title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-52

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-41

status: Public on Jun 01 2022

type: SRA

city: Beijing

first: Hua-nan

last: Zhao

state: Beijing

address: 5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

description: Targeted deep sequencing

library_source: genomic

data_processing:
alignment: BWA
mpileup: samtools mpileup
bmat: parse-mpileup-V04.py
plot base mutation ratio using Python tool: plot-targetseq-bmat-V04.py
Assembly: hg38
Supplementary files format and content: Excel table, the off-target editing ratio list
Library strategy: Targeted deep sequencing

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cells

extract_protocol: Primers containing the paired Illumina adaptor sequences in the overhangs were designed based on regions flanking the targeting sites (Supplementary Table 2). A 10-nt barcode was also added into each primer pairs to reduce the detection limit from 0.1% to 0.005%10. 10-100 ng of genomic DNA was used for the first round of PCR amplification using NEBNext® Q5U® Hot Start HiFi PCR Master Mix (NEB, M0515L) for approximately 10 cycles. Q5U is capable of reading and amplifying templates containing uracil bases and hence ensures accurate measurement of off-target editing level. The PCR products were purified with 1× Agencourt AMPure XP beads and eluted in nuclease-free water. The second round of amplification was performed on the purified DNA samples with different index primers for about 15 cycles. The PCR products were purified with 0.8× Agencourt AMPure XP beads and eluted in nuclease-free water. The libraries were quantified using Qubit dsDNA HS Assay kit (Invitrogen) and Qubit 2.0 Fluorometer (INVITROGEN), and then pooled together for high-throughput sequencing by Illumina HiSeq X Ten or MGISEQ-2000.

tag: cell line

value: HEK293T cells

tag: treatment

tag: cell type


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-51

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-50

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-40

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-3

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-39

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-19

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-16

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-25

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-10

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_SupFig7_ND4-L1397N-LTX21-rep1_ND4-Extend-4

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-27

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-25

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-3

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-29

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-1

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.IND-38

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-15

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-7

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-6

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-20

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-5

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-9

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-1

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-3

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-6

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-TAS.DR-13

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-11

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-10

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep2_ND4-TAS.IND-48_ND5.1-TAS.IND-410_ND6-TAS.IND-484

description: Targeted deep sequencing

value: Untreated


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep2_ND4-TAS.IND-6_ND5.1-TAS.IND-47_ND6-TAS.IND-48

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SupFig7_ND4-L1397N-LTX21-rep1_ND4-Extend-2

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep2_ND4-TAS.IND-46_ND5.1-TAS.IND-371_ND6-TAS.IND-436

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep2_ND4-TAS.IND-17_ND5.1-TAS.IND-134_ND6-TAS.IND-154

description: Targeted deep sequencing


title: ExtendFig3_ND4-L1397N-LTX21-rep1_ND4-Extend-7

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_SFig11_ND6-L1397N-LTX21-WT-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-DL-71

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep1_ND4-Extend-2_ND5.1-TAS.IND-60_ND6-TAS.IND-63

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep2_ND4-Extend-2_ND5.1-TAS.IND-60_ND6-TAS.IND-63

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep1_ND4-TAS.IND-46_ND5.1-TAS.IND-371_ND6-TAS.IND-436

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep1_ND4-TAS.IND-48_ND5.1-TAS.IND-410_ND6-TAS.IND-484

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig3f_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-484

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig3f_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-436

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_SFig11_ND6-L1397N-LTX21-WT-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-DL-19

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig25_SupFig7_Untreated-rep1_ND4-TAS.IND-31_ND5.1-TAS.IND-230_ND6-TAS.IND-271

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig25_SupFig7_Untreated-rep2_ND4-Extend-15_ND5.1-TAS.IND-388_ND6-TAS.IND-454

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig25_SupFig7_Untreated-rep1_ND4-Extend-15_ND5.1-TAS.IND-388_ND6-TAS.IND-454

description: Targeted deep sequencing


title: ExtendFig3_ExtendFig7_Fig3f_SupFig7_Untreated-rep1_ND4-TAS.IND-34_ND5.1-TAS.IND-257_ND6-TAS.IND-297

description: Targeted deep sequencing


title: ExtendFig3_ExtendFig7_Fig3f_SupFig7_Untreated-rep1_ND4-TAS.IND-44_ND5.1-TAS.IND-346_ND6-TAS.IND-405

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig3f_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-154

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep1_ND4-TAS.IND-17_ND5.1-TAS.IND-134_ND6-TAS.IND-154

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig25_SupFig7_Untreated-rep2_ND4-TAS.IND-31_ND5.1-TAS.IND-230_ND6-TAS.IND-271

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_SFig11_ND6-L1397N-LTX21-WT-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-DL-71

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig3f_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-454

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_SFig11_ND6-L1397N-LTX21-WT-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-DL-19

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig3f_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-63

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_Fig3f_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-63

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_Fig3f_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-48

description: Targeted deep sequencing


title: ExtendFig3_Fig3f_SupFig7_Untreated-rep1_ND4-TAS.IND-6_ND5.1-TAS.IND-47_ND6-TAS.IND-48

description: Targeted deep sequencing


title: ExtendFig3_ExtendFig7_Fig3f_SupFig7_Untreated-rep2_ND4-TAS.IND-44_ND5.1-TAS.IND-346_ND6-TAS.IND-405

description: Targeted deep sequencing


title: ExtendFig3_ExtendFig7_Fig3f_SupFig7_Untreated-rep2_ND4-TAS.IND-34_ND5.1-TAS.IND-257_ND6-TAS.IND-297

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig3f_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-48

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig3f_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-271

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_Fig3f_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-454

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-47

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-60

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_Fig2d_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-DL-49

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_Fig3f_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-154

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-410

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_Fig3f_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-436

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-257

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-184

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep1_Fig3f_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-271

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-388

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-371

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-342

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-230

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-207

description: Targeted deep sequencing


title: EFig3_ND6-L1397N-LTX21-rep2_Fig2d_ND6-L1397N-LTX21-rep2_SFig7_ND6-L1397N-LTX21-rep2_ND6-DL-49

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-388

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-346

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-60

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-47

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-342

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-346

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-257

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-371

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-230

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-207

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-44

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-46

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-6

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep2_Fig3f_ND5.1-L1397N-LTX21-rep2_SFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-IND-134

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-184

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-134

description: Targeted deep sequencing


title: EFig3_ND5.1-L1397N-LTX21-rep1_Fig3f_ND5.1-L1397N-LTX21-rep1_SFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-IND-410

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-34

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-42

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-Extend-15

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-6

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-27

description: Targeted deep sequencing


title: ExtendFig3_ND5.1-L1397N-LTX21-rep1_ND5.1-TAS.IND-369

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-30

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-17

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-44

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-46

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-17

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-27

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-Extend-15

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-31

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-30

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-34

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-405

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-398

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-48

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep2_Fig3f_ND4-L1397N-LTX21-rep2_SFig7_ND4-L1397N-LTX21-rep2_ND4-IND-31

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-48

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-215

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-241

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-405

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-297

description: Targeted deep sequencing


title: EFig3_ND4-L1397N-LTX21-rep1_Fig3f_ND4-L1397N-LTX21-rep1_SFig7_ND4-L1397N-LTX21-rep1_ND4-IND-42

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-215

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig25_SFig7_Untreated-rep2_ND4-IND-27_ND5.1-IND-184_ND6-IND-215

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig25_SFig7_Untreated-rep1_ND4-IND-30_ND5.1-IND-207_ND6-IND-241

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig25_SFig7_Untreated-rep1_ND4-IND-42_ND5.1-IND-342_ND6-IND-398

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-241

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-398

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig25_SFig7_Untreated-rep2_ND4-IND-30_ND5.1-IND-207_ND6-IND-241

description: Targeted deep sequencing


title: EFig3_EFig7_Fig3f_SFig25_SFig7_Untreated-rep1_ND4-IND-27_ND5.1-IND-184_ND6-IND-215

description: Targeted deep sequencing


title: ChIP-seq of BRCA2 in ZFP281 KO-2 mESC

status: Public on May 31 2022

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

data_processing:
ChipSeq samples were aligned using Bowtie2 (v2.2.5)  allowing uniquely mapping reads only
Peak calling was performed with MACS2 (v2.1.1) and filtered at FDR < 5 (0.05)
Assembly: UCSC mm9
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: murine embryonic stem cells

growth_protocol: Mouse ES cell lines WT and ZFP281 KO were cultured in N2B27 medium supplemented with 2i/LIF in 0.1% gelatin-coated tissue culture flask

extract_protocol:
For ChIP-Seq, 5×10^7 cells were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's ChIP-Seq sample prep kit (0801-0303).
NEBNext® DNA Library Prep Master Mix Set for Illumina

treatment_protocol: WT and ZFP281 KO ES cells were cross-linked in PBS containing 1% paraformaldehyde

tag: strain

value: C57BL/6 (female) x 129/S (male)

value: murine embryonic stem cells

tag: genotype

value: ZFP281 KO

tag: chip antibody


title: EFig3_ND6-L1397N-LTX21-rep1_Fig3f_ND6-L1397N-LTX21-rep1_SFig7_ND6-L1397N-LTX21-rep1_ND6-IND-484

description: Targeted deep sequencing


title: HTISA.ASLV.total.1

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
fastq raw reads files were split into the individual Total and GFP-negative libraries by their barcodes, using fastqx toolkit fastx_barcode_splitter.pl program with ---bol --exact parameters (search exact match of barcode at the beginning of the read).
For each library, the viral LTR sequence spanning the first 41 base-pairs of the read was trimmed and processed reads were mapped to the human grch37/hg19 genome build using Bowtie (version 1.1.2) software with seed length 25 and 3 mismatches allowed. To reduce background, integration sites with only a single read were discarded.
The genome was divided into 25 kb bins and the number of reads for each bin was counted. Covered bins were defined as those with at least 3 unique integration sites and total 50 or more reads. Bins that did not match these criteria were discarded from the analysis. For each covered bin, enrichment of reads in the GFP-negative population was determined as follows. First, the reads that were mapped to Ig loci were discarded. Next, the reads in the Total population were normalized to have the same total number of reads as the GFP-negative population. The resulting normalized number of reads per bin in the total population was used as the Poisson l parameter against which the number of reads in the GFP-negative population at the same bin were compared in the Poisson test.  This generated an array of p-value to which we applied Benjamini-Hochberg criteria using FDR of 0.05 to determine the significant GFP-negative enriched bins for this pair of Total/GFP-negative libraries.
Assembly: human GRCh37/hg19
Supplementary files format and content: Aligned-reads bed files were first converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).

source_name: Ramos cell line

growth_protocol: Ramos cells were propagated in RPMI 1640 medium (Sigma) supplemented with 10% fetal calf serum (GIBCO) and antibiotic mixture (Sigma) in a 5% CO2 atmosphere at 37°C

extract_protocol:
Total and GFP-negative cultures were harvested for genomic DNA isolation on the same day so that culture times after infection with GFP7 were the same. Genomic DNA was isolated using a salt-extraction method (Aljanabi and Martinez, 1997).
HTISA libraries were prepared and sequenced from GFP-negative and Total populations ("B" culture genomic DNAs were combined to yield a GFP-negative "Pool" library and a Total "Pool" library, so that finally, we obtained one pooled and 4 separate GFP-negative samples and one pooled and 4 separate Total samples). We used a linear amplification–PCR protocol based on a previously published high-throughput, genome-wide, translocation sequencing (HTGTS) method (Frock et al., 2015). The adaptation of the protocol was as follows: Retroviral integration sites were linearly amplified from the vector 5' LTR using biotinylated Bio_L7a (HIV-derived vector integrations) or Bio_A7a (ASLV-derived vector integrations) primers. Nested PCR was performed with barcoded inner primer I5_bar75_L7a (HIV-derived vector integrations) or I5_bar75_A7a (ASLV-derived vector integrations). The blocking digestion of the nested PCR product was omitted. The resulting PCR product were gel purified and sequenced using a NextSeq500 (Illumina) sequencer.

treatment_protocol: 10e7 Ramos cells were infected (4 independent infections) with no-DIVAC GFP7 vector at low multiplicity resulting in 0.5-1% GFP-positive cells 2 days after infection. Blasticidin (final concentration 5 µg/ml) was added 2 days post infection. Three days post infection the blasticidin concentration was increased to 6.5 µg/ml and kept until the 5th day. Seven days post infection, GFP positive cells were sorted and cultured for two days. Nine days post infection, GFP-positive cells were sorted again. Each culture was split in half to create duplicate "A" and "B" cultures. After 20 days of propagation, the culture was selected with blasticidin (12 µg/ml) to remove cells with silenced vector. After 4 days of blasticidin selection, GFP-negative cells (containing mostly vectors integrated into SHM-susceptible sites) were then sorted from each of the 8 cultures ("A" and "B" duplicates of 4 infections) and sorted again 3 days later to remove the remaining GFP-positive cells.

value: B lymphocyte

value: WT

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: age

value: Unknown

tag: Sex

value: male


title: HTISA.ASLV.gneg.1


title: HTISA.ASLV.total.2


title: ChIP-seq of BRCA2 in ZFP281 KO-1 mESC


title: HTISA.ASLV.total.3


title: HTISA.ASLV.gneg.2


title: EFig3_EFig7_Fig3f_SFig7_ND6-L1397N-LTX21-rep2_ND6-IND-297

description: Targeted deep sequencing


title: RNA-seq_iPSC-derived HPC DNMT3A exon 23-/- clone 2

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description:
iPSC-derived hematopoietic progenitor cells after 16 days of differentiation
SAMPLE 7

library_source: transcriptomic

data_processing:
Adapter trimming and rRNA removal in raw fastq files was performed using TrimGalore (Babraham Bioinformatics, Cambridge, UK). Reads were aligned to the human genome build GRCh38 with STAR aligner (Dobin et al. 2013). Read counts were retrieved with Subread/featureCounts and further analyzed with the R package DESeq2.
Genome_build: GRCh38

molecule: total RNA

source_name: iPSC from bone marrow KIT+ cells

growth_protocol: For hematopoietic differentation of iPSCs, EBs were generated by self-detachment from microcontact-printed vitronectin spots generated with PDMS stamps. EBs were carefully resuspended in serum free medium containing 50% IMDM, 50% Ham’s F12, 0.5% BSA, 1% chemically defined lipid concentrate, 2 mM GlutaMAX (all Thermo Fisher Scientific), 400 µM 1-thioglycerol, 50 µg/mL L-ascorbic acid, and 6 µg/mL holo transferrin (all Sigma Aldrich) supplemented with 10 ng/mL FGF-2 (Peprotech), 10 ng/mL BMP-4 (Miltenyi Biotec), and 10 µM Y-27632 (Abcam). EBs were seeded on 0.1% gelatin coated 6-well plates. From day 2 to 16 EBs were cultured in serum free medium supplemented with 10 ng/mL FGF 2, 10 ng/mL BMP-4, 50 ng/mL SCF (Peprotech), 10 ng/mL VEGF-A (Peprotech) and 10 U/mL penicillin/streptomycin (Thermo Fisher Scientific). The non-adherent iHPC were harvested at day 16 and separated with a 40 µm cell strainer.

extract_protocol:
RNA of iPSC-derived hematopoietic progenitor cells was isolated with the NucleoSpin RNA Plus kit (Macherey-Nagel).
QuantSeq 3´-mRNA Library Prep FWD/Lexogen, Standard 3' Seq (10 M 50 bp single reads)

value: Induced pluripotent stem cell derived hematopoietic progenitor cells

tag: parent cell line

value: iPSC DNMT3A exon 23-/- clone 2

tag: mutation

value: KRAS (A146T)


title: RNA-seq_iPSC-derived HPC DNMT3A exon 23-/- clone 1

description:
iPSC-derived hematopoietic progenitor cells after 16 days of differentiation
SAMPLE 6

source_name: iPSC from bone marrow MSC

value: iPSC DNMT3A exon 23-/- clone 1


title: RNA-seq_iPSC-derived HPC DNMT3A exon 19-/- clone 2

description:
iPSC-derived hematopoietic progenitor cells after 16 days of differentiation
SAMPLE 5

value: iPSC DNMT3A exon 19-/- clone 2


title: EFig3_EFig7_Fig3f_SFig25_SFig7_Untreated-rep2_ND4-IND-42_ND5.1-IND-342_ND6-IND-398

description: Targeted deep sequencing


title: RNA-seq_iPSC-derived HPC wildtype 3

description:
iPSC-derived hematopoietic progenitor cells after 16 days of differentiation
SAMPLE 3

value: iPSC wildtype 3


title: RNA-seq_iPSC-derived HPC DNMT3A exon 19-/- clone 1

description:
iPSC-derived hematopoietic progenitor cells after 16 days of differentiation
SAMPLE 4

value: iPSC DNMT3A exon 19-/- clone 1


title: RNA-seq_iPSC-derived HPC wildtype 2

description:
iPSC-derived hematopoietic progenitor cells after 16 days of differentiation
SAMPLE 2

value: iPSC wildtype 2


title: HTISA.ASLV.gneg.3


title: ChIP-seq of BRCA2 in ZFP281 WT mESC

value: ZFP281 WT


title: RNA-seq_iPSC-derived HPC wildtype 1

description:
iPSC-derived hematopoietic progenitor cells after 16 days of differentiation
SAMPLE 1

value: iPSC wildtype 1


title: EB-B-suspension

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

country: USA

institute: UCLA

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on Illumina NovaSeq 6000.
The raw reads were mapped to human reference genome (refdata-cellranger-GRCh38-1.2.0) using cellranger count.
Assembly: hg38
Supplementary files format and content: Sparse matrix with raw gene counts for each cell

extract_protocol:
For the generation of single-cell gel beads in emulsion, cells were loaded on a Chromium single cell instrument (10x Genomics) with an estimated targeted cell recovery of ~5,000 cells as per manufacturer’s protocol. In brief, single-cell suspension of cells in 0.4% BSA-PBS were added to each channel on the 10X chip. Cells were partitioned with Gel Beads into emulsion in the Chromium instrument where cell lysis and barcoded reverse transcription of RNA occurred following amplification.
Single-cell RNAseq libraries were prepared by using the Chromium single cell 3’ library and gel bead kit v3 (10X Genomics).

tag: tissue

value: RM3.5 iPSCs RM3.5, expressing a tdTOMATO from the GAPDH locus

value: Normal karyotype

value: Swirler EB as described in Motazedian et al. NCB,2022


title: EB-B-adherent

value: Swirler EB as described in Motazedian et al. NCB,2021


title: EB-A-suspension

value: Swirler EB as described in Motazedian et al. NCB,2020


title: EB-A-adherent

value: Swirler EB as described in Motazedian et al. NCB,2019


title: fastGRO_siZNF827_d4TGFB_ R2

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

country: Denmark

institute: Queen’s University Belfast

data_processing:
Low quality bases were trimmed from pre-aligned reads, then aligned to hg19 reference genome using STAR v2.7, followed by quantification using salmon v1.4.
Raw read counts were filtered to remove counts where maximum <=1. Differential analysis was performed with DESeq2 (R, v3.14) with default parameters, with the median of ratios method of normalisation performed prior to differntial analysis.
After library size normalization using DESeq (v3.14), expression was quantified and differential expression analysis was performed using DESeq2.
Gene set enrichment analysis for biological processes was performed using GSEA Preranked module
fastGRO analysis were performed as indicated in the published manuscript (Barbieri, Elisa, et al. , Cell reports  (2020)
CUT&Tag analysis were performed as indicated in the published manuscript (Kaya-Okur, Hatice S., et al. ,Nature communications (2019)
Assembly: hg19
Supplementary files format and content: Matrix table with gene counts from DESeq2, for every gene and every sample
Supplementary files format and content: ChIP  provided as Peak and Bigwig file format
Supplementary files format and content: CUT&Tag  provided as Peak  file format
Supplementary files format and content: fastGRO provided as Bigwig  file format
Library strategy: fastGRO

source_name: HMLE cell line

extract_protocol:
fastGRO was performed as indicated in the published manuscript (Barbieri, Elisa, et al. , Cell reports  (2020)
RNA libraries were prepared for sequencing using "NEBNext Ultra II RNA Library Prep Directional" kit according to manufacturer instructions

value: siZNF827 d4 TGF-B

tag: tag

value: ZNF827 depletion


title: fastGRO_siZNF827_d4TGFB_ R1


title: fastGRO_Untreated_R1

value: Untreated HMLE

value: Untreated


title: iPSC-derived HPC DNMT3A exon 23-/- clone 2

type: genomic

description: iPSC-derived hematopoietic progenitor cells after 16 days of differentiation

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

growth_protocol: iPSCs were cultured on tissue culture plastic coated with Matrigel Matrix (Corning) in StemMACS iPS-Brew XF (Miltenyi Biotec) with 100 U/mL penicillin and 100 μg/mL streptomycin. For iMSC generation, iPSC medium was switched to MSC medium, consisting of Dulbecco‘s modified Eagle’s medium-low glucose (Thermo Fisher Scientific) supplemented with 10% human platelet lysate, and 5 U/ml heparin (Rotexmedica) for 35 days. Cells were passaged when reaching a confluency of 70% with 0.5% Trypsin-EDTA (Thermo Fisher Scientific) and seeded at 400,000 cells/6-well on 0.1% gelatine coated plates. For hematopoietic differentation of iPSCs, EBs were generated by self-detachment from microcontact-printed vitronectin spots generated with PDMS stamps. EBs were carefully resuspended in serum free medium containing 50% IMDM, 50% Ham’s F12, 0.5% BSA, 1% chemically defined lipid concentrate, 2 mM GlutaMAX (all Thermo Fisher Scientific), 400 µM 1-thioglycerol, 50 µg/mL L-ascorbic acid, and 6 µg/mL holo transferrin (all Sigma Aldrich) supplemented with 10 ng/mL FGF-2 (Peprotech), 10 ng/mL BMP-4 (Miltenyi Biotec), and 10 µM Y-27632 (Abcam). EBs were seeded on 0.1% gelatin coated 6-well plates. From day 2 to 16 EBs were cultured in serum free medium supplemented with 10 ng/mL FGF 2, 10 ng/mL BMP-4, 50 ng/mL SCF (Peprotech), 10 ng/mL VEGF-A (Peprotech) and 10 U/mL penicillin/streptomycin (Thermo Fisher Scientific). The non-adherent iHPC were harvested at day 16 and separated with a 40 µm cell strainer.

extract_protocol: Genomic DNA of iPSCs, iPSC-derived mesenchymal stromal cells, and iPSC-derived hematopoietic cells was harvested with the NucleoSpin Tissue kit (Macherey-Nagel).

value: Induced pluripotent stem cell derived hematopoietic progenitor cells

value: iPSC DNMT3A exon 23-/- clone 2

value: KRAS (A146T)


title: fastGRO_Untreated_R2


title: ZNF827_Cut&Tag_d4TGFB_R2

data_processing:
Low quality bases were trimmed from pre-aligned reads, then aligned to hg19 reference genome using STAR v2.7, followed by quantification using salmon v1.4.
Raw read counts were filtered to remove counts where maximum <=1. Differential analysis was performed with DESeq2 (R, v3.14) with default parameters, with the median of ratios method of normalisation performed prior to differntial analysis.
After library size normalization using DESeq (v3.14), expression was quantified and differential expression analysis was performed using DESeq2.
Gene set enrichment analysis for biological processes was performed using GSEA Preranked module
fastGRO analysis were performed as indicated in the published manuscript (Barbieri, Elisa, et al. , Cell reports  (2020)
CUT&Tag analysis were performed as indicated in the published manuscript (Kaya-Okur, Hatice S., et al. ,Nature communications (2019)
Assembly: hg19
Supplementary files format and content: Matrix table with gene counts from DESeq2, for every gene and every sample
Supplementary files format and content: ChIP  provided as Peak and Bigwig file format
Supplementary files format and content: CUT&Tag  provided as Peak  file format
Supplementary files format and content: fastGRO provided as Bigwig  file format
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed as indicated in the published manuscript (Kaya-Okur, Hatice S., et al. ,Nature communications (2019)
DNA libraries were prepared for sequencing using "NEBNext® Ultra™ II for DNA Library Prep" kit according to manufacturer instructions

value: FLAG-ZNF828 d4TGFB

value: ChIP antibody


title: iPSC-derived HPC DNMT3A exon 19-/- clone 2

label_protocol: Standard Infinium HD Methylation Assay protocol

value: iPSC DNMT3A exon 19-/- clone 2


title: ZNF827_Cut&Tag_d4TGFB_R1

value: FLAG-ZNF827 d4TGFB


title: iPSC-derived MSC DNMT3A exon 23-/- clone 2

description: iPSC-derived mesenchymal stromal cells after 35 days of differentiation

value: Induced pluripotent stem cell derived mesenchymal stromal cells


title: iPSC-derived MSC wildtype 2

value: iPSC wildtype 2


title: iPSC-derived HPC wildtype 3

value: iPSC wildtype 3


title: fastGRO_siControl_d4TGFB_ R1

value: siControl d4 TGF-B

value: TGFbeta treatment


title: iPSC-derived HPC DNMT3A exon 19-/- clone 1

value: iPSC DNMT3A exon 19-/- clone 1


title: Ki67_aid_HCT116_IAA_interphase_ChIP_input_r1

status: Public on May 27 2022

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: interphase_IAA, target: input.

data_processing:
1. pA-DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts;  remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17;  reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 1.30.1 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq and 4. ChIP-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for pA-DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
5. Hi-C: Reads were mapped with HiC-Pro, which performed read mapping, generation of contact matrices and ICE-normalization.
Assembly: hg38
Supplementary files format and content: 1. pA-DamID: BigWig files of log2-normalized pADamID scores for 50 kb genomic bins, tsv files with genomic coordinates and all scores per replicate / average scores per condition (including previously published pA-DamID data used in this study), tsv file with complete metadata that includes target/Dam control combinations; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios.; 4. ChIP-seq: BigWig tracks of Ki-67/input log2-ratios; 5. Hi-C: ICE-normalized matrices (100 kb resolution) and one index file with genomic coordinates.

source_name: HCT116 (ATCC CCL-247)

growth_protocol: hTERT-RPE, HCT116 and K562 cells (all from ATCC) were cultured according to their ATCC guidelines.

extract_protocol:
1. pA-DamID: 1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a primary antibody and for a Dam control condition, to specifically deposit m6A marks at chromatin nearby the primary antibody. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2. RNA-seq: RNA was isolated using the Qiagen RNeasy column purification kit; 3. Repli-Seq: cells were harvested as for pA-DamID and immediately fixed in ice-cold ethanol. 4. ChIP-seq: Cells were crosslinked (1% FA, 10 minutes) and quenced with glycine (2.0M). 5. Hi-C: Cells were harvested and crosslinked (2% FA, 10 minutes).
1. pA-DamID: the full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; 2: RNA-seq: sequencing libraries were prepared using the Illumina TruSeq polyA stranded RNA kit; 3. Repli-seq: replicated DNA was enriched for with a BrdU IP, before libraries were prepared as described in Marchal, 2018; 4. ChIP-seq: Chromatin was fragmented to ~300 bp fragments with a Bioruptor Plus sonication device (Diagenode). Ki-67 antibody (ab15580, Abcam; 5 μL per ChIP) was coupled with Protein G beads (Thermo Fisher Scientific) and incubated with fragmented chromatin overnight at 4 °C. Released DNA fragments were purified with the MinElute PCR Purification kit (Qiagen). The purified DNA fragments were prepared with the KAPA HTP Library Preparation kit (Roche); 5. Hi-C: Cross-linked nuclei were digested with MboI and biotinylated nucleotides incorporated in the overhangs. Following blunt-end ligation, the ligated fragments were extracted using streptavidin pulldown and prepared for sequencing using a standard end-repair / 3A-tailing procedure.

treatment_protocol: 1. Wildtype: no treatment; 2. Cell cycle: cells were synchronized with a sequential treatment of G2 enrichment (16 hours, with RO-3306) and metaphase blocking (90 minutes, with nocodazole). Synchronized cells were harvested with a mitotic shake-off, and immediately processed for pA-DamID or replated for interphase time points; 3. Ki67-AID: protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich, in DMSO, 24 h depletion), a similar amount of DMSO was used as control; 4. Actinomycin D: nucleoli were disrupted with a low dose of actinomycin D (50 ng/mL, in DMSO, 3 h treatment), a similar amount of DMSO was used as control; 5. Osmotic shock: nucleoli were disrupted with a short osmotic shock (0.2x PBS, 15 minutes), cells were harvested at two time points during nucleolar recovery; 6. Repli-seq: BrdU was added to a final concentration of 100 uM and cells were incubated at 37 °C for another 2 h.

value: Colorectal carcinoma cells

tag: library type

value: ChIP-seq

tag: genetic modification

value: OsTir1; Ki67-miniAID-mClover

tag: experiment

tag: condition

tag: target

value: input


title: Ki67_aid_HCT116_IAA_mitosis_ChIP_Ki67_r1

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: mitosis_IAA, target: Ki67.


title: iPSC DNMT3A exon 23-/- clone 1

value: Induced pluripotent stem cells

value: iPSC wildtype 1


title: iPSC-derived MSC wildtype 3

value: KRAS (A146T)


title: Ki67_aid_HCT116_interphase_ChIP_input_r1

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: interphase, target: input.

value: interphase


title: iPSC-derived HPC wildtype 2

value: Induced pluripotent stem cell derived hematopoietic progenitor cells


title: Ki67_aid_HCT116_IAA_interphase_ChIP_Ki67_r1

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: interphase_IAA, target: Ki67.


title: iPSC-derived MSC DNMT3A exon 23-/- clone 1

value: iPSC DNMT3A exon 23-/- clone 1


title: iPSC DNMT3A exon 2-/- clone 1


title: iPSC-derived MSC DNMT3A exon 19-/- clone 2

value: iPSC DNMT3A exon 19-/- clone 2


title: iPSC-derived HPC wildtype 1


title: Ki67_aid_HCT116_mitosis_ChIP_input_r1

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: mitosis, target: input.

value: mitosis


title: Ki67_aid_HCT116_interphase_HiC_r2

description: Hi-C on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: interphase.

value: Hi-C


title: iPSC-derived HPC DNMT3A exon 23-/- clone 1


title: iPSC DNMT3A exon 23-/- clone 2

value: iPSC wildtype 3


title: iPSC wildtype 2


title: iPSC-derived MSC DNMT3A exon 2-/- clone 1

value: Induced pluripotent stem cell derived mesenchymal stromal cells

value: iPSC DNMT3A exon 2-/- clone 1


title: Ki67_aid_HCT116_interphase_ChIP_Ki67_r1

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: interphase, target: Ki67.


title: iPSC DNMT3A exon 19-/- clone 2

value: iPSC wildtype 2


title: iPSC wildtype 3


title: iPSC DNMT3A exon 19-/- clone 1


title: Ki67_aid_HCT116_mitosis_HiC_r1

description: Hi-C on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: mitosis.

value: Colorectal carcinoma cells


title: Mg3_mac

status: Public on May 25 2022

city: Houston

first: Michael

last: Lorenz

state: TX

address: 6431 Fannin

institute: UTHealth Houston

data_processing:
Base-calling was performed by Macrogen using Illumina Real Time Analysis RTA software followed by fastq file generation with the Illumina package bcl2fastq.
Adapters were trimmed using Trimmomatic v0.39, with additional removal of bases below a read quality of 3 at the start and end of the read and total removal of reads less than 36 bp after trimming.
Reads were mapped to a concatenated mouse-M. guilliermondii transcriptome using Salmon v1.1.0 with --gcBias and --seqBias flags. The transcriptome file was generated from a concatenated genome file using GffRead v0.11.6.
Genome_build: The concatenated genome file was generated from the GRCm38.p6 Mus musculus reference genome (Ensembl release 98) and the M. guilliermondii reference genome obtained from the Candida Genome Database (http://candidagenome.org/) using the current version as of January 16, 2020, 11:57 am.
Supplementary_files_format_and_content: Salmon output files (.quant.sf). These contain gene name, length, and effective length (modeled based on factors affecting the probablility of sampling fragments from this transcript), TPM (transcripts per million, a normalized measure of abundance) and estimated number of mapped reads. For more information, see https://salmon.readthedocs.io/en/latest/file_formats.html.

organism:
Mus musculus
Meyerozyma guilliermondii ATCC 6260

source_name: Whole cell

growth_protocol: M. guilliermondii cultures were grown overnight in YPD medium at 30 °C then diluted back into YPD medium at 30 °C to allow return to exponential phase. Cultures were then washed twice in phosphate buffered saline followed by dilution into Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
M. guilliermondii-only cultures were scraped to detach fungal cells and pelleted by centrifugation, followed by resuspension in ice cold water and centrifugation again. For M. guilliermondii-macrophage co-cultures, medium was aspirated and ice cold water was added to lyse macrophages. Wells were then scraped and samples were pelleted by centrifugation, resuspended again in ice-cold water followed by further centrifugation. Fungal cell walls were digested with zymolyase at 37 °C, followed by RNA extraction using the SV Total RNA Isolation System (Promega).
Libraries were constructed using the TruSeq Stranded RNA library preparation protocol. Sequencing was carried out using the NovaSeq platform (Illumina) to obtain 19-57 million 2 x 151 paired-end reads. All library preparation and sequencing was performed by Macrogen.

treatment_protocol: M. guilliermondii cultures were incubated for 1 hr at 37 °C, 5% CO2 in the presence or absence of primary murine bone marrow derived macrophages after which time the vast majority of fungal cells had been taken up by phagocytosis.

value: co-culture with macrophage


title: iPSC DNMT3A exon 2-/- clone 2


title: iPSC-derived MSC wildtype 1


title: Ki67_aid_HCT116_IAA_mitosis_HiC_r1

description: Hi-C on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: mitosis_IAA.

value: OsTir1; Ki67-miniAID-mClover


title: iPSC-derived MSC DNMT3A exon 2-/- clone 2

value: iPSC DNMT3A exon 2-/- clone 2


title: iPSC-derived MSC DNMT3A exon 19-/- clone 1

value: iPSC DNMT3A exon 19-/- clone 1


title: Mg1_only

organism: Meyerozyma guilliermondii ATCC 6260

value: only (no co-culture)


title: Ki67_aid_HCT116_IAA_interphase_HiC_r1

description: Hi-C on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: interphase_IAA.


title: Mouse brain_rep2_control

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

data_processing:
Adapter seqeucnes were trimmed by using trim_galore
fastuniq is used to remove PCR duplication. Then use seqtk trimfq '-e 10' or '-b 6 -e 10' remove random sequences added in library construction
Clean reads were mapped to genome by using HISAT2; with parameter "--mp 4,2 --rna-strandness RF --no-softclip --no-mixed --no-discordant".
A custom python script was used to parse the pileup format into a tabular format summarizing the mutation at each position.
Assembly: hg38 and mm10
Library strategy: Slic-seq

source_name: mouse brain

growth_protocol: HEK293T cells were cultured in DMEM medium without sodium pyruvate (Dulbecco’s Modified Eagle Medium, HyClone) supplemented with 10% FBS (Cegrogen) and 1% penicillin/streptomycin (Genview). The cells were maintained at 37 ℃ under a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from cell lines or mouse tissues with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25 (NEB)
Fragmented RNA was first subjected to end repair by T4 PNK. For the treated sample, the RNA was treated with periodate followed by Endonuclease V cleavage.3′-adapter ligation (3′ adapter, /5rApp/NNNNNNTGGAATTCTCGGGTGCCAAGG/3ddC/) followed by the 3′ adapter removing by 5′-deadenylase and RecJf digestion. After purification, SuperScript III was used to perform RT (RT primer, /ACACGACGCTCTTCCGATCT). After cDNA synthesis, 5′ adapter (5′ adapter, /5Phos/NNNNNNNNNNAGATCGGAAGAGCACACGTCTG/3ddC/) ligation were performed. After purification, qPCR was performed to evaluate the cycle numbers of each samples to avoid over-amplification. Library PCR amplification was performed using the NEB primers. The products were purified by NEBNext Sample Purification Beads or low melting point agarose gel and used for sequencing.

treatment_protocol: Total RNA was isolated from cell lines or mouse tissues with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25(NEB) and gDNA was removed by TURBO DNase (Invitrogen). Purified polyadenylated RNA was fragmented using RNA fragmentation reagents (Ambion) at 70 °C for 10 min. Fragmented RNA was incubated with freshly prepared 50 mM NaIO4 at 25°C for 30 min in the dark.The RNA cleave assays were performed using Endonuclease V (NEB) with standard reaction buffer (10mM Tris-HCl pH 7.5, 0.5mM MnCl2, 50mM KCl, 1mM dithiothreitol and 5% glycerol)  and then perform next-generation sequencing (NGS).

value: control

tag: tissue type

value: brain tissue


title: Mg2_mac


title: Mouse brain_rep1_control

tag: treatment


title: HEK293T_rep2_treated

source_name: cell line

value: treated

value: human cell line


title: Mg1_mac


title: Mg3_only


title: fastGRO_siControl_d4TGFB_ R2

value: siControl d4 TGF-B

value: TGFbeta treatment


title: Mg2_only


title: EndoVIPER-seq_rep2


title: EndoVIPER-seq_rep1


title: HEK293T_rep1_treated


title: Ki67_aid_HCT116_interphase_HiC_r1

tag: cell type

value: Hi-C

value: interphase


title: Ki67_aid_HCT116_IAA_mitosis_ChIP_input_r1

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: mitosis_IAA, target: input.

value: ChIP-seq

value: input


title: HEK293T_rep3_treated

tag: strain


title: Human brain_rep1_control

source_name: Human brain


title: Human brain_rep2_treated


title: primed-to-naïve day 14

status: Public on May 24 2022

city: Shanghai

first: Bi

last: Yan

address: Siping Road 1239

institute: Tongji university

description: Single Cell 3' v3

data_processing:
10× Genomics single-cell data were pre-processed using the Cell Ranger pipeline (v.4.0.0) with default parameters.
Integration, Dimensionality reduction,clusering and visualization were done by Seurat (v.3.2.3)
Assembly: hg38
Supplementary files format and content: tsv files of cell barcodes and features. mtx files of UMI matrix

source_name: primed-to-naïve day 14

extract_protocol:
Standard 10× genomics scRNA-seq protocol
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) , according to the manufacturer’s instructions. Briefly, cells were washed with 0.04% BSA DPBS for three times and were resuscitated to a concentration of 700~1200 cells/ul (viability≥85%). Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcription step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification. Amplified cDNA was then used for 3’gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads.

value: pluripotent stem cells

tag: cell status

value: primed-to-naïve

value: male


title: naïve hPSC

description: Single Cell 3' v3

source_name: naïve hPSC

value: naïve


title: Mouse brain_rep1_treated


title: Human brain_rep2_control


title: primed hPSC

description: Single Cell 3' v3

source_name: primed hPSC

value: primed


title: Mouse brain_rep2_treated


title: WB_oF5

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Cellranger 4.0
Seurat 4.0
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 sparce matrix

molecule: polyA RNA

source_name: peripheral blood

extract_protocol: 10X 3' (3.1 chemistry)

treatment_protocol: various purification schemes (see purification column)

tag: purification

value: RBC depletion, STEMCELL cat. 01738

tag: cells

value: RBC depleted whole blood

value: female


title: WB_M3_sc_50K

tag: Sex

tag: age


title: WB_oM4


title: Human brain_rep1_treated

value: brain tissue


title: WB_F2_sc_50K


title: Neut_M1_sc_25K

value: negative selection, STEMCELL cat. 19666

value: purified neutrophils


title: Neut_M3_sc_50K


title: iPSC wildtype 1

value: Induced pluripotent stem cells


title: Neut_F3_sc_50K


title: Neut_F1_sc_50K


title: Neut_F2_sc_50K


title: Neut_M0_sc_50K


title: Gran_M2_sc_50K

value: Ficoll/Hypaque gradient, dextran sed.

value: granulocytes, density gradient


title: Neut_M2_sc_50K


title: Ki67_aid_HCT116_mitosis_ChIP_Ki67_r1

description: ChIP-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: mitosis, target: Ki67.

value: Colorectal carcinoma cells

value: OsTir1; Ki67-miniAID-mClover

value: mitosis


title: Gran_M3_sc_50K


title: Gran_F3_sc_50K


title: Gran_F1_sc_50K


title: Gran_F2_sc_50K


title: ChIP-CBP-T3-rep2

status: Public on May 23 2022

city: New York

first: Siqian

last: Feng

state: New York

address: 625 W. 130th Street

institute: Columbia University

data_processing:
For ChIP-seq and ATAC-seq, mapping was done against dm3 with the “Map with Bowtie for Illumina” tool on usegalaxy.org, and only uniquely mapped reads were kept.
ChIP-seq peak calling was performed using the galaxy version of MACS2 (“MACS2 callpeak” on usegalaxy.org), with the following setting: --nomodel –extsize 200, and all other parameters were default
ATAC-seq peak calling was also performed with the galaxy version of MACS2, with the following setting: --nomodel –extsize 200 - -shift -100.
For RNA-seq, the cutadaptor tool on usegalaxy.eu was used to trim reads and remove reads shorter than 100bp. The filtered reads were then mapped to the genome build dm6 using the RNA STAR tool with the following parameters: --sjdbOverhang 149. The featurecount tool was used to obtain the transcript count tables.
Selex-seq data were processed using the NRLB algorithm
Assembly: dm3 for ChIP-seq and ATAC-seq, dm6 for RNA-seq
Supplementary files format and content: bigwig (ChIP-seq and ATAC-seq) and count table (RNA-seq)

organism: Drosophila melanogaster

source_name: T3 leg imaginal discs, wandering larvae

growth_protocol: Drosophila larvae were grown on standard cornmeal or molasses food at 25°C.

extract_protocol:
Tissues were crosslinked with 1% formaldehyde for 10 minutes at RT, and were sonicated. DNA was purified from input and ChIP samples.
ChIP-seq libraries were constructed using illumina TruSeq ChIP Library Preparation Kit

tag: genotype

value: isogenic w1118 (BL5905)

tag: chip antibody

value: rabbit anti-CBP

tag: genome build


title: Gran_M1_sc_50K

value: male


title: ChIP-CBP-T3-rep1


title: input-CBP-T3-rep2


title: WB_F3_sc_50K


title: input-CBP-T1-rep2

source_name: T1 leg imaginal discs, wandering larvae


title: ChIP-CBP-T1-rep1


title: input-CBP-T1-rep1


title: WB_oF4


title: ChIP-Hth-T1-rep2

value: Goat anti Hth dG20 (sc-26187, lot A1204)


title: input-Hth-T1-rep2


title: input-Hth-T1-rep1


title: input-CBP-T3-rep1


title: ChIP-Hth-T1-rep1


title: Bleo4

status: Public on May 22 2022

city: Winnipeg

first: Peter

last: Thompson

state: MB

address: 715 McDermot ave

department: Physiology & Pathophysiology

country: Canada

institute: University of Manitoba

description:
TreatedVSControl_Gene_differential_expression2
TreatedVSControl_Known_lncRNA_differential_expression2
TreatedVSControl_Novel_lncRNA_differential_expression2

data_processing:
All bioinformatic analysis was carried out by an independent company, LC Sciences. Briefly, Cutadapt (v1.10) and perl scripts used to filter adapter contamination and undetermined bases
FastQC (v0.10.1) used to quality check sequences
BowTie2 and HISAT (v2.0.4) used to map sequences to hg38
Mapped reads assembled for each sample with StringTie (v1.3)
Comprehensive transcriptome built with perl scripts and gffcompare, StringTie and edgeR used to estimate transcript expression levels
LncRNAs identified based on filtering transcripts overlapping with known mRNAs and transcripts <200 bps. CPC and CNCI used to predict coding potential, with CPC score <-1 and CNCI score <0 removed. Remaining transcripts were considered lncRNAs. Differential expression performed using StringTie and edgeR to calculate FPKM
Assembly: GRCh38.p12 (ENSEMBL v96) and lncRNA (v27)
Supplementary files format and content: Normalized gene and lncRNA expression levels (FPKM) from edgeR

source_name: Pancreatic Islets of Langerhans_Bleo

growth_protocol: Human islets from a second donor (50 year old female) were rested in culture for 24 h prior treatments

extract_protocol:
Total RNA was extracted with TRIzol-based kit and DNAse I treated
Illumina TruSeq libaries done by LC Sciences

treatment_protocol: After resting, islets wered culture in vehicle (DMSO) or 50 uM bleomycin in normal human islet media (RPMI1640, 10% FBS, 5.5 mM glucose, 1Xantibiotic-antimycotic) for 48 h. Islets were transferred to fresh media for 4 days of culture prior to harvest

tag: individual

value: donor 2

tag: tissue

value: Endocrine Pancreas

value: 50 uM bleomycin for 48 h

value: Adult

value: Female

tag: disease state

value: Non-diabetic


title: Bleo6


title: Veh5

source_name: Pancreatic Islets of Langerhans_Veh

value: vehicle (DMSO) for 48 h


title: Bleo5


title: Ki67_aid_HCT116_IAA_interphase_HiC_r2

tag: library type

value: Hi-C

tag: genetic modification

tag: experiment

tag: condition


title: Veh4

tag: treatment


title: Input-24hDOX-Rep2

status: Public on May 18 2022

city: Brussels

first: Cedric

last: Blanpain

state: anderlecht

address: Route de Lennik 808, Bat C, C6-126

country: Belgium

institute: Université Libre de Bruxelles (ULB)

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Assembly: mm10
Supplementary files format and content: bigwig file for each sample

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Mesp1 is dox-inducible

growth_protocol: Pluripotent stem cells were differentiated using published hanging drop protocols (1000 initial cells in serum-condtining medium)

extract_protocol: NEB Next Ultra II DNA library Prep Kit for Illumina

treatment_protocol: Doxycyclin was added to induce the expression of Mesp1

tag: target-protein

value: Input

value: dox

value: WT


title: Input-12hDOX-Rep2


title: Mesp1-ChIP-seq-ESC-2i-24hdox-Rep2

source_name: mouse embryonic pluripotent stem cells culture in 2i medium where forced expression of Mesp1 is dox-inducible

value: Rabbit anti-HA (cat:ab9110, Abcam, ChIP-grade)


title: ChIP-CBP-T1-rep2


title: Input-ESC-2i-24hdox-Rep2


title: Input-24hND-Rep2


title: Input-d2-5-0h-Rep2


title: Zic2-ChIP-seq-Mesp1WT-24hdox-Rep2

value: Rabbit anti-Zic2 (Cat:epr7790,Abcam, ChIP-grade)


title: Zic3-ChIP-seq-Mesp1WT-24hdox-Rep2

value: Rabbit anti-Zic3 (Cat:ab222124,Abcam, ChIP-grade)


title: Zic2-ChIP-seq-Mesp1WT-24hnodox-Rep2


title: Mesp1-ChIP-seq-24h-DOX-Rep2


title: Zic3-ChIP-seq-Mesp1WT-0h-Rep2


title: Zic2-ChIP-seq-Mesp1WT-0h-Rep2


title: Mesp1-ChIP-seq-12h-DOX-Rep2


title: RNA-SEQ-WT-day4-Sorted-Flk1+/Pdgfra+_rep5

data_processing:
Quality filtering using Trimmomatic
alignment using STAR
Read counting in genes using HT-seq count
Differential expression analysis using DESeq2
Assembly: mm10
Supplementary files format and content: Table of normalized (read per million) reads for the three different batches

extract_protocol: Qiagen RNA extraction kit

tag: differentiation time


title: Input_Zic23-dKO-Rep2


title: Zic3-ChIP-seq-Mesp1WT-24hnodox-Rep2


title: M1-3HA-Zic23dKO-Rep2


title: RNA-SEQ-WT-day4-Sorted-Flk1-/Pdgfra-_rep5


title: RNA-SEQ-WT-day4-Sorted-Flk1-/Pdgfra-_rep4


title: RNA-SEQ-WT-day4-Sorted-Flk1+/Pdgfra+_rep3


title: RNA-SEQ-WT-day4-Sorted-Flk1+/Pdgfra+_rep4


title: RNA-SEQ-WT-day4-Sorted-Flk1-/Pdgfra-_rep3


title: ATAC-seq-Zic2-3-dKO-24h-dox_Rep3

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Assembly: mm10
Supplementary files format and content: BED file of peaks and bigwig files for each sample

extract_protocol: Nextera DNA sample Preparation Kit

tag: time


title: ATAC-SEQ-Sorted_Flk1-/Pdgfra-_Rep3

source_name: Differentiating mouse embryonic pluripotent stem cells at day 4


title: ATAC-SEQ-Sorted_Flk1+/Pdgfra+_Rep2


title: ATAC-seq-Zic2-3-dKO-24h-dox_Rep2


title: ATAC-SEQ-Sorted_Flk1-/Pdgfra-_Rep2


title: ATAC-SEQ-Sorted_Flk1-/Pdgfra-


title: iMGL_ci2_scCRISPRi_sgRNA

status: Public on May 17 2022

first: Mark

last: Cookson

address: 35 Convent Drive

department: National Institute on Aging

institute: National Institutes of Health

data_processing:
A custom demultiplexing workflow using cellranger v6.1.1 from 10x Genomics was used to align fastqs and count reads mapping to the genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Barcode-feature count matrix (HDF5) and sgRNA protospacer calls per cell (CSV).
Supplementary_files_format_and_content: sgPeaknnn refers to a specific genomic region targeted for repression in the CRISPRi experiment. These are noncoding regions upstream of the LRRK2 gene that were found to be accessible in microglia in our ATACseq experiments, that overlie Parkinson's disease genetic risk variants. A tiling approach was used for sgRNA design across the regions, so that there were 11-367 sgRNAs targeting each region in the sgRNA library.

source_name: single guide RNA read (per single cell)

extract_protocol:
Live, transduced (RFP+), CMO-labeled iMicroglia were purified by FACS.
Libraries were constructed according to the Chromium Single Cell 3' Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for CRISRP Screening and Cell Multiplexing User Guide from 10x Genomics.

tag: rs76904798 genotype

value: not available

value: iPSC-derived microglia cells

tag: differentiation protocol

value: iPSC were differentiated to microglia-like cells according to Abud et al 2017 (PMID 28426964), McQuade et al 2018 (PMID 30577865).

tag: cell line


title: iMGL_ci3_scCRISPRi_sgRNA


title: iMGL_ci2_scCRISPRi_CMO

source_name: cell multiplexing oligonucleotide (CMO) label read (per single cell)


title: iMGL_ci3_scCRISPRi_GEX

source_name: gene expression data (single cell RNAseq)


title: iMGL_ci1_scCRISPRi_CMO


title: iMGL_ci1_scCRISPRi_sgRNA


title: iMGL_ci2_scCRISPRi_GEX


title: SN_S2942_snMulti-seq_ATAC

data_processing:
10x Genomics cellranger-arc count algorithm (v1.0.1) was used to align fastqs and count reads mapping to the genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Per barcode cell metrics file (CSV), fragment file (TSV), and barcode-feature count matrix (HDF5).
Library strategy: snMulti-seq (ATAC + GEX)

source_name: frozen substantia nigra tissue

extract_protocol:
Nuclei were extracted from frozen tissue by ultracentrifugation using the Nuclei PURE Prep nuclei isolation kit from Sigma Aldrich.
Libraries were constructed according to the Chromium Single Cell Multiome ATAC + Gene Expression User Guide (v1 Chemistry) from 10x Genomics.

value: substantia nigra

tag: molecule subtype

value: nuclear RNA and genomic DNA


title: ATAC-SEQ-Sorted_Flk1+/Pdgfra+_Rep3

tag: genotype


title: SN_S2942_snMulti-seq_GEX

molecule: nuclear RNA


title: SN_S2960_snMulti-seq_GEX


title: SN_S2972_snMulti-seq_ATAC


title: SN_S2960_snMulti-seq_ATAC


title: FCtx_S1209_snATACseq

data_processing:
10x Genomics cellranger-atac count algorithm (v1.2.0) was used to align fastqs and count reads mapping to the genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Per barcode singlecell.csv file (CSV), fragment file (TSV), and barcode-feature count matrix (HDF5).
Library strategy: snATACseq

source_name: frozen frontal cortex tissue

extract_protocol:
Nuclei were extracted from frozen tissue by ultracentrifugation using the Nuclei PURE Prep nuclei isolation kit from Sigma Aldrich.
Libraries were constructed according to the Chromium Single Cell ATAC Reagent Kits User Guide (v1 Chemistry) from 10x Genomics.

value: CT

value: frontal cortex


title: iMGL_ci1_scCRISPRi_GEX


title: SN_S2972_snMulti-seq_GEX


title: FCtx_S1135_snATACseq


title: FCtx_S4022_snATACseq

value: TT


title: FCtx_S4924_snATACseq


title: FCtx_S1363_snATACseq

value: CC


title: Veh6

value: donor 2

value: Endocrine Pancreas

value: vehicle (DMSO) for 48 h

tag: age

value: Adult

tag: Sex

value: Female

value: Non-diabetic


title: FCtx_S5123_snATACseq

tag: tissue


title: 005_hglPB5

status: Public on May 16 2022

city: Rochester

first: Stephan

last: Emmrich

state: NY

address: 213 Hutchison Hall, River Campus

institute: University of Rochester

description: 3' mRNA UMI

data_processing:
Cellranger 3.1.0 was used to generate count matrices from either an ENSEMBL94 mouse reference ("mmuBM") or FRAMA naked mole-rat BM transcriptome assembly ("hglBM")
RNA features were uniquefied using data.table by sum-up each duplicate
ADT features from each sample were concatenated
Annotation of features, molecules/cells and samples was indexed against the feature matrices
Supplementary files format and content: R workspace containing RNA count matrix and cell annotation

organism: Heterocephalus glaber

source_name: hematopoietic system

growth_protocol: Naked mole-rat or Mouse primary bone marrow cells from healthy specimen

extract_protocol:
Cells were DAPI-sorted as viable unfractionated marrow tissue
Chromium Single-Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)

treatment_protocol: Cells were processed for TotalSeq™ CITE reagents according to the manufacturers instructions (BioLegend), using both human and mouse Fc blocking reagents (BioLegend)

value: peripheral blood

value: 3 years

value: wildtype


title: 113_hglPB7

description: 3' mRNA UMI


title: iMGL_ci3_scCRISPRi_CMO

value: not available

value: iPSC-derived microglia cells


title: FCtx_S630_snATACseq


title: 003_hglPB3

description: 3' mRNA UMI


title: 001_hglPB1

description: 3' mRNA UMI

value: 11 years


title: Iso CD4+ T cells VDJ seq 3

status: Public on May 13 2022

city: Seoul

first: Kyungsoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

country: South Korea

institute: Yonsei University

description:
Single-cell RNA-seq with 10x Genomics 5' v1 V(D)J
Iso CD4+ T cells VDJ seq 3

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.2.1) was used to filter (cutoffs as follows: 1. number of genes per cell, at least 200 and 6000 at most; 2. percentage of mitochondrial counts per cell, 5% at most), normalize (LogNormalize function with default parameters) and scale the UMI matrix (ScaleData function regressing the variables mitochondrial gene percentage and number of UMIs per cell).
Assembly: mm10-3.0.0
Supplementary files format and content: annotations.tsv, normalized_counts.tsv, umi_counts.tsv

extract_protocol:
For single cell RNA sequencing, Lungs from TC-1 tumor bearing Pdcd1fl/fl × Foxp3eGFP-Cre-ERT2(+/-) mice were digested with type IV collagenase and DNaseI mixture. Digested lung samples were stained with CD4 antibody and the LIVE/DEAD fixable dead cell stain kit for sorting of live CD4+ T cells. Tumor infiltrating CD4+ T cells were sorted from isotype control or anti-PD-1 antibody treated Pdcd1fl/fl × Foxp3eGFP-Cre-ERT2(+/-) mice. Single-cell sequencing libraries were prepared by using Chromium 10X Genomics platform with a VDJ Enrichment Kit and 5’ Library & Gel Bead Kit according to the manufacturer’s instructions.
Libraries were constructed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol

treatment_protocol: PD-1 hetero conditional KO mice were treated with tamoxifen on days 0-4. TC-1 tumor cells were intravenously injected on day 12 into PD-1 hetero conditional KO mice. Isotype control or anti-PD-1 antibody were injected into tamoxifen treated PD-1 hetero conditional KO mice on every 3 days after day 13. TC-1 bearing PD-1 hetero conditional KO mice were euthanized at 14 days after TC-1 tumor injection.

tag: strain

tag: cell type

value: Tumor infiltrating CD4+ T cells

value: PD-1fl/fl X Foxp3eGFP-Cre-ERT2(+/-)

tag: antibody

value: Isotype control antibody


title: 004_hglPB4

description: 3' mRNA UMI


title: [alpha]PD-1 CD4+ T cells VDJ seq 3

description:
Single-cell RNA-seq with 10x Genomics 5' v1 V(D)J
αPD-1 CD4+ T cells VDJ seq 3

value: αPD-1 antibody (RMP1-14)


title: Iso CD4+ T cells GEX seq 3

description:
Single-cell RNA-seq with 10x Genomics 5' v1 paired-end
Iso CD4+ T cells GEX seq 3


title: [alpha]PD-1 CD4+ T cells VDJ seq 2

description:
Single-cell RNA-seq with 10x Genomics 5' v1 V(D)J
αPD-1 CD4+ T cells VDJ seq 2


title: FCtx_S4724_snATACseq

value: CT

value: frontal cortex


title: Iso CD4+ T cells VDJ seq 2

description:
Single-cell RNA-seq with 10x Genomics 5' v1 V(D)J
Iso CD4+ T cells VDJ seq 2


title: [alpha]PD-1 CD4+ T cells GEX seq 2

description:
Single-cell RNA-seq with 10x Genomics 5' v1 paired-end
αPD-1 CD4+ T cells GEX seq 2


title: [alpha]PD-1 CD4+ T cells GEX seq 3

description:
Single-cell RNA-seq with 10x Genomics 5' v1 paired-end
αPD-1 CD4+ T cells GEX seq 3


title: Input for TP1 (GSM4081683)

status: Public on May 12 2022

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
50nt sequence reads were identified by the Sequencing Service (using Illumina’s Genome Analyzer 2).
Reads were mapped to the human genome hg19 using the BWA algorithm.
Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Assembly: hg19
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

source_name: Myometrium

growth_protocol: Not applicable

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays
Libraries were prepared by Active Motif Services - Factor Path assays

treatment_protocol: Not applicable

tag: Stage

value: TNL

value: Tissue


title: Input for TP2 (GSM4081684)

value: TL


title: EM_8_rep2 [M_8_3]

status: Public on May 11 2022

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis.
We used FastqC (v0.11.8) and MultiQC (v0.9) to evaluate the raw read quality statistics.
eads were mapped to the zebrafish genome (Ensembl v93) by Hisat2 (v2.0.5) with parameters “--dta -x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation in GTF format (Ensembl v93).
The output of Hisat2 were converted to BAM format and sorted by Samtools (v1.5). The tool Picard MarkDuplicates (v2.18.15) was used to remove duplicates.
Genome_build: GRCz11
Supplementary_files_format_and_content: HTSeq (0.9.1) was used to count reads mapped to each gene with parameters “-t exon –i gene_id -r pos -s reverse”.

organism: Danio rerio

source_name: EM 8d_whole body

growth_protocol: Zebrafish were obtained from Institute of Hydrobiology, Chinese Academy of Sciences (Wuhan). Embryos were incubated in petri dishes after 0 dpf. Each petri dish contained 50 embryos, which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr, and fed twice daily in tank (paramecium at 6-10 dpf, paramecium and fairy shrimp at 11-15 dpf, and fairy shrimp at 16-32 dpf).

extract_protocol:
We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL, measured its purity with NanoPhotometer spectrophotometer (IMPLEN, CA, USA), quantified its concentration with Qubit 3.0 Flurometer (Life Technologies, CA, USA), and checked its integrity by Agilent 2100 bioanalyzer (Agilent Technologies, CA, USA).
Stranded PolyA+ RNA libraries were prepared at Anoroad (Beijing, China) with in-house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System (Illumina Inc., San Diego, CA).

treatment_protocol: Zebrafish were treated with EM and/or E2 continuously before sampling for RNA-seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM (10μg/L) and E2 (100ng/L) either together or alone, as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM, E2 and DMSO to ensure the effectiveness of drugs.

value: AB

value: EM (10μg/L)

value: whole body

tag: library type

value: fr-firststrand (dUTP)


title: 114_hglPB7

description: 3' mRNA UMI

value: peripheral blood

value: wildtype


title: EM_8_rep1 [M_8_1]

tag: treatment


title: EM_32_rep3 [M_32_3]

source_name: EM 32d_whole body


title: EM_64_rep1 [M_64_1]

source_name: EM 64d_whole body


title: EM_64_rep2 [M_64_2]


title: EM_32_rep2 [M_32_2]


title: EM_2_rep2 [M_2_2]

source_name: EM  2d_whole body


title: EM_32_rep1 [M_32_1]


title: EM_2_rep3 [M_2_3]


title: Iso CD4+ T cells GEX seq 2

description:
Single-cell RNA-seq with 10x Genomics 5' v1 paired-end
Iso CD4+ T cells GEX seq 2


title: EM_16_rep2 [M_16_3]

source_name: EM 16d_whole body


title: EM_16_rep2 [M_16_2]


title: EM_2_rep1 [M_2_1]


title: 002_hglPB2

description: 3' mRNA UMI

value: 3 years


title: EM_16_rep1 [M_16_1]


title: DMSO_8_rep1 [D_8_1]

source_name: DMSO 8d_whole body

value: DMSO (100μl/L)


title: DMSO_8_rep3 [D_8_3]


title: DMSO_64_rep1 [D_64_1]

source_name: DMSO 64d_whole body


title: DMSO_8_rep2 [D_8_2]


title: DMSO_64_rep2 [D_64_2]


title: DMSO_32_rep2 [D_32_2]

source_name: DMSO 32d_whole body


title: DMSO_32_rep1 [D_32_1]


title: DMSO_16_rep3 [D_16_3]

source_name: DMSO 16d_whole body


title: DMSO_2_rep2 [D_2_2]

source_name: DMSO 2d_whole body


title: EM_8_rep2 [M_8_2]


title: DMSO_32_rep3 [D_32_3]


title: DMSO_2_rep1 [D_2_1]


title: DMSO_16_rep1 [D_16_1]


title: JUNB_CutTag

status: Public on May 10 2022

city: Beijing

first: Jie

address: Qing Hua Yuan

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description: cultured cells

data_processing:
for bulk RNA-seq data, adapter sequences were trimmed from raw fastq file using TrimGalore (v0.6.4), clean data were mapped to the human reference genome (GRCh38) using STAR (2.7.3a) with --quantMode GeneCounts option to output read count tables, differential gene expression analysis was performed using DESeq2 (v1.24.0)
for single cell RAN-seq data, UMI count matrx was generated using cellranger (v2.0.1) software
for ATAC-seq, CUT & Tag, and ChIP-seq, all of the paired-end raw reads were processed using TrimGalore to trim adaptor and low-quality reads. Adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq were aligned to hg38 by bowtie2 (version 2.3.5) with the parameters: --t --q --N 1 --L 25. PCR duplicates and multiple mapped reads were removed. The replicate BAM files for each time point were merged and removed reads aligning to blacklisted genomic regions before calling peaks with MACS2 (version 2.2.6) and the enriched TF motifs were analyzed by Homer (version 4.10.4, findMotifsGenome).
Assembly: GRCh38

Supplementary files format and content: bed
Library strategy: Cut & Tag

source_name: cultured cells

growth_protocol: Undifferentiated hPSCs were cultured in E8 medium without feeders.

extract_protocol:
Total RNA was isolated from the fresh tissues with RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions and treated with RNase-free DNase.
For RNA-seq, 100ng total RNA in each sample are used for SMART-seq2 library construction.For ATAC-seq, ATAC-seq library was prepared followed the omini-ATAC-seq protocol. For ChIP-seq, ChIP-seq library was prepared followed the ULI-ChIP protocol. For CUT &Tag, 50000 fresh cells were subjected to library construction.

value: Embryonic stem cells

value: human embryonic stem cell line H1


title: RNA_HEC_WT_rep1

description: cultured cells

data_processing:
for bulk RNA-seq data, adapter sequences were trimmed from raw fastq file using TrimGalore (v0.6.4), clean data were mapped to the human reference genome (GRCh38) using STAR (2.7.3a) with --quantMode GeneCounts option to output read count tables, differential gene expression analysis was performed using DESeq2 (v1.24.0)
for single cell RAN-seq data, UMI count matrx was generated using cellranger (v2.0.1) software
for ATAC-seq, CUT & Tag, and ChIP-seq, all of the paired-end raw reads were processed using TrimGalore to trim adaptor and low-quality reads. Adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq were aligned to hg38 by bowtie2 (version 2.3.5) with the parameters: --t --q --N 1 --L 25. PCR duplicates and multiple mapped reads were removed. The replicate BAM files for each time point were merged and removed reads aligning to blacklisted genomic regions before calling peaks with MACS2 (version 2.2.6) and the enriched TF motifs were analyzed by Homer (version 4.10.4, findMotifsGenome).
Assembly: GRCh38

Supplementary files format and content: tab-delimited text files include read count values for all samples


title: RNA_HEC_KO_rep2

description: cultured cells


title: RNA_HEC_KO_rep1

description: cultured cells


title: RNA_HEC_WT_rep2

description: cultured cells


title: DMSO_16_rep2 [D_16_2]


title: hSMG organoid, late passages

status: Public on May 05 2022

first: Jae-Yol

last: Lim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Otorhinolaryngology

institute: Yonsei University College of Medicine

description: 10x genomics

data_processing:
Gene counting with CellRanger 4.0.0
De-multiplexing with Souporcell
Batch-effect corrected via Harmony (version 0.0.5)
Assembly: GRCh38
Supplementary files format and content: Clustering analysis results as h5ad format

source_name: human submandibular gland

extract_protocol:
human SMG organoids were dissociated with TrypLE for 10 min. Dissociated cells were subjected to live cell enrichment with Dead cell Removal kit (Miltenyi). Enriched live cells were processed for single cell RNA-seq as intructions.
Library was performed according to the manufacter’s instructions (10× chromium next GEM single cell 3’v3.1 protocol, #CG000204).

value: human submandibular gland

value: Organoid cells derived from human submandibular gland

value: Cultured for 3 months


title: Ccne1SD Mesoderm day 4, 3' end count mRNA, G2M, replicate 2

status: Public on May 02 2022

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way, RMB, Pod B, 912E, UCSF

institute: UCSF

data_processing:
Quant-seq RNA-seq libraries were all processed as follows. Adapters were trimmed with Cutadapt v1.18 using input parameters of "-m 20 -a "A{18}" -a "T{18}" -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC". Trimmed reads were aligned using STAR v2.7.1a to mm10/Gencode M14 using input commands of "--outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.05 --seedSearchStartLmax 25 --winAnchorMultimapNmax 100". Aligned reads were counted using FeatureCounts v1.6.4.
Assembly: mm10
Supplementary files format and content: Raw Counts

source_name: Ccne1SD SBR

growth_protocol: Differentiation was performed as desribed in Ying et al., 2003

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions (Invitrogen)
Libraries were prepared according to the manufacturer's instructions (Quant-seq, Lexogen)
RNA-seq (Quant-seq 3' end counting (Lexogen))

treatment_protocol: Cells were dissociated at 37°C in HBSS containing 1% trypsin and 10uM EDTA, and then stained for DNA content by incubation with 10ng/ml Hoechst 33342 (ThermoFisher) in HBSS +2% FBS for 45 minutes at 37°C prior to sorting.

value: Ccne1SD SBR

value: Mesoderm Differentiation assay (day 4)

value: Ccne1 mutant

tag: cell cycle_phase

tag: library

value: Quant-seq


title: Ccne1SD Mesoderm day 4, 3' end count mRNA, G2M, replicate 1


title: wt Mesoderm day 4, 3' end count mRNA, G2M, replicate 2

source_name: Sox1 Bry Reporter (SBR)

value: Sox1 Bry Reporter (SBR)

value: wild type


title: ESC 3' end count mRNA, G2M, replicate 6

source_name: ESC

value: ESC


title: Ccne1SD Mesoderm day 4, 3' end count mRNA, G1, replicate 1


title: ESC 3' end count mRNA, G2M, replicate 3


title: wt Mesoderm day 4, 3' end count mRNA, G1, replicate 2


title: wt Mesoderm day 4, 3' end count mRNA, G2M, replicate 1


title: Ccne1SD Mesoderm day 4, 3' end count mRNA, G1, replicate 2


title: ESC 3' end count mRNA, G1, replicate 5


title: ESC 3' end count mRNA, G2M, replicate 1


title: ESC 3' end count mRNA, G1, replicate 4


title: ESC 3' end count mRNA, G1, replicate 3


title: 3T3 3' end count mRNA, G2M, replicate 6

value: fibroblast


title: 3T3 3' end count mRNA, G2M, replicate 5


title: 3T3 3' end count mRNA, G2M, replicate 4


title: ESC 3' end count mRNA, G1, replicate 1


title: 3T3 3' end count mRNA, G2M, replicate 3


title: 3T3 3' end count mRNA, G2M, replicate 2


title: 3T3 3' end count mRNA, G1, replicate 6


title: 3T3 3' end count mRNA, G2M, replicate 1


title: 3T3 3' end count mRNA, G1, replicate 4


title: 3T3 3' end count mRNA, G1, replicate 3


title: wt Mesoderm day 4, 3' end count mRNA, G1, replicate 1


title: ESC 3' end count mRNA, G2M, replicate 5


title: 3T3 3' end count mRNA, G1, replicate 1


title: ESC 3' end count mRNA, G2M, replicate 4


title: ESC 3' end count mRNA, G2M, replicate 2


title: ESC 3' end count mRNA, G1, replicate 6


title: ESC 3' end count mRNA, G1, replicate 2


title: scRNA_post_Liveseq.IBA.1h.8_1.sample1007

status: Public on May 01 2022

city: Lausanne

first: Wanze

address: SV IBI-SV UPDELA, Station 19

country: Switzerland

institute: EPFL

description: merged data from different sequencing lanes

data_processing:
Basecalls performed using bcl2fastq v2.19.1
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR 2.6.1c with parameters "--runMode alignReads --runThreadN 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMultimapNmax 1 --outSAMtype BAM Unsorted SortedByCoordinate"
The bam files were used for generate gene couting matrix using HTSeq with parameters "htseq-count -s no -m union -f"
Assembly: mm10
Supplementary files format and content: A comma-separated values file of read counting for all samples

source_name: IBA

growth_protocol: All these cells are culture in high-glucose DMEM medium (Life Technologies, Carlsbad, CA)  supplemented with 10% fetal bovine serum (FBS) (Gibco), and 1× penicillin/streptomycin solution (Life Technologies) in a 5% CO2 humidified atmosphere at 37 °C and maintained at less than 80% confluence before passaging

extract_protocol:
scRNA_post_Liveseq
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752
Tn5 tagmentation

treatment_protocol:
1h
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752

tag: batch


title: scRNA_post_Liveseq.IBA.4h.8_1.sample1012

treatment_protocol:
4h
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752


title: scRNA_post_Liveseq.IBA.4h.8_1.sample1009


title: scRNA_post_Liveseq.IBA.1h.8_1.sample1005


title: scRNA_post_Liveseq.IBA.1h.8_1.sample1008


title: scRNA_post_Liveseq.IBA.1h.8_1.sample1003


title: scRNA_post_Liveseq.IBA.1h.8_1.sample1001


title: scRNA_post_Liveseq.IBA.0h.8_1.sample1010

treatment_protocol:
0h
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752


title: scRNA_post_Liveseq.IBA.0h.8_1.sample1000


title: scRNA_post_Liveseq.IBA.4h.8_1.sample1011


title: scRNA_post_Liveseq.IBA.4h.8_1.sample999


title: scRNA_post_Liveseq.IBA.1h.8_1.sample998


title: scRNA_post_Liveseq.IBA.1h.8_1.sample1004


title: 3T3 3' end count mRNA, G1, replicate 5


title: scRNA_post_Liveseq.IBA.4h.8_1.sample997


title: scRNA_post_Liveseq.IBA.0h.8_1.sample995


title: scRNA_post_Liveseq.IBA.4h.8_1.sample996


title: 3T3 3' end count mRNA, G1, replicate 2


title: scRNA_post_Liveseq.IBA.0h.8_1.sample993


title: scRNA_post_Liveseq.IBA.0h.8_1.sample994


title: scRNA_post_Liveseq.IBA.0h.8_1.sample992


title: scRNA_post_Liveseq.IBA.0h.8_1.sample991


title: scRNA_post_Liveseq.IBA.1h.8_1.sample987


title: scRNA_post_Liveseq.IBA.4h.8_1.sample986


title: scRNA_post_Liveseq.IBA.0h.8_1.sample1002


title: scRNA_post_Liveseq.IBA.1h.8_1.sample985


title: scRNA_post_Liveseq.IBA.0h.8_1.sample988


title: scRNA_post_Liveseq.IBA.0h.8_1.sample990


title: scRNA_post_Liveseq.IBA.0h.8_1.sample983


title: scRNA_post_Liveseq.IBA.4h.8_1.sample982


title: scRNA_post_Liveseq.IBA.1h.8_1.sample980


title: scRNA_post_Liveseq.IBA.1h.8_1.sample979


title: scRNA_post_Liveseq.IBA.0h.8_1.sample975


title: scRNA_post_Liveseq.IBA.1h.8_1.sample977


title: scRNA_post_Liveseq.IBA.4h.8_1.sample973


title: scRNA_post_Liveseq.IBA.0h.8_1.sample1006


title: scRNA_post_Liveseq.IBA.1h.8_1.sample976


title: scRNA_post_Liveseq.IBA.4h.8_1.sample978


title: scRNA_post_Liveseq.IBA.0h.8_1.sample972


title: scRNA_post_Liveseq.IBA.4h.8_1.sample984


title: scRNA_post_Liveseq.IBA.1h.8_1.sample971


title: scRNA_post_Liveseq.IBA.0h.8_1.sample970


title: scRNA_post_Liveseq.IBA.1h.8_1.sample989


title: scRNA_post_Liveseq.IBA.4h.8_1.sample968


title: scRNA_post_Liveseq.IBA.0h.8_1.sample965


title: scRNA_post_Liveseq.IBA.4h.8_1.sample967


title: scRNA_post_Liveseq.IBA.0h.8_1.sample966


title: scRNA_post_Liveseq.IBA.4h.8_1.sample963


title: scRNA_post_Liveseq.IBA.1h.8_1.sample969


title: scRNA_post_Liveseq.IBA.0h.8_1.sample962


title: scRNA_post_Liveseq.IBA.0h.8_1.sample961


title: scRNA_post_Liveseq.IBA.4h.8_1.sample960


title: scRNA_post_Liveseq.IBA.0h.8_1.sample981


title: scRNA_post_Liveseq.IBA.4h.8_1.sample959


title: scRNA_post_Liveseq.IBA.1h.8_1.sample958


title: scRNA_post_Liveseq.IBA.0h.8_1.sample974


title: scRNA_post_Liveseq.IBA.0h.8_1.sample957


title: scRNA_post_Liveseq.IBA.4h.8_1.sample954


title: scRNA_post_Liveseq.IBA.1h.8_1.sample956


title: scRNA_post_Liveseq.IBA.1h.8_1.sample953


title: scRNA_post_Liveseq.IBA.1h.8_1.sample952


title: scRNA_post_Liveseq.IBA.4h.8_1.sample951


title: scRNA_post_Liveseq.IBA.0h.8_1.sample950


title: scRNA_post_Liveseq.IBA.4h.8_1.sample949


title: scRNA_post_Liveseq.IBA.0h.8_1.sample944


title: scRNA_post_Liveseq.IBA.0h.8_1.sample943


title: scRNA_post_Liveseq.IBA.0h.8_1.sample945


title: scRNA_post_Liveseq.IBA.1h.8_1.sample948


title: scRNA_post_Liveseq.IBA.1h.8_1.sample964


title: scRNA_post_Liveseq.IBA.0h.8_1.sample942


title: scRNA_post_Liveseq.IBA.4h.8_1.sample947


title: scRNA_post_Liveseq.IBA.4h.8_1.sample941


title: scRNA_post_Liveseq.IBA.1h.8_1.sample940


title: scRNA_post_Liveseq.IBA.0h.8_1.sample937


title: scRNA_post_Liveseq.IBA.1h.8_1.sample935


title: scRNA_post_Liveseq.IBA.0h.8_1.sample936


title: scRNA_post_Liveseq.IBA.0h.8_1.sample939


title: scRNA_post_Liveseq.IBA.0h.8_1.sample934


title: scRNA_post_Liveseq.IBA.0h.8_1.sample938


title: scRNA_post_Liveseq.IBA.4h.8_1.sample933


title: scRNA_post_Liveseq.IBA.0h.8_1.sample955


title: scRNA_post_Liveseq.IBA.0h.8_1.sample930


title: scRNA_post_Liveseq.IBA.1h.8_1.sample932


title: scRNA_post_Liveseq.IBA.1h.8_1.sample929


title: scRNA_post_Liveseq.IBA.1h.8_1.sample928


title: scRNA_post_Liveseq.IBA.1h.8_1.sample925


title: scRNA_post_Liveseq.IBA.0h.8_1.sample927


title: scRNA_post_Liveseq.IBA.4h.8_1.sample926


title: scRNA_post_Liveseq.IBA.1h.8_1.sample924


title: scRNA_post_Liveseq.IBA.4h.8_1.sample946


title: scRNA_post_Liveseq.IBA.0h.8_1.sample923


title: scRNA_post_Liveseq.IBA.0h.8_1.sample922


title: scRNA_post_Liveseq.IBA.0h.8_1.sample919


title: scRNA_post_Liveseq.IBA.0h.8_1.sample920


title: scRNA_post_Liveseq.IBA.1h.8_1.sample921


title: scRNA_post_Liveseq.IBA.1h.8_1.sample931


title: scRNA_post_Liveseq.IBA.0h.8_1.sample916


title: scRNA_post_Liveseq.IBA.4h.8_1.sample914


title: scRNA_post_Liveseq.IBA.1h.8_1.sample915


title: scRNA_post_Liveseq.IBA.1h.8_1.sample910


title: scRNA_post_Liveseq.IBA.0h.8_1.sample912


title: scRNA_post_Liveseq.IBA.0h.8_1.sample911


title: scRNA_post_Liveseq.IBA.1h.8_1.sample908


title: scRNA_post_Liveseq.IBA.4h.8_1.sample907


title: scRNA_post_Liveseq.IBA.0h.8_1.sample909


title: scRNA_post_Liveseq.IBA.0h.8_1.sample903


title: scRNA_post_Liveseq.IBA.4h.8_1.sample902


title: scRNA_post_Liveseq.IBA.0h.8_1.sample905


title: scRNA_post_Liveseq.IBA.4h.8_1.sample901


title: scRNA_post_Liveseq.IBA.1h.8_1.sample904


title: scRNA_post_Liveseq.IBA.4h.8_1.sample900


title: scRNA_post_Liveseq.IBA.1h.8_1.sample898


title: scRNA_post_Liveseq.IBA.4h.8_1.sample899


title: scRNA_post_Liveseq.IBA.0h.8_1.sample918


title: scRNA_post_Liveseq.IBA.0h.8_1.sample894


title: scRNA_post_Liveseq.IBA.1h.8_1.sample917


title: scRNA_post_Liveseq.IBA.4h.8_1.sample895


title: scRNA_post_Liveseq.IBA.0h.8_1.sample893


title: scRNA_post_Liveseq.IBA.0h.8_1.sample892


title: scRNA_post_Liveseq.IBA.4h.8_1.sample890


title: scRNA_post_Liveseq.IBA.1h.8_1.sample891


title: scRNA_post_Liveseq.IBA.0h.8_1.sample913


title: scRNA_post_Liveseq.IBA.4h.8_1.sample888


title: scRNA_post_Liveseq.IBA.1h.8_1.sample889


title: scRNA_post_Liveseq.IBA.0h.8_1.sample886


title: scRNA_post_Liveseq.IBA.1h.8_1.sample885


title: scRNA_post_Liveseq.IBA.0h.8_1.sample883


title: scRNA_post_Liveseq.IBA.0h.8_1.sample884


title: scRNA_post_Liveseq.IBA.0h.8_1.sample881


title: scRNA_post_Liveseq.IBA.0h.8_1.sample882


title: scRNA_post_Liveseq.IBA.4h.8_1.sample880


title: scRNA_post_Liveseq.IBA.4h.8_1.sample897


title: scRNA_post_Liveseq.IBA.0h.8_1.sample876


title: scRNA_post_Liveseq.IBA.0h.8_1.sample877


title: scRNA_post_Liveseq.IBA.4h.8_1.sample878


title: scRNA_post_Liveseq.IBA.0h.8_1.sample896


title: scRNA_post_Liveseq.IBA.1h.8_1.sample879


title: scRNA_post_Liveseq.IBA.4h.8_1.sample875


title: scRNA_post_Liveseq.IBA.1h.8_1.sample873


title: scRNA_post_Liveseq.IBA.4h.8_1.sample870


title: scRNA_post_Liveseq.IBA.0h.8_1.sample874


title: scRNA_post_Liveseq.IBA.4h.8_1.sample869


title: scRNA_post_Liveseq.IBA.0h.8_1.sample872


title: scRNA_post_Liveseq.IBA.0h.8_1.sample871


title: scRNA_post_Liveseq.IBA.0h.8_1.sample887


title: scRNA_post_Liveseq.IBA.0h.8_1.sample867


title: scRNA_post_Liveseq.IBA.0h.8_1.sample868


title: scRNA_post_Liveseq.IBA.4h.8_1.sample864


title: scRNA_post_Liveseq.IBA.0h.8_1.sample865


title: scRNA_post_Liveseq.IBA.0h.8_1.sample863


title: scRNA_post_Liveseq.IBA.1h.8_1.sample862


title: scRNA_post_Liveseq.IBA.4h.8_1.sample861


title: scRNA_post_Liveseq.IBA.4h.8_1.sample860


title: scRNA_post_Liveseq.IBA.0h.8_1.sample859


title: scRNA_post_Liveseq.IBA.1h.8_1.sample858


title: scRNA_post_Liveseq.IBA.1h.8_1.sample857


title: scRNA_post_Liveseq.IBA.0h.8_1.sample855


title: scRNA_post_Liveseq.IBA.1h.8_1.sample856


title: Live_seq.ASPC.not_treated.9_4.sample847

source_name: ASPC

extract_protocol:
Live_seq
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752
Tn5 tagmentation

treatment_protocol:
not_treated
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752


title: scRNA_post_Liveseq.IBA.1h.8_1.sample851


title: Live_seq.ASPC.not_treated.9_4.sample848


title: Live_seq.ASPC.DMIR_treated.9_4.sample849

treatment_protocol:
DMIR_treated
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752


title: scRNA_post_Liveseq.IBA.4h.8_1.sample906


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample846


title: scRNA_post_Liveseq.IBA.1h.8_1.sample852


title: scRNA_post_Liveseq.IBA.0h.8_1.sample853


title: Live_seq.ASPC.DMIR_treated.9_4.sample850


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample841

treatment_protocol:
LPS_treated
Please refer the detailed protocol here: https://doi.org/10.1101/2021.03.24.436752


title: Live_seq.ASPC.not_treated.9_4.sample840


title: Live_seq.ASPC.DMIR_treated.9_4.sample843


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample842


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample838


title: Live_seq.ASPC.DMIR_treated.9_4.sample844


title: scRNA_post_Liveseq.IBA.0h.8_1.sample866


title: Live_seq.ASPC.DMIR_treated.9_4.sample837


title: Live_seq.ASPC.DMIR_treated.9_4.sample836


title: Live_seq.ASPC.not_treated.9_4.sample834


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample835


title: Live_seq.ASPC.DMIR_treated.9_4.sample839


title: Live_seq.ASPC.not_treated.9_4.sample832


title: Live_seq.ASPC.not_treated.9_4.sample833


title: Live_seq.ASPC.not_treated.9_4.sample831


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample830


title: Live_seq.ASPC.not_treated.9_4.sample829


title: scRNA_post_Liveseq.IBA.1h.8_1.sample854


title: Live_seq.ASPC.DMIR_treated.9_4.sample828


title: Live_seq.IBA.not_treated.9_4.sample827


title: Live_seq.ASPC.not_treated.9_4.sample845


title: Live_seq.ASPC.not_treated.9_4.sample825


title: Live_seq.IBA.not_treated.9_4.sample824


title: Live_seq.IBA.not_treated.9_4.sample823


title: Live_seq.ASPC.not_treated.9_4.sample822


title: Live_seq.ASPC.DMIR_treated.9_4.sample826


title: Live_seq.ASPC.not_treated.9_4.sample820


title: Live_seq.ASPC.not_treated.9_4.sample821


title: Live_seq.ASPC.not_treated.9_4.sample818


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample815


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample816


title: Live_seq.IBA.not_treated.9_4.sample811


title: Live_seq.ASPC.DMIR_treated.9_4.sample812


title: Live_seq.IBA.not_treated.9_4.sample813


title: Live_seq.ASPC.DMIR_treated.9_4.sample817


title: Live_seq.ASPC.not_treated.9_4.sample809


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample806


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample819


title: Live_seq.IBA.not_treated.9_4.sample804


title: Live_seq.ASPC.DMIR_treated.9_4.sample810


title: Live_seq.ASPC.DMIR_treated.9_4.sample807


title: Live_seq.ASPC.not_treated.9_4.sample805


title: Live_seq.ASPC.DMIR_treated.9_4.sample802


title: Live_seq.ASPC.DMIR_treated.9_4.sample801


title: Live_seq.ASPC.DMIR_treated.9_4.sample800


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample808


title: Live_seq.ASPC.not_treated.9_4.sample803


title: Live_seq.IBA.not_treated.9_4.sample799


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample798


title: Live_seq.ASPC.not_treated.9_4.sample794


title: Live_seq.IBA.not_treated.9_4.sample797


title: Live_seq.IBA.not_treated.9_4.sample792


title: Live_seq.IBA.not_treated.9_4.sample793


title: Live_seq.ASPC.DMIR_treated.9_4.sample795


title: Live_seq.ASPC.DMIR_treated.9_4.sample791


title: Live_seq.ASPC.DMIR_treated.9_4.sample814


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample796


title: Live_seq.ASPC.DMIR_treated.9_4.sample787


title: Live_seq.ASPC.DMIR_treated.9_4.sample788


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample786


title: Live_seq.ASPC.not_treated.9_4.sample783


title: Live_seq.ASPC.not_treated.9_4.sample780


title: Live_seq.ASPC.not_treated.9_4.sample779


title: Live_seq.ASPC.not_treated.9_4.sample781


title: Live_seq.Raw264.7_G9.LPS_treated.9_4.sample775


title: Live_seq.IBA.not_treated.9_4.sample776


title: Live_seq.ASPC.not_treated.9_4.sample773


title: Live_seq.ASPC.DMIR_treated.9_4.sample771


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample778


title: Live_seq.ASPC.DMIR_treated.9_4.sample784


title: Live_seq.ASPC.not_treated.9_4.sample770


title: Live_seq.ASPC.not_treated.9_4.sample782


title: Live_seq.ASPC.not_treated.9_4.sample769


title: Live_seq.ASPC.DMIR_treated.9_4.sample777


title: Live_seq.ASPC.not_treated.9_4.sample789


title: Live_seq.ASPC.DMIR_treated.9_4.sample790


title: Live_seq.ASPC.DMIR_treated.9_4.sample767


title: Live_seq.IBA.not_treated.9_4.sample764


title: Live_seq.Raw264.7_G9.not_treated.9_4.sample766


title: Live_seq.ASPC.not_treated.9_4.sample768


title: Live_seq.IBA.not_treated.9_4.sample761


title: Live_seq.ASPC.not_treated.9_4.sample762


title: Live_seq.ASPC.DMIR_treated.9_4.sample765


title: Live_seq.ASPC.not_treated.9_4.sample763


title: Live_seq.ASPC.not_treated.9_4.sample760


title: Live_seq.ASPC.not_treated.9_4.sample758


title: Live_seq.ASPC.not_treated.9_4.sample774