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Perturb-seq

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Hello to all Perturb-seq users! Feel free to use this forum for any questions, especially those related to troubleshooting experiments or computational methods.

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Atray Dixit, … Timothy Tickle4

3/10/17

Data Availability of Single Cell Portal

GSE90063_dc3hr_umi_wt.txt only contains data from unperturbed cells

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Data Availability of Single Cell Portal

GSE90063_dc3hr_umi_wt.txt only contains data from unperturbed cells

3/10/17

7/15/25

Upstream related to perturb-seq

Hello everyone, I currently re-process upstream analyses using SRR files as input to generate the

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Upstream related to perturb-seq

Hello everyone, I currently re-process upstream analyses using SRR files as input to generate the

7/15/25

6/28/24

knock out based perturb seq data analysis questions

Hi, May I ask whether there is standard method to analysis perturb seq data? And what plots are

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knock out based perturb seq data analysis questions

Hi, May I ask whether there is standard method to analysis perturb seq data? And what plots are

6/28/24

8/10/23

WT / Unperturbed data BAM files in GEO

Hello, I know its been quite few years after the publication but I wanted to give this a try. First

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WT / Unperturbed data BAM files in GEO

Hello, I know its been quite few years after the publication but I wanted to give this a try. First

8/10/23

Paul Klein, … Catherine Z5

5/16/23

Guidelines for UMI thresholding for sgRNA attribution to cells

Hi,I find scAR just directly compare several sgRNA UMI size ... 在2022年10月21日星期五 UTC+8 17:48:09<

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Guidelines for UMI thresholding for sgRNA attribution to cells

Hi,I find scAR just directly compare several sgRNA UMI size ... 在2022年10月21日星期五 UTC+8 17:48:09<

5/16/23

Revathy Venukuttan

4/3/23

Market matrix files for the sgRNAs

Hi authors, Thank you for the nice paper! I was wondering if you have generated the market matrix

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Market matrix files for the sgRNAs

Hi authors, Thank you for the nice paper! I was wondering if you have generated the market matrix

4/3/23

9/29/22

Including quality covariates

Dear authors, Thank you for the nice paper! I am trying to run the pipeline on K562 cells, and I

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Including quality covariates

Dear authors, Thank you for the nice paper! I am trying to run the pipeline on K562 cells, and I

9/29/22

alexande...@fbb.msu.ru, … 李威毅8

12/7/21

Data not available

Dear sir could you please add the full (non-sparse) expression matrices (genes x cells) to GEO? I can

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Data not available

Dear sir could you please add the full (non-sparse) expression matrices (genes x cells) to GEO? I can

12/7/21

yyshe...@gmail.com

5/14/20

Hi, I have a question regarding the input file. If I use 10X platform, when we use "cellranger

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Hi, I have a question regarding the input file. If I use 10X platform, when we use "cellranger

5/14/20

rosela...@gmail.com

9/4/19

Dear Perturb-seq team, I have doubt about the meaning of the z-score in the image 5E of the paper.

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Dear Perturb-seq team, I have doubt about the meaning of the z-score in the image 5E of the paper.

9/4/19

6/11/19

recreate regulatory matrix BMDC 0hr

Dear Pertub-seq team, I'm trying to reproduce some of your results using the data provided on GEO

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recreate regulatory matrix BMDC 0hr

Dear Pertub-seq team, I'm trying to reproduce some of your results using the data provided on GEO

6/11/19

david...@gmail.com, … acellix...@gmail.com3

4/22/19

Covariate matrix?

Hi Atray, I'm still a little bit confused about how to get sgRNA covariates. I clicked the link

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Covariate matrix?

Hi Atray, I'm still a little bit confused about how to get sgRNA covariates. I clicked the link

4/22/19

2/8/19

Hello, Firstly Thank you for the very nice paper! I was just wondering about the cloning of the Guide

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Hello, Firstly Thank you for the very nice paper! I was just wondering about the cloning of the Guide

2/8/19

helen...@gmail.com, Atray Dixit5

1/11/19

K562 BAM files do not contain paired end data

Great, thanks for this! Best, Helen

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K562 BAM files do not contain paired end data

Great, thanks for this! Best, Helen

1/11/19

Andrew, … Atray Dixit5

1/9/19

Estimation of capture rate and moi with generative model

Nice catch, and I believe that is correct! Looks like there were a couple of typos in the equation in

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Estimation of capture rate and moi with generative model

Nice catch, and I believe that is correct! Looks like there were a couple of typos in the equation in

1/9/19

orewa...@gmail.com, Atray Dixit9

6/19/18

Problem about the number of detected sgRNA/cell

Thanks for all your reply! These technical details are really helpful. Best wishes, Dongyang

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Problem about the number of detected sgRNA/cell

Thanks for all your reply! These technical details are really helpful. Best wishes, Dongyang

6/19/18

alsi...@gmail.com

3/7/18

Dear Atray, I'm very interested in your paper. Since I will have to expose your results to my

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Dear Atray, I'm very interested in your paper. Since I will have to expose your results to my

3/7/18

xujin...@gmail.com, Atray Dixit7

1/16/18

expression matrices and high MOI data

Hi Atray, Thank you very much! They are really helpful! :) Best, Jinyuan

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expression matrices and high MOI data

Hi Atray, Thank you very much! They are really helpful! :) Best, Jinyuan

1/16/18

Ashu Seq, Atray Dixit4

11/9/17

Thank you Atray! That was helpful! With kind regards, Ashu

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Thank you Atray! That was helpful! With kind regards, Ashu

11/9/17

eric....@gmail.com, Atray Dixit4

8/16/17

Cell state as output

Hi Eric, I see. Yes I see what you mean. If your dependent variable (outputs) are truly binary, then

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Cell state as output

Hi Eric, I see. Yes I see what you mean. If your dependent variable (outputs) are truly binary, then

8/16/17

Tian Luyi, Atray Dixit4

8/3/17

GBC - gRNA dictionary?

Hi Tian, My apologies. It depends on the manner in which cloning is performed. If, as in most of our

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GBC - gRNA dictionary?

Hi Tian, My apologies. It depends on the manner in which cloning is performed. If, as in most of our

8/3/17

jan.gl...@gmail.com, Atray Dixit9

8/1/17

cbc_gbc_dicts, batches

Thank you, Atray! Don't worry about the delay, I was on vacation anyway :). best, Jan

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cbc_gbc_dicts, batches

Thank you, Atray! Don't worry about the delay, I was on vacation anyway :). best, Jan

8/1/17

Eduardo Gade Gusmão, Atray Dixit5

4/8/17

DE Genes by Perturbation

Hi Atray, thank you very much, this was really helpful! Best, Eduardo

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DE Genes by Perturbation

Hi Atray, thank you very much, this was really helpful! Best, Eduardo

4/8/17

sarah.ku...@gmail.com, Atray Dixit2

4/8/17

Genes in programs P1-P5

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Genes in programs P1-P5

4/8/17

Eduardo Gade Gusmão, Atray Dixit2

3/29/17

Data Matrix in GEO

Hi Eduardo, The GEO UMI matrix contains no additional preprocessing beyond what is intrinsically part

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Data Matrix in GEO

Hi Eduardo, The GEO UMI matrix contains no additional preprocessing beyond what is intrinsically part

3/29/17

Jin, Atray Dixit3

3/22/17

Cloning protocol

Hi Atray, Thank you so much for the information! Your explanation is very clear. I just placed an

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Cloning protocol

Hi Atray, Thank you so much for the information! Your explanation is very clear. I just placed an

3/22/17

Iwo, Atray Dixit4

3/14/17

Linear model and cell perturbation probability

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Linear model and cell perturbation probability

3/14/17

3/10/17

Question on GEO data discussion

(1) The file you refer to is in matrix market format and can be read with a function like scipy's

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Question on GEO data discussion

(1) The file you refer to is in matrix market format and can be read with a function like scipy's

3/10/17

dmd...@nyu.edu, Atray Dixit2

2/22/17

regulatory matrices

Hi Dayanne, The regulatory matrices correspond to the coefficient matrix obtained after we fit our

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regulatory matrices

Hi Dayanne, The regulatory matrices correspond to the coefficient matrix obtained after we fit our

2/22/17

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