title: Tumor methylation  CW8

description: Tumor methylation


title: Tumor methylation  CW10

status: Public on Aug 21 2024

type: genomic

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

description: Tumor methylation

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip (850K) as per standard Illumina protocols.

scan_protocol: Infinium MethylationEPIC

data_processing:
Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.
Average Beta or normalized (provide the normalization method) Normalized Beta using preprocessNoob
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Meningioma

label_protocol: Infinium MethylationEPIC

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded or fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles using the Infinium MethylationEPIC array

treatment_protocol: not applicable

tag: sample type

value: Tumor methylation


title: Tumor methylation  CW9

description: Tumor methylation


title: Tumor methylation  CW7

description: Tumor methylation


title: Tumor methylation  CW3

description: Tumor methylation


title: Tumor methylation  CW20

description: Tumor methylation


title: Tumor methylation  CW4

description: Tumor methylation


title: Tumor methylation  CW6

description: Tumor methylation


title: Tumor methylation  CW1

description: Tumor methylation


title: Tumor methylation  CW56

description: Tumor methylation


title: Tumor methylation  CW58

description: Tumor methylation


title: Tumor methylation  CW2

description: Tumor methylation


title: Tumor methylation  CW18

description: Tumor methylation


title: Tumor methylation  CW13

description: Tumor methylation


title: Tumor methylation  I310

description: Tumor methylation


title: Tumor methylation  I272

description: Tumor methylation


title: Tumor methylation  I266

description: Tumor methylation


title: Tumor methylation  I306

description: Tumor methylation


title: Tumor methylation  I258

description: Tumor methylation


title: Tumor methylation  CW29

description: Tumor methylation


title: Tumor methylation  CW12

description: Tumor methylation


title: Tumor methylation  CW52

description: Tumor methylation


title: Tumor methylation  I317

description: Tumor methylation


title: Tumor methylation  I315

description: Tumor methylation


title: Tumor methylation  I314

description: Tumor methylation


title: Tumor methylation  I312

description: Tumor methylation


title: Tumor methylation  I311

description: Tumor methylation


title: Tumor methylation  CW5

description: Tumor methylation


title: Tumor methylation  I313

description: Tumor methylation


title: Tumor methylation  I309

description: Tumor methylation


title: Tumor methylation  CW55

description: Tumor methylation


title: Tumor methylation  I308

description: Tumor methylation


title: Tumor methylation  I304

description: Tumor methylation


title: Tumor methylation  I303

description: Tumor methylation


title: Tumor methylation  I301

description: Tumor methylation


title: Tumor methylation  I302

description: Tumor methylation


title: Tumor methylation  I307

description: Tumor methylation


title: Tumor methylation  I279

description: Tumor methylation


title: Tumor methylation  I300

description: Tumor methylation


title: Tumor methylation  I299

description: Tumor methylation


title: Tumor methylation  I298

description: Tumor methylation


title: Tumor methylation  I297

description: Tumor methylation


title: Tumor methylation  I316

description: Tumor methylation


title: Tumor methylation  I293

description: Tumor methylation


title: Tumor methylation  I295

description: Tumor methylation


title: Tumor methylation  I296

description: Tumor methylation


title: Tumor methylation  I292

description: Tumor methylation


title: Tumor methylation  I291

description: Tumor methylation


title: Tumor methylation  I294

description: Tumor methylation


title: Tumor methylation  I290

description: Tumor methylation


title: Tumor methylation  I286

description: Tumor methylation


title: Tumor methylation  I284

description: Tumor methylation


title: Tumor methylation  I288

description: Tumor methylation


title: Tumor methylation  I287

description: Tumor methylation


title: Tumor methylation  I283

description: Tumor methylation


title: Tumor methylation  I281

description: Tumor methylation


title: Tumor methylation  I280

description: Tumor methylation


title: Tumor methylation  I282

description: Tumor methylation


title: Tumor methylation  I273

description: Tumor methylation


title: Tumor methylation  I277

description: Tumor methylation


title: Tumor methylation  I305

description: Tumor methylation


title: Tumor methylation  I278

description: Tumor methylation


title: Tumor methylation  I274

description: Tumor methylation


title: Tumor methylation  I276

description: Tumor methylation


title: Tumor methylation  I271

description: Tumor methylation


title: Tumor methylation  I270

description: Tumor methylation


title: Tumor methylation  I289

description: Tumor methylation


title: Tumor methylation  I269

description: Tumor methylation


title: Tumor methylation  I268

description: Tumor methylation


title: Tumor methylation  I261

description: Tumor methylation


title: Tumor methylation  I260

description: Tumor methylation


title: Tumor methylation  I264

description: Tumor methylation


title: Tumor methylation  I267

description: Tumor methylation


title: Tumor methylation  I263

description: Tumor methylation


title: Tumor methylation  I285

description: Tumor methylation


title: Tumor methylation  I257

description: Tumor methylation


title: Tumor methylation  I262

description: Tumor methylation


title: Tumor methylation  I253

description: Tumor methylation


title: Tumor methylation  I255

description: Tumor methylation


title: Tumor methylation  I259

description: Tumor methylation


title: Tumor methylation  I251

description: Tumor methylation


title: Tumor methylation  I252

description: Tumor methylation


title: Tumor methylation  I256

description: Tumor methylation


title: Tumor methylation  UHN62

description: Tumor methylation


title: Tumor methylation  I275

description: Tumor methylation


title: Tumor methylation  I248

description: Tumor methylation


title: Tumor methylation  I254

description: Tumor methylation


title: Tumor methylation  I250

description: Tumor methylation


title: Tumor methylation  I249

description: Tumor methylation


title: Tumor methylation  I216

description: Tumor methylation


title: Tumor methylation  I235

description: Tumor methylation


title: Tumor methylation  I246

description: Tumor methylation


title: Tumor methylation  I247

description: Tumor methylation


title: Tumor methylation  I244

description: Tumor methylation


title: Tumor methylation  I243

description: Tumor methylation


title: Tumor methylation  I242

description: Tumor methylation


title: Tumor methylation  I265

description: Tumor methylation


title: Tumor methylation  I236

description: Tumor methylation


title: Tumor methylation  I239

description: Tumor methylation


title: Tumor methylation  I234

description: Tumor methylation


title: Tumor methylation  I240

description: Tumor methylation


title: Tumor methylation  I238

description: Tumor methylation


title: Tumor methylation  I233

description: Tumor methylation


title: Tumor methylation  I230

description: Tumor methylation


title: Tumor methylation  I232

description: Tumor methylation


title: Tumor methylation  I231

description: Tumor methylation


title: Tumor methylation  I237

description: Tumor methylation


title: Tumor methylation  I229

description: Tumor methylation


title: Tumor methylation  I226

description: Tumor methylation


title: Tumor methylation  I228

description: Tumor methylation


title: Tumor methylation  I227

description: Tumor methylation


title: Tumor methylation  I224

description: Tumor methylation


title: Tumor methylation  I222

description: Tumor methylation


title: Tumor methylation  I221

description: Tumor methylation


title: Tumor methylation  I219

description: Tumor methylation


title: Tumor methylation  I218

description: Tumor methylation


title: Tumor methylation  I225

description: Tumor methylation


title: Tumor methylation  I241

description: Tumor methylation


title: Tumor methylation  I245

description: Tumor methylation


title: Tumor methylation  I217

description: Tumor methylation


title: Tumor methylation  I183

description: Tumor methylation


title: Tumor methylation  I206

description: Tumor methylation


title: Tumor methylation  I96

description: Tumor methylation


title: Tumor methylation  I104

description: Tumor methylation


title: Tumor methylation  I215

description: Tumor methylation


title: Tumor methylation  I159

description: Tumor methylation


title: Tumor methylation  I214

description: Tumor methylation


title: Tumor methylation  I213

description: Tumor methylation


title: Tumor methylation  I211

description: Tumor methylation


title: Tumor methylation  I212

description: Tumor methylation


title: Tumor methylation  I210

description: Tumor methylation


title: Tumor methylation  I205

description: Tumor methylation


title: Tumor methylation  I208

description: Tumor methylation


title: Tumor methylation  I204

description: Tumor methylation


title: Tumor methylation  I209

description: Tumor methylation


title: Tumor methylation  I203

description: Tumor methylation


title: Tumor methylation  I202

description: Tumor methylation


title: Tumor methylation  I200

description: Tumor methylation


title: Tumor methylation  I198

description: Tumor methylation


title: Tumor methylation  I199

description: Tumor methylation


title: Tumor methylation  I220

description: Tumor methylation


title: Tumor methylation  I201

description: Tumor methylation


title: Tumor methylation  I197

description: Tumor methylation


title: Tumor methylation  I196

description: Tumor methylation


title: Tumor methylation  I194

description: Tumor methylation


title: Tumor methylation  I193

description: Tumor methylation


title: Tumor methylation  I195

description: Tumor methylation


title: Tumor methylation  I192

description: Tumor methylation


title: Tumor methylation  I191

description: Tumor methylation


title: Tumor methylation  I189

description: Tumor methylation


title: Tumor methylation  I190

description: Tumor methylation


title: Tumor methylation  I188

description: Tumor methylation


title: Tumor methylation  I187

description: Tumor methylation


title: Tumor methylation  I186

description: Tumor methylation


title: Tumor methylation  I184

description: Tumor methylation


title: Tumor methylation  I182

description: Tumor methylation


title: Tumor methylation  I181

description: Tumor methylation


title: Tumor methylation  I207

description: Tumor methylation


title: Tumor methylation  I177

description: Tumor methylation


title: Tumor methylation  I175

description: Tumor methylation


title: Tumor methylation  I174

description: Tumor methylation


title: Tumor methylation  I178

description: Tumor methylation


title: Tumor methylation  I173

description: Tumor methylation


title: Tumor methylation  I176

description: Tumor methylation


title: Tumor methylation  I171

description: Tumor methylation


title: Tumor methylation  I170

description: Tumor methylation


title: Tumor methylation  I169

description: Tumor methylation


title: Tumor methylation  I166

description: Tumor methylation


title: Tumor methylation  I167

description: Tumor methylation


title: Tumor methylation  I165

description: Tumor methylation


title: Tumor methylation  I168

description: Tumor methylation


title: Tumor methylation  I163

description: Tumor methylation


title: Tumor methylation  I164

description: Tumor methylation


title: Tumor methylation  I162

description: Tumor methylation


title: Tumor methylation  I185

description: Tumor methylation


title: Tumor methylation  I158

description: Tumor methylation


title: Tumor methylation  I160

description: Tumor methylation


title: Tumor methylation  I161

description: Tumor methylation


title: Tumor methylation  I155

description: Tumor methylation


title: Tumor methylation  I157

description: Tumor methylation


title: Tumor methylation  I156

description: Tumor methylation


title: Tumor methylation  I152

description: Tumor methylation


title: Tumor methylation  I180

description: Tumor methylation


title: Tumor methylation  I179

description: Tumor methylation


title: Tumor methylation  I153

description: Tumor methylation


title: Tumor methylation  I154

description: Tumor methylation


title: Tumor methylation  I151

description: Tumor methylation


title: Tumor methylation  I148

description: Tumor methylation


title: Tumor methylation  I150

description: Tumor methylation


title: Tumor methylation  I172

description: Tumor methylation


title: Tumor methylation  I149

description: Tumor methylation


title: Tumor methylation  I146

description: Tumor methylation


title: Tumor methylation  I145

description: Tumor methylation


title: Tumor methylation  I142

description: Tumor methylation


title: Tumor methylation  I143

description: Tumor methylation


title: Tumor methylation  I144

description: Tumor methylation


title: Tumor methylation  I141

description: Tumor methylation


title: Tumor methylation  I140

description: Tumor methylation


title: Tumor methylation  I139

description: Tumor methylation


title: Tumor methylation  I138

description: Tumor methylation


title: Tumor methylation  I136

description: Tumor methylation


title: Tumor methylation  I135

description: Tumor methylation


title: Tumor methylation  I134

description: Tumor methylation


title: Tumor methylation  I131

description: Tumor methylation


title: Tumor methylation  I130

description: Tumor methylation


title: Tumor methylation  I133

description: Tumor methylation


title: Tumor methylation  I129

description: Tumor methylation


title: Tumor methylation  I128

description: Tumor methylation


title: Tumor methylation  I127

description: Tumor methylation


title: Tumor methylation  I132

description: Tumor methylation


title: Tumor methylation  I125

description: Tumor methylation


title: Tumor methylation  I126

description: Tumor methylation


title: Tumor methylation  I147

description: Tumor methylation


title: Tumor methylation  I121

description: Tumor methylation


title: Tumor methylation  I124

description: Tumor methylation


title: Tumor methylation  I123

description: Tumor methylation


title: Tumor methylation  I120

description: Tumor methylation


title: Tumor methylation  I119

description: Tumor methylation


title: Tumor methylation  I117

description: Tumor methylation


title: Tumor methylation  I115

description: Tumor methylation


title: Tumor methylation  I118

description: Tumor methylation


title: Tumor methylation  I113

description: Tumor methylation


title: Tumor methylation  I114

description: Tumor methylation


title: Tumor methylation  I110

description: Tumor methylation


title: Tumor methylation  I116

description: Tumor methylation


title: Tumor methylation  I108

description: Tumor methylation


title: Tumor methylation  I111

description: Tumor methylation


title: Tumor methylation  I137

description: Tumor methylation


title: Tumor methylation  I109

description: Tumor methylation


title: Tumor methylation  I106

description: Tumor methylation


title: Tumor methylation  I107

description: Tumor methylation


title: Tumor methylation  I105

description: Tumor methylation


title: Tumor methylation  I103

description: Tumor methylation


title: Tumor methylation  I102

description: Tumor methylation


title: Tumor methylation  I101

description: Tumor methylation


title: Tumor methylation  I99

description: Tumor methylation


title: Tumor methylation  I98

description: Tumor methylation


title: Tumor methylation  I100

description: Tumor methylation


title: Tumor methylation  I97

description: Tumor methylation


title: Tumor methylation  I94

description: Tumor methylation


title: Tumor methylation  I92

description: Tumor methylation


title: Tumor methylation  I93

description: Tumor methylation


title: Tumor methylation  I95

description: Tumor methylation


title: Tumor methylation  I90

description: Tumor methylation


title: Tumor methylation  I89

description: Tumor methylation


title: Tumor methylation  I91

description: Tumor methylation


title: Tumor methylation  I87

description: Tumor methylation


title: Tumor methylation  I86

description: Tumor methylation


title: Tumor methylation  I82

description: Tumor methylation


title: Tumor methylation  I84

description: Tumor methylation


title: Tumor methylation  I83

description: Tumor methylation


title: Tumor methylation  I79

description: Tumor methylation


title: Tumor methylation  I85

description: Tumor methylation


title: Tumor methylation  I75

description: Tumor methylation


title: Tumor methylation  I77

description: Tumor methylation


title: Tumor methylation  I88

description: Tumor methylation


title: Tumor methylation  I76

description: Tumor methylation


title: Tumor methylation  I72

description: Tumor methylation


title: Tumor methylation  I81

description: Tumor methylation


title: Tumor methylation  I80

description: Tumor methylation


title: Tumor methylation  I78

description: Tumor methylation


title: Tumor methylation  I70

description: Tumor methylation


title: Tumor methylation  I71

description: Tumor methylation


title: Tumor methylation  I69

description: Tumor methylation


title: Tumor methylation  I67

description: Tumor methylation


title: Tumor methylation  I65

description: Tumor methylation


title: Tumor methylation  I68

description: Tumor methylation


title: Tumor methylation  I66

description: Tumor methylation


title: Tumor methylation  I54

description: Tumor methylation


title: Tumor methylation  I59

description: Tumor methylation


title: Tumor methylation  I53

description: Tumor methylation


title: Tumor methylation  I49

description: Tumor methylation


title: Tumor methylation  I42

description: Tumor methylation


title: Tumor methylation  I64

description: Tumor methylation


title: Tumor methylation  I63

description: Tumor methylation


title: Tumor methylation  I60

description: Tumor methylation


title: Tumor methylation  I74

description: Tumor methylation


title: Tumor methylation  I57

description: Tumor methylation


title: Tumor methylation  I73

description: Tumor methylation


title: Tumor methylation  I56

description: Tumor methylation


title: Tumor methylation  I50

description: Tumor methylation


title: Tumor methylation  I52

description: Tumor methylation


title: Tumor methylation  I51

description: Tumor methylation


title: Tumor methylation  I55

description: Tumor methylation


title: Tumor methylation  I46

description: Tumor methylation


title: Tumor methylation  I45

description: Tumor methylation


title: Tumor methylation  I44

description: Tumor methylation


title: Tumor methylation  I43

description: Tumor methylation


title: Tumor methylation  I39

description: Tumor methylation


title: Tumor methylation  I41

description: Tumor methylation


title: Tumor methylation  I58

description: Tumor methylation


title: Tumor methylation  I40

description: Tumor methylation


title: Tumor methylation  I38

description: Tumor methylation


title: Tumor methylation  I36

description: Tumor methylation


title: Tumor methylation  I47

description: Tumor methylation


title: Tumor methylation  I35

description: Tumor methylation


title: Tumor methylation  I34

description: Tumor methylation


title: Tumor methylation  I33

description: Tumor methylation


title: Tumor methylation  I32

description: Tumor methylation


title: Tumor methylation  I62

description: Tumor methylation


title: Tumor methylation  I30

description: Tumor methylation


title: Tumor methylation  I29

description: Tumor methylation


title: Tumor methylation  I31

description: Tumor methylation


title: Tumor methylation  I27

description: Tumor methylation


title: Tumor methylation  I25

description: Tumor methylation


title: Tumor methylation  I48

description: Tumor methylation


title: Tumor methylation  I24

description: Tumor methylation


title: Tumor methylation  I23

description: Tumor methylation


title: Tumor methylation  I21

description: Tumor methylation


title: Tumor methylation  I37

description: Tumor methylation


title: Tumor methylation  I20

description: Tumor methylation


title: Tumor methylation  I18

description: Tumor methylation


title: Tumor methylation  I15

description: Tumor methylation


title: Tumor methylation  I16

description: Tumor methylation


title: Tumor methylation  I17

description: Tumor methylation


title: Tumor methylation  I19

description: Tumor methylation


title: Tumor methylation  I7

description: Tumor methylation


title: Tumor methylation  I9

description: Tumor methylation


title: Tumor methylation  I4

description: Tumor methylation


title: Tumor methylation  I13

description: Tumor methylation


title: Tumor methylation  I14

description: Tumor methylation


title: Tumor methylation  I8

description: Tumor methylation


title: Tumor methylation  I6

description: Tumor methylation


title: Tumor methylation  I1

description: Tumor methylation


title: Tumor methylation  I28

description: Tumor methylation


title: Tumor methylation  I3

description: Tumor methylation


title: Tumor methylation  I5

description: Tumor methylation


title: Tumor methylation  I22

description: Tumor methylation


title: Tumor methylation  I26

description: Tumor methylation


title: Tumor methylation  I11

description: Tumor methylation


title: Tumor methylation  I12

description: Tumor methylation


title: Tumor methylation  I10

description: Tumor methylation


title: Tumor methylation  I61

description: Tumor methylation


title: CD4, 20170216_20170216YT_12_TGF+IL4_3_12

type: RNA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

country: USA

institute: national Institute of Health

description: miRNA microarray

hyb_protocol: Total RNA samples were profiled by nCounter mouse v1.5 miRNA Expression Assay Kit (Nanostring technology).

data_processing: The expressed data were normalized using the median normalization analysis. Statistically significant differentially expressed microRNAs were defined as p < 0.05 and fold change > 2. Scanned images were imported into GenePix Pro 6.0 (Axon) for grid alignment and data extraction.

molecule: total RNA

organism: Mus musculus

extract_protocol: Total RNA was derived from cultured cells with an RNeasy Mini kit (Qiagen).

tag: cell line

value: CD4 primary cell

tag: treatment


title: CD4, 20170216_20170216YT_10_TGF_3_10

description: miRNA microarray

value: TGF


title: CD4, 20170216_20170216YT_11_IL4_3_11

description: miRNA microarray


title: CD4, 20170216_20170216YT_09_CTRL_3_09

description: miRNA microarray

value: CTRL


title: Tumor methylation  I2

description: Tumor methylation


title: 2-Air_x484

type: SRA

city: Kyoto

first: Ryo

last: Niwa

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

library_source: transcriptomic

data_processing:
We quantified gene expression using the analysis pipeline (2.3.4) described in the ENCODE project (https://www.encodeproject.org/pipelines/ENCPL002LPE/), using GRCh38 ENSEMBL release 98 as a reference sequence and GRCh38 GENCODE release 32 for gene definitions.
Assembly: GRCh38
Supplementary files format and content: Text file with TPM values

source_name: Human SFTPC-GFP 201B7 iPSC reporter line (B2-3)

growth_protocol: Both airway and alveolar epithelial cells were differentiated from B2-3 SFTPC-GFP reporter (wild type) iPS cells or gene-edited ACE2 KO iPS cells via NKX2-1+ lung progenitor cells, respectively (Gotoh et al., 2014; Konishi et al., 2016; Yamamoto et al., 2017). In brief, iPS cells were stepwise differentiated into definitive endodermal cells, anterior foregut endodermal cells, and NKX2-1+ lung progenitor cells, followed by cell sorting using anti-carboxypeptidase M (CPM) antibody, as previously described (Yamamoto et al., 2017). Upon airway cell induction, isolated CPM+ cells were seeded onto iMatrix-511 silk (Takara Bio) (20 μg/cm3)-coated 24-well cell culture inserts (Falcon) at a density of 1.8 × 106 cells/cm2 with PneumaCult-ALI Maintenance medium (STEMCELL Technologies) supplemented with 10 µM Y-27632 (LC Laboratories), 4 µg/mL heparin (Nacalai Tesque) and 1 µM hydrocortisone (Sigma-Aldrich). After the cells became confluent, the medium was further supplemented with 10 µM DAPT (Wako) and replenished every 2–7 days for a period of 1 month. Upon alveolar epithelial cell induction, isolated CPM+ lung progenitor cells were seeded onto Geltrex (Gibco)-coated 24-well cell culture inserts at a density of 8.3 × 105 cells/cm2 and the cells were cultured for 1-week in ALI in fibroblast-free alveolarization medium exchanged every other day, as described previously (Yamamoto et al., 2017).

extract_protocol:
To extract total RNA, we used the RNeasy Mini Kit following the manufacturer’s instructions.
For preparing sequencing libraries, we used the TruSeq Stranded Total RNA kit from Illumina.

tag: cell type

value: Airway epithelial cells

tag: genotype


title: 3-Air_WT

value: Human SFTPC-GFP 201B7 iPSC reporter line (B2-3)

value: WT


title: 2-Air_1371


title: CD4, 20170216_20170216YT_02_TGF_1_02

description: miRNA microarray


title: 1-Air_x1371


title: 1-Air_x484


title: CD4, 20170216_20170216YT_03_IL4_1_03

description: miRNA microarray


title: CD4, 20170216_20170216YT_07_IL4_2_07

description: miRNA microarray


title: CD4, 20170216_20170216YT_04_TGF+IL4_1_04

description: miRNA microarray


title: CD4, 20170216_20170216YT_06_TGF_2_06

description: miRNA microarray


title: 3-Alv_x484

value: Alveolar epithelial cells


title: 3-Alv_1371


title: 3-Air_x484


title: 2-Air_WT


title: CD4, 20170216_20170216YT_05_CTRL_2_05

description: miRNA microarray


title: CD4, 20170216_20170216YT_08_TGF+IL4_2_08

description: miRNA microarray


title: 3-Alv_WT


title: 1-Air_WT


title: 2-Alv_1371


title: 2-Alv_x484


title: 2-Alv_WT


title: 3-Air_1371


title: 1-Alv_x1371


title: 1-Alv_x484


title: 1-Alv_WT


title: CD4, 20170216_20170216YT_01_CTRL_1_01

description: miRNA microarray


title: HbSS #1 (3xNLS)

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell data was analyzed using cellranger count (v7.0.0) with default parameters. The transcriptome database was based on cellranger GRCh38-2020-A_build.
Seurat v4.3.0 was used for the downstream analysis. The single-cell data were filtered by: (1) number of expressed genes (i.e., nFeature_RNA) between 200-6000, (2) percentage of mitochondrial reads (i.e.,percent.mt) less than 10% and (3) the total read (i.e., nCount_RNA) less than 50000.
The "FindMarkers" function was used for differential gene expression analysis comparing edited and unedited cells. Single-cell data integration was based on the "anchor" method. The UMAP (Uniform Manifold Approximation and Projection) plot was generated using the first 50 PCs. Cell clustering was performed on the UMAP space with resolution of 0.1.
Assembly: hg38
Supplementary files format and content: R data format

molecule: polyA RNA

source_name: Derived from transplanted mouse BM

growth_protocol: All mouse studies were approved by the Institutional Animal Care and Use Committee (IACUC,protocol number #192-100553) at St. Jude Children’s Research Hospital and maintained under specific pathogen-free conditions.

extract_protocol:
Bone marrow (BM) harvested from control and treated mice after 17 weeks and purified with glycophorin-A beads to extract CD235a+ human erythroid cells. Purified cells were processed using 10X genomics according to manufacturer’s protocol.
CD235+ cells pooled from each mice respective to their donors and treatment. Later, cells were loaded separately on the 10x Chromium platform. Gel beads-in-emulsion (GEM) generation, cDNA amplification, and library construction were performed following the protocol of Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, 10x Genomics) with target recovery of 8,000–10,000 cells per library or sample. A total of 13 cycles of PCR were then conducted using the Chromium Single Cell 3′ Library and Gel Bead Kit (10x Genomics) according to the manufacturer’s manuals, to amplify the cDNA library for sufficient RNA libraries. Libraries were prepared following the manufacturer’s manual (10x Genomics), followed by quantification using Agilent Tapestation.

treatment_protocol: 0.5 million cells (control or edited) administered by tail-vein injection to 8- to 12- week-old female mice. Seventeen weeks post transplantation, BM was harvested and evaluated for donor chimerism and indels.

tag: tissue

value: Derived from transplanted mouse BM

value: Human CD34+ HSPCs

value: Human CD235a+

value: Edited


title: HbSC #3 (3xNLS)

description: 10X Genomics


title: HbSS #2 (Control)

description: 10X Genomics

value: Control


title: HK252_PALMITATE_FASNI

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: HK252 PALMITATE FASNI

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCh38 (hg38) as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCh38
Supplementary files format and content: Counts

source_name: cell line

growth_protocol: Serum free GBM media( DMEMF12/B27/Penstrep)

extract_protocol:
Qiagen Mini RNA extraction kit, total RNA
Conventional library prep RNA (Stranded mRNA (Poly-A)

treatment_protocol: Primary GBM cell lines were cultured in GBM media (DMEMF12/B27/Penstrep), treated with either DMS0(control) or DRUG(TVB-2640), palmiate or both for 4 days before collected for RNA extraction

value: cell line

value: primary tumor cell line

value: IDH Mutant


title: HCC2 CSCs culture on  MEFs   3

city: Guang Zhou

first: Tingting

last: Guo

state: Guang Dong

address: University Town Campus (South Campus): 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre,

country: China

institute: South China University of Technology

description: count-MEF.txt

data_processing:
we used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads.
Discard a paired reads if either one read contains adapter contamination;
Discard a paired reads if more than 10% of bases are uncertain in either one read;
Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read
reads from each sample in FASTQ format were aligned to the genome using Hisat2 to generate SAM files, which were then converted to BAM format using Samtools. Gene quantification was performed using FeatureCounts to obtain a raw count matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver cancer

growth_protocol: HCC2 CSCs were cultured under three different conditions, with the incubator with  5% CO2 at 37C

extract_protocol:
Total RNAs from cells were extracted using Universal RNA Extraction Kit (TaKaRa)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: ALDH-positive HCC2 CSCs were cultured in three different ways: on MEFs, in suspension conditions, and in differentiation conditions using DMEM medium containing 10% FBS.

value: liver cancer

value: HCC CELL

value: culture on MEFs


title: HCC2 CSCs culture in DMEM with 10%FBS 2

description: count-FBS.txt

value: culture in DMEM with 11%FBS


title: HCC2 CSCs culture by spheriod 1

description: count-SP.txt

value: culture by  spheriod


title: HCC2 CSCs culture in DMEM with 10%FBS 1

description: count-FBS.txt

value: culture in DMEM with 10%FBS


title: HCC2 CSCs culture by spheriod 3

description: count-SP.txt


title: BT142_PALMITATE_FASNI

description: BT142 PALMITATE FASNI


title: HCC2 CSCs culture in DMEM with 10%FBS 3

description: count-FBS.txt

value: culture in DMEM with 12%FBS


title: HK252_PALMITATE

description: HK252 PALMITATE

value: Palmitate


title: HCC2 CSCs culture on  MEFs   2

description: count-MEF.txt

value: WT


title: BT142_PALMITATE

description: BT142 PALMITATE


title: HbSS #1 (Control)

description: 10X Genomics

value: Derived from transplanted mouse BM


title: 20_213_VPA

description: 213 VPA

extract_protocol:
Qiagen Mini RNA extraction kit, total RNA
Conventional library prep RNA (Stranded mRNA (Poly-A))

treatment_protocol: Primary GBM cell lines were cultured in GBM media (DMEMF12/B27/Penstrep), treated with either DMS0(control) or DRUG(VPA) for 48hrs, collected for RNA extraction

value: IDH MT

value: VPA


title: BT142_CONTROL

description: BT142 CONTROL


title: BT142_FASNI

description: BT142 FASNI

value: Fasni


title: HK252_FASNI

description: HK252 FASNI


title: 19_213_Control

description: 213 Control

value: Control


title: HK252_CONTROL

description: HK252 CONTROL

value: cell line


title: 16_MGG119_VPA

description: MGG119 VPA

value: primary tumor cell line


title: 14_BT142_VPA

description: BT142 VPA


title: 15_MGG119_Control

description: MGG119 Control


title: HbSS #2 (3xNLS)

description: 10X Genomics

value: Human CD34+ HSPCs

value: Human CD235a+

value: Edited


title: HCC2 CSCs culture by spheriod 2

description: count-SP.txt

value: liver cancer

value: HCC CELL


title: 13_BT142_Control

description: BT142 Control


title: HCC2 CSCs culture on  MEFs 1

description: count-MEF.txt

value: culture on MEFs


title: 12_252_VPA

description: 252 VPA


title: HbSC #3 (Control)

description: 10X Genomics


title: 11_252_Control

description: 252 Control


title: 10_206_VPA

description: 206 VPA

value: IDH WT


title: 9_206_Control

description: 206 Control


title: 7_350_Control

description: 350 Control


title: 3_408_Control

description: 408 Control


title: 8_350_VPA

description: 350 VPA


title: 1_157_Control

description: 157 Control


title: 2_157_VPA

description: 157 VPA


title: GS9_Rego_C

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using megSAP (version 0.2-135-gd002274) combined with ngs-bits package (version 2019_11-42-gflb98e63).
Reads were aligned using STAR v2.7.3a
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each replicate.

source_name: tumor, central nervous system

growth_protocol: LN18, LN229, and LNZ308 glioma cell lines were cultured in DMEM (Gibco, Carlsbad, CA, US) supplemented with 10% fetal calf serum (Thermo Fisher Scientific, Waltham, MA, US) and 50 µg/mL Gentamicin (Thermo Fisher Scientific, Waltham, MA, US). GS-9 cells were grown in Neurobasal®-A medium (Gibco, Carlsbad, CA, US) supplemented with 2% B27 without vitamin A (Invitrogen, Waltham, MA, US), 1% GlutaMAX (Thermo Fisher Scientific, Waltham, MA, US), and 0.02 µg/mL fibroblast growth factor (FGF) and epidermal growth factor (EGF) (PeproTech, Cranbury, NJ, US).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

treatment_protocol: All cells were treated with their calculated IC50 concentrations of regorafenib 24 hours, or corresponding concentration of DMSO solvent.

value: tumor, central nervous system

value: glioma

value: regorafenib


title: GS9_DMSO_C

value: DMSO


title: GS9_Rego_A


title: GS9_DMSO_B


title: GS9_Rego_B


title: GS9_DMSO_A


title: LN18_Rego_C


title: LN18_Rego_B


title: 4_408_VPA

description: 408 VPA


title: 5_393_Control

description: 393 Control


title: LN18_Rego_A


title: LNZ308_Rego_B


title: LN18_DMSO_B


title: LNZ308_DMSO_C


title: LNZ308_Rego_C


title: LNZ308_Rego_A


title: LNZ308_DMSO_B


title: LNZ308_DMSO_A


title: LN229_Rego_C


title: LN229_Rego_B


title: LN18_DMSO_A


title: LN229_DMSO_C


title: 6_393_VPA

description: 393 VPA


title: UV-RIP-seq_IgG_rep1

city: Chicago

first: Mannan

last: Bhola

state: IL

address: 303 E Superior St

department: BMG

institute: Northwestern university

description: UV-RIP-seq

data_processing:
The quality control of raw data was evaluated with FastQC and MultiQC (Ewels et al., 2016b).
Reads were mapped uniquely with STAR v2.7.5 (Dobin et al., 2013) to the human genome (hg38) and to the ERCC genome (ERCC92) for sample-level normalization across all IP samples. Only de-duplicated and uniquely mapped reads were used further.
FeatureCounts v2.0.3 (Liao et al., 2014) was used to get the read counts for UV-RIP-seq samples across all transcripts using GENCODE v45 annotation (Frankish et al., 2023).
Transcripts significantly enriched for TOP1 binding were determined by analyzing the differential enrichment of TOP1 IP over IgG using DESeq2 v1.38.3 (Love et al., 2014).
BigWig files were generated by calculating the log2 ratio as RPKM of the TOP1 IP with respect to IgG IP. The BigWig files were visualized in IGV (Thorvaldsdottir et al., 2013).
Assembly: hg38
processed data files format and content: BigWig

growth_protocol: Human SW480 cells were grown at 37°C, supplied with 5% CO₂ in Dulbecco’s modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted from samples using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Total RNA-seq (ribo-depleted) libraries for total RNA-seq and UV-RIP-seq samples were generated and sequenced by Admera Health. Briefly, isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Libraries were constructed with KAPA™ RNA HyperPrep with RiboErase (Roche, Indiana, USA) and performed based on manufacturer’s recommendations. Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). The final library size was about 430 bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used.

treatment_protocol: SW480 cells were crosslinked by UV irradiation (150 mJ/cm−2 at 254 nm) using CL-3000 UV Crosslinker (Analytik Jena).

value: Colorectal Cancer Cell


title: LN229_DMSO_B


title: UV-RIP-seq_TOP1_rep2

description: UV-RIP-seq


title: LN229_DMSO_A


title: UV-RIP-seq_IgG_rep2

description: UV-RIP-seq


title: LN18_DMSO_C


title: UV-RIP-seq_TOP1_rep1

description: UV-RIP-seq


title: LN229_Rego_A


title: TB97

data_processing:
Quality of reads assessed by FastQC tool.
The reads were aligned to the human reference genome using Star aligner.
RNA-Seq reads were counted using HtSeq.
Assembly: GRCh38
Supplementary files format and content: count matrix (txt.file)

extract_protocol:
RNA was extracted from a combination of fresh frozen and paraffin-embedded tissue for meningiomas using the RNeasy Mini Kit, and the AllPrep RNA FFPE Kit (Qiagen, USA) and quantified using the Nanodrop 1000 Instrument (Thermo Scientific, USA) and Agilent Bioanalyzer.
mRNA libraries were generated using NEB Ultra II directional mRNA library prep kit according to the manufacturer’s protocol.

value: Meningioma


title: TB96


title: TB99


title: TB92


title: TB95


title: TB89


title: TB91


title: TB86


title: TB93


title: TB98


title: TB90


title: TB85


title: TB88


title: TB82


title: TB81


title: TB84


title: TB87


title: TB80


title: TB83


title: TB8


title: TB79


title: TB76


title: TB94


title: TB78


title: TB75


title: TB73


title: TB77


title: TB74


title: TB72


title: TB71


title: TB7


title: TB6


title: TB55


title: TB69


title: TB51


title: TB50


title: TB43


title: TB42


title: TB70


title: TB46


title: TB41


title: TB40


title: TB39


title: TB5


title: TB38


title: TB34


title: TB33


title: TB35


title: TB3


title: TB36


title: TB30


title: TB29


title: TB28


title: TB25


title: TB31


title: TB64


title: TB4


title: TB23


title: TB24


title: TB20


title: TB22


title: TB16


title: TB14


title: TB2


title: TB18


title: TB21


title: TB105


title: TB15


title: TB104


title: TB102


title: TB13


title: TB10


title: TB11


title: TB101


title: TB1


title: TB27


title: UHN221


title: UHN12


title: UHN16


title: TB26


title: UHN212


title: UHN90


title: UHN171


title: I316


title: I317


title: I315


title: I313


title: I311


title: I312


title: I309


title: I308


title: I304


title: I303


title: I305


title: TB103


title: I298


title: I314


title: I301


title: I302


title: I300


title: I307


title: I295


title: I296


title: I297


title: I293


title: I291


title: I299


title: I288


title: I294


title: I292


title: I289


title: I290


title: I286


title: I287


title: I284


title: I283


title: I285


title: I282


title: I281


title: I274


title: I280


title: I277


title: I276


title: I278


title: I270


title: I273


title: I275


title: I267


title: I269


title: I268


title: I264


title: I263


title: I265


title: I261


title: I262


title: I260


title: I256


title: I255


title: I257


title: I253


title: I252


title: I254


title: I271


title: I247


title: I250


title: I246


title: I251


title: I242


title: I243


title: I239


title: I240


title: I241


title: I238


title: I237


title: I259


title: I236


title: I232


title: I234


title: I228


title: I233


title: I229


title: I227


title: I225


title: I221


title: I219


title: I220


title: I218


title: I214


title: I213


title: I222


title: I217


title: I215


title: I209


title: I210


title: I231


title: I205


title: I212


title: I207


title: I230


title: I208


title: I202


title: I203


title: I201


title: I223


title: I224


title: I226


title: I211


title: I200


title: I199


title: I198


title: I195


title: I197


title: I194


title: I193


title: I192


title: I190


title: I188


title: I187


title: I189


title: I186


title: I184


title: I182


title: I181


title: I179


title: I177


title: I174


title: I176


title: I173


title: I172


title: I171


title: I170


title: I196


title: I191


title: I166


title: I168


title: I165


title: I167


title: I185


title: I163


title: I158


title: I155


title: I178


title: I164


title: I160


title: I152


title: I162


title: I157


title: I154


title: I150


title: I149


title: I169


title: I153


title: I148


title: I151


title: I156


title: I143


title: I180


title: I144


title: I141


title: I140


title: I139


title: I138


title: I131


title: I133


title: I137


title: I129


title: I126


title: I147


title: I134


title: I146


title: I127


title: I124


title: P1 cortex CUT&Tag-seq of histones [H3K27me3_S34]

city: SHANGHAI

first: MENGGE

last: SUN

address: FENGLIN ROAD

institute: FUDAN UNIVERSITY

description: CUT&Tag positive control sample

library_source: genomic

data_processing:
Sequence tags were analyzed by MACS3 software version 3.0.0 to detect genomic regions enriched with multiple overlapping DNA fragments (peaks), which were identified as potential putative binding sites. After that, the peaks that appeared in both repeated experiments were marked as consensus peak.
Use GenomicFeatures version 1.54.4 to create a txdb file for mm39 by parsing GTF files, which will be used for subsequent peak annotation. Afterwards, Chipseeker version 1.38.0 was used to annotate and visualize the consensus peak, where the TSS (transcription start site) region was defined as -3kb to +3kb.
Using the consensus peak as the target sequence, motif enrichment analysis was performed using Homer version 5.0.1 to obtain p-values. The background sequence was the mm39 whole genome sequence, and the motif lengths sought were 8, 10, and 12.
The data for VISTA Enhancer comes from the beta version of VISTA Enhancer Browser, which can be accessed from https://enhancer.lbl.gov. The genome coordinate transformation of this data was achieved through liftOver version 1.26.0 in the R studio environment. Peak and VISTA enhancer distribution along genomic regions of genes of interest was visualized using the Integrative Genomics Viewer (IGV).
Assembly: mm39
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

source_name: cortex

extract_protocol:
The hGFAP-GFP mice were sacrificed at E18 or P1. The green brain dorsal cortices were collected, minced and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufacturer’s instruction (Miltenyi Biotec, catalog no. 130-092-628). The GFP+ cells were captured and harvested through fluorescence-activated cell sorting (FACS).
Paired-end Illumina sequencing was performed on an Illumina NovaSeq platform following the manufacturer’s instructions and produced 150 bp paired-end reads. All raw sequence data were quality trimmed to a minimum Phred score of 20 using trim_galore version 0.6.7. Apparent PCR duplicates were removed using Picard MarkDuplicates vl.107. All paired-end reads generated from the CUT&Tag-Seq of pERK and GLI3 were aligned to the mm39 mouse genome using subread-align version 2.0.6. The removal of obvious PCR duplicates and filtering of BAM files were achieved through sambamba markdup version 0.8.2 and samtools view version 1.13, respectively.

value: cortex

value: hGFAP-GFP

tag: developmental stage


title: I125


title: P1 cortex CUT&Tag-seq of histones [H3K4me3_S33]

description: CUT&Tag positive control sample


title: I135


title: I145


title: I128


title: I123


title: I122


title: P1 cortex CUT&Tag-seq of histones [H3K27ac_S36]

description: CUT&Tag positive control sample


title: E18 GLI3 cortex CUT&Tag-seq [GLI3_S45]

description: CUT&Tag sample


title: I142


title: I136


title: I130


title: I132


title: I121


title: P1 GLI3 cortex CUT&Tag-seq [GLI3-5_S89]

description: CUT&Tag sample


title: I120


title: I204


title: I119


title: I117


title: I175


title: P1 pERK cortex CUT&Tag-seq [pERK-1_S1]

description: CUT&Tag sample


title: I118


title: P1 pERK cortex CUT&Tag-seq [pERK-2_S2]

description: CUT&Tag sample


title: I115


title: I114


title: I116


title: I113


title: Fresh hepatic tissues,OP-treated,rep2

city: Nanchang

first: Yaojun

last: Cai

address: 1519 Dongyue Avenue

department: Department of Endocrinology and Metabolism

institute: The First Affiliated Hospital, Jiangxi Medical College, Nanchang University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research  species > was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq  approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from  the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following  assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt  (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9).  including the Q20, Q30 and GC-content of the clean data.
Assembly: GRCm39
Supplementary files format and content: txt;row_counts

source_name: Fresh hepatic tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total  RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA,  5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA  was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two  rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under  elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the  cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen,  cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I  (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An  A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter  contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to  the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB,  cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the  following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃  for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final  cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina  Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.  A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research  species > was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq  approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from  the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following  assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt  (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:  1) removing reads containing adapters;  2) removing reads containing polyA and polyG;  3) removing reads containing more than 5% of unknown nucleotides (N);  4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases.  Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9).  including the Q20, Q30 and GC-content of the clean data.
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total  RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA,  5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA  was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two  rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under  elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the  cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen,  cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I  (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An  A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter  contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to  the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB,  cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the  following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃  for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina  Novaseq™ 6000  following the vendor's recommended protocol.

value: Fresh hepatic tissues

tag: strain


title: I111


title: I110


title: I109


title: Fresh hepatic tissues,high fat/cholesterol/fructose diet,rep3


title: Fresh hepatic tissues,OP-treated,rep1


title: PBS Control and Dual ADC Treatment mixed sample

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

description:
10x Genomics
sample 1 and sample 2

data_processing:
The raw reads from the sequencing, stored in three FASTQ files (index reads, forward reads, and reverse reads), were processed using the 10X Genomics Cloud Analysis embedded in Cell Ranger Multi version 7.1.0. The mouse reference genome mm10 2020-A was used for alignment. Sequencing quality control (QC) was performed using FastQC (version 0.12.1) on both Windows and Linux platforms. The count-by-gene matrix was analyzed using the Seurat package (version 4.3.0.1, PMID: 34062119) in R (version 4.3.0). Data normalization and scaling were performed using the SCTransform function developed by Christoph Hafemeister and Rahul Satija. Cell type annotation was done using CellMarker 2.0, PanglaoDB, and the Tabula Muris database.
Assembly: mm10 2020-A
Supplementary files format and content: The processed data files were saved in matrix format, specifically the count-by-gene matrix. This matrix contains gene expression counts for each cell, with genes as rows and cells as columns. The data is used for downstream analysis, including cell clustering, differential gene expression analysis, and cell type annotation. The processed files are typically in the form of text files or compressed archive formats suitable for further analysis using bioinformatics tools.

source_name: TNBC

extract_protocol:
A 10X single-cell library was prepared using the Chromium Fixed RNA Kit (Cat# 1000497, 10X Genomics). Approximately 16,500 cells were hybridized with probe hybridization to target polyadenylated RNA. The hybridized cells were then loaded onto the Chromium X instrument (PN-1000326, 10X Genomics) to generate barcode-labeled single-cell gel beads-in-emulsion (GEMs) with a target cell count of ~10,000. The GEMs were subsequently lysed using a recovery agent to release the hybridized RNA.
cDNA was synthesized from the released RNA, followed by amplification and sample index PCR for indexing. The quality control of cDNA was evaluated using an Agilent Bioanalyzer to ensure the final library molecules contained P5 and P7 priming sites for Illumina sequencers. Single-cell library construction was initiated using the 10X barcoded ligated probe products, and sequencing was performed using the NovaSeq 6000 flow cell 100-cycle kit (Illumina, San Diego, CA, USA) in a Read1:i7:i5 format of 28:10:10:90 bp.

value: TNBC

tag: tissue type

value: PDX tumor harvest from mice

value: PDX TNBC

value: PBS or CD276 mAb-MMAF/IMQ


title: Fresh hepatic tissues,high fat/cholesterol/fructose diet,rep2


title: I108


title: I107


title: Fresh hepatic tissues,high fat/cholesterol/fructose diet,rep1


title: CAR NKT CD45 scRNAs, rep2

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

description: 10x Genomics

data_processing:
Sequencing reads were mapped to mm10, and unique molecular identifier (UMI) counts were collapsed based on the 10x Genomics Cell Ranger software (version 6.1.2). Resulting datasets were analyzed via the Seurat package (v4.0.4) in R (v4.1.1).
Assembly: Sequencing reads were mapped to mm10,
Supplementary files format and content: Tap-separated values files and matrix files

source_name: Melanoma tumor

extract_protocol:
Mice bearing B16-OVA-hCD19 tumors received non-transduced T cells, CAR.CD19 T cells or CAR.CD19 NKTs and 16 days later, CD45+ cells were sorted from multiple pooled tumors from each group and processed for single-cell RNA sequencing analysis.
Barcoding and library preparation were performed following manufacture instructions with the 10x Genomics Chromium Next GEM Single Cell 3’ kit v3.1.

value: Melanoma tumor

value: Immune cells in the Melanoma

value: Wild type

value: CAR NKT


title: NT T CD45 scRNAs, rep2

description: 10x Genomics

value: Nontransduced T


title: CAR T CD45 scRNAs, rep2

description: 10x Genomics

value: CAR T


title: NT NKT CD45 scRNAs, rep2

description: 10x Genomics

value: Nontransduced NKT


title: CAR19/CSF1R T CD45 scRNAs

description: 10x Genomics

value: CAR19/CSF1R T


title: I112


title: I106


title: Fresh hepatic tissues,OP-treated,rep3


title: I103


title: I105


title: NoinductionABX005

city: Beijing

first: Qingrong

last: Ni

address: No.30 Fucheng Road

department: Department of dermatology

institute: Air force medical center

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release109
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: tail skin

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: tail skin

value: wild type with ABX treated


title: I102

value: Meningioma


title: NoinductionABX004


title: NoinductionABX003


title: I101


title: I99


title: NoinductionABX002


title: NoinductionABX001


title: I100


title: I97


title: I98


title: VitiligoABX004

value: vitiligo induction with ABX treated


title: VitiligoABX005


title: VitiligoABX006


title: VitiligoABX003


title: I95


title: I94


title: NoinductionABX006


title: VitiligoABX002


title: Ctrl-HA-5

value: wild type with hippuric acid i.p.


title: VitiligoABX001


title: I93


title: I161


title: I92


title: I91


title: Ctrl-HA-4


title: Ctrl-HA-3


title: I90


title: I89


title: I87


title: Vehicle002

value: wild type with vehicle i.p.


title: I85


title: I88


title: Ctrl-HA-1


title: I86


title: Vehicle001


title: I84


title: I83


title: Ctrl-HA-2


title: Vehicle003


title: Noinduction023

value: wild type


title: Noinduction021


title: I81


title: Noinduction022


title: I82


title: I80


title: Noinduction011


title: I79


title: I77


title: I78


title: Noinduction005


title: Noinduction003


title: Noinduction002


title: Noinduction001


title: I75


title: Vitiligo261

value: vitiligo induction


title: I74


title: I72


title: I73


title: Vitiligo260


title: Vitiligo000


title: I70


title: I68


title: Vitiligo062


title: Vitiligo063


title: Vitiligo047


title: I67


title: I66


title: I71


title: Vitiligo006


title: Noinduction012


title: LG31E4_R47H_101

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with a unique gene count over 5000 or less than 300, cells with UMI counts over 15000, and cells with a high fraction of mitochondrial reads (>1%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v4.0.0 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: hippocampus

tag: Sex

value: Male

tag: age

value: Human ApoE4:E4/E4; P301S tau:+; R47H Human TREM2 KI:+/KI


title: I69


title: I76


title: I28


title: CW56


title: CW58


title: I65


title: LG31E4_R47H_68

description: mRNA expression in mouse hippocampus


title: CW55


title: LG31E4_R47H_82

description: mRNA expression in mouse hippocampus

value: Human ApoE4:E4/E4; P301S tau:+; R47H Human TREM2 KI:+/+


title: LG31E4_R47H_60

description: mRNA expression in mouse hippocampus


title: LG31E4_R47H_61

description: mRNA expression in mouse hippocampus


title: Vitiligo001


title: LG31E4_R47H_94

description: mRNA expression in mouse hippocampus

value: Human ApoE4:E4/E4; P301S tau:-; R47H Human TREM2 KI:+/+


title: FH168


title: LG31E4_R47H_32

description: mRNA expression in mouse hippocampus


title: CW29


title: Vitiligo039


title: CW13


title: I64


title: LG31E4_R47H_78

description: mRNA expression in mouse hippocampus


title: pSabatiniLabsMMrCTXM2i22d221004B

city: Cambridge

first: Evan

last: Macosko

state: MA

address: 75 Ames St

institute: Broad Institute

description: 10x Genomics v.3

data_processing:
Sequencing was performed on Illumina NovaSeq 6000
Sequencing reads were demultiplexed and aligned to the custom-annotated GRCm38 genome using CellRanger v5
CellRanger v5 filtering was performed including 10x barcode correction, UMI correction, and cell barcode calling to produce the filtered_feature_bc_matrix
Assembly: GRCm38 (custom annotated for readout of transgenes)
Supplementary files format and content: barcodes.tsv.gz contains filtered cell barcode information corresponding to column indices of matrix.mtx.gz
Supplementary files format and content: features.tsv.gz contains filtered feature information corresponding to row indices of matrix.mtx.gz
Supplementary files format and content: matrix.mtx.gz contains filtered gene expression counts matrix

source_name: frontal cortex, brain

extract_protocol:
Please see: https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge
10X Chromium Single Cell 3' (V3), manufacturer's protocol

value: frontal cortex, brain

value: C

tag: mouse


title: MDSC_hCD84_2

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
STAR (v2.7.10a) was used for sequence alignments to human genome (GRCh38). Genes with zero expression in all samples were removed and DESeq269 (alpha = 0.05 and Independent Filtering feature= T) was used to obtain differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: IVD-hMDSCs

growth_protocol: Human immunosuppressive myeloid cells were differentiated in vitro from CD33+ enriched cells. Human PBMCs were isolated from healthy volunteer donors by venipuncture, followed by differential density gradient separation (Ficoll-Hypaque; Sigma-Aldrich, St. Louis, MO). CD33+ myeloid cells were then isolated using anti-CD33 magnetic microbeads and LS column separation (Miltenyi Biotec, Germany) as per manufacturer’s instructions. The purity of the isolated cell population was greater than 90% by flow cytometry and the viability of isolated cells was confirmed using trypan blue dye exclusion. Purified CD33+ cells were then cultured in RPMI 1640 (Thermo Fisher Scientific) 10% heat-inactivated FBS (Capricorn Scientific GmbH), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Sigma-Aldrich) in the presence of 50 ng/ml hGM-CSF (Peprotech) and 50 ng/ml hIL-6 (Peprotech) for one week. Cytokines were refreshed after 4 days. At day 7, cells were analysed by flow cytometry and used for in vitro experiments.

extract_protocol:
RNA from IVD-hMDSCs was extracted using RNeasy Micro Kit (Qiagen, Cat n=74004), following manufacturers’ guidelines. RNA integrity was checked with Agilent 2100 Bioanalyzer system.
RNA integrity was checked with Agilent 2100 Bioanalyzer system. NEBNext UltraExpress™ RNA Library Prep Kit (New England BioLabs Inc,) and NEBNext poly (A) mRNA magnetic isolation module (New England BioLabs Inc) were used for cDNA synthesis. The libraries were sequenced using the NextSeq 2000 and P2 kit High (100 cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads.

treatment_protocol: At day 5 of their differentiation, 1 x 106 hIVD-MDSC were exposed with either 2.5 ug/ml of CD84 (Novus Biologicals, Clone 152-1D5) stimulating antibody47,86,87 or recombinant human CD84 (1855-CD, R&D Systems 10µg/ml). Stimulation was performed in RPMI 1640 (Thermo Fisher Scientific) 10% heat-inactivated FBS (Capricorn Scientific GmbH), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Sigma-Aldrich) in the presence of 50 ng/ml hGM-CSF (Peprotech) and 50 ng/ml hIL-6 (Peprotech) at for 48 hours.

value: IVD-hMDSCs

value: recombinant CD84


title: MDSC_hCD84_1


title: MDSCs_untreated_2

value: Untreated


title: tumor048, IF_PDL1L

city: Seoul

first: Jaemoon

last: Koh

address: 101, Daehak-ro Jongno-gu

department: Department of Pathology

country: South Korea

institute: Seoul National University Hospital

description:
tumor048
DSP-1012340070601-C-H11

data_processing:
Fastq files were further processed by a DND system, and raw and Q3 normalized counts of all WTA targets in each ROI were obtained through GeoMx DSP data analysis software. GeoMx DSP counts from each ROI were scaled to the 75th percentile of the expression. ROIs were categorized according to their spatial locations for subsequent analysis.
Assembly: hg38
Supplementary files format and content: CSV file of Q3 normalized counts

source_name: Lung adenocarcinoma

extract_protocol:
We studied 38 resected pADC specimens at Seoul National University Hospital (SNUH) with heterogeneous PD-L1 expression (n = 8). To characterize the heterogeneity of tumor PD-L1 expression and spatial distribution of IC infiltration in the TME, TMAs were constructed from formalin-fixed, paraffin-embedded (FFPE) tissue blocks from eight patients with pADC. For each patient, two to four 2-mm-diameter cores containing the following components were arrayed: IC-inflamed area, high tumor PD-L1 expression (IF PDL1H); IC-inflamed area, low tumor PD-L1 expression (IF PDL1L); IC-deficient area, high tumor PD-L1 expression (ID PDL1H); and IC-deficient area, low tumor PD-L1 expression (ID PDL1L).
ROIs were placed on 20× fluorescent images scanned using by GeoMx DSP. Oligoes from PanCK+ and PanCK− regions were collected separately via ultraviolet-induced cleavage. The oligoes then were uniquely indexed using the Illumina i5 × i7 dual indexing system (Illumina, San Diego, CA, USA). Polymerase chain reactions (PCR) were purified, and libraries were paired-end sequenced (2 × 75) on a NextSeq550 system (Illumina).

value: Lung adenocarcinoma

value: tumor

value: EGFRmt

tag: group

tag: case

value: case8 IF


title: pSabatiniLabsMMrCTXM2i21d221004B

description: 10x Genomics v.3


title: UHN102

city: Toronto

first: Vikas

last: Patil

address: 610 University Ave.

institute: Princess Margaret Cancer Center

value: Meningioma


title: tumor047, IF_PDL1L

description:
tumor047
DSP-1012340070601-C-H09


title: I57


title: I46


title: pSabatiniLabsMMrCTXM2i20d221004B

description: 10x Genomics v.3


title: immune045, IF_PDL1L

description:
immune045
DSP-1012340070601-C-H06

value: immune cell


title: MDSCs_untreated_1


title: I245


title: pSabatiniLabsMMrCTXM2i22d221004A

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2i21d221004A

description: 10x Genomics v.3


title: tumor046, IF_PDL1L

description:
tumor046
DSP-1012340070601-C-H07


title: LG31E4_R47H_80

description: mRNA expression in mouse hippocampus


title: immune046, IF_PDL1L

description:
immune046
DSP-1012340070601-C-H08


title: immune048, IF_PDL1L

description:
immune048
DSP-1012340070601-C-H12


title: immune047, IF_PDL1L

description:
immune047
DSP-1012340070601-C-H10


title: tumor045, IF_PDL1L

description:
tumor045
DSP-1012340070601-C-H05


title: immune044, IF_PDL1L

description:
immune044
DSP-1012340070601-C-H04

value: case7 IF


title: pSabatiniLabsMMrCTXM2i20d221004A

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2i18d221004C

description: 10x Genomics v.3


title: tumor044, IF_PDL1L

description:
tumor044
DSP-1012340070601-C-H03


title: immune043, IF_PDL1L

description:
immune043
DSP-1012340070601-C-H02


title: pSabatiniLabsMMrCTXM2i18d221004B

description: 10x Genomics v.3


title: I43


title: tumor043, IF_PDL1L

description:
tumor043
DSP-1012340070601-C-H01


title: UHN97


title: immune042, IF_PDL1L

description:
immune042
DSP-1012340070601-C-G12


title: I40


title: tumor041, IF_PDL1L

description:
tumor041
DSP-1012340070601-C-G09


title: pSabatiniLabsMMrCTXM2i17d221004C

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2i17d221004B

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2i18d221004A

description: 10x Genomics v.3


title: tumor040, ID_PDL1L

description:
tumor040
DSP-1012340070601-C-G07

value: case6 ID


title: tumor042, IF_PDL1L

description:
tumor042
DSP-1012340070601-C-G11


title: pSabatiniLabsMMrCTXM2i15d221004B

description: 10x Genomics v.3


title: UHN147


title: UHN149


title: UHN142


title: tumor037, ID_PDL1L

description:
tumor037
DSP-1012340070601-C-G01


title: pSabatiniLabsMMrCTXM2i15d221004A

description: 10x Genomics v.3


title: immune040, ID_PDL1L

description:
immune040
DSP-1012340070601-C-G08


title: immune039, ID_PDL1L

description:
immune039
DSP-1012340070601-C-G06


title: tumor036, IF_PDL1L

description:
tumor036
DSP-1012340070601-C-F11

value: case6 IF


title: immune035, IF_PDL1L

description:
immune035
DSP-1012340070601-C-F10


title: tumor039, ID_PDL1L

description:
tumor039
DSP-1012340070601-C-G05


title: pSabatiniLabsMMrCTXM2i17d221004A

description: 10x Genomics v.3


title: tumor038, ID_PDL1L

description:
tumor038
DSP-1012340070601-C-G03


title: UHN104


title: UHN148


title: immune038, ID_PDL1L

description:
immune038
DSP-1012340070601-C-G04


title: pSabatiniLabsMMrCTXM2i14d221004A

description: 10x Genomics v.3


title: UHN145


title: immune037, ID_PDL1L

description:
immune037
DSP-1012340070601-C-G02


title: immune036, IF_PDL1L

description:
immune036
DSP-1012340070601-C-F12


title: immune041, IF_PDL1L

description:
immune041
DSP-1012340070601-C-G10


title: pSabatiniLabsMMrCTXM2i13d221004C

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2i14d221004C

description: 10x Genomics v.3


title: immune032, IF_PDL1L

description:
immune032
DSP-1012340070601-C-F04

value: case5 IF


title: tumor032, IF_PDL1L

description:
tumor032
DSP-1012340070601-C-F03


title: UHN10


title: immune031, ID_PDL1L

description:
immune031
DSP-1012340070601-C-F02

value: case5 ID


title: UHN111


title: tumor031, ID_PDL1L

description:
tumor031
DSP-1012340070601-C-F01


title: UHN139


title: pSabatiniLabsMMrCTXM2i14d221004B

description: 10x Genomics v.3


title: immune030, IF_PDL1H

description:
immune030
DSP-1012340070601-C-E12


title: UHN109


title: immune034, IF_PDL1H

description:
immune034
DSP-1012340070601-C-F08


title: tumor035, IF_PDL1L

description:
tumor035
DSP-1012340070601-C-F09


title: UHN138


title: immune033, IF_PDL1H

description:
immune033
DSP-1012340070601-C-F06


title: tumor034, IF_PDL1H

description:
tumor034
DSP-1012340070601-C-F07


title: UHN140


title: UHN1


title: tumor033, IF_PDL1H

description:
tumor033
DSP-1012340070601-C-F05


title: pSabatiniLabsMMrCTXM2i13d221004B

description: 10x Genomics v.3


title: UHN80


title: pSabatiniLabsMMrCTXM2i13d221004A

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2i10d221004C

description: 10x Genomics v.3

value: DN-THRB


title: tumor030, IF_PDL1H

description:
tumor030
DSP-1012340070601-C-E11


title: UHN152


title: tumor026, ID_PDL1L

description:
tumor026
DSP-1012340070601-C-E03


title: immune029, ID_PDL1H

description:
immune029
DSP-1012340070601-C-E10


title: UHN18


title: UHN105


title: tumor029, ID_PDL1H

description:
tumor029
DSP-1012340070601-C-E09


title: immune028, ID_PDL1H

description:
immune028
DSP-1012340070601-C-E08


title: tumor028, ID_PDL1H

description:
tumor028
DSP-1012340070601-C-E07


title: pSabatiniLabsMMrCTXM2i10d221004B

description: 10x Genomics v.3

value: frontal cortex, brain


title: FH96


title: immune027, IF_PDL1H

description:
immune027
DSP-1012340070601-C-E06


title: pSabatiniLabsMMrCTXM2i8d221004C

description: 10x Genomics v.3

value: WT-THRB

value: C


title: pSabatiniLabsMMrCTXM2i10d221004A

description: 10x Genomics v.3


title: tumor027, IF_PDL1H

description:
tumor027
DSP-1012340070601-C-E05


title: UHN122


title: pSabatiniLabsMMrCTXM2i8d221004B

description: 10x Genomics v.3


title: immune026, ID_PDL1L

description:
immune026
DSP-1012340070601-C-E04


title: pSabatiniLabsMMrCTXM2i9d221004B

description: 10x Genomics v.3


title: UHN64


title: immune024, IF_PDL1H

description:
immune024
DSP-1012340070601-C-D12

value: wt

value: case4 IF


title: immune021, IF_PDL1H

description:
immune021
DSP-1012340070601-C-D06

value: Lung adenocarcinoma


title: tumor025, IF_PDL1L

description:
tumor025
DSP-1012340070601-C-E01

value: tumor


title: pSabatiniLabsMMrCTXM2i9d221004A

description: 10x Genomics v.3


title: immune025, IF_PDL1L

description:
immune025
DSP-1012340070601-C-E02

value: EGFRmt


title: tumor024, IF_PDL1H

description:
tumor024
DSP-1012340070601-C-D11


title: pSabatiniLabsMMrCTXM2i9d221004C

description: 10x Genomics v.3


title: UHN95


title: immune020, ID_PDL1L

description:
immune020
DSP-1012340070601-C-D04

value: case3 ID


title: pSabatiniLabsMMrCTXM2i8d221004A

description: 10x Genomics v.3


title: tumor019, ID_PDL1H

description:
tumor019
DSP-1012340070601-C-D01


title: tumor022, IF_PDL1H

description:
tumor022
DSP-1012340070601-C-D07


title: immune018, IF_PDL1L

description:
immune018
DSP-1012340070601-C-C12

value: case3 IF


title: pSabatiniLabsMMrCTXM2i7d221004A

description: 10x Genomics v.3


title: tumor018, IF_PDL1L

description:
tumor018
DSP-1012340070601-C-C11


title: tumor023, IF_PDL1H

description:
tumor023
DSP-1012340070601-C-D09


title: UHN154

value: Meningioma


title: UHN78


title: pSabatiniLabsMMrCTXM2i7d221004C

description: 10x Genomics v.3


title: immune023, IF_PDL1H

description:
immune023
DSP-1012340070601-C-D10

value: immune cell


title: pSabatiniLabsMMrCTXM2i7d221004B

description: 10x Genomics v.3


title: immune017, IF_PDL1L

description:
immune017
DSP-1012340070601-C-C10


title: immune022, IF_PDL1H

description:
immune022
DSP-1012340070601-C-D08


title: FH83


title: pSabatiniLabsMMrCTXM2iDd2210042

description: 10x Genomics v.3


title: tumor017, IF_PDL1L

description:
tumor017
DSP-1012340070601-C-C09


title: tumor021, IF_PDL1H

description:
tumor021
DSP-1012340070601-C-D05


title: immune016, IF_PDL1H

description:
immune016
DSP-1012340070601-C-C08


title: immune019, ID_PDL1H

description:
immune019
DSP-1012340070601-C-D02


title: tumor020, ID_PDL1L

description:
tumor020
DSP-1012340070601-C-D03


title: immune015, IF_PDL1H

description:
immune015
DSP-1012340070601-C-C06


title: UHN63


title: pSabatiniLabsMMrCTXM2iDd2210043

description: 10x Genomics v.3


title: CW52


title: tumor015, IF_PDL1H

description:
tumor015
DSP-1012340070601-C-C05


title: FH75


title: FH89


title: UHN36


title: tumor014, ID_PDL1L

description:
tumor014
DSP-1012340070601-C-C03

value: case2 ID


title: pSabatiniLabsMMrCTXM2iDd2210041

description: 10x Genomics v.3


title: tumor013, ID_PDL1L

description:
tumor013
DSP-1012340070601-C-C02


title: pSabatiniLabsMMrCTXM2iCd2210043

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2iCd2210042

description: 10x Genomics v.3


title: tumor012, IF_PDL1L

description:
tumor012
DSP-1012340070601-C-B12

value: case2 IF


title: FH78


title: pSabatiniLabsMMrCTXM2iCd2210041

description: 10x Genomics v.3


title: pSabatiniLabsMMrCTXM2iBd2210043

description: 10x Genomics v.3


title: FH42


title: tumor016, IF_PDL1H

description:
tumor016
DSP-1012340070601-C-C07


title: immune010, IF_PDL1L

description:
immune010
DSP-1012340070601-C-B09


title: pSabatiniLabsMMrCTXM2iBd2210042

description: 10x Genomics v.3


title: UHN57


title: pSabatiniLabsMMrCTXM2iBd2210041

description: 10x Genomics v.3


title: immune009, IF_PDL1L

description:
immune009
DSP-1012340070601-C-B07


title: tumor009, IF_PDL1L

description:
tumor009
DSP-1012340070601-C-B06


title: immune014, ID_PDL1L

description:
immune014
DSP-1012340070601-C-C04


title: immune008, ID_PDL1L

description:
immune008
DSP-1012340070601-C-B05

value: case1 ID


title: pSabatiniLabsMMrCTXM2iAd2210043

description: 10x Genomics v.3


title: tumor008, ID_PDL1L

description:
tumor008
DSP-1012340070601-C-B04


title: UHN48


title: pSabatiniLabsMMrCTXM2iAd2210042

description: 10x Genomics v.3


title: immune007, ID_PDL1L

description:
immune007
DSP-1012340070601-C-B03


title: immune012, IF_PDL1L

description:
immune012
DSP-1012340070601-C-C01


title: UHN27


title: tumor007, ID_PDL1L

description:
tumor007
DSP-1012340070601-C-B02


title: UHN15


title: tumor011, ID_PDL1L

description:
tumor011
DSP-1012340070601-C-B10


title: immune011, ID_PDL1L

description:
immune011
DSP-1012340070601-C-B11


title: I52


title: pSabatiniLabsMMrCTXM2iAd2210041

description: 10x Genomics v.3


title: immune006, IF_PDL1L

description:
immune006
DSP-1012340070601-C-B01

value: case1 IF


title: pSabatiniLabsMMrCTXMOpiBd220318BR2

description: 10x Genomics v.3

value: DN-THRB


title: tumor006, IF_PDL1L

description:
tumor006
DSP-1012340070601-C-A12


title: immune005, IF_PDL1H

description:
immune005
DSP-1012340070601-C-A11


title: immune004, IF_PDL1L

description:
immune004
DSP-1012340070601-C-A09


title: pSabatiniLabsMMrCTXMOpiBd220318BR1

description: 10x Genomics v.3

value: frontal cortex, brain


title: I51


title: tumor010, IF_PDL1L

description:
tumor010
DSP-1012340070601-C-B08


title: UHN43


title: tumor004, IF_PDL1L

description:
tumor004
DSP-1012340070601-C-A08


title: FH136


title: pSabatiniLabsMMrCTXMOpiBd220318BL

description: 10x Genomics v.3


title: tumor005, IF_PDL1H

description:
tumor005
DSP-1012340070601-C-A10


title: immune002, ID_PDL1H

description:
immune002
DSP-1012340070601-C-A05


title: I50


title: tumor003, IF_PDL1H

description:
tumor003
DSP-1012340070601-C-A06


title: pSabatiniLabsMMrCTXMOpiAd220318AR

description: 10x Genomics v.3


title: tumor002, ID_PDL1H

description:
tumor002
DSP-1012340070601-C-A04


title: I48


title: I44


title: immune001, ID_PDL1H

description:
immune001
DSP-1012340070601-C-A03


title: pSabatiniLabsMMrCTXMOpiAd220318AL

description: 10x Genomics v.3


title: I63


title: wt_HSPC_IgG_1

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

institute: DKFZ (German Cancer Research Center)

data_processing:
TrimGalore v. 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was deployed together with Cutadapt v. 1.14 (https://cutadapt.readthedocs.io/en/stable/) using the non-default parameters “--paired”, “--nextera”, “--length_1 35”, and “--length_2 35” to perform adapter and quality trimming.
Bowtie2 v. 2.2.6 (PMID: 22388286) was used with the “--very-sensitive” flag and a maximum insertion length of 2500 bp to map trimmed reads against the GRCh37/hg19 reference genome.
Aligned reads belonging to the same lane-multiplexed library were combined using SAMtools merge v. 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).
Discordant mappings and alignments with a Phred score below 20 were removed using SAMtools view.
Trimmed reads were additionally aligned against the S. cerevisiae R64 reference genome followed by post-alignment filtering as described above. To derive a library-specific scaling factor, the multiplicative inverse of the number of filtered alignments against the yeast genome were calculated. Coverage tracks were generated using the bamCoverage functionality of Deeptools v. 3.1.1 (https://anaconda.org/bioconda/deeptools/files?version=3.1.1) with the non-default parameters “--ignoreForNormalization chrM chrY chrX” and “--effectiveGenomeSize 2652783500” as well as the “--scaleRatio” option to specify the spike-in-derived scaling factor.
Peak calling was performed with MACS v.2.2.6 (https://pypi.org/project/MACS2/) using a wrapper script callpeaks provided by Encode (https://www.encodeproject.org/chip-seq/histone/); to identify HSPC-specific peaks, ACT-seq data from corresponding iPSCs were used as reference.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)
Library strategy: Antibody-guided chromatin tagmentation (ACT-seq)

source_name: HSPC

growth_protocol: Cell line ChiPSC22 and its t(7;12) derivatives were grown in the feeder free DEF-CS culture system (Cellartis/Takara Bio Europe) under standard conditions.

extract_protocol:
Cell permeabilization of native cells and tagmentation reaction with pA-Tn5 transposome-antibody complex for "Antibody-guided chromatin tagmentation (ACT-seq)" according to Carter et al (PMID: 31431618). For normalization of sequence reads between biological replicates, ~4,000 permeabilized nuclei of yeast Saccharomyces cerevisiae, prepared according to (PMID: 25827087) and incubated with pA-Tn5ome-ab complex targeting yeast H2B, were spiked into each mix of cells and pA-Tn5ome-ab complex.  Tagmented DNA was purified with MinElute (Qiagen) columns (ACTseq) according to the provider's instruction.
Libraries were prepared according to Weichenhan et al. (PMID: 29224141). Briefly, tagmented DNA was amplified by PCR under real-time conditions using a universal Illumina forward and a barcoded reverse primer and the NEBNext High Fidelity 2x PCR Master-Mix (NEB), and amplfication was monitored by inspecting real time the amplification curves. DNA was HighPrep bead-purified, Qubit (Invitrogen) quantitated and sized by TapeStation (Agilent) profiling.

treatment_protocol: Before differentiation of CHIPSC22 and its t(7;12) derivatives to HSPCs, they were transferred to Matrigel (BD Biosciences, Stockholm, Sweden) and mTeSR1 medium (StemCell Technologies Inc., Grenoble, France) for 2-3 passages. They were then grown for 3-4 passages as clusters using Gentle Cell Dissociation Reagent (Stemcell Technologies Inc.). The STEMdiff Hematopoietic kit (Stemcell Technologies Inc.) was used for the differentiations according to the protocol. On day 12 of the differentiation, the hematopoietic cells were harvested and analyzed by ATAC-seq.

value: HSPC

tag: chip antibody

value: IgG (Millipore PP64)


title: tumor001, ID_PDL1H

description:
tumor001
DSP-1012340070601-C-A02

value: wt


title: I41


title: translocation_HSPC_IgG_1

value: translocation t(7;12)


title: immune003, IF_PDL1H

description:
immune003
DSP-1012340070601-C-A07

value: Lung adenocarcinoma


title: translocation_HSPC_IgG_3


title: scTCR-seq of pooled anti-PDL1 antibody-treated cells derived from flow cell 2

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

data_processing:
The analysis was performed with using CellRanger (version 7.0.1) with default parameters. Demultiplexing was done allowing 1 mismatch in the barcodes.
Assembly: not provided
Supplementary files format and content: Cellranger output files:
Supplementary files format and content: sample_id_filtered_feature_bc_matrix.h5, sample_id_clonotypes.csv, sample_id_filtered_contig_annotations.csv
Supplementary files format and content: sample_id_vdj_contig_info.pb (these files should be used to aggregate [cellranger aggr] TCR sequences from X_T1_TCR and X_T2_TCR samples within each treatment condition).

source_name: Tumor

extract_protocol:
Cells were concentrated to 1000 cells/ml and loaded onto the Chromium Controller (10X Genomics, Pleasanton, CA) with a target of 10,000 cells per sample. Two captures per treatment condition were performed. Cells were mixed with barcoded gel beads and 5’ GEM Kit v3 reagents and single cell capture was performed (10X Genomics).
Following reverse transcription, cDNA and murine TCRs were amplified, and gene expression and TCR sequencing libraries were constructed according to the manufacturer’s recommendations. Each DNA library was loaded into a sequencing lane on a NovaSeq system (Illumina, USA) and was sequenced with pair-end reads of 75 bp.

value: Tumor

value: T cells

value: anti-PDL1 antibody


title: translocation_HSPC_IgG_2


title: I56

source_name: Meningioma


title: translocation_iPSC_IgG_3

source_name: iPSC

value: iPSC


title: scTCR-seq of pooled anti-PDL1 antibody-treated cells derived from flow cell 1


title: translocation_iPSC_IgG_2


title: I62

value: Meningioma


title: I45


title: wt_HSPC_H3K27ac_3

value: H3K27ac (Abcam ab4729)


title: scTCR-seq of pooled bintrafusp control cells derived from flow cell 2

value: control


title: translocation_iPSC_IgG_1


title: I60


title: I55


title: translocation_HSPC_H3K27ac_2


title: wt_HSPC_H3K27ac_2


title: wt_HSPC_H3K27ac_1


title: scTCR-seq of pooled bintrafusp alfa-treated cells derived from flow cell 2

value: bintrafusp alpha


title: scTCR-seq of pooled anti-TGF-beta antibody-treated cells derived from flow cell 1

value: anti-TGF-beta antibody


title: scTCR-seq of pooled control cells derived from flow cell 1


title: scTCR-seq of pooled bintrafusp alfa-treated cells derived from flow cell 1


title: wt_iPSC_IgG_1


title: wt_iPSC_H3K27ac_2


title: translocation_HSPC_H3K27ac_1


title: eCLIP_IgG_rep2

data_processing:
The quality control of raw data was evaluated with FastQC and MultiQC (Ewels et al., 2016b).
Reads were mapped uniquely with STAR v2.7.5 (Dobin et al., 2013) to the human genome (hg38).
FeatureCounts v2.0.3 (Liao et al., 2014) was used to get the read counts for eCLIP samples across all transcripts using GENCODE v45 annotation (Frankish et al., 2023).
Transcripts significantly enriched for TOP1 binding were determined by analyzing the differential enrichment of TOP1 IP over IgG using DESeq2 v1.38.3 (Love et al., 2014).
BigWig files were generated by calculating the log2 ratio as RPKM of the TOP1 IP with respect to IgG IP. The BigWig files were visualized in IGV (Thorvaldsdottir et al., 2013).
Assembly: hg38
processed data files format and content: BigWig
Library strategy: eCLIP-seq

extract_protocol:
TOP1-RNA complexes were separated by SDS-PAGE, transferred to a nitrocellulosemembrane, and RNA was extracted from the membrane using proteinase K (NEB).
3’ RNA adaptor was ligated onto the RNA with T4 RNA ligase. RNA was reverse transcribed with Superscript IV (Invitrogen), free primer was removed (ExoSap-IT, Affymetrix) and a 3’ DNA adaptor was ligated onto the cDNA product with T4 RNA ligase (NEB). Complementary DNA was amplified by PCR using Q5 Master Mix (NEB) and purified before Illumina sequencing. The sequencing was done using Illumina NextSeq 1000 with a read length configuration of 75bp for 40M reads per sample.

treatment_protocol: SW480 cells (20 × 10^6) were UV crosslinked (400 mJ/cm−2 at 254 nm) and saved at -80ºC until processing.

value: Colorectal Cancer Cell


title: wt_iPSC_H3K27ac_3


title: wt_iPSC_H3K27ac_1


title: TOP1cc-seq RBR Input rep2

description: CHIP-seq / TOP1cc-seq

data_processing:
The quality control of raw data was evaluated with FastQC and MultiQC (Ewels et al., 2016b).Trimgalore was used to filter out low quality reads (with a phred score threshold of 30) and adapter sequences.
The samples were aligned using Bowtiev2.4.5 to GRCh38 (+major SNVs). Only reads with high mapping quality were considered using a MAPQ threshold of 10 in Samtools v1.6. The BAM files were further deduplicated using Samtools.
The samples were also aligned to Drosophila melanogaster genome (BDGP6) using Bowtie2 for spike-in normalization.
Deeptools v3.5.1 (Ramirez et al., 2014) was used to generate normalized bigwig files, heatmap, and profile plots. The bins per million mapped normalized reads were used and the log2 ratio between the IP over the Input was calculated. The bigwig files were visualized in IGV (Thorvaldsdottir et al., 2013).
Assembly: GRCh38
processed data files format and content: BigWig

growth_protocol: TOP1 knockdown Human SW480 cells were grown at 37°C, supplied with 5% CO₂ in Dulbecco’s modified Eagle medium (DMEM, Gibco) supplemented with 10% FBS and 1.5 mg/mL puromycin

extract_protocol:
Cell resuspensions were next dounced ten times in a prechilled glass homogenizer. Nuclei were collected and resuspended in shearing buffer (0.1% SDS, 0.5% N-lauroylsarcosine, 1% Triton X-100, 10 mM Tris-HCl pH 8.1, 100 mM NaCl, 1 mM EDTA, 1 mM PMSF, PICs) and incubated on ice for 30 min. Chromatin was fragmented using an E220 Focused-Ultrasonicator (Covaris) to an average size of 200-600 bp.
The eluted DNA was quantified with a Qubit 4.0 fluorometer, and 10 ng of DNA was used to prepare the sequencing libraries using KAPA Hyper Prep Kit according to the manufacturer’s instructions. Briefly, purified DNA was subjected to end-repair, adaptor ligation followed by indexed PCR. Libraries were size selected for average size of 300 bp. The sequencing was done using Illumina NovaSeq 6000 with a read length configuration of 150 PE for 50 M PE reads per sample (25M in each direction).

treatment_protocol: SW480 cells transiently expressing EV, GFP-FLAG-TOP1 WT or GFP-FLAG-TOP1 RBR were treated with 10 mM CPT for 4 min followed by immediate washing with ice-cold 1X PBS, scraped, and resuspended in lysis buffer (20 mM Tris-HCl pH 7.5, 300 mM NaCl, 2 mM EDTA, 0.5% NP40, 1% Triton X-100, 1 mM PMSF, PICs), and incubated on ice for 30 min.


title: scRNA-seq of pooled anti-TGF-beta antibody-treated cells derived from flow cell 1


title: translocation_iPSC_H3K27ac_2


title: translocation_iPSC_H3K27ac_3


title: scRNA-seq of pooled anti-PDL1 antibody-treated cells derived from flow cell 2


title: TOP1cc-seq RBR Input rep1

description: CHIP-seq / TOP1cc-seq


title: TOP1cc-seq RBR IP rep2

description: CHIP-seq / TOP1cc-seq

value: GFP


title: translocation_iPSC_H3K27ac_1


title: wt_HSPC_H3K4me1_2

value: H3K4me1 (Abcam ab8895)


title: scRNA-seq of pooled anti-PDL1 antibody-treated cells derived from flow cell 1


title: TOP1cc-seq RBR IP rep1

description: CHIP-seq / TOP1cc-seq


title: TOP1cc-seq WT Input rep2

description: CHIP-seq / TOP1cc-seq


title: scRNA-seq of pooled bintrafusp control cells derived from flow cell 2


title: translocation_HSPC_H3K4me1_2

value: HSPC


title: wt_iPSC_H3K4me1_3


title: scRNA-seq of pooled control cells derived from flow cell 1


title: wt_HSPC_H3K4me1_3


title: translocation_HSPC_H3K4me1_1


title: wt_HSPC_H3K4me1_1


title: scRNA-seq of pooled anti-TGF-beta antibody-treated cells derived from flow cell 2


title: wt_iPSC_H3K4me1_1


title: scRNA-seq of pooled bintrafusp alfa-treated cells derived from flow cell 2


title: wt_iPSC_H3K4me1_2


title: scTCR-seq of pooled anti-TGF-beta antibody-treated cells derived from flow cell 2


title: translocation_HSPC_H3K27ac_3


title: TOP1cc-seq WT IP rep1

description: CHIP-seq / TOP1cc-seq


title: translocation_iPSC_H3K4me1_3


title: TOP1cc-seq WT IP rep2

description: CHIP-seq / TOP1cc-seq


title: translocation_iPSC_H3K4me1_2


title: translocation_iPSC_H3K4me1_1


title: scRNA-seq of pooled bintrafusp alfa-treated cells derived from flow cell 1


title: K14 Abl 1

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adaptor sequences were removed with Trimmomatic PE using options ‘HEADCROP:10 CROP:70 ILLUMINACLIP: adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50’.
ATAC–seq paired-end reads were then aligned to mouse reference genome mm10 using Bowtie2 (v.2.3.4.2) using options ‘‘-X 2000 -q -p 6 -t –fr –very-sensitive –no-discordant –no-unal –no-mixed’.
Mitochondrial reads, reads from unmapped or random counting and reads with a mapping quality <20 was removed using SAM tools.
Duplicate reads were removed by Picard MarkDuplicates module.
Peak calling was performed on each individual sample by MACS2 (v.2.1.0.20151222) using options ‘-f BAMPE -g mm -q 0.01 –nomodel –shift 0.
Peaks from the different subpopulations were merged for downstream analysis
Reads counts of each merged peak for each individual sample were calculated by HTSeq-count using options ‘-f bam -r pos -m intersection-nonempty’.
These counts were normalized for one million mapped reads in merged peaks and fold-change was calculated compared to control.
Peaks were associated to genes with GREAT software (v4.0.4) with the following parameters: 5.0 kb in proximal upstream, 1.0 kb in proximal downstream and 100.0 kb in distal.
Assembly: mm10
Supplementary files format and content: .csv / normalized peak intensity

source_name: Skin epidermis

extract_protocol:
For ATAC-seq, 50000 sorted basal cells (α6High/CD34-/Lrig1-/YFP+/GFP+/RFP+) were collected in 1 ml PBS supplemented with 3% FBS at 4 °C. Cells were centrifuged and cell pellets were resuspended in 100 μl lysis buffer (TrisHCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0.1%) and centrifuged at 500g for 25 min at 4 °C. Supernatant was carefully discarded and nuclei were resuspended in 50 μl reaction buffer (Tn5 transposase 2.5 μl, TD buffer 22.5 μl, from Nextera DNA sample preparation kit, Illumina, and 25 μl H20). The reaction was performed at 37 °C for 30 min and was stopped by adding 5 μl clean up buffer (NaCl 900 mM, EDTA 300 mM). DNA was purified using the MiniElute purification kit (QIAGEN) following the manufacturer’s protocol.
DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800 bp (BluePippin, Sage Sciences), following the manufacturer’s recommendations.

value: Skin epidermis

value: Epithelial

value: Basal lineage ablation