title: TMA4 | 016 | Full ROI

description: Library name: Sample 357

value: TMA4 | 015 | Full ROI


title: TMA4 | 015 | Full ROI

status: Public on Dec 06 2025

type: SRA

city: Baltimore

first: Ie-Ming

last: Shih

state: Maryland

address: 1550 Orleans Street, room 305

department: Department of Gynecology and Obstetrics

country: USA

institute: Johns Hopkins Medical Institutions

description: Library name: Sample 356

library_source: transcriptomic

data_processing:
Raw sequencing data were processed using either NanoString GeoMx NGS Pipeline v2.3.4 or  v2.3.5.
Assembly: GRCh38
Supplementary files format and content: geo_count_data.xlsx: count data for each ROIs
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: fallopian tube

extract_protocol:
Following probe hybridization, UV‐cleavable indexing oligonucleotides were released from each ROI by targeted UV illumination on the GeoMx DSP instrument.
Spatial transcriptome sequencing library

tag: tissue

value: fallopian tube

tag: tissue type

value: epithelium

tag: diagnosis

value: Normal fallopian tube epithelium

tag: batch


title: TMA4 | 019 | Full ROI

description: Library name: Sample 360


title: TMA4 | 018 | Full ROI

description: Library name: Sample 359

value: stroma

value: STIC

tag: corresponding epithelium

value: TMA4 | 017 | Full ROI


title: TMA4 | 014 | Full ROI

description: Library name: Sample 355

value: TMA4 | 013 | Full ROI


title: TMA4 | 013 | Full ROI

description: Library name: Sample 354


title: TMA4 | 012 | Full ROI

description: Library name: Sample 353

value: TMA4 | 011 | Full ROI


title: TMA4 | 009 | Full ROI

description: Library name: Sample 350


title: TMA4 | 010 | Full ROI

description: Library name: Sample 351

value: TMA4 | 009 | Full ROI


title: TMA4 | 011 | Full ROI

description: Library name: Sample 352


title: TMA4 | 007 | Full ROI

description: Library name: Sample 348


title: TMA4 | 002 | Full ROI

description: Library name: Sample 343


title: TMA4 | 004 | Full ROI

description: Library name: Sample 345

value: TMA4 | 001 | Full ROI


title: TMA4 | 028 | Full ROI

description: Library name: Sample 369

value: TMA4 | 027 | Full ROI


title: TMA3 | 015 | Full ROI

description: Library name: Sample 341


title: TMA4 | 005 | Full ROI

description: Library name: Sample 346


title: TMA4 | 006 | Full ROI

description: Library name: Sample 347

value: TMA4 | 005 | Full ROI


title: TMA3 | 014 | Full ROI

description: Library name: Sample 340

value: High grade serous carcinoma


title: TMA3 | 009 | Full ROI

description: Library name: Sample 335


title: TMA3 | 010 | Full ROI

description: Library name: Sample 336


title: TMA3 | 011 | Full ROI

description: Library name: Sample 337


title: TMA3 | 012 | Full ROI

description: Library name: Sample 338


title: TMA3 | 008 | Full ROI

description: Library name: Sample 334


title: TMA3 | 013 | Full ROI

description: Library name: Sample 339


title: TMA4 | 017 | Full ROI

description: Library name: Sample 358


title: TMA4 | 008 | Full ROI

description: Library name: Sample 349

value: TMA4 | 007 | Full ROI


title: TMA3 | 006 | Full ROI

description: Library name: Sample 332


title: TMA3 | 007 | Full ROI

description: Library name: Sample 333


title: TMA3 | 002 | Full ROI

description: Library name: Sample 328


title: TMA3 | 001 | Full ROI

description: Library name: Sample 327


title: TMA2_2 | 019 | Full ROI

description: Library name: Sample 326


title: TMA2_2 | 018 | Full ROI

description: Library name: Sample 325


title: TMA3 | 003 | Full ROI

description: Library name: Sample 329


title: TMA2_2 | 017 | Full ROI

description: Library name: Sample 324


title: TMA2_2 | 014 | Full ROI

description: Library name: Sample 321


title: TMA4 | 001 | Full ROI

description: Library name: Sample 342


title: TMA4 | 003 | Full ROI

description: Library name: Sample 344

value: TMA4 | 002 | Full ROI


title: TMA2_2 | 015 | Full ROI

description: Library name: Sample 322


title: TMA2_2 | 013 | Full ROI

description: Library name: Sample 320


title: TMA2_2 | 012 | Full ROI

description: Library name: Sample 319


title: TMA2_2 | 011 | Full ROI

description: Library name: Sample 318


title: TMA2_2 | 008 | Full ROI

description: Library name: Sample 315


title: TMA2_2 | 009 | Full ROI

description: Library name: Sample 316


title: TMA2_2 | 010 | Full ROI

description: Library name: Sample 317


title: TMA2_2 | 006 | Full ROI

description: Library name: Sample 313


title: TMA2_2 | 007 | Full ROI

description: Library name: Sample 314


title: TMA3 | 004 | Full ROI

description: Library name: Sample 330


title: TMA2_2 | 005 | Full ROI

description: Library name: Sample 312


title: TMA2_2 | 002 | Full ROI

description: Library name: Sample 309


title: TMA2_2 | 004 | Full ROI

description: Library name: Sample 311


title: TMA2_2 | 003 | Full ROI

description: Library name: Sample 310


title: TMA3 | 005 | Full ROI

description: Library name: Sample 331


title: TMA1 | 009 | Full ROI

description: Library name: Sample 307

value: Clear cell carcinoma


title: TMA2_2 | 001 | Full ROI

description: Library name: Sample 308

value: STIL


title: TMA1 | 006 | Full ROI

description: Library name: Sample 304

value: fallopian tube


title: TMA1 | 007 | Full ROI

description: Library name: Sample 305

value: epithelium


title: TMA1 | 005 | Full ROI

description: Library name: Sample 303


title: TMA1 | 003 | Full ROI

description: Library name: Sample 301

value: Normal fallopian tube epithelium


title: TMA1 | 008 | Full ROI

description: Library name: Sample 306


title: TMA2_2 | 016 | Full ROI

description: Library name: Sample 323


title: TMA1 | 004 | Full ROI

description: Library name: Sample 302


title: STIC_TMA3 | 006 | Full ROI

description: Library name: Sample 286


title: TMA1 | 002 | Full ROI

description: Library name: Sample 300


title: TMA1 | 001 | Full ROI

description: Library name: Sample 299


title: STIC_TMA3 | 005 | Full ROI

description: Library name: Sample 285


title: STIC_TMA3 | 004 | Full ROI

description: Library name: Sample 284


title: STIC_TMA3 | 003 | Full ROI

description: Library name: Sample 283


title: STIC_TMA3 | 001 | Full ROI

description: Library name: Sample 281


title: MSK10 | 003 | Full ROI

description: Library name: Sample 265


title: MSK10 | 005 | Full ROI

description: Library name: Sample 267


title: MSK10 | 004 | Full ROI

description: Library name: Sample 266


title: MSK10 | 001 | Full ROI

description: Library name: Sample 263


title: MSK10 | 002 | Full ROI

description: Library name: Sample 264


title: STIC_TMA3 | 002 | Full ROI

description: Library name: Sample 282


title: MSK02 | 005 | Full ROI

description: Library name: Sample 262


title: MSK02 | 004 | Full ROI

description: Library name: Sample 261


title: MSK02 | 003 | Full ROI

description: Library name: Sample 260


title: MSK02 | 001 | Full ROI

description: Library name: Sample 258


title: MSK02 | 002 | Full ROI

description: Library name: Sample 259


title: MSK01 | 008 | Full ROI

description: Library name: Sample 255

value: stroma

value: MSK01 | 007 | Full ROI


title: MSK01 | 004 | Full ROI

description: Library name: Sample 251

value: STIC

value: MSK01 | 003 | Full ROI


title: MSK01 | 005 | Full ROI

description: Library name: Sample 252


title: MSK01 | 006 | Full ROI

description: Library name: Sample 253

value: MSK01 | 005 | Full ROI


title: MSK01 | 007 | Full ROI

description: Library name: Sample 254


title: MSK01 | 002 | Full ROI

description: Library name: Sample 249

value: MSK01 | 001 | Full ROI


title: MSK01 | 001 | Full ROI

description: Library name: Sample 248


title: MHC | 016 | Full ROI

description: Library name: Sample 247


title: MHC | 015 | Full ROI

description: Library name: Sample 246


title: MHC | 013 | Full ROI

description: Library name: Sample 244


title: MHC | 012 | Full ROI

description: Library name: Sample 243


title: MHC | 014 | Full ROI

description: Library name: Sample 245


title: MHC | 009 | Full ROI

description: Library name: Sample 240


title: MHC | 010 | Full ROI

description: Library name: Sample 241


title: MHC | 008 | Full ROI

description: Library name: Sample 239


title: MHC | 003 | Full ROI

description: Library name: Sample 234


title: MHC | 007 | Full ROI

description: Library name: Sample 238


title: MHC | 006 | Full ROI

description: Library name: Sample 237


title: MHC | 011 | Full ROI

description: Library name: Sample 242


title: MHC | 005 | Full ROI

description: Library name: Sample 236


title: MSK01 | 009 | Full ROI

description: Library name: Sample 256


title: MSK01 | 010 | Full ROI

description: Library name: Sample 257

value: MSK01 | 009 | Full ROI


title: MHC | 001 | Full ROI

description: Library name: Sample 232


title: FTE485 | 006 | Full ROI

description: Library name: Sample 137


title: FTE485 | 005 | Full ROI

description: Library name: Sample 136


title: FTE485 | 004 | Full ROI

description: Library name: Sample 135

value: p53 signature


title: FTE485 | 008 | Full ROI

description: Library name: Sample 139


title: FTE485 | 007 | Full ROI

description: Library name: Sample 138


title: FTE485 | 002 | Full ROI

description: Library name: Sample 133


title: FTE483_1K | 008 | Full ROI

description: Library name: Sample 131

value: FTE483_1K | 007 | Full ROI


title: FTE483_1K | 007 | Full ROI

description: Library name: Sample 130


title: FTE483_1K | 006 | Full ROI

description: Library name: Sample 129

value: FTE483_1K | 005 | Full ROI


title: MSK01 | 003 | Full ROI

description: Library name: Sample 250


title: FTE485 | 001 | Full ROI

description: Library name: Sample 132


title: FTE483_1K | 005 | Full ROI

description: Library name: Sample 128


title: FTE483_1K | 004 | Full ROI

description: Library name: Sample 127

value: FTE483_1K | 003 | Full ROI


title: FTE483_1K | 001 | Full ROI

description: Library name: Sample 124


title: FTE406 | 006 | Full ROI

description: Library name: Sample 073


title: MHC | 004 | Full ROI

description: Library name: Sample 235


title: FTE483_1K | 003 | Full ROI

description: Library name: Sample 126


title: FTE483_1K | 002 | Full ROI

description: Library name: Sample 125

value: FTE483_1K | 001 | Full ROI


title: MHC | 002 | Full ROI

description: Library name: Sample 233


title: FTE406 | 002 | Full ROI

description: Library name: Sample 069


title: FTE406 | 001 | Full ROI

description: Library name: Sample 068


title: FTE406 | 005 | Full ROI

description: Library name: Sample 072


title: FTE403-7A_2 | 005 | Full ROI

description: Library name: Sample 067


title: FTE403-7A_2 | 004 | Full ROI

description: Library name: Sample 066


title: FTE406 | 003 | Full ROI

description: Library name: Sample 070

value: High grade serous carcinoma


title: FTE406 | 004 | Full ROI

description: Library name: Sample 071


title: FTE403-7A_2 | 001 | Full ROI

description: Library name: Sample 063

value: STIL


title: FTE387-6Z_2 | 003 | Full ROI

description: Library name: Sample 062

value: fallopian tube


title: FTE387-6Z_2 | 002 | Full ROI

description: Library name: Sample 061

value: epithelium


title: FTE387-6Z_2 | 001 | Full ROI

description: Library name: Sample 060


title: FTE384-1A | 004 | Full ROI

description: Library name: Sample 059

value: Normal fallopian tube epithelium


title: FTE403-7A_2 | 003 | Full ROI

description: Library name: Sample 065


title: FTE485 | 003 | Full ROI

description: Library name: Sample 134


title: FTE384-1A | 003 | Full ROI

description: Library name: Sample 058


title: FTE403-7A_2 | 002 | Full ROI

description: Library name: Sample 064


title: FTE384-1A | 001 | Full ROI

description: Library name: Sample 056


title: FTE384-1A | 002 | Full ROI

description: Library name: Sample 057


title: FTE384_2A | 010 | Full ROI

description: Library name: Sample 054


title: FTE384_2A | 007 | Full ROI

description: Library name: Sample 051


title: FTE384_2A | 009 | Full ROI

description: Library name: Sample 053


title: FTE384_2A | 006 | Full ROI

description: Library name: Sample 050


title: FTE384_2A | 003 | Full ROI

description: Library name: Sample 047


title: FTE384_2A | 004 | Full ROI

description: Library name: Sample 048


title: FTE384_2A | 005 | Full ROI

description: Library name: Sample 049


title: FTE384_2A | 001 | Full ROI

description: Library name: Sample 045


title: FTE128_B8_rescan | 020 | Full ROI

description: Library name: Sample 044

value: stroma

value: Normal mesothelium

value: FTE128_B8_rescan | 019 | Full ROI


title: FTE034_4 | 008 | PanCK+

description: Library name: Sample 024


title: FTE034_4 | 006 | PanCK+

description: Library name: Sample 021


title: FTE034_4 | 005 | PanCK+

description: Library name: Sample 020


title: FTE034_4 | 007 | PanCK

description: Library name: Sample 022


title: FTE034_4 | 005 | PanCK

description: Library name: Sample 019


title: FTE034_4 | 001 | PanCK+

description: Library name: Sample 014


title: FTE034_4 | 002 | PanCK

description: Library name: Sample 015


title: FTE034_4 | 003 | PanCK+

description: Library name: Sample 017


title: FTE029_A5_3 | 007 | PanCK+

description: Library name: Sample 012


title: FTE029_A5_3 | 007 | PanCK

description: Library name: Sample 011


title: FTE034_4 | 001 | PanCK

description: Library name: Sample 013


title: FTE034_4 | 004 | PanCK+

description: Library name: Sample 018


title: FTE029_A5_3 | 005 | PanCK+

description: Library name: Sample 009


title: FTE029_A5_3 | 006 | PanCK+

description: Library name: Sample 010


title: FTE384_2A | 008 | Full ROI

description: Library name: Sample 052


title: FTE029_A5_3 | 002 | PanCK+

description: Library name: Sample 004


title: FTE029_A5_3 | 003 | PanCK

description: Library name: Sample 005


title: FTE029_A5_3 | 004 | PanCK+

description: Library name: Sample 008


title: FTE029_A5_3 | 003 | PanCK+

description: Library name: Sample 006


title: FTE034_4 | 002 | PanCK+

description: Library name: Sample 016


title: FTE034_4 | 007 | PanCK+

description: Library name: Sample 023


title: FTE029_A5_3 | 001 | PanCK+

description: Library name: Sample 002


title: FTE384_2A | 002 | Full ROI

description: Library name: Sample 046

value: STIC


title: GFP2-NC_rep2

city: 北京

first: yuhong

last: wang

state: 北京市

address: 北京大学吕志和楼106

country: China

institute: Peking university

library_source: genomic

data_processing:
Paired-end sequencing data were aligned and analyased by CRISPResso (version 2.2.14)
Assembly: GFP  gene used in this study
Supplementary files format and content: xlsx files including the output statistic modifications from different libraries
Library strategy: Amplicon-Seq

molecule: genomic DNA

extract_protocol:
About 20 w cells were harvested to extract genomic DNA
The targeted GFP loci were PCR-amplified from 500 ng genomic DNA using primers listed in the supplementary table. An initial PCR of 25 cycles was performed with TranStart Fastpfu high-fidelity DNA polymerase, and a second round of 15 cycles was used to add sequencing adaptor and barcodes. The final PCR products were gel-purified, quantified by DeNovix, and sequenced by PE150 on NovaSeq 6000 platform (GENEWIZ)

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: GFP knockin at AAVS1


title: FTE029_A5_3 | 001 | PanCK

description: Library name: Sample 001


title: GFP1-NC_rep2


title: FTE029_A5_3 | 002 | PanCK

description: Library name: Sample 003


title: FTE384_2A | 011 | Full ROI

description: Library name: Sample 055


title: Tm-HAE1-GFP-RY23


title: Tm-HAE1-GFP-RY21


title: Tm-HAE1-GFP-RY20


title: Tm-HAE1-GFP-RY22


title: Tm-HAE1-GFP-RY19


title: Tm-HAE1-GFP-RY17


title: Tm-HAE1-GFP-RY18


title: Tm-HAE1-GFP-RY15


title: Tm-HAE1-GFP-RY13


title: Tm-HAE1-GFP-RY12


title: Tm-HAE1-GFP-RY14


title: Tm-HAE1-GFP-RY11


title: Tm-HAE1-GFP-RY10


title: FTE029_A5_3 | 004 | PanCK

description: Library name: Sample 007


title: Tm-HAE1-GFP-RY9


title: Tm-HAE1-GFP-RY7


title: Tm-HAE1-GFP-RY1


title: Am-HAE1-GFP-RY22


title: Am-HAE1-GFP-RY20


title: Am-HAE1-GFP-RY19


title: Tm-HAE1-GFP-RY8


title: Am-HAE1-GFP-RY23


title: STIC_TMA4 | 009 | PanCK+

description: Library name: Sample 298


title: Am-HAE1-GFP-RY18


title: STIC_TMA4 | 009 | PanCK

description: Library name: Sample 297

value: STIC_TMA4 | 009 | PanCK+


title: Am-HAE1-GFP-RY17


title: Am-HAE1-GFP-RY16


title: Am-HAE1-GFP-RY15


title: Am-HAE1-GFP-RY14


title: STIC_TMA4 | 008 | PanCK

description: Library name: Sample 295

value: STIC_TMA4 | 008 | PanCK+


title: Am-HAE1-GFP-RY12


title: Am-HAE1-GFP-RY13


title: STIC_TMA4 | 006 | PanCK+

description: Library name: Sample 293


title: STIC_TMA4 | 005 | PanCK+

description: Library name: Sample 292


title: Am-HAE1-GFP-RY11


title: STIC_TMA4 | 004 | PanCK+

description: Library name: Sample 291


title: Am-HAE1-GFP-RY9


title: STIC_TMA4 | 003 | PanCK+

description: Library name: Sample 290


title: Am-HAE1-GFP-RY10


title: Am-HAE1-GFP-RY8


title: Am-HAE1-GFP-RY21


title: STIC_TMA4 | 008 | PanCK+

description: Library name: Sample 296


title: STIC_TMA4 | 002 | PanCK+

description: Library name: Sample 289


title: STIC_TMA4 | 001 | PanCK+

description: Library name: Sample 288


title: Am-HAE1-GFP-RY7


title: Am-HAE1-GFP-RY1


title: STIC_TMA4 | 001 | PanCK

description: Library name: Sample 287

value: STIC_TMA4 | 001 | PanCK+


title: STIC_TMA1 | 007 | PanCK+

description: Library name: Sample 280


title: HAE1-GFP-RY22


title: STIC_TMA4 | 007 | PanCK+

description: Library name: Sample 294


title: Tm-HAE1-GFP-RY16


title: HAE1-GFP-RY23


title: STIC_TMA1 | 006 | PanCK+

description: Library name: Sample 278


title: STIC_TMA1 | 007 | PanCK

description: Library name: Sample 279

value: STIC_TMA1 | 007 | PanCK+


title: STIC_TMA1 | 005 | PanCK+

description: Library name: Sample 276

value: Endometrial endometrioid carcinoma


title: HAE1-GFP-RY19


title: STIC_TMA1 | 006 | PanCK

description: Library name: Sample 277

value: STIC_TMA1 | 006 | PanCK+


title: HAE1-GFP-RY21


title: STIC_TMA1 | 004 | PanCK+

description: Library name: Sample 275


title: STIC_TMA1 | 004 | PanCK

description: Library name: Sample 274

value: STIC_TMA1 | 004 | PanCK+


title: HAE1-GFP-RY17


title: HAE1-GFP-RY16


title: STIC_TMA1 | 003 | PanCK+

description: Library name: Sample 273


title: STIC_TMA1 | 003 | PanCK

description: Library name: Sample 272

value: STIC_TMA1 | 003 | PanCK+


title: HAE1-GFP-RY15


title: HAE1-GFP-RY14


title: STIC_TMA1 | 002 | PanCK

description: Library name: Sample 270

value: fallopian tube

value: STIC_TMA1 | 002 | PanCK+


title: STIC_TMA1 | 001 | PanCK+

description: Library name: Sample 269

value: epithelium

value: STIL


title: HAE1-GFP-RY12


title: HAE1-GFP-RY13


title: STIC_TMA1 | 001 | PanCK

description: Library name: Sample 268

value: stroma

value: STIC_TMA1 | 001 | PanCK+


title: HAE1-GFP-RY11


title: HAE1-GFP-RY10


title: HAE1-GFP-RY9


title: HAE1-GFP-RY8


title: HAE1-GFP-RY20


title: FTE547_1C | 017 | Full ROI

description: Library name: Sample 230

value: Normal fallopian tube epithelium


title: FTE547_1C | 014 | Full ROI

description: Library name: Sample 227

value: STIC

value: FTE547_1C | 013 | Full ROI


title: FTE547_1C | 018 | Full ROI

description: Library name: Sample 231

value: FTE547_1C | 017 | Full ROI


title: HAE1-GFP-RY1

value: Human embryonic kidney

value: GFP knockin at AAVS1


title: HAE1-GFP-RY7


title: GFP2-NC_rep1


title: FTE547_1C | 015 | Full ROI

description: Library name: Sample 228


title: FTE547_1C | 013 | Full ROI

description: Library name: Sample 226


title: HAE1-GFP-RY18


title: FTE547_1C | 011 | Full ROI

description: Library name: Sample 224


title: FTE547_1C | 012 | Full ROI

description: Library name: Sample 225

value: FTE547_1C | 011 | Full ROI


title: STIC_TMA1 | 002 | PanCK+

description: Library name: Sample 271


title: PAMless-AID-GFP-RY23


title: PAMless-AID-GFP-RY22


title: FTE547_1C | 010 | Full ROI

description: Library name: Sample 223

value: FTE547_1C | 009 | Full ROI


title: PAMless-AID-GFP-RY21


title: PAMless-AID-GFP-RY20


title: FTE547_1C | 008 | Full ROI

description: Library name: Sample 221

value: FTE547_1C | 007 | Full ROI


title: FTE547_1C | 007 | Full ROI

description: Library name: Sample 220


title: FTE547_1C | 016 | Full ROI

description: Library name: Sample 229

value: FTE547_1C | 015 | Full ROI


title: PAMless-AID-GFP-RY18


title: FTE547_1C | 006 | Full ROI

description: Library name: Sample 219

value: FTE547_1C | 005 | Full ROI


title: PAMless-AID-GFP-RY17


title: FTE547_1C | 003 | Full ROI

description: Library name: Sample 216

value: fallopian tube


title: Ecsenius pulcher. Post-hypoxia time point. Hypoxic group. Rep 6

city: Abu Dhabi

first: Daniel

middle: Michael

last: Ripley

address: NYUAD

country: United Arab Emirates

institute: New York University Abu Dhabi

description: Library name: F31

data_processing:
Reads trimmed (trimmomatic), filtered (sortmeRNA, DeconSeq), and assembled intro transcripts (Trinity). The raw count data were generated using RSEM to align the cleaned trimmed reads to the de-novo assembled transcriptome.
Assembly: de novo transcriptome assembly. FASTA file with transcript sequences is available on the series record.
Supplementary files format and content: .csv file containing transcript ID, length, effective length, and estimated counts from Kallisto

organism: Ecsenius pulcher

source_name: anterior tail muscle cross section.

extract_protocol:
Qiagen RNeasy minikit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: anterior tail muscle cross section.

tag: treatment

value: Post-hypoxia time point. Hypoxic group


title: PAMless-AID-GFP-RY16


title: PAMless-AID-GFP-RY15


title: FTE547_1C | 001 | Full ROI

description: Library name: Sample 214

value: epithelium


title: GFP1-NC_rep1


title: FTE545_2G | 010 | Full ROI

description: Library name: Sample 213

value: stroma

value: FTE545_2G | 009 | Full ROI


title: FTE547_1C | 002 | Full ROI

description: Library name: Sample 215

value: FTE547_1C | 001 | Full ROI


title: FTE545_2G | 009 | Full ROI

description: Library name: Sample 212

value: Normal fallopian tube epithelium


title: Ecsenius pulcher. Post-hypoxia time point. Hypoxic group. Rep 4

description: Library name: F23


title: FTE547_1C | 005 | Full ROI

description: Library name: Sample 218

value: STIC


title: PAMless-AID-GFP-RY19


title: Ecsenius pulcher. Post-hypoxia time point. Hypoxic group. Rep 5

description: Library name: F29


title: FTE547_1C | 009 | Full ROI

description: Library name: Sample 222


title: PAMless-AID-GFP-RY14


title: FTE545_2G | 008 | Full ROI

description: Library name: Sample 211

value: STIL

value: FTE545_2G | 007 | Full ROI


title: FTE545_2G | 007 | Full ROI

description: Library name: Sample 210


title: Ecsenius pulcher. Post-hypoxia time point. Hypoxic group. Rep 1

description: Library name: F1


title: PAMless-AID-GFP-RY13

value: Human embryonic kidney

value: GFP knockin at AAVS1


title: PAMless-AID-GFP-RY12


title: FTE547_1C | 004 | Full ROI

description: Library name: Sample 217

value: FTE547_1C | 003 | Full ROI


title: FTE545_2G | 003 | Full ROI

description: Library name: Sample 206


title: FTE545_2G | 002 | Full ROI

description: Library name: Sample 205

value: FTE545_2G | 001 | Full ROI


title: Ecsenius pulcher. Post-hypoxia time point. Hypoxic group. Rep 2

description: Library name: F9


title: FTE545_2G | 005 | Full ROI

description: Library name: Sample 208


title: Ecsenius pulcher. Post-hypoxia time point. Control group. Rep 5

description: Library name: F26

value: Post-hypoxia time point. Control group


title: FTE545_2G | 004 | Full ROI

description: Library name: Sample 207

value: FTE545_2G | 003 | Full ROI


title: FTE544_1V | 009 | Full ROI

description: Library name: Sample 202

value: fallopian tube


title: Ecsenius pulcher. Post-hypoxia time point. Hypoxic group. Rep 3

description: Library name: F21

value: anterior tail muscle cross section.


title: Ecsenius pulcher. Post-hypoxia time point. Control group. Rep 4

description: Library name: F25


title: FTE544_1V | 008 | Full ROI

description: Library name: Sample 201

value: FTE544_1V | 007 | Full ROI


title: PAMless-AID-GFP-RY8


title: PAMless-AID-GFP-RY11


title: Ecsenius pulcher. Post-hypoxia time point. Control group. Rep 6

description: Library name: F28


title: FTE545_2G | 001 | Full ROI

description: Library name: Sample 204

value: epithelium


title: PAMless-AID-GFP-RY10


title: FTE544_1V | 005 | Full ROI

description: Library name: Sample 198


title: FTE544_1V | 010 | Full ROI

description: Library name: Sample 203

value: stroma

value: FTE544_1V | 009 | Full ROI


title: Ecsenius pulcher. Post-hypoxia time point. Control group. Rep 3

description: Library name: F18


title: FTE545_2G | 006 | Full ROI

description: Library name: Sample 209

value: FTE545_2G | 005 | Full ROI


title: PAMless-AID-GFP-RY9


title: FTE544_1V | 006 | Full ROI

description: Library name: Sample 199

value: FTE544_1V | 005 | Full ROI


title: PAMless-AID-GFP-RY7


title: FTE544_1V | 004 | Full ROI

description: Library name: Sample 197

value: Normal fallopian tube epithelium

value: FTE544_1V | 003 | Full ROI


title: Ecsenius pulcher. Post-hypoxia time point. Control group. Rep 1

description: Library name: F5


title: Ecsenius pulcher. Acute time point. Hypoxic group. Rep 6

description: Library name: LH7

value: Acute time point. Hypoxic group


title: FTE544_1V | 003 | Full ROI

description: Library name: Sample 196


title: FTE544_1V | 002 | Full ROI

description: Library name: Sample 195

value: STIL

value: FTE544_1V | 001 | Full ROI


title: FTE544_1V | 001 | Full ROI

description: Library name: Sample 194


title: Ecsenius pulcher. Post-hypoxia time point. Control group. Rep 2

description: Library name: F16


title: PAMless-AID-GFP-RY1

value: Human embryonic kidney

value: GFP knockin at AAVS1


title: FTE541_A26 | 014 | Full ROI

description: Library name: Sample 193

value: FTE541_A26 | 013 | Full ROI


title: FTE541_A26 | 013 | Full ROI

description: Library name: Sample 192


title: FTE541_A26 | 012 | Full ROI

description: Library name: Sample 191

value: FTE541_A26 | 011 | Full ROI


title: FTE541_A26 | 011 | Full ROI

description: Library name: Sample 190

value: fallopian tube


title: Ecsenius pulcher. Acute time point. Hypoxic group. Rep 5

description: Library name: LH6

value: anterior tail muscle cross section.


title: X121 cells, doxorubicin production, Day6, L002

city: Turku

first: Mikko

last: Metsä-Ketelä

address: Tykistökatu 6A

department: Department of Life Technologies

country: Finland

institute: University of Turku

description:
Library name: Sample 18, L002
Column name in Speucetius_counts.txt: 180087_18_X121_6d_S10_L002_R1_001.fastq.gz

data_processing:
Chipster (CSC)
Reads were trimmed using TRIMMOMATIC (default parameters)
Trimmed reads were mapped using BowTie2 (default parameters)
Mapped reads were counted using HTSeq
Differential expression was done using edgeR
Assembly: CP022438.1
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

organism: Streptomyces peucetius

source_name: bacterial cells

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
Illumina PCR-free library

tag: strain

value: mutant

value: bacterial cells

tag: phenotype

value: doxorubicin producer

tag: time


title: Ecsenius pulcher. Acute time point. Hypoxic group. Rep 4

description: Library name: LH5


title: X121 cells, doxorubicin production, Day5, L002

description:
Library name: Sample 17, L002
Column name in Speucetius_counts.txt: 180087_17_X121_5d_S9_L002_R1_001.fastq.gz


title: FTE544_1V | 007 | Full ROI

description: Library name: Sample 200

value: epithelium


title: Ecsenius pulcher. Acute time point. Hypoxic group. Rep 3

description: Library name: LH4


title: FTE541_A26 | 009 | Full ROI

description: Library name: Sample 188


title: FTE541_A26 | 008 | Full ROI

description: Library name: Sample 187

value: stroma

value: FTE541_A26 | 007 | Full ROI


title: FTE541_A26 | 007 | Full ROI

description: Library name: Sample 186

value: Normal fallopian tube epithelium


title: X121 cells, doxorubicin production, Day2, L002

description:
Library name: Sample 14, L002
Column name in Speucetius_counts.txt: 180087_14_X121_2d_S6_L002_R1_001.fastq.gz


title: FTE541_A26 | 004 | Full ROI

description: Library name: Sample 183

value: STIC

value: FTE541_A26 | 003 | Full ROI


title: Ecsenius pulcher. Acute time point. Hypoxic group. Rep 1

description: Library name: LH1

value: Acute time point. Hypoxic group


title: FTE541_A26 | 006 | Full ROI

description: Library name: Sample 185

value: FTE541_A26 | 005 | Full ROI


title: Ecsenius pulcher. Acute time point. Hypoxic group. Rep 2

description: Library name: LH2


title: FTE541_A26 | 002 | Full ROI

description: Library name: Sample 181

value: FTE541_A26 | 001 | Full ROI


title: Ecsenius pulcher. Acute time point. Control group. Rep 5

description: Library name: LC6

value: Acute time point. Control group


title: FTE541_A24 | 009 | Full ROI

description: Library name: Sample 178


title: X121 cells, doxorubicin production, Day4, L002

description:
Library name: Sample 16, L002
Column name in Speucetius_counts.txt: 180087_16_X121_4d_S8_L002_R1_001.fastq.gz


title: FTE541_A26 | 005 | Full ROI

description: Library name: Sample 184


title: GOO1 cells, daunorubicin production, Day6, L002

description:
Library name: Sample 12, L002
Column name in Speucetius_counts.txt: 180087_12_G001_6d_S4_L002_R1_001.fastq.gz

value: daunorubicin over-producer


title: X121 cells, doxorubicin production, Day1, L002

description:
Library name: Sample 13, L002
Column name in Speucetius_counts.txt: 180087_13_X121_1d_S5_L002_R1_001.fastq.gz


title: X121 cells, doxorubicin production, Day3, L002

description:
Library name: Sample 15, L002
Column name in Speucetius_counts.txt: 180087_15_X121_3d_S7_L002_R1_001.fastq.gz


title: GOO1 cells, daunorubicin production, Day3, L002

description:
Library name: Sample 9, L002
Column name in Speucetius_counts.txt: 180087_9_G001_3d_S18_L002_R1_001.fastq.gz


title: GOO1 cells, daunorubicin production, Day4, L002

description:
Library name: Sample 10, L002
Column name in Speucetius_counts.txt: 180087_10_G001_4d_S2_L002_R1_001.fastq.gz


title: FTE541_A26 | 001 | Full ROI

description: Library name: Sample 180


title: FTE541_A24 | 010 | Full ROI

description: Library name: Sample 179

value: FTE541_A24 | 009 | Full ROI


title: FTE541_A24 | 005 | Full ROI

description: Library name: Sample 174

value: fallopian tube


title: FTE541_A24 | 004 | Full ROI

description: Library name: Sample 173

value: FTE541_A24 | 003 | Full ROI


title: FTE541_A26 | 003 | Full ROI

description: Library name: Sample 182


title: FTE541_A24 | 002 | Full ROI

description: Library name: Sample 171

value: FTE541_A24 | 001 | Full ROI


title: FTE541_A24 | 003 | Full ROI

description: Library name: Sample 172


title: FTE541_A26 | 010 | Full ROI

description: Library name: Sample 189

value: FTE541_A26 | 009 | Full ROI


title: FTE541_A24 | 008 | Full ROI

description: Library name: Sample 177

value: FTE541_A24 | 007 | Full ROI


title: FTE541_A24 | 007 | Full ROI

description: Library name: Sample 176

value: epithelium


title: Ecsenius pulcher. Acute time point. Control group. Rep 6

description: Library name: LC7

value: anterior tail muscle cross section.


title: GOO1 cells, daunorubicin production, Day5, L002

description:
Library name: Sample 11, L002
Column name in Speucetius_counts.txt: 180087_11_G001_5d_S3_L002_R1_001.fastq.gz

value: mutant

value: bacterial cells


title: Ecsenius pulcher. Acute time point. Control group. Rep 1

description: Library name: LC1


title: FTE541_A24 | 006 | Full ROI

description: Library name: Sample 175

value: stroma

value: STIC

value: FTE541_A24 | 005 | Full ROI


title: Ecsenius pulcher. Acute time point. Control group. Rep 4

description: Library name: LC5


title: ATCC27952 cells, control, Day6, L002

description:
Library name: Sample 6, L002
Column name in Speucetius_counts.txt: 180087_6_WT_6d_S15_L002_R1_001.fastq.gz

value: wild type

value: daunorubicin producer


title: Ecsenius pulcher. Acute time point. Control group. Rep 3

description: Library name: LC4

value: Acute time point. Control group


title: GOO1 cells, daunorubicin production, Day1, L002

description:
Library name: Sample 7, L002
Column name in Speucetius_counts.txt: 180087_7_G001_1d_S16_L002_R1_001.fastq.gz

value: daunorubicin over-producer


title: FTE515_6A | 020 | Full ROI

description: Library name: Sample 167

value: Normal fallopian tube epithelium

value: FTE515_6A | 019 | Full ROI


title: GOO1 cells, daunorubicin production, Day2, L002

description:
Library name: Sample 8, L002
Column name in Speucetius_counts.txt: 180087_8_G001_2d_S17_L002_R1_001.fastq.gz


title: FTE515_6A | 022 | Full ROI

description: Library name: Sample 169

value: fallopian tube

value: FTE515_6A | 021 | Full ROI


title: ATCC27952 cells, control, Day5, L002

description:
Library name: Sample 5, L002
Column name in Speucetius_counts.txt: 180087_5_WT_5dA_S14_L002_R1_001.fastq.gz


title: Ecsenius pulcher. Acute time point. Control group. Rep 2

description: Library name: LC2


title: FTE541_A24 | 001 | Full ROI

description: Library name: Sample 170


title: FTE515_6A | 021 | Full ROI

description: Library name: Sample 168


title: FTE515_6A | 018 | Full ROI

description: Library name: Sample 165

value: FTE515_6A | 017 | Full ROI


title: PANC1-Vector3

city: hefei

first: Yajun

last: Chen

state: anhui

address: No.1688, Lianhua Road, Hefei 230601, Anhui, China.

institute: Hefei Normal University

description: Library name: Sample 6

data_processing:
Basecalling is performed by Illumina RTA software in sequencer.
Raw data (raw reads) of FASTQ format were firstly processed through fastp to generate clean reads.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Differential expression analysis of two conditions/groups (five biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Genes with an  P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package.
Assembly: GRCh38
Supplementary files format and content: processed data file.xls

organism: Mus musculus

source_name: tissue liver

extract_protocol:
After sacrifice, mouse liver samples were likewise snap-frozen in liquid nitrogen and stored at −80℃. After the tissues were homogenized, total RNA was extracted employing Trizol reagent (Invitrogen, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries  for lncRNA-seq were prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reversetranscribed using fragmented RNA and dNTPs . RNA was degraded using RNase H, and second strand cDNA was synthesised using DNA polymerase I and dNTPs. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3’ ends of DNA fragments,sequencing adaptors were ligated to the cDNA. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Uridine digestion was performed using Uracil-N-Glycosylase, which was followed by the cDNA amplification using PCR.

value: tissue liver

value: Solvent administration


title: PANC1-Vector1

description: Library name: Sample 4


title: ATCC27952 cells, control, Day4, L002

description:
Library name: Sample 4, L002
Column name in Speucetius_counts.txt: 180087_4_WT_4d_S13_L002_R1_001.fastq.gz


title: FTE515_6A | 019 | Full ROI

description: Library name: Sample 166

value: epithelium


title: FTE515_6A | 017 | Full ROI

description: Library name: Sample 164


title: ATCC27952 cells, control, Day3, L002

description:
Library name: Sample 3, L002
Column name in Speucetius_counts.txt: 180087_3_WT_3dA_S12_L002_R1_001.fastq.gz


title: PANC1-OE3

description: Library name: Sample 3

value: Gigantol administration


title: FTE515_6A | 016 | Full ROI

description: Library name: Sample 163

value: FTE515_6A | 015 | Full ROI


title: FTE515_6A | 015 | Full ROI

description: Library name: Sample 162


title: ATCC27952 cells, control, Day1, L002

description:
Library name: Sample 1, L002
Column name in Speucetius_counts.txt: 180087_1_WT_1d_S1_L002_R1_001.fastq.gz

value: bacterial cells


title: FTE515_6A | 014 | Full ROI

description: Library name: Sample 161

value: stroma

value: FTE515_6A | 013 | Full ROI


title: FTE515_6A | 013 | Full ROI

description: Library name: Sample 160


title: FTE515_6A | 012 | Full ROI

description: Library name: Sample 159

value: STIL

value: FTE515_6A | 011 | Full ROI


title: PANC1-OE2

description: Library name: Sample 2


title: PANC1-OE1

description: Library name: Sample 1


title: ATCC27952 cells, control, Day2, L002

description:
Library name: Sample 2, L002
Column name in Speucetius_counts.txt: 180087_2_WT_2d_S11_L002_R1_001.fastq.gz

value: wild type

value: daunorubicin producer


title: FTE515_6A | 010 | Full ROI

description: Library name: Sample 157

value: Normal fallopian tube epithelium

value: FTE515_6A | 009 | Full ROI


title: FTE515_6A | 006 | Full ROI

description: Library name: Sample 153

value: fallopian tube

value: STIC

value: FTE515_6A | 005 | Full ROI


title: X121 cells, doxorubicin production, Day6, L001

description:
Library name: Sample 18, L001
Column name in Speucetius_counts.txt: 180087_18_X121_6d_S10_L001_R1_001.fastq.gz

value: mutant

value: doxorubicin producer


title: FTE515_6A | 011 | Full ROI

description: Library name: Sample 158

value: epithelium


title: FTE515_6A | 008 | Full ROI

description: Library name: Sample 155

value: FTE515_6A | 007 | Full ROI


title: FTE515_6A | 009 | Full ROI

description: Library name: Sample 156


title: Lung of tumor-bearing (KP) mice replicate 3 (scATAC-seq)

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
Library name: mm_scATACseq_Lung_KP_Rep3
10x Genomics

library_source: genomic single cell

data_processing:
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: mm10
Supplementary files format and content: scATAC-seq: cellranger processed outputs (barcode, peak/feature matrix).

source_name: Lung

extract_protocol:
Mouse: myeloid cells were sorted from respective tissues (Lung/BM/blood) based on markers described in Methods section. For scATAC-seq, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei or cells were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Mouse: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. scRNA-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell pooled on the Illumina NovaSeq 6000 S2 100 cycle kit. scATAC-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol: Mouse: myeloid cells excluding mature neutrophils were sorted from processed tissues (Lung/BM/blood) of naïve or KP Tumor-bearing mice in PBS+0.04% BSA, based on surface markers described in Methods section.

value: Lung

value: immune

value: Tumor-bearing


title: PANC1-Vector2

description: Library name: Sample 5

value: tissue liver

value: Solvent administration


title: X121 cells, doxorubicin production, Day5, L001

description:
Library name: Sample 17, L001
Column name in Speucetius_counts.txt: 180087_17_X121_5d_S9_L001_R1_001.fastq.gz

value: bacterial cells


title: FTE515_6A | 002 | Full ROI

description: Library name: Sample 149

value: stroma

value: FTE515_6A | 001 | Full ROI


title: FTE489_3AA | 008 | Full ROI

description: Library name: Sample 147

value: Normal fallopian tube epithelium

value: FTE489_3AA | 007 | Full ROI


title: FTE515_6A | 007 | Full ROI

description: Library name: Sample 154

value: fallopian tube


title: X121 cells, doxorubicin production, Day4, L001

description:
Library name: Sample 16, L001
Column name in Speucetius_counts.txt: 180087_16_X121_4d_S8_L001_R1_001.fastq.gz


title: GOO1 cells, daunorubicin production, Day6, L001

description:
Library name: Sample 12, L001
Column name in Speucetius_counts.txt: 180087_12_G001_6d_S4_L001_R1_001.fastq.gz

value: daunorubicin over-producer


title: Lung of tumor-bearing (KP) mice replicate 2 (scATAC-seq)

description:
Library name: mm_scATACseq_Lung_KP_Rep2
10x Genomics


title: WTDSS

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description:
Library name: NOVA0466.XW3
Single colon cells pooled from 3 mice were analyzed by scRNA-seq

library_source: transcriptomic single cell

data_processing:
Demultiplexed FASTQ files (paired-end,Read 1: 30bp, Read 2:100bp) were generated using the CellRanger mkfastq command. The primary data analyses which included alignment, filtering, barcode counting and UMI quantification, quality control, clustering and statistical analysis were performed using CellRanger count command. Gene positions were annotated using Ensembl build 93 and filtered for biotype. Raw gene expression matrices were imported into R (version 3.6.1) and converted to a Seurat object using the Seurat R package (version 3.1.0). To remove dead cells and doublets, the total number of UMIs and genes and the percentage of UMIs derived from the mitochondrial genome for each cell were counted.  The upper and lower bounds were defined as the mean +/- two standard deviations for both the total UMIs and genes, respectively. Cells which had over 10% UMIs derived from mitochondrial genome were discarded. Finally, cells with total UMIs or genes outside of the upper and lower bounds were removed. For the remaining 5534 out of 6290 cells, gene expression matrices were normalized to the total cellular read count and to mitochondrial read count. Highly variably genes (HVG) were selected from the normalized data using Seurat SCTransform function. The top 3000 HVGs were used as features for dimensionality reduction and clustering. The Seurat RunPCA and JackStraw functions were performed to calculate and to select significant (P-value <0.05) principal components (PCs), respectively.  The RunUMAP function was then applied to plot the selected significant PCs. The FindNeighbors constructed a Shared Nearest Neighbor (SNN) Graph, and FindClusters function with “resolution = 0.1” parameter was carried out to cluster cells into different groups. Marker genes were defined based on the following criteria: 1) the average expression value in the cluster of interest was at least 1.2-fold higher than the average expression in the rest of clusters; 2) there are greater than 10% of cells in the cluster of interest which were detectable; and 3) marker genes should have the highest mean expression in the cluster of interest compared to the rest of clusters. Canonical marker genes were used to annotate cell clusters.
Assembly: mm10
Supplementary files format and content: hd5 file, data matrix from cell ranger export

molecule: polyA RNA

source_name: colon

growth_protocol: Mice were housed in regular growth conditions

extract_protocol:
Following the removal of the mesentery/fat and connective tissue, colons from three mice were combined, flushed with ice-cold CMF-PBS, longitudinally opened, and rinsed with ice-cold CMF-PBS. The colons were then cut into 0.5-1 centimeter pieces and washed once in rinse buffer containing 5.6 mM Na2HPO4 x2H2O, 8.0 mM KH2PO4, 96.2 mM NaCl, 1.6 mM KCl, 43.4 mM Sucrose, 54.9 mM D-sorbitol. Then, the colon pieces were resuspended in isolation buffer (2mM EDTA and 0.5mM DTT in rinse buffer) and incubated on a rotation platform for 20 min at room temperature. Subsequently, supernatants were removed and the remaining tissue was resuspended in 10 ml ice-cold rinse buffer and pipetted 25 times up and down with a 25 ml pipette. Following the settling of the large tissue pieces, the supernatants containing crypts were transferred to a new tube.  After additional pipetting 25 times up and down with a 25 ml pipette and settling of the tissue pieces, the supernatants were centrifuged at 300 g, 4°C for 3 min, and the pellets were resuspended in 10 ml room-temperature single-cell-isolation-buffer (1 mg/ml DNaseI, 5 mM MgCl2, 20 μM Y27 in TrypLE Express) and incubated on 100 RPM at 37°C for 20 min. Then,  the cell solution was passed through the 40 mm cell strainers. Digestion was stopped by the addition of 35 ml ice-cold CMF-PBS, and centrifugation at 500 g, 4°C for 4 min. The cell pellets were resuspended in ice-cold PBS with 2% FBS.
Single cell libraries were prepared on a 10x Genomics Chromium controller (10x Genomics, Pleasanton, CA) using the version 3 reagent kit according to the manufacturer’s instructions. The reagent mixture was calculated for capturing 6000 cells. The libraries were sequenced on a NovaSeq (Illumina, San Diego, CA) by the NIEHS Epigenomics core laboratory. Raw read processing was carried out using the Cell Ranger Single-Cell Software Suite (version 3.0.1, 10X Genomics).

treatment_protocol: None-treated WT females,  WT females treated with 2.5% DSS in drinking water for 5 days, and NAPRT KO females  treated with 2.5% DSS in drinking water for 5 days

value: colon

value: WT

value: 2.5% DSS in drinking water for 5 days


title: Bone marrow of naive mice replicate 2 (scATAC-seq)

description:
Library name: mm_scATACseq_BM_naive_Rep2
10x Genomics

source_name: Bone marrow

value: Bone marrow

value: Naive


title: FTE515_6A | 004 | Full ROI

description: Library name: Sample 151

value: FTE515_6A | 003 | Full ROI


title: WT1

description:
Library name: NOVA0466.XW1
Single colon cells pooled from 3 mice were analyzed by scRNA-seq


title: GOO1 cells, daunorubicin production, Day5, L001

description:
Library name: Sample 11, L001
Column name in Speucetius_counts.txt: 180087_11_G001_5d_S3_L001_R1_001.fastq.gz

value: mutant


title: FTE515_6A | 005 | Full ROI

description: Library name: Sample 152

value: epithelium

value: STIC


title: FTE515_6A | 003 | Full ROI

description: Library name: Sample 150


title: X121 cells, doxorubicin production, Day2, L001

description:
Library name: Sample 14, L001
Column name in Speucetius_counts.txt: 180087_14_X121_2d_S6_L001_R1_001.fastq.gz

value: doxorubicin producer


title: Bone marrow of tumor-bearing (KP) mice replicate 3 (scATAC-seq)

description:
Library name: mm_scATACseq_BM_KP_Rep3
10x Genomics

value: immune

value: Tumor-bearing


title: KODSS

description:
Library name: NOVA0466.XW4
Single colon cells pooled from 3 mice were analyzed by scRNA-seq

value: KO


title: FTE515_6A | 001 | Full ROI

description: Library name: Sample 148


title: X121 cells, doxorubicin production, Day1, L001

description:
Library name: Sample 13, L001
Column name in Speucetius_counts.txt: 180087_13_X121_1d_S5_L001_R1_001.fastq.gz

value: bacterial cells


title: X121 cells, doxorubicin production, Day3, L001

description:
Library name: Sample 15, L001
Column name in Speucetius_counts.txt: 180087_15_X121_3d_S7_L001_R1_001.fastq.gz


title: FTE489_3AA | 007 | Full ROI

description: Library name: Sample 146

value: Normal fallopian tube epithelium


title: FTE489_3AA | 006 | Full ROI

description: Library name: Sample 145

value: fallopian tube

value: stroma

value: STIL

value: FTE489_3AA | 005 | Full ROI


title: FTE489_3AA | 004 | Full ROI

description: Library name: Sample 143

value: FTE489_3AA | 003 | Full ROI


title: FTE489_3AA | 003 | Full ROI

description: Library name: Sample 142


title: FTE479_3R | 010 | Full ROI

description: Library name: Sample 121

value: High grade serous carcinoma

value: FTE478_2C | 001 | Full ROI


title: FTE489_3AA | 002 | Full ROI

description: Library name: Sample 141

value: FTE489_3AA | 001 | Full ROI


title: GOO1 cells, daunorubicin production, Day1, L001

description:
Library name: Sample 7, L001
Column name in Speucetius_counts.txt: 180087_7_G001_1d_S16_L001_R1_001.fastq.gz

value: mutant

value: daunorubicin over-producer


title: CB_3G

city: Stanford

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

description:
Library name: CB_3G
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 with --expect-cells=5000 --nosecondary --include-introns commands.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Brain, Cerebellum

extract_protocol:
Nuclei were isolated from the fresh-frozen cerebellum as previously described (Tsai et al., 2023). NeuN-negative nuclei were separately sorted into 1.5 mL DNA LoBind tubes containing 1 mL of Dijon buffer. A total of 50,000 single nuclei were sorted per sample. Nuclei were then counted, and their concentrations were adjusted to approximately 1 million nuclei/mL.
Library preparation was performed using the Chromium Single Cell 3ʹ Library & Gel Bead Kit v3 (10X Genomics). The nuclei/master mix solution was adjusted to target 10,000 nuclei per sample, with an equal distribution of 5,000 nuclei from male and 5,000 from female mice. The prepared samples were loaded onto a standard Chromium Controller (10X Genomics) for processing. Sequencing of the 10X snRNA-seq libraries was conducted by Novogene Co. Inc.

value: Brain, Cerebellum

tag: age

value: NeuN-


title: FTE479_3R | 008 | Full ROI

description: Library name: Sample 119

value: epithelium


title: FTE489_3AA | 001 | Full ROI

description: Library name: Sample 140


title: ATCC27952 cells, control, Day6, L001

description:
Library name: Sample 6, L001
Column name in Speucetius_counts.txt: 180087_6_WT_6d_S15_L001_R1_001.fastq.gz

value: wild type

value: daunorubicin producer


title: CB_3MN

description:
Library name: CB_3MN
10x Genomics

value: NeuN+


title: FTE479_3R | 012 | Full ROI

description: Library name: Sample 123

value: FTE479_3R | 011 | Full ROI


title: GOO1 cells, daunorubicin production, Day4, L001

description:
Library name: Sample 10, L001
Column name in Speucetius_counts.txt: 180087_10_G001_4d_S2_L001_R1_001.fastq.gz

value: bacterial cells


title: FTE489_3AA | 005 | Full ROI

description: Library name: Sample 144

value: fallopian tube


title: FTE479_3R | 005 | Full ROI

description: Library name: Sample 116

value: stroma

value: p53 signature

value: FTE479_3R | 004 | Full ROI


title: CB_24FN

description:
Library name: CB_24FN
10x Genomics


title: FTE479_3R | 007 | Full ROI

description: Library name: Sample 118

value: STIC

value: FTE479_3R | 006 | Full ROI


title: CB_3FN

description:
Library name: CB_3FN
10x Genomics


title: FTE479_3R | 006 | Full ROI

description: Library name: Sample 117


title: GOO1 cells, daunorubicin production, Day2, L001

description:
Library name: Sample 8, L001
Column name in Speucetius_counts.txt: 180087_8_G001_2d_S17_L001_R1_001.fastq.gz


title: FTE479_3R | 011 | Full ROI

description: Library name: Sample 122

value: STIL


title: FTE479_3R | 004 | Full ROI

description: Library name: Sample 115


title: CB_24MN

description:
Library name: CB_24MN
10x Genomics


title: FTE479_3R | 009 | Full ROI

description: Library name: Sample 120

value: Normal fallopian tube epithelium

value: FTE479_3R | 008 | Full ROI


title: GOO1 cells, daunorubicin production, Day3, L001

description:
Library name: Sample 9, L001
Column name in Speucetius_counts.txt: 180087_9_G001_3d_S18_L001_R1_001.fastq.gz

value: mutant

value: daunorubicin over-producer


title: CB_24G

description:
Library name: CB_24G
10x Genomics

value: Brain, Cerebellum

value: NeuN-


title: FTE479_3R | 003 | Full ROI

description: Library name: Sample 114

value: FTE479_3R | 002 | Full ROI


title: CB_18MN

description:
Library name: CB_18MN
10x Genomics

value: NeuN+


title: FTE479_3R | 002 | Full ROI

description: Library name: Sample 113

value: epithelium


title: ATCC27952 cells, control, Day4, L001

description:
Library name: Sample 4, L001
Column name in Speucetius_counts.txt: 180087_4_WT_4d_S13_L001_R1_001.fastq.gz

value: wild type

value: bacterial cells

value: daunorubicin producer


title: FTE479_3R | 001 | Full ROI

description: Library name: Sample 112

value: fallopian tube

value: High grade serous carcinoma


title: ATCC27952 cells, control, Day5, L001

description:
Library name: Sample 5, L001
Column name in Speucetius_counts.txt: 180087_5_WT_5dA_S14_L001_R1_001.fastq.gz


title: CB_18G

description:
Library name: CB_18G
10x Genomics


title: FTE478_2C | 004 | Full ROI

description: Library name: Sample 111

value: stroma

value: FTE478_2C | 003 | Full ROI


title: FTE478_2C | 003 | Full ROI

description: Library name: Sample 110


title: ATCC27952 cells, control, Day2, L001

description:
Library name: Sample 2, L001
Column name in Speucetius_counts.txt: 180087_2_WT_2d_S11_L001_R1_001.fastq.gz


title: CB_18FN

description:
Library name: CB_18FN
10x Genomics


title: FTE478_2C | 002 | Full ROI

description: Library name: Sample 109

value: STIL

value: FTE478_2C | 001 | Full ROI


title: ATCC27952 cells, control, Day3, L001

description:
Library name: Sample 3, L001
Column name in Speucetius_counts.txt: 180087_3_WT_3dA_S12_L001_R1_001.fastq.gz


title: CB_12MN

description:
Library name: CB_12MN
10x Genomics


title: ATCC27952 cells, control, Day1, L001

description:
Library name: Sample 1, L001
Column name in Speucetius_counts.txt: 180087_1_WT_1d_S1_L001_R1_001.fastq.gz


title: FTE476_1E | 004 | Full ROI

description: Library name: Sample 107

value: Normal fallopian tube epithelium

value: FTE476_1E | 003 | Full ROI


title: CB_12G

description:
Library name: CB_12G
10x Genomics


title: FTE478_2C | 001 | Full ROI

description: Library name: Sample 108


title: CB_12FN

description:
Library name: CB_12FN
10x Genomics


title: FTE476_1E | 002 | Full ROI

description: Library name: Sample 105

value: STIC

value: FTE476_1E | 001 | Full ROI


title: 50_A110_C24_5_single-end

first: Miriam

last: Goetting

address: Yliopistonmäki

department: Dept of Biology

description: sequencing run made in 2 lanes

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Read alignment was done using Tophat (v2.1.0) to  salmon genome reference
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: ICSASG v2 (International Cooperation to Sequence the Atlantic Salmon Genome from NCBI)
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

organism: Salmo salar

source_name: blood

growth_protocol: Blood was sampled from landlocked salmon by caudal puncture and stored on ice.

extract_protocol:
Erythrocyte samples were  homogenized in TissueLyser (Qiagen, Austin, USA) and RNA was isolated using NucleoZol (Macherey-Nagel).
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047). Same samples were paired-end and single-end sequenced (paired-end: 3 biological replicates). For the single-end sequencing there are additional biological replicates for the treatments (single-end: 5 biological replicates).

treatment_protocol: Blood samples were centrifuged and top layer containing white blood cells and plasma was removed. Samples were immediately frozen in liquid nitrogen.

tag: acclimation condition

value: cold, 8 C, 3 weeks

tag: environmental stress

value: hypoxia, 12 hours + reoxygenation 12 hours

value: erythrocyte

tag: developmental stage

value: juvenile


title: FTE476_1E | 001 | Full ROI

description: Library name: Sample 104

value: epithelium


title: FTE472_2K | 008 | Full ROI

description: Library name: Sample 101

value: Endometrioid carcinoma

value: FTE472_2K | 007 | Full ROI


title: FTE472_2K | 010 | Full ROI

description: Library name: Sample 103

value: fallopian tube

value: FTE472_2K | 009 | Full ROI


title: FTE472_2K | 009 | Full ROI

description: Library name: Sample 102


title: FTE472_2K | 007 | Full ROI

description: Library name: Sample 100


title: FTE472_2K | 006 | Full ROI

description: Library name: Sample 099

value: stroma

value: FTE472_2K | 005 | Full ROI


title: 47_A88_C12_4_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours


title: FTE476_1E | 003 | Full ROI

description: Library name: Sample 106


title: AKI_2

city: Hangzhou

first: Xiaofeng

last: Peng

address: Yuhangtang Road 866,Hangzhou,Zhejiang

institute: Zhejiang University

description: Library name: Sample 7

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data. Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: Species: mus_musculus Origin: ensembl Version: GRCm39.104  Genome: http://ftp.ensembl.org/pub/release-104/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz Gff3: http://ftp.ensembl.org/pub/release-104/gff3/mus_musculus/Mus_musculus.GRCm39.104.chr.gff3.gz Transcript: http://ftp.ensembl.org/pub/release-104/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz
Supplementary files format and content: all.fpkm_anno.xls

source_name: Kidney

extract_protocol:
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.
Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Kidney

value: Kidney IRI surgery


title: FTE472_2K | 004 | Full ROI

description: Library name: Sample 097

value: STIL

value: FTE472_2K | 003 | Full ROI


title: AKI_3

description: Library name: Sample 8


title: 46_A105_C6_5_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 6 hours


title: 48_A108_C12_5_single-end

description: sequencing run made in 2 lanes

value: cold, 8 C, 3 weeks


title: FTE472_2K | 002 | Full ROI

description: Library name: Sample 095

value: FTE472_2K | 001 | Full ROI


title: 49_A109_C24_4_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours + reoxygenation 12 hours

value: erythrocyte


title: FTE472_2K | 003 | Full ROI

description: Library name: Sample 096

value: epithelium


title: 45_A86_C6_4_single-end

description: sequencing run made in 2 lanes

value: juvenile


title: AKI_5

description: Library name: Sample 10


title: FTE472_2K | 001 | Full ROI

description: Library name: Sample 094


title: FTE471_4O | 005 | Full ROI

description: Library name: Sample 092

value: Normal fallopian tube epithelium


title: 44_A103_C1_5_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 1 hour


title: Ctrl_5

description: Library name: Sample 5

value: Sham surgery


title: FTE471_4O | 004 | Full ROI

description: Library name: Sample 091

value: fallopian tube

value: stroma

value: p53 signature

value: FTE471_4O | 003 | Full ROI


title: AKI_1

description: Library name: Sample 6

value: Kidney

value: Kidney IRI surgery


title: FTE471_4O | 006 | Full ROI

description: Library name: Sample 093

value: FTE471_4O | 005 | Full ROI


title: FTE471_4O | 002 | Full ROI

description: Library name: Sample 089

value: STIC

value: FTE471_4O | 001 | Full ROI


title: 43_A84_C1_4_single-end

description: sequencing run made in 2 lanes

value: cold, 8 C, 3 weeks


title: Ctrl_4

description: Library name: Sample 4


title: 42_A102_C0_5_single-end

description: sequencing run made in 2 lanes

value: control


title: FTE472_2K | 005 | Full ROI

description: Library name: Sample 098

value: STIL


title: FTE471_4O | 001 | Full ROI

description: Library name: Sample 088

value: epithelium


title: Ctrl_3

description: Library name: Sample 3


title: FTE470_1H | 006 | Full ROI

description: Library name: Sample 087

value: FTE470_1H | 005 | Full ROI


title: Ctrl_2

description: Library name: Sample 2


title: 41_A101_C0_4_single-end

description: sequencing run made in 2 lanes

value: erythrocyte

value: juvenile


title: FTE470_1H | 005 | Full ROI

description: Library name: Sample 086

value: Normal fallopian tube epithelium


title: FTE470_1H | 004 | Full ROI

description: Library name: Sample 085

value: fallopian tube

value: FTE470_1H | 003 | Full ROI


title: Ctrl_1

description: Library name: Sample 1

value: Sham surgery


title: 40_A90_C24_3_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours + reoxygenation 12 hours


title: FTE470_1H | 003 | Full ROI

description: Library name: Sample 084


title: 38_A85_C6_3_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 6 hours


title: FTE467_1S | 006 | Full ROI

description: Library name: Sample 079

value: stroma

value: FTE467_1S | 003 | Full ROI


title: FTE467_1S | 001 | Full ROI

description: Library name: Sample 074


title: FTE467_1S | 004 | Full ROI

description: Library name: Sample 077

value: FTE467_1S | 001 | Full ROI


title: FTE470_1H | 001 | Full ROI

description: Library name: Sample 082


title: colon, D21_AOM_48h_9

data_processing:
RNA-SEQ reads (30-60M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Assembly: mm10
Supplementary files format and content: excel table; log2 transformed and normalized abundance measurements by DESeq2

extract_protocol:
Total RNA was isolated using TRIzol™ Plus RNA Purification Kit (Thermo Fisher Scientific) from frozen colon tissue after pulverization in liquid nitrogen with mortar and pestle.
The integrity of the total RNA was determined using a Tapestation (Agilent) and concentration were assessed by Qubit (ThermoFisher Scientific).  Libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina, San Diego, CA) with Ribo-Zero technology. The indexed samples were sequenced on the Nova-seq 6000 (Illumina) employing a 75-bp single-end protocol

treatment_protocol: WT and NAPRT KO mice were supplemented with 3 g/L NA in the drinking water. Twenty-four hours later, they were i.p. injected with one dose of 10 mg/Kg AOM with a continuous supply of the NA water for the rest of the experiment. Colon tissues were then harvested at 12 or 48 hours after injection

value: colon

value: NAPRT KO

value: AOM 10 mg/kg


title: colon, D21_AOM_48h_8


title: FTE128_B8_rescan | 019 | Full ROI

description: Library name: Sample 043

value: mesothelium

value: Normal mesothelium


title: FTE470_1H | 002 | Full ROI

description: Library name: Sample 083

value: STIL

value: FTE470_1H | 001 | Full ROI


title: colon, WT2

description: 10x  Genomics

value: WT

value: NAM


title: FTE467_1S | 003 | Full ROI

description: Library name: Sample 076

value: fallopian tube

value: epithelium


title: 35_A20_C24_2_single-end

description: sequencing run made in 2 lanes

value: cold, 8 C, 3 weeks

value: erythrocyte

value: juvenile


title: FTE467_1S | 002 | Full ROI

description: Library name: Sample 075


title: 37_A8_C1_3_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 1 hour


title: FTE471_4O | 003 | Full ROI

description: Library name: Sample 090

value: p53 signature


title: colon, D21_AOM_48h_5


title: FTE467_1S | 008 | Full ROI

description: Library name: Sample 081

value: stroma

value: Normal fallopian tube epithelium

value: FTE467_1S | 007 | Full ROI


title: 34_A18_C24_1_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours + reoxygenation 12 hours


title: FTE467_1S | 007 | Full ROI

description: Library name: Sample 080


title: FTE128_B8_rescan | 018 | Full ROI

description: Library name: Sample 042

value: FTE128_B8_rescan | 019 | Full ROI


title: colon, D21_AOM_48h_7

value: colon

value: NAPRT KO

value: AOM 10 mg/kg


title: FTE467_1S | 005 | Full ROI

description: Library name: Sample 078

value: STIL

value: FTE467_1S | 002 | Full ROI


title: colon, D21_AOM_48h_4


title: 36_A4_C0_3_single-end

description: sequencing run made in 2 lanes

value: control


title: colon, D21_AOM_48h_6


title: 33_A15_C12_2_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours


title: FTE128_B8_rescan | 017 | Full ROI

description: Library name: Sample 041

value: fallopian tube

value: mesothelium

value: Normal mesothelium


title: FTE128_B8_rescan | 016 | Full ROI

description: Library name: Sample 040

value: FTE128_B8_rescan | 017 | Full ROI


title: 32_A14_C12_1_single-end

description: sequencing run made in 2 lanes

value: cold, 8 C, 3 weeks

value: erythrocyte

value: juvenile


title: colon, D21_AOM_48h_3


title: FTE128_B8_rescan | 015 | Full ROI

description: Library name: Sample 039


title: FTE128_B8_rescan | 014 | Full ROI

description: Library name: Sample 038

value: stroma

value: FTE128_B8_rescan | 013 | Full ROI


title: colon, D21_AOM_48h_2


title: FTE128_B8_rescan | 011 | Full ROI

description: Library name: Sample 035

value: epithelium

value: Normal fallopian tube epithelium


title: 31_A11_C6_2_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 6 hours


title: FTE128_B8_rescan | 010 | Full ROI

description: Library name: Sample 034

value: FTE128_B8_rescan | 009 | Full ROI


title: FTE128_B8_rescan | 013 | Full ROI

description: Library name: Sample 037


title: colon, WT_AOM_48h_8

value: colon

value: wild-type

value: AOM 10 mg/kg


title: 29_A7_C1_2_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 1 hour


title: 39_A16_C12_3_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours


title: FTE128_B8_rescan | 009 | Full ROI

description: Library name: Sample 033

value: fallopian tube


title: FTE128_B8_rescan | 008 | Full ROI

description: Library name: Sample 032


title: FTE128_B8_rescan | 005 | Full ROI

description: Library name: Sample 029

value: FTE128_B8_rescan | 004 | Full ROI


title: 27_A3_C0_2_single-end

description: sequencing run made in 2 lanes

value: control


title: colon, WT_AOM_48h_7


title: 28_A5_C1_1_single-end

description: sequencing run made in 2 lanes

value: cold, 8 C, 3 weeks


title: FTE128_B8_rescan | 004 | Full ROI

description: Library name: Sample 028


title: FTE128_B8_rescan | 007 | Full ROI

description: Library name: Sample 031


title: 26_A1_C0_1_single-end

description: sequencing run made in 2 lanes

value: erythrocyte


title: FTE128_B8_rescan | 006 | Full ROI

description: Library name: Sample 030

value: FTE128_B8_rescan | 007 | Full ROI


title: FTE128_B8_rescan | 003 | Full ROI

description: Library name: Sample 027


title: colon, WT_AOM_48h_5


title: FTE128_B8_rescan | 002 | Full ROI

description: Library name: Sample 026

value: stroma

value: STIL

value: FTE128_B8_rescan | 001 | Full ROI


title: colon, WT_AOM_48h_6


title: colon, WT_AOM_48h_4


title: FTE128_B8_rescan | 001 | Full ROI

description: Library name: Sample 025

value: epithelium


title: 25_A120_W24_5_single-end

description: sequencing run made in 2 lanes

value: warm, 15 C, 3 weeks

value: hypoxia, 12 hours + reoxygenation 12 hours

value: juvenile


title: FTE128_B8_rescan | 012 | Full ROI

description: Library name: Sample 036

value: Normal fallopian tube epithelium

value: FTE128_B8_rescan | 011 | Full ROI


title: HAE1-evolution2-A2

data_processing:
The adapter and low-quality sequence were trimmed using cutadapt
The MIXCR tool was used to remove PCR duplicates and retain biological duplicates, thereby reducing the background of PCR-induced mutations.
The assembled antibody sequences from MIXCR output files were converted to FASTQ files and subsequently analyzed using CRISPResso (version 2.2.14)
Assembly: Antibody (CV07-209) VH gene used in this study
Supplementary files format and content: tsv files including the assembled and deduplicated antibody sequences
Library strategy: Antibody-sequencing

extract_protocol:
Cells were harvested to extract genomic DNA after transfection or each round of FACS enrichment.
DNA libraries from 293F#209 cells were prepared using an additional linear random barcoded primer extension step with 1-2 μg genomic DNA before the conventional amplicon PCR procedure. This process yielded ~570 bp DNA products, which were gel-purified, quantified by DeNovix, and sequenced by PE300 on NextSeq 2000 platform (GENEWIZ)

value: Human embryonic kidney

value: CV07-209 knockin at AAVS1


title: colon, WT_AOM_48h_3

value: colon

value: wild-type

value: AOM 10 mg/kg


title: colon, WT_AOM_48h_2


title: 170_wt24hcutHigh, WT tailcut 24hpi irg1KI:GFP activated, 300 cells

city: Chapel Hill

first: Celia

middle: E

last: Shiau

state: NC

address: 2159 Genome Sciences Building

institute: UNC Chapel Hill

description:
Library name: Sample 18: 170_wt24hcutHigh
2x50 base pairs

data_processing:
iTerm2 Build 3.4.14
Sequence reads were trimmed using Trimmomatic and quality control checks were performed using MultiQC.
Sequences post trimming and that passed quality control check were aligned to the most up to date zebrafish reference genome using BBMap.
Subsequent counts based on alignment to the zebrafish genome were obtained using Featurecounts.
Raw counts were normalized and differential expression analysis was performed using DESeq2.
Assembly: GRCz11
Supplementary files format and content: Two tab-delimited text files for each dataset, each includes raw counts for each sample.
Supplementary files format and content: Two xlsx files for each dataset, each include differential gene expression for each sample.

organism: Danio rerio

source_name: whole embryo 3dpf

extract_protocol:
RNA was isolated using the RNAqueous-Micro kit RNA Isolation Procedure (Ambion). Whole larvae were lysed in 100–300 uL RNA lysis buffer.
Library preparation was done using the SMARTr HT+ Nextera XT for low input samples.

treatment_protocol: N/A for Samples 1-12. Samples 13-19: Embryo tails were amputated at 2 dpf and tissues collected for RNA extraction at 24 hours post amputation; samples 13-15 were staged-matched siblings embryos that were not injured, called "uncut".

value: whole embryo 3dpf

value: macrophages

value: WT

value: tail amputation


title: 23_A116_W6_5_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 6 hours

value: erythrocyte


title: HAE1-evolution2-A1


title: 24_A118_W12_5_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours


title: 178_wt24hcutHigh, WT tailcut 24hpi irg1KI:GFP activated, 1.65k cells

description:
Library name: Sample 19: 178_wt24hcutHigh
2x50 base pairs


title: HAE1-evolution1-A3


title: 22_A114_W1_5_single-end

description: sequencing run made in 2 lanes

value: warm, 15 C, 3 weeks

value: hypoxia, 1 hour


title: HAE1-evolution1-A2


title: 21_A113_W1_4_single-end

description: sequencing run made in 2 lanes

value: juvenile


title: 177_wt24hcutBase, WT tailcut 24hpi irg1KI:GFP baseline, 25 embryos, 2k cells

description:
Library name: Sample 17: 177_wt24hcutBase
2x50 base pairs


title: colon, D21_AOM_12h_8

value: NAPRT KO


title: colon, WT_AOM_48h_1


title: HAE1-evolution1-A1


title: 20_A111_W0_5_single-end

description: sequencing run made in 2 lanes

value: control


title: colon, D21_AOM_12h_7


title: 176_wt24huncPOS, WT uncut irg1KI:GFP positive, 960 cells

description:
Library name: Sample 15: 176_wt24huncPOS
2x50 base pairs


title: colon, D21_AOM_48h_1


title: 19_A99_W24_4_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours + reoxygenation 12 hours


title: colon, D21_AOM_12h_6


title: 168_wt24huncPOS, WT uncut irg1KI:GFP positive, 1.5k cells

description:
Library name: Sample 13: 168_wt24huncPOS
2x50 base pairs


title: colon, D21_AOM_12h_5


title: NC-VH-rep1

value: Human embryonic kidney

value: CV07-209 knockin at AAVS1


title: 17_A97_W12_4_single-end

description: sequencing run made in 2 lanes


title: 88_73MH, st73 mut "high peak" irg1-KI:GFP positive, 54 embryos, 2k cells

description:
Library name: Sample 12: 88_73MH
2x50 base pairs


title: AIDmono-VH-rep3


title: colon, D21_AOM_12h_4

value: colon


title: 16_A36_W12_3_single-end

description: sequencing run made in 2 lanes


title: 84_73MH, st73 mut "high peak" irg1-KI:GFP positive, 48 embryos, 3k cells

description:
Library name: Sample 11: 84_73MH
2x50 base pairs


title: 30_A9_C6_1_single-end

description: sequencing run made in 2 lanes

value: cold, 8 C, 3 weeks


title: colon, D21_AOM_12h_3

value: AOM 10 mg/kg


title: 169_wt24hcutBase, WT tailcut 24hpi irg1KI:GFP baseline, 29 embryos, 4.6k cells

description:
Library name: Sample 16: 169_wt24hcutBase
2x50 base pairs

value: whole embryo 3dpf

value: macrophages


title: AIDmono-VH-rep2


title: 15_A96_W6_4_single-end

description: sequencing run made in 2 lanes


title: AIDmono-VH-rep1


title: 14_A95_W6_3_single-end

description: sequencing run made in 2 lanes


title: 172_wt24huncPOS, WT uncut irg1KI:GFP positive, 519 cells

description:
Library name: Sample 14: 168_wt24huncPOS
2x50 base pairs

value: WT


title: colon, D21_AOM_12h_2


title: 13_A94_W1_3_single-end

description: sequencing run made in 2 lanes


title: 83_73ML, st73 mut "low peak" irg1-KI:GFP positive, 48 embryos, 3.2k cells

description:
Library name: Sample 8: 83_73ML
2x50 base pairs


title: 50_73MH, st73 mut "high peak" irg1-KI:GFP positive, 33 embryos, 1.26k cells

description:
Library name: Sample 10: 50_73MH
2x50 base pairs


title: NC-VH-rep3


title: colon, WT_AOM_12h_8

value: wild-type


title: NC-VH-rep2


title: colon, D21_AOM_12h_1


title: 18_A40_W24_3_single-end

description: sequencing run made in 2 lanes

value: erythrocyte


title: HAE1-VH-rep2


title: 12_A92_W0_4_single-end

description: sequencing run made in 2 lanes


title: 49_73ML, st73 mut "low peak" irg1-KI:GFP positive, 33 embryos, 1.16k cells

description:
Library name: Sample 7: 49_73ML
2x50 base pairs


title: colon, WT_AOM_12h_7


title: 85_73SPOS, st73 sibs irg1-KI:GFP positive, 54 embryos, 2.4k cells

description:
Library name: Sample 6: 85_73SPOS
2x50 base pairs

value: nlrc3l+/+; nlrc3l+/-


title: HAE1-VH-rep1


title: 11_A91_W0_3_single-end

description: sequencing run made in 2 lanes

value: warm, 15 C, 3 weeks


title: 81_73SPOS, st73 sibs irg1-KI:GFP positive, 48 embryos, 3.8k cells

description:
Library name: Sample 5: 81_73SPOS
2x50 base pairs


title: colon, WT_AOM_12h_5


title: EVadMu-3

city: Xi'an

first: Qi

last: Liu

address: No.127, Changle West Road

institute: Air Force Medical University

description:
Library name: 6
adMu_EV3

data_processing:
Base-calling: CASAVA (Illumina Casava 1.8) Data filtering:  Custom filter (remove adapter/N-containing/low-quality reads) Read Alignment: HISAT2 Bam sort: SAMtools Read count: FeatureCounts
Assembly: mm39
Supplementary files format and content: Processed data files.xlsx

organism: Rattus norvegicus

source_name: Primary DRG neurons

extract_protocol:
Total RNA was extracted from primary dorsal root ganglion (DRG) neurons using TRIzol® Reagent according to the manufacturer’s instructions with minor modifications.
Poly(A)+ mRNA was enriched from total RNA using Oligo(dT) magnetic beads, then randomly fragmented. First-strand cDNA was synthesized with random hexamer primers, followed by second-strand cDNA synthesis. The resulting cDNA underwent end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification to generate the final sequencing library.

value: Primary DRG neurons


title: colon, WT_AOM_12h_6


title: 87_73ML, st73 mut "low peak" irg1-KI:GFP positive, 54 embryos, 2.6k cells

description:
Library name: Sample 9: 87_73ML
2x50 base pairs


title: EVadMu-2

description:
Library name: 5
adMu_EV2


title: 9_A38_W24_1_single-end

description: sequencing run made in 2 lanes

value: juvenile


title: HAE1-VH-rep3


title: 48_73SPOS, st73 sibs irg1-KI:GFP positive, 33 embryos, 2.5k cells

description:
Library name: Sample 4: 48_73SPOS
2x50 base pairs


title: 10_A39_W24_2_single-end

description: sequencing run made in 2 lanes


title: 86_73SNEG, st73 sibs irg1-KI:GFP negative, 54 embryos, 50k cells

description:
Library name: Sample 3: 86_73SNEG
2x50 base pairs


title: 8_A35_W12_2_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 12 hours


title: colon, WT_AOM_12h_3


title: 7_A34_W12_1_single-end

description: sequencing run made in 2 lanes


title: EVMu-3

description:
Library name: 3
Mu_EV3


title: EVadMu-1

description:
Library name: 4
adMu_EV1


title: colon, WT_AOM_12h_4


title: 82_73SNEG, st73 sibs irg1-KI:GFP negative, 48 embryos, 54k cells

description:
Library name: Sample 2: 82_73SNEG
2x50 base pairs


title: colon, WT_AOM_12h_1


title: 5_A31_W6_1_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 6 hours


title: 6_A32_W6_2_single-end

description: sequencing run made in 2 lanes


title: EVMu-1

description:
Library name: 1
Mu_EV1


title: EVMu-2

description:
Library name: 2
Mu_EV2


title: 47_73SNEG, st73 sibs irg1-KI:GFP negative, 33 embryos, 50k cells

description:
Library name: Sample 1: 47_73SNEG
2x50 base pairs


title: AECs, H3N2, R1R2, 3

city: Boston

first: Yuncheng

last: Man

state: MA

address: 201 Brookline Ave

institute: Wyss Institute, Harvard University

data_processing:
The paired reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b, and unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: GRCh38 (NCBI, p.14, release 110)
Supplementary files format and content: raw counts

source_name: Human Alveolar Epithelial Cells

extract_protocol:
Total RNA was extracted using Qiagen Micro Plus kit and sent to Genewiz
Genewiz prepared the libraries for standard bulk RNA-seq

value: Human Alveolar Epithelial Cells


title: Chimonocalamus delicatus, Bamboo rhizomes, replicate 3

city: kunming

first: Jiangbonan

last: jiang

state: Yunnan

address: panlongqu

institute: Southwest Forestry University

description:
Library name: B3
Different parts of the plant

data_processing:
Phyllostachys edulis
The resulting cDNA library was sequenced using IlluminaNovaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China)
An index of the reference genome was built, and paired-end clean reads were mapped to thereference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1in areference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: PRJEB2955
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Chimonocalamus delicatus

source_name: Bamboo rhizomes

extract_protocol:
Aroma gene analysis of Chimonocalamus delicatus at different stem ages and in different parts
mRNA was collected from Chimonocalamus delicatus samples from different parts of different stem ages.

value: Bamboo rhizomes

value: Bamboo rhizomes quality


title: AKI_4

description: Library name: Sample 9

value: Kidney

value: Kidney IRI surgery


title: colon, WT_AOM_12h_2

value: colon

value: AOM 10 mg/kg


title: colon, D21_Ctrl_6

value: NAPRT KO


title: 4_A26_W1_2_single-end

description: sequencing run made in 2 lanes

value: hypoxia, 1 hour


title: AECs, H3N2, R1R2, 2


title: colon, D21_Ctrl_7


title: 2_A23_W0_2_single-end

description: sequencing run made in 2 lanes

value: control


title: colon, D21_Ctrl_5


title: Chimonocalamus delicatus, Bamboo stems, replicate 3

description:
Library name: G3
Different parts of the plant

source_name: Bamboo stems

value: Bamboo stems

value: Bamboo stems quality


title: Chimonocalamus delicatus, Bamboo rhizomes, replicate 1

description:
Library name: B1
Different parts of the plant


title: colon, D21_Ctrl_4


title: AECs, H3N2, R1R2, 1


title: AECs, H3N2, Scramble, 3

value: H3N2, Scramble


title: AECs, H3N2, Scramble, 4


title: 1_A21_W0_1_single-end

description: sequencing run made in 2 lanes

value: warm, 15 C, 3 weeks

value: erythrocyte


title: Chimonocalamus delicatus, Bamboo stems, replicate 2

description:
Library name: G2
Different parts of the plant


title: colon, D21_Ctrl_3


title: Chimonocalamus delicatus, Bamboo stems, replicate 1

description:
Library name: G1
Different parts of the plant


title: colon, D21_Ctrl_2


title: A96_W6_4_paired-end

value: juvenile


title: AECs, H3N2, Scramble, 1


title: AECs, H3N2, R1R2, 4


title: 3_A25_W1_1_single-end

description: sequencing run made in 2 lanes


title: colon, D21_Ctrl_1


title: colon, WT_Ctrl_6

value: wild-type


title: colon, D21_Ctrl_8


title: A95_W6_3_paired-end

value: hypoxia, 6 hours


title: AECs, H3N2, Scramble, 2

value: Human Alveolar Epithelial Cells


title: colon, WT_Ctrl_5


title: A120_W24_5_paired-end

value: hypoxia, 12 hours + reoxygenation 12 hours


title: Chimonocalamus delicatus, Bamboo branches, replicate 3

description:
Library name: Z3
Different parts of the plant

source_name: Bamboo branches

value: Bamboo branches

value: Bamboo branches quality


title: Chimonocalamus delicatus, Bamboo rhizomes, replicate 2

description:
Library name: B2
Different parts of the plant

value: Bamboo rhizomes

value: Bamboo rhizomes quality


title: A116_W6_5_paired-end


title: A36_W12_3_paired-end

value: hypoxia, 12 hours


title: colon, WT_Ctrl_7

value: colon


title: AECs, H3N2, Vehicle, 1

value: H3N2, Vehicle


title: Chimonocalamus delicatus, Bamboo branches, replicate 1

description:
Library name: Z1
Different parts of the plant


title: Chimonocalamus delicatus, Bamboo leaves, replicate 1

description:
Library name: Y1
Different parts of the plant

source_name: Bamboo leaves

value: Bamboo leaves

value: Bamboo leaves quality


title: A38_W24_1_paired-end


title: AECs, H3N2, Vehicle, 3


title: colon, WT_Ctrl_4


title: AECs, H3N2, Vehicle, 4


title: A35_W12_2_paired-end


title: Chimonocalamus delicatus, Bamboo leaves, replicate 3

description:
Library name: Y3
Different parts of the plant


title: Chimonocalamus delicatus, Bamboo branches, replicate 2

description:
Library name: Z2
Different parts of the plant


title: AECs, H3N2, Vehicle, 2


title: colon, WT_Ctrl_3


title: Chimonocalamus delicatus, Bamboo leaves, replicate 2

description:
Library name: Y2
Different parts of the plant


title: AECs, Mock, Vehicle, 4

value: Mock, Vehicle


title: colon, WT_Ctrl_2


title: Chimonocalamus delicatus, Three years old bamboo stem, replicate 2

description:
Library name: san2
growth stage

source_name: Three years old bamboo stem

value: Three years old bamboo stem

value: Three years old bamboo stem quality


title: A94_W1_3_paired-end

value: warm, 15 C, 3 weeks

value: hypoxia, 1 hour

value: erythrocyte

value: juvenile


title: AECs, Mock, Vehicle, 3

value: Human Alveolar Epithelial Cells


title: A39_W24_2_paired-end

value: hypoxia, 12 hours + reoxygenation 12 hours


title: A34_W12_1_paired-end


title: AECs, Mock, Vehicle, 1


title: colon, WT-4

treatment_protocol: Eight to twelve-week-old WT or NAPRT KO female mice were treated with or without 2.5% DSS in drinking water together with 3 g/L nicotinamide (NAM) for 7 days.

value: WT

value: control


title: Chimonocalamus delicatus, Two years old bamboo stem, replicate 3

description:
Library name: er3
growth stage

source_name: Two years old bamboo stem

value: Two years old bamboo stem

value: Two years old bamboo stem quality


title: AECs, Mock, Vehicle, 2


title: colon, WT_Ctrl_1

value: colon

value: wild-type


title: colon, WT-3


title: Chimonocalamus delicatus, Three years old bamboo stem, replicate 1

description:
Library name: san1
growth stage


title: A113_W1_4_paired-end


title: Rat facial nerve tissue following injury  Model3

city: Chengdu

first: Guihua

last: Wei

address: No.111, North 1st Section, 2nd Ring Rd

institute: Southwest Jiaotong University

description: Library name: LIB-B3

data_processing:
Raw paired-end reads were quality-checked using FastQC (v0.11.9). Adapters and low-quality bases were trimmed using fastp (v0.22.0) with a minimum read length of 75 bp after trimming. Cleaned reads were aligned to the reference genome using STAR (v2.4.2a). Gene expression levels were quantified using RSEM (v1.2.29). Differential expression analysis between groups was performed using edgeR (v3.28.1) with a threshold of |FC|>=2 and adjusted p-value (padj) < 0.05
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPkM walues for each sample

source_name: facial nerve tissue

extract_protocol:
Total RNA was extracted from samples using TRIzol reagent. RNA concentration was measured using NanoDrop. The integrity of RNA was assessed by agarose gel electrophoresis.
Sequencing libraries were constructed following the standard Illumina protocol. Briefly, mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, and reverse-transcribed into double-stranded cDNA. After end repair, A-tailing, and adapter ligation, the cDNA fragments were PCR-amplified. Final library quality and size distribution were validated using Qubit and an Agilent Fragment Analyzer.

value: facial nerve tissue

value: primary nerve tissue

value: wild type

value: facial nerve injury (FNI) model

value: batch 6


title: Chimonocalamus delicatus, Two years old bamboo stem, replicate 2

description:
Library name: er2
growth stage


title: Chimonocalamus delicatus, Three years old bamboo stem, replicate 3

description:
Library name: san3
growth stage

value: Three years old bamboo stem

value: Three years old bamboo stem quality


title: colon, WT-2


title: Chimonocalamus delicatus, Two years old bamboo stem, replicate 1

description:
Library name: er1
growth stage


title: A91_W0_3_paired-end

value: warm, 15 C, 3 weeks

value: erythrocyte


title: Chimonocalamus delicatus, One year old bamboo stem, replicate 3

description:
Library name: yi3
growth stage

source_name: One year old bamboo stem

value: One year old bamboo stem

value: One year old bamboo stem quality


title: A92_W0_4_paired-end

value: juvenile


title: A111_W0_5_paired-end

value: control


title: colon, KO-4

value: NAPRT KO


title: A25_W1_1_paired-end

value: hypoxia, 1 hour


title: A9_C6_1_paired-end

value: cold, 8 C, 3 weeks

value: hypoxia, 6 hours


title: Chimonocalamus delicatus, One year old bamboo stem, replicate 1

description:
Library name: yi1
growth stage


title: Chimonocalamus delicatus, One year old bamboo stem, replicate 2

description:
Library name: yi2
growth stage


title: Rat facial nerve tissue following injury and C-Gel-light treatment 2

description: Library name: LIB-A2

value: facial nerve tissue

value: C-Gel-light treatment post-FNI

value: batch 2


title: colon, KO-3

value: colon


title: A85_C6_3_paired-end


title: Rat facial nerve tissue following injury  Model2

description: Library name: LIB-B2

value: primary nerve tissue

value: wild type

value: facial nerve injury (FNI) model

value: batch 5


title: Rat facial nerve tissue following injury and C-Gel-light treatment 1

description: Library name: LIB-A1

value: batch 1


title: colon, WT-1

value: WT


title: Chimonocalamus delicatus, Half a year bamboo stem, replicate 3

description:
Library name: ban3
growth stage

source_name: Half a year bamboo stem

value: Half a year bamboo stem

value: Half a year bamboo stem quality


title: A11_C6_2_paired-end

value: erythrocyte

value: juvenile


title: colon, KO-1

source_name: colon

value: NAPRT KO

value: control


title: Rat facial nerve tissue following injury  Model1

description: Library name: LIB-B1

value: batch 4


title: Chimonocalamus delicatus, Half a year bamboo stem, replicate 2

description:
Library name: ban2
growth stage


title: colon, KONAM-8

value: 2.5% DSS+ 3g/l NAM


title: colon, KO-2


title: Rat facial nerve tissue following injury and C-Gel-light treatment 3

description: Library name: LIB-A3

value: facial nerve tissue

value: C-Gel-light treatment post-FNI

value: batch 3


title: Chimonocalamus delicatus, Half a year bamboo stem, replicate 1

description:
Library name: ban1
growth stage


title: retinal organoid, RDH12_AR_3

city: LONDON

first: Mariya

last: Moosajee

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: AR_D1_01_03

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (version 3.4) before alignment.
Reads were mapped and subsequent gene-level counted using RSEM 1.3.1 and STAR 2.7.10a against the human genome GRCh38 using annotation release 95, both from Ensembl.
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.38.3) within the R programming environment (version 4.2.2).
Assembly: GRCh38
Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.

source_name: Organoid

extract_protocol:
RNA was isolated, quantified and cDNA generated from 2 pooled organoids at day 303 week 44 (Qiagen, UK).
cDNA libraries were sequenced on a HiSeq 2500 with paired-end reads of 150 bp using Illumina Stranded Total RNA with Ribo-Zero Plus (Illumina, UK)

value: Organoid


title: A18_C24_1_paired-end

value: cold, 8 C, 3 weeks

value: hypoxia, 12 hours + reoxygenation 12 hours


title: Chimonocalamus delicatus, Bamboo shoot, replicate 3

description:
Library name: ck3
growth stage

source_name: Bamboo shoot

value: Bamboo shoot

value: Bamboo shoot quality


title: retinal organoid, RDH12_AR_4

description: Library name: AR_D1_02_01


title: retinal organoid, RDH12_AR_1

description: Library name: AR_D1_01_01


title: Chimonocalamus delicatus, Bamboo shoot, replicate 2

description:
Library name: ck2
growth stage


title: retinal organoid, RDH12_AR_2

description: Library name: AR_D1_01_02


title: colon, KONAM-7

value: colon


title: A16_C12_3_paired-end

source_name: blood

value: hypoxia, 12 hours


title: Chimonocalamus delicatus, Bamboo shoot, replicate 1

description:
Library name: ck1
growth stage


title: A109_C24_4_paired-end


title: A20_C24_2_paired-end


title: A14_C12_1_paired-end


title: A88_C12_4_paired-end


title: retinal organoid, RDH12_AD_9

description: Library name: AD_A2_01_03


title: A84_C1_4_paired-end

value: hypoxia, 1 hour


title: retinal organoid, RDH12_AD_12

description: Library name: AD_A2_02_03


title: LOW2

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: Library name: LOW2

data_processing:
Reads were trimmed with Trim Galore, aligned with BWA-MEM (release 0.7.17-r1188), to the human genome (GRCh38 primary assembly).
Mus musculus (GRCm39) and Bos taurus (GCF_002263795.3) genomes were used for sequential disambiguation to remove potential contaminant reads from FBS and host DNA of the in-vivo experiment.
Bam files were filtered for mitochondrial, Y chromosome and PCR duplicated reads with Picard (2.25.0-0). Blacklisted regions were filtered using as reference ENCODE blacklist  (hg38 v2). Soft-clipped reads were filtered out with gatk when the ratio of clipped over the total bases exceeded 0.25.  Finally, only properly paired reads, with non-secondary alignment and mapping quality of at least 15 and length > 45 bp were retained.
To quantify open chromatin regions, bedtools multibamcov (with parameters -q 10) was used against the Rank6 signatures regions unique of old and young conditions, generated from the previous experiment.
Differential accessibility was computed with DESeq2, filtering regions with less then 10 counts, and testing for the contrast High vs Low dose (FDR 0.05).
The analysis of known motif enriched in DARs was conducted with Homer software115 (parameters -size 200 -mask)
Assembly: GRCh38 primary assembly
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

source_name: Bone marrow

extract_protocol:
Purify transposed DNA using a QUIAGEN MinElute Reaction Cleanup kit (28204)
customized Nextera PCR primer mix 1/2

value: Bone marrow

value: hematopoietic stem and progenitor cells

value: WT

value: in vivo after cell culture over night


title: colon, WTNAM-7


title: A5_C1_1_paired-end

value: erythrocyte

value: juvenile


title: retinal organoid, RDH12_AD_11

description: Library name: AD_A2_02_02


title: colon, WTNAM-6

value: 2.5% DSS+ 3g/l NAM


title: colon, KONAM-4

value: NAPRT KO


title: colon, WTNAM-5


title: colon, WTNAM-8


title: LOW3

description: Library name: LOW3


title: HIGH2

description: Library name: HIGH2


title: retinal organoid, RDH12_AD_10

description: Library name: AD_A2_02_01


title: colon, KONAM-6


title: retinal organoid, RDH12_AD_5

description: Library name: AD_A1_02_02


title: A102_C0_5_paired-end

value: control


title: colon, WTNAM-3


title: colon, KONAM-5


title: LOW1

description: Library name: LOW1


title: A1_C0_1_paired-end


title: HIGH3

description: Library name: HIGH3


title: retinal organoid, RDH12_AD_4

description: Library name: AD_A1_02_01

value: Organoid


title: retinal organoid, RDH12_AD_3

description: Library name: AD_A1_01_03


title: retinal organoid, RDH12_AD_8

description: Library name: AD_A2_01_02


title: colon, WTNAM-1


title: ON_Young1C

data_processing:
Reads wuality control checked with FASTQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters -s 2 --minOverlap 10)
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

extract_protocol:
miRNeasy Mini Kit (QIAGEN)
Ultra-low input RNA Seq directly

value: Primary HSPCs patient sample

value: cell culture over night


title: colon, KONAM-3


title: A103_C1_5_paired-end

value: cold, 8 C, 3 weeks


title: retinal organoid, RDH12_AD_7

description: Library name: AD_A2_01_01


title: wild type (VC2010) 1st biological replicate

city: St Louis

first: Hieu

last: Hoang

state: MO

address: 660 South Euclid Avenue, 4th floor entry 1

department: Pediatrics

institute: Washington University in St Louis

description:
Library name: VC2010-1
wild-type mRNA seq 1st replicate

data_processing:
Demultiplexing with Illumina BCLconvert
Fastq files were combined and aligned with STAR 2.7.11b
Gene counts quantitated with Subread:featureCount 2.0.8 with CPM and RPKM transformations added with custom Rscripting.
Isoform counts quantitated with Salmon 1.10.0
Assembly: Ensembl WBcel235.108
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

organism: Caenorhabditis elegans

source_name: Whole worms mixed stages, mostly adults

growth_protocol: C. elegans mix staged mostly adults grown in Nematode Growth Medium plates at 20oC

extract_protocol: Trizol chroloform extraction with isopropanol precipitation and ethanol wash

value: Whole worms mixed stages, mostly adults

value: all cell types from whole worms

value: wild type (VC2010)


title: ON_Young1B


title: cmd-1(E141G) 3rd biological replicate

description:
Library name: udn96-3
cmd-1(E141G) mRNA seq 3rd replicate


title: cmd-1(E141G) 2nd biological replicate

description:
Library name: udn96-2
cmd-1(E141G) mRNA seq 2nd replicate


title: retinal organoid, WT_7

description: Library name: WT_35_05_02