title: lib8404

description:
07-02-010-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8403

status: Public on Mar 27 2018

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

description:
07-08-144-3-NS
Processed data file: raw_counts_ureca23.txt

library_source: transcriptomic

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_ureca23.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted using TRIzol following the manufacturer's protocol (Invitrogen).
RNA quality was assessed using RNA electrophoresis (Agilent). All samples had RIN values ≥7. Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina).

tag: cell type

value: Peripheral blood mononuclear cell (PBMC)

tag: stim

value: NS

tag: group

value: Asthma

tag: full cohort classification

tag: bla g 1 bedroom level

tag: bla g 1 living room level

tag: der f 1 bedroom level

tag: der p 1 bedroom level

tag: der f 1 living room level

tag: der p 1 living room level

tag: phase


title: lib8402

description:
07-08-144-3-CR
Processed data file: raw_counts_ureca23.txt

value: CR


title: lib8400

description:
07-02-059-0-CR
Processed data file: raw_counts_ureca23.txt

value: CR sensitized


title: lib8401

description:
07-02-059-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8398

description:
07-08-148-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8397

description:
07-08-076-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8396

description:
07-08-076-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8393

description:
07-01-044-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8392

description:
07-01-044-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8434

description:
07-01-154-6-CR
Processed data file: raw_counts_ureca23.txt

value: Control

tag: cohort 2 classification

value: Neither


title: lib8388

description:
07-01-076-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8389

description:
07-01-076-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8390

description:
07-01-009-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8383

description:
07-02-085-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8386

description:
07-08-147-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib8387

description:
07-08-147-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8381

description:
07-08-153-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8382

description:
07-02-085-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8376

description:
07-02-033-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib8377

description:
07-02-033-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8379

description:
07-01-092-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8380

description:
07-08-153-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8378

description:
07-01-092-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8375

description:
07-02-069-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8374

description:
07-02-069-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8373

description:
07-08-125-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8372

description:
07-08-125-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8368

description:
07-08-126-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8369

description:
07-08-126-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8371

description:
07-08-158-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8370

description:
07-08-158-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8367

description:
07-08-165-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8391

description:
07-01-009-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8363

description:
07-01-013-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8399

description:
07-08-148-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8366

description:
07-08-165-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8362

description:
07-01-013-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8359

description:
07-01-155-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8357

description:
07-02-076-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8358

description:
07-01-155-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8356

description:
07-02-076-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8354

description:
07-07-013-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8348

description:
07-08-042-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8349

description:
07-08-042-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8347

description:
07-02-146-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8338

description:
07-08-097-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8346

description:
07-02-146-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8343

description:
07-01-100-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8337

description:
07-02-091-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8334

description:
07-07-005-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8336

description:
07-02-091-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib8341

description:
07-01-156-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8340

description:
07-01-156-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8332

description:
07-08-077-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8331

description:
07-08-065-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8329

description:
07-02-070-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8355

description:
07-07-013-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8330

description:
07-08-065-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8327

description:
07-02-024-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8325

description:
07-08-129-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8326

description:
07-02-024-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8322

description:
07-01-082-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8320

description:
07-08-163-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8321

description:
07-08-163-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8316

description:
07-01-167-6-CR
Processed data file: raw_counts_ureca23.txt

value: Case

value: CR-Late


title: lib8323

description:
07-01-082-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8342

description:
07-01-100-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8311

description:
07-02-061-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8335

description:
07-07-005-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8339

description:
07-08-097-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8333

description:
07-08-077-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8315

description:
07-01-124-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8314

description:
07-01-124-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8307

description:
07-08-082-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8310

description:
07-02-061-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8306

description:
07-08-082-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8328

description:
07-02-070-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8308

description:
07-07-035-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib8304

description:
07-01-088-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8324

description:
07-08-129-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8302

description:
07-08-050-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8301

description:
07-08-061-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8296

description:
07-08-075-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8300

description:
07-08-061-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8317

description:
07-01-167-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8295

description:
07-02-138-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8305

description:
07-01-088-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8289

description:
07-08-090-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8282

description:
07-08-154-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8283

description:
07-08-154-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8297

description:
07-08-075-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8279

description:
07-01-126-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8288

description:
07-08-090-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8280

description:
07-01-074-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib3230

status: Public on Dec 05 2018

description:
923066A-32
923066A-32_S14_L002

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts_TN-05.txt is a tab-delimited matrix. The first column ("geneName") contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

source_name: Active_Wk 52

extract_protocol:
RNA was isolated from whole blood samples using the Total RNA Isolation chemistry on an ABI Prism 6100 (Applied Biosystems, CA).
Samples were globin- reduced with the GLOBINclear kit (Ambion, CA), and libraries were constructed from globin- reduced RNA using the Illumina TruSeq RNA Sample Preparation kit v2.

tag: subject id

tag: subject status

value: newly diagnosed T1D patient

tag: age

tag: gender

value: Female

tag: race

value: White

tag: ethnicity

value: Not Hispanic or Latino

tag: visit

value: Wk 52

tag: treatment

value: Active

tag: responder

value: N

tag: tissue

value: whole blood


title: lib8281

description:
07-01-074-3-NS
Processed data file: raw_counts_ureca23.txt

tag: cell type

value: Peripheral blood mononuclear cell (PBMC)

tag: stim

tag: group

tag: full cohort classification

tag: bla g 1 bedroom level

tag: bla g 1 living room level


title: lib8271

description:
07-01-069-6-NS
Processed data file: raw_counts_ureca23.txt

value: NS

tag: der f 1 bedroom level

tag: der p 1 bedroom level

tag: der f 1 living room level

tag: der p 1 living room level

tag: phase


title: lib8270

description:
07-01-069-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8278

description:
07-01-126-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8268

description:
07-08-150-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8265

description:
07-02-047-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8267

description:
07-01-055-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8264

description:
07-02-047-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8303

description:
07-08-050-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8269

description:
07-08-150-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8309

description:
07-07-035-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8266

description:
07-01-055-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib3240

description:
914644A-30
914644A-30_S24_L002

source_name: Placebo_Wk 26

tag: subject id

tag: subject status

tag: age

tag: gender

tag: race

value: Wk 26

value: Placebo


title: lib8261

description:
07-08-014-1-NS
Processed data file: raw_counts_ureca23.txt

value: Asthma


title: lib8294

description:
07-02-138-3-CR
Processed data file: raw_counts_ureca23.txt

value: CR

value: Control


title: lib8263

description:
07-02-114-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8260

description:
07-08-014-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8262

description:
07-02-114-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8254

description:
07-02-073-3-CR
Processed data file: raw_counts_ureca23.txt

value: CR sensitized


title: lib8253

description:
07-02-015-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8259

description:
07-01-083-8-NS
Processed data file: raw_counts_ureca23.txt

tag: cohort 2 classification

value: Neither


title: lib8258

description:
07-01-083-8-CR
Processed data file: raw_counts_ureca23.txt

tag: cell type


title: lib8252

description:
07-02-015-8-CR
Processed data file: raw_counts_ureca23.txt

tag: stim


title: lib8250

description:
07-02-113-7-CR
Processed data file: raw_counts_ureca23.txt

tag: group


title: lib8242

description:
07-08-026-9-CR
Processed data file: raw_counts_ureca23.txt

tag: full cohort classification


title: lib8240

description:
07-08-141-5-CR
Processed data file: raw_counts_ureca23.txt

tag: bla g 1 bedroom level


title: lib8241

description:
07-08-141-5-NS
Processed data file: raw_counts_ureca23.txt

tag: bla g 1 living room level


title: lib8239

description:
07-02-022-1-NS
Processed data file: raw_counts_ureca23.txt

tag: der f 1 bedroom level


title: lib8243

description:
07-08-026-9-NS
Processed data file: raw_counts_ureca23.txt

tag: der p 1 bedroom level


title: lib8238

description:
07-02-022-1-CR
Processed data file: raw_counts_ureca23.txt

tag: der f 1 living room level


title: lib8234

description:
07-02-144-0-CR
Processed data file: raw_counts_ureca23.txt

tag: der p 1 living room level


title: lib8223

description:
07-08-055-5-NS
Processed data file: raw_counts_ureca23.txt

tag: phase


title: lib8225

description:
07-02-056-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8222

description:
07-08-055-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8228

description:
07-02-036-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8224

description:
07-02-056-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8221

description:
07-02-067-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8220

description:
07-02-067-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8229

description:
07-02-036-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8255

description:
07-02-073-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8218

description:
07-02-042-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8217

description:
07-08-080-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8219

description:
07-02-042-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8216

description:
07-08-080-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8215

description:
07-07-042-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8214

description:
07-07-042-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8210

description:
07-08-068-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8251

description:
07-02-113-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8209

description:
07-08-118-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8213

description:
07-08-081-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8235

description:
07-02-144-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8200

description:
07-08-112-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib8198

description:
07-01-025-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8208

description:
07-08-118-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8199

description:
07-01-025-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8197

description:
07-01-068-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8076

description:
07-08-046-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8073

description:
07-01-107-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8072

description:
07-01-107-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8074

description:
07-02-133-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8071

description:
07-02-105-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib8077

description:
07-08-046-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8069

description:
07-07-075-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8070

description:
07-02-105-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib8067

description:
07-08-113-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8212

description:
07-08-081-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib8211

description:
07-08-068-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8066

description:
07-08-113-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8065

description:
07-02-136-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8194

description:
07-08-029-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8075

description:
07-02-133-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8060

description:
07-08-128-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8195

description:
07-08-029-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8061

description:
07-08-128-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8064

description:
07-02-136-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8201

description:
07-08-112-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib8068

description:
07-07-075-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8059

description:
07-07-001-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8046

description:
07-01-139-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8196

description:
07-01-068-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib8044

description:
07-08-133-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8054

description:
07-01-056-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8058

description:
07-07-001-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8055

description:
07-01-056-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8045

description:
07-08-133-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8043

description:
07-01-040-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8040

description:
07-08-022-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8042

description:
07-01-040-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8041

description:
07-08-022-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8037

description:
07-08-085-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8036

description:
07-08-085-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8035

description:
07-07-055-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8034

description:
07-07-055-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8038

description:
07-08-105-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8032

description:
07-02-009-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8031

description:
07-01-034-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8033

description:
07-02-009-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8030

description:
07-01-034-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib8028

description:
07-02-118-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib8047

description:
07-01-139-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib8021

description:
07-08-102-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib8024

description:
07-08-121-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8017

description:
07-08-146-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib8012

description:
07-01-039-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib8015

description:
07-01-053-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8016

description:
07-08-146-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib8020

description:
07-08-102-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib8010

description:
07-01-098-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib8011

description:
07-01-098-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8005

description:
07-02-080-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8039

description:
07-08-105-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib8013

description:
07-01-039-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib8001

description:
07-01-047-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib8003

description:
07-08-160-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib7996

description:
07-07-014-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib8002

description:
07-08-160-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib7997

description:
07-07-014-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8000

description:
07-01-047-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib7995

description:
07-08-044-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib7989

description:
07-01-079-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib7994

description:
07-08-044-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib7991

description:
07-08-161-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib7987

description:
07-07-100-0-NS
Processed data file: raw_counts_ureca23.txt

value: Case

value: CR-Late


title: lib7988

description:
07-01-079-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib7983

description:
07-02-140-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib8029

description:
07-02-118-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7981

description:
07-01-023-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib7977

description:
07-01-158-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib8014

description:
07-01-053-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib7986

description:
07-07-100-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib7982

description:
07-02-140-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib7980

description:
07-01-023-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib7976

description:
07-01-158-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib7972

description:
07-08-034-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib7973

description:
07-08-034-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib7971

description:
07-08-041-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib7970

description:
07-08-041-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib7967

description:
07-08-132-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib7968

description:
07-01-132-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib7969

description:
07-01-132-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib7990

description:
07-08-161-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib7961

description:
07-07-017-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib7965

description:
07-07-074-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib7963

description:
07-08-032-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib7955

description:
07-08-040-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib7962

description:
07-08-032-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib7964

description:
07-07-074-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib7960

description:
07-07-017-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib7958

description:
07-08-033-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib7954

description:
07-08-040-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib7952

description:
07-01-010-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib7951

description:
07-08-109-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib7953

description:
07-01-010-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7937

description:
07-08-123-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib7939

description:
07-01-135-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7941

description:
07-01-146-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7943

description:
07-01-085-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7942

description:
07-01-085-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib7966

description:
07-08-132-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib7938

description:
07-01-135-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib7936

description:
07-08-123-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib7934

description:
07-02-109-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib7935

description:
07-02-109-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib7930

description:
07-02-003-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib7931

description:
07-02-003-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib7928

description:
07-01-011-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib7929

description:
07-01-011-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib7927

description:
07-01-084-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib7959

description:
07-08-033-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib7925

description:
07-01-127-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib7926

description:
07-01-084-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib7919

description:
07-07-108-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7924

description:
07-01-127-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib7918

description:
07-07-108-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib7940

description:
07-01-146-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib7950

description:
07-08-109-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib7916

description:
07-08-007-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib7917

description:
07-08-007-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib7913

description:
07-01-070-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib7914

description:
07-02-021-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib7915

description:
07-02-021-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib7903

description:
07-02-045-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib7904

description:
07-01-162-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib7912

description:
07-01-070-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib7905

description:
07-01-162-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib7902

description:
07-02-045-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib7901

description:
07-07-008-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib7896

description:
07-08-067-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib7900

description:
07-07-008-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib7895

description:
07-02-039-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7894

description:
07-02-039-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib7893

description:
07-08-114-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib7892

description:
07-08-114-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib7891

description:
07-01-012-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5928

description:
07-02-046-3-NS
Processed data file: raw_counts_ureca23.txt

tag: cohort 1 classification

value: CR-Early/DM-Early


title: lib7898

description:
07-02-048-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib5929

description:
07-02-046-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib5925

description:
07-02-038-2-CR
Processed data file: raw_counts_ureca23.txt

value: CR-Early


title: lib7889

description:
07-08-012-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib5927

description:
07-01-080-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib5923

description:
07-01-095-7-DM
Processed data file: raw_counts_ureca23.txt

value: DM


title: lib7890

description:
07-01-012-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib5922

description:
07-01-095-7-TT
Processed data file: raw_counts_ureca23.txt

value: TT


title: lib5921

description:
07-01-095-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib5924

description:
07-02-038-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5918

description:
07-02-046-3-TT
Processed data file: raw_counts_ureca23.txt


title: lib5917

description:
07-08-071-2-DM
Processed data file: raw_counts_ureca23.txt


title: lib5919

description:
07-02-046-3-DM
Processed data file: raw_counts_ureca23.txt


title: lib5915

description:
07-08-071-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib7899

description:
07-02-048-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib7888

description:
07-08-012-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib5913

description:
07-01-086-4-DM
Processed data file: raw_counts_ureca23.txt


title: lib5920

description:
07-01-095-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib5916

description:
07-08-071-2-TT
Processed data file: raw_counts_ureca23.txt


title: lib5914

description:
07-08-071-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5908

description:
07-01-080-1-TT
Processed data file: raw_counts_ureca23.txt


title: lib5911

description:
07-01-086-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib5912

description:
07-01-086-4-TT
Processed data file: raw_counts_ureca23.txt


title: lib5910

description:
07-01-086-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib5907

description:
07-01-078-9-DM
Processed data file: raw_counts_ureca23.txt

value: DM-Early

value: Not Included


title: lib5902

description:
07-07-024-7-TT
Processed data file: raw_counts_ureca23.txt

value: Peripheral blood mononuclear cell (PBMC)


title: lib5904

description:
07-01-078-9-NS
Processed data file: raw_counts_ureca23.txt

value: NS


title: lib5901

description:
07-07-024-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib5899

description:
07-01-066-5-DM
Processed data file: raw_counts_ureca23.txt


title: lib5900

description:
07-07-024-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib5898

description:
07-01-066-5-TT
Processed data file: raw_counts_ureca23.txt


title: lib5893

description:
07-02-040-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib5897

description:
07-01-066-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib5891

description:
07-02-038-2-DM
Processed data file: raw_counts_ureca23.txt


title: lib5892

description:
07-02-040-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib5896

description:
07-01-066-5-NS
Processed data file: raw_counts_ureca23.txt


title: lib5890

description:
07-02-038-2-TT
Processed data file: raw_counts_ureca23.txt


title: lib5889

description:
07-01-048-4-DM
Processed data file: raw_counts_ureca23.txt


title: lib5887

description:
07-01-048-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib5909

description:
07-01-080-1-DM
Processed data file: raw_counts_ureca23.txt


title: lib5883

description:
07-08-157-3-DM
Processed data file: raw_counts_ureca23.txt


title: lib5882

description:
07-08-157-3-TT
Processed data file: raw_counts_ureca23.txt


title: lib5905

description:
07-01-078-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib5886

description:
07-01-048-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib5884

description:
07-07-019-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib5888

description:
07-01-048-4-TT
Processed data file: raw_counts_ureca23.txt


title: lib5881

description:
07-08-157-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib5885

description:
07-07-019-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib5879

description:
07-08-156-0-DM
Processed data file: raw_counts_ureca23.txt


title: lib5878

description:
07-08-156-0-TT
Processed data file: raw_counts_ureca23.txt


title: lib5880

description:
07-08-157-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib5877

description:
07-08-156-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib5926

description:
07-01-080-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib5876

description:
07-08-156-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib5873

description:
07-01-004-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib5872

description:
07-01-004-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib7897

description:
07-08-067-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib5875

description:
07-01-004-8-DM
Processed data file: raw_counts_ureca23.txt


title: lib5868

description:
07-07-020-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib5871

description:
07-08-015-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib5870

description:
07-08-015-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib5867

description:
07-07-011-7-DM
Processed data file: raw_counts_ureca23.txt


title: lib5862

description:
07-01-036-0-TT
Processed data file: raw_counts_ureca23.txt


title: lib5864

description:
07-07-011-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib5866

description:
07-07-011-7-TT
Processed data file: raw_counts_ureca23.txt


title: lib5865

description:
07-07-011-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib5861

description:
07-01-036-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib5860

description:
07-01-036-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib5859

description:
07-07-019-3-DM
Processed data file: raw_counts_ureca23.txt


title: lib5858

description:
07-07-019-3-TT
Processed data file: raw_counts_ureca23.txt


title: lib5863

description:
07-01-036-0-DM
Processed data file: raw_counts_ureca23.txt


title: lib5850

description:
07-02-016-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5852

description:
07-02-016-2-TT
Processed data file: raw_counts_ureca23.txt


title: lib5851

description:
07-02-016-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib5849

description:
07-08-027-6-DM
Processed data file: raw_counts_ureca23.txt


title: lib5874

description:
07-01-004-8-TT
Processed data file: raw_counts_ureca23.txt


title: lib5848

description:
07-08-027-6-TT
Processed data file: raw_counts_ureca23.txt


title: lib5869

description:
07-07-020-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib5846

description:
07-08-027-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib5845

description:
07-02-013-6-DM
Processed data file: raw_counts_ureca23.txt


title: lib5843

description:
07-02-013-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib5844

description:
07-02-013-6-TT
Processed data file: raw_counts_ureca23.txt


title: lib5842

description:
07-02-013-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib5853

description:
07-02-016-2-DM
Processed data file: raw_counts_ureca23.txt


title: lib8025

description:
07-08-121-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5841

description:
07-08-028-2-DM
Processed data file: raw_counts_ureca23.txt


title: lib8004

description:
07-02-080-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib5839

description:
07-08-028-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib5829

description:
07-08-010-2-TT
Processed data file: raw_counts_ureca23.txt


title: lib5830

description:
07-08-010-2-DM
Processed data file: raw_counts_ureca23.txt


title: lib5828

description:
07-08-010-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib5832

description:
07-07-010-1-TT
Processed data file: raw_counts_ureca23.txt


title: lib5831

description:
07-07-010-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib5827

description:
07-08-010-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5825

description:
07-08-002-8-TT
Processed data file: raw_counts_ureca23.txt


title: lib5823

description:
07-08-002-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib5906

description:
07-01-078-9-TT
Processed data file: raw_counts_ureca23.txt


title: lib5821

description:
07-01-006-9-TT
Processed data file: raw_counts_ureca23.txt


title: lib5822

description:
07-01-006-9-DM
Processed data file: raw_counts_ureca23.txt


title: lib5824

description:
07-08-002-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib5820

description:
07-01-006-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib5819

description:
07-01-006-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib5818

description:
07-02-143-8-DM
Processed data file: raw_counts_ureca23.txt


title: lib5814

description:
07-08-049-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib5817

description:
07-02-143-8-TT
Processed data file: raw_counts_ureca23.txt


title: lib5812

description:
07-07-096-5-CR
Processed data file: raw_counts_ureca23.txt


title: lib5840

description:
07-08-028-2-TT
Processed data file: raw_counts_ureca23.txt


title: lib5815

description:
07-02-143-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib5813

description:
07-08-049-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib5833

description:
07-07-010-1-DM
Processed data file: raw_counts_ureca23.txt


title: lib5810

description:
07-01-145-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib5806

description:
07-02-121-4-DM
Processed data file: raw_counts_ureca23.txt


title: lib5808

description:
07-08-049-0-DM
Processed data file: raw_counts_ureca23.txt


title: lib5805

description:
07-02-121-4-TT
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title: lib5807

description:
07-08-049-0-TT
Processed data file: raw_counts_ureca23.txt


title: lib5804

description:
07-02-121-4-CR
Processed data file: raw_counts_ureca23.txt


title: lib5799

description:
07-01-163-0-NS
Processed data file: raw_counts_ureca23.txt


title: lib5803

description:
07-02-121-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib5798

description:
07-07-096-5-TT
Processed data file: raw_counts_ureca23.txt


title: lib5802

description:
07-01-163-0-DM
Processed data file: raw_counts_ureca23.txt


title: lib5801

description:
07-01-163-0-TT
Processed data file: raw_counts_ureca23.txt


title: lib5800

description:
07-01-163-0-CR
Processed data file: raw_counts_ureca23.txt


title: lib5797

description:
07-01-157-9-DM
Processed data file: raw_counts_ureca23.txt


title: lib5793

description:
07-01-145-4-DM
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title: lib5816

description:
07-02-143-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib5792

description:
07-01-145-4-TT
Processed data file: raw_counts_ureca23.txt


title: lib5795

description:
07-01-157-9-CR
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title: lib5790

description:
07-01-153-3-TT
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title: lib5791

description:
07-01-153-3-DM
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title: lib5789

description:
07-01-153-3-CR
Processed data file: raw_counts_ureca23.txt


title: lib5811

description:
07-07-096-5-NS
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title: lib5787

description:
07-01-141-2-DM
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title: lib5788

description:
07-01-153-3-NS
Processed data file: raw_counts_ureca23.txt


title: lib5786

description:
07-01-141-2-TT
Processed data file: raw_counts_ureca23.txt


title: lib5785

description:
07-01-141-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib5784

description:
07-01-141-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5771

description:
07-08-051-7-DM
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title: lib5768

description:
07-02-079-8-TT
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title: lib5770

description:
07-08-051-7-TT
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title: lib5775

description:
07-07-076-9-DM
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title: lib5769

description:
07-02-079-8-DM
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title: lib5774

description:
07-07-076-9-TT
Processed data file: raw_counts_ureca23.txt


title: lib5796

description:
07-01-157-9-TT
Processed data file: raw_counts_ureca23.txt


title: lib5794

description:
07-01-157-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib5756

description:
07-08-051-7-NS
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title: lib5762

description:
07-02-077-9-NS
Processed data file: raw_counts_ureca23.txt


title: lib5755

description:
07-07-063-5-CR
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title: lib5764

description:
07-02-077-9-TT
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title: lib5765

description:
07-02-077-9-DM
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title: lib5757

description:
07-08-051-7-CR
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title: lib5766

description:
07-02-079-8-NS
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title: lib5754

description:
07-07-063-5-NS
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title: lib5751

description:
07-01-119-7-DM
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title: lib5749

description:
07-01-119-7-CR
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title: lib5772

description:
07-07-076-9-NS
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title: lib5750

description:
07-01-119-7-TT
Processed data file: raw_counts_ureca23.txt


title: lib5773

description:
07-07-076-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib5748

description:
07-01-119-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib5745

description:
07-02-066-4-CR
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title: lib5747

description:
07-02-066-4-DM
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title: lib5744

description:
07-02-066-4-NS
Processed data file: raw_counts_ureca23.txt


title: lib5767

description:
07-02-079-8-CR
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title: lib5743

description:
07-02-062-9-DM
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title: lib5739

description:
07-07-063-5-DM
Processed data file: raw_counts_ureca23.txt


title: lib5740

description:
07-02-062-9-NS
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title: lib5742

description:
07-02-062-9-TT
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title: lib5738

description:
07-07-063-5-TT
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title: lib5736

description:
07-08-100-1-TT
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title: lib5753

description:
07-01-116-6-CR
Processed data file: raw_counts_ureca23.txt


title: lib5732

description:
07-08-099-7-TT
Processed data file: raw_counts_ureca23.txt


title: lib5735

description:
07-08-100-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib5752

description:
07-01-116-6-NS
Processed data file: raw_counts_ureca23.txt


title: lib5737

description:
07-08-100-1-DM
Processed data file: raw_counts_ureca23.txt


title: lib5734

description:
07-08-100-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib5725

description:
07-01-116-6-DM
Processed data file: raw_counts_ureca23.txt


title: lib5733

description:
07-08-099-7-DM
Processed data file: raw_counts_ureca23.txt


title: lib5731

description:
07-08-099-7-CR
Processed data file: raw_counts_ureca23.txt


title: lib5730

description:
07-08-099-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib5746

description:
07-02-066-4-TT
Processed data file: raw_counts_ureca23.txt


title: lib5723

description:
07-07-052-8-DM
Processed data file: raw_counts_ureca23.txt


title: lib5722

description:
07-07-052-8-TT
Processed data file: raw_counts_ureca23.txt


title: lib5721

description:
07-07-052-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib5717

description:
07-02-054-2-CR
Processed data file: raw_counts_ureca23.txt


title: lib5724

description:
07-01-116-6-TT
Processed data file: raw_counts_ureca23.txt


title: lib5719

description:
07-02-054-2-DM
Processed data file: raw_counts_ureca23.txt


title: lib5718

description:
07-02-054-2-TT
Processed data file: raw_counts_ureca23.txt


title: lib5715

description:
07-01-108-1-DM
Processed data file: raw_counts_ureca23.txt


title: lib5716

description:
07-02-054-2-NS
Processed data file: raw_counts_ureca23.txt


title: lib5720

description:
07-07-052-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib5714

description:
07-01-108-1-TT
Processed data file: raw_counts_ureca23.txt


title: lib5741

description:
07-02-062-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib5713

description:
07-01-108-1-CR
Processed data file: raw_counts_ureca23.txt


title: lib5763

description:
07-02-077-9-CR
Processed data file: raw_counts_ureca23.txt


title: lib5711

description:
07-01-106-8-DM
Processed data file: raw_counts_ureca23.txt


title: lib5710

description:
07-01-106-8-TT
Processed data file: raw_counts_ureca23.txt


title: lib5712

description:
07-01-108-1-NS
Processed data file: raw_counts_ureca23.txt


title: lib5707

description:
07-01-104-7-DM
Processed data file: raw_counts_ureca23.txt


title: lib5708

description:
07-01-106-8-NS
Processed data file: raw_counts_ureca23.txt


title: lib5706

description:
07-01-104-7-TT
Processed data file: raw_counts_ureca23.txt


title: lib5709

description:
07-01-106-8-CR
Processed data file: raw_counts_ureca23.txt


title: lib5704

description:
07-01-104-7-NS
Processed data file: raw_counts_ureca23.txt


title: lib5705

description:
07-01-104-7-CR
Processed data file: raw_counts_ureca23.txt


title: PTPR, B, sample 2163 [reference set]

status: Public on Jan 14 2018

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'
Average beta

label: biotin/DNP

molecule: genomic DNA

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: methylation class

value: PTPR, B

tag: material

value: FFPE


title: PTPR, B, sample 2227 [reference set]

value: Frozen


title: PTPR, A, sample 470 [validation set]

status: Public on Jan 18 2018

description:
SAMPLE 470
Methylation data from brain tumor sample.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'.

tag: tissue

value: brain tumor

value: PTPR, A


title: PTPR, A, sample 1909 [reference set]


title: PTPR, B, sample 2164 [reference set]


title: PTPR, B, sample 123 [validation set]

description:
SAMPLE 123
Methylation data from brain tumor sample.


title: PTPR, A, sample 1587 [reference set]


title: PTPR, B, sample 1669 [reference set]


title: PTPR, B, sample 1078 [reference set]


title: PTPR, B, sample 1079 [reference set]


title: PTPR, B, sample 1077 [reference set]


title: PTPR, B, sample 1080 [reference set]


title: PTPR, B, sample 1074 [reference set]


title: PTPR, B, sample 1158 [reference set]


title: PTPR, A, sample 1076 [reference set]


title: PTPR, B, sample 1075 [reference set]


title: PTPR, A, sample 1073 [reference set]


title: PTPR, A, sample 1072 [reference set]


title: PTPR, B, sample 1071 [reference set]


title: PTPR, A, sample 1069 [reference set]


title: PTPR, A, sample 1068 [reference set]


title: PTPR, B, sample 1776 [reference set]


title: PTPR, B, sample 2162 [reference set]


title: PTPR, B, sample 1067 [reference set]


title: PTPR, B, sample 2511 [reference set]


title: PTPR, B, sample 1081 [reference set]


title: PTPR, B, sample 851 [reference set]


title: PTPR, B, sample 346 [reference set]


title: PTPR, B, sample 137 [reference set]


title: PTPR, B, sample 2510 [reference set]


title: PTPR, A, sample 2678 [reference set]


title: PTPR, B, sample 1070 [reference set]


title: RelA_IRF3KO_60min

status: Public on Jun 11 2017

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

library_source: genomic

data_processing:
Reads were aligned to mm9 genome assembly using Bowtie 2. The uniquely mapped reads were kept for peak calling.
Peaks were called using the HOMER software with an FDR threshold of 0.01.
Peaks were annotated and assigned to the nearest genes.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow cells isolated from 6- to 10-week-old C57BL/6 male mice and were incubated in the macrophage differentiation medium (DMEM, 20% FBS, 12% CMG cell supernant containing M-CSF, 1% L-glutamine, 1% Pen/Strep, 0.5% sodium pyruvate, 0.1% β-mercaptoethanol) for six days.

extract_protocol:
Forty million of bone marrow-derived macrophages were cross-linked with 4mM DSG for 1 hr and 1% formaldehyde for 10 min. Nuclei pellets were isolated and sonicated using Misonix 3000 sonicator to fragments between 200bp to 1000bp. Chromatin lysate was incubated with the antibody overnight. The immune complexes were pulled down with Protein G Dynabeads (Invitrogen, 10004D) and washed for four times. The purified immune complexes were incubated with proteinase K at 60°C overnight for reverse cross-linking and protein digestion. IP DNA was purified by phenol-chloroform. DNA concentration was quantified by Qubit kit (Thermo Fisher, Q32854).
ChIP-seq library was prepared using KAPA LTP library preparation kit (KK8500) following the manufacturer’s instructions. About 10ng DNA was used following the standard end repair, A-tailing, and adapter ligation steps. Each library was amplified with fewer than 12 PCR cycles. An additional size selection was performed after PCR to remove the big fragments. The final library size is between 300bp to 600bp.

treatment_protocol: Bone marrow-derived macrophages were stimulated with 100ng/ml lipid A for 0, 15, 30, 60, and 120 min before cross-linking for ChIP experiments.

tag: strain

tag: genotype

value: IRF3 KO

tag: stimulus

value: lipid A

tag: time

value: 60 min

tag: chip antibody

value: RelA (Santa Cruz, catalgo# sc-372, lot# H1114)


title: RelA_IRF3KO_15min

value: 15 min


title: RelA_IRF3KO_30min

value: 30 min


title: Input

value: wildtype

value: pooled samples stimulated by lipid A for 0, 15, 30, 60, 120 min

value: none (input)


title: RelA_IRF3KO_120min

value: 120 min


title: RelA_IRF3KO_0min

value: 0 min


title: Input_RelA_IRF3KO


title: RelA_WT_120min


title: CREB_120min_rep2

value: CREB (Santa Cruz, catalog# sc-186 lot# C0614)


title: CREB_60min_rep2


title: CREB_30min_rep2


title: RelA_WT_0min


title: Input_RelA_WT


title: 7677145100_J

status: Public on Oct 05 2017

type: RNA

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using the Illumina HiScan and the standard Illumina scanning protocol.

data_processing: Background subtracted data was floored to a value of 10 and quantile normalized, no filtering was performed.

label: Biotin

source_name: Whole Blood

label_protocol: Standard Illumina labeling protocol.

extract_protocol: GLOBINclear (Life Technologies) was used to deplete globin mRNA from total whole blood RNA from the 12-month visit. cRNA was prepared by amplification and labelling using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) and hybridized to Human HT-12 Beadarray Chips (Illumina).

tag: donor id

tag: subset

tag: markers

value: CD4+ CD45RO+ CRTH2- CCR6+ CXCR3-

tag: status

value: Stimulated


title: RelA_WT_30min


title: 7677145100_G

value: CD4+ CD45RO+ CRTH2- CCR6- CXCR3+


title: 7677145074_I

value: CD4+ CD45RO+ CD27- CRTH2+ CD161-

value: Ctrl


title: 7677145100_B


title: 7677145100_D


title: 7677145100_E


title: 7677145100_K

value: CD4+ CD45RO+ CD27- CRTH2+ CD161+


title: 7677145074_A


title: CREB_15min_rep2

value: lipid A


title: 7677145074_L


title: 7677145100_L


title: 7677145074_D


title: RelA_WT_60min

value: 60 min


title: 7677145074_J


title: CREB_120min_rep1


title: CREB_0min_rep1


title: CREB_60min_rep1


title: CREB_30min_rep1


title: ATF3_60min

value: ATF3 (Santa Cruz, catalog# sc-188, lot# L2214)


title: ATF3_120min


title: ATF3_15min

value: 15 min


title: ATF3_0min


title: JunD_60min

value: JunD (Santa Cruz, catalog# sc-74, lot3 A3015)


title: JunD_120min

value: wildtype


title: ATF3_30min

value: 30 min


title: JunD_0min


title: 7677145074_F


title: JunD_15min


title: JunB_60min

value: JunB (Santa Cruz, catalog# sc-46, lot# F1814)


title: JunD_30min


title: JunB_120min

value: 120 min


title: JunB_0min

value: 0 min


title: CREB_0min_rep2

value: CREB (Santa Cruz, catalog# sc-186 lot# C0614)


title: JunB_15min


title: CREB_15min_rep1


title: Fos_120min

value: Fos (Santa Cruz, catalog# sc-253, lot# I0808)


title: Fos_30min


title: Fos_15min


title: JunB_30min


title: CEBPd_120min

value: CEBPd (Santa Cruz, catalog# sc-151, lot# K1711)


title: CEBPd_60min


title: CEBPd_30min


title: CEBPd_15min


title: Fos_60min


title: CEBPd_0min


title: CEBPb_15min

value: CEBPb (in-house rabbit polyclonal antisera for mouse CEBPβ aa 22-195)


title: CEBPb_120min


title: CEBPb_60min


title: CEBPb_30min


title: CEBPb_0min


title: Brg1_60min

value: Brg1 (Abcam, ab110641)


title: Brg1_15min


title: Brg1_120min


title: Brg1_0min


title: RelA_WT_15min

value: RelA (Santa Cruz, catalgo# sc-372, lot# H1114)


title: Fos_0min


title: S34798_T1D2_redraw_C60

status: Public on Jun 08 2017

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: log10(PF_ALIGNED_BASES)>6.5, MEDIAN_CV_COVERAGE<1 & MEDIAN_CV_COVERAGE >0.4.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts_T1D_single_cell.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

source_name: Islet antigen-reactive CD4+ sorted T-cells

extract_protocol:
Single cells were captured on a C1 system, using a 5-10 um mRNA Seq IFC according to manufacturer’s instructions (Fluidigm, South San Francisco, CA).  Full-length cDNA was prepared using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

tag: samplelabel

tag: sampleID

tag: samplename

value: 1_T1D2-REDRAW _C60

tag: pid

tag: visit

tag: numcellssorted

tag: libraryid

tag: cdnasynthesis

value: C1+SMARTer v1

tag: libraryprep

tag: projectid

tag: seqsite

value: BRI

value: single cell

tag: flowcellid

tag: runchemistry

value: HiSeq SBS Kit v4

tag: lane


title: S34802_T1D2_redraw_C94

tag: tissue

value: Islet antigen-reactive CD4+ sorted T-cells

value: 1_T1D2-REDRAW _C94


title: S34800_T1D2_redraw_C82

value: 1D_T1D2-REDRAW _C82

value: single cell +debris


title: S34799_T1D2_redraw_C66

value: 1D_T1D2-REDRAW _C66


title: S34793_T1D2_redraw_C53

value: 1_T1D2-REDRAW _C53


title: S34796_T1D2_redraw_C83

value: 1D_T1D2-REDRAW _C83


title: S34801_T1D2_redraw_C88

value: 1_T1D2-REDRAW _C88


title: S34795_T1D2_redraw_C77

value: 1D_T1D2-REDRAW _C77


title: S34791_T1D2_redraw_C78

value: 1_T1D2-REDRAW _C78


title: S34794_T1D2_redraw_C65

value: 1_T1D2-REDRAW _C65


title: S34788_T1D2_redraw_C30

value: 1D_T1D2-REDRAW _C30


title: S34790_T1D2_redraw_C42

value: 1_T1D2-REDRAW _C42


title: S34789_T1D2_redraw_C36

value: 1D_T1D2-REDRAW _C36

value: C1+SMARTer v1


title: S34785_T1D2_redraw_C04

value: 1_T1D2-REDRAW _C04

value: BRI

value: single cell


title: S34786_T1D2_redraw_C16

value: Islet antigen-reactive CD4+ sorted T-cells

value: 1D_T1D2-REDRAW _C16

value: HiSeq SBS Kit v4


title: S34784_T1D2_redraw_C47

value: 1_T1D2-REDRAW _C47


title: S34782_T1D2_redraw_C35

value: 1_T1D2-REDRAW _C35


title: S34780_T1D2_redraw_C11

value: 1_T1D2-REDRAW _C11


title: S34775_T1D2_redraw_C24

value: 1_T1D2-REDRAW _C24


title: Brg1_30min

tag: strain

tag: genotype

value: wildtype

tag: stimulus

value: lipid A

tag: time

value: 30 min

tag: chip antibody

value: Brg1 (Abcam, ab110641)


title: S34787_T1D2_redraw_C22

tag: samplelabel

tag: sampleID

tag: samplename

value: 1_T1D2-REDRAW _C22

tag: status

tag: pid


title: S34778_T1D2_redraw_C40

value: 1D_T1D2-REDRAW _C40

tag: visit

tag: numcellssorted

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

value: single cell +debris


title: S34777_T1D2_redraw_C34

value: 1D_T1D2-REDRAW _C34

value: C1+SMARTer v1

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S34773_T1D2_redraw_C06

tag: tissue

value: 1_T1D2-REDRAW _C06

value: BRI

value: single cell


title: S34772_T1D2_redraw_C91

value: Islet antigen-reactive CD4+ sorted T-cells

value: 1D_T1D2-REDRAW _C91

value: HiSeq SBS Kit v4


title: S34774_T1D2_redraw_C12

value: 1_T1D2-REDRAW _C12


title: S34769_T1D2_redraw_C63

value: 1_T1D2-REDRAW _C63


title: S34768_T1D2_redraw_C51

value: 1_T1D2-REDRAW _C51


title: S34770_T1D2_redraw_C79

value: 1D_T1D2-REDRAW _C79


title: S34761_T1D2_redraw_C75

value: 1D_T1D2-REDRAW _C75


title: S34765_T1D2_redraw_C62

value: 1_T1D2-REDRAW _C62


title: S34760_T1D2_redraw_C61

value: 1_T1D2-REDRAW _C61


title: S34764_T1D2_redraw_C56

value: 1_T1D2-REDRAW _C56


title: S34754_T1D2_redraw_C19

value: 1D_T1D2-REDRAW _C19

value: single cell +debris


title: S34767_T1D2_redraw_C92

value: 1D_T1D2-REDRAW _C92

value: C1+SMARTer v1


title: S34762_T1D2_redraw_C87

value: 1D_T1D2-REDRAW _C87

value: BRI


title: S34766_T1D2_redraw_C80

value: Islet antigen-reactive CD4+ sorted T-cells

value: 1D_T1D2-REDRAW _C80


title: S34763_T1D2_redraw_C50

value: 1_T1D2-REDRAW _C50

value: single cell

value: HiSeq SBS Kit v4


title: S34756_T1D2_redraw_C33

value: 1D_T1D2-REDRAW _C33


title: S34781_T1D2_redraw_C23

value: 1D_T1D2-REDRAW _C23


title: S34757_T1D2_redraw_C45

value: 1_T1D2-REDRAW _C45


title: S34751_T1D2_redraw_C38

value: 1D_T1D2-REDRAW _C38


title: S34753_T1D2_redraw_C13

value: 1_T1D2-REDRAW _C13


title: S34749_T1D2_redraw_C20

value: 1_T1D2-REDRAW _C20


title: S34752_T1D2_redraw_C44

value: 1D_T1D2-REDRAW _C44


title: S34742_T1D2_redraw_C15

value: 1_T1D2-REDRAW _C15


title: S34745_T1D2_redraw_C37

value: 1D_T1D2-REDRAW _C37

value: single cell +debris


title: S34748_T1D2_redraw_C08

value: 1_T1D2-REDRAW _C08

value: C1+SMARTer v1


title: S34747_T1D2_redraw_C02

value: Islet antigen-reactive CD4+ sorted T-cells

value: 1_T1D2-REDRAW _C02

value: BRI


title: S34746_T1D2_redraw_C43

value: 1_T1D2-REDRAW _C43

value: single cell


title: S34744_T1D2_redraw_C31

value: 1D_T1D2-REDRAW _C31

value: HiSeq SBS Kit v4


title: S34740_T1D2_redraw_C03

value: 1_T1D2-REDRAW _C03


title: S34731_Ctl5_redraw_C72

value: HC


title: S34730_Ctl5_redraw_C95


title: S34724_Ctl5_redraw_C42


title: S34729_Ctl5_redraw_C83


title: S34758_T1D2_redraw_C49

value: 1_T1D2-REDRAW _C49


title: S34720_Ctl5_redraw_C35


title: S34723_Ctl5_redraw_C36


title: S34711_Ctl5_redraw_C45


title: S34722_Ctl5_redraw_C10


title: S34718_Ctl5_redraw_C28


title: S34725_Ctl5_redraw_C48


title: S34715_Ctl5_redraw_C85


title: S34712_Ctl5_redraw_C74


title: S34710_Ctl5_redraw_C39


title: S34719_Ctl5_redraw_C40


title: S34707_Ctl5_redraw_C13


title: S34705_Ctl5_redraw_C38


title: S34706_Ctl5_redraw_C44


title: S34704_Ctl5_redraw_C32


title: S34708_Ctl5_redraw_C27


title: S34709_Ctl5_redraw_C33


title: S34703_Ctl5_redraw_C14


title: S34701_Ctl5_redraw_C37


title: S31803_T1D5_C64


title: S31805_T1D5_C78


title: S31813_T1D5_C82


title: S31796_T1D5_C41


title: S31807_T1D5_C53


title: S31804_T1D5_C70


title: S31808_T1D5_C59


title: S31791_T1D5_C40


title: S31787_T1D5_C06


title: S31773_T1D5_C55


title: S31784_T1D5_C69


title: S31786_T1D5_C91


title: S31793_T1D5_C05


title: S31795_T1D5_C29


title: S31782_T1D5_C57


title: S31772_T1D5_C45


title: S31794_T1D5_C23


title: S31764_T1D5_C31


title: S31769_T1D5_C44


title: S31765_T1D5_C37


title: S31771_T1D5_C19


title: S31767_T1D5_C20


title: S30174_T1D4_ROpos_C94


title: S31792_T1D5_C46


title: S30167_T1D4_ROpos_C96


title: S30170_T1D4_ROpos_C89


title: S30172_T1D4_ROpos_C72


title: S31763_T1D5_C21


title: S30171_T1D4_ROpos_C60


title: S31802_T1D5_C58


title: S31781_T1D5_C51


title: S30166_T1D4_ROpos_C90


title: S31779_T1D5_C86


title: S31776_T1D5_C62


title: S30169_T1D4_ROpos_C59


title: S30164_T1D4_ROpos_C70


title: S30163_T1D4_ROpos_C30


title: S30165_T1D4_ROpos_C78


title: S30162_T1D4_ROpos_C47


title: S30159_T1D4_ROpos_C23


title: S30161_T1D4_ROpos_C41


title: S30156_T1D4_ROpos_C46


title: S30152_T1D4_ROpos_C92


title: S30155_T1D4_ROpos_C28


title: S30149_T1D4_ROpos_C93


title: S30157_T1D4_ROpos_C11


title: S30154_T1D4_ROpos_C24


title: S30153_T1D4_ROpos_C73


title: S30148_T1D4_ROpos_C67


title: S30150_T1D4_ROpos_C56


title: S30158_T1D4_ROpos_C17


title: S30147_T1D4_ROpos_C39


title: S30143_T1D4_ROpos_C32


title: S30144_T1D4_ROpos_C19


title: S30141_T1D4_ROpos_C02


title: S30142_T1D4_ROpos_C08


title: S30139_T1D4_ROpos_C37


title: S30140_T1D4_ROpos_C43


title: S30135_Ctl3_ROpos_C94


title: S30160_T1D4_ROpos_C35


title: S30132_Ctl3_ROpos_C60


title: S30133_Ctl3_ROpos_C76


title: S30126_Ctl3_ROpos_C90


title: S30129_Ctl3_ROpos_C65


title: S30124_Ctl3_ROpos_C16


title: S30130_Ctl3_ROpos_C89


title: S30146_T1D4_ROpos_C33


title: S30122_Ctl3_ROpos_C41


title: S30125_Ctl3_ROpos_C36


title: S30145_T1D4_ROpos_C27


title: S30121_Ctl3_ROpos_C46


title: S30123_Ctl3_ROpos_C04


title: S30119_Ctl3_ROpos_C34


title: S30117_Ctl3_ROpos_C12


title: S30114_Ctl3_ROpos_C93


title: S30115_Ctl3_ROpos_C86


title: S30111_Ctl3_ROpos_C49


title: S30118_Ctl3_ROpos_C28


title: S30110_Ctl3_ROpos_C45


title: S30134_Ctl3_ROpos_C88


title: S30109_Ctl3_ROpos_C33


title: S30108_Ctl3_ROpos_C27


title: S30106_Ctl3_ROpos_C01


title: S30105_Ctl3_ROpos_C38


title: S30107_Ctl3_ROpos_C19


title: S13436_413Tmr_C72

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
Reads were aligned using Omicsoft Sequence Aligner (OSA, v.1.7.3) with OShell (v.6.1.0.2) using default parameters and a gene models index provided for Ensembl version 66.
Read counts per Ensembl gene ID were estimated using htseq-count (v.0.5.4p3).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: PF_ALIGNED_BASES>3.5e6, MEDIAN_CV_COVERAGE<=2.0 & MEDIAN_CV_COVERAGE >=0.4, PCT_USABLE_BASES>=0.25, log10(MEDIAN_3PRIME_BIAS+1)<=0.4 &  log10(MEDIAN_3PRIME_BIAS+1)>=0.1, and >=1 detected in-frame rearranged TCR junction.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_clone_single_cell.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

source_name: T-cell clone BRI4.13

value: T-cell clone BRI4.13

tag: stim

value: Tetramer stimulated

value: single cell, damaged

value: TruSeq SBS Kit v3


title: S30104_Ctl3_ROpos_C26

tag: samplelabel

value: single cell +debris


title: S30120_Ctl3_ROpos_C40

tag: sampleID


title: S13435_413Tmr_C54

tag: samplename


title: S30102_Ctl3_ROpos_C08

tag: status


title: S13433_413Tmr_C83


title: S30103_Ctl3_ROpos_C20

tag: pid


title: S28989_Ctl2_ROpos_C94

tag: visit


title: S30112_Ctl3_ROpos_C55

tag: numcellssorted


title: S30113_Ctl3_ROpos_C87

tag: libraryid


title: S13432_413Tmr_C77

tag: cdnasynthesis


title: S30100_Ctl3_ROpos_C15

tag: libraryprep


title: S28987_Ctl2_ROpos_C77

tag: projectid


title: S28986_Ctl2_ROpos_C65

tag: seqsite


title: S28988_Ctl2_ROpos_C88

tag: flowcellid


title: S13430_413Tmr_C59

tag: runchemistry


title: S13431_413Tmr_C65

tag: lane


title: S13428_413Tmr_C78

tag: tissue


title: S13426_413Tmr_C58

tag: stim


title: S13424_413Tmr_C48

tag: samplelabel


title: S28983_Ctl2_ROpos_C84

tag: sampleID


title: S13423_413Tmr_C36

tag: samplename


title: S28982_Ctl2_ROpos_C78

tag: status


title: S28984_Ctl2_ROpos_C90

tag: pid


title: S28981_Ctl2_ROpos_C70

tag: visit


title: S13434_413Tmr_C95

tag: numcellssorted


title: S13422_413Tmr_C30

tag: libraryid


title: S13420_413Tmr_C16

tag: cdnasynthesis


title: S28980_Ctl2_ROpos_C64

tag: libraryprep


title: S13421_413Tmr_C22

tag: projectid


title: S28985_Ctl2_ROpos_C53

tag: seqsite


title: S13415_413Tmr_C23

tag: flowcellid


title: S28976_Ctl2_ROpos_C04

tag: runchemistry


title: S28975_Ctl2_ROpos_C41

tag: lane


title: S13417_413Tmr_C47

tag: tissue


title: S28973_Ctl2_ROpos_C34


title: S28978_Ctl2_ROpos_C22


title: S13427_413Tmr_C70

tag: stim


title: S28971_Ctl2_ROpos_C06

tag: samplelabel


title: S28970_Ctl2_ROpos_C91

tag: sampleID


title: S13412_413Tmr_C40

tag: samplename


title: S28969_Ctl2_ROpos_C73

tag: status


title: S13411_413Tmr_C34


title: S13413_413Tmr_C05


title: S13410_413Tmr_C28


title: S28967_Ctl2_ROpos_C57

tag: pid


title: S13408_413Tmr_C12


title: S28965_Ctl2_ROpos_C62

tag: visit


title: S28964_Ctl2_ROpos_C50

tag: numcellssorted


title: S13407_413Tmr_C85

tag: libraryid


title: S28979_Ctl2_ROpos_C58

tag: cdnasynthesis


title: S13406_413Tmr_C79

tag: libraryprep


title: S13419_413Tmr_C10

tag: projectid


title: S28963_Ctl2_ROpos_C87

tag: seqsite


title: S13405_413Tmr_C73

tag: flowcellid


title: S28972_Ctl2_ROpos_C12

tag: runchemistry


title: S13414_413Tmr_C11

tag: lane


title: S28961_Ctl2_ROpos_C75

tag: tissue


title: S28958_Ctl2_ROpos_C33


title: S13403_413Tmr_C57

tag: stim


title: S28957_Ctl2_ROpos_C19

tag: samplelabel


title: S28959_Ctl2_ROpos_C39

tag: sampleID


title: S28960_Ctl2_ROpos_C55

tag: samplename


title: S13402_413Tmr_C92


title: S28956_Ctl2_ROpos_C13

tag: status


title: S28954_Ctl2_ROpos_C32

tag: pid


title: S28953_Ctl2_ROpos_C08

tag: visit


title: S28955_Ctl2_ROpos_C07

tag: numcellssorted


title: S13401_413Tmr_C80

tag: libraryid


title: S13400_413Tmr_C74

tag: cdnasynthesis


title: S13399_413Tmr_C68

tag: libraryprep


title: S28951_Ctl2_ROpos_C37

tag: projectid


title: S28950_Ctl2_ROpos_C25

tag: seqsite


title: S13398_413Tmr_C62

tag: flowcellid


title: S28949_Ctl2_ROpos_C15

tag: runchemistry


title: S13392_413Tmr_C45

tag: lane


title: S28962_Ctl2_ROpos_C81

tag: tissue


title: S28548_T1D2 redraw_C60

value: 1_T1D#2 ReDraw_C60


title: S13391_413Tmr_C39

tag: stim

value: C1+SMARTer v1


title: S28545_T1D2 redraw_C77

value: Islet antigen-reactive CD4+ sorted T-cells

tag: samplelabel

value: 1_T1D#2 ReDraw_C77


title: S13397_413Tmr_C56

tag: sampleID

value: BRI


title: S28544_T1D2 redraw_C65

tag: samplename

value: 1_T1D#2 ReDraw_C65


title: S13390_413Tmr_C33


title: S28543_T1D2 redraw_C53

value: 1_T1D#2 ReDraw_C53

tag: status

value: single cell


title: S13389_413Tmr_C27


title: S28952_Ctl2_ROpos_C02

tag: pid

value: HiSeq SBS Kit v4


title: S13385_413Tmr_C32


title: S28541_T1D2 redraw_C22

value: 1_T1D#2 ReDraw_C22

tag: visit


title: S13388_413Tmr_C19

tag: numcellssorted


title: S28540_T1D2 redraw_C29

value: 1_T1D#2 ReDraw_C29

tag: libraryid


title: S28539_T1D2 redraw_C17

value: 1_T1D#2 ReDraw_C17

tag: cdnasynthesis


title: S13384_413Tmr_C02

value: T-cell clone BRI4.13

tag: libraryprep


title: S28536_T1D2 redraw_C34

value: 1_T1D#2 ReDraw_C34

tag: projectid


title: S28533_T1D2 redraw_C85

value: 1_T1D#2 ReDraw_C85

tag: seqsite


title: S13382_413Tmr_C25

value: Tetramer stimulated

value: single cell, damaged

tag: flowcellid

value: TruSeq SBS Kit v3


title: S13380_413Tmr_C15

value: C1+SMARTer v1

tag: runchemistry


title: S28530_T1D2 redraw_C57

value: Islet antigen-reactive CD4+ sorted T-cells

value: 1_T1D#2 ReDraw_C57

tag: lane


title: S28529_T1D2 redraw_C51

tag: tissue

value: 1_T1D#2 ReDraw_C51

value: BRI


title: S13381_413Tmr_C21

tag: stim


title: S13379_413Tmr_C09

tag: samplelabel


title: S13337_413aCD3_C94

tag: sampleID

value: anti-CD3 anti-CD28 Stimulated


title: S28528_T1D2 redraw_C92

tag: samplename

value: 1_T1D#2 ReDraw_C92

value: single cell


title: S13335_413aCD3_C72


title: S28527_T1D2 redraw_C56

value: 1_T1D#2 ReDraw_C56

tag: status

value: HiSeq SBS Kit v4


title: S30173_T1D4_ROpos_C82

tag: pid

value: single cell +debris


title: S30168_T1D4_ROpos_C53

tag: visit


title: S13386_413Tmr_C44

value: T-cell clone BRI4.13

tag: numcellssorted


title: S13334_413aCD3_C66

tag: libraryid


title: S13333_413aCD3_C60

tag: cdnasynthesis


title: S28521_T1D2 redraw_C26

value: 1_T1D#2 ReDraw_C26

tag: libraryprep


title: S13336_413aCD3_C88

tag: projectid

value: single cell, dead


title: S13330_413aCD3_C83

tag: seqsite


title: S25526_T1D_CD154pos_C54

tag: flowcellid


title: S28520_T1D2 redraw_C08

value: 1_T1D#2 ReDraw_C08

tag: runchemistry


title: S13328_413aCD3_C65

value: single cell, damaged

tag: lane


title: S13329_413aCD3_C71

tag: tissue

value: TruSeq SBS Kit v3


title: S28522_T1D2 redraw_C32

value: 1_T1D#2 ReDraw_C32

value: C1+SMARTer v1


title: S28523_T1D2 redraw_C44

value: Islet antigen-reactive CD4+ sorted T-cells

value: 1_T1D#2 ReDraw_C44


title: S13326_413aCD3_C53

tag: stim

value: BRI


title: S13327_413aCD3_C59

tag: samplelabel

value: anti-CD3 anti-CD28 Stimulated


title: S13325_413aCD3_C96

tag: sampleID


title: S25524_T1D_CD154pos_C77

tag: samplename


title: S25521_T1D_CD154pos_C59

tag: status


title: S13323_413aCD3_C64


title: S25519_T1D_CD154pos_C84

tag: pid


title: S13322_413aCD3_C58


title: S25518_T1D_CD154pos_C78

tag: visit


title: S13321_413aCD3_C52

tag: numcellssorted


title: S25517_T1D_CD154pos_C36

tag: libraryid


title: S28526_T1D2 redraw_C49

value: 1_T1D#2 ReDraw_C49

tag: cdnasynthesis


title: S25515_T1D_CD154pos_C22

tag: libraryprep

value: single cell


title: S13320_413aCD3_C42

tag: projectid


title: S25514_T1D_CD154pos_C29

tag: seqsite


title: S13319_413aCD3_C36

tag: flowcellid


title: S28517_T1D2 redraw_C15

value: 1_T1D#2 ReDraw_C15

tag: runchemistry


title: S13318_413aCD3_C22

tag: lane


title: S13317_413aCD3_C10

tag: tissue


title: S25510_T1D_CD154pos_C18


title: S25507_T1D_CD154pos_C63


title: S13316_413aCD3_C47

tag: stim


title: S13315_413aCD3_C11

tag: samplelabel


title: S13312_413aCD3_C40

tag: sampleID


title: S25506_T1D_CD154pos_C57

tag: samplename


title: S13314_413aCD3_C05


title: S25508_T1D_CD154pos_C91

tag: status


title: S25501_T1D_CD154pos_C68

tag: pid


title: S13310_413aCD3_C18


title: S25495_T1D_CD154pos_C55

tag: visit


title: S13309_413aCD3_C12

tag: numcellssorted


title: S25497_T1D_CD154pos_C75

tag: libraryid


title: S13308_413aCD3_C91

tag: cdnasynthesis


title: S25489_T1D_CD154pos_C38

tag: libraryprep


title: S13307_413aCD3_C73

tag: projectid


title: S25488_T1D_CD154pos_C32

tag: seqsite


title: S25522_T1D_CD154pos_C65

tag: flowcellid


title: S13306_413aCD3_C69

tag: runchemistry


title: S13304_413aCD3_C92

tag: lane


title: S13305_413aCD3_C51

tag: tissue


title: S25483_T1D_CD154pos_C15


title: S25482_T1D_CD154pos_C09


title: S25048_FluTmrposCD8pos_C66

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in three steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2; SMARTer adapter sequence trimming with fastq-mcf (FastqMcf tool, v.1.0.0); 3) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: PF_ALIGNED_BASES>3.5e6, MEDIAN_CV_COVERAGE<=2.0 & MEDIAN_CV_COVERAGE >=0.4, PCT_USABLE_BASES>=0.25, log10(MEDIAN_3PRIME_BIAS+1)<=0.4 &  log10(MEDIAN_3PRIME_BIAS+1)>=0.1, and >=1 detected in-frame rearranged TCR junction.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_influenza_CD8.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

source_name: Tmr-positive CD8+ sorted T-cells

value: Tmr-positive CD8+ sorted T-cells


title: S25047_FluTmrposCD8pos_C60


title: S13301_413aCD3_C68

tag: stim


title: S13302_413aCD3_C74

tag: samplelabel


title: S25046_FluTmrposCD8pos_C54

tag: sampleID


title: S13297_413aCD3_C75

tag: samplename


title: S25045_FluTmrposCD8pos_C95


title: S25499_T1D_CD154pos_C93

tag: status


title: S25044_FluTmrposCD8pos_C65


title: S13300_413aCD3_C50


title: S25043_FluTmrposCD8pos_C53


title: S25042_FluTmrposCD8pos_C90


title: S13296_413aCD3_C67


title: S13295_413aCD3_C61


title: S13293_413aCD3_C45


title: S25040_FluTmrposCD8pos_C70


title: S25041_FluTmrposCD8pos_C78


title: S25487_T1D_CD154pos_C20

tag: pid


title: S25039_FluTmrposCD8pos_C52


title: S13290_413aCD3_C27


title: S13291_413aCD3_C33


title: S13292_413aCD3_C39


title: S13303_413aCD3_C86


title: S25037_FluTmrposCD8pos_C30


title: S25038_FluTmrposCD8pos_C42


title: S13289_413aCD3_C01


title: S13288_413aCD3_C44


title: S25035_FluTmrposCD8pos_C23


title: S25036_FluTmrposCD8pos_C47


title: S13287_413aCD3_C32


title: S25034_FluTmrposCD8pos_C17


title: S25033_FluTmrposCD8pos_C11


title: S13285_413aCD3_C43


title: S13286_413aCD3_C08


title: S25032_FluTmrposCD8pos_C05


title: S13284_413aCD3_C31


title: S13218_413Unstim_C82

value: Unstimulated


title: S25031_FluTmrposCD8pos_C46


title: S13191_413Unstim_C72

value: T-cell clone BRI4.13


title: S25029_FluTmrposCD8pos_C34


title: S25030_FluTmrposCD8pos_C40


title: S13219_413Unstim_C66


title: S25027_FluTmrposCD8pos_C18


title: S13225_413Unstim_C83


title: S13211_413Unstim_C95


title: S25026_FluTmrposCD8pos_C06


title: S13194_413Unstim_C89


title: S25024_FluTmrposCD8pos_C73


title: S25023_FluTmrposCD8pos_C69


title: S13294_413aCD3_C55


title: S25022_FluTmrposCD8pos_C51


title: S25028_FluTmrposCD8pos_C28


title: S25020_FluTmrposCD8pos_C74


title: S13206_413Unstim_C77


title: S25021_FluTmrposCD8pos_C92


title: S13189_413Unstim_C71


title: S13202_413Unstim_C53


title: S13199_413Unstim_C58


title: S25017_FluTmrposCD8pos_C50


title: S13186_413Unstim_C84


title: S13238_413Unstim_C70


title: S25018_FluTmrposCD8pos_C56


title: S25013_FluTmrposCD8pos_C49


title: S25014_FluTmrposCD8pos_C55


title: S13217_413Unstim_C10


title: S13216_413Unstim_C52


title: S13188_413Unstim_C16


title: S25009_FluTmrposCD8pos_C44


title: S25016_FluTmrposCD8pos_C87


title: S13203_413Unstim_C17


title: S13232_413Unstim_C41


title: S25012_FluTmrposCD8pos_C19


title: S25019_FluTmrposCD8pos_C62


title: S13192_413Unstim_C47


title: S13230_413Unstim_C59


title: S13220_413Unstim_C29


title: S25007_FluTmrposCD8pos_C14


title: S25006_FluTmrposCD8pos_C08


title: S13236_413Unstim_C18


title: S25008_FluTmrposCD8pos_C26


title: S13201_413Unstim_C06


title: S25010_FluTmrposCD8pos_C01


title: S13208_413Unstim_C91


title: S25005_FluTmrposCD8pos_C43


title: S13209_413Unstim_C85


title: S25004_FluTmrposCD8pos_C25


title: S25002_FluTmrposCD8pos_C03


title: S13229_413Unstim_C79


title: S25011_FluTmrposCD8pos_C07


title: S13223_413Unstim_C69


title: S13224_413Unstim_C57


title: S13207_413Unstim_C51


title: S13226_413Unstim_C86


title: S13197_413Unstim_C11


title: S13204_413Unstim_C73


title: S13234_413Unstim_C56


title: S13237_413Unstim_C93


title: S13213_413Unstim_C74


title: S13196_413Unstim_C81


title: S13227_413Unstim_C50


title: S13221_413Unstim_C87


title: S13195_413Unstim_C05


title: S13198_413Unstim_C67


title: S13190_413Unstim_C61


title: S13231_413Unstim_C19


title: S13215_413Unstim_C07


title: S25003_FluTmrposCD8pos_C09


title: S13228_413Unstim_C01


title: S13235_413Unstim_C26


title: S13222_413Unstim_C55


title: S13212_413Unstim_C20


title: S13214_413Unstim_C43


title: S13239_413Unstim_C37


title: S13210_413Unstim_C08


title: S13233_413Unstim_C21


title: S13200_413Unstim_C15


title: S19596_413aCD3_bulk_lib2377

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: PF_ALIGNED_BASES>3.5e6, MEDIAN_CV_COVERAGE<=2.0 & MEDIAN_CV_COVERAGE >=0.4, PCT_USABLE_BASES>=0.25, log10(MEDIAN_3PRIME_BIAS+1)<=0.4 &  log10(MEDIAN_3PRIME_BIAS+1)>=0.1, and >=1 detected in-frame rearranged TCR junction.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_clone_bulk.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

extract_protocol:
Full-length cDNA was prepared from 500-1000 cells using SMARTer Ultra Low Input RNA Kit for Sequencing - v3 according to manufacturer’s instructions (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

tag: replicate

value: SMARTer v3

value: NexteraXT


title: S19597_413Tmr_bulk_lib2378

value: Tmr

tag: numcellssorted


title: S19790_413Unstim_bulk_lib2368

value: Unstim

tag: libraryid


title: S19597_413Tmr_bulk_lib2373

tag: cdnasynthesis

value: TruSeq SBS Kit v3


title: S19596_413aCD3_bulk_lib2372

tag: libraryprep


title: S19790_413Unstim_bulk_lib2367

tag: projectid


title: S13439_413Tmr_C88

value: Tetramer stimulated

tag: seqsite

value: single cell, damaged


title: S13437_413Tmr_C76

value: C1+SMARTer v1

tag: flowcellid


title: S19597_413Tmr_bulk_lib2269

tag: runchemistry


title: S13438_413Tmr_C82

tag: lane


title: S13240_413Unstim_C39

tag: tissue


title: Sup_Fig_2_HK_KO_30_2_KO_analysis

status: Public on Jun 06 2017

data_processing:
Bioinformatics analyses were conducted using Galaxy (Goecks & Nekrutenko, 2010. https://galaxyproject.org/). Reads were aligned to the mouse genome (NCBI37/mm9) with TopHat v1.3.3 and allowed a maximum of one alignment with up to two mismatches per read. opHat v1.3.3  tophat -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --no-coverage-search --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --segment-length 25 --min-segment-intron 50 --max-mismatches 2 --s.
RPKM values were calculated using Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). RPKMs were calculated by dividing mapped exonic reads by the length of the mature mRNA product.
All RPKMs represent an average from at least two biological replicates. A gene was included in the analysis if it met all of the following criteria: The maximum RPKM reached 1 at any time point, the gene was induced at least 5-fold, and the induced expression was significantly different from the basal (P<0.05) as determined by the DESeq package in R Bioconductor[52]. P-values were adjusted using the Benjamini-Hochberg procedure for multiple hypothesis testing[53]. The splice variant with the largest RPKM was included in the analysis.
To normalize the data, the basal RPKM in WT samples was set at 0% and the maximum WT RPKM at 100% for each gene. In the mutant strains, percent expression was calculated using this scale substituting only the maximum WT RPKM with the maximum mutant RPKM.
For promoter enrichment, PScan software (http://159.149.160.88/pscan) using Jaspar 2016 motif analysis examining -450 to +50 base pairs of the promoter of groups of interest. For Gene Ontogeny analysis, gene families were inputted into ENRICHR software[28,54]. The GO Biologic Process function was used for gene ontogeny classification. The top 5 significant GO terms were used. Both the lighter color and longer length of the bars denote stronger significance of the identified pathway.  Bedgraph files were generated from aligned BAM files using the Bedtools suite: genomeCoverageBed -bg -split, using the mouse mm9 reference genome.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position

molecule: polyA RNA

source_name: Bone Marrow Derived Macrophages

growth_protocol: BMDMs were isolated and differentiated from WT or mutant/deficient mice as previously described in (Bhatt et al., 2012). Briefly, bone marrow isolated from femurs and tibias from male mice at 6-10 weeks of age were cultured in BMDM media consisting of DMEM with 20% FBS, CMG conditioned media containing M-CSF, and 1X Pen/Strep for 6 days. All media was washed twice with PBS, then antibiotic-free BMDM media was added prior to addition of bacteria.

extract_protocol:
RNA was extracted using TRI-reagent (Molecular Research Center), treated with RNase-free DNaseI, and purified using an RNeasy kit (Qiagen)
Strand-specific libraries were generated from 400 ng total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina), with modifications using the “dUTP” method (Levin et al., 2010). cDNA libraries were single-end sequenced with a length of 50bp on an Illumina HiSeq 2000.

treatment_protocol: Mouse macrophages were stimulated on day 6 following differentiation. Human and mouse macrophages were infected with S. aureus strain DU5938 at 10 M.O.I. in antibiotic free MDM and BMDM media. Macrophages were infected with S. aureus for 0, 30, 60, 120, and 240 minutes at 37 °C or treated with HK S. aureus for the same time points. Media was obtained at the 240-minute time point for cytokine determination by ELISA.

tag: strain

tag: gender

value: male

tag: genotype

value: KO

value: bone marrow

tag: cell type

value: macrophage

tag: bacteria

value: Heat-Killed S. aureus


title: Sup_Fig_2_HK_WT_240_KO_analysis

value: WT


title: Sup_Fig_2_HK_WT_120_KO_analysis


title: Sup_Fig_2_HK_KO_60_1_KO_analysis


title: Sup_Fig_2_HK_KO_60_2_KO_analysis


title: Sup_Fig_2_HK_KO_240_2_KO_analysis


title: Sup_Fig_2_HK_WT_30_KO_analysis


title: Sup_Fig_2_HK_DKO_60_2_DKO_analysis

value: DKO


title: Sup_Fig_2_HK_KO_30_1_KO_analysis


title: Sup_Fig_2_HK_DKO_120_2_DKO_analysis


title: Sup_Fig_2_HK_DKO_240_2_DKO_analysis


title: Sup_Fig_2_HK_DKO_240_1_DKO_analysis


title: Sup_Fig_2_HK_DKO_60_1_DKO_analysis


title: Sup_Fig_2_HK_KO_120_2_KO_analysis


title: S19790_413Unstim_bulk_lib2366

tag: samplelabel

tag: sampleID

tag: samplename

tag: status

tag: stim

value: BRI


title: Figure_3_Sup_Fig_2_WT_0h_DKO_analysis_live_and_hk

value: Uninfected


title: Sup_Fig_2_HK_KO_240_1_KO_analysis


title: S13193_413Unstim_C49

value: T-cell clone BRI4.13

value: Unstimulated

tag: numcellssorted

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

value: single cell


title: Figure_3_Live_WT_60_DKO_analysis

value: Live S. aureus


title: Sup_Fig_2_HK_WT_60_KO_analysis


title: Figure_3_Live_WT_30_DKO_analysis


title: Sup_Fig_2_HK_DKO_30_1_DKO_analysis


title: S19596_413aCD3_bulk_lib2268

tag: replicate

value: SMARTer v3

value: NexteraXT

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3


title: Figure_3_Live_WT_240_DKO_analysis

tag: strain

tag: gender

tag: genotype

tag: tissue


title: Figure_3_Live_WT_120_DKO_analysis

tag: cell type

tag: bacteria


title: Figure_3_Live_KO_30_2_KO_analysis


title: Figure_3_Live_KO_240_2_KO_analysis


title: Figure_3_Live_KO_30_1_KO_analysis


title: Sup_Fig_2_HK_DKO_30_2_DKO_analysis


title: Figure_3_Sup_Fig_2_KO_0_2_KO_analysis_live_and_hk


title: Figure_3_Live_KO_120_2_KO_analysis


title: Figure_3_Live_KO_120_1_KO_analysis


title: Figure_3_Live_DKO_60_2_DKO_analysis


title: Figure_3_Sup_Fig_2_DKO_0_1_DKO_analysis_live_and_hk


title: Figure_3_Sup_Fig_2_KO_0_1_KO_analysis_live_and_hk


title: Figure_3_Live_KO_60_2_KO_analysis


title: Sup_Fig_2_HK_KO_120_1_KO_analysis


title: Sup_Fig_2_HK_DKO_120_1_DKO_analysis


title: Figure_3_Live_KO_60_1_KO_analysis


title: Figure_3_Live_DKO_240_1_DKO_analysis


title: Figure_3_Live_DKO_240_2_DKO_analysis


title: Figure_3_Live_DKO_120_2_DKO_analysis


title: Sup_Fig_2_DKO_0_2_DKO_analysis


title: Figure_3_Live_DKO_60_1_DKO_analysis


title: Figure_1B_4_Sup_Fig_2_HK_WT_60_1_DKO_analysis_KO_analysis


title: Figure_3_Live_DKO_30_1_DKO_analysis


title: Figure_3_Live_DKO_30_2_DKO_analysis


title: Figure_1B_4_Sup_Fig_2_HK_WT_240_1_DKO_analysis_KO_analysis


title: Figure_3_Live_KO_240_1_KO_analysis


title: Figure_1A_3_4_Live_WT_60_4


title: Figure_3_Live_DKO_120_1_DKO_analysis


title: Figure_1B_4_Sup_Fig_2_HK_WT_60_2_DKO_analysis


title: Figure_3_DKO_0_2_DKO_analysis_live


title: Figure_1B_4_Sup_Fig_2_HK_WT_120_1_DKO_analysis_KO_analysis


title: Figure_1A_3_4_Live_WT_30_2_KO_analysis


title: Figure_1B_4_Sup_Fig_2_HK_WT_30_2_DKO_analysis


title: Figure_1B_4_Sup_Fig_2_HK_WT_30_1_DKO_analysis_KO_analysis


title: Figure_1B_4_Sup_Fig_2_HK_WT_240_2_DKO_analysis


title: Figure_1A_3_4_Live_WT_240_3_KO_analysis


title: Figure_1A_3_4_Live_WT_240_1_DKO_analysis


title: Figure_1A_3_4_Live_WT_60_3_KO_analysis


title: Figure_1A_3_4_Live_WT_120_2_KO_analysis


title: Figure_1A_3_4_Live_WT_120_3_KO_analysis


title: Figure_1A_3_4_Live_WT_120_4


title: Figure_1A_3_4_Live_WT_30_3_KO_analysis


title: Figure_1A_3_4_Live_WT_120_1_DKO_analysis


title: Figure_1A_3_4_Live_WT_60_2_KO_analysis


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_8


title: Figure_1A_3_4_Live_WT_240_4


title: Figure_1B_4_Sup_Fig_2_HK_WT_120_2_DKO_analysis


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_6_KO_analysis_live_hk


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_4


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_9


title: Figure_1A_3_4_Live_WT_30_1_DKO_analysis


title: Figure_1A_3_4_Live_WT_30_4


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_2


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_3


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_7


title: Figure_1A_3_4_Live_WT_60_1_DKO_analysis


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_12


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_13


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_11_KO_analysis_live_hk


title: Figure_1A_1B_3_4_Sup_Fig_2_Figure_1A_WT_0h_1


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_10


title: Figure_1A_1B_3_4_Sup_Fig_2_WT_0h_5_DKO_analysis_live_and_hk


title: Figure_1A_3_4_Live_WT_240_2_KO_analysis


title: T1D#25_PPIC3

status: Public on Aug 15 2016

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalised using quantile normalization, values less than 10 were floored to 10, and the data was transformed to log2 scale within R.

label: biotin

source_name: PBMC

label_protocol: Biotinylated cRNA targets were prepared from 250 ng of total RNA, using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: PBMCs were cultured in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.

extract_protocol: RNA was extracted with Qiagen Rneasy mini kit, followed by DNase I treatment and clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer.

treatment_protocol: 1x10^6 PBMCs were stimulated with peptides derived from type 1 diabetogenic protein (IGRP, PPI), and cultured for 24 hours in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.

tag: stimulation

tag: time point


title: T1D#20_PPIC3


title: T1D#26_PPIC3


title: HC#35_PPIC3


title: T1D#30_PPIC3


title: T1D#18_PPIC3


title: HC#23_PPIC3


title: HC#20_PPIC3


title: HC#34_PPIC3


title: T1D#23_PPIC3


title: T1D#29_PPIC3


title: T1D#27_PPIC3


title: T1D#22_PPIC3


title: T1D#28_PPIC3


title: HC#32_PPIC3


title: T1D#24_PPIC3


title: HC#30_PPIC3


title: HC#25_PPIC3


title: HC#31_PPIC3


title: HC#27_PPIC3


title: T1D#19_PPIC3


title: HC#22_PPIC3


title: HC#28_PPIC3


title: HC#33_PPIC3


title: HC#26_PPIC3


title: HC#24_PPIC3


title: HC#19_PPIC3


title: HC#17_PPIC3


title: HC#16_PPIC3


title: HC#21_PPIC3


title: T1D#30_None


title: T1D#27_None


title: T1D#26_None


title: T1D#29_None


title: T1D#22_None


title: T1D#17_None


title: T1D#23_None


title: T1D#28_None


title: HC#35_None


title: T1D#16_None


title: HC#28_None


title: HC#31_None


title: T1D#25_None


title: HC#32_None


title: T1D#19_None


title: HC#29_None


title: HC#34_None


title: T1D#21_None


title: HC#27_None


title: T1D#24_None


title: HC#24_None


title: T1D#20_None


title: HC#18_PPIC3


title: HC#25_None


title: T1D#18_None


title: HC#23_None


title: HC#18_None


title: HC#30_None


title: HC#26_None


title: HC#33_None


title: HC#16_None


title: HC#22_None


title: HC#21_None


title: T1D#23_IGRPp14


title: T1D#28_IGRPp14


title: HC#20_None


title: HC#17_None


title: T1D#30_IGRPp14


title: T1D#29_IGRPp14


title: HC#19_None


title: T1D#22_IGRPp14


title: T1D#26_IGRPp14


title: HC#30_IGRPp14


title: HC#34_IGRPp14


title: T1D#24_IGRPp14


title: T1D#20_IGRPp14


title: HC#19_IGRPp14


title: T1D#27_IGRPp13


title: HC#21_IGRPp14


title: HC#22_IGRPp14


title: HC#18_IGRPp14


title: T1D#26_IGRPp13


title: T1D#16_IGRPp13


title: HC#27_IGRPp14


title: T1D#23_IGRPp13


title: T1D#24_IGRPp13


title: T1D#29_IGRPp13


title: T1D#19_IGRPp13


title: T1D#22_IGRPp13


title: HC#33_IGRPp13


title: HC#34_IGRPp13


title: HC#18_IGRPp13


title: HC#30_IGRPp13


title: HC#23_IGRPp13


title: HC#19_IGRPp13


title: HC#17_IGRPp13


title: T1D#27_IGRPp12


title: HC#24_IGRPp13


title: HC#16_IGRPp13


title: T1D#22_IGRPp12


title: T1D#25_IGRPp12


title: T1D#16_IGRPp12


title: HC#18_IGRPp12


title: HC#21_IGRPp13


title: T1D#24_IGRPp12


title: T1D#28_IGRPp12


title: HC#21_IGRPp12


title: HC#16_IGRPp14


title: HC#30_IGRPp12


title: T1D#23_IGRPp12


title: HC#34_IGRPp12


title: T1D#27_IGRPp11


title: T1D#30_IGRPp11


title: T1D#26_IGRPp11


title: HC#33_IGRPp11


title: HC#16_IGRPp12


title: T1D#22_IGRPp11


title: T1D#17_IGRPp12


title: HC#30_IGRPp11


title: HC#23_IGRPp11


title: T1D#23_IGRPp11


title: T1D#26_IGRPp12


title: HC#24_IGRPp11


title: HC#27_IGRPp11


title: T1D#29_IGRPp11


title: HC#21_IGRPp11


title: HC#34_IGRPp11


title: HC#16_IGRPp11


title: T1D#28_IGRPC4


title: HC#22_IGRPp13


title: T1D#29_IGRPC4


title: T1D#26_IGRPC4


title: HC#18_IGRPp11


title: T1D#30_IGRPC4


title: T1D#21_IGRPC4


title: HC#25_IGRPC4


title: T1D#18_IGRPC4


title: HC#24_IGRPC4


title: T1D#17_IGRPC4


title: T1D#25_IGRPC4


title: HC#33_IGRPC4


title: HC#30_IGRPC4


title: HC#35_IGRPC4


title: T1D#20_IGRPC4


title: HC#27_IGRPC4


title: HC#22_IGRPC4


title: HC#20_IGRPC4


title: HC#32_IGRPC4


title: HC#23_IGRPC4


title: HC#28_IGRPC4


title: HC#31_IGRPC4


title: T1D#16_IGRPC4


title: T1D#24_IGRPC4


title: HC#19_IGRPC4


title: HC#18_IGRPC4


title: HC#34_IGRPC4


title: T1D#9_ZnT8p18

treatment_protocol: 1x10^6 PBMCs were stimulated with peptides derived from type 1 diabetogenic protein (GAD65, IGRP, PPI, ZnT8) and influenza virus M, and cultured for 24 hours in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.


title: T1D#19_IGRPC4


title: HC#16_IGRPC4


title: T1D#9_Flu-MP

value: Flu-MP


title: T1D#23_IGRPC4


title: HC#17_IGRPC4


title: T1D#9_ZnT8C5


title: HC#26_IGRPC4


title: T1D#9_None


title: T1D#9_GAD65C1


title: HC#29_IGRPC4


title: T1D#27_IGRPC4


title: T1D#22_IGRPC4


title: T1D#9_IGRPC4


title: T1D#9_PPIC3


title: T1D#8_IGRPC4


title: T1D#8_GAD65C1


title: T1D#8_ZnT8C5


title: T1D#8_None


title: T1D#7_ZnT8p17


title: T1D#7_ZnT8C5


title: T1D#7_None


title: T1D#7_ZnT8p16


title: T1D#7_IGRPp11


title: T1D#7_IGRPC4


title: T1D#6_None


title: T1D#7_GAD65C1


title: T1D#6_PPIC3


title: T1D#5_None


title: T1D#4_IGRPp13


title: T1D#5_ZnT8p16


title: T1D#6_GAD65C1


title: HC#21_IGRPC4


title: T1D#5_IGRPp13


title: T1D#4_PPIC3


title: T1D#6_Flu-MP


title: T1D#7_PPIC3


title: T1D#5_ZnT8p17


title: T1D#5_IGRPp14


title: T1D#5_ZnT8C5


title: T1D#4_None


title: T1D#4_ZnT8C5


title: T1D#6_IGRPC4


title: T1D#5_IGRPp12


title: T1D#6_ZnT8C5


title: T1D#5_ZnT8p15


title: T1D#5_IGRPC4


title: T1D#4_IGRPC4


title: T1D#3_ZnT8p15


title: T1D#4_GAD65C1


title: T1D#3_None


title: T1D#4_Flu-MP


title: T1D#3_ZnT8C5


title: T1D#3_PPIC3


title: T1D#3_GAD65C1


title: T1D#2_ZnT8p17


title: T1D#3_Flu-MP


title: T1D#2_GAD65C1


title: T1D#15_IGRPp12


title: T1D#3_IGRPp13


title: T1D#2_IGRPp13


title: T1D#2_ZnT8C5


title: T1D#2_PPIC3


title: T1D#2_IGRPC4


title: T1D#14_IGRPC4


title: T1D#2_IGRPp12


title: T1D#3_IGRPC4


title: T1D#15_None


title: T1D#2_ZnT8p15


title: T1D#15_IGRPC4


title: T1D#2_IGRPp14


title: T1D#2_IGRPp11


title: T1D#2_None


title: T1D#14_GAD65C1


title: T1D#14_ZnT8C5


title: T1D#15_ZnT8C5


title: T1D#15_GAD65C1


title: T1D#13_ZnT8p18


title: T1D#14_PPIC3


title: T1D#13_ZnT8p17


title: T1D#14_None


title: T1D#13_None


title: T1D#13_IGRPp12


title: T1D#13_IGRPp13


title: T1D#13_IGRPC4


title: T1D#12_ZnT8C5


title: T1D#13_IGRPp11


title: T1D#12_None


title: T1D#12_ZnT8p17


title: T1D#12_IGRPC4


title: T1D#12_IGRPp11


title: T1D#11_ZnT8p15


title: T1D#11_ZnT8C5


title: T1D#12_IGRPp12


title: T1D#11_None


title: T1D#11_GAD65C1


title: T1D#10_IGRPp14


title: T1D#12_GAD65C1


title: T1D#11_PPIC3


title: T1D#10_ZnT8C5


title: T1D#1_ZnT8C5