title: BLA_FearRecall_fr13_I7_S2119

description: Smartseq


title: BLA_FearRecall_fr13_I1_S2113

status: Public on Oct 26 2023

type: SRA

city: Stanford

first: Wenfei

last: Sun

address: 318 Campus Dr.

country: USA

institute: Stanford University

description: Smartseq

library_source: transcriptomic single cell

data_processing:
Fastq reads were mapped with STAR(2.7.9a)
Assembly: mm10
Supplementary files format and content: Cell by gene matrix format

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
OligodT primers were used to enrich mRNA
Brain tissues were dissociated with Worthington Papain Digestion Kit RNA libraries were prepared using smart seq 3
Novaseq 6000 was used for sequencing with standard Illumina protocols

treatment_protocol: Fear conditioning paradigm

tag: tissue

tag: genotype

value: TRAP2 Ai14

tag: treatment

value: Fear recall


title: case0218-tumour01

city: Bergen

first: Oleksii

last: Nikolaienko

state: Vestland

address: Jonas Lies veg 87

department: Department of Clinical Science

country: Norway

institute: University of Bergen

library_source: genomic

data_processing:
For BRCA1 methylation analysis, sequencing reads were mapped/aligned to the GRCh38 reference genome using the Illumina DRAGEN Bio-IT Platform (v3.6.3).
All reads mapping outside of the target BRCA1 promoter area (GRCh38 chr17:43124861-43126026) were filtered out to disallow identification of individuals
Cytosine methylation and its allele specificity was evaluated using the epialleleR R package (v1.3.5).
Assembly: GRCh38
Supplementary files format and content: epialleleR BED report: frequency of hypermethylated epialleles at the level of individual amplicons
Supplementary files format and content: epialleleR CG report: conventional cytosine methylation report for cytosines in CpG context
Supplementary files format and content: epialleleR VCF report: frequency of SNP variants within hyper- and hypomethylated epialleles
Supplementary files format and content: epialleleR VEF report: frequency of hypermethylated epialleles at the level of individual cytosines in CpG context

molecule: genomic DNA

organism: Homo sapiens

source_name: tumour

extract_protocol:
All patients underwent an incisional or Tru-Cut tumor biopsy prior to treatment. Tumor biopsies were snap-frozen in liquid nitrogen at removal and stored in liquid nitrogen, while WBC specimens were stored at –80°C after centrifugation of EDTA whole blood and plasma removal. Genomic DNA for methylation analyses was extracted from tumor and WBC samples using QIAamp DNA Mini kit (Qiagen, Valencia, CA).
500 ng of genomic DNA were bisulfite converted and subjected to BRCA1 gene promoter fragment amplification using four pairs of primers, that do not overlap with any of the CpG dinucleotides (GRCh38 genomic coordinates: CpG00–13 chr17:43125624–43126026, CpG14–31 chr17:43125270–43125640, CpG17–34 chr17:43125171–43125550, CpG33–49 chr17:43124861–43125249). All four amplicons were combined, indexed, and sequenced by 2x226 bp reads using Illumina MiSeq System (Illumina, San Diego, CA), resulting in an ultradeep coverage of about 30000x for each amplicon.

value: tumour

value: pretreatment


title: case0223-tumour01


title: case0217-tumour01


title: BLA_FearRecall_fr13_H4_S2092

description: Smartseq


title: case0226-tumour01


title: case0221-tumour01


title: case0216-tumour01


title: BLA_FearRecall_fr13_H24_S2112

description: Smartseq


title: case0215-tumour01


title: BLA_FearRecall_fr13_H2_S2090

description: Smartseq


title: BLA_FearRecall_fr13_H18_S2106

description: Smartseq


title: case0214-tumour01


title: case0224-tumour01


title: BLA_FearRecall_fr13_H11_S2099

description: Smartseq


title: case0213-tumour01


title: BLA_FearRecall_fr13_G8_S2072

description: Smartseq


title: BLA_FearRecall_fr13_I22_S2134

description: Smartseq


title: case0225-tumour01


title: BLA_FearRecall_fr13_G7_S2071

description: Smartseq


title: case0212-tumour01


title: case0210-tumour01


title: BLA_FearRecall_fr13_G6_S2070

description: Smartseq


title: BLA_FearRecall_fr13_G17_S2081

description: Smartseq


title: BLA_FearRecall_fr13_G15_S2079

description: Smartseq


title: BLA_FearRecall_fr13_G5_S2069

description: Smartseq


title: case0208-tumour01


title: case0207-tumour01


title: case0206-tumour01


title: BLA_FearRecall_fr13_G11_S2075

description: Smartseq


title: BLA_FearRecall_fr13_F8_S2048

description: Smartseq


title: BLA_FearRecall_fr13_F7_S2047

description: Smartseq


title: case0204-tumour01


title: BLA_FearRecall_fr13_F5_S2045

description: Smartseq


title: case0202-tumour01


title: case0203-tumour01


title: BLA_FearRecall_fr13_F19_S2059

description: Smartseq


title: case0201-tumour01


title: BLA_FearRecall_fr13_F16_S2056

description: Smartseq


title: case0211-tumour01


title: case0200-tumour01


title: case0199-tumour01


title: BLA_FearRecall_fr13_F14_S2054

description: Smartseq


title: BLA_FearRecall_fr13_F13_S2053

description: Smartseq


title: case0198-tumour01


title: BLA_FearRecall_fr13_F11_S2051

description: Smartseq


title: case0209-tumour01


title: case0197-tumour01


title: BLA_FearRecall_fr13_F10_S2050

description: Smartseq


title: BLA_FearRecall_fr13_E8_S2024

description: Smartseq


title: BLA_FearRecall_fr13_E9_S2025

description: Smartseq


title: case0205-tumour01


title: case0196-tumour01


title: case0194-tumour01


title: BLA_FearRecall_fr13_E7_S2023

description: Smartseq


title: BLA_FearRecall_fr13_E19_S2035

description: Smartseq


title: case0195-tumour01


title: case0192-tumour01


title: BLA_FearRecall_fr13_E17_S2033

description: Smartseq


title: case0191-tumour01


title: case0190-tumour01


title: case0189-tumour01


title: BLA_FearRecall_fr13_D9_S2001

description: Smartseq


title: BLA_FearRecall_fr13_E14_S2030

description: Smartseq


title: case0188-tumour01


title: BLA_FearRecall_fr13_D6_S1998

description: Smartseq


title: BLA_FearRecall_fr13_D20_S2012

description: Smartseq


title: case0187-tumour01


title: BLA_FearRecall_fr13_D4_S1996

description: Smartseq


title: BLA_FearRecall_fr13_D17_S2009

description: Smartseq


title: case0185-tumour01


title: BLA_FearRecall_fr13_D16_S2008

description: Smartseq


title: case0184-tumour01


title: BLA_FearRecall_fr13_D15_S2007

description: Smartseq


title: BLA_FearRecall_fr13_E3_S2019

description: Smartseq


title: case0183-tumour01


title: case0193-tumour01


title: case0182-tumour01


title: case0181-tumour01


title: BLA_FearRecall_fr13_D1_S1993

description: Smartseq


title: BLA_FearRecall_fr13_D10_S2002

description: Smartseq


title: BLA_FearRecall_fr13_C5_S1973

description: Smartseq


title: BLA_FearRecall_fr13_C7_S1975

description: Smartseq


title: case0178-tumour01


title: case0179-tumour01


title: case0177-tumour01


title: BLA_FearRecall_fr13_C4_S1972

description: Smartseq


title: BLA_FearRecall_fr13_C3_S1971

description: Smartseq


title: case0176-tumour01


title: BLA_FearRecall_fr13_C23_S1991

description: Smartseq


title: case0174-tumour01


title: case0186-tumour01


title: case0175-tumour01


title: BLA_FearRecall_fr13_C22_S1990

description: Smartseq


title: BLA_FearRecall_fr13_C21_S1989

description: Smartseq


title: BLA_FearRecall_fr13_C16_S1984

description: Smartseq


title: case0173-tumour01


title: BLA_FearRecall_fr13_C13_S1981

description: Smartseq


title: case0172-tumour01


title: case0171-tumour01


title: case0180-tumour01


title: case0170-tumour01


title: case0168-tumour01


title: BLA_FearRecall_fr13_C11_S1979

description: Smartseq


title: case0167-tumour01


title: BLA_FearRecall_fr13_C8_S1976

description: Smartseq


title: case0165-tumour01


title: BLA_FearRecall_fr13_C10_S1978

description: Smartseq


title: BLA_FearRecall_fr13_B7_S1951

description: Smartseq


title: BLA_FearRecall_fr13_B3_S1947

description: Smartseq


title: case0164-tumour01


title: case0169-tumour01


title: BLA_FearRecall_fr13_B4_S1948

description: Smartseq


title: BLA_FearRecall_fr13_B19_S1963

description: Smartseq


title: BLA_FearRecall_fr13_B13_S1957

description: Smartseq


title: BLA_FearRecall_fr13_B17_S1961

description: Smartseq


title: case0161-tumour01


title: case0159-tumour01


title: case0162-tumour01


title: case0163-tumour01


title: case0160-tumour01


title: BLA_FearRecall_fr13_B2_S1946

description: Smartseq


title: BLA_FearRecall_fr13_A7_S1927

description: Smartseq


title: case0158-tumour01


title: BLA_FearRecall_fr13_A8_S1928

description: Smartseq


title: BLA_FearRecall_fr13_A4_S1924

description: Smartseq


title: case0157-tumour01


title: case0156-tumour01


title: BLA_FearRecall_fr13_B22_S1966

description: Smartseq


title: BLA_FearRecall_fr13_A2_S1922

description: Smartseq


title: BLA_FearRecall_fr13_A22_S1942

description: Smartseq


title: case0153-tumour02


title: case0154-tumour01


title: case0155-tumour01


title: BLA_FearRecall_fr13_A19_S1939

description: Smartseq


title: case0166-tumour01


title: BLA_FearRecall_fr13_A16_S1936

description: Smartseq


title: BLA_FearRecall_fr13_B18_S1962

description: Smartseq


title: BLA_FearRecall_fr13_A14_S1934

description: Smartseq


title: case0151-tumour01


title: BLA_FearRecall_fr13_A11_S1931

description: Smartseq


title: case0150-tumour01


title: BLA_FearRecall_fr12_G8_S7448

description: Smartseq


title: case0148-tumour01


title: case0149-tumour01


title: BLA_FearRecall_fr13_A10_S1930

description: Smartseq


title: BLA_FearRecall_fr12_H11_S7475

description: Smartseq


title: case0146-tumour01


title: case0147-tumour01


title: case0145-tumour01


title: BLA_FearRecall_fr12_G20_S7460

description: Smartseq


title: BLA_FearRecall_fr13_A23_S1943

description: Smartseq


title: BLA_FearRecall_fr12_G18_S7458

description: Smartseq


title: BLA_FearRecall_fr12_G24_S7464

description: Smartseq


title: case0152-tumour01


title: BLA_FearRecall_fr12_G15_S7455

description: Smartseq


title: case0153-tumour01


title: case0141-tumour01


title: case0140-tumour01


title: case0144-tumour01


title: BLA_FearRecall_fr12_G23_S7463

description: Smartseq


title: BLA_FearRecall_fr12_G14_S7454

description: Smartseq


title: case0142-tumour01


title: BLA_FearRecall_fr12_F9_S7425

description: Smartseq


title: BLA_FearRecall_fr12_H4_S7468

description: Smartseq


title: BLA_FearRecall_fr12_G10_S7450

description: Smartseq


title: case0137-tumour01


title: BLA_FearRecall_fr12_F8_S7424

description: Smartseq


title: case0136-tumour01


title: case0135-tumour01


title: case0138-tumour01


title: BLA_FearRecall_fr12_F23_S7439

description: Smartseq


title: BLA_FearRecall_fr12_F19_S7435

description: Smartseq


title: BLA_FearRecall_fr12_G17_S7457

description: Smartseq


title: case0134-tumour01


title: BLA_FearRecall_fr12_F18_S7434

description: Smartseq


title: case0139-tumour01


title: BLA_FearRecall_fr12_F15_S7431

description: Smartseq


title: case0131-tumour01


title: case0129-tumour01


title: BLA_FearRecall_fr12_F11_S7427

description: Smartseq


title: BLA_FearRecall_fr12_E7_S7399

description: Smartseq


title: case0128-tumour01


title: case0143-tumour01


title: case0132-tumour01


title: BLA_FearRecall_fr12_E17_S7409

description: Smartseq


title: case0127-tumour01


title: case0126-tumour01


title: BLA_FearRecall_fr12_E13_S7405

description: Smartseq


title: BLA_FearRecall_fr12_E14_S7406

description: Smartseq


title: case0130-tumour01


title: case0124-tumour01


title: BLA_FearRecall_fr12_F7_S7423

description: Smartseq


title: case0125-tumour01


title: case0133-tumour01


title: BLA_FearRecall_fr12_D15_S7383

description: Smartseq


title: BLA_FearRecall_fr12_D6_S7374

description: Smartseq


title: case0122-tumour01


title: case0121-tumour01


title: BLA_FearRecall_fr12_D13_S7381

description: Smartseq


title: case0120-tumour01


title: BLA_FearRecall_fr12_D10_S7378

description: Smartseq


title: BLA_FearRecall_fr12_F14_S7430

description: Smartseq


title: case0118-tumour01


title: BLA_FearRecall_fr12_D1_S7369

description: Smartseq


title: BLA_FearRecall_fr12_C24_S7368

description: Smartseq


title: case0116-tumour01


title: BLA_FearRecall_fr12_E16_S7408

description: Smartseq


title: BLA_FearRecall_fr12_D9_S7377

description: Smartseq


title: case0115-tumour01


title: BLA_FearRecall_fr12_C10_S7354

description: Smartseq


title: case0113-tumour01


title: case0123-tumour01


title: case0112-tumour01


title: case0111-tumour01


title: case0114-tumour01


title: BLA_FearRecall_fr12_B9_S7329

description: Smartseq


title: BLA_FearRecall_fr12_C19_S7363

description: Smartseq


title: case0117-tumour02


title: BLA_FearRecall_fr12_D14_S7382

description: Smartseq


title: BLA_FearRecall_fr12_B2_S7322

description: Smartseq


title: case0110-tumour01


title: case0119-tumour01


title: BLA_FearRecall_fr12_A23_S7319

description: Smartseq


title: BLA_FearRecall_fr12_C14_S7358

description: Smartseq


title: BLA_FearRecall_fr12_A17_S7313

description: Smartseq


title: case0109-tumour01


title: BLA_FearRecall_fr12_C6_S7350

description: Smartseq


title: BLA_FearRecall_fr12_A16_S7312

description: Smartseq


title: BLA_FearRecall_fr12_A1_S7297

description: Smartseq


title: case0107-tumour01


title: BLA_FearRecall_fr11_H9_S1329

description: Smartseq


title: case0106-tumour01


title: BLA_FearRecall_fr11_H4_S1324

description: Smartseq


title: case0105-tumour01


title: BLA_FearRecall_fr11_H3_S1323

description: Smartseq


title: BLA_FearRecall_fr11_H20_S1340

description: Smartseq


title: case0104-tumour01


title: BLA_FearRecall_fr11_H11_S1331

description: Smartseq


title: case0103-tumour01


title: case0102-tumour01


title: BLA_FearRecall_fr11_G9_S1305

description: Smartseq


title: case0101-tumour01


title: case0100-tumour01


title: case0108-tumour01


title: BLA_FearRecall_fr11_G6_S1302

description: Smartseq


title: BLA_FearRecall_fr11_G8_S1304

description: Smartseq


title: case0097-tumour01


title: case0099-tumour01


title: case0098-tumour01


title: case0096-tumour01


title: BLA_FearRecall_fr11_G24_S1320

description: Smartseq


title: BLA_FearRecall_fr11_G22_S1318

description: Smartseq


title: case0095-tumour01


title: BLA_FearRecall_fr11_G21_S1317

description: Smartseq


title: case0094-tumour01


title: BLA_FearRecall_fr11_G20_S1316

description: Smartseq


title: case0093-tumour01


title: case0091-tumour01


title: BLA_FearRecall_fr11_G17_S1313

description: Smartseq


title: BLA_FearRecall_fr11_G2_S1298

description: Smartseq


title: BLA_FearRecall_fr11_G19_S1315

description: Smartseq


title: case0090-tumour01


title: case0092-tumour01


title: case0089-tumour01


title: case0088-tumour01


title: BLA_FearRecall_fr11_G3_S1299

description: Smartseq


title: case0087-tumour01


title: BLA_FearRecall_fr11_G14_S1310

description: Smartseq


title: BLA_FearRecall_fr11_G10_S1306

description: Smartseq


title: BLA_FearRecall_fr11_G23_S1319

description: Smartseq


title: BLA_FearRecall_fr11_F9_S1281

description: Smartseq


title: case0085-tumour01


title: BLA_FearRecall_fr11_F8_S1280

description: Smartseq


title: BLA_FearRecall_fr11_G15_S1311

description: Smartseq


title: case0086-tumour01


title: case0084-tumour01


title: case0083-tumour01


title: BLA_FearRecall_fr11_F5_S1277

description: Smartseq


title: BLA_FearRecall_fr11_F7_S1279

description: Smartseq


title: case0082-tumour01


title: BLA_FearRecall_fr11_F4_S1276

description: Smartseq


title: BLA_FearRecall_fr11_F3_S1275

description: Smartseq


title: case0081-tumour01


title: case0080-tumour01


title: case0079-tumour01


title: BLA_FearRecall_fr11_F23_S1295

description: Smartseq


title: BLA_FearRecall_fr11_F19_S1291

description: Smartseq


title: BLA_FearRecall_fr11_G13_S1309

description: Smartseq


title: BLA_FearRecall_fr11_F18_S1290

description: Smartseq


title: case0076-tumour01


title: case0078-tumour01


title: BLA_FearRecall_fr11_F16_S1288

description: Smartseq


title: BLA_FearRecall_fr11_F15_S1287

description: Smartseq


title: case0077-tumour01


title: case0074-tumour01


title: BLA_FearRecall_fr11_F14_S1286

description: Smartseq


title: case0075-tumour01


title: case0072-tumour01


title: case0071-tumour01


title: BLA_FearRecall_fr11_F12_S1284

description: Smartseq


title: BLA_FearRecall_fr11_F11_S1283

description: Smartseq


title: BLA_FearRecall_fr11_F13_S1285

description: Smartseq


title: case0073-tumour01


title: case0070-tumour01


title: BLA_FearRecall_fr11_E7_S1255

description: Smartseq


title: BLA_FearRecall_fr11_E4_S1252

description: Smartseq


title: BLA_FearRecall_fr11_E20_S1268

description: Smartseq


title: BLA_FearRecall_fr11_E17_S1265

description: Smartseq


title: case0065-tumour01


title: case0066-tumour01


title: case0067-tumour01


title: BLA_FearRecall_fr11_E14_S1262

description: Smartseq


title: BLA_FearRecall_fr11_E15_S1263

description: Smartseq


title: case0063-tumour01


title: case0064-tumour01


title: BLA_FearRecall_fr11_E13_S1261

description: Smartseq


title: BLA_FearRecall_fr11_E11_S1259

description: Smartseq


title: case0061-tumour01


title: case0060-tumour01


title: case0062-tumour01


title: case0059-tumour01


title: BLA_FearRecall_fr11_F10_S1282

description: Smartseq


title: case0069-tumour01


title: BLA_FearRecall_fr11_D4_S1228

description: Smartseq


title: case0058-tumour01


title: case0068-tumour01


title: BLA_FearRecall_fr11_D9_S1233

description: Smartseq


title: case0056-tumour01


title: BLA_FearRecall_fr11_D6_S1230

description: Smartseq


title: BLA_FearRecall_fr11_D20_S1244

description: Smartseq


title: BLA_FearRecall_fr11_D18_S1242

description: Smartseq


title: case0057-tumour01


title: case0055-tumour01


title: BLA_FearRecall_fr11_D15_S1239

description: Smartseq


title: BLA_FearRecall_fr12_A8_S7304

description: Smartseq


title: BLA_FearRecall_fr11_E16_S1264

description: Smartseq


title: BLA_FearRecall_fr11_D13_S1237

description: Smartseq


title: case0053-tumour01


title: case0052-tumour01


title: BLA_FearRecall_fr11_D10_S1234

description: Smartseq


title: BLA_FearRecall_fr11_D12_S1236

description: Smartseq


title: case0050-tumour01


title: BLA_FearRecall_fr11_D14_S1238

description: Smartseq


title: BLA_FearRecall_fr11_D1_S1225

description: Smartseq


title: case0054-tumour01


title: case0049-tumour01


title: BLA_FearRecall_fr11_C6_S1206

description: Smartseq


title: case0047-tumour01


title: case0048-tumour01


title: BLA_FearRecall_fr11_C22_S1222

description: Smartseq


title: BLA_FearRecall_fr11_C21_S1221

description: Smartseq


title: case0051-tumour01


title: BLA_FearRecall_fr11_C2_S1202

description: Smartseq


title: case0045-tumour01


title: case0043-tumour01


title: BLA_FearRecall_fr11_C18_S1218

description: Smartseq


title: case0044-tumour01


title: BLA_FearRecall_fr11_C15_S1215

description: Smartseq


title: case0046-tumour01


title: case0040-tumour01


title: case0041-tumour01


title: BLA_FearRecall_fr11_C14_S1214

description: Smartseq


title: BLA_FearRecall_fr11_C13_S1213

description: Smartseq


title: case0039-tumour01


title: BLA_FearRecall_fr11_C11_S1211

description: Smartseq


title: BLA_FearRecall_fr11_C24_S1224

description: Smartseq


title: case0038-tumour01


title: BLA_FearRecall_fr11_C10_S1210

description: Smartseq


title: BLA_FearRecall_fr11_B6_S1182

description: Smartseq


title: case0037-tumour01


title: BLA_FearRecall_fr11_B9_S1185

description: Smartseq


title: case0036-tumour01


title: case0035-tumour01


title: BLA_FearRecall_fr11_B2_S1178

description: Smartseq


title: case0033-tumour01


title: BLA_FearRecall_fr11_C19_S1219

description: Smartseq


title: case0034-tumour01


title: BLA_FearRecall_fr11_B5_S1181

description: Smartseq


title: case0117-tumour01


title: case0032-tumour01


title: BLA_FearRecall_fr11_B20_S1196

description: Smartseq


title: case0031-tumour02


title: BLA_FearRecall_fr11_A7_S1159

description: Smartseq


title: case0030-tumour01


title: BLA_FearRecall_fr11_B19_S1195

description: Smartseq


title: BLA_FearRecall_fr11_B11_S1187

description: Smartseq


title: case0028-tumour01


title: BLA_FearRecall_fr11_A17_S1169

description: Smartseq


title: case0027-tumour01


title: BLA_FearRecall_fr11_A23_S1175

description: Smartseq


title: case0029-tumour01


title: case0026-tumour01


title: BLA_FearRecall_fr11_A16_S1168

description: Smartseq


title: case0025-tumour01


title: BLA_FearRecall_fr11_A1_S1153

description: Smartseq


title: case0024-tumour01


title: case0022-tumour01


title: case0021-tumour01


title: case0023-tumour01


title: case0019-tumour01


title: BLA_FearRecall_fr10_P3_S7275

description: Smartseq


title: BLA_FearRecall_fr10_P23_S7295

description: Smartseq


title: BLA_FearRecall_fr10_P18_S7290

description: Smartseq


title: case0017-tumour01


title: case0031-tumour01


title: BLA_FearRecall_fr10_P21_S7293

description: Smartseq


title: case0020-tumour01


title: BLA_FearRecall_fr10_P13_S7285

description: Smartseq


title: case0014-tumour01


title: BLA_FearRecall_fr11_B10_S1186

description: Smartseq


title: BLA_FearRecall_fr10_P20_S7292

description: Smartseq


title: case0013-tumour01


title: BLA_FearRecall_fr10_P2_S7274

description: Smartseq


title: BLA_FearRecall_fr11_A24_S1176

description: Smartseq


title: case0018-tumour01


title: BLA_FearRecall_fr10_P17_S7289

description: Smartseq


title: case0011-tumour01


title: BLA_FearRecall_fr10_P14_S7286

description: Smartseq


title: case0010-tumour01


title: case0016-tumour01


title: case0042-tumour01


title: case0015-tumour01


title: case0008-tumour01


title: BLA_FearRecall_fr11_A15_S1167

description: Smartseq


title: BLA_FearRecall_fr10_O17_S7265

description: Smartseq


title: BLA_FearRecall_fr10_P11_S7283

description: Smartseq


title: case0012-tumour01


title: BLA_FearRecall_fr10_N6_S7230

description: Smartseq


title: BLA_FearRecall_fr10_O21_S7269

description: Smartseq


title: case0009-tumour01


title: case0003-tumour01


title: BLA_FearRecall_fr10_O19_S7267

description: Smartseq


title: BLA_FearRecall_fr10_O2_S7250

description: Smartseq


title: BLA_FearRecall_fr10_N3_S7227

description: Smartseq


title: BLA_FearRecall_fr10_N24_S7248

description: Smartseq


title: case0001-tumour01


title: BLA_FearRecall_fr10_O18_S7266

description: Smartseq


title: BLA_FearRecall_fr10_N21_S7245

description: Smartseq


title: FV3

city: Shenzhen

first: Rufan

last: Huang

address: No.66,Gongchang Road,Guangming District

country: China

institute: Sun Yat-sen University

description: miRNA-seq of fusion vesicles

library_source: transcriptomic

data_processing:
reads connector and quality filtering software:  First round: fastp, version 0.19.5, parameters -q 20, -f 1, --length_required 18  Second round: cutadapt, version 1.18, parameter -m 20-j 50
Rfam comparison:bowtie, version 1.2.2, parameter -n 1-e 80-l 18-a-m 3
Genome comparison:bowtie, version 1.2.2, parameters -n 1-e 80-l 18-a-m 3 --best
Small RNA identification：miRDeep2, version 2.0.1.2, mapper parameter -c - i-j-l 18
DESeq2 (with replicated samples) or EdgeR (without replicated samples) were used for differential expression analysis
Assembly: Citrus_clementina_v1.0
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Citrus x paradisi

source_name: fusion vesicles

extract_protocol:
RNA was extracted using an RNA miRNeasy Micro Kit (Qiagen), and the quantity and purity were quantified by Quantus Fluorometer (Promega, USA) and Qsep100 (BIOptic, China)
Library construction was performed using Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following manufacturer's protocols.

value: fusion vesicles


title: case0005-tumour01


title: EV3

description: miRNA-seq of grapefruit exosomes

source_name: exosomes

value: exosomes


title: BLA_FearRecall_fr10_O15_S7263

description: Smartseq


title: BLA_FearRecall_fr10_N18_S7242

description: Smartseq


title: case0006-tumour01


title: BLA_FearRecall_fr10_O14_S7262

description: Smartseq


title: BLA_FearRecall_fr10_O13_S7261

description: Smartseq


title: case0004-tumour01


title: BLA_FearRecall_fr10_P1_S7273

description: Smartseq


title: BLA_FearRecall_fr10_N16_S7240

description: Smartseq


title: EV1

description: miRNA-seq of grapefruit exosomes


title: case0002-tumour01


title: MDAMB436_EPZ_Day5_A

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
Data were quantified as reads per kilobase of transcript per million reads mapped (RPKM) using Rubsread and featureCounts
Assembly: GRCh38
Supplementary files format and content: Excel file includes RPKM values for each sample

extract_protocol:
Total RNA using RNeasy Plus Mini Kit form Qiagen per manufactuer's instructions
Poly-A RNA libraries for RNA-seq were prepared by Novogene company

treatment_protocol: Cells were treated with either DMSO vehicle control or 5 micromolar EPZ015666 for 3 days or 5 days prior to RNA isolation and stranded RNAseq.

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: replicate

value: A

tag: time point


title: MDAMB436_EPZ_Day5_B

value: B


title: FV2

description: miRNA-seq of fusion vesicles


title: BLA_FearRecall_fr10_N20_S7244

description: Smartseq


title: case0007-tumour01


title: COV362_EPZ_Day5_B

value: Ovarian cancer cell line


title: COV362_DMSO_Day5_B

value: DMSO


title: BLA_FearRecall_fr10_N17_S7241

description: Smartseq


title: BLA_FearRecall_fr10_M7_S7207

description: Smartseq


title: BLA_FearRecall_fr10_M3_S7203

description: Smartseq


title: BLA_FearRecall_fr10_M21_S7221

description: Smartseq


title: BLA_FearRecall_fr10_N2_S7226

description: Smartseq


title: FV1

description: miRNA-seq of fusion vesicles


title: BLA_FearRecall_fr10_M20_S7220

description: Smartseq


title: BLA_FearRecall_fr10_N19_S7243

description: Smartseq


title: OVCAR8_EPZ_Day3_B


title: BLA_FearRecall_fr10_M18_S7218

description: Smartseq


title: EV2

description: miRNA-seq of grapefruit exosomes


title: BLA_FearRecall_fr10_M15_S7215

description: Smartseq


title: OVCAR8_EPZ_Day5_B


title: BLA_FearRecall_fr10_N15_S7239

description: Smartseq


title: BLA_FearRecall_fr10_N12_S7236

description: Smartseq


title: MDAMB436_DMSO_Day5_B


title: BLA_FearRecall_fr10_M9_S7209

description: Smartseq


title: OVCAR8_EPZ_Day5_A


title: BLA_FearRecall_fr10_L24_S7200

description: Smartseq


title: COV362_EPZ_Day5_A


title: COV362_DMSO_Day5_A


title: BT549_EPZ_Day3_B


title: BLA_FearRecall_fr10_L2_S7178

description: Smartseq


title: hBEC, signaling perturbations, pooled donors no. 221175 and 323353 [ali13]

city: Boston

first: Kalki

last: Kukreja

state: MA

address: 200 Longwood Avenue

institute: Harvard University

description: Signaling perturbations performed on air-liquid interface (ALI) hBEC organotypic cultures

data_processing:
Raw FASTQ were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. We ran the experiment with individual donor ( donor ID: 429581) using nextseq. Each nextseq run results in 16 FASTQ files (4 lanes x 4 reads per lane). We ran the nextseq run twice and hence have 16x2 = 32 raw files for this experiment. These contain 16 samples corresponding to 16 different conditions that are multiplexed for sequencing. For the second experiment, we ran 17 total samples with pooled donors (donor IDs: 221175 and 323353 ) on novaeseq platform. Each novaseq run results in 8 FASTQ files (2 lanes x 4 reads). The read files from an inDrops run have the following content:
*_R1_001.fastq.gz : contains the 3' UTR cDNA read
*_R2_001.fastq.gz : contains the first half of the cell barcode
*_R3_001.fastq.gz : contains the library index for demultiplexing libraries
*_R4_001.fastq.gz : contains the second half of the barcode and the UMI.
All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis (github.com/indrops), using the parameter values specified in the .yaml files provided in the supplementary material. The yaml files also provide library indices that can be used for demultiplexing.
When cells were pooled prior to droplet capture, the cell barcodes were then assigned to each donor respectively by their SNP profiles using the scSplit (https://github.com/jon-xu/scSplit).
To obtain the final counts matrix used for data analysis, total count and a mitochondrial count filters were applied as described in McCauley,Kukreja et. al. 2022, biorXiv
Assembly: GRCh38/91
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, gene names, and raw counts for all cells
Supplementary files format and content: Library barcodes and metadata (metadata.csv.gz): library identity, barcode, and associated metadata for all cells across in the sample

source_name: Airway epthelium

growth_protocol: Primary human bronchial epithelial cells (HBECs) from normal donors were obtained from Lonza (Cat. # CC-2540) and were expanded for two passages with Growth Medium (BEGM supplemented with one SingleQuots kit, Lonza Cat. # CC-3171) in uncoated T75 flasks (Corning Cat. # 430641U). After expansion, cells were seeded on uncoated 12-well TransWell (Corning Cat. # 3460) plates at a density of 1e6 cells per plate and expanded for 7 days in Differentiation Medium (50:50 BEGM (Lonza Cat. # CC-3171)/high-glucose DMEM (ThermoFisher Cat. # 11965175)) supplemented with one SingleQuots kit with no T3 and final retinoic acid concentration of 50 nM (Lonza # CC-4175). After 7 days, media was removed from the apical surface and cells were differentiated at air-liquid interface for an additional 30-45 days with media replaced every 48-72 hours.

extract_protocol:
HBECs were collected 14 days post-injury by treating with 0.05% Trypsin-EDTA (prepared by dilution of 0.25% Trypsin- EDTA, ThermoFisher Cat. # 25200056, with calcium/magnesium-free PBS), for 20 minutes at 37 °C. Trypsin dissociation was halted with Trypsin Neutralizer Solution (ThermoFisher Cat. # R002100) at 1:1 dilution and cells were filtered through a 40 μm strainer and pelleted by centrifugation at 300x g for 5 minutes. Cells were resuspended in phosphate buffered saline (ThermoFisher Cat. # 10010072) with 0.1% bovine serum albumin (ThermoFisher Cat. # B14) and counted on a Countess Cell Counter (ThermoFisher) to determine cell number and viability. For cell counting, 10 μL of cell suspension was mixed with 10 μL of Trypan Blue Solution (ThermoFisher Cat. # 15250061) and 10 μL of that 1:1 mix was loaded into Countess chip and read with default program. Viable cell numbers were used to determine cell concentration. Optiprep Density Gradient Medium (Sigma Cat. # D1556) was added to achieve a final concentration of 15% Optiprep and 120-150,000 cells/ml. Cells were captured by inDrops as detailed in Zilionis, R. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat. Protoc. 12, 44–73 (2017).
inDrops v3 scRNA-seq; Library construction as detailed in Zilionis, R. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat. Protoc. 12, 44–73 (2017).

treatment_protocol: After air-liquid interface differentiation, cells were washed 3X with warm 1XS PBS and treated with MEM (ThermoFisher Cat. # 10370088, 500 μL apical, 1 mL basal) for 1 hour at 37°C to remove differentiated luminal cells. Following incubation, luminal cells were removed by pipetting gently up and down 3-5X before removing apical media and washing with 500 μL MEM in apical chamber. Cytokines were diluted in Differentiation Medium at concentrations indicated. Cells were cultured for an additional 14 days, replacing media every 48-72 hours.

value: Airway epthelium

tag: donor ids

value: signaling molecules as specficied


title: BT549_DMSO_Day3_A


title: BLA_FearRecall_fr10_N13_S7237

description: Smartseq


title: OVCAR8_EPZ_Day3_A


title: BT549_EPZ_Day5_B


title: BLA_FearRecall_fr10_N11_S7235

description: Smartseq


title: BLA_FearRecall_fr10_M17_S7217

description: Smartseq


title: OVCAR8_DMSO_Day3_B


title: MDAMB436_DMSO_Day5_A


title: BT549_DMSO_Day5_B


title: OVCAR8_DMSO_Day3_A


title: BT549_DMSO_Day3_B


title: BLA_FearRecall_fr10_M13_S7213

description: Smartseq


title: BLA_FearRecall_fr10_M12_S7212

description: Smartseq


title: OVCAR8_DMSO_Day5_B


title: BLA_FearRecall_fr10_L8_S7184

description: Smartseq


title: BLA_FearRecall_fr10_K3_S7155

description: Smartseq


title: OVCAR8_DMSO_Day5_A


title: BLA_FearRecall_fr10_L23_S7199

description: Smartseq


title: BLA_FearRecall_fr10_K2_S7154

description: Smartseq


title: GSC23_shCONT_Rep_3

city: New York

first: Shuai

last: Wang

state: NY

address: 550 First Avenue

institute: NYU Grossman School of Medicine

data_processing:
Illumina PE150 technology is employed to sequence the sample
The qulity control step was performed before sequencing
FASTQ to row count was analyzed by bioinformatians in Novogene
Assembly: hg19
Supplementary files format and content: Tab-delimited text file contain raw counts

source_name: Primary GBM cells

extract_protocol:
Cells were lysed by using Trizol (Invitrogen, 15596026) and RNA was extracted with Direct-zol RNA Microprep kit (Zymo Research, R2062) according to the manufacturer’s protocol.
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA.

value: Primary GBM cells


title: GSC23_shCBX3_1


title: BLA_FearRecall_fr10_L22_S7198

description: Smartseq


title: BT549_EPZ_Day3_A


title: GSC23_shCONT_Rep_1


title: BLA_FearRecall_fr10_L18_S7194

description: Smartseq


title: BLA_FearRecall_fr10_K7_S7159

description: Smartseq


title: BLA_FearRecall_fr10_K6_S7158

description: Smartseq


title: Input_shCONT

data_processing:
For the downstream analysis of ChIP-Seq data, TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim raw FASTQ files. Trimmed data were aligned to the hg19 human genome assembly using Bowtie2, followed by sorting and indexing BAM files with SamTools. ChIP signals were visualized using bigwig files generated by DeepTools. “ComputeMatrix,” “plotHeatmap,” and “plotProfile” functions wrapped in DeepTools were used to generate heat maps.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% methanol-free formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a 130 Watt Ultrasonic Processors.
ChIP and input DNA was prepared using EZ-ChIP kit (Milliopre, 17-371), ChIP-Seq library was prepared by Novogene.


title: BLA_FearRecall_fr10_L16_S7192

description: Smartseq


title: ChIP_shCBX3_Kla


title: Input_shCBX3


title: BT549_EPZ_Day5_A


title: BT549_DMSO_Day5_A


title: BLA_FearRecall_fr10_K21_S7173

description: Smartseq


title: BLA_FearRecall_fr10_L10_S7186

description: Smartseq


title: BLA_FearRecall_fr10_J4_S7132

description: Smartseq


title: BLA_FearRecall_fr10_J5_S7133

description: Smartseq


title: BLA_FearRecall_fr10_J20_S7148

description: Smartseq


title: Pat.6_POST_ROI.013_CD68-CD31-

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

description:
Initial_dataset.xlsx
Q3_normalized_dataset.xlsx

data_processing:
The sequencing data was demultiplexed and converted into FASTQ files with bcl2fastq2 Conversion Software (Illumina, v2.2.0).
Raw FASTQ files were subjected to adapter removal, merging of paired-end reads, read alignment to barcode IDs and PCR duplicate removal with GeoMx NGS Pipeline software (NanoString), and resulting DCC files were uploaded into GeoMx DSP Control Center (Nanostring, v.2.4).
For QC, negative probes identified as outliers by Grubbs test were excluded in each segment.
Signal-to-noise ratio [Q3 / geoMean(Negative probes)] was calculated for each segment and segments with signal-to-noise ratio < 1 were excluded from further analyses.
Genes exceeding both the limit of quantitation calculated based on negative probe counts and value 2 in at least 15% of segments were defined as confidently expressed and used in further analyses. For analyses not directly comparing different segment types (differential gene expression and pathway analyses), this gene filtering was performed separately for CD68+, CD31+ and CD68-CD31- segments.
Filtered data were normalized by Q3 values calculated based on all genes passing the aforementioned filters.
Assembly: NanoString's GeoMx Human Whole Transcriptome Atlas, cat. GMX-RNA-NGS-HuWTA; GRCh38.p13
Supplementary files format and content: DCC files that were imported into GeoMx DSP Control Center
Supplementary files format and content: .xlsx file containing Initial Dataset (unnormalized and unfiltered) exported from GeoMx DSP Control Center
Supplementary files format and content: .xlsx files containing Q3 normalized count data (four sheets of data: all segments, CD68+, CD31+ and CD68-CD31- segments)
Library strategy: Spatial Transcriptomics

source_name: FFPE BRCA biopsy

growth_protocol: FFPE biopsy

extract_protocol:
FFPE biopsies were cut into 5μm sections and each patient’s pre- and post-treatment samples were placed on the same slide for subsequent simultaneous analysis. Biopsies were hybridized with RNA probes and stained for CD68, CD31, pan-cytokeratin and nuclei. Using the GeoMx DSP instrument, selected regions of interest (ROIs) were segmented into following areas: 1.) CD68+pan-cytokeratin- area, 2.) CD31+ area and 3.) remaining DNA+ area, and the hybridized RNA probes were collected separately from these three areas.
Spatial transcriptome libraries were prepared using NanoString's GeoMx Human Whole Transcriptome Atlas kit and GeoMx Digital Spatial Prolifer instrument according to manufacturer's instructions.

treatment_protocol: Patients from ER+ breast cancer (BRCA) and biliary tract cancer (BTC) cohorts of the phase I/II first-in-human MATINS trial (https://clinicaltrials.gov/ct2/show/NCT03733990) were treated with bexmarilimab (FP-1305). FFPE biopsies were collected from target lesions before (PRE) and after (POST) bexmarilimab therapy.

tag: cancer

value: BTC

tag: biopsy type

value: POST

tag: patient response_to_bex

value: nDC

tag: segment

tag: roi

tag: patient

tag: geomx batch

tag: roi exclusion

value: No

tag: q3 normalized_data_sheets

value: FFPE BRCA biopsy


title: Pat.6_POST_ROI.013_CD68+

tag: tissue


title: GSC23_shCONT_Rep_2


title: BLA_FearRecall_fr10_K9_S7161

description: Smartseq

tag: genotype

value: TRAP2 Ai14

value: Fear recall


title: Pat.6_POST_ROI.013_CD31+


title: BLA_FearRecall_fr10_J19_S7147

description: Smartseq

tag: treatment


title: BLA_FearRecall_fr10_J6_S7134

description: Smartseq


title: BLA_FearRecall_fr10_J13_S7141

description: Smartseq


title: scRNA-seq of 6 single rosette organoids at 1-month old each with CMO

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Raw paired-end 10x scRNA-seq data were processed and aligned using CellRanger v4.0.0.
Raw RNA UMI count matrix were filtered to keep cells with >500 detected genes and <10% mitochondrial transcripts.
Raw paired-end HTO data were processed using CITE-seq-Count v1.4.4.
Cell barcodes present in both raw RNA UMI count matrix and raw HTO count matrix were kept for joint analysis.
Assembly: GRCh38
Supplementary files format and content: raw RNA UMI count matrix; raw HTO counts matrix

source_name: Brain organoid cells

growth_protocol: iPSC lines were passaged using Accutase (Innovative cell) and replated onto Geltrex-coated (1:50 dilution in DMEM/F12) 12-well plates at 3-4 x 105 cells/well  in mTeSR1 with 10 µM rho-kinase inhibitor (Y-27632; Tocris, 1254). Medium without the inhibitor was replaced daily until the cells reach 80-100% confluency. The medium was then changed to 3N (50:50 DMEM/F12:neurobasal with N2 and B27 supplements)36 without vitamin A with 2 µM DMH1 (Tocris, 4126), 2 µM XAV939 (Cayman Chemical, 13596) , and 10 µM SB431542 (Cayman Chemical, 13031) (2 mL of media per well). Daily 75% media changes with 1 µM cyclopamine (Cayman Chemical, 11321) added began on day 1. On day 4, the monolayer was cut into squares using the StemPro EZ passage tool, and 1 mL of conditioned media was reserved. The squares were incubated for 1 minute with L7 hPSC passaging solution (Lonza). After aspirating the L7 solution, the squares were sprayed off the bottom of the culture plate with the 1 mL of preconditioned culture media with a P1000 micropipette. An additional 2 mL of fresh culture medium with the 4 inhibitors was added for a final volume of 3 mL. Approximately 200 µL of resuspended squares were then transferred into each well of a 96-well plate preincubated at 37 C for 20 minutes with 35 µL of 100% Geltrex solution/well. Up to 16 wells can be made using one monolayer. Higher densities will result in fusion between nearby SOSRS forming multi-rosette doublets or “strings”. After 48 hours, daily 50% media changes were performed. On day 6 (2 days after cutting), the four inhibitors were no longer added but replaced with 3 µM CHIR99021. After 3-4 additional days of culture. The organoids were individually removed using the STRIPPER Micropipetter (Cooper Surgical) with 275 µM tips and plated individually in the wells of a low-adherence U-bottom 96-well plate with 200 µL of 3N medium without vitamin A with 3 µM CHIR99021, BDNF (20 ng/mL), and NT3 (20 ng/mL). The ideal diameter for picking the SOSRS is ~ 250 µM. Starting 2 days later, half-media changes of 3N with vitamin A, BDNF (20 ng/mL), and NT3 (20 ng/mL) were repeated every other day. After 35 days of differentiation, 3N media with vitamin A (but without BDNF and NT3) was used for half-media changes every other day. At this time, SOSRS were transferred from the low-adherence 96-well plates to low-adherence 24-well plates for a necessary increase in media volume due to expanded SOSRS size.

extract_protocol:
One-, three-, or five-month SOSRS were dissociated using the Worthington papain dissociation kit. Cells from each organoid were labelled with sample-specific hashtag-labelled antibodies (HTO-A, Biolegend) to allow multi-sample pooled analyses to reduce batch effects, with subsequent de-multiplexing of scRNA-seq data based on the hashtags.
Single-cell suspensions were processed using the 10X Genomics Chromium platform, and scRNA-seq libraries were sequenced by Illumina NovaSeq. Each paired-end read contains a cell barcode and a UMI in Read 1, and the transcript-specific read in Read 2 with a read length of 151 nt.  Separately, each cell generates an HTO count vector for the hashtags used, allowing the cells to be assigned to organoid samples they come from.
10x Chromium scRNA-seq

treatment_protocol: No treatment

value: Induced pluripotent stem cells

tag: cell line

value: CC1, E9


title: BLA_FearRecall_fr10_K22_S7174

description: Smartseq


title: BLA_FearRecall_fr10_K15_S7167

description: Smartseq


title: BLA_FearRecall_fr10_I8_S7112

description: Smartseq


title: ChIP_shCONT_Kla


title: Pat.6_POST_ROI.011_CD68-CD31-

value: Yes, healthy tissue


title: BLA_FearRecall_fr10_K13_S7165

description: Smartseq


title: GSC23_shCBX3_2


title: BLA_FearRecall_fr10_K12_S7164

description: Smartseq


title: BLA_FearRecall_fr10_J9_S7137

description: Smartseq


title: GSC23_shCBX3_3


title: BLA_FearRecall_fr10_I19_S7123

description: Smartseq


title: scRNA-seq of 6 single rosette organoids at 3-month old each with CMO

tag: cell type


title: BLA_FearRecall_fr10_I15_S7119

description: Smartseq


title: BLA_FearRecall_fr10_K16_S7168

description: Smartseq


title: BLA_FearRecall_fr10_J21_S7149

description: Smartseq


title: BLA_FearRecall_fr10_I11_S7115

description: Smartseq


title: Pat.6_POST_ROI.012_CD68-CD31-


title: Pat.6_PRE_ROI.008_CD68-CD31-

value: PRE


title: Pat.6_POST_ROI.012_CD31+


title: Pat.6_POST_ROI.012_CD68+


title: BLA_FearRecall_fr10_I7_S7111

description: Smartseq


title: BLA_FearRecall_fr10_I13_S7117

description: Smartseq


title: Organoid_Expansion_Bulk_BR1

city: Utrecht

first: Jeff

last: DeMartino

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

data_processing:
Reads were demultiplexed requiring a perfect match to a designed 8-nt index (Ilumina Nextera DNA adapter series) and up to 1 mismatch to a designed 3-nt to 9-nt staggered barcode residing at the beginning of the read.
gRNAs were counted by requiring a perfect match to a designed 19-nt, 20-nt, or 21-nt gRNA in the library using mageck count from MaGeCK CRISPR screen analysis toolkit (0.5.9.5)
Assembly: Custom TFome sgRNA library
Supplementary files format and content: Tab delimited files containing sgRNA read counts

source_name: human small intenstinal organoids

extract_protocol:
Genomic DNA was isolated from different cell populations using DNeasy Blood & Tissue kit (QIAGEN) following the manufacturer’s protocol.
CRISPR screen sequencing libraries were constructed as previously described (L. Lin, B. Holmes, M. W. Shen, D. Kammeron, N. Geijsen, D. K. Gifford, R. I. Sherwood, Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression. Cell Rep. 33, 108426 (2020).) Briefly, two sequential PCR reactions were performed to amplify the gRNA fragments integrated in the genomic DNA, using primers flanking the gRNA protospacers containing staggered barcodes and primers with full-length Illumina sequencing adapters. All primer sequences are listed in Table S3.

value: human small intenstinal organoids


title: Organoid_Differentiation_Bulk_BR2


title: BLA_FearRecall_fr10_I24_S7128

description: Smartseq


title: BLA_FearRecall_fr10_I20_S7124

description: Smartseq


title: BLA_FearRecall_fr10_I10_S7114

description: Smartseq


title: Pat.6_POST_ROI.011_CD31+


title: Pat.6_POST_ROI.011_CD68+


title: Pat.6_POST_ROI.010_CD68-CD31-


title: BLA_FearRecall_fr10_I17_S7121

description: Smartseq


title: Pat.6_POST_ROI.010_CD31+


title: Pat.6_POST_ROI.010_CD68+


title: anti-FLAG, rep 2

data_processing:
Read mapping to the human genome (hg38) was done with Bowtie2 (2.4.1) using parameters: -q -N 0 -L 22 -X 500 --no-unal.
Unmapped reads, low mapping quality reads (Q<30) were discarded.
Peak calling was performed by using MACS2’s callpeak function (2.2.6) with a cutoff of q<0.01
Assembly: hg38
Supplementary files format and content: bigWig (except for Input sample)

source_name: Human small intestinal organoids

extract_protocol:
Organoids were briefly dissociated with TrypLE (Thermo Fisher), fixed with formaldehyde (final concentration: 1%) and quenched by Glycine (final concentration: 0.125M). Chromatin was extracted by two-step lysis protocol in the presence of protease inhibitors: leupeptin hemisulfate, pepstatin A and phenylmethylsulfonyl fluoride. Chromatin was further sheared by sonication using Bioruptor Pico (Diagenode) with 7 cycles of 30s “ON” and 30s “OFF”.
Sequencing libraries for ChIP-seq were constructed by using NEBNext Ultra II DNA Library Prep kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) (NEB)

value: Human small intestinal organoids

tag: chip antibody

value: anti-FLAG (Thermo)


title: anti-FLAG, rep 1


title: Pat.6_PRE_ROI.008_CD68+


title: Sorted_Negative_BR2


title: Sorted_Negative_BR1


title: Pat.6_POST_ROI.009_CD68-CD31-


title: BLA_FearRecall_fr10_I14_S7118

description: Smartseq


title: Sorted_mNeongreen_BR2


title: Sorted_mNeongreen_BR1


title: anti-ZNF800, rep3

value: anti-ZNF800 (Atlas)


title: Pat.6_PRE_ROI.007_CD31+


title: BLA_FearRecall_fr10_H20_S7100

description: Smartseq


title: anti-ZNF800, rep1


title: Pat.6_POST_ROI.009_CD31+


title: BLA_FearRecall_fr10_H5_S7085

description: Smartseq


title: BLA_FearRecall_fr10_I12_S7116

description: Smartseq


title: Pat.6_PRE_ROI.007_CD68+


title: Sorted_iRFP_BR2


title: BLA_FearRecall_fr10_H16_S7096

description: Smartseq


title: Sorted_iRFP_BR1


title: Pat.6_PRE_ROI.006_CD68-CD31-


title: Pat.6_POST_ROI.009_CD68+


title: Organoid_Expansion_Bulk_BR2


title: Pat.6_PRE_ROI.008_CD31+


title: Organoid_Differentiation_Bulk_BR1


title: Hgfac KO day2 wounds, 3 biological reps

city: Cambridge

first: Ramnik

last: Xavier

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing BCL files were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to generate gene expression counts using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: distal colon

extract_protocol:
Fresh frozen intact tissues or day2 wounds of Hgfac WT and KO mice were OCT embedded, and 10um frozen sections were cut with cryostat.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit following the manufacturer's instruction.

value: distal colon

tag: condition

value: day2 wounds

value: Hgfac KO


title: Input


title: Pat.6_PRE_ROI.006_CD31+

value: BTC


title: BLA_FearRecall_fr10_H7_S7087

description: Smartseq


title: ESC_CRISPRa_Il17rb_CapHiC_rep2

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

country: France

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

description:
restriction enzyme: DpnII
ESC_CRISPRa_Il17rb_CapHiC_pooled.mat.gz

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq.
Assembly: mm10
Supplementary files format and content: The captured regions from the Capture Hi-C data are represented as text (.mat) files, consisting of headed columns: chr, ID (of capture region), coord_bin1, coord_bin2, from1, to1 (coordinates of first region), to1, to2 (coordinates of second region), and a final column with the normalized interaction score.

source_name: J1 embryonic stem cell

growth_protocol: J1 mouse ES cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (4.5 g/L glucose-DMEN, 15% FCS, 0.1 mM non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1 mM glutamine, 500 U/mL LIF, gentamicin), then passaged onto feeder-free 0.2% gelatin-coated plates for at least two passages to remove feeder cells.

extract_protocol:
Five million aliquots of cells were fixed in 2% formaldehyde for 10 min, quenched with 125 mM cold glycine, then collected by centrifugation and washed with PBS. Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 0.2% NP-40, protease inhibitor cocktail) on ice for 30 min and nuclei collected by centrifugation and resuspended in DpnII restriction buffer. ESCs were permeabilized by treatment with 0.4% SDS for 1 h at 37°C, followed by 1.6% Triton X-100 for 1 h at 37°C. Nuclei aliquots were digested overnight at 37°C with 1500 U DpnII, then cohesive ends were filled in with biotin tags by incubating for 90 min at 37°C with 15 μM dATP, 15 μM dTTP, 15 μM dGTP, 15 μM biotin-14-dCTP and 25 U DNA polymerase I Klenow fragment. Nuclei were collected by centrifugation and in situ ligation was performed overnight at 16°C in 500 μL volumes of 1X ligase buffer (NEB) with 20,000 U T4 DNA ligase, before de-crosslinking overnight at 65°C with 0.75 mg/mL proteinase K. DNA was purified by RNase A treatment, phenol/chloroform extraction and isopropanol precipitation. Five microgram aliquots of DNA were sonicated to a fragment size of ~100-400 bp in a Covaris sonicator E220 and bound to Steptavidin MyOne T1 beads, following the manufacturer’s instructions. The DNA was then end-repaired by incubating for 1 h at 20°C with 0.8 mM dNTPs, 0.3 U/μL T4 DNA polymerase, 1 U/μL T4 polynucleotide kinase and 0.1 U/μL DNA polymerase I Klenow fragment in ligase buffer, then A-tailed by incubating for 1 h at 37°C with 200 μM dATP and 0.2 U/μL Klenow fragment (3’-5’ exo-) in NEBuffer 2 (NEB), then Illumina PE adapter was added by incubating overnight at 20°C with 15 μM PE adapter and 2000 U T4 DNA ligase in ligase buffer, washing the beads with appropriate buffers in between each treatment. Hi-C material was then amplified from the beads with 7-9 cycles of PCR using Herculase II Fusion DNA polymerase (Agilent) according to the manufacturer’s instructions. Material at this stage was quantified on a BioAnalyzer (Agilent) and DpnII and HindIII Hi-C material was sequenced (2x50 nt) on a NextSeq 2000 (Illumina) following the manufacturer’s instructions). 750 ng of this DpnII Hi-C material was concentrated in a SpeedVac vacuum concentrator and then target capture was performed using the SureSelect XT Target Enrichment system (Agilent) with the custom-designed library, following the manufacturer’s instructions
Products resulting from extract protocol are immediately ready for cluster generation on Illumina HiSeq 4000, following manufacturer's instructions.

treatment_protocol: Twenty million cell batches of J1 ESCs were transfected each with 20 μg dCas9-VPR vector (Addgene #63798) and 20 μg plasmid constructed by the IGBMC molecular biology platform, containing optimized scaffold for 4 gRNAs alongside a puromycin resistance gene and mCherry reporter, with Lipofectamine 2000 according to the manufacturer’s instructions. After 24 h, transfected cells were treated with 3 μg/mL puromycin and 1 mg/mL G418, and after another 24 h, mCherry-positive cells were sorted by FACS before immediate processing.

value: J1 embryonic stem cell

tag: strain

value: WT

value: CRISPRa induction of Il17rb


title: Hgfac WT intact tissues, 3 biological reps

value: intact tissues

value: Hgfac WT


title: BLA_FearRecall_fr10_G9_S7065

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: anti-FLAG, rep 3


title: Colon_MSP_6h_2

data_processing:
RNA-seq data were processed using the nf-core/rnaseq workflow (version 3.3)
Sequencing reads were preprocessed using FastQC, Trim Galore!, and SortMeRNA to remove low-quality reads, adapters, and ribosomal RNA, respectively.
The remaining reads were then aligned to reference using STAR and gene abundances were quantified using Salmon
Supplementary files format and content: Tab delimited files for counts and TPM values of transcripts derived from Salmon (*quant.sf)
Supplementary files format and content: Tab delimited files for counts and TPM values of genes derived from Salmon (*quant.genes.sf)

source_name: Primary colonic epithelial cells

growth_protocol: Colon spheroids were maintained in 50% L-WRN conditioned medium and passaged every 3-4 days.

extract_protocol:
RNA was extracted using DynaBeads mRNA DIRECT Purification Kit (Life Technologies) following the manufacturer's protocols
RNA libraries for RNA-seq were parepared using Nextera XT DNA library Preparation Kit (Illumina) following the manufacturer's protocols.

treatment_protocol: Colon spheroids were cultured in 0% L-WRN CM (Advanced DMEM F/12 supplemented with 1%(v/v) GlutaMAX, 1%(v/v) HEPES and 100U/ml pen/Strep) with PBS or recombinant mouse MSP protein for indicated time.

value: Primary colonic epithelial cells

value: MSP (100ng/ml)

tag: time


title: Colon_MSP_6h_1


title: Colon_MSP_4h_3


title: Colon_MSP_4h_2


title: Pat.6_PRE_ROI.005_CD68-CD31-

tag: cancer

tag: biopsy type

value: PRE

value: nDC

value: No

value: FFPE BRCA biopsy


title: Pat.6_PRE_ROI.005_CD31+

tag: patient response_to_bex

tag: segment


title: Colon_MSP_2h_2


title: Colon_MSP_4h_1


title: BLA_FearRecall_fr10_H22_S7102

description: Smartseq


title: Pat.6_PRE_ROI.007_CD68-CD31-

tag: roi

tag: patient


title: BLA_FearRecall_fr10_G23_S7079

description: Smartseq


title: BLA_FearRecall_fr10_G19_S7075

description: Smartseq


title: anti-ZNF800, rep2

value: Human small intestinal organoids

value: anti-ZNF800 (Atlas)


title: Colon_Control_6h_2

value: PBS


title: BLA_FearRecall_fr10_H12_S7092

description: Smartseq


title: Plasmid library

organism: synthetic construct

source_name: Library plasmid

value: Library plasmid


title: Colon_MSP_0h_2


title: Hgfac WT day2 wounds, 3 biological reps

value: distal colon

value: day2 wounds


title: Colon_Control_4h_3

value: WT


title: Pat.6_PRE_ROI.004_CD68-CD31-

value: BTC

tag: geomx batch

tag: roi exclusion

value: Yes, healthy tissue


title: Colon_MSP_0h_1


title: Pat.6_PRE_ROI.003_CD68-CD31-

tag: q3 normalized_data_sheets

tag: tissue


title: ESC_CRISPRa_Il17rb_CapHiC_rep1

value: J1 embryonic stem cell

tag: genotype

tag: treatment

value: CRISPRa induction of Il17rb


title: Pat.6_PRE_ROI.006_CD68+


title: Colon_MSP_6h_3

tag: cell type

value: Primary colonic epithelial cells


title: BLA_FearRecall_fr10_H10_S7090

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: BLA_FearRecall_fr10_G8_S7064

description: Smartseq


title: Colon_Control_2h_2


title: Pat.6_PRE_ROI.002_CD68-CD31-

value: PRE

value: nDC


title: Colon_Control_2h_1


title: Colon_Control_0h_3


title: Pat.6_PRE_ROI.003_CD31+

value: No

value: FFPE BRCA biopsy


title: BLA_FearRecall_fr10_G7_S7063

description: Smartseq


title: Colon_Control_0h_2


title: Colon_MSP_2h_3

value: MSP (100ng/ml)


title: Pat.6_PRE_ROI.005_CD68+


title: Colon_MSP_2h_1


title: BLA_FearRecall_fr10_F2_S7034

description: Smartseq


title: NIH3T3 cells, control, 16h, 3

growth_protocol: NIH3T3 cells were maintained in DMEM supplemeted with 10% fetal bovine serum (FBS), 1%(v/v) GlutaMAX, 1%(v/v) HEPES and 100U/ml pen/Strep

treatment_protocol: Treated cells with DMSO or 1uM ATRA for indicated time.

tag: cell line

value: fibroblast cells

value: parental

value: DMSO


title: Colon_MSP_0h_3


title: Pat.6_PRE_ROI.004_CD31+


title: BLA_FearRecall_fr10_G18_S7074

description: Smartseq


title: BLA_FearRecall_fr10_F19_S7051

description: Smartseq


title: Colon_Control_6h_3

value: PBS


title: NIH3T3 cells, control, 16h, 2


title: NIH3T3 cells, RA, 8h, 2

value: 1uM ATRA


title: Pat.6_PRE_ROI.001_CD68+

value: BTC


title: Pat.6_PRE_ROI.004_CD68+

value: Yes, healthy tissue


title: NIH3T3 cells, RA, 8h, 1


title: BLA_FearRecall_fr10_G17_S7073

description: Smartseq


title: NIH3T3 cells, control, 8h, 3


title: Colon_Control_6h_1

value: WT


title: BLA_FearRecall_fr10_G15_S7071

description: Smartseq


title: Colon_Control_4h_2


title: Pat.3_POST_ROI.013_CD31+

value: POST

value: DC

value: Yes, low signal-to-noise ratio


title: Colon_Control_4h_1

value: Primary colonic epithelial cells


title: NIH3T3 cells, control, 8h, 1


title: BLA_FearRecall_fr10_G14_S7070

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: Colon_Control_2h_3


title: BLA_FearRecall_fr10_F11_S7043

description: Smartseq


title: Pat.6_PRE_ROI.003_CD68+

value: PRE

value: nDC

value: No


title: BLA_FearRecall_fr10_G1_S7057

description: Smartseq


title: BLA_FearRecall_fr10_F7_S7039

description: Smartseq


title: Pat.3_POST_ROI.013_CD68+

value: FFPE BRCA biopsy


title: Pat.6_PRE_ROI.002_CD31+


title: BLA_FearRecall_fr10_F23_S7055

description: Smartseq


title: Colon_Control_0h_1


title: Pat.3_POST_ROI.012_CD68-CD31-


title: NIH3T3 cells, RA, 16h, 3

value: fibroblast cells

value: parental


title: NIH3T3 cells, control, 0h, 1

value: DMSO


title: BLA_FearRecall_fr10_E9_S7017

description: Smartseq


title: mESCs, zfCh_2

city: Edinburgh

first: Theresa

last: Schöpp

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

data_processing:
adaptor sequences were removedfrom the reads with cutadapt (1.18) using default settings
consensus sequences of rodent retrotransposons were retrieved from Repbase (24.01) and used to map the processed reads using bowtie2 (2.4.2) with default setting
number of mapped reads per retrotransposon were counted and analyzed using DESeq2 (1.32.0)
Assembly: Repbase
Supplementary files format and content: tab-delimited text file includes log2 fold change

source_name: E14Tg2a mESCs

growth_protocol: cells were maintained in LIF/FCS mESC media

extract_protocol:
RNA was extracted using QIAzol reagent (total RNA, rRNA depleted)
Librarieswere prepared with NEBNext Ultra II Directional RNA Library Kit for Illumina with prior use ofNEBNext rRNA Depletion Kit v2 (E7405, NEB) following the manufacturer’s protocol.

value: E14Tg2a mESCs

value: embryonic stem cells

value: Tasor -/-; zfChimera

value: reconstitution of zfTex15-hTasor chimera


title: mESCs, delD_2

value: Tasor -/-; delDUF

value: reconstitution of hsTasor-delDUF


title: Pat.6_PRE_ROI.002_CD68+

value: BTC

value: Yes, healthy tissue


title: BLA_FearRecall_fr10_F21_S7053

description: Smartseq

value: TRAP2 Ai14


title: NIH3T3 cells, RA, 16h, 2

value: 1uM ATRA


title: NIH3T3 cells, RA, 16h, 1


title: Pat.6_PRE_ROI.001_CD31+

value: PRE


title: Pat.6_PRE_ROI.001_CD68-CD31-

value: nDC


title: BLA_FearRecall_fr10_F10_S7042

description: Smartseq

value: Fear recall


title: Pat.3_POST_ROI.012_CD68+

value: POST

value: DC

value: No

value: FFPE BRCA biopsy


title: Pat.3_PRE_ROI.011_CD68-CD31-


title: NIH3T3 cells, RA, 8h, 3

value: fibroblast cells

value: parental


title: NIH3T3 cells, control, 16h, 1

value: DMSO


title: BLA_FearRecall_fr10_F15_S7047

description: Smartseq


title: BLA_FearRecall_fr10_E22_S7030

description: Smartseq


title: Pat.3_POST_ROI.013_CD68-CD31-


title: mESCs, hCh_1

value: E14Tg2a mESCs

value: embryonic stem cells

value: Taso -/-; hChimera

value: reconstitution of hsTex15-hsTasor chimera


title: Pat.3_PRE_ROI.011_CD68+

value: BTC


title: NIH3T3 cells, control, 8h, 2


title: BLA_FearRecall_fr10_F12_S7044

description: Smartseq

value: TRAP2 Ai14


title: NIH3T3 cells, control, 0h, 3


title: mESCs, PB_1

value: Tasor -/-; PB

value: reconstitution of empty vector PB


title: NIH3T3 cells, control, 0h, 2


title: Pat.3_POST_ROI.010_CD68+


title: mESCs, Control_1

value: Tasor +/+


title: O77-P5-con_S7_L004_Small intestinal epithelium_control

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

description:
Capture-C
cd_IFNg.txt

data_processing:
Paired-end reads were aligned to mm10 and filtered for Hi-C artefacts using HiCUP (Wingett et al., 2015) and Bowtie 2 (Langmead and Salzberg, 2012), with fragment filter set to 100-800 bp. Quality was evaluated by ensuring a high proportion of valid reads (generally high, above 50%, for two IFNg-treated samples of organoid 77 36.8 and 37.7%, respectively). High restriction digestion efficiency was assessed by evaluating the percentage of religated fragments, suggesting that digestion efficiency was above 70% for all samples (lowest: 73.1%).
Read counts of reads aligning to captured gene promoters were then called by CHiCAGO (Cairns et al., 2016).
For scatterplots we first determined all interactions between promoters and a given set of intervals (i.e. ATAC peaks). To enable a robust analysis of the Low Input data, ATAC peaks were extended for this to cover two adjacent DpnII restriction fragments on each side. Next, for each promoter-interval interaction we quantified the sum of read counts across all DpnII fragments overlapping this interval. This number was then divided by the total number of interval-overlapping DpnII fragments and total read coverage of the interacting promoter to obtain mean normalized read counts.
Assembly: mm10
Supplementary files format and content: txt files representing read counts and scores of reads aligning to sites interacting with captured gene promoters.
Library strategy: Capture-C

source_name: Small intestinal epithelium

growth_protocol: Small intestinal organoids were cultured for 3-6 weeks (passage 2-5) and passaged every week

extract_protocol:
Chromatin was extracted and fixed as described previously (Downes et al., 2022), following the protocol for low input and adapting centrifugation steps to organoid cells (400 g). Briefly, 25,000 organoid cells were trypsinized, collected in 1ml medium and crosslinked with 134µl of 16% formaldehyde (1.89% final; ThermoFisher Scientific, #10751395) while rotating for 10 min at room temperature. Cells were quenched with 162µl 1M cold glycine, washed with cold PBS and lysed for 20 minutes at 4°C in 500µl lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40, supplemented with cOmplete proteinase inhibitors (Roche)) prior to snap freezing on dry ice. Fixed chromatin was stored at -80°C.
Capture-C libraries were prepared as described previously, following the recommendations for Low Input samples (Downes et al., 2022). Briefly, lysates were thawed on ice, pelleted and resuspended in 200µl 1x DpnII buffer (New England Biology). The nuclei were subsequently permeabilized with SDS (ThermoFischer Scientific, AM9820, 0.28% final concentration, 1hr, 37°C, interval shaking 500rpm, 30 sec on/off), quenched with Triton X 100 (1.67% final concentration, 1hr, 37°C, interval shaking 500rpm, 30 sec on/off) and digested for 24 hours with 3x10µl DpnII (homemade, 37°C, interval shaking 500rpm, 30 sec on/off). The digested chromatin was then in situ ligated with 8µl T4 Ligase (240U, ThemoFirsher Scientific, EL0013) in a volume of 1440µl (20 hours, 16°C). Following this, the nuclei containing ligated chromatin were pelleted to remove any non-nuclear chromatin, reverse-crosslinked and the ligated DNA was phenol-chloroform purified. The sample was resuspended in 100µl water and sonicated 13x (Bioruptor Pico, 30sec on/off) to obtain fragments of ~200bp, followed by a concentration using AmpureX beads (Beckman Coulter #A63881, ratio: 1.8x). All material was adaptor-ligated and indexed in one reaction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs: E7645L) and NEBNext Multiplex Oligos for Illumina Primer sets 1 (New England Biolabs #E7335S/L) and 2 (New England Biolabs #E7500S/L). The libraries were amplified with 8 PCR cycles using Herculase II Fusion Polymerase kit (Agilent #600677) and their appropriate size assessed via Bioanalyzer. Libraries were next hybridized in the following way: For each promoter-containing DpnII restriction fragment we designed one-two capture probes (aligned to mm10, 70bp each) using the online tool designed by the Hughes lab (CapSequm2: http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) with the following filtering parameters: Duplicates: <2, Density <30, SRepeatLength <30, Duplication: FALSE. Note that only one capture probe could be designed for the first Ciita TSS (Supplementary Table 6). The 5’ biotinylated probes were pooled at a 2.9 nM each and the samples were multiplexed by mass prior to hybridization (2ug each, according to Qubit dsDNA BR Assay, Invitrogen #Q32850). Hybridization was carried out using the KAPA HyperCapture system (Roche, KAPA HyperCapture Reagent Kit #9075828001, KAPA HyperCapture Bead Kit #9075798001) according to Roche protocol for 72 hours followed by a 24 hours hybridization (double Capture). During the PCR amplification steps libraries were amplified for 18 cycles to ensure all of the low input sample is captured. Captured libraries were quantified by qPCR using the KAPA Sybr Fast Universal kit (KAPA #KK4602) and sequenced on Illumina NextSeq 500.

treatment_protocol: Organoids were treated 3 days after splitting with 500pg/ml IFNg diluted in organoid growth medium for 3 hours. Control organoids were treated with organoid growth medium without IFNg for the same time.

value: Small intestinal epithelium

tag: age

value: aged

value: organoids

tag: passage

tag: biological replicate

value: control


title: Pat.3_POST_ROI.012_CD31+

tag: cancer

value: POST

value: DC

value: No

value: FFPE BRCA biopsy


title: mESCs, hCh_2

value: E14Tg2a mESCs

value: Tasor -/-; hChimera


title: BLA_FearRecall_fr10_E1_S7009

description: Smartseq

value: Fear recall


title: O77-P5-con_S7_L003_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

tag: strain


title: BLA_FearRecall_fr10_E8_S7016

description: Smartseq


title: BLA_FearRecall_fr10_D8_S6992

description: Smartseq


title: mESCs, del3_2

value: embryonic stem cells

value: reconstitution of hsTasor-del3-332


title: mESCs, hT_2

value: Tasor -/-; hTasor

value: reconstitution of hsTasor


title: BLA_FearRecall_fr10_E6_S7014

description: Smartseq

value: TRAP2 Ai14


title: O77-P5-IFN_S8_L004_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

value: IFNg


title: O77-P5-con_S7_L001_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

value: Small intestinal epithelium


title: Pat.3_POST_ROI.009_CD31+

value: BTC

tag: biopsy type

tag: patient response_to_bex


title: BLA_FearRecall_fr10_D24_S7008

description: Smartseq


title: O77-P5-IFN_S8_L003_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

value: aged

value: organoids


title: Pat.3_POST_ROI.009_CD68+

value: POST

tag: segment

tag: roi


title: mESCs, KO_2

value: Tasor -/-


title: O77-P5-IFN_S8_L002_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt


title: mESCs, zfCh_1

value: Tasor -/-; zfChimera

value: reconstitution of zfTex15-hTasor chimera


title: Pat.3_PRE_ROI.011_CD31+

value: PRE

value: DC

tag: patient

tag: geomx batch

value: No

value: FFPE BRCA biopsy


title: BLA_FearRecall_fr10_E20_S7028

description: Smartseq

value: Fear recall


title: mESCs, delD_1

value: E14Tg2a mESCs

value: embryonic stem cells

value: Tasor -/-; delDUF

value: reconstitution of hsTasor-delDUF


title: BLA_FearRecall_fr10_E14_S7022

description: Smartseq

value: TRAP2 Ai14


title: O77-P4-can_S5_L004_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

value: Small intestinal epithelium

value: control


title: mESCs, del3_1

value: reconstitution of hsTasor-del3-332


title: O77-P4-can_S5_L003_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

value: aged

value: organoids


title: Pat.3_POST_ROI.010_CD68-CD31-

value: BTC

value: POST

tag: roi exclusion

tag: q3 normalized_data_sheets


title: mESCs, hT_1

tag: genotype

value: Tasor -/-; hTasor

value: reconstitution of hsTasor


title: BLA_FearRecall_fr10_D23_S7007

description: Smartseq

tag: tissue

tag: treatment


title: BLA_FearRecall_fr10_D11_S6995

description: Smartseq


title: BLA_FearRecall_fr10_C6_S6966

description: Smartseq


title: Pat.3_POST_ROI.007_CD68-CD31-

value: DC

value: No


title: O77-P4-IFN_S6_L003_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

tag: cell type

value: IFNg


title: O77-P4-IFN_S6_L002_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

tag: age


title: mESCs, PB_2

tag: cell line

value: E14Tg2a mESCs

value: Tasor -/-; PB

value: reconstitution of empty vector PB


title: BLA_FearRecall_fr10_E11_S7019

description: Smartseq

value: Fear recall


title: mESCs, Control_2

value: embryonic stem cells

value: Tasor +/-


title: BLA_FearRecall_fr10_C23_S6983

description: Smartseq

value: TRAP2 Ai14


title: Pat.3_POST_ROI.010_CD31+

value: FFPE BRCA biopsy


title: mESCs, KO_1

value: Tasor -/-


title: O76-P3-con_S3_L002_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

value: Small intestinal epithelium

value: aged

value: organoids

tag: passage

tag: biological replicate

value: control


title: BLA_FearRecall_fr10_E10_S7018

description: Smartseq


title: Pat.3_POST_ROI.009_CD68-CD31-

tag: cancer

value: BTC

value: POST


title: O76-P3-con_S3_L001_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

tag: strain


title: O77-P5-con_S7_L002_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt


title: BLA_FearRecall_fr10_C13_S6973

description: Smartseq


title: O76-P2-con_S1_L003_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt


title: Pat.3_POST_ROI.006_CD68+

tag: biopsy type

tag: patient response_to_bex

value: DC

value: No


title: O77-P5-IFN_S8_L001_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

value: IFNg


title: BLA_FearRecall_fr10_C14_S6974

description: Smartseq


title: Pat.3_POST_ROI.006_CD68-CD31-

tag: segment

tag: roi


title: BLA_FearRecall_fr10_D16_S7000

description: Smartseq


title: O77-P4-can_S5_L002_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt


title: O76-P3-IFN_S4_L004_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt


title: Pat.3_POST_ROI.008_CD31+

tag: patient

tag: geomx batch

value: Yes, low signal-to-noise ratio


title: Pat.3_POST_ROI.008_CD68+

tag: roi exclusion

tag: q3 normalized_data_sheets


title: O77-P4-can_S5_L001_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

tag: tissue


title: O76-P2-con_S1_L004_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

tag: treatment


title: Pat.3_POST_ROI.007_CD31+


title: Pat.3_POST_ROI.008_CD68-CD31-


title: O76-P3-con_S3_L004_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

tag: cell type


title: O77-P4-IFN_S6_L001_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

tag: age


title: BLA_FearRecall_fr10_D13_S6997

description: Smartseq

tag: genotype


title: Pat.3_POST_ROI.007_CD68+


title: O76-P3-con_S3_L003_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt

tag: passage


title: O76-P3-IFN_S4_L003_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

tag: biological replicate


title: Pat.3_POST_ROI.006_CD31+

tag: cancer


title: BLA_FearRecall_fr10_C17_S6977

description: Smartseq


title: BLA_FearRecall_fr10_B9_S6945

description: Smartseq


title: O77-P4-IFN_S6_L004_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

tag: strain


title: BLA_FearRecall_fr10_B24_S6960

description: Smartseq


title: O76-P2-IFN_S2_L001_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt


title: O76-P2-con_S1_L001_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt


title: O76-P3-IFN_S4_L002_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt


title: BLA_FearRecall_fr10_C10_S6970

description: Smartseq


title: BLA_FearRecall_fr10_C1_S6961

description: Smartseq


title: Pat.3_POST_ROI.005_CD68-CD31-

tag: biopsy type


title: O76-P2-con_S1_L002_Small intestinal epithelium_control

description:
Capture-C
cd_IFNg.txt


title: Young4_S5_L001_Small intestinal epithelium_Young_rep4

description:
genomic DNA of freshly isolated small intestinal epithelial cells, subjected to transposase reaction for adapter insertion in open chromatin regions
consensus_peaks.mLb.clN.annotatePeaks.txt
consensus_peaks.mLb.clN.featureCounts.txt
In featureCounts.txt, Y_R3.mLb.clN.bam matches to Young4

data_processing:
nf-core/atacseq  v1.2.1
Nextflow  v20.04.1
FastQC  v0.11.9
Trim Galore! v0.6.4_dev
BWA v0.7.17-r1188
Samtools v1.10
BEDTools v2.29.2
BamTools v2.1.0
deepTools v3.4.3
Picard v2.23.1
R v3.6.2
Pysam v0.15.3
MACS2 v2.2.7.1
ataqv v1.1.1
featureCounts v2.0.1
Preseq v2.0.3
MultiQC v1.9
Assembly: GRCm38
Supplementary files format and content: consensus peak annotation txt file
Supplementary files format and content: consensus peak feature counts txt file

growth_protocol: Cells were directly isolated from in vivo small intestine

extract_protocol:
Cells were isolated from the small intestine by EDTA & Trypsin-based digestion and then FACS sorted (EpCam+ ; CD45-)
Illumina sequencing libraries were prepared using Tn5 Transposase to fragment chromatin and insert sequencing adapters at regions of open chromatin. 10ul of isolated DNA was used for library PCR (17 cycles total), using index i5 and index i7 primer (Illumine Nextera). Libraries were size selected and purified via AMPure XP beads

value: small intestinal epithelial cells

value: Young


title: Pat.3_POST_ROI.004_CD31+

tag: patient response_to_bex


title: Pat.3_POST_ROI.005_CD31+

tag: segment


title: O76-P2-IFN_S2_L004_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt


title: Pat.3_POST_ROI.004_CD68+

tag: roi


title: Young2_S3_L004_Small intestinal epithelium_Young_rep2

description:
genomic DNA of freshly isolated small intestinal epithelial cells, subjected to transposase reaction for adapter insertion in open chromatin regions
consensus_peaks.mLb.clN.annotatePeaks.txt
consensus_peaks.mLb.clN.featureCounts.txt
In featureCounts.txt, Y_R2.mLb.clN.bam matches to Young2


title: Pat.3_POST_ROI.005_CD68+

tag: patient


title: O76-P2-IFN_S2_L002_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt


title: BLA_FearRecall_fr10_B21_S6957

description: Smartseq

data_processing:
Fastq reads were mapped with STAR(2.7.9a)
Assembly: mm10
Supplementary files format and content: Cell by gene matrix format

extract_protocol:
OligodT primers were used to enrich mRNA
Brain tissues were dissociated with Worthington Papain Digestion Kit RNA libraries were prepared using smart seq 3
Novaseq 6000 was used for sequencing with standard Illumina protocols

value: Fear recall


title: Young4_S5_L004_Small intestinal epithelium_Young_rep4


title: Young2_S3_L002_Small intestinal epithelium_Young_rep2


title: Young2_S3_L001_Small intestinal epithelium_Young_rep2


title: Young1_S1_L003_Small intestinal epithelium_Young_rep1

description:
genomic DNA of freshly isolated small intestinal epithelial cells, subjected to transposase reaction for adapter insertion in open chromatin regions
consensus_peaks.mLb.clN.annotatePeaks.txt
consensus_peaks.mLb.clN.featureCounts.txt
In featureCounts.txt, Y_R1.mLb.clN.bam matches to Young1


title: Young4_S5_L003_Small intestinal epithelium_Young_rep4


title: Young4_S5_L002_Small intestinal epithelium_Young_rep4


title: BLA_FearRecall_fr10_B18_S6954

description: Smartseq


title: Pat.3_POST_ROI.003_CD68+

tag: geomx batch


title: Pat.3_POST_ROI.003_CD68-CD31-

tag: roi exclusion


title: Pat.3_POST_ROI.004_CD68-CD31-

tag: q3 normalized_data_sheets


title: Young1_S1_L004_Small intestinal epithelium_Young_rep1


title: Pat.3_POST_ROI.002_CD68-CD31-

tag: tissue


title: O76-P2-IFN_S2_L003_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

tag: treatment


title: Young1_S1_L001_Small intestinal epithelium_Young_rep1

tag: cell type


title: BLA_FearRecall_fr10_B10_S6946

description: Smartseq


title: Young1_S1_L002_Small intestinal epithelium_Young_rep1

tag: age


title: Young2_S3_L003_Small intestinal epithelium_Young_rep2


title: BLA_FearRecall_fr10_B13_S6949

description: Smartseq

tag: genotype


title: Aged4_S6_L003_Small intestinal epithelium_Aged_rep4

description:
genomic DNA of freshly isolated small intestinal epithelial cells, subjected to transposase reaction for adapter insertion in open chromatin regions
consensus_peaks.mLb.clN.annotatePeaks.txt
consensus_peaks.mLb.clN.featureCounts.txt
In featureCounts.txt, A_R3.mLb.clN.bam matches to Aged4

value: Aged


title: Aged4_S6_L002_Small intestinal epithelium_Aged_rep4


title: BLA_FearRecall_fr10_B11_S6947

description: Smartseq

value: TRAP2 Ai14


title: Pat.3_POST_ROI.002_CD31+

value: FFPE BRCA biopsy


title: Pat.3_POST_ROI.002_CD68+


title: BLA_FearRecall_fr10_A5_S6917

description: Smartseq


title: BLA_FearRecall_fr10_A20_S6932

description: Smartseq


title: Pat.3_POST_ROI.003_CD31+


title: BLA_FearRecall_fr10_A21_S6933

description: Smartseq


title: Pat.3_POST_ROI.001_CD68-CD31-


title: Aged2_S4_L003_Small intestinal epithelium_Aged_rep2

description:
genomic DNA of freshly isolated small intestinal epithelial cells, subjected to transposase reaction for adapter insertion in open chromatin regions
consensus_peaks.mLb.clN.annotatePeaks.txt
consensus_peaks.mLb.clN.featureCounts.txt
In featureCounts.txt, A_R2.mLb.clN.bam matches to Aged2


title: Aged2_S4_L001_Small intestinal epithelium_Aged_rep2


title: BLA_FearRecall_fr10_A19_S6931

description: Smartseq


title: Pat.3_POST_ROI.001_CD31+


title: Aged1_S2_L004_Small intestinal epithelium_Aged_rep1

description:
genomic DNA of freshly isolated small intestinal epithelial cells, subjected to transposase reaction for adapter insertion in open chromatin regions
consensus_peaks.mLb.clN.annotatePeaks.txt
consensus_peaks.mLb.clN.featureCounts.txt
In featureCounts.txt, A_R1.mLb.clN.bam matches to Aged1


title: Aged4_S6_L004_Small intestinal epithelium_Aged_rep4


title: Aged4_S6_L001_Small intestinal epithelium_Aged_rep4


title: BLA_FearRecall_fr10_A7_S6919

description: Smartseq


title: BLA_FearRecall_fr10_A11_S6923

description: Smartseq


title: Pat.3_POST_ROI.001_CD68+


title: Aged1_S2_L002_Small intestinal epithelium_Aged_rep1


title: Aged1_S2_L001_Small intestinal epithelium_Aged_rep1


title: Aged2_S4_L002_Small intestinal epithelium_Aged_rep2


title: Pat.5_POST_ROI.013_CD68-CD31-

value: BRCA

value: nDC


title: BLA_FearRecall_fr10_A12_S6924

description: Smartseq


title: BLA_FearRecall_fr10_A1_S6913

description: Smartseq


title: Pat.5_POST_ROI.013_CD31+


title: Pten null with AMPK (GoF) rep4

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava2.20 software used for basecalling.
Reads were aligned to Ensembl mouse genome (GRCh38) using Tophat2 (2.11.3).
Gene-based read counts were performed using Rsubread from FeatureCounts.
Assembly: Ensembl mouse genome (GRCh38).
Supplementary files format and content: count.csv: Comma-separated text file includes gene counts for each sample.

source_name: Prostate

extract_protocol:
Immediately following dissection, whole prostates were snap frozen in liquid nitrogen. Frozen tissue was ground under liquid nitrogen and RNA isolated by subsequent homogenization in Trizol reagent (Invitrogen) according to the manufacturer's instructions, followed by purification on an RNeasy column (Qiagen).
RNA quality was assessed using the Agilent 2100 RNA 6000 Nano assay and libraries prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module following manufacturer’s instructions. Library quality was evaluated using the Agilent 2100 High-Sensitivity DNA assay, and concentrations measured using the Qubit™ dsDNA HS Assay Kit.
RNAseq 40 million Paired End 41bp reads per sample.

value: Pten null with AMPK (GoF)

value: Prostate

value: 17 weeks


title: Pat.5_POST_ROI.013_CD68+


title: BLA_FearRecall_fr1_P9_S214

description: Smartseq


title: Pten null with AMPK (GoF) rep2


title: Pat.5_POST_ROI.012_CD68-CD31-


title: Pten null rep5

value: Pten null


title: BLA_FearRecall_fr1_P8_S213

description: Smartseq


title: Pten null with AMPK (GoF) rep6


title: BLA_FearRecall_fr1_P7_S212

description: Smartseq


title: Aged1_S2_L003_Small intestinal epithelium_Aged_rep1


title: Pat.5_POST_ROI.012_CD31+

value: POST


title: Pten null rep4


title: Pten null with AMPK (GoF) rep1


title: Pten null rep3


title: BLA_FearRecall_fr1_P6_S211

description: Smartseq


title: Pat.5_POST_ROI.012_CD68+


title: BLA_FearRecall_fr1_P5_S210

description: Smartseq


title: Pten null rep1


title: Pat.5_POST_ROI.011_CD68-CD31-


title: Pten null with AMPK (GoF) rep3


title: TII-6

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

country: Canada

institute: Université Laval

data_processing:
Trimgalore / cutadapt
STAR
featurecounts
DEESEQ2
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw counts for each sample in .csv file
Supplementary files format and content: NDA

organism: Bos taurus

source_name: Morula

extract_protocol:
The SMART-Seq®HT kit (Takara Bio, USA)
NextEra XT Stranded mRNA Sample Prep kit following manufacturer instructions

value: Morula

tag: developmental stage

value: Embryo

value: Haploid

tag: parthenogenesis


title: BLA_FearRecall_fr1_P4_S209

description: Smartseq


title: TII-5


title: TII-4


title: Pten null with AMPK (GoF) rep5


title: BLA_FearRecall_fr1_P3_S208

description: Smartseq


title: TII-1


title: Pat.5_POST_ROI.011_CD68+

tag: cancer

value: No


title: Pat.5_POST_ROI.011_CD31+


title: BLA_FearRecall_fr1_P2_S207

description: Smartseq


title: ICSI-5

value: Diploid


title: Pten null rep6

tag: strain


title: Pat.5_POST_ROI.010_CD68-CD31-

tag: biopsy type


title: ICSI-2


title: Pat.5_POST_ROI.010_CD31+

tag: patient response_to_bex


title: Pten null rep2


title: ICSI-3


title: ICSI-4


title: ICSI-1


title: BLA_FearRecall_fr1_O9_S191

description: Smartseq


title: BLA_FearRecall_fr1_P10_S215

description: Smartseq


title: CHX-6


title: Pat.5_POST_ROI.010_CD68+

tag: segment


title: CHX-5


title: Pat.5_POST_ROI.009_CD68-CD31-

tag: roi


title: CHX-3


title: BLA_FearRecall_fr1_O7_S189

description: Smartseq


title: TII-2


title: CHX-2


title: BLA_FearRecall_fr1_O6_S188

description: Smartseq


title: Pat.5_POST_ROI.009_CD31+

tag: patient


title: CHX-1


title: Pat.5_POST_ROI.009_CD68+

tag: geomx batch


title: NV50_untreated_rep5 [248-23]

city: Düsseldorf

first: Natascia

last: Ventura

address: Auf'm Hennekamp 50

institute: Heinrich Heine University  and the IUF- Leibniz Research Institute for Environmental Medicine

data_processing:
Illumina bcl2fastq v2.20.0.422 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina TrueSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2), then mapped to C. elegans (WBcel235.99) (March 26, 2020) genome sequence using CLC Genomics Workbench v20.0.4 and v21.0.4 with standard parameters.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v21.0.4 with standard parameters. After grouping of samples according to their respective experimental condition, the statistical differential expression was determined using the CLC Differential Expression for RNA-Seq tool (version 2.5). The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value of ≤ 0.05 was considered significant.
Assembly: WBcel235.99
Supplementary files format and content: The Excel file includes RPKM values for every gene and each sample.

organism: Caenorhabditis elegans

source_name: whole nematode pellet, RNA extracted

growth_protocol: All strains were maintained and kept synchronized by egg lay at 20 °C on Nematode Growth Media (NGM) agar supplemented with Escherichia coli OP50 unless otherwise indicated. Worms

extract_protocol:
RNeasy Mini Plus Kit, Qiagen according to manufacturer with optional DNAse treatment
Libraries were prepared according to Illumina instructions accompanying the Illumina® ‘TruSeq Stranded mRNA Library Prep’ Kit. Briefly, 350 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA), following the manufacturer's protocols, with a read setup of 1 × 150 bp.

treatment_protocol: Quercetin (Q4951 Sigma-Aldrich), Lutein (PHR1699 Sigma-Aldrich), where dissolved in a solution of Dimethylsulfoxid (DMSO, 276855 Sigma-Aldrich) containing 1% of Tween 80 (P1754 Sigma-Aldrich) and mixed with bacteria to the following concentrations: Quercetin 100µM, lutein µM100. Control worms were fed bacteria containing the same amount of solvent (0.5% DMSO plus 0.005% Tween 80) used to prepare the above compound. Treatement started from eggs on plates seeded with HT115 (pl4440)

tag: cell line

value: NV50:abl-1 KO, isolated from crossing XR1 with GRU102,

value: untreated

tag: time point

value: 3 days old worms on Empty vector (pL4440)


title: NV48_quercetin_rep5 [248-22]

value: NV48:(wild type isolated from crossing XR1 with GRU102 straisn)

value: quercetin 100µM


title: NV50_quercetin_rep5 [248-24]


title: Pat.5_PRE_ROI.008_CD68-CD31-

value: BRCA

value: PRE

tag: roi exclusion

tag: q3 normalized_data_sheets

tag: tissue

value: FFPE BRCA biopsy


title: BLA_FearRecall_fr1_O5_S187

description: Smartseq

value: TRAP2 Ai14

tag: treatment

value: Fear recall


title: BLA_FearRecall_fr1_O4_S186

description: Smartseq

tag: genotype


title: NV48_untreated_rep5 [248-21]


title: Pat.5_PRE_ROI.008_CD31+

value: nDC


title: BLA_FearRecall_fr1_O8_S190

description: Smartseq


title: NV50_untreated_rep4 [248-19]


title: NV48_lutein_rep4 [248-18]

value: lutein 100µM


title: BLA_FearRecall_fr1_O3_S185

description: Smartseq


title: BLA_FearRecall_fr1_O2_S184

description: Smartseq


title: NV48_untreated_rep4 [248-16]


title: NV50_quercetin_rep4 [248-20]


title: NV50_quercetin_rep3 [248-15]


title: NV48_quercetin_rep4 [248-17]


title: Pat.5_PRE_ROI.007_CD68-CD31-


title: BLA_FearRecall_fr1_O10_S192

description: Smartseq


title: NV50_untreated_rep3 [248-14]


title: Pat.5_PRE_ROI.007_CD31+


title: NV48_lutein_rep3 [248-13]


title: NV48_quercetin_rep3 [248-12]


title: NV48_untreated_rep3 [248-11]


title: Pat.5_PRE_ROI.007_CD68+


title: BLA_FearRecall_fr1_N9_S168

description: Smartseq


title: BLA_FearRecall_fr1_N8_S167

description: Smartseq


title: NV48_quercetin_rep2 [248-7]


title: Pat.5_PRE_ROI.006_CD68-CD31-


title: NV48_lutein_rep2 [248-8]


title: NV50_quercetin_rep2 [248-10]


title: Pat.5_PRE_ROI.006_CD31+


title: NV50_untreated_rep2 [248-9]


title: NV48_untreated_rep2 [248-6]


title: Pat.5_PRE_ROI.008_CD68+


title: NV50_quercetin_rep1 [248-5]


title: Pat.5_PRE_ROI.006_CD68+


title: BLA_FearRecall_fr1_N7_S166

description: Smartseq


title: NV50_untreated_rep1 [248-4]


title: NV48_lutein_rep1 [248-3]


title: BLA_FearRecall_fr1_N5_S164

description: Smartseq


title: BLA_FearRecall_fr1_N6_S165

description: Smartseq


title: NV48_quercetin_rep1 [248-2]


title: Pat.5_PRE_ROI.005_CD68-CD31-


title: Pat.5_PRE_ROI.005_CD31+


title: O76-P3-IFN_S4_L001_Small intestinal epithelium_IFNg

description:
Capture-C
cd_con.txt

value: Small intestinal epithelium

tag: age

value: aged

tag: cell type

value: organoids

tag: passage

tag: biological replicate

value: IFNg


title: BLA_FearRecall_fr1_O1_S183

description: Smartseq


title: Aged2_S4_L004_Small intestinal epithelium_Aged_rep2

value: small intestinal epithelial cells

tag: strain

value: Aged


title: NV48_untreated_rep1 [248-1]

value: untreated


title: BLA_FearRecall_fr1_N4_S163

description: Smartseq


title: ISC/EB ATACseq H1 RNAi C

city: Gif-sur-Yvette

first: Katarzyna

last: Siudeja

address: 1, Avenue de la Terrasse

institute: Institute for Integrative Biology of the Cell (I2BC), INSERM U1280, CEA, CNRS, Université Paris-Saclay

data_processing:
bioinfo-pf-curie/ATAC-seq: v1.0.2 pipeline for ATAC-seq data processing developed by the Curie Bioinformatics Core facility was used (https://doi.org/10.5281/zenodo.7576558)
Raw reads were trimmed for adapters using trimgalore and aligned to the Drosophila melanogaster reference genome (dm6) using bowtie2
Duplicated reads were removed from the aligned results with Picard, and filtered to discard low mapping quality reads <20, aligned to mitochondrial chromosome reads as well as singleton reads.
Only valid pairs were considered. Read shifting was applied to account for Tn5 insertions (+ strand reads adjusted by 4 bp, and - strand reads adjusted by -5bp).
Peaks were called using MACS2 and Narrow peaks with q<0.01 were reported.
Assembly: dmelr6.28
Supplementary files format and content: narrowPeak

organism: Drosophila melanogaster

source_name: ISC/EB

growth_protocol: 3-day old female flies with esgts, UAS-GFP (control) or esgts, UAS-GFP UAS-H1 RNAi 1 were kept at 18°C for 2 days and shifted to 29°C for 4 days on poor food to induce RNAi expression

extract_protocol:
Tagmented DNA purified with Qiagen Minelute Cleanup Kit
Tagmentation of DNA with Tn5 transposase from Illumina (#FC-121-1030)

treatment_protocol: For each replicate, 70 guts (control and H1 RNAi) were dissected in cold PBS, dissociated in elastase and FACS-sorted to isolate 50-100,000 GFP+ progenitor cells

value: ISC/EB

value: Intestinal cells

value: esgts, UAS-GFP UAS H1 RNAi 1

value: H1 RNAi 1

tag: time

value: 4 days induction at 29°C


title: Pat.5_PRE_ROI.005_CD68+

tag: cancer

value: BRCA

tag: biopsy type

value: PRE

tag: patient response_to_bex

tag: segment

value: No

value: FFPE BRCA biopsy


title: ISC/EB ATACseq H1 RNAi B

tag: cell line


title: ISC/EB ATACseq H1 RNAi A


title: Pat.5_PRE_ROI.004_CD68-CD31-

value: nDC

tag: roi

tag: patient

tag: geomx batch


title: ISC/EB ATACseq control C

value: esgts, UAS-GFP

value: control


title: ISC/EB ATACseq control A


title: Pat.5_PRE_ROI.004_CD31+

tag: roi exclusion

tag: q3 normalized_data_sheets

tag: tissue


title: BLA_FearRecall_fr1_N2_S161

city: Stanford

first: Wenfei

last: Sun

address: 318 Campus Dr.

institute: Stanford University

description: Smartseq

tag: genotype

value: TRAP2 Ai14

tag: treatment

value: Fear recall


title: ISC/EB RNAseq H1 RNAi C

data_processing:
Nextflow pipeline for RNA-seq data processing developed by the Curie Bioinformatics Core facility was used (https://doi.org/10.5281/zenodo.7443721)
FastQ files were generated with bcl2Fastq, demultiplexed and trimmed to remove adaptors using the Raw-QC and RNA-seq analysis pipelines
Reads were aligned to the Drosophila reference genome (dm6) to generate raw counts tables.
Assembly: dmelr6.28
Supplementary files format and content: tab-delimited text file include tpm values for each Sample

growth_protocol: Crosses and adults were kept at 18°C, the GAL80 permissive temperature. 3 day old flies were shifted to 29°C for 1 day to induce Dam expression

extract_protocol:
RNA isolation and purification was then performed with the Arcturus PicoPure RNA Isolation kit (Thermofisher)
RNA libraries were prepared with the Illumina Stranded mRNA Prep kit

tag: cell type


title: BLA_FearRecall_fr1_N10_S169

description: Smartseq


title: Pat.5_PRE_ROI.004_CD68+


title: Pat.5_PRE_ROI.003_CD68-CD31-


title: ISC/EB RNAseq H1 RNAi B


title: BLA_FearRecall_fr1_N1_S160

description: Smartseq


title: BLA_FearRecall_fr1_M9_S145

description: Smartseq


title: ISC/EB RNAseq H1 RNAi A


title: ISC/EB RNAseq control A


title: ISC/EB RNAseq control B


title: Pat.5_PRE_ROI.003_CD68+


title: Pat.5_PRE_ROI.003_CD31+


title: Pat.5_PRE_ROI.002_CD68-CD31-


title: BLA_FearRecall_fr1_M8_S144

description: Smartseq


title: BLA_FearRecall_fr1_M6_S142

description: Smartseq


title: BLA_FearRecall_fr1_N3_S162

description: Smartseq


title: BLA_FearRecall_fr1_M7_S143

description: Smartseq


title: Pat.5_PRE_ROI.002_CD31+


title: ISC/EB ATACseq control B


title: T9-RE02-1

city: Beijing

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

institute: Fifth Medical Center of Chinese PLA General Hospital

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file includes UMI values for each cell

source_name: Peripheral blood

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner

value: CAR-T cells

tag: cells enriched from

value: Peripheral blood

tag: disease state

value: B-ALL

tag: sampling stage

tag: individual

tag: responses

value: Complete Remission


title: T9-RE03-4

value: Relapse


title: T9-RE03-1


title: T9-RE03-3


title: T9-RE02-4


title: T9-CR10-7


title: BLA_FearRecall_fr1_M5_S141

description: Smartseq


title: ISC/EB RNAseq control C

value: ISC/EB

value: Intestinal cells

tag: time


title: T9-CR10-2


title: T9-CR10-4


title: T9-CR10-6