title: WTCHG_306606_247

value: U/ml

value: IU/ml

value: Yes

value: Current Smoker

value: Asian or Asian British - Any other Asian background

value: Oral

value: Twice daily

value: Weekly

value: Intramuscular

value: SDAI Class 2

value: Hand-rolled tobacco

value: Completed


title: WTCHG_306606_249

status: Public on May 12 2021

type: SRA

city: London

first: Michael

middle: R

last: Barnes

address: William Harvey Research Institute, Charterhouse Square

country: United Kingdom

institute: QMUL

library_source: transcriptomic

data_processing:
Adaptors were clipped off the reads using Trimmomatic version 0.33
Reads were aligned to the GRCh38 genome using Bowtie version 2.3.0
Alignments to miRNAs were counted with the htseq-count function from HTSeq version 0.6.1p2 and the miRBase annotation release 21.
Genome_build: GRCh38
Supplementary_files_format_and_content: Alignments to miRNAs were counted with the htseq-count function from HTSeq version 0.6.1p2 (Anders, 2014) and the miRBase annotation release 21.

molecule: total RNA

organism: Homo sapiens

source_name: BASELINE

extract_protocol:
Cell subset RNA was extracted using miRNeasy minikits (Qiagen) following the manufacturer’s protocol. Whole blood RNA was extracted from Tempus Blood tubes using MagMAX RNA isolation kits (Ambion) and then was subjected to removal of globin mRNA using GLOBINclear human 20 reaction kits (Ambion) following the manufacturer’s protocol.
Prepared using the NEBNext small RNA library prep set for Illumina

tag: cell type

value: RNA-Tempus

tag: matchingarrayid

tag: patientid

value: U/mL

value: No

value: Previous Smoker

value: White- British

value: DAS28CRP Class 3

value: Female

value: Cigarrette


title: WTCHG_306606_248

value: u/ml

value: iu/ml

value: Yes

value: Black or Black British - Caribbean

value: U/ml


title: WTCHG_306606_246

value: Kunits/L

value: Oral

value: IU/ml

value: Never Smoked

value: Weekly

value: Asian or Asian British - Indian

value: Once daily

value: DAS28CRP Class 1

value: SDAI Class 1

value: Ku/L


title: WTCHG_306606_243

value: RNA-Tempus

value: U/ML

value: No

value: IU/ML

value: White- British

value: 5 days/week

value: DAS28CRP Class 2

value: Female

value: Completed

value: 1-2 days a month


title: WTCHG_306606_244

value: Oral

value: Yes

value: Never Smoked

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: U/ml

value: 3 - 4 days a week


title: WTCHG_306606_242

value: RNA-Tempus

value: U/mL

value: IU/mL

value: Previous Smoker

value: 3 days/week

value: Weekly

value: Twice daily

value: DAS28CRP Class 1

value: Cigarrette

value: Enrolled

value: 1-2 days a week


title: WTCHG_306606_241

value: Oral

value: No

value: Yes

value: Never Smoked

value: IU/ml

value: Other ethnic groups - Any other ethnic group

value: Intramuscular

value: Subcutaneous

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Completed


title: WTCHG_306606_240

value: RNA-Tempus

value: U/mL

value: lU/mL

value: Weekly

value: Black or Black British - African

value: Twice daily

value: SDAI Class 3


title: WTCHG_306606_239

value: U/ml

value: Oral

value: No

value: Current Smoker

value: Yes

value: White- British

value: 6 days/week

value: DAS28CRP Class 3

value: Cigarrette

value: 1-2 days a year


title: WTCHG_306606_257

value: RNA-Tempus

value: u/ml

value: IU/ml

value: 3 days/week

value: DAS28CRP Class 1

value: SDAI Class 2

value: Female

value: Completed


title: WTCHG_306606_236

value: U/mL

value: Oral

value: Previous Smoker

value: Once daily

value: kU/L

value: Weekly

value: DAS28CRP Class 2

value: SDAI Class 1

value: 1-2 days a week


title: WTCHG_306606_233

value: RNA-Tempus

value: No

value: iu/ml

value: Yes

value: White- British

value: DAS28CRP Class 3

value: Male

value: Cigarrette


title: WTCHG_306606_234

value: U/ml

value: IU/ml

value: Current Smoker

value: Twice daily

value: Intramuscular

value: SDAI Class 2

value: Female

value: U/ML

value: Completed


title: WTCHG_306606_231

value: RNA-Tempus

value: kunit/L

value: Oral

value: IU/ML

value: Weekly

value: White - any other White background

value: DAS28CRP Class 2

value: SDAI Class 1

value: Kunits/l

value: 1-2 days a year


title: WTCHG_306606_232

value: eu/ml

value: No

value: IU/ml

value: Yes

value: Previous Smoker

value: White- British

value: Once daily

value: DAS28CRP Class 1

value: Male

value: Cigarrette

value: iu/ml


title: WTCHG_306606_238

value: RNA-Tempus

value: U/ml

value: Oral

value: 3 days/week

value: Weekly

value: Cigar

value: Completed

value: 1-2 days a week


title: WTCHG_306606_230

value: No

value: Never Smoked

value: Intramuscular

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female


title: WTCHG_306606_235

value: IU/ml

value: Yes

value: Previous Smoker

value: White- British

value: 5 days/week

value: DAS28CRP Class 1

value: Male

value: 5 or more days a week


title: WTCHG_306606_228

value: RNA-Tempus

value: U/ml

value: Oral

value: iu/mL

value: Weekly

value: Once daily

value: DAS28CRP Class 2

value: SDAI Class 1


title: WTCHG_306606_237

value: U/mL

value: No

value: kU/L

value: SDAI Class 2

value: Female

value: Hand-rolled tobacco

value: Completed

value: 1-2 days a year


title: WTCHG_306606_224

value: u/mL

value: Yes

value: Current Smoker

value: White- British

value: DAS28CRP Class 1

value: Cigarrette

value: u/ml


title: WTCHG_306606_226

value: RNA-Tempus

value: iu/ml

value: Weekly

value: Oral

value: Black or Black British - Caribbean

value: Once daily

value: DAS28CRP Class 2

value: 3 - 4 days a week


title: WTCHG_306606_229

value: U/mL

value: No

value: Previous Smoker

value: IU/ml

value: SDAI Class 1

value: Female

value: Completed


title: WTCHG_306606_221

value: U/ml

value: Yes

value: Never Smoked

value: White- British

value: 6 days/week

value: U/ML

value: Lost to follow-up

value: 1-2 days a year


title: WTCHG_306606_223

value: RNA-Tempus

value: u/ml

value: Oral

value: Black or Black British - Caribbean

value: Weekly

value: Subcutaneous

value: DAS28CRP Class 1

value: SDAI Class 3

value: Withdrawn -lost to follow up

value: Intramuscular


title: WTCHG_306606_220

value: U/ml

value: No

value: IU/ml

value: Yes

value: Previous Smoker

value: Twice daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Cigarrette

value: Completed

value: 3 - 4 days a week


title: WTCHG_306606_222

value: RNA-Tempus

value: u/ml

value: Oral

value: Weekly

value: Asian or Asian British - Bangladeshi

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: 2 days/week


title: WTCHG_306606_218

value: No

value: KU/L

value: Yes

value: Previous Smoker

value: 3 days/week

value: White- British

value: Once daily

value: Hand-rolled tobacco

value: 1-2 days a week


title: WTCHG_306606_214

value: RNA-Tempus

value: IU/ml

value: Female

value: Cigarrette

value: U/ml

value: Withdrawn -lost to follow up

value: 1-2 days a year


title: WTCHG_306606_217

value: u/ml

value: Oral

value: iu/ml

value: Never Smoked

value: Weekly

value: Asian or Asian British - Indian

value: Twice daily

value: Intramuscular

value: DAS28CRP Class 3

value: SDAI Class 2

value: Completed


title: WTCHG_306606_212

value: RNA-Tempus

value: kunits/L

value: No

value: IU/ML

value: Yes

value: Previous Smoker

value: 5 days/week

value: White- British

value: Once daily

value: DAS28CRP Class 1

value: SDAI Class 3


title: WTCHG_306606_215

value: U/ml

value: Oral

value: Weekly

value: IU/ml

value: Male

value: Cigarrette

value: 1-2 days a month


title: WTCHG_306606_211

value: RNA-Tempus

value: kU/L

value: Never Smoked

value: Asian or Asian British - Indian

value: Twice daily

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female

value: Completed


title: WTCHG_306606_216

value: U/ML

value: No

value: KU/L

value: Yes

value: Previous Smoker

value: 3 days/week

value: White- British

value: Once daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: u/ml

value: 1-2 days a week


title: WTCHG_306606_207

value: RNA-Tempus

value: u/mL

value: Oral

value: Current Smoker

value: Weekly

value: Intramuscular

value: DAS28CRP Class 1

value: Male

value: Cigarrette

value: Withdrawn -lost to follow up

value: Twice daily

value: Intraarticular

value: Knee (right)


title: WTCHG_306606_208

value: U/ml

value: No

value: IU/ml

value: Yes

value: Previous Smoker

value: 6 days/week

value: White- British

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female

value: Completed


title: WTCHG_306606_210

value: RNA-Tempus

value: Kunits/L

value: Oral

value: Never Smoked

value: Weekly

value: Asian or Asian British - Indian

value: Intramuscular

value: DAS28CRP Class 1

value: SDAI Class 3


title: WTCHG_306606_204

value: U/ml

value: No

value: IU/ml

value: Yes

value: Cigarrette

value: u/ml

value: Withdrawn -lost to follow up

value: iu/ml

value: Twice daily


title: WTCHG_306606_209

value: RNA-Tempus

value: u/mL

value: Current Smoker

value: White- British

value: DAS28CRP Class 2

value: SDAI Class 1

value: Male

value: Hand-rolled tobacco

value: Enrolled

value: Once daily

value: 1-2 days a year


title: WTCHG_306606_206

value: Oral

value: No

value: Yes

value: Never Smoked

value: Weekly

value: Asian or Asian British - Indian

value: Intramuscular

value: Female

value: Completed

value: Subcutaneous


title: WTCHG_306606_225

value: RNA-Tempus

value: U/ml

value: IU/ml

value: Black or Black British - Caribbean

value: Shoulder (left)

value: DAS28CRP Class 3

value: u/ml

value: Lost to follow-up

value: 1-2 days a week


title: WTCHG_306606_202

value: Oral

value: No

value: Yes

value: Previous Smoker

value: White- British

value: Twice daily

value: SDAI Class 2

value: Cigarrette

value: Withdrawn -lost to follow up

value: 1-2 days a month


title: WTCHG_306409_303

value: RNA-Tempus

value: U/ml

value: iu/ml

value: Current Smoker

value: 4 days/week

value: Weekly

value: Once daily

value: Intramuscular

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Completed

value: 5 or more days a week

value: more than 20


title: WTCHG_306409_294

value: kunits/L

value: Oral

value: IU/ml

value: Yes

value: No

value: Other ethnic groups - Any other ethnic group

value: DAS28CRP Class 3

value: SDAI Class 3

value: Cigarrette

value: Twice daily


title: WTCHG_306606_201

value: RNA-Tempus

value: U/mL

value: iu/mL

value: Current Smoker

value: 6 days/week

value: White- British

value: Weekly

value: SDAI Class 2

value: Male

value: Hand-rolled tobacco

value: 3 - 4 days a week

value: iu/ml


title: WTCHG_306409_295

value: kunits/L

value: No

value: IU/ml

value: Yes

value: Oral

value: Intramuscular

value: Completed

value: 1-2 days a week


title: WTCHG_306409_302

value: RNA-Tempus

value: U/ml

value: IU/mL

value: Never Smoked

value: White - any other White background

value: Twice daily

value: DAS28CRP Class 3

value: Female

value: 1-2 days a year


title: WTCHG_306409_293

value: u/ml

value: iu/ml

value: Previous Smoker

value: 3 days/week

value: White- British

value: Weekly

value: 2 days/week

value: DAS28CRP Class 1

value: SDAI Class 3

value: Cigarrette


title: WTCHG_306409_301

value: RNA-Tempus

value: U/ml

value: Oral

value: No

value: Yes

value: 6 days/week

value: DAS28CRP Class 2

value: SDAI Class 1

value: Completed


title: WTCHG_306409_296

value: u/ml

value: ku/l

value: Never Smoked

value: Once daily

value: DAS28CRP Class 3

value: Male

value: 1-2 days a month


title: WTCHG_306606_219

value: Current Smoker

value: 3 days/week

value: White- British

value: Weekly

value: Hand-rolled tobacco

value: 5 or more days a week

value: more than 20


title: WTCHG_306409_290

value: RNA-Tempus

value: U/ml

value: Oral

value: No

value: Yes

value: Previous Smoker

value: Twice daily

value: Intramuscular

value: SDAI Class 2

value: Female

value: Cigarrette


title: WTCHG_306409_288

value: IU/ml

value: DAS28CRP Class 2

value: SDAI Class 1

value: Male

value: Completed

value: 1-2 days a week


title: WTCHG_306409_287

value: RNA-Tempus

value: EU/ml

value: Current Smoker

value: Weekly

value: White- British

value: Once daily

value: DAS28CRP Class 3


title: WTCHG_306409_289

value: U/ml

value: Oral

value: No

value: Yes

value: Previous Smoker

value: Twice daily

value: Intramuscular

value: 3 - 4 days a week


title: WTCHG_306409_285

value: U/ML

value: IU/ML

value: DAS28CRP Class 1

value: SDAI Class 3

value: Female

value: Cigarrette

value: u/ml

value: Completed


title: WTCHG_306409_284

value: RNA-Tempus

value: KU/L

value: 3 days/week

value: White- British

value: Weekly

value: Once daily

value: SDAI Class 1

value: Male

value: Hand-rolled tobacco

value: 1-2 days a week

value: ku/l


title: WTCHG_306409_282

value: Oral

value: No

value: iu/ml

value: Yes

value: Previous Smoker

value: DAS28CRP Class 2

value: 3 - 4 days a week


title: WTCHG_306409_280

value: RNA-Tempus

value: U/ml

value: IU/ml

value: Current Smoker

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female

value: Cigarrette

value: Completed


title: WTCHG_306409_281

value: Weekly

value: White- British

value: Once daily

value: SDAI Class 1

value: Male

value: 5 or more days a week


title: WTCHG_306409_276

value: U/ML

value: No

value: IU/ML

value: Yes

value: Never Smoked

value: Oral

value: 5 days/week

value: u/ml

value: more than 20


title: WTCHG_306409_277

value: RNA-Tempus

value: u/mL

value: Current Smoker

value: DAS28CRP Class 1

value: SDAI Class 2

value: Cigarrette

value: Withdrawn -lost to follow up


title: WTCHG_306606_203

value: U/mL

value: Previous Smoker

value: Weekly

value: Shoulder (right)

value: IU/mL

value: White- British

value: Once daily

value: Intramuscular

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Completed


title: WTCHG_306409_279

value: RNA-Tempus

value: u/mL

value: Oral

value: KU/L

value: Yes

value: No

value: Current Smoker

value: Mixed - White and Black African

value: DAS28CRP Class 3

value: u/ml

value: 1-2 days a week

value: KU/l


title: WTCHG_306409_275

value: EU/ml

value: IU/ml

value: Never Smoked

value: White- British

value: Weekly

value: DAS28CRP Class 1

value: SDAI Class 3

value: Once daily

value: 5 or more days a week

value: Twice daily

value: Intramuscular


title: WTCHG_306409_274

value: RNA-Tempus

value: U/ml

value: Oral

value: Yes

value: No

value: Current Smoker

value: SDAI Class 2

value: Male

value: Cigarrette

value: Lost to follow-up

value: 1-2 days a month


title: WTCHG_306409_272

value: IU/ml

value: Never Smoked

value: 4 days/week

value: White- British

value: Weekly

value: DAS28CRP Class 3

value: Female

value: Completed

value: 1-2 days a week


title: WTCHG_306409_291

value: RNA-Tempus

value: Oral

value: IU/ML

value: Yes

value: Previous Smoker

value: White - any other White background

value: Twice daily

value: Intramuscular

value: 2 days/week

value: DAS28CRP Class 1

value: SDAI Class 1

value: iu/ml


title: WTCHG_306409_273

value: U/ml

value: No

value: IU//ML

value: Current Smoker

value: Weekly

value: White- British

value: 5 days/week

value: SDAI Class 2

value: Male

value: Cigarrette


title: WTCHG_306409_292

value: RNA-Tempus

value: u/ml

value: Oral

value: Yes

value: Previous Smoker

value: Black or Black British - Caribbean

value: Female

value: Enrolled


title: WTCHG_306409_270

value: U/ml

value: No

value: IU/ml

value: White - any other White background

value: Twice daily

value: Intramuscular

value: DAS28CRP Class 3

value: Completed


title: WTCHG_306409_271

value: u/mL

value: Never Smoked

value: 2 days/week

value: Other ethnic groups - Chinese

value: Weekly

value: Once daily

value: SDAI Class 2

value: 1-2 days a week


title: WTCHG_306409_268

value: RNA-Tempus

value: u/ml

value: iu/ml

value: Yes

value: Oral

value: Asian or Asian British - Indian

value: Male


title: WTCHG_306409_269

value: U/ml

value: No

value: Previous Smoker

value: IU/ml

value: White- British

value: DAS28CRP Class 3

value: Cigarrette

value: 3 - 4 days a week


title: WTCHG_306409_262

value: Current Smoker

value: 6 days/week

value: Weekly

value: Once daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: Hand-rolled tobacco

value: Completed

value: 5 or more days a week


title: WTCHG_306409_267

value: RNA-Tempus

value: Oral

value: IU/mL

value: Yes

value: Intraarticular

value: Intramuscular

value: Ankle (right)

value: Female

value: 1-2 days a month


title: WTCHG_306409_263

value: U/ML

value: IU/ML

value: No

value: Previous Smoker

value: White- British

value: SDAI Class 3

value: Male

value: Cigarrette

value: Withdrawn -lost to follow up

value: 1-2 days a year

value: 5 days/week


title: WTCHG_306409_265

value: RNA-Tempus

value: u/mL

value: Oral

value: Never Smoked

value: Weekly

value: Yes

value: DAS28CRP Class 3

value: SDAI Class 1

value: Completed


title: WTCHG_306409_266

value: u/ml

value: No

value: iu/ml

value: Current Smoker

value: Subcutaneous

value: DAS28CRP Class 2

value: Female

value: Hand-rolled tobacco


title: WTCHG_306409_264

value: RNA-Tempus

value: U/ml

value: IU/ml

value: White- British

value: Cigarrette

value: Once daily

value: Intramuscular


title: WTCHG_306409_261

value: Yes

value: Weekly

value: Oral

value: Twice daily

value: SDAI Class 1


title: WTCHG_306409_259

value: kunits/L

value: No

value: Never Smoked

value: Asian or Asian British - Any other Asian background

value: DAS28CRP Class 1

value: SDAI Class 2

value: Completed


title: WTCHG_306409_286

value: RNA-Tempus

value: u/ml

value: iu/ml

value: Previous Smoker

value: Black or Black British - Caribbean

value: Female

value: 1-2 days a week


title: WTCHG_306409_256

value: EU/ml

value: Oral

value: IU/ml

value: Yes

value: Weekly

value: SDAI Class 3

value: Cigarrette

value: Once daily

value: Alternate days

value: 1-2 days a month


title: WTCHG_306409_258

value: RNA-Tempus

value: kunits/L

value: No

value: White- British

value: DAS28CRP Class 2

value: SDAI Class 1

value: Withdrawn -lost to follow up

value: Twice daily


title: WTCHG_306409_257

value: U/mL

value: Oral

value: iU/mL

value: Previous Smoker

value: White - Irish

value: Intramuscular

value: 6 days/week

value: DAS28CRP Class 1

value: Female

value: u/mL

value: Completed

value: iu/mL


title: WTCHG_306409_253

value: RNA-Tempus

value: U/ml

value: No

value: IU/ml

value: Current Smoker

value: Weekly

value: Yes

value: White- British

value: DAS28CRP Class 3

value: SDAI Class 2

value: Cigarrette

value: 1-2 days a month


title: WTCHG_306409_254

value: Oral

value: Never Smoked

value: 3 days/week


title: WTCHG_306409_252

value: kunits/L

value: IU/L

value: 2 days/week

value: Mixed - Any other mixed background

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Completed

value: Once daily


title: WTCHG_306409_255

value: RNA-Tempus

value: U/ml

value: No

value: IU/ml

value: Yes

value: Previous Smoker

value: White- British

value: Twice daily

value: Male

value: 1-2 days a week

value: iu/ml


title: WTCHG_306409_251

value: kU/L

value: Oral

value: IU/L

value: Never Smoked

value: Weekly

value: Black or Black British - African

value: DAS28CRP Class 3

value: SDAI Class 2

value: KU/L


title: WTCHG_306409_278

value: RNA-Tempus

value: u/mL

value: No

value: 6 days/week

value: Knee (right)

value: Once daily

value: Intraarticular

value: DAS28CRP Class 1

value: Female

value: u/ml

value: Completed

value: Subcutaneous

value: 1-2 days a month


title: WTCHG_306409_249

value: Oral

value: iu/ml

value: Yes

value: Current Smoker

value: Weekly

value: White- British

value: SDAI Class 3

value: Cigarrette

value: IU/ml


title: WTCHG_306409_246

value: RNA-Tempus

value: U/ML

value: No

value: IU/ML

value: Previous Smoker

value: 5 days/week

value: Intramuscular

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: U/ml

value: 3 - 4 days a week

value: more than 20


title: WTCHG_306409_250

value: kunits/l

value: Oral

value: Yes

value: Weekly

value: Asian or Asian British - Bangladeshi

value: DAS28CRP Class 1

value: Completed


title: WTCHG_306409_248

value: RNA-Tempus

value: No

value: iu/ml

value: Current Smoker

value: White- British

value: Once daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: Cigarrette

value: 5 or more days a week


title: WTCHG_306409_245

value: u/ml

value: Previous Smoker

value: 6 days/week

value: Intramuscular

value: Knee (right)

value: SDAI Class 2

value: Male

value: 1-2 days a week


title: WTCHG_306409_247

value: RNA-Tempus

value: U/ml

value: Oral

value: No

value: Yes

value: Weekly

value: Completed


title: WTCHG_306409_243

value: IU/ml

value: Never Smoked

value: White- British

value: DAS28CRP Class 2

value: SDAI Class 1

value: 3 - 4 days a week

value: Once daily

value: Intraarticular

value: Wrist (right)


title: WTCHG_306409_242

value: u/ml

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female

value: U/ML

value: 1-2 days a week


title: WTCHG_306409_244

value: RNA-Tempus

value: eu/ml

value: Oral

value: No

value: iu/ml

value: Yes

value: Weekly

value: DAS28CRP Class 1

value: Shoulder (left)

value: Intramuscular


title: WTCHG_306409_239

value: U/ml

value: IU/ml

value: Current Smoker

value: White- British

value: Twice daily

value: Cigarrette

value: Completed


title: WTCHG_306409_241

value: RNA-Tempus

value: U/m

value: IU/ML

value: Previous Smoker

value: 5 days/week

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female


title: WTCHG_306409_240

value: U/mL

value: No

value: IU/mL

value: Yes

value: 3 days/week

value: Oral

value: Weekly

value: Once daily

value: DAS28CRP Class 3

value: SDAI Class 2

value: u/ml

value: 3 - 4 days a week

value: iu/ml


title: WTCHG_306409_238

value: RNA-Tempus

value: Current Smoker

value: White- British

value: DAS28CRP Class 1

value: Male

value: Hand-rolled tobacco

value: Completed

value: 1-2 days a week


title: WTCHG_306409_236

value: U/mL

value: No

value: Eu/mL

value: Yes

value: Previous Smoker

value: 6 days/week

value: Intraarticular

value: Elbow (right)

value: DAS28CRP Class 2

value: SDAI Class 1

value: Cigarrette

value: Intramuscular


title: WTCHG_306409_237

value: RNA-Tempus

value: Oral

value: White- British

value: Weekly

value: Subcutaneous

value: DAS28CRP Class 1

value: SDAI Class 3

value: Female

value: 1-2 days a year


title: WTCHG_306409_234

value: U/mL

value: No

value: Eu/mL

value: Yes

value: Current Smoker

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: Completed

value: 1-2 days a week


title: WTCHG_306409_233

value: RNA-Tempus

value: Oral

value: Previous Smoker

value: White- British

value: Intramuscular

value: 6 days/week

value: Cigarrette

value: Once daily


title: WTCHG_306409_231

value: U/ml

value: No

value: IU/ml

value: Never Smoked

value: Weekly

value: Twice daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: 1-2 days a month

value: Shoulder (left)

value: Intraarticular


title: WTCHG_306409_232

value: RNA-Tempus

value: U/ML

value: IU/ML

value: Yes

value: Current Smoker

value: Asian or Asian British - Pakistani

value: Oral

value: DAS28CRP Class 1

value: SDAI Class 2

value: Male

value: Lost to follow-up


title: WTCHG_306409_230

value: U/ml

value: No

value: iu/ml

value: Never Smoked

value: Weekly

value: White- British

value: Twice daily

value: Intramuscular

value: DAS28CRP Class 2

value: Completed

value: 1-2 days a year

value: IU/ml


title: WTCHG_306409_229

value: RNA-Tempus

value: Oral

value: Yes

value: 6 days/week

value: Black or Black British - Caribbean

value: SDAI Class 1

value: Female


title: WTCHG_306409_228

value: No

value: Previous Smoker

value: White - any other White background

value: Cigarrette


title: WTCHG_306409_226

value: U/mL

value: iU/mL

value: White- British

value: Weekly

value: u/ml

value: 1-2 days a month

value: iu/ml


title: WTCHG_306409_225

value: RNA-Tempus

value: U/ml

value: Oral

value: IU/ml

value: Twice daily

value: Intramuscular

value: DAS28CRP Class 2

value: Male

value: Cigar

value: Completed

value: 5 or more days a week

value: more than 20


title: WTCHG_306409_224

value: No

value: Yes

value: Current Smoker

value: White- British

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female

value: Cigarrette

value: 1-2 days a week


title: WTCHG_306606_213

value: RNA-Tempus

value: u/ml

value: iu/ml

value: Never Smoked

value: Weekly

value: Oral

value: Black or Black British - Caribbean

value: Twice daily

value: U/ml

value: 1-2 days a month


title: WTCHG_306409_223

value: kunits/L

value: No

value: IU/ML

value: Yes

value: Male

value: Completed

value: iu/ML


title: WTCHG_321773_202

value: RNA-Tempus

value: U/ML

value: White- British

value: 5 days/week

value: DAS28CRP Class 3

value: SDAI Class 2

value: 5 or more days a week

value: more than 20

value: IU/ml


title: WTCHG_306409_221

value: U/ml

value: Oral

value: Never Smoked

value: Weekly

value: Other ethnic groups - Any other ethnic group

value: Twice daily

value: Intramuscular

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: 1-2 days a month


title: WTCHG_306409_217

value: RNA-Tempus

value: No

value: IU

value: Yes

value: Previous Smoker

value: White- British

value: 5 days/week

value: Cigarrette

value: Completed

value: 3 - 4 days a week

value: iu/ml

value: Intraarticular

value: Knee (right)


title: WTCHG_306409_216

value: U/mL

value: Eu/mL

value: Never Smoked

value: 6 days/week

value: Oral

value: Weekly

value: DAS28CRP Class 2

value: 1-2 days a year

value: Intramuscular


title: WTCHG_306409_215

value: RNA-Tempus

value: No

value: lu/ml

value: Yes

value: Current Smoker

value: White- British

value: Twice daily

value: SDAI Class 1

value: Female

value: Hand-rolled tobacco

value: IU/ml

value: Once daily


title: WTCHG_306409_222

value: Oral

value: Cigarrette

value: U/ml

value: Completed


title: WTCHG_306409_219

value: U/mL

value: Never Smoked

value: DAS28CRP Class 2

value: 1-2 days a week


title: WTCHG_306409_210

value: RNA-Tempus

value: No

value: IU/mL

value: Yes

value: Previous Smoker

value: Weekly

value: DAS28CRP Class 3

value: SDAI Class 2

value: 3 - 4 days a week

value: iU/mL

value: Intramuscular


title: WTCHG_306409_220

value: U/ml

value: Oral

value: IU/ml

value: Other ethnic groups - Chinese

value: Twice daily

value: DAS28CRP Class 1

value: Female


title: WTCHG_306409_213

value: RNA-Tempus

value: No

value: 6 days/week

value: White- British

value: Cigarrette

value: Completed

value: Soft tissue


title: WTCHG_306409_218

value: kunits/L

value: Yes

value: IU/L

value: Previous Smoker

value: Weekly

value: Wrist (left)

value: Mixed - White and Black African

value: Intraarticular

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: Hand-rolled tobacco

value: 1-2 days a year

value: Wrist (right)


title: WTCHG_306409_208

value: RNA-Tempus

value: U/ml

value: Oral

value: No

value: IU/ml

value: Current Smoker

value: White- British

value: Twice daily

value: Intramuscular

value: 6 days/week

value: SDAI Class 1

value: Female

value: Cigarrette

value: u/ml

value: Lost to follow-up

value: 1-2 days a month

value: iu/ml


title: WTCHG_306409_206

value: RNA-Tempus

value: Never Smoked

value: Weekly

value: Yes

value: DAS28CRP Class 3

value: SDAI Class 2

value: IU

value: Completed

value: 3 - 4 days a week

value: more than 20


title: WTCHG_306409_235

value: U/mL

value: Oral

value: No

value: Eu/mL

value: Current Smoker

value: 6 days/week

value: White- British

value: DAS28CRP Class 2

value: SDAI Class 1

value: Intramuscular


title: WTCHG_306409_209

value: RNA-Tempus

value: U/ml

value: Yes

value: Previous Smoker

value: Weekly

value: IU/ml

value: Twice daily

value: Subcutaneous

value: Female

value: Cigarrette


title: WTCHG_306409_204

value: u/mL

value: Oral

value: No

value: Never Smoked

value: Mixed - White and Black Caribbean

value: DAS28CRP Class 3

value: SDAI Class 2

value: u/ml

value: Completed

value: 1-2 days a year


title: WTCHG_306409_203

value: RNA-Tempus

value: U/ml

value: Yes

value: Previous Smoker

value: White- British

value: 1-2 days a week


title: WTCHG_306409_205

value: IU/ml

value: Asian or Asian British - Indian

value: Weekly

value: Once daily

value: Intramuscular

value: Female

value: Cigarrette

value: 3 - 4 days a week


title: WTCHG_306409_201

value: Oral

value: No

value: Current Smoker

value: Twice daily

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male


title: WTCHG_306409_202

value: RNA-Tempus

value: U/ml

value: Never Smoked

value: Yes

value: White- British

value: DAS28CRP Class 1

value: Completed

value: 1-2 days a month


title: WTCHG_306408_303

value: iu/ml

value: 4 days/week

value: Weekly

value: Once daily

value: Intramuscular

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Cigarrette

value: 5 or more days a week

value: more than 20


title: WTCHG_306408_301

value: RNA-Tempus

value: U/ml

value: Oral

value: No

value: Previous Smoker

value: 6 days/week


title: WTCHG_306408_296

value: u/ml

value: ku/l

value: Yes

value: Never Smoked

value: 3 days/week

value: White- British

value: DAS28CRP Class 3

value: Male

value: Completed

value: 1-2 days a month


title: WTCHG_306408_295

value: kunits/L

value: IU/ml

value: Current Smoker

value: Weekly

value: Twice daily

value: Intramuscular

value: SDAI Class 2

value: Cigarrette

value: 1-2 days a week


title: WTCHG_306408_302

value: RNA-Tempus

value: U/ml

value: No

value: IU/mL

value: Yes

value: White - any other White background

value: Oral

value: Female

value: 1-2 days a year


title: WTCHG_306408_294

value: kunits/L

value: IU/ml

value: Other ethnic groups - Any other ethnic group

value: DAS28CRP Class 3

value: SDAI Class 3

value: Withdrawn -lost to follow up


title: WTCHG_306408_293

value: u/ml

value: iu/ml

value: Previous Smoker

value: 3 days/week

value: White- British

value: Weekly

value: 2 days/week

value: DAS28CRP Class 1

value: Cigarrette

value: Completed


title: WTCHG_306408_292

value: RNA-Tempus

value: Oral

value: Yes

value: No

value: Black or Black British - Caribbean

value: SDAI Class 2

value: Female

value: Enrolled

value: Twice daily


title: WTCHG_306409_214

value: U/ml

value: IU/ml

value: Current Smoker

value: Intramuscular

value: 6 days/week

value: DAS28CRP Class 2

value: SDAI Class 1

value: Withdrawn -lost to follow up

value: 1-2 days a month


title: WTCHG_306409_211

value: RNA-Tempus

value: Never Smoked

value: Once daily

value: Oral

value: White- British

value: Weekly

value: DAS28CRP Class 1

value: Completed

value: 5 or more days a week


title: WTCHG_306408_288

value: U/ml

value: No

value: IU/ml

value: Yes

value: Previous Smoker

value: Twice daily

value: Male

value: Cigarrette

value: 1-2 days a week


title: WTCHG_306409_212

value: RNA-Tempus

value: U/mL

value: iu/mL

value: Never Smoked

value: 6 days/week

value: Wrist (right)

value: Intraarticular

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female


title: WTCHG_306408_290

value: U/ml

value: Oral

value: No

value: Weekly

value: White- British

value: Intramuscular

value: Completed


title: WTCHG_306409_207

value: RNA-Tempus

value: u/ml

value: iu/ml

value: Yes

value: Current Smoker

value: 2 days/week

value: Hand-rolled tobacco

value: 1-2 days a week


title: WTCHG_306408_286

value: Previous Smoker

value: Black or Black British - Caribbean

value: Twice daily

value: DAS28CRP Class 1

value: SDAI Class 2

value: Cigarrette


title: WTCHG_306408_284

value: No

value: KU/L

value: 3 days/week

value: Oral

value: White- British

value: Weekly

value: Once daily

value: SDAI Class 1

value: Male

value: U/ml

value: ku/l


title: WTCHG_306408_287

value: RNA-Tempus

value: EU/ml

value: IU/ml

value: Current Smoker

value: Yes

value: DAS28CRP Class 3

value: Female

value: Completed


title: WTCHG_306408_285

value: U/ML

value: IU/ML

value: No

value: Intramuscular

value: DAS28CRP Class 1

value: SDAI Class 3

value: Cigarrette

value: u/ml


title: WTCHG_306408_281

value: U/ml

value: Oral

value: iu/ml

value: Previous Smoker

value: Weekly

value: White- British

value: Once daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: Male

value: 5 or more days a week


title: WTCHG_306408_282

value: RNA-Tempus

value: No

value: Yes

value: Female

value: Completed

value: 3 - 4 days a week


title: WTCHG_306408_280

value: U/ml

value: IU/ml

value: Current Smoker

value: DAS28CRP Class 3

value: SDAI Class 2

value: Cigarrette

value: 1-2 days a week


title: WTCHG_306408_279

value: u/mL

value: Oral

value: KU/L

value: Mixed - White and Black African

value: Weekly

value: u/ml

value: KU/l

value: Intramuscular

value: Once daily


title: WTCHG_306408_278

value: RNA-Tempus

value: No

value: Yes

value: Never Smoked

value: 6 days/week

value: Knee (right)

value: Black or Black British - African

value: Intraarticular

value: DAS28CRP Class 1

value: Female

value: Completed

value: Subcutaneous

value: 1-2 days a month


title: WTCHG_306408_277

value: u/mL

value: Oral

value: Current Smoker

value: White- British

value: Weekly

value: SDAI Class 2

value: Male

value: Cigarrette

value: u/ml

value: Withdrawn -lost to follow up

value: 5 or more days a week


title: WTCHG_306408_276

value: RNA-Tempus

value: U/ML

value: No

value: IU/ML

value: Yes

value: Never Smoked

value: 5 days/week

value: DAS28CRP Class 3

value: more than 20

value: IU/ml


title: WTCHG_306408_275

value: EU/ml

value: Oral

value: White- British

value: Weekly

value: DAS28CRP Class 1

value: SDAI Class 3

value: Female

value: Completed

value: Once daily

value: Twice daily

value: Intramuscular


title: WTCHG_306408_274

value: RNA-Tempus

value: U/ml

value: Yes

value: No

value: Current Smoker

value: SDAI Class 2

value: Male

value: Cigarrette

value: Lost to follow-up

value: 1-2 days a month


title: WTCHG_306408_273

value: Oral

value: IU//ML

value: Weekly

value: White- British

value: 5 days/week

value: DAS28CRP Class 3


title: WTCHG_306408_291

value: IU/ML

value: Previous Smoker

value: White - any other White background

value: Twice daily

value: Intramuscular

value: 2 days/week

value: DAS28CRP Class 1

value: SDAI Class 1

value: Female

value: Completed

value: iu/ml


title: WTCHG_306408_272

value: RNA-Tempus

value: U/ml

value: Oral

value: No

value: IU/ml

value: Yes

value: Never Smoked

value: 4 days/week

value: SDAI Class 2

value: 1-2 days a week


title: WTCHG_306408_266

value: u/ml

value: Current Smoker

value: Weekly

value: White- British

value: Subcutaneous

value: DAS28CRP Class 2

value: Hand-rolled tobacco


title: WTCHG_306408_268

value: RNA-Tempus

value: iu/ml

value: 2 days/week

value: Asian or Asian British - Indian

value: Once daily

value: DAS28CRP Class 3

value: Male

value: Completed


title: WTCHG_306408_271

value: u/mL

value: Oral

value: No

value: Yes

value: Never Smoked

value: Other ethnic groups - Chinese

value: SDAI Class 2

value: Female


title: WTCHG_306408_264

value: U/ml

value: IU/ml

value: Current Smoker

value: White- British

value: Weekly

value: DAS28CRP Class 2

value: SDAI Class 1

value: Cigarrette

value: Intramuscular


title: WTCHG_306408_267

value: RNA-Tempus

value: IU/mL

value: Previous Smoker

value: Intraarticular

value: Ankle (right)

value: Completed

value: 1-2 days a month

value: Once daily


title: WTCHG_306408_269

value: U/ml

value: Oral

value: No

value: Yes

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: 3 - 4 days a week


title: WTCHG_306408_265

value: u/mL

value: Never Smoked

value: Weekly

value: White- British

value: SDAI Class 1

value: Female

value: 1-2 days a year


title: WTCHG_306408_270

value: RNA-Tempus

value: IU/ml

value: Previous Smoker

value: White - any other White background

value: Twice daily

value: Intramuscular

value: Cigarrette

value: Completed


title: WTCHG_306408_263

value: U/ML

value: IU/ML

value: Yes

value: No

value: DAS28CRP Class 2

value: SDAI Class 3

value: Male

value: Withdrawn -lost to follow up

value: 5 days/week

value: Oral


title: WTCHG_306408_258

value: RNA-Tempus

value: kunits/L

value: IU/ml

value: White- British

value: Weekly

value: SDAI Class 1

value: Female


title: WTCHG_306408_259

value: Never Smoked

value: Asian or Asian British - Any other Asian background

value: DAS28CRP Class 1

value: SDAI Class 2

value: Completed


title: WTCHG_306408_262

value: u/ml

value: No

value: iu/ml

value: Yes

value: Current Smoker

value: 6 days/week

value: Once daily

value: DAS28CRP Class 2

value: Hand-rolled tobacco

value: 5 or more days a week


title: WTCHG_306408_261

value: RNA-Tempus

value: U/ml

value: IU/ml

value: Weekly

value: Oral

value: White- British

value: Twice daily

value: SDAI Class 1

value: Cigarrette


title: WTCHG_306408_289

value: No

value: Previous Smoker

value: Intramuscular

value: Female

value: Completed

value: 3 - 4 days a week


title: WTCHG_306408_253

value: Current Smoker

value: Yes

value: DAS28CRP Class 3

value: SDAI Class 2

value: Withdrawn -lost to follow up

value: 1-2 days a month


title: WTCHG_306408_254

value: RNA-Tempus

value: U/ml

value: Oral

value: IU/ml

value: Never Smoked

value: 3 days/week

value: Weekly


title: WTCHG_306408_256

value: EU/ml

value: No

value: Previous Smoker

value: Black or Black British - Caribbean

value: DAS28CRP Class 1

value: SDAI Class 3

value: Cigarrette

value: Once daily

value: Alternate days


title: WTCHG_306408_252

value: kunits/L

value: Yes

value: IU/L

value: 2 days/week

value: Mixed - Any other mixed background

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Completed

value: 1-2 days a month


title: WTCHG_306408_251

value: RNA-Tempus

value: kU/L

value: Oral

value: No

value: Never Smoked

value: Weekly

value: Black or Black British - African

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: KU/L


title: WTCHG_306408_248

value: U/ml

value: iu/ml

value: Yes

value: Current Smoker

value: White- British

value: Once daily

value: Intramuscular

value: Cigarrette

value: 5 or more days a week

value: more than 20


title: WTCHG_306408_249

value: RNA-Tempus

value: u/ml

value: Oral

value: No

value: DAS28CRP Class 1

value: SDAI Class 3

value: Female

value: Completed

value: 1-2 days a month

value: IU/ml

value: Intraarticular


title: WTCHG_320982_266

value: U/ml

value: Yes

value: Current Smoker

value: Weekly

value: White- British

value: Twice daily

value: DAS28CRP Class 3

value: SDAI Class 2

value: Male

value: 1-2 days a week


title: WTCHG_306408_244

value: RNA-Tempus

value: eu/ml

value: Oral

value: No

value: iu/ml

value: Never Smoked

value: DAS28CRP Class 1

value: SDAI Class 1

value: Shoulder (left)

value: Intramuscular


title: WTCHG_306408_246

value: U/ML

value: IU/ML

value: Yes

value: Previous Smoker

value: Weekly

value: 5 days/week

value: Cigarrette

value: U/ml

value: Completed

value: 3 - 4 days a week

value: more than 20


title: WTCHG_306408_245

value: RNA-Tempus

value: u/ml

value: Oral

value: No

value: iu/ml

value: 6 days/week

value: White- British

value: Knee (right)

value: SDAI Class 2

value: Male

value: 1-2 days a week

value: Once daily


title: WTCHG_306408_241

value: U/m

value: IU/ML

value: Yes

value: Previous Smoker

value: Weekly

value: 5 days/week

value: Intramuscular

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Cigarrette

value: IU/ml


title: WTCHG_306408_240

value: RNA-Tempus

value: U/mL

value: No

value: IU/mL

value: 3 days/week

value: Oral

value: White- British

value: DAS28CRP Class 3

value: u/ml

value: Completed

value: 3 - 4 days a week

value: iu/ml


title: WTCHG_306408_243

value: U/ml

value: Yes

value: Never Smoked

value: 6 days/week

value: Weekly

value: Intramuscular

value: DAS28CRP Class 2

value: Male

value: Once daily

value: Intraarticular

value: Wrist (right)


title: WTCHG_306408_234

value: RNA-Tempus

value: U/mL

value: Oral

value: No

value: Eu/mL

value: Current Smoker

value: White- British

value: SDAI Class 2

value: Cigarrette

value: 1-2 days a week


title: WTCHG_306408_238

value: u/ml

value: iu/ml

value: Yes

value: Weekly

value: DAS28CRP Class 1

value: Hand-rolled tobacco

value: Completed


title: WTCHG_306408_237

value: RNA-Tempus

value: Previous Smoker

value: 6 days/week

value: Subcutaneous

value: SDAI Class 3

value: Female

value: 1-2 days a year

value: Intramuscular


title: WTCHG_306408_236

value: U/mL

value: Oral

value: No

value: Eu/mL

value: White- British

value: Intraarticular

value: Elbow (right)

value: DAS28CRP Class 2

value: SDAI Class 1

value: Male

value: Cigarrette

value: 3 - 4 days a week


title: WTCHG_306408_235

value: RNA-Tempus

value: Yes

value: Current Smoker

value: 6 days/week

value: Weekly

value: Completed


title: WTCHG_306408_239

value: U/ml

value: Oral

value: IU/ml

value: Twice daily

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female

value: 1-2 days a week


title: WTCHG_306408_233

value: U/mL

value: No

value: Previous Smoker

value: White- British

value: Intramuscular

value: Once daily


title: WTCHG_306408_232

value: RNA-Tempus

value: U/ML

value: IU/ML

value: Yes

value: Current Smoker

value: Asian or Asian British - Pakistani

value: DAS28CRP Class 1

value: Male

value: Cigarrette

value: Lost to follow-up


title: WTCHG_306408_231

value: U/ml

value: Oral

value: IU/ml

value: Never Smoked

value: Weekly

value: Twice daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Completed

value: 1-2 days a month

value: Shoulder (left)

value: Intraarticular


title: WTCHG_306408_242

value: RNA-Tempus

value: u/ml

value: No

value: Yes

value: White- British

value: Once daily

value: DAS28CRP Class 3

value: SDAI Class 2

value: U/ML

value: 1-2 days a week


title: WTCHG_306408_257

value: U/mL

value: Oral

value: iU/mL

value: Previous Smoker

value: White - Irish

value: Intramuscular

value: 6 days/week

value: DAS28CRP Class 1

value: SDAI Class 3

value: Weekly

value: Cigarrette

value: u/mL

value: iu/mL


title: WTCHG_306408_250

value: RNA-Tempus

value: kunits/l

value: Yes

value: IU/ML

value: No

value: Asian or Asian British - Bangladeshi

value: Male

value: Completed


title: WTCHG_306408_255

value: U/ml

value: IU/ml

value: Previous Smoker

value: White- British

value: Oral

value: Twice daily

value: DAS28CRP Class 3

value: SDAI Class 2

value: 1-2 days a week

value: iu/ml

value: Once daily


title: WTCHG_306408_229

value: RNA-Tempus

value: Yes

value: Never Smoked

value: 6 days/week

value: Black or Black British - Caribbean

value: Weekly

value: Intramuscular

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female


title: WTCHG_306408_228

value: No

value: IU/ml

value: Previous Smoker

value: Oral

value: White - any other White background

value: Cigarrette

value: Completed

value: 1-2 days a year


title: WTCHG_306408_226

value: RNA-Tempus

value: U/mL

value: iU/mL

value: Yes

value: White- British

value: u/ml

value: 1-2 days a month

value: iu/ml


title: WTCHG_306408_225

value: U/ml

value: Weekly

value: Twice daily

value: Intramuscular

value: DAS28CRP Class 2

value: SDAI Class 1

value: Male

value: Cigar

value: 5 or more days a week

value: more than 20


title: WTCHG_306408_224

value: RNA-Tempus

value: Oral

value: No

value: IU/ml

value: Current Smoker

value: DAS28CRP Class 3

value: SDAI Class 2

value: Female

value: Cigarrette

value: Completed

value: 1-2 days a week


title: WTCHG_306408_221

value: U/ml

value: Yes

value: Never Smoked

value: Weekly

value: Other ethnic groups - Any other ethnic group

value: Twice daily

value: Intramuscular

value: DAS28CRP Class 2

value: 1-2 days a month


title: WTCHG_306408_247

value: RNA-Tempus

value: Oral

value: No

value: iu/ml

value: Previous Smoker

value: White- British

value: Once daily

value: SDAI Class 1

value: Male


title: WTCHG_306408_220

value: U/ml

value: IU/ml

value: Yes

value: Other ethnic groups - Chinese

value: DAS28CRP Class 1

value: SDAI Class 2

value: Female

value: Completed


title: WTCHG_306408_219

value: RNA-Tempus

value: U/mL

value: Never Smoked

value: DAS28CRP Class 2

value: 1-2 days a week


title: WTCHG_306408_223

value: kunits/L

value: Oral

value: No

value: IU/ML

value: Weekly

value: White- British

value: Twice daily

value: DAS28CRP Class 3

value: iu/ML


title: WTCHG_306408_218

value: Yes

value: IU/L

value: Previous Smoker

value: Wrist (left)

value: Mixed - White and Black African

value: Intraarticular

value: Intramuscular

value: SDAI Class 2

value: Male

value: Hand-rolled tobacco

value: 1-2 days a year

value: Wrist (right)


title: WTCHG_306408_208

value: RNA-Tempus

value: U/ml

value: Oral

value: No

value: IU/ml

value: Current Smoker

value: Weekly

value: 6 days/week

value: SDAI Class 1

value: Female

value: Cigarrette

value: u/ml

value: Lost to follow-up

value: 1-2 days a month

value: iu/ml


title: WTCHG_306408_209

value: Yes

value: Previous Smoker

value: White- British

value: Twice daily

value: Subcutaneous

value: DAS28CRP Class 2

value: Completed

value: 3 - 4 days a week

value: Intramuscular


title: WTCHG_306408_211

value: RNA-Tempus

value: U/ml

value: No

value: Never Smoked

value: Once daily

value: Oral

value: IU/ml

value: Weekly

value: DAS28CRP Class 1

value: SDAI Class 2

value: 5 or more days a week


title: WTCHG_306408_216

value: U/mL

value: Eu/mL

value: Yes

value: 6 days/week

value: White- British

value: SDAI Class 1

value: Female

value: 1-2 days a year

value: Knee (right)

value: Intraarticular


title: WTCHG_306408_206

value: RNA-Tempus

value: U/ml

value: No

value: Never Smoked

value: Twice daily

value: DAS28CRP Class 3

value: IU

value: Completed

value: 3 - 4 days a week

value: more than 20


title: WTCHG_306408_207

value: u/ml

value: Oral

value: iu/ml

value: Yes

value: Current Smoker

value: 2 days/week

value: Weekly

value: SDAI Class 2

value: Hand-rolled tobacco

value: 1-2 days a week


title: WTCHG_306408_215

value: RNA-Tempus

value: No

value: lu/ml

value: White- British

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: IU/ml

value: Intramuscular

value: Once daily


title: WTCHG_306408_210

value: U/mL

value: Oral

value: IU/mL

value: Yes

value: Previous Smoker

value: DAS28CRP Class 3

value: Cigarrette

value: Completed

value: 3 - 4 days a week

value: iU/mL


title: WTCHG_306408_205

value: RNA-Tempus

value: U/ml

value: No

value: Asian or Asian British - Indian

value: Weekly

value: SDAI Class 2


title: WTCHG_306408_213

value: 6 days/week

value: White- British

value: DAS28CRP Class 1

value: Female

value: Soft tissue


title: CD34+_cells_after_8days_culture

city: New York

first: Minkui

last: Luo

address: 1275 York Avenue

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina bcl2fastq2 v2.19 was used for demultiplexing and fastq generation.
Raw fastq data were processed and converted to single-cell expression counts matrix following the standard Drop-seq computational pipeline v1.12 developed by McCarrol lab (http://mccarrolllab.org/dropseq/). Briefly, barcodes and unique molecular identifiers (UMIs) were extracted and corrected for bead synthesis errors. Raw reads were trimmed for adapter and ploy-A sequences, followed by alignment to human GRCh37 reference genome using STAR v2.5.2b (Dobin et al., 2013). The number of captured cells was determined by selecting the “knee” point in the cumulative distribution of reads. The matrices of single-cell expression count were generated by counting UMIs per gene in captured cells.
Genome_build: hg19
Supplementary_files_format_and_content: UMI counts matrix in txt format; each row represents a gene and each column represents a cell; cells from each sample were labeled with the following prefix: 'R1M1' and 'R1M2' for Sample 1, 'R1M3' and 'R1M4' for Sample 2, 'R1M5' and 'R1M6' for Sample 3, 'R1M7' and 'R1M8' for Sample 4.

source_name: cord blood

extract_protocol:
The procedure of scRNA-seq followed the C version 3.1 from Steve McCarroll’s lab (http://mccarrolllab.org/wp-content/uploads/2015/05/Online-Dropseq-Protocol-v.- 3.1-Dec-2015.pdf). Briefly, 1 mL of the samples containing approximately 100,000 cells with 90% viability were processed using microfluidic devices (PMDS Microfluidic Devices, FlowJEM). 8,000~10,000 cells were encapsulated in microfluidic droplets with 3000~4000 single cells recovered after washing and enzymatic steps. The resultant emulsion droplets were broken and subject to reverse transcription, followed by 14 cycles of PCR amplification---95 °C for 3 min, 4 x (98 °C for 20 s, 65 °C for 45 s, 72 °C for 3 min), 10 x (98 °C for 20 s, 67 °C for 20 s, 72 °C for 3 min), and 72 °C for 5 min. After purification with AMPure XP beads (Beckman Coulter), 600 pg barcoded cDNA was fragmented by Amplicon Tagment enzyme using Nextera XT Kit (Illumina), followed by indexing PCR--95 °C for 30 s, 12 x (95 °C for 10 s, 55 °C for 30 s, 72 °C for 30 s), and 72 °C for 5 min. The resulting DNA library was further purified with 0.6 x AMPure XP beads before sequencing.
Libraries were sequenced on Illumina NextSeq 500 platform (R1- 20 cycles, index1- 8 cycles, R2- 64 cycles). Samples were demultiplexed and raw fastq data were generated using bcl2fastq2 v2.19

tag: population

value: cultured CD34 cells in TPO and SCF


title: CD41+CD42+_cells

value: sorted from sample 2

tag: sort

value: sorted megakaryocytes


title: non-CD41+CD42+_cells

value: cells other than megakaryocytes


title: WTCHG_306408_212

value: U/mL

value: iu/mL

value: Yes

value: Never Smoked

value: Wrist (right)

value: Oral

value: Intraarticular

value: DAS28CRP Class 3

value: Completed

value: 1-2 days a week


title: WTCHG_306408_203

value: RNA-Tempus

value: U/ml

value: No

value: IU/ml

value: Previous Smoker

value: Weekly

value: White- British

value: Twice daily

value: SDAI Class 2

value: Cigarrette


title: WTCHG_306408_202

value: Never Smoked

value: Yes

value: Intramuscular

value: DAS28CRP Class 1

value: Female

value: 1-2 days a month

value: Once daily


title: MOLM13_dgSTK35-PDIK1L_rep4

city: Cold Spring Harbor

first: Sofya

middle: A

last: Polyanskaya

state: NY

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

description:
210311_Salmon_tpm_MOLM13_SCP4_STK35PDIK1L.txt
200701_DeSeq2_MOLM13_dgSTK35_PDIK1L.txt
210203_Kallisto_MOLM13_dgSTK35_PDIK1L_vs_sgROSA_Polyanskaya.csv

data_processing:
Sequencing reads were mapped onto reference human genome hg19 using STAR v.2.5.2b-1
The mapped reads were assigned to genes using HTSeq-Count v.0.6.1p1
The differential expression gene analysis was performed using DESeq2, with four replicates for each sample
Pesudo-alignment to the reference human transcriptome (gencode v.35), assignment of reads to genes, and TPM calculation were all performed using Salmon (v.1.0)
This, GSE109491, and GSE104308 datasets raw data were re-analyzed together using Kallisto pipeline
This, GSE109491, and GSE104308 datasets were aligned (pseudo-alignment) using Kallisto to hg38, bootstrap 100
The differential expression gene analysis was performed using DESeq2, with [MOLM13_sgROSA_rep1; MOLM13_sgROSA_rep2; MOLM13_sgROSA_rep3; MOLM13_sgROSA_rep4]; [MOLM13_sgSCP4_rep1; MOLM13_sgSCP4_rep2; MOLM13_sgSCP4_rep3; MOLM13_sgSCP4_rep4]; [MOLM13_dgSTK35-PDIK1L_rep1; MOLM13_dgSTK35-PDIK1L_rep2; MOLM13_dgSTK35-PDIK1L_rep3; MOLM13_dgSTK35-PDIK1L_rep4]; [GSM2944342; GSM2944341]; [GSM2944348; GSM2944347]; [GSM2944344; GSM2944343]; [GSM2794837; GSM2794836]; [GSM2794841;GSM2794840]; [GSM2794839; GSM2794838] treated as replicates.
Genome_build: hg19; hg38
Supplementary_files_format_and_content: two tab-delimited text files of DeSeq2 outputs for sgSCP4 and dgSTK35PDIK1L vs sgROSA
Supplementary_files_format_and_content: matrix table with Salmon tpm counts for every gene and every sample in this dataset
Supplementary_files_format_and_content: six comma-separated values files of Kallisto outputs for knockouts from this, GSE109493 ([GSM2794837; GSM2794836]; [GSM2794841;GSM2794840]; [GSM2794839; GSM2794838]), and GSE104309 ([GSM2944342; GSM2944341]; [GSM2944348; GSM2944347]; [GSM2944344; GSM2944343]) datasets

molecule: polyA RNA

source_name: acute myeloid leukemia

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin/streptomycin

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: Cells were lentivirally infected with sgSTK35-sgPDIK1L bi-cistronic vector encoding two guideRNAs coupled to the blasticidin resistance gene for simultaneous knockout of STK35 and PDIK1L, 1 μg/mL blasticidin was added 24 hours post-infection, cells were harvested on day 5 post-infection

tag: cell line

tag: treatment

value: :day 5 after sgSTK35-sgPDIK1L bi-cistronic vector encoding two guideRNAs infection


title: WTCHG_306408_201

value: RNA-Tempus

value: U/ml

value: Oral

value: Current Smoker

value: DAS28CRP Class 3

value: Male

value: Completed

value: 1-2 days a week


title: WTCHG_306408_230

value: No

value: iu/ml

value: Weekly

value: White- British

value: Twice daily

value: DAS28CRP Class 2

value: SDAI Class 1

value: 1-2 days a year

value: IU/ml


title: MOLM13_dgSTK35-PDIK1L_rep3

value: :day 5 after sgSTK35-sgPDIK1L bi-cistronic vector encoding two guideRNAs infection


title: MOLM13_dgSTK35-PDIK1L_rep2


title: MOLM13_dgSTK35-PDIK1L_rep1


title: MOLM13_sgSCP4_rep4

description:
210311_Salmon_tpm_MOLM13_SCP4_STK35PDIK1L.txt
200701_DeSeq2_MOLM13_sgSCP4.txt
210203_Kallisto_MOLM13_sgSCP4_vs_sgROSA_Polyanskaya.csv

treatment_protocol: Cells were lentivirally infected with sgSCP4 guideRNA coupled to the blasticidin resistance gene for knockout, 1 μg/mL blasticidin was added 24 hours post-infection, cells were harvested on day 5 post-infection

value: :day 5 after sgSCP4 guideRNA infection


title: WTCHG_306408_222

value: RNA-Tempus

value: Oral

value: Yes

value: Once daily

value: Intramuscular

value: Female

value: Cigarrette

value: U/ml


title: MOLM13_sgSCP4_rep2


title: MOLM13_sgSCP4_rep1


title: MOLM13_sgROSA_rep4

description: 210311_Salmon_tpm_MOLM13_SCP4_STK35PDIK1L.txt

treatment_protocol: Cells were lentivirally infected with sgROSA guideRNA coupled to the blasticidin resistance gene for knockout, 1 μg/mL blasticidin was added 24 hours post-infection, cells were harvested on day 5 post-infection

value: :day 5 after sgROSA guideRNA infection


title: WTCHG_306408_217

value: No

value: IU

value: Previous Smoker

value: Weekly

value: White- British

value: 5 days/week

value: Completed

value: 3 - 4 days a week

value: iu/ml

value: Intraarticular

value: Knee (right)


title: MOLM13_sgROSA_rep2


title: MOLM13_sgROSA_rep1


title: MOLM13_sgROSA_rep3


title: Crohns_Treatment naïve 29

city: Southampton

first: Sarah

last: Ennis

state: Hampshire

address: Southampton General Hospital, SO16 6YD

department: Human Development and Health

institute: University of Southampton

data_processing:
Sequencing output basecalls were converted int FASTQ and demultiplexed using module bcl2fastq2/2.18 on IRIDIS HPS (UoS), adding the option --barcode-mismatches 0.
FASTQ files were parsed on HTG EdgeSeq parser (v 5.2.823).
Construction of  a gene expression count matrix for each gene and each patient. They were merged to form a single output file containing all genes and all counts.
HTG Reveal, a web-based, GDPR-compliant data analysis suite.
Quality control of RNA sequencing data was performed in line with recommendations from HTG, to satisfy cut-offs for sample quality, sufficient read depth and minimal expression variability across probes.
Differential expression was assessed using DESeq2 package (Python, within Reveal software, 2020 version).
Gene-co-expression networks enable regulatory hubs and gene-gene associations to be determined. CEMiTool (2020 version) was used to assess weighted gene co-expression networks within normalized data, and to determine modules and hub regulatory genes observed in different categorical group.
Gene-Gene interactions within co-expressed genes were determined using the HitPredict database.
WGCNA (R package) was used to establish gene co-expression modules and assess correlation between continuous clinical outcome variables.
Assessment for enrichment of genes in specific WGCNA modules, and differentially expressed genes (DEGs), in specific pathways using ToppFun, EnRichR and BioPlanet.

source_name: Ileal

extract_protocol:
Biopsies were homogenised using Qiagen TissueLyser. RNA was extracted using Promega Maxwell RSC (simplyRNA tissue). RNA quality was assessed using the  Agilent Bioanalyzer (RNA Nano).
RNA samples were thawed, diluted and 25ng of RNA per sample was plated in 96 wells and loaded onto the HTG EdgeSeq instrument. HTG fully automated nuclease target protection chemistry includes hybridization of mRNA to target-specific Nuclease Protection Probes (NPPs), addition of S1 nuclease to digest excess NPPs and non-hybridized RNA followed by heat denaturation of S1. The processed samples contain 5’ and 3’-end wing sequences and were used as a template for PCR reactions with primers complementary to the “wings” which also contain barcode sequences and common adaptors required for cluster generation and sequencing (P5, P7). Libraries were cleaned-up following a standard clean-up procure (AMPureXP, PEG8000) and quantified with qPCR using KAPA Library quantification (Roche) kit. Libraries were normalized accordingly, were pooled in a 3pM concentration and were loaded on the Illumina NextSeq500 for single read deep sequencing (Read1: 50bp, Index1: 6bp, Index2: 6bp).

tag: tissue

value: Ileal

tag: type

value: Biopsy frozen in RNALater

value: Crohns_Treatment naive


title: WTCHG_306408_214

value: RNA-Tempus

value: Oral

value: IU/ml

value: Yes

value: Current Smoker

value: Twice daily

value: Intramuscular

value: 6 days/week

value: DAS28CRP Class 2

value: SDAI Class 1

value: Female

value: Cigarrette

value: Withdrawn -lost to follow up

value: 1-2 days a month


title: Crohns_Treatment naïve 28

value: Ileal


title: Control 17

value: Biopsy frozen in RNALater

value: Control


title: Crohns_Treatment naïve 27

value: Crohns_Treatment naive


title: Crohns_Established disease 28

value: Crohns_Established disease


title: Native_CD34+_cells

value: CD34+ cells


title: Control 15


title: WTCHG_306408_204

value: RNA-Tempus

value: u/mL

value: Oral

value: No

value: Yes

value: Never Smoked

value: Weekly

value: Mixed - White and Black Caribbean

value: DAS28CRP Class 3

value: SDAI Class 2

value: u/ml

value: Completed

value: 1-2 days a year


title: Control 16

value: Ileal

value: Biopsy frozen in RNALater

value: Control


title: UC_Established disease 26

value: UC_Established disease


title: IBDU_Treatment naïve 4

value: IBDU_Treatment naive


title: Crohns_Established disease 26

value: Crohns_Established disease


title: Crohns_Treatment naïve 23

value: Crohns_Treatment naive


title: UC_Treatment naïve 15

value: UC_Treatment naive


title: Crohns_Established disease 27


title: Crohns_Treatment naïve 25


title: UC_Treatment naïve 13


title: UC_Treatment naïve 14


title: Crohns_Treatment naïve 24


title: Control 14


title: Control 13


title: Crohns_Treatment naïve 21


title: Crohns_Treatment naïve 22


title: Crohns_Established disease 25


title: Control 12


title: Control 11


title: MOLM13_sgSCP4_rep3

value: :day 5 after sgSCP4 guideRNA infection


title: Crohns_Treatment naïve 20


title: Control 10


title: Crohns_Established disease 29


title: Late_Comp_Screen_YPD_Day5_Rep3

city: Berkeley

first: Tina

middle: Lynn

last: Sing

state: California

address: Barker Hall, Rm 616, University of California, Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Inducible cDNA library transformed into yeast
Sample 175

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Sequencing reads were aligned to the SK1 genome using HISAT2
Transcripts per million reads (TPM) were calculated with STRINGTIE
Genome_build: SK1 genome from Saccharomyces Genome Resequencing Project (Sanger Institute)
Supplementary_files_format_and_content: Tab-delimited text output files from STRINGTIE include TPM values for each gene

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: All cells were grown in the indicated liquid media. E. coli were grown at 37˚C and S. cerevisiae were grown at 30˚C. G418 was added to all S. cerevisiae cultures to maintain plasmid selection.

extract_protocol:
mRNA and plasmid extracts were all performed using standard techniques.
mRNA was isolated with Oligo(dT)25 Dynabeads (Ambion) and libraries were preparerd with the NEXTFLEX Rapid Directional RNA-seq Kit (PerkinElmer). cDNA sequencing libraries were prepared with the NEXTFLEX Rapid DNA-seq Kit (PerkinElmer).
mRNA-seq (Samples 1-10) and DNA-seq (Samples 11-175)

treatment_protocol: cDNA libraries were induced by growing S. cerevisiae in media containing galactose (YPGR) or uninduced by growing in media containing glucose (YPD).

tag: strain

value: UB20279 + pUB914-<Late cDNA library>

tag: meiotic cdna library

value: Late Meiosis

tag: growth condition

value: YPD + G418


title: Crohns_Treatment naïve 18


title: Crohns_Treatment naïve 19


title: Crohns_Treatment naïve 17


title: Late_Comp_Screen_YPD_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 174


title: Late_Comp_Screen_YPD_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 172


title: Late_Comp_Screen_YPD_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 171


title: Late_Comp_Screen_YPD_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 173


title: Crohns_Treatment naïve 26


title: Control 9


title: UC_Established disease 25


title: Late_Comp_Screen_YPGR_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 170

value: YPGR + G418


title: Crohns_Treatment naïve 14


title: Crohns_Treatment naïve 15


title: Late_Comp_Screen_YPGR_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 169


title: Crohns_Treatment naïve 16


title: Late_Comp_Screen_YPGR_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 166


title: Late_Comp_Screen_YPD_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 164


title: Late_Comp_Screen_YPGR_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 167


title: Late_Comp_Screen_YPD_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 163


title: Late_Comp_Screen_YPGR_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 168


title: Crohns_Established disease 24


title: UC_Treatment naïve 12


title: Crohns_Treatment naïve 11


title: Crohns_Treatment naïve 12


title: Late_Comp_Screen_YPD_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 165


title: UC_Treatment naïve 11


title: UC_Treatment naïve 10


title: Crohns_Treatment naïve 10


title: Late_Comp_Screen_YPD_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 161


title: Late_Comp_Screen_YPGR_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 160


title: Crohns_Treatment naïve 9


title: Late_Comp_Screen_YPGR_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 159


title: Late_Comp_Screen_YPGR_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 158


title: Crohns_Treatment naïve 13


title: Control 8


title: Crohns_Treatment naïve 8


title: Late_Comp_Screen_YPGR_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 157


title: Late_Comp_Screen_YPGR_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 156


title: Late_Comp_Screen_YPD_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 155


title: Crohns_Established disease 23


title: Control 7


title: Late_Comp_Screen_YPD_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 162


title: Late_Comp_Screen_YPD_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 154


title: Late_Comp_Screen_YPD_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 153


title: Crohns_Established disease 22


title: UC_Treatment naïve 8


title: Late_Comp_Screen_YPGR_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 146


title: Control 6


title: UC_Established disease 8


title: UC_Treatment naïve 9


title: Control 4


title: Crohns_Treatment naïve 7


title: Late_Comp_Screen_YPD_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 151


title: Late_Comp_Screen_YPD_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 152


title: Crohns_Treatment naïve 6


title: Late_Comp_Screen_YPGR_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 150


title: Late_Comp_Screen_YPGR_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 149


title: Crohns_Established disease 21


title: Late_Comp_Screen_YPGR_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 147


title: Late_Comp_Screen_YPGR_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 148


title: UC_Established disease 6


title: Crohns_Treatment naïve 4


title: Control 3


title: Crohns_Treatment naïve 5


title: Control 5


title: MeiosisI_Comp_Screen_YPD_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 115

value: UB20279 + pUB914-<Meiosis I cDNA library>

value: Meiosis I


title: Crohns_Established disease 18


title: UC_Established disease 7


title: MeiosisI_Comp_Screen_YPD_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 112


title: MeiosisI_Comp_Screen_YPD_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 114


title: IBDU_Treatment naïve 3


title: MeiosisI_Comp_Screen_YPGR_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 110


title: MeiosisI_Comp_Screen_YPD_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 104


title: Crohns_Established disease 20


title: MeiosisI_Comp_Screen_YPGR_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 109


title: Control 1


title: MeiosisI_Comp_Screen_YPGR_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 100


title: MeiosisI_Comp_Screen_YPGR_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 108


title: UC_Established disease 5


title: Crohns_Established disease 19


title: MeiosisI_Comp_Screen_YPGR_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 107


title: Crohns_Treatment naïve 2


title: MeiosisI_Comp_Screen_YPD_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 113


title: IBDU_Treatment naïve 2


title: MeiosisI_Comp_Screen_YPGR_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 106


title: MeiosisI_Comp_Screen_YPD_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 105


title: MeiosisI_Comp_Screen_YPD_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 111


title: Crohns_Established disease 15


title: MeiosisI_Comp_Screen_YPD_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 103


title: Crohns_Established disease 12


title: Control 2


title: MeiosisI_Comp_Screen_YPD_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 102


title: MeiosisI_Comp_Screen_YPGR_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 99


title: Crohns_Established disease 11


title: IBDU_Treatment naive 1


title: Crohns_Established disease 17


title: Crohns_Established disease 10


title: MeiosisI_Comp_Screen_YPD_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 101


title: Crohns_Established disease 16


title: Crohns_Established disease 14


title: MeiosisI_Comp_Screen_YPGR_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 97


title: MeiosisI_Comp_Screen_YPGR_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 98


title: MeiosisI_Comp_Screen_YPD_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 94


title: MeiosisI_Comp_Screen_YPGR_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 90


title: MeiosisI_Comp_Screen_YPD_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 91


title: Crohns_Established disease 6


title: MeiosisI_Comp_Screen_YPD_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 95


title: MeiosisI_Comp_Screen_YPGR_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 96


title: MeiosisI_Comp_Screen_YPD_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 93


title: MeiosisI_Comp_Screen_YPD_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 92


title: Crohns_Treatment naïve 1


title: UC_Established disease 3


title: Early_Comp_Screen_YPD_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 83

value: UB20279 + pUB914-<Early cDNA library>

value: Early Meiosis


title: Crohns_Established disease 9

value: Ileal


title: Early_Comp_Screen_YPD_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 85


title: Early_Comp_Screen_YPD_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 82


title: Crohns_Established disease 8

value: Biopsy frozen in RNALater


title: Crohns_Established disease 7


title: MeiosisI_Comp_Screen_YPGR_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 89


title: MeiosisI_Comp_Screen_YPGR_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 88


title: Early_Comp_Screen_YPGR_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 79


title: Crohns_Established disease 13


title: Crohns_Established disease 5


title: MeiosisI_Comp_Screen_YPGR_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 86


title: Early_Comp_Screen_YPGR_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 78


title: Early_Comp_Screen_YPGR_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 77


title: Crohns_Established disease 4


title: MeiosisI_Comp_Screen_YPGR_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 87


title: Early_Comp_Screen_YPD_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 84


title: UC_Established disease 4


title: Crohns_Established disease 3


title: Early_Comp_Screen_YPD_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 73


title: WT_norm_R2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Reads were mapped against the human genome (GRCh38) and human rRNA sequences using ContextMap 2.7.9 with BWA as internal alignment program.
Read counts per gene (from ENSEMBL version 85) were calculated using the featureCounts program from the subread package (v1.4.6-p3).
Genome_build: GRCh38
Supplementary_files_format_and_content: read counts

source_name: 1205Lu WT cells

growth_protocol: 1205Lu cells were cultivated in DMEM supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/l penicillin, 0.1 mg/ml streptomycin (all gibco®, Thermo Fisher Scientific, Karlsruhe, Germany).

extract_protocol:
Total cellular RNA was isolated using PeqGold Total RNA Kit (VWR International GmbH, Darmstadt, Germany) according to manufacturer’s recommendations.
Contaminating DNA was removed with RapidOut DNA Removal Kit (Thermo Fisher Scientific). mRNA enrichment and cDNA library preparation were done using Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra II Directional RNA Library Prep Kit (both New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: Cells were plated in 12 well plates with or without 1000 U/ml human IFN-α2a (research grade (Miltenyi)) the day before transfection. 3p-RNA was transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s instructions.  0.1 nmol of RNA was complexed using 2.5 µl of transfection reagent.

tag: genotype

value: WT (no KO)

value: no IFN-alpha2a (1000 U/ml) stimulation, no RNA stimulation


title: Early_Comp_Screen_YPD_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 72


title: Crohns_Established disease 2


title: Early_Comp_Screen_YPD_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 81


title: Early_Comp_Screen_YPGR_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 80


title: WT_3p6h_R2

value: 3p-RNA (160 nM) for 6 h


title: Early_Comp_Screen_YPGR_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 70


title: WT_3p6h_R1


title: UC_Established disease 2

value: UC_Established disease


title: Crohns_Established disease 1

value: Crohns_Established disease


title: Early_Comp_Screen_YPGR_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 69


title: Early_Comp_Screen_YPGR_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 68


title: Early_Comp_Screen_YPGR_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 67


title: UC_Established disease 1


title: KO_i4h_R3

source_name: 1205Lu RIG-IKO cells

value: DDX58 KO (RIG-I)

value: IFN-alpha2a (1000 U/ml) stimulation for 4 h


title: Early_Comp_Screen_YPGR_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 76


title: KO_i18h_R3

value: IFN-alpha2a (1000 U/ml) pre-stimulation for 18 h, no RNA stimulation


title: Early_Comp_Screen_YPD_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 63


title: Early_Comp_Screen_YPD_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 62


title: SOPR0472

first: James

middle: David

last: Davies

address: LE57, Lab and Pathology block, Tremona Road

department: Clinical and Experimental Sciences

data_processing:
A total of 1000 STAMPs from each donor were subjected to sequencing. STAMPs from each donor were split equally over two shared NextSeq runs to minimise batch effects between samples.
Samples were de-multiplexed with bcl2fastq tool from Illumina
Reads were  aligned to human_hg19 reference genome using STAR
Genome_build: hg19
Supplementary_files_format_and_content: aligned reads; raw counts

source_name: SOPR0472 donor ileal tissue

growth_protocol: IBD patient ileal biopsies were collected and digested with liberase TM (90 minutes, +37C). Single cell suspensions of whole ileal tissue was then processed through the Drop-seq single cell RNA-sequencing pipeline.

extract_protocol: Single cell suspensions of ileal biopsy tissue were co-encapsulated with genetically-encoded beads (Drop-seq). Monodisperse droplets at 1 nl in size were generated using the microfluidic devices fabricated in the Centre for Hybrid Biodevices, University of Southampton. Following encapsulation, approximately 1000 STAMPS (beads exposed to a single cell) for each donor were taken further for library prep. The resulting libraries were run on 2 shared NextSeq runs (1.5x105 reads for maximal coverage) at the Wessex Investigational Sciences Hub laboratory, University of Southampton, to obtain single cell sequencing data.

tag: subject status

value: Inflammatory bowel disease (IBD) patient

value: ileal biopsies


title: SOPR0476

source_name: SOPR0476 donor ileal tissue

value: digested with liberase TM (90 minutes, +37C)


title: KO_norm_R3


title: Early_Comp_Screen_YPD_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 75

value: YPD + G418


title: KO_i18h_R1


title: WT_norm_R3


title: KO_3p6i18h_R2

value: IFN-alpha2a (1000 U/ml) pre-stimulation for 18 h, 3p-RNA (160 nM) for 6 h


title: KO_3p6i18h_R3


title: Early_Comp_Screen_YPD_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 74

value: UB20279 + pUB914-<Early cDNA library>


title: WT_norm_R1


title: Early_Comp_Screen_YPD_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 65

value: Early Meiosis


title: KO_3p6i18h_R1


title: Early_Comp_Screen_YPD_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 71


title: WT_3p6h_R3


title: Early_Comp_Screen_YPGR_Day_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 57

value: YPGR + G418


title: Early_Comp_Screen_YPGR_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 56


title: KO_norm_R1


title: KO_norm_R2


title: Early_Comp_Screen_YPGR_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 66


title: KO_i4h_R1


title: Starvation_Comp_Screen_YPD_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 53

value: UB20279 + pUB914-<Starvation cDNA library>

value: Starvation


title: KMS-11_sh9_B

city: Pamplona

first: Teresa

last: Ezponda

state: Navarra

address: Pio XII 55

department: Hematology/Oncology

country: Spain

institute: Center for Applied Medical Research

description:
KMS11 cell line infected with the shRNA.B targeting LINC-SMILO 4 days after lentiviral infection.
Low input 3’ end RNA-Seq.
processed data file: DataRaw_ReadCounts.txt

data_processing:
Illumina Casava software used for basecalling (NexSeq 500).
Demultiplexing with bcl2fastq2 Conversion Software v2.19 of Illumina.
Quality control analyzed with FastQC.
The reads in the FASTQ files were aligned to the GRCh19/hg19 human genome (GENECODE 25) with Bowtie 2 version 2.3.1.
Data was sorted, indexed and converted to BAM files with SAMtools v1.6.
Aligned reads were quantified using quant3p script.
Genome_build: hg19 (GENECODE v25)
Supplementary_files_format_and_content: DataRaw_ReadCounts.txt: Tab-delimited text file including raw counts for each Sample.

source_name: Myeloma plasma cell

growth_protocol: KMS-11 cell line was cultured in RMPI-1640 medium supplemented with 10% FBS, 1% Penicillin/Streptomycin and 2% HEPES. Cell line was maintained at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol:
One million cells of each KMS-11 infected condition were collected and washed with Phosphate Buffered Saline (PBS) 1X. RNA was harvested using Trizol reagent following the manufacturer’s recommendations.
Protocol reproduced from: Jaitin, D. A. et al. (2014) ‘Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.’, Science, 343(6172), pp. 776–9.

treatment_protocol: After 48 hours of infection KMS-11 cells were selected with puromycin (2ug/ml). Cells were harvested after 4 days of lentiviral infection.

value: Multiple myeloma cell line

tag: Sex

value: Female

tag: age

tag: shRNA

value: LINC-SMILO


title: KMS-11_sh9_A

tag: cell type


title: KMS-11_Scramble_A

description:
KMS11 cell line infected with the pLKO.1-puro_scramble vector 4 days after lentiviral infection.
Low input 3’ end RNA-Seq.
processed data file: DataRaw_ReadCounts.txt

value: Scramble


title: Starvation_Comp_Screen_YPGR_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 48


title: Starvation_Comp_Screen_YPGR_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 49


title: Early_Comp_Screen_YPGR_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 60


title: KO_i18h_R2

value: DDX58 KO (RIG-I)


title: Early_Comp_Screen_YPD_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 61


title: Early_Comp_Screen_YPGR_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 59


title: KO_i4h_R2

value: IFN-alpha2a (1000 U/ml) stimulation for 4 h


title: Early_Comp_Screen_YPGR_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 58


title: PSlow

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Partek
Trim tags, Align to STAR - 2.7.3a, Deduplicate UMIs, Filter Barcodes -> Single Cell Counts
Filter Total reads: (Min: 1,766, Max: 150,213)  Expressed genes: (Min: 500, Max: 4,000)  Mitochondrial reads percent: (Min: 0%, Max: 15.00%)
Normalize CPM (counts per million)  Add: 1.0  Log: 2.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
Nick Ceglia
Filtered gene expression matrices were generated using 10X CellRanger (version 3.1.0).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 4.0.0) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each sample with five mouse using antibody barcode patterns from TotalSeq.
Mouse specific barcodes were demultiplexed by HTO using Seurat (version 3.1).
Genome_build: Ensembl mm10
Supplementary_files_format_and_content: _matrix.mtx mtx (matrix market format) Gene by Cell Count Matrix
Supplementary_files_format_and_content: _genes.tsv tsv Ensembl Transcript Ids and Gene Symbols
Supplementary_files_format_and_content: _barcodes.tsv tsv Filtered Cell Barcodes
Supplementary_files_format_and_content: _filtered_contig_annotations.csv csv Barcoded VDJ sequences and annotation data
Supplementary_files_format_and_content: _demultiplexed_barcodes.csv csv Cell barcode to mouse by HTO

organism: Mus musculus

source_name: Sorted CD8 T cells from peritoneal cavity

growth_protocol: Sorted in vivo CD8 TIL

extract_protocol:
The single cell suspension was loaded onto a Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, and cDNA amplification.
Library preparation of 10,000 cells proceeded using the Chromium Single Cell 5’ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 16 cycles and 11-50ng of the material was used to prepare sequencing libraries with 14-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 or NextSeq 500 in a 26bp or 28bp/91bp paired end run using the NovaSeq 6000 S1 or S2 Reagent Kit (100 cycles) or NextSeq 500/550 High Output Kit v2.5 (150 cycles) (Illumina). An average of 256 million paired reads was generated per sample.
scRNA/TCR sequencing with feature barcoding

treatment_protocol: Mice were treated with anti-Tim-4 and anti-PD-1 on days 7 and 10 after tumor challenge

tag: cd8 t cell subset

value: PSlow


title: Early_Comp_Screen_YPD_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 64


title: KO_3p6h_R2

value: 3p-RNA (160 nM) for 6 h


title: KMS-11_Scramble_B


title: Starvation_Comp_Screen_YPD_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 55


title: Starvation_Comp_Screen_YPD_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 52


title: Starvation_Comp_Screen_YPD_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 54


title: Starvation_Comp_Screen_YPGR_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 50


title: Starvation_Comp_Screen_YPD_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 43


title: RNASeq CD8T REH 1.5h rep1

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: CD8T REH 1.5h

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.1.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Genome_build: mm10

source_name: spleen & lymph node

growth_protocol: Tregs were isolated from B6-Foxp3EGFP mice using CD4+ T cell isolation kit (Miltinyi) followed by fluorescence activated cell sorting (FACS) for GFP expression to isolate Tregs. CD8+ T cells were isolated from C57BL/6J mice using CD8+ T cell isolation kit (Miltinyi).

extract_protocol:
RNA was extracted using the Zymo RNA miniprep kit (Zymo Research). 500 ng RNA was used for RNA-Seq library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems)
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq3000 system.

treatment_protocol: Isolated cells were stimulated with 200nM IL-2 or IL-2-REH

value: CD8+ T cells

value: REH

tag: time


title: KO_3p6h_R1


title: Starvation_Comp_Screen_YPGR_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 47


title: PShigh

value: PShigh


title: Starvation_Comp_Screen_YPD_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 45

value: YPD + G418


title: KO_3p6h_R3


title: Starvation_Comp_Screen_YPD_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 51


title: Starvation_Comp_Screen_YPD_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 44


title: Starvation_Comp_Screen_YPGR_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 46


title: Starvation_Comp_Screen_YPGR_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 40


title: RNASeq Treg REH 4h rep3

description: Treg REH 4h

value: Tregs


title: Starvation_Comp_Screen_YPD_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 41


title: RNASeq CD8T REH 4h rep1

description: CD8T REH 4h


title: RNASeq CD8T IL2 4h rep1

description: CD8T IL2 4h


title: RNASeq Treg IL2 1.5h rep3

description: Treg IL2 1.5h


title: Starvation_Comp_Screen_YPGR_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 39


title: RNASeq CD8T IL2 1.5h rep1

description: CD8T IL2 1.5h


title: Starvation_Comp_Screen_YPD_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 42


title: RNASeq CD8T 0h rep1

description: CD8T 0h


title: RNASeq Treg 0h rep3

description: Treg 0h


title: RNASeq Treg IL2 4h rep2

description: Treg IL2 4h


title: RNASeq Treg REH 1.5h rep3

description: Treg REH 1.5h


title: RNASeq Treg REH 4h rep2

description: Treg REH 4h


title: RNASeq Treg REH 1.5h rep2

description: Treg REH 1.5h


title: Starvation_Comp_Screen_YPGR_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 38


title: Starvation_Comp_Screen_YPGR_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 36


title: RNASeq Treg REH 1.5h rep1

description: Treg REH 1.5h


title: RNASeq Treg IL2 4h rep3

description: Treg IL2 4h


title: RNASeq Treg 0h rep1

description: Treg 0h


title: RNASeq Treg IL2 1.5h rep2

description: Treg IL2 1.5h


title: Starvation_Comp_Screen_YPGR_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 37


title: RNASeq Treg REH 4h rep1

description: Treg REH 4h


title: RNASeq Treg 0h rep2

description: Treg 0h


title: Control_1_1

city: Shanghai

first: Hong

last: Tang

state: Shanghai

address: Life Science Research Building 320 Yueyang Road, Xuhui District, 200031

country: China

institute: Institut Pasteur of Shanghai, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 (version 2.0.5) and counts of transcripts were calculated using htseq-count.
Differential analyses between groups were performed using a count-based method limma, where voom is employed for normalization (Law et al., 2014; Liu et al., 2015). Genes of significant change were scored when the BH-adjusted P-value (Yoav Benjamini, 1995) was less than 0.05 and fold-change more than 2.
Functional analysis was performed using GSEA v3.0 PreRanked mode (Broad Institute) to identify the enriched of KEGG pathways and comparing targets gene sets of designated transcription factors (curated TRANSFAC) between groups. T-statistic output from limma was used as the metrics for ranking and 1,000 gene set permutations were set as default. A gene set with a FDR q value less than 0.05 was considered as significantly enriched.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD169+ macrophages

extract_protocol:
Total RNA extracted by Trizol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wt mice were i.v. injected with 2 μg HBsAg or OVA. After 2 hours, dLN and splenic macrophages were FACS sorted.

value: lymph node and spleen-derived CD169+ macrophages

value: wt


title: RNASeq Treg IL2 4h rep1

description: Treg IL2 4h


title: Starvation_Comp_Screen_YPGR_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 30

value: UB20279 + pUB914-<Starvation cDNA library>

value: YPGR + G418


title: Starvation_Comp_Screen_YPD_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 31

value: Starvation


title: Starvation_Comp_Screen_YPD_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 35


title: Starvation_Comp_Screen_YPGR_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 29


title: RNASeq Treg IL2 1.5h rep1

description: Treg IL2 1.5h


title: OVA_2_1


title: Starvation_Comp_Screen_YPGR_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 28


title: Starvation_Comp_Screen_YPD_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 34


title: Starvation_Comp_Screen_YPGR_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 27


title: Starvation_Comp_Screen_YPD_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 33


title: Starvation_Comp_Screen_YPD_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 32


title: Col_root_rep2

type: RNA

city: Guangzhou

first: Xianhai

last: Zhao

state: Guangdong

address: Wushan

department: College of Forestry and Landscape Architecture

institute: South China Agricultural University

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring (version13.1,Agilent Technologies) were employed to finish the basic analysis with the raw data.

organism: Arabidopsis thaliana

source_name: Wild-type Col-0, root sample

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: Seedlings were grown on vertical MS plates under long-day condition.

extract_protocol: Total RNA was extracted with the RNeasy Plant Kit (Qiagen).

treatment_protocol: Roots of 12 dpg seedlings were cut and about 30 roots were pooled as one biological replicates.

tag: ecotype background

tag: genotype/variation

value: wild type control

value: root

tag: developmental stage

value: 12 day after germination


title: Col_root_rep3


title: Control_2_1


title: OVA_3_1


title: HBV_3_1


title: HBV_4_1


title: Col_root_rep1


title: HBV_2_1


title: axs1-1 axs2-1/+_root_rep1

source_name: axs1-1 axs2-1/+ double mutant, root sample

value: axs1-1 axs2-1/+ mutant


title: axs1-1 axs2-1/+_root_rep3


title: KO-CCI TJ-41

city: Pittsburgh

first: Travis

middle: C.

last: Jackson

state: Pennsylvania

address: 3550 Terrace Street

department: Critical Care Medicine

institute: University of Pittsburgh

description:
KO-CCI
Gene expression data from mouse cortical brain tissue

hyb_protocol: 5 micrograms of fragmented and labeled ds-cDNA was incubated overnight (16h) hybridization at 45 degrees C with rotational mixing at 60 RPM. Arrays were processed on a GeneChip® 450 Fluidics Station using manufacturer specified protocols. To remove unbound sample, arrays were first washed with non-stringent wash buffer A. The GeneChips® were then stained for ten minutes in Stain cocktail 1.  Buffer A was again used to wash-off excess stain. Signal amplification was achieved by ten minutes incubation with Stain Cocktail 2 followed by a second ten minute incubation with Stain Cocktail 1.

scan_protocol: GeneChips were scanned using theGeneArray® 3000 scanner

data_processing: The data were analyzed with Tanscriptome Analysis Console (TAC) 4.0.

label: Biotin

source_name: Cortical Brain Tissue

label_protocol: Biotinylated cDNA were prepared and applified according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: 12-15wk old mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Animals were given anestheisa. Control animals were allowed to recover. Injured animals were given a crainotomy folled by a CCI-TBI. 48h later animals were pufused transcardially with cold PBS, brain tissue harvested, immediately flash-frozen in liquid nitrogen, and stored at -80C.

value: KO

tag: injury

value: CCI

tag: gender

value: Female


title: KO-CCI TJ-42


title: HBV_1_1


title: OVA_4_1


title: Starvation_Comp_Screen_YPGR_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 26


title: axs1-1 axs2-1/+_root_rep2

tag: tissue


title: Late_Yeast

description:
Inducible cDNA library transformed into yeast
Sample 25

tag: strain

value: UB20279 + pUB914-<Late cDNA library>

value: Late Meiosis


title: OVA_1_1


title: MeiosisII_Yeast

description:
Inducible cDNA library transformed into yeast
Sample 24

value: UB20279 + pUB914-<Meiosis II cDNA library>

tag: meiotic cdna library

value: Meiosis II


title: Starvation_Yeast

description:
Inducible cDNA library transformed into yeast
Sample 21

tag: growth condition

value: YPD + G418


title: KO-CCI TJ-40

tag: genotype

value: Male


title: Late_mRNA_Rep1

description:
mRNA isolated from synchronized meiotic time course
Sample 9

data_processing:
Sequencing reads were aligned to the SK1 genome using HISAT2
Transcripts per million reads (TPM) were calculated with STRINGTIE
Genome_build: SK1 genome from Saccharomyces Genome Resequencing Project (Sanger Institute)
Supplementary_files_format_and_content: Tab-delimited text output files from STRINGTIE include TPM values for each gene

value: sporulation media


title: MeiosisI_Yeast

description:
Inducible cDNA library transformed into yeast
Sample 23

value: UB20279 + pUB914-<Meiosis I cDNA library>

value: Meiosis I


title: Early_Yeast

description:
Inducible cDNA library transformed into yeast
Sample 22

value: UB20279 + pUB914-<Early cDNA library>

value: Early Meiosis


title: Late_mRNA_Rep2

description:
mRNA isolated from synchronized meiotic time course
Sample 10


title: KO-CCI TJ-24


title: KO-Sham TJ-32

description:
KO-Sham
Gene expression data from mouse cortical brain tissue

value: Sham


title: MeiosisI_mRNA_Rep1

description:
mRNA isolated from synchronized meiotic time course
Sample 5


title: KO-Sham TJ-31


title: KO-Sham TJ-11


title: KO-CCI TJ-23


title: Early_mRNA_Rep2

description:
mRNA isolated from synchronized meiotic time course
Sample 4


title: KO-Sham TJ-10


title: KO-Sham TJ-33


title: KO-CCI TJ-22


title: MeiosisII_mRNA_Rep2

description:
mRNA isolated from synchronized meiotic time course
Sample 8


title: WT-CCI TJ-36

description:
WT-CCI
Gene expression data from mouse cortical brain tissue

value: WT


title: KO-CCI TJ-21


title: WT-CCI TJ-35


title: KO-Sham TJ-12


title: MeiosisII_mRNA_Rep1

description:
mRNA isolated from synchronized meiotic time course
Sample 7


title: KO-Sham TJ-9


title: WT-CCI TJ-13


title: WT-Sham TJ-26

description:
WT-Sham
Gene expression data from mouse cortical brain tissue


title: MeiosisI_mRNA_Rep2

description:
mRNA isolated from synchronized meiotic time course
Sample 6


title: WT-Sham TJ-25


title: WT-CCI TJ-34


title: WT-CCI TJ-15


title: WT-CCI TJ-14