title: EUHM1003V2, Healthy, D1

status: Public on Feb 28 2025

type: SRA

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

description: Library name: EUHM1003V2

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (vl.5.6)102 by (l) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: GRCh38.108
Supplementary files format and content: tab delimited text file including raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Periphery blood

extract_protocol:
Oligo (dT)-attached magnetic beads were used to purify mRNA.
Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription. A second-strand cDNA synthesis is followed and dUTP was used instead of dTTP. Afterwards, the purified double-stranded cDNA was End Repaired, A-Tailed, and adapter ligated. The cDNA fragments obtained from previous step were digested with UDG enzyme to remove the U-labeled second-strand template and were amplified by PCR.  The final products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer DNA analysis for quality control. The double-stranded PCR products from previous step were heat denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 (in-lane control) together to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray, and pair-end 100 bases reads were generated on BGI-G400 platform.

tag: tissue

value: Periphery blood

tag: cell line

value: Primary cells

tag: cell type

value: Whole blood

tag: condition

value: Healthy

tag: treatment


title: EUHM1007V1, Healthy, Baseline

description: Library name: EUHM1007V1

value: Baseline


title: EUHM1003V3, Healthy, D7

description: Library name: EUHM1003V3


title: EUHM1007V2, Healthy, D1

description: Library name: EUHM1007V2


title: EUHM1004V2, Healthy, D1

description: Library name: EUHM1004V2


title: EUH1009V3, Healthy, D7

description: Library name: EUH1009V3


title: Peripheral whole blood DNA from fILD patient 478

type: genomic

city: Vancouver

first: Gillian

middle: Catherine

last: Goobie

state: British Columbia

address: Centre for Heart Lung Innovation, St. Paul's Hospital, 1081 Burrard Street

department: Division of Respiratory Medicine

country: Canada

institute: University of British Columbia

description:
206139130072
206139130072_R06C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium MethylatioEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner settings

data_processing:
A multi-package approach to processing and analyzing raw DNAm data produced from the Infinium MethylationEPIC array was implemented. First, raw .idat files for each sample underwent pre-processing, quality control, filtering, and analysis using R statistical computing environment (version 4.2.1, www.r-project.org). Using the minfi package, samples with a mean detection p-value >0.05 were excluded (n=2). The detection p-value compares the total unmethylated and methylated signal at each CpG location and compares it to the background signal inferred from negative control probes, such that p-values >0.05 or >0.01 indicate a failed probe where the signal from the probe is not significantly different from the background. All samples are from blood, and thus it was not expected there would be major global differences in methylation patterns between the samples. This enabled normalization using a subset quantile procedure, which helps to mitigate the impacts of artifacts in the data that are the result of differences between Type-I and Type-II methylation probes and other technical sources of variation. Next, for probe filtering, we removed any CpG probes whose detection p-value was >0.01 on one or more samples. We also removed sex chromosome probes given that our study includes patients of male and female sex. Next, we removed probes that had a single nucleotide polymorphism (SNP) at the CpG site, as this can result in impaired hybridization and detection of methylation for individuals with a variant allele at that locus. Subsequently, we removed cross-reactive probes that do not uniquely hybridize to a single CpG site on the MethylationEPIC array.
*processed value definition = Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Whole blood DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral whole blood samples taken from patients enrolled in the UPitt cohort using the Puregene DNA isolation kit or QiaAmp blood DNA isolation kit (Qiagen) and from the UBC cohort using the DNeasy Blood and Tissue Kit (Qiagen), all according to the manufacturer’s instructions. UBC samples were transferred to UPitt for simultaneous analysis alongside the UPitt samples. Prior to analysis, all DNA samples were stored at -20°C. DNA concentration and purity were assessed using the Infinite M200 Pro NanoQuant Plate Reader. Samples with an A260/A280 absorbance ratio outside of the 1.7-2.0 range were excluded.

tag: cohort

value: UBC

tag: Sex

value: M

tag: smokehx

value: Former

value: IPF

value: Whole blood DNA

tag: genotype


title: Peripheral whole blood DNA from fILD patient 479

description:
206139130072
206139130072_R07C01


title: Peripheral whole blood DNA from fILD patient 480

description:
206139130072
206139130072_R08C01


title: Peripheral whole blood DNA from fILD patient 477

description:
206139130072
206139130072_R05C01

value: UPitt

value: UNCLASSIFIABLE


title: Peripheral whole blood DNA from fILD patient 476

description:
206139130072
206139130072_R04C01


title: EUH1009V1, Healthy, Baseline

description: Library name: EUH1009V1


title: Peripheral whole blood DNA from fILD patient 475

description:
206139130072
206139130072_R03C01

value: F


title: EUH1006V2, Healthy, D1

description: Library name: EUH1006V2


title: EUH1006V3, Healthy, D7

description: Library name: EUH1006V3


title: EUH1003V3, Healthy, D7

description: Library name: EUH1003V3


title: Peripheral whole blood DNA from fILD patient 472

description:
206144080012
206144080012_R08C01

value: Always


title: EUH1006V1, Healthy, Baseline

description: Library name: EUH1006V1


title: EUHM1004V1, Healthy, Baseline

description: Library name: EUHM1004V1


title: Peripheral whole blood DNA from fILD patient 470

description:
206144080012
206144080012_R06C01

value: Never


title: EUH1003V1, Healthy, Baseline

description: Library name: EUH1003V1


title: Peripheral whole blood DNA from fILD patient 473

description:
206139130072
206139130072_R01C01


title: Peripheral whole blood DNA from fILD patient 469

description:
206144080012
206144080012_R05C01


title: EUHM1003V1, Healthy, Baseline

description: Library name: EUHM1003V1


title: EUH1003V2, Healthy, D1

description: Library name: EUH1003V2


title: Peripheral whole blood DNA from fILD patient 471

description:
206144080012
206144080012_R07C01


title: EUH1009V2, Healthy, D1

description: Library name: EUH1009V2


title: CTRU2059CE.04, Healthy, Baseline

description: Library name: CTRU2059CE.04


title: CTRU2057CE.06, Healthy, D1

description: Library name: CTRU2057CE.06


title: Peripheral whole blood DNA from fILD patient 467

description:
206144080012
206144080012_R03C01


title: Peripheral whole blood DNA from fILD patient 474

description:
206139130072
206139130072_R02C01


title: CTRU2057CE.05, Healthy, Baseline

description: Library name: CTRU2057CE.05


title: Peripheral whole blood DNA from fILD patient 468

description:
206144080012
206144080012_R04C01


title: Peripheral whole blood DNA from fILD patient 466

description:
206144080012
206144080012_R02C01


title: CTRU2059CE.05, Healthy, D1

description: Library name: CTRU2059CE.05


title: Peripheral whole blood DNA from fILD patient 464

description:
206144080007
206144080007_R08C01


title: Peripheral whole blood DNA from fILD patient 463

description:
206144080007
206144080007_R07C01


title: CTRU2028CE.07, Healthy, D1

description: Library name: CTRU2028CE.07


title: CTRU2028CE.08, Healthy, D7

description: Library name: CTRU2028CE.08


title: Peripheral whole blood DNA from fILD patient 465

description:
206144080012
206144080012_R01C01


title: CTRU2024CE.08, Healthy, D7

description: Library name: CTRU2024CE.08


title: CTRU2024CE.06, Healthy, D1

description: Library name: CTRU2024CE.06


title: CTRU2015CE.06, Healthy, D7

description: Library name: CTRU2015CE.06


title: Peripheral whole blood DNA from fILD patient 462

description:
206144080007
206144080007_R06C01


title: Peripheral whole blood DNA from fILD patient 457

description:
206144080007
206144080007_R01C01


title: CTRU2014CE.07, Healthy, D7

description: Library name: CTRU2014CE.07


title: Peripheral whole blood DNA from fILD patient 460

description:
206144080007
206144080007_R04C01


title: CTRU2024CE.05, Healthy, Baseline

description: Library name: CTRU2024CE.05


title: Peripheral whole blood DNA from fILD patient 459

description:
206144080007
206144080007_R03C01


title: Peripheral whole blood DNA from fILD patient 458

description:
206144080007
206144080007_R02C01


title: Peripheral whole blood DNA from fILD patient 461

description:
206144080007
206144080007_R05C01


title: Peripheral whole blood DNA from fILD patient 456

description:
206139130080
206139130080_R08C01


title: CTRU2014CE.06, Healthy, D1

description: Library name: CTRU2014CE.06


title: CTRU2014CE.05, Healthy, Baseline

description: Library name: CTRU2014CE.05


title: CTRU2015CE.05, Healthy, Baseline

description: Library name: CTRU2015CE.05


title: Peripheral whole blood DNA from fILD patient 454

description:
206139130080
206139130080_R06C01


title: Peripheral whole blood DNA from fILD patient 455

description:
206139130080
206139130080_R07C01


title: CTRU2010CE.06, Healthy, Baseline

description: Library name: CTRU2010CE.06


title: Peripheral whole blood DNA from fILD patient 453

description:
206139130080
206139130080_R05C01


title: Peripheral whole blood DNA from fILD patient 452

description:
206139130080
206139130080_R04C01


title: CTRU2010CE.07, Healthy, D1

description: Library name: CTRU2010CE.07


title: CTRU2007CE.08, Healthy, D7

description: Library name: CTRU2007CE.08


title: CTRU2028CE.06, Healthy, Baseline

description: Library name: CTRU2028CE.06


title: Peripheral whole blood DNA from fILD patient 451

description:
206139130080
206139130080_R03C01

value: HP


title: CTRU2007CE.07, Healthy, D1

description: Library name: CTRU2007CE.07


title: Peripheral whole blood DNA from fILD patient 450

description:
206139130080
206139130080_R02C01


title: Peripheral whole blood DNA from fILD patient 449

description:
206139130080
206139130080_R01C01

value: CTD-ILD


title: CTRU2006CE.06, Healthy, D7

description: Library name: CTRU2006CE.06

value: Periphery blood


title: Peripheral whole blood DNA from fILD patient 447

description:
206139130041
206139130041_R07C01


title: CTRU2006CE.05, Healthy, D1

description: Library name: CTRU2006CE.05

value: Primary cells


title: Peripheral whole blood DNA from fILD patient 448

description:
206139130041
206139130041_R08C01


title: Peripheral whole blood DNA from fILD patient 446

description:
206139130041
206139130041_R06C01


title: CTRU2005CE.05, Healthy, Baseline

description: Library name: CTRU2005CE.05

value: Whole blood


title: CTRU2010CE.08, Healthy, D7

description: Library name: CTRU2010CE.08

value: Healthy


title: Peripheral whole blood DNA from fILD patient 442

description:
206139130041
206139130041_R02C01


title: Peripheral whole blood DNA from fILD patient 445

description:
206139130041
206139130041_R05C01


title: Peripheral whole blood DNA from fILD patient 444

description:
206139130041
206139130041_R04C01


title: Peripheral whole blood DNA from fILD patient 441

description:
206139130041
206139130041_R01C01


title: CTRU2004CE.07, Healthy, D7

description: Library name: CTRU2004CE.07


title: CTRU2004CE.05, Healthy, Baseline

description: Library name: CTRU2004CE.05

value: Baseline


title: Peripheral whole blood DNA from fILD patient 440

description:
206139130040
206139130040_R08C01

value: UBC


title: CTRU2002CE.07, Healthy, D7

description: Library name: CTRU2002CE.07


title: CTRU2007CE.06, Healthy, Baseline

description: Library name: CTRU2007CE.06


title: Peripheral whole blood DNA from fILD patient 435

description:
206139130040
206139130040_R03C01

value: M


title: CTRU2001CE.06, Healthy, Baseline

description: Library name: CTRU2001CE.06


title: CTRU2001CE.07, Healthy, D1

description: Library name: CTRU2001CE.07


title: CTRU2001CE.08, Healthy, D7

description: Library name: CTRU2001CE.08


title: Peripheral whole blood DNA from fILD patient 434

description:
206139130040
206139130040_R02C01

value: Former


title: CTRU2006CE.04, Healthy, Baseline

description: Library name: CTRU2006CE.04


title: Peripheral whole blood DNA from fILD patient 437

description:
206139130040
206139130040_R05C01


title: CTRU2005CE.06, Healthy, D7

description: Library name: CTRU2005CE.06


title: Peripheral whole blood DNA from fILD patient 433

description:
206139130040
206139130040_R01C01

value: IPF


title: Peripheral whole blood DNA from fILD patient 443

description:
206139130041
206139130041_R03C01

value: Whole blood DNA


title: 626610019V2, LTX, D1

description: Library name: 626610019V2

value: Lung transplant


title: 626610019V3, LTX, D7

description: Library name: 626610019V3


title: Peripheral whole blood DNA from fILD patient 431

description:
206139130026
206139130026_R07C01


title: CTRU2004CE.06, Healthy, D1

description: Library name: CTRU2004CE.06


title: 626610018V3, LTX, D7

description: Library name: 626610018V3


title: Peripheral whole blood DNA from fILD patient 429

description:
206139130026
206139130026_R05C01


title: 626610017V3, LTX, D7

description: Library name: 626610017V3


title: Peripheral whole blood DNA from fILD patient 430

description:
206139130026
206139130026_R06C01


title: Peripheral whole blood DNA from fILD patient 439

description:
206139130040
206139130040_R07C01


title: Peripheral whole blood DNA from fILD patient 428

description:
206139130026
206139130026_R04C01

value: UNCLASSIFIABLE


title: CTRU2002CE.06, Healthy, D1

description: Library name: CTRU2002CE.06


title: Peripheral whole blood DNA from fILD patient 438

description:
206139130040
206139130040_R06C01


title: 626610018V1, LTX, Baseline

description: Library name: 626610018V1


title: 626610017V2, LTX, D1

description: Library name: 626610017V2


title: CTRU2002CE.05, Healthy, Baseline

description: Library name: CTRU2002CE.05


title: Peripheral whole blood DNA from fILD patient 436

description:
206139130040
206139130040_R04C01

value: F


title: Peripheral whole blood DNA from fILD patient 427

description:
206139130026
206139130026_R03C01


title: 626610019V1, LTX, Baseline

description: Library name: 626610019V1


title: Peripheral whole blood DNA from fILD patient 432

description:
206139130026
206139130026_R08C01


title: 626610016V2, LTX, D1

description: Library name: 626610016V2


title: Peripheral whole blood DNA from fILD patient 426

description:
206139130026
206139130026_R02C01


title: 626610016V3, LTX, D7

description: Library name: 626610016V3


title: Peripheral whole blood DNA from fILD patient 421

description:
206139130054
206139130054_R05C01


title: Peripheral whole blood DNA from fILD patient 420

description:
206139130054
206139130054_R04C01

value: Always


title: Peripheral whole blood DNA from fILD patient 418

description:
206139130054
206139130054_R02C01


title: Peripheral whole blood DNA from fILD patient 425

description:
206139130026
206139130026_R01C01


title: 626610013V2, LTX, D1

description: Library name: 626610013V2


title: Peripheral whole blood DNA from fILD patient 424

description:
206139130054
206139130054_R08C01


title: 626610016V1, LTX, Baseline

description: Library name: 626610016V1


title: 626610018V2, LTX, D1

description: Library name: 626610018V2


title: 626610011V3, LTX, D7

description: Library name: 626610011V3


title: 626610015V1, LTX, Baseline

description: Library name: 626610015V1


title: Peripheral whole blood DNA from fILD patient 423

description:
206139130054
206139130054_R07C01

value: Never


title: Peripheral whole blood DNA from fILD patient 412

description:
206144080140
206144080140_R04C01


title: Peripheral whole blood DNA from fILD patient 422

description:
206139130054
206139130054_R06C01


title: 626610014V1, LTX, Baseline

description: Library name: 626610014V1


title: Peripheral whole blood DNA from fILD patient 411

description:
206144080140
206144080140_R03C01


title: Peripheral whole blood DNA from fILD patient 419

description:
206139130054
206139130054_R03C01


title: 626610014V2, LTX, D1

description: Library name: 626610014V2


title: 626610013V3, LTX, D7

description: Library name: 626610013V3


title: Peripheral whole blood DNA from fILD patient 409

description:
206144080140
206144080140_R01C01


title: Peripheral whole blood DNA from fILD patient 417

description:
206139130054
206139130054_R01C01


title: Peripheral whole blood DNA from fILD patient 408

description:
206144080148
206144080148_R08C01


title: Peripheral whole blood DNA from fILD patient 415

description:
206144080140
206144080140_R07C01


title: 626610011V1, LTX, Baseline

description: Library name: 626610011V1


title: Peripheral whole blood DNA from fILD patient 416

description:
206144080140
206144080140_R08C01


title: Peripheral whole blood DNA from fILD patient 414

description:
206144080140
206144080140_R06C01


title: 626610012V3, LTX, D7

description: Library name: 626610012V3


title: 626610017V1, LTX, Baseline

description: Library name: 626610017V1


title: 626610012V2, LTX, D1

description: Library name: 626610012V2


title: Peripheral whole blood DNA from fILD patient 413

description:
206144080140
206144080140_R05C01


title: 626610010V2, LTX, D1

description: Library name: 626610010V2


title: 626610012V1, LTX, Baseline

description: Library name: 626610012V1


title: 626610015V3, LTX, D7

description: Library name: 626610015V3


title: 626610010V1, LTX, Baseline

description: Library name: 626610010V1


title: Peripheral whole blood DNA from fILD patient 410

description:
206144080140
206144080140_R02C01


title: 626610011V2, LTX, D1

description: Library name: 626610011V2


title: Peripheral whole blood DNA from fILD patient 404

description:
206144080148
206144080148_R04C01


title: 626610013V1, LTX, Baseline

description: Library name: 626610013V1


title: 626610010V3, LTX, D7

description: Library name: 626610010V3


title: 626610015V2, LTX, D1

description: Library name: 626610015V2


title: Peripheral whole blood DNA from fILD patient 403

description:
206144080148
206144080148_R03C01


title: 626610007V3, LTX, D7

description: Library name: 626610007V3


title: Peripheral whole blood DNA from fILD patient 399

description:
206144080124
206144080124_R07C01


title: Peripheral whole blood DNA from fILD patient 402

description:
206144080148
206144080148_R02C01


title: Peripheral whole blood DNA from fILD patient 406

description:
206144080148
206144080148_R06C01


title: Peripheral whole blood DNA from fILD patient 407

description:
206144080148
206144080148_R07C01


title: Peripheral whole blood DNA from fILD patient 405

description:
206144080148
206144080148_R05C01

value: HP


title: 626610009V3, LTX, D7

description: Library name: 626610009V3


title: 626610009V2, LTX, D1

description: Library name: 626610009V2


title: Peripheral whole blood DNA from fILD patient 396

description:
206144080124
206144080124_R04C01


title: 626610008V3, LTX, D7

description: Library name: 626610008V3


title: 626610006V3, LTX, D7

description: Library name: 626610006V3


title: 626610007V1, LTX, Baseline

description: Library name: 626610007V1


title: 626610009V1, LTX, Baseline

description: Library name: 626610009V1


title: Peripheral whole blood DNA from fILD patient 394

description:
206144080124
206144080124_R02C01


title: Peripheral whole blood DNA from fILD patient 393

description:
206144080124
206144080124_R01C01


title: 626610005V1, LTX, Baseline

description: Library name: 626610005V1


title: Peripheral whole blood DNA from fILD patient 401

description:
206144080148
206144080148_R01C01


title: 626610008V2, LTX, D1

description: Library name: 626610008V2


title: Peripheral whole blood DNA from fILD patient 400

description:
206144080124
206144080124_R08C01


title: 626610008V1, LTX, Baseline

description: Library name: 626610008V1


title: Peripheral whole blood DNA from fILD patient 398

description:
206144080124
206144080124_R06C01


title: 626610004V3, LTX, D7

description: Library name: 626610004V3


title: Peripheral whole blood DNA from fILD patient 397

description:
206144080124
206144080124_R05C01


title: Peripheral whole blood DNA from fILD patient 395

description:
206144080124
206144080124_R03C01


title: 626610007V2, LTX, D1

description: Library name: 626610007V2


title: Peripheral whole blood DNA from fILD patient 392

description:
206144080149
206144080149_R08C01


title: 626610003V3, LTX, D7

description: Library name: 626610003V3


title: Peripheral whole blood DNA from fILD patient 389

description:
206144080149
206144080149_R05C01


title: 626610006V2, LTX, D1

description: Library name: 626610006V2


title: Peripheral whole blood DNA from fILD patient 388

description:
206144080149
206144080149_R04C01


title: Peripheral whole blood DNA from fILD patient 386

description:
206144080149
206144080149_R02C01


title: 626610002V3, LTX, D7

description: Library name: 626610002V3


title: Peripheral whole blood DNA from fILD patient 391

description:
206144080149
206144080149_R07C01


title: 626610003V1, LTX, Baseline

description: Library name: 626610003V1


title: 626610003V2, LTX, D1

description: Library name: 626610003V2


title: Peripheral whole blood DNA from fILD patient 385

description:
206144080149
206144080149_R01C01


title: Peripheral whole blood DNA from fILD patient 390

description:
206144080149
206144080149_R06C01


title: 626610004V2, LTX, D1

description: Library name: 626610004V2


title: 626610004V1, LTX, Baseline

description: Library name: 626610004V1


title: Peripheral whole blood DNA from fILD patient 387

description:
206144080149
206144080149_R03C01


title: 626610005V2, LTX, D1

description: Library name: 626610005V2


title: Peripheral whole blood DNA from fILD patient 384

description:
206144080146
206144080146_R08C01


title: Peripheral whole blood DNA from fILD patient 383

description:
206144080146
206144080146_R07C01


title: 626610002V2, LTX, D1

description: Library name: 626610002V2


title: 626610001V3, LTX, D7

description: Library name: 626610001V3


title: 626610006V1, LTX, Baseline

description: Library name: 626610006V1


title: 626610001V2, LTX, D1

description: Library name: 626610001V2


title: 626610002V1, LTX, Baseline

description: Library name: 626610002V1


title: Peripheral whole blood DNA from fILD patient 382

description:
206144080146
206144080146_R06C01


title: Peripheral whole blood DNA from fILD patient 379

description:
206144080146
206144080146_R03C01


title: Peripheral whole blood DNA from fILD patient 381

description:
206144080146
206144080146_R05C01


title: Peripheral whole blood DNA from fILD patient 377

description:
206144080146
206144080146_R01C01

value: CTD-ILD


title: 626610001V1, LTX, Baseline

description: Library name: 626610001V1

value: Periphery blood


title: Peripheral whole blood DNA from fILD patient 380

description:
206144080146
206144080146_R04C01


title: Peripheral whole blood DNA from fILD patient 378

description:
206144080146
206144080146_R02C01


title: Peripheral whole blood DNA from fILD patient 376

description:
206144080127
206144080127_R08C01


title: Peripheral whole blood DNA from fILD patient 375

description:
206144080127
206144080127_R07C01


title: Peripheral whole blood DNA from fILD patient 374

description:
206144080127
206144080127_R06C01


title: Peripheral whole blood DNA from fILD patient 373

description:
206144080127
206144080127_R05C01


title: Peripheral whole blood DNA from fILD patient 372

description:
206144080127
206144080127_R04C01


title: Peripheral whole blood DNA from fILD patient 371

description:
206144080127
206144080127_R03C01


title: Peripheral whole blood DNA from fILD patient 370

description:
206144080127
206144080127_R02C01


title: Peripheral whole blood DNA from fILD patient 369

description:
206144080127
206144080127_R01C01


title: Peripheral whole blood DNA from fILD patient 368

description:
206139120093
206139120093_R08C01


title: Peripheral whole blood DNA from fILD patient 363

description:
206139120093
206139120093_R03C01


title: Peripheral whole blood DNA from fILD patient 362

description:
206139120093
206139120093_R02C01


title: Peripheral whole blood DNA from fILD patient 367

description:
206139120093
206139120093_R07C01


title: Peripheral whole blood DNA from fILD patient 364

description:
206139120093
206139120093_R04C01


title: Peripheral whole blood DNA from fILD patient 366

description:
206139120093
206139120093_R06C01


title: Peripheral whole blood DNA from fILD patient 359

description:
206139120091
206139120091_R07C01


title: Peripheral whole blood DNA from fILD patient 361

description:
206139120093
206139120093_R01C01


title: Peripheral whole blood DNA from fILD patient 358

description:
206139120091
206139120091_R06C01


title: Peripheral whole blood DNA from fILD patient 355

description:
206139120091
206139120091_R03C01


title: Peripheral whole blood DNA from fILD patient 360

description:
206139120091
206139120091_R08C01


title: Peripheral whole blood DNA from fILD patient 365

description:
206139120093
206139120093_R05C01


title: Peripheral whole blood DNA from fILD patient 357

description:
206139120091
206139120091_R05C01


title: Peripheral whole blood DNA from fILD patient 349

description:
206139120086
206139120086_R05C01


title: Peripheral whole blood DNA from fILD patient 352

description:
206139120086
206139120086_R08C01


title: Peripheral whole blood DNA from fILD patient 350

description:
206139120086
206139120086_R06C01


title: Peripheral whole blood DNA from fILD patient 354

description:
206139120091
206139120091_R02C01


title: Peripheral whole blood DNA from fILD patient 351

description:
206139120086
206139120086_R07C01


title: Peripheral whole blood DNA from fILD patient 348

description:
206139120086
206139120086_R04C01


title: Peripheral whole blood DNA from fILD patient 346

description:
206139120086
206139120086_R02C01


title: Peripheral whole blood DNA from fILD patient 345

description:
206139120086
206139120086_R01C01


title: Peripheral whole blood DNA from fILD patient 344

description:
206139120082
206139120082_R08C01


title: Peripheral whole blood DNA from fILD patient 356

description:
206139120091
206139120091_R04C01


title: Peripheral whole blood DNA from fILD patient 343

description:
206139120082
206139120082_R07C01


title: Peripheral whole blood DNA from fILD patient 341

description:
206139120082
206139120082_R05C01


title: Peripheral whole blood DNA from fILD patient 347

description:
206139120086
206139120086_R03C01


title: Peripheral whole blood DNA from fILD patient 338

description:
206139120082
206139120082_R02C01


title: Peripheral whole blood DNA from fILD patient 339

description:
206139120082
206139120082_R03C01


title: Peripheral whole blood DNA from fILD patient 340

description:
206139120082
206139120082_R04C01


title: Peripheral whole blood DNA from fILD patient 334

description:
206139120117
206139120117_R06C01


title: Peripheral whole blood DNA from fILD patient 335

description:
206139120117
206139120117_R07C01


title: Peripheral whole blood DNA from fILD patient 336

description:
206139120117
206139120117_R08C01


title: Peripheral whole blood DNA from fILD patient 337

description:
206139120082
206139120082_R01C01


title: Peripheral whole blood DNA from fILD patient 331

description:
206139120117
206139120117_R03C01


title: Peripheral whole blood DNA from fILD patient 332

description:
206139120117
206139120117_R04C01


title: Peripheral whole blood DNA from fILD patient 333

description:
206139120117
206139120117_R05C01


title: Peripheral whole blood DNA from fILD patient 353

description:
206139120091
206139120091_R01C01


title: Peripheral whole blood DNA from fILD patient 327

description:
206139120087
206139120087_R07C01


title: Peripheral whole blood DNA from fILD patient 329

description:
206139120117
206139120117_R01C01


title: Peripheral whole blood DNA from fILD patient 330

description:
206139120117
206139120117_R02C01


title: Peripheral whole blood DNA from fILD patient 328

description:
206139120087
206139120087_R08C01


title: Peripheral whole blood DNA from fILD patient 324

description:
206139120087
206139120087_R04C01


title: Peripheral whole blood DNA from fILD patient 326

description:
206139120087
206139120087_R06C01

value: UPitt


title: COL0_D_S6

city: Columbia

first: Jose Roberto

last: Da Silva Nascimento

state: MO

address: 1201 Rollins Street

department: Life Sciences Center

institute: University of MIssouri

data_processing:
raw Illumina sequencing data was passed through the protocol of Cufflinks suite tools in Linux
The raw paired reads were mapped to the reference genome (TAIR10) by using Tophat
Gene expression was compared by Cuffdiff
Log2 fold change of FPKM for all identified genes was calculated
Assembly: TAIR10
Supplementary files format and content: .txt files containing the number of normalyzed read counts mapped for each gene per sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Developing seed

growth_protocol: Arabidopsis thaliana WT and badc1/3 T-DNA insertion mutant crosses were grown in a growth chamber under 16 h day length with 100-150 µmol photons m-2 sec-1 white light measured at the soil surface. Temperatures ranged from 21-23°C during the day and 18-20°C at night.

extract_protocol:
Total RNA was purified using the NucleoSpin® RNA Plant kit (MACHEREY-NAGEL), as recommended by the manufacturer
mRNA Stranded Library Preparation (Poly A)

treatment_protocol: Arabidopsis thaliana WT and badc1/3 T-DNA insertion.

value: Developing seed

value: WT


title: COL0_C_S7


title: Peripheral whole blood DNA from fILD patient 322

description:
206139120087
206139120087_R02C01


title: badc-tdna13_E_S9

value: badc1/badc3 double knock out


title: Peripheral whole blood DNA from fILD patient 325

description:
206139120087
206139120087_R05C01

value: UBC


title: Peripheral whole blood DNA from fILD patient 323

description:
206139120087
206139120087_R03C01


title: Peripheral whole blood DNA from fILD patient 342

description:
206139120082
206139120082_R06C01


title: badc-tdna13_D_S10


title: Peripheral whole blood DNA from fILD patient 318

description:
206137500047
206137500047_R06C01


title: COL0_B_S8


title: Peripheral whole blood DNA from fILD patient 321

description:
206139120087
206139120087_R01C01


title: Peripheral whole blood DNA from fILD patient 316

description:
206137500047
206137500047_R04C01

value: M


title: Peripheral whole blood DNA from fILD patient 317

description:
206137500047
206137500047_R05C01

value: Former


title: Peripheral whole blood DNA from fILD patient 320

description:
206137500047
206137500047_R08C01


title: Peripheral whole blood DNA from fILD patient 319

description:
206137500047
206137500047_R07C01


title: badc-tdna13_A_S2


title: Peripheral whole blood DNA from fILD patient 314

description:
206137500047
206137500047_R02C01


title: Peripheral whole blood DNA from fILD patient 315

description:
206137500047
206137500047_R03C01


title: Peripheral whole blood DNA from fILD patient 313

description:
206137500047
206137500047_R01C01


title: Peripheral whole blood DNA from fILD patient 312

description:
206137500048
206137500048_R08C01


title: Peripheral whole blood DNA from fILD patient 310

description:
206137500048
206137500048_R06C01

value: IPF


title: Peripheral whole blood DNA from fILD patient 311

description:
206137500048
206137500048_R07C01

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 309

description:
206137500048
206137500048_R05C01


title: Peripheral whole blood DNA from fILD patient 308

description:
206137500048
206137500048_R04C01


title: T4121 GSCs, shMCU#2-1

city: Shanghai

first: Gguangqin

last: Liu

address: No. 130 Dong-An Road

country: China

institute: Fudan university

description:
Library name: sample16
4-2-1_1

data_processing:
Raw reads were filtered using Seqtk and mapped to the reference genome using HISAT2 (version 2.0.4).
Gene expression was quantified using StringTie (v1.3.3b), followed by TMM (trimmed mean of M values) normalization.
Assembly: GRCh38
Supplementary files format and content: FPKM and count values for each sample

source_name: T4121 GSCs

extract_protocol:
Total RNA was harvested using MJzol Animal RNA Isolation Kit (Majorivd).
RNA libraries for RNA-seq were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following the manufacturer's instructions. Library quality and size distribution were assessed using an Agilent 4200 Bioanalyzer.

value: T4121 GSCs

value: Glioblastoma stem cells


title: T4121 GSCs, shMCU#1-2

description:
Library name: sample14
4-1-2_1


title: T4121 GSCs, shMCU#2-2

description:
Library name: sample17
4-2-2_1


title: T4121 GSCs, shNT-3

description:
Library name: sample12
4-0-3_1


title: T4121 GSCs, shMCU#1-1

description:
Library name: sample13
4-1-1_1


title: T4121 GSCs, shMCU#2-3

description:
Library name: sample18
4-2-3_1


title: Peripheral whole blood DNA from fILD patient 307

description:
206137500048
206137500048_R03C01

value: UNCLASSIFIABLE


title: T4121 GSCs, shMCU#1-3

description:
Library name: sample15
4-1-3_1


title: T4121 GSCs, shNT-2

description:
Library name: sample11
4-0-2_1


title: Peripheral whole blood DNA from fILD patient 305

description:
206137500048
206137500048_R01C01


title: Peripheral whole blood DNA from fILD patient 306

description:
206137500048
206137500048_R02C01

value: F


title: 08-387 GSCs, shMCU#2-2

description:
Library name: sample8
3-2-2_1


title: Peripheral whole blood DNA from fILD patient 304

description:
206137500045
206137500045_R08C01

value: Never


title: T4121 GSCs, shNT-1

description:
Library name: sample10
4-0-1_1


title: Peripheral whole blood DNA from fILD patient 303

description:
206137500045
206137500045_R07C01


title: 08-387 GSCs, shMCU#2-1

description:
Library name: sample7
3-2-1_1


title: Peripheral whole blood DNA from fILD patient 302

description:
206137500045
206137500045_R06C01


title: 08-387 GSCs, shMCU#1-1

description:
Library name: sample4
3-1-1_1


title: Peripheral whole blood DNA from fILD patient 301

description:
206137500045
206137500045_R05C01


title: 08-387 GSCs, shMCU#1-2

description:
Library name: sample5
3-1-2_1


title: Peripheral whole blood DNA from fILD patient 300

description:
206137500045
206137500045_R04C01

value: Unknown


title: 08-387 GSCs, shMCU#1-3

description:
Library name: sample6
3-1-3_1


title: Peripheral whole blood DNA from fILD patient 299

description:
206137500045
206137500045_R03C01


title: Peripheral whole blood DNA from fILD patient 298

description:
206137500045
206137500045_R02C01

value: CTD-ILD


title: 08-387 GSCs, shNT-2

description:
Library name: sample2
3-0-2_1


title: Peripheral whole blood DNA from fILD patient 297

description:
206137500045
206137500045_R01C01


title: 08-387 GSCs, shNT-1

description:
Library name: sample1
3-0-1_1


title: 08-387 GSCs, shMCU#2-3

description:
Library name: sample9
3-2-3_1


title: Peripheral whole blood DNA from fILD patient 296

description:
206137500043
206137500043_R08C01

value: HP


title: Peripheral whole blood DNA from fILD patient 295

description:
206137500043
206137500043_R07C01

value: UPitt


title: Peripheral whole blood DNA from fILD patient 292

description:
206137500043
206137500043_R04C01

value: Always


title: Peripheral whole blood DNA from fILD patient 291

description:
206137500043
206137500043_R03C01


title: Peripheral whole blood DNA from fILD patient 294

description:
206137500043
206137500043_R06C01


title: Peripheral whole blood DNA from fILD patient 290

description:
206137500043
206137500043_R02C01


title: Peripheral whole blood DNA from fILD patient 289

description:
206137500043
206137500043_R01C01


title: Peripheral whole blood DNA from fILD patient 287

description:
206139130021
206139130021_R07C01


title: CARD11 KO Jurkat, Unstimulated, JNK inhibitor IX, rep5

city: Bethesda

first: Bradly

last: Bauman

state: MD

address: 4301 Jones Bridge Rd. C2033

institute: Uniformed Services University of the Health Sciences

description: Library name: KO-NS-JNKIX-05

data_processing:
Nextflow nf-core/rnaseq (version 3.4) workflow was used to estimate a matrix of sample gene expression values.
Paired-end DNA sequence FastQ files were merged by sample (two/sample) and underwent read quality control (FastQC v0.11.9) prior to adapter and quality trimming (Trim Galore! v0.6.7), then input into Salmon's (v1.5.2) mapping-mode for gene expression matrix quantification.
Further sequencing quality control was performed via subsequent trimmed read alignment using STAR (v2.6.1d), SAMtools (v1.13), and Picard (v2.25.7), followed by RSeQC (v3.0.1), Qualimap (v2.2.2-dev), and Preseq (v3.1.1).
Differential expression analysis was performed using the DESeq2 package (v1.32.0).
Assembly: GRCh37; Ensembl release 75
Supplementary files format and content: tsv file includes raw count values for each Sample (library name)
Supplementary files format and content: tsv file includes TPM values for each Sample (library name)

source_name: Jurkat E6.1

growth_protocol: Jurkat T cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), penicillin/streptomycin/normocin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells resuspended in Trizol (Invitrogen) using a Direct-zol RNA MiniPrep Kit (Zymo Research), including on-column DNaseI treatment.
Library preparation was performed with 140 ng total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina) and IDT for Illumina RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples). Sequencing libraries were quantified by real-time PCR using KAPA Library Quantification Kit for NGS (Roche) and assessed for size distribution on a Fragment Analyzer (Agilent) to confirm absence of adapter dimers and unligated library molecules.

treatment_protocol: WT or CARD11 KO Jurkat T cells were incubated for 2 hours with DMSO (No inhibitor), JNK inhibitor IX or JNK-IN-8 prior to stimulation with 20 ng/mL PMA and 1 ug/mL ionomycin for 2 hours.

value: Jurkat E6.1

value: T lymphocyte cell

value: CARD11 KO

tag: stimulus

value: No stimulus

tag: inhibitor

value: JNK inhibitor IX

tag: batch


title: Peripheral whole blood DNA from fILD patient 288

description:
206139130021
206139130021_R08C01

value: M


title: CARD11 KO Jurkat, Stimulated, No inhibitor, rep5

description: Library name: KO-PI-NI-05

value: PMA/ionomycin

value: No inhibitor


title: CARD11 KO Jurkat , Unstimulated, JNK-IN-8, rep5

description: Library name: KO-NS-JNK8-05


title: CARD11 KO Jurkat, Unstimulated, No inhibitor, rep5

description: Library name: KO-NS-NI-05


title: CARD11 KO Jurkat, Stimulated, JNK inhibitor IX, rep5

description: Library name: KO-PI-JNKIX-05


title: CARD11 KO Jurkat , Stimulated, JNK-IN-8, rep5

description: Library name: KO-PI-JNK8-05


title: WT Jurkat, Stimulated, No inhibitor, rep5

description: Library name: WT-PI-NI-05

value: WT


title: WT Jurkat , Unstimulated, JNK-IN-8, rep5

description: Library name: WT-NS-JNK8-05


title: WT Jurkat , Stimulated, JNK-IN-8, rep5

description: Library name: WT-PI-JNK8-05


title: WT Jurkat, Unstimulated, JNK inhibitor IX, rep5

description: Library name: WT-NS-JNKIX-05


title: Peripheral whole blood DNA from fILD patient 286

description:
206139130021
206139130021_R06C01

value: Former

value: Whole blood DNA


title: 08-387 GSCs, shNT-3

description:
Library name: sample3
3-0-3_1

value: Glioblastoma stem cells


title: Peripheral whole blood DNA from fILD patient 285

description:
206139130021
206139130021_R05C01

value: F


title: WT Jurkat, Unstimulated, No inhibitor, rep5

description: Library name: WT-NS-NI-05


title: Peripheral whole blood DNA from fILD patient 284

description:
206139130021
206139130021_R04C01

value: Never

value: CTD-ILD


title: Peripheral whole blood DNA from fILD patient 293

description:
206137500043
206137500043_R05C01

value: UPitt

value: HP


title: CARD11 KO Jurkat, Stimulated, JNK inhibitor IX, rep4

description: Library name: KO-PI-JNKIX-04

value: Jurkat E6.1


title: Peripheral whole blood DNA from fILD patient 283

description:
206139130021
206139130021_R03C01


title: Peripheral whole blood DNA from fILD patient 282

description:
206139130021
206139130021_R02C01


title: CARD11 KO Jurkat, Stimulated, No inhibitor, rep4

description: Library name: KO-PI-NI-04

value: T lymphocyte cell


title: CARD11 KO Jurkat , Unstimulated, JNK-IN-8, rep4

description: Library name: KO-NS-JNK8-04

value: CARD11 KO


title: WT Jurkat, Stimulated, JNK inhibitor IX, rep5

description: Library name: WT-PI-JNKIX-05


title: Peripheral whole blood DNA from fILD patient 281

description:
206139130021
206139130021_R01C01

value: IPF


title: Peripheral whole blood DNA from fILD patient 280

description:
206139130057
206139130057_R08C01


title: CARD11 KO Jurkat, Unstimulated, JNK inhibitor IX, rep4

description: Library name: KO-NS-JNKIX-04

value: No stimulus

value: JNK inhibitor IX


title: Peripheral whole blood DNA from fILD patient 279

description:
206139130057
206139130057_R07C01

value: M


title: WT Jurkat , Stimulated, JNK-IN-8, rep4

description: Library name: WT-PI-JNK8-04

value: PMA/ionomycin


title: WT Jurkat, Stimulated, No inhibitor, rep4

description: Library name: WT-PI-NI-04

value: WT

value: No inhibitor


title: Peripheral whole blood DNA from fILD patient 276

description:
206139130057
206139130057_R04C01

value: Former

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 274

description:
206139130057
206139130057_R02C01


title: Peripheral whole blood DNA from fILD patient 275

description:
206139130057
206139130057_R03C01


title: WT Jurkat, Unstimulated, JNK inhibitor IX, rep4

description: Library name: WT-NS-JNKIX-04


title: Peripheral whole blood DNA from fILD patient 278

description:
206139130057
206139130057_R06C01

value: F

value: UNCLASSIFIABLE


title: WT Jurkat , Unstimulated, JNK-IN-8, rep4

description: Library name: WT-NS-JNK8-04


title: CARD11 KO Jurkat , Stimulated, JNK-IN-8, rep3

description: Library name: KO-PI-JNK8-03


title: WT Jurkat, Stimulated, JNK inhibitor IX, rep4

description: Library name: WT-PI-JNKIX-04


title: Peripheral whole blood DNA from fILD patient 272

description:
206139130058
206139130058_R08C01

value: Unknown

value: CTD-ILD


title: Peripheral whole blood DNA from fILD patient 273

description:
206139130057
206139130057_R01C01

value: UPitt


title: WT Jurkat, Unstimulated, No inhibitor, rep4

description: Library name: WT-NS-NI-04

value: Jurkat E6.1


title: CARD11 KO Jurkat , Stimulated, JNK-IN-8, rep4

description: Library name: KO-PI-JNK8-04

value: T lymphocyte cell


title: CARD11 KO Jurkat, Stimulated, JNK inhibitor IX, rep3

description: Library name: KO-PI-JNKIX-03

value: CARD11 KO


title: Peripheral whole blood DNA from fILD patient 271

description:
206139130058
206139130058_R07C01


title: Peripheral whole blood DNA from fILD patient 270

description:
206139130058
206139130058_R06C01


title: Peripheral whole blood DNA from fILD patient 269

description:
206139130058
206139130058_R05C01


title: CARD11 KO Jurkat, Stimulated, No inhibitor, rep3

description: Library name: KO-PI-NI-03


title: CARD11 KO Jurkat , Unstimulated, JNK-IN-8, rep3

description: Library name: KO-NS-JNK8-03


title: CARD11 KO Jurkat, Unstimulated, JNK inhibitor IX, rep3

description: Library name: KO-NS-JNKIX-03


title: Peripheral whole blood DNA from fILD patient 268

description:
206139130058
206139130058_R04C01


title: Peripheral whole blood DNA from fILD patient 267

description:
206139130058
206139130058_R03C01

value: IPF


title: CARD11 KO Jurkat, Unstimulated, No inhibitor, rep3

description: Library name: KO-NS-NI-03

value: No stimulus


title: CARD11 KO Jurkat, Unstimulated, No inhibitor, rep4

description: Library name: KO-NS-NI-04


title: Peripheral whole blood DNA from fILD patient 277

description:
206139130057
206139130057_R05C01


title: WT Jurkat , Stimulated, JNK-IN-8, rep3

description: Library name: WT-PI-JNK8-03


title: Peripheral whole blood DNA from fILD patient 266

description:
206139130058
206139130058_R02C01


title: Peripheral whole blood DNA from fILD patient 265

description:
206139130058
206139130058_R01C01

value: Always


title: WT Jurkat, Stimulated, JNK inhibitor IX, rep3

description: Library name: WT-PI-JNKIX-03

value: JNK inhibitor IX


title: Peripheral whole blood DNA from fILD patient 264

description:
206139130042
206139130042_R08C01

value: M

value: Never


title: Peripheral whole blood DNA from fILD patient 263

description:
206139130042
206139130042_R07C01


title: WT Jurkat , Unstimulated, JNK-IN-8, rep3

description: Library name: WT-NS-JNK8-03

value: WT


title: Peripheral whole blood DNA from fILD patient 262

description:
206139130042
206139130042_R06C01

value: Former


title: Peripheral whole blood DNA from fILD patient 261

description:
206139130042
206139130042_R05C01

value: HP

value: Whole blood DNA


title: WT Jurkat, Unstimulated, JNK inhibitor IX, rep3

description: Library name: WT-NS-JNKIX-03


title: Peripheral whole blood DNA from fILD patient 260

description:
206139130042
206139130042_R04C01

value: F


title: CARD11 KO Jurkat , Stimulated, JNK-IN-8, rep2

description: Library name: KO-PI-JNK8-02

value: PMA/ionomycin


title: Peripheral whole blood DNA from fILD patient 259

description:
206139130042
206139130042_R03C01

value: UNCLASSIFIABLE


title: WT Jurkat, Unstimulated, No inhibitor, rep3

description: Library name: WT-NS-NI-03

value: No inhibitor


title: CARD11 KO Jurkat, Stimulated, JNK inhibitor IX, rep2

description: Library name: KO-PI-JNKIX-02

value: Jurkat E6.1


title: Peripheral whole blood DNA from fILD patient 258

description:
206139130042
206139130042_R02C01

value: UPitt

value: CTD-ILD


title: CARD11 KO Jurkat, Stimulated, No inhibitor, rep2

description: Library name: KO-PI-NI-02

value: T lymphocyte cell

value: CARD11 KO


title: CARD11 KO Jurkat, Unstimulated, JNK inhibitor IX, rep2

description: Library name: KO-NS-JNKIX-02

value: No stimulus


title: Peripheral whole blood DNA from fILD patient 257

description:
206139130042
206139130042_R01C01


title: CARD11 KO Jurkat , Unstimulated, JNK-IN-8, rep2

description: Library name: KO-NS-JNK8-02


title: CARD11 KO Jurkat, Unstimulated, No inhibitor, rep2

description: Library name: KO-NS-NI-02


title: Peripheral whole blood DNA from fILD patient 256

description:
206139120125
206139120125_R08C01


title: WT Jurkat , Stimulated, JNK-IN-8, rep2

description: Library name: WT-PI-JNK8-02


title: Peripheral whole blood DNA from fILD patient 254

description:
206139120125
206139120125_R06C01


title: Peripheral whole blood DNA from fILD patient 253

description:
206139120125
206139120125_R05C01

value: Unknown


title: WT Jurkat, Stimulated, JNK inhibitor IX, rep2

description: Library name: WT-PI-JNKIX-02

value: JNK inhibitor IX


title: Peripheral whole blood DNA from fILD patient 252

description:
206139120125
206139120125_R04C01

value: M


title: WT Jurkat, Stimulated, No inhibitor, rep3

description: Library name: WT-PI-NI-03

value: WT


title: WT Jurkat, Stimulated, No inhibitor, rep2

description: Library name: WT-PI-NI-02


title: WT Jurkat, Unstimulated, JNK inhibitor IX, rep2

description: Library name: WT-NS-JNKIX-02


title: Peripheral whole blood DNA from fILD patient 250

description:
206139120125
206139120125_R02C01


title: Peripheral whole blood DNA from fILD patient 249

description:
206139120125
206139120125_R01C01

value: Never


title: WT Jurkat, Unstimulated, No inhibitor, rep2

description: Library name: WT-NS-NI-02


title: CARD11 KO Jurkat, Stimulated, JNK inhibitor IX, rep1

description: Library name: KO-PI-JNKIX-01


title: CARD11 KO Jurkat , Stimulated, JNK-IN-8, rep1

description: Library name: KO-PI-JNK8-01


title: CARD11 KO Jurkat, Stimulated, No inhibitor, rep1

description: Library name: KO-PI-NI-01


title: Peripheral whole blood DNA from fILD patient 247

description:
206139120039
206139120039_R07C01


title: CARD11 KO Jurkat, Unstimulated, JNK inhibitor IX, rep1

description: Library name: KO-NS-JNKIX-01


title: CARD11 KO Jurkat , Unstimulated, JNK-IN-8, rep1

description: Library name: KO-NS-JNK8-01


title: Peripheral whole blood DNA from fILD patient 245

description:
206139120039
206139120039_R05C01


title: Peripheral whole blood DNA from fILD patient 255

description:
206139120125
206139120125_R07C01

value: Former


title: Peripheral whole blood DNA from fILD patient 243

description:
206139120039
206139120039_R03C01

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 244

description:
206139120039
206139120039_R04C01

value: IPF


title: CARD11 KO Jurkat, Unstimulated, No inhibitor, rep1

description: Library name: KO-NS-NI-01


title: WT Jurkat, Stimulated, JNK inhibitor IX, rep1

description: Library name: WT-PI-JNKIX-01

value: PMA/ionomycin


title: Peripheral whole blood DNA from fILD patient 242

description:
206139120039
206139120039_R02C01

value: F


title: WT Jurkat, Stimulated, No inhibitor, rep1

description: Library name: WT-PI-NI-01

value: No inhibitor


title: Peripheral whole blood DNA from fILD patient 239

description:
206139120037
206139120037_R07C01

value: HP


title: Peripheral whole blood DNA from fILD patient 251

description:
206139120125
206139120125_R03C01

value: UPitt


title: WT Jurkat , Unstimulated, JNK-IN-8, rep2

description: Library name: WT-NS-JNK8-02

value: Jurkat E6.1


title: Peripheral whole blood DNA from fILD patient 240

description:
206139120037
206139120037_R08C01

value: CTD-ILD


title: WT Jurkat, Unstimulated, JNK inhibitor IX, rep1

description: Library name: WT-NS-JNKIX-01

value: T lymphocyte cell


title: WT Jurkat, Unstimulated, No inhibitor, rep1

description: Library name: WT-NS-NI-01

value: No stimulus


title: Peripheral whole blood DNA from fILD patient 238

description:
206139120037
206139120037_R06C01

value: Unknown


title: Peripheral whole blood DNA from fILD patient 248

description:
206139120039
206139120039_R08C01


title: Peripheral whole blood DNA from fILD patient 246

description:
206139120039
206139120039_R06C01


title: Peripheral whole blood DNA from fILD patient 236

description:
206139120037
206139120037_R04C01


title: Peripheral whole blood DNA from fILD patient 235

description:
206139120037
206139120037_R03C01


title: WT Jurkat , Stimulated, JNK-IN-8, rep1

description: Library name: WT-PI-JNK8-01


title: Peripheral whole blood DNA from fILD patient 233

description:
206139120037
206139120037_R01C01


title: Peripheral whole blood DNA from fILD patient 241

description:
206139120039
206139120039_R01C01

value: UNCLASSIFIABLE


title: Sample_41_GEX_ADT Memory B Cell Run5

first: Sarah

last: Andrews

state: Maryland

address: 9000 Rockville Pike

institute: National Institutes of Health

description:
Library name: Sample_41_GEX_ADT
Run5

library_source: transcriptomic single cell

data_processing:
CellRanger v6.0.0
GEX and ADT libraries were run through CellRanger count together to produce one matrix file
Assembly: GRCh38 human reference genome 3.0.0
Supplementary files format and content: Sample_GEX_ADT_barcodes.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_features.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_matrix.mtx.gz
Supplementary files format and content: FeatureReferenceFile.csv

source_name: pbmc

extract_protocol:
Single-cells were encapsulated in Gel-beads-in-emulsion using the 10x Genomics Chromium Controller and a Single Cell Immune Profiling Next GEM v2 Chemistry Kit.
10x Genomics Single Cell Immune Profiling Next GEM v2 Chemistry Kit

value: pbmc

value: Memory B Cell

value: H2 Influenza Vaccination

tag: library type


title: Sample_43_GEX_ADT Plasmablast Run5

description:
Library name: Sample_43_GEX_ADT
Run5

value: Plasmablast


title: Peripheral whole blood DNA from fILD patient 232

description:
206139120079
206139120079_R08C01

value: M

value: Never

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 231

description:
206139120079
206139120079_R07C01

value: F


title: Sample_40_GEX_ADT Memory B Cell Run5

description:
Library name: Sample_40_GEX_ADT
Run5


title: Peripheral whole blood DNA from fILD patient 229

description:
206139120079
206139120079_R05C01


title: Peripheral whole blood DNA from fILD patient 228

description:
206139120079
206139120079_R04C01


title: Sample_39_GEX_ADT Plasmablast Run5

description:
Library name: Sample_39_GEX_ADT
Run5


title: Peripheral whole blood DNA from fILD patient 227

description:
206139120079
206139120079_R03C01

value: Former


title: WT Jurkat , Unstimulated, JNK-IN-8, rep1

description: Library name: WT-NS-JNK8-01

value: WT


title: Sample_36_GEX_ADT Memory B Cell Run5

description:
Library name: Sample_36_GEX_ADT
Run5


title: Sample_35_GEX_ADT Memory B Cell Run5

description:
Library name: Sample_35_GEX_ADT
Run5


title: Sample_45_GEX_ADT Plasmablast Run5

description:
Library name: Sample_45_GEX_ADT
Run5


title: Peripheral whole blood DNA from fILD patient 237

description:
206139120037
206139120037_R05C01

value: UPitt


title: Peripheral whole blood DNA from fILD patient 225

description:
206139120079
206139120079_R01C01


title: Sample_34_GEX_ADT Plasmablast Run5

description:
Library name: Sample_34_GEX_ADT
Run5


title: Peripheral whole blood DNA from fILD patient 224

description:
206139120038
206139120038_R08C01

value: IPF


title: Peripheral whole blood DNA from fILD patient 226

description:
206139120079
206139120079_R02C01


title: Sample_33_GEX_ADT Memory B Cell Run5

description:
Library name: Sample_33_GEX_ADT
Run5


title: Sample_44_GEX_ADT Memory B Cell Run5

description:
Library name: Sample_44_GEX_ADT
Run5


title: Sample_42_GEX_ADT Memory B Cell Run5

description:
Library name: Sample_42_GEX_ADT
Run5


title: Peripheral whole blood DNA from fILD patient 234

description:
206139120037
206139120037_R02C01

value: CTD-ILD


title: Peripheral whole blood DNA from fILD patient 223

description:
206139120038
206139120038_R07C01


title: Peripheral whole blood DNA from fILD patient 222

description:
206139120038
206139120038_R06C01


title: Peripheral whole blood DNA from fILD patient 220

description:
206139120038
206139120038_R04C01


title: Peripheral whole blood DNA from fILD patient 230

description:
206139120079
206139120079_R06C01


title: Sample_30_GEX_ADT Plasmablast Run4

description:
Library name: Sample_30_GEX_ADT
Run4


title: Peripheral whole blood DNA from fILD patient 219

description:
206139120038
206139120038_R03C01


title: Sample_29_GEX_ADT Plasmablast Run4

description:
Library name: Sample_29_GEX_ADT
Run4


title: Sample_31_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_31_GEX_ADT
Run4


title: Sample_37_GEX_ADT Plasmablast Run5

description:
Library name: Sample_37_GEX_ADT
Run5


title: Peripheral whole blood DNA from fILD patient 217

description:
206139120038
206139120038_R01C01


title: Sample_27_GEX_ADT Plasmablast Run4

description:
Library name: Sample_27_GEX_ADT
Run4


title: Peripheral whole blood DNA from fILD patient 218

description:
206139120038
206139120038_R02C01


title: Peripheral whole blood DNA from fILD patient 216

description:
206137500008
206137500008_R08C01


title: Peripheral whole blood DNA from fILD patient 221

description:
206139120038
206139120038_R05C01


title: Peripheral whole blood DNA from fILD patient 215

description:
206137500008
206137500008_R07C01

value: HP


title: Sample_38_GEX_ADT Memory B Cell Run5

description:
Library name: Sample_38_GEX_ADT
Run5


title: Sample_24_GEX_ADT Plasmablast Run4

description:
Library name: Sample_24_GEX_ADT
Run4


title: Sample_28_GEX_ADT Plasmablast Run4

description:
Library name: Sample_28_GEX_ADT
Run4


title: Sample_32_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_32_GEX_ADT
Run4


title: Peripheral whole blood DNA from fILD patient 214

description:
206137500008
206137500008_R06C01


title: Sample_23_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_23_GEX_ADT
Run4


title: Sample_22_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_22_GEX_ADT
Run4


title: Sample_25_GEX_ADT Plasmablast Run4

description:
Library name: Sample_25_GEX_ADT
Run4


title: Peripheral whole blood DNA from fILD patient 213

description:
206137500008
206137500008_R05C01


title: Peripheral whole blood DNA from fILD patient 212

description:
206137500008
206137500008_R04C01


title: Peripheral whole blood DNA from fILD patient 211

description:
206137500008
206137500008_R03C01


title: Sample_21_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_21_GEX_ADT
Run4


title: Peripheral whole blood DNA from fILD patient 209

description:
206137500008
206137500008_R01C01


title: Sample_26_GEX_ADT Plasmablast Run4

description:
Library name: Sample_26_GEX_ADT
Run4


title: Sample_18_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_18_GEX_ADT
Run4


title: Sample_20_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_20_GEX_ADT
Run4


title: Sample_19_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_19_GEX_ADT
Run4


title: Sample_17_GEX_ADT Memory B Cell Run4

description:
Library name: Sample_17_GEX_ADT
Run4


title: Peripheral whole blood DNA from fILD patient 205

description:
206139120084
206139120084_R05C01


title: Peripheral whole blood DNA from fILD patient 208

description:
206139120084
206139120084_R08C01


title: Peripheral whole blood DNA from fILD patient 206

description:
206139120084
206139120084_R06C01


title: HUDEP-2, DNMT3A gRNA, sample September2

city: Frankfurt

first: Darja

last: Karpova

address: Sandhofstrasse 1

department: Cell Therapeutics

country: Germany

institute: German Red Cross Blood Donor Service

description: Library name: sample.Lib34

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software. RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Gene level raw transcript counts calculated as average counts from all transcripts (RAWCountsHUDEP_GEO.xlsx) mapped to a given gene were used for analysis of differential expression using DESeq2 (v.1.34.0) within R (version 4.1.1) programming environment. Design parameter was set on “gRNA+ Isolation time point of RNA samples”.
Assembly: Human Ensembl release 101 primary assembly
Supplementary files format and content: Demultiplexed, aligned raw trancripts level reads (RAWCountsHUDEP_GEO.xlsx) as well as normallized count table genrated as output from DESeq2 analysis (ProcessedCountsHUDEP_GEO.xls)

source_name: Cord Blood Derived Cell Line

growth_protocol: Endogenous expression of DNMT3A gene was downregulated in the cord blood CD34 cell derived erythroid cell line HUDEP-2 using the CRISPR interference. A dCas9 fused with the transcriptional repressors KRAB and MeCP2 (Expression vector: pLV[Exp]-CBh>dCas9-KRAB-MeCP2:T2A:Hygro from VectorBuilder) was introduced into HUDEP-2 cells together with either a scramble sgRNA (Expression vector: pLV[gRNA]-EGFP:T2A:Neo-U6>Scramble[gRNA#1], guide sequence: GTGTAGTTCGACCATTCGTG, marker: EGFP:T2A:Neo from VectorBuilder] or with a gRNA targeting the DNMT3A promoter (Expression vector: pLV[gRNA]-TagBFP2:T2A:Neo-U6>{DNMT3A_antisense_2}, guide sequence: ACGGTAATGAGCGCCGCTGC, marker: TagBFP2:T2A:Neo from VectorBuilder). Lentiviral transduction of HUDEP-2 cells with dCas9-KRAB-MeCP2 + control (scramble) gRNA or dCas9-KRAB-MeCP2 + DNMT3A gRNA in form of lentiviral particles packaged using third generation lentiviral packaging system. Regular HUDEP-2 culture media (Li, C. et al. In Vivo HSC Gene Therapy Using a Bi-modular HDAd5/35++ Vector Cures Sickle Cell  Disease in a Mouse Model. Mol Ther 29, 822–837 (2021)) was supplemented with hygromycin (100 µg/ml the first two weeks, 50 µg/ml the following six weeks due to visibly higher sensitivity of the cells during the initial culture period and 200 µg/ml for the remainder of the culture, up to seven months after transduction) starting on day 6 after transduction. Transduction efficiency was >90% at all times.

extract_protocol:
Following a fluorescence-based sort of transduced cells (> 99%), purity was monitored and RNA samples were isolated using RNAeasy Plus Kit (Qiagen) the between four and seven months after transduction; RNA integrity was verified using  Agilent 2100 Bioanalyzer trace analysis (Agilent Technologies).
25 total RNA were processed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs) as per manufacturer’s instructions. cDNA (20 ng input standardized for fragmentation, end repair, 5’ phosphorylation and dA tailing followed by adapter ligation) and final library quality was monitored using Agilent 2100 Bioanalyzer trace analysis (Agilent Technologies). Pooled libraries were sequenced on an Illumina NovaSeq X Plus 10B (2x150) flow cell to a depth of 100 M read pairs (150 bp) per sample at Genome Technology Access Center (GTAC) and McDonnell Genome Institute at the Washington University School of Medicine.

value: Cord Blood Derived Cell Line

value: CD34 derived erythroid cells

value: DNMT3A downregulated

value: DNMT3A promoter targeting gRNA

value: September


title: Peripheral whole blood DNA from fILD patient 207

description:
206139120084
206139120084_R07C01

value: Unknown


title: HUDEP-2, DNMT3A gRNA, sample August

description: Library name: sample.Lib26

value: August


title: HUDEP-2, DNMT3A gRNA, sample June

description: Library name: sample.Lib28

value: June


title: Sample_16_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_16_GEX_ADT
Run3

value: pbmc

value: Memory B Cell

value: H2 Influenza Vaccination


title: HUDEP-2, DNMT3A gRNA, sample September6

description: Library name: sample.Lib46


title: Sample_14_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_14_GEX_ADT
Run3


title: HUDEP-2, DNMT3A gRNA, sample September4

description: Library name: sample.Lib40


title: HUDEP-2, DNMT3A gRNA, sample September5

description: Library name: sample.Lib44


title: HUDEP-2, DNMT3A gRNA, sample July

description: Library name: sample.Lib30

value: July


title: Peripheral whole blood DNA from fILD patient 210

description:
206137500008
206137500008_R02C01

value: M

value: Former

value: Whole blood DNA


title: HUDEP-2, control gRNA, sample September6

description: Library name: sample.Lib45

value: control

value: control gRNA


title: HUDEP-2, DNMT3A gRNA, sample September1

description: Library name: sample.Lib32

value: Cord Blood Derived Cell Line


title: Sample_13_GEX_ADT Plasmablast Run3

description:
Library name: Sample_13_GEX_ADT
Run3

value: Plasmablast


title: Peripheral whole blood DNA from fILD patient 204

description:
206139120084
206139120084_R04C01

value: UPitt

value: F

value: CTD-ILD


title: HUDEP-2, DNMT3A gRNA, sample September3

description: Library name: sample.Lib38

value: CD34 derived erythroid cells

value: DNMT3A downregulated

value: DNMT3A promoter targeting gRNA

value: September


title: Sample_12_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_12_GEX_ADT
Run3

value: pbmc

value: Memory B Cell


title: HUDEP-2, control gRNA, sample September5

description: Library name: sample.Lib43


title: Peripheral whole blood DNA from fILD patient 202

description:
206139120084
206139120084_R02C01

value: Unknown

value: UNCLASSIFIABLE


title: Peripheral whole blood DNA from fILD patient 203

description:
206139120084
206139120084_R03C01


title: HUDEP-2, control gRNA, sample September3

description: Library name: sample.Lib37


title: Peripheral whole blood DNA from fILD patient 201

description:
206139120084
206139120084_R01C01

value: IPF


title: Peripheral whole blood DNA from fILD patient 200

description:
206139120085
206139120085_R08C01

value: Never

value: Whole blood DNA


title: Sample_10_GEX_ADT Plasmablast Run3

description:
Library name: Sample_10_GEX_ADT
Run3

value: H2 Influenza Vaccination


title: HUDEP-2, control gRNA, sample September4

description: Library name: sample.Lib39

value: Cord Blood Derived Cell Line

value: control

value: control gRNA


title: T4121 GSCs, shMCU,H3K27ac (Input3)

description: Library name: T4121 GSCs_shMCU, Input3

library_source: genomic

data_processing:
Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: BIGWIG

extract_protocol:
A total of 2×107 cells were washed with phosphate-buffered saline (PBS) and cross-linked with a 1% formaldehyde solution for 10 minutes at room temperature. Cross-linking was quenched with 0.125 M glycine for 5 minutes, after which the cells were pelleted and washed twice with PBS. The cell pellets were lysed on ice for 5 minutes using a cell lysis buffer containing 10 mM HEPES (pH 7.5), 0.1 mM EDTA, 0.5% NP-40, and a protease inhibitor cocktail.
Libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, China, cat. no. ND607). Library products corresponding to fragments ranging from 200 to 500 base pairs were enriched and quantified. Sequencing was performed on a Novaseq X Plus (Illumina) using the PE150 sequencing mode to generate paired-end reads.

value: T4121 GSCs

value: Glioblastoma stem cells

value: shMCU


title: Peripheral whole blood DNA from fILD patient 198

description:
206139120085
206139120085_R06C01

value: UPitt

value: F


title: HUDEP-2, control gRNA, sample September2

description: Library name: sample.Lib33

value: CD34 derived erythroid cells

value: September


title: Peripheral whole blood DNA from fILD patient 197

description:
206139120085
206139120085_R05C01


title: Sample_6_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_6_GEX_ADT
Run3

value: pbmc

value: Memory B Cell


title: Sample_8_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_8_GEX_ADT
Run3


title: HUDEP-2, control gRNA, sample September1

description: Library name: sample.Lib31


title: Sample_7_GEX_ADT Plasmablast Run3

description:
Library name: Sample_7_GEX_ADT
Run3

value: Plasmablast


title: Sample_11_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_11_GEX_ADT
Run3


title: Sample_5_GEX_ADT Plasmablast Run3

description:
Library name: Sample_5_GEX_ADT
Run3


title: HUDEP-2, control gRNA, sample July

description: Library name: sample.Lib29

value: July


title: HUDEP-2, control gRNA, sample August

description: Library name: sample.Lib25

value: August


title: T4121 GSCs, shMCU,H3K27ac (ChIP2)

description: Library name: T4121 GSCs_shMCU, ChIP2


title: HUDEP-2, control gRNA, sample June

description: Library name: sample.Lib27

value: June


title: Peripheral whole blood DNA from fILD patient 196

description:
206139120085
206139120085_R04C01

value: M

value: Unknown

value: HP

value: Whole blood DNA


title: T4121 GSCs, shMCU,H3K27ac (Input1)

description: Library name: T4121 GSCs_shMCU, Input1

value: T4121 GSCs


title: T4121 GSCs, shMCU,H3K27ac (ChIP3)

description: Library name: T4121 GSCs_shMCU, ChIP3

value: Glioblastoma stem cells


title: T4121 GSCs, shMCU,H3K27ac (Input2)

description: Library name: T4121 GSCs_shMCU, Input2

value: shMCU


title: T4121 GSCs, shNT,H3K27ac (Input3)

description: Library name: T4121 GSCs_shNT, Input3

value: shNT


title: T4121 GSCs, shMCU,H3K27ac (ChIP1)

description: Library name: T4121 GSCs_shMCU, ChIP1


title: Peripheral whole blood DNA from fILD patient 195

description:
206139120085
206139120085_R03C01

value: UPitt

value: F

value: Former

value: IPF


title: Sample_9_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_9_GEX_ADT
Run3

value: pbmc

value: Memory B Cell

value: H2 Influenza Vaccination


title: Peripheral whole blood DNA from fILD patient 194

description:
206139120085
206139120085_R02C01


title: Peripheral whole blood DNA from fILD patient 192

description:
206139120077
206139120077_R08C01

value: Always


title: T4121 GSCs, shNT,H3K27ac (ChIP2)

description: Library name: T4121 GSCs_shNT, ChIP2


title: Peripheral whole blood DNA from fILD patient 193

description:
206139120085
206139120085_R01C01


title: Peripheral whole blood DNA from fILD patient 191

description:
206139120077
206139120077_R07C01


title: Sample_45_BCR Plasmablast Run5

description:
Library name: Sample_45_BCR
Run5

value: Plasmablast

value: BCR


title: Sample_4_GEX_ADT Memory B Cell Run3

description:
Library name: Sample_4_GEX_ADT
Run3


title: T4121 GSCs, shNT,H3K27ac (ChIP3)

description: Library name: T4121 GSCs_shNT, ChIP3


title: T4121 GSCs, shNT,H3K27ac (Input1)

description: Library name: T4121 GSCs_shNT, Input1


title: Peripheral whole blood DNA from fILD patient 189

description:
206139120077
206139120077_R05C01

value: Unknown

value: CTD-ILD


title: T4121 GSCs, shNT,H3K27ac (Input2)

description: Library name: T4121 GSCs_shNT, Input2


title: Sample_2_GEX_ADT Plasmablast Run2

description:
Library name: Sample_2_GEX_ADT
Run2


title: Sample_1_GEX_ADT Memory B Cell Run2

description:
Library name: Sample_1_GEX_ADT
Run2


title: Peripheral whole blood DNA from fILD patient 190

description:
206139120077
206139120077_R06C01

value: Never

value: Whole blood DNA


title: T4121 GSCs, shNT,H3K27ac (ChIP1)

description: Library name: T4121 GSCs_shNT, ChIP1

value: T4121 GSCs

value: Glioblastoma stem cells


title: Cattle_Yak_testis

city: Lanzhou

first: Xingdong

last: Wang

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Yak, LU_Bosgru_v3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos grunniens x Bos taurus

source_name: Testicular tissue of cattle_yak after sexual maturity for single-cell RNA sequencing

extract_protocol:
The frozen testicular tissue was removed and immediately placed in a 37 ℃ water bath for 2 min. After the tissue was melted, take it out with tweezers, place it in the resuscitation solution (DMEM/F12 medium+0.5mol/L sucrose+20% FBS), place it in a 37 ℃ water bath for 2min, preheat the DPBS to wash the tissue block for 2-3 times, place the tissue block in DMEM/F12 medium (Gibco, Waltham, MA, USA), and cut the tissue with ophthalmic scissors. Transfer the testicular tissue of cutted to a 15mL centrifuge tube, and add a solution with 0.2% collagenase IV (2 mg/mL) (Sigma, City of Saint Louis, USA) and hyaluronidase (2 mg/mL) solution (Sigma, City of Saint Louis, USA) (1:1) of 8~10 times the total amount of tissue. The centrifuge tube was placed in a 37℃ constant temperature shaker at 120 rpm (30 min, after 15min, 200μL tissue digestive fluid was taken every 3min to observe the digestive condition under the microscope until the free tubules with no mass tissue could be clearly observed), centrifuge at 1000 r/min for 5 min and drain the supernatant. 0.25% trypsin solution (2.5 mg/mL) (Gibco, Waltham, MA, USA), 8-10 times the total amount of tissue blocks, was added again. Finally, the tissue digestible solution was placed in a constant temperature shaker at 37℃ at 120 rpm (40 min, after 15min, 200μL tissue digestible solution was taken every 3min to observe the digestion condition under the microscope until the single cell suspension could be clearly observed). Fetal bovine serum was added to terminate digestion. The mixed cell suspension was blown evenly and filtered through 70μm and 40μm screens successively. The filtrate was collected and centrifuged at 300×g 4℃ for 5 min, the supernatant was abandoned, and the cells were re-suspended in DMEM/F12 complete medium containing 10% FBS, and cultured at 37 ℃ with 5% CO2. Part of the cell suspension was stained with Trypan blue and counted by automatic counter to calculate the number of cells and viability. The concentration was ~1000 cells/uL and cell viability>90% were used for scRNA seq.
The Cell suspension was loaded onto the Chromium Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) and the bead and cells with Cell Barcode were wrapped in the droplet. The droplet containing cells was collected, and then the cells were lysed in the droplet, so that the mRNA in the cells combined with the bead Cell Barcode to form a Single Cell GEMs, and the reverse transcription reaction was performed in the droplet to construct the cDNA library. GEM-RT-PCR was performed with a 96-hole reaction module (Bio-Rad; CT022510) in the C1000 Touch thermal cycler to generate barcode cDNA using the following procedures: 53°C for 45 min; 85°C for 5 minutes; Maintain at 4°C. The sample index on the library sequence is used to distinguish the source of the target sequence.

value: testis

value: Germ cell

tag: developmental stage

value: Postsexual maturity


title: Sample_43_BCR Plasmablast Run5

description:
Library name: Sample_43_BCR
Run5


title: Sample_3_GEX_ADT Plasmablast Run3

description:
Library name: Sample_3_GEX_ADT
Run3


title: 1001660006709_NTC

city: Kansas City

first: Andrew

last: Godwin

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: Kansas University Medical Center

description: Library name: DSP-1001660006709-D-A01

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Initial quality control and data analyses were performed using the GeoMxWorkflows, NanoStringNCTools, and GeoMxTools packages provided on Bioconductor, following the vignette “Analyzing GeoMx-NGS RNA Expression Data with GeoMxTools” provided by NanoString.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 cycles) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

tag: region

tag: patient

tag: roi

tag: segment

tag: area


title: Peripheral whole blood DNA from fILD patient 188

description:
206139120077
206139120077_R04C01

value: UPitt

value: M

value: Former

tag: tissue


title: Sample_44_BCR Memory B Cell Run5

description:
Library name: Sample_44_BCR
Run5

value: pbmc

tag: cell type

value: Memory B Cell


title: Sample_15_GEX_ADT Plasmablast Run3

description:
Library name: Sample_15_GEX_ADT
Run3

tag: treatment

value: H2 Influenza Vaccination


title: 7-day ligated sample 3

city: Albany

first: Melinda

last: Larsen

state: NY

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

description:
Library name: 7_day_ligated_3
10X Genomics

data_processing:
Initial processing steps included aligning to the GRCm39-8 genome with the addition of a tdTomato transcript and generating counts files, which was completed using CellRanger version 8.0.0.
Background noise was removed using CellBender (Fleming et al. 2023). Data files were imported using Seurat v5.0.1 in R v4.3.1 (R Project for Statistical Computing, 2021; Stuart et al., 2019)
Dead or apoptotic cells were removed if >25% of unique molecular identifiers (UMIs) mapped to mitochondrial genes.
Any cells with less than 200 or over 9,000 genes were excluded.
Integration was performed on 12 datasets to create one dataset. Clusters were calculated following the default pipeline (Seurat Guided Clustering Tutorial, 2023). All analysis of the integrated dataset was performed using the Seurat package in combination with other R packages.
Assembly: GRCm39-8
Supplementary files format and content: output_CellBender_T41.h5

organism: Mus musculus

source_name: Submandibular Salivary Gland

extract_protocol:
For enrichment of stromal cell populations, tThree mice were used for each timepoint with the mouse’s right submandibular and sublingual gland both being harvested. Excess fat and interstitial tissue were removed. The glands were then transferred to a dish containing 1X PBS, liberase TL Research Grade low Thermolysin (Roche 05401020001) at 0.25 mg/ml, DNase I (Stemcell Technologies 07900) at 15mg/ml, and dispase (Gibco 17105-041) at 0.53 u/ml and microdissected for 10 minutes. The sample was then incubated in a 37°C incubator for 15 minutes then triturated 1200 times . After trituration, the sample was incubated for an additional 5 minutes in a 37°C incubator and triturated once more. A 15 mL conical tube was placed on ice and the entire sample was transferred to the conical tube and incubated for 10 minutes. The supernatant was isolated and transferred to a fresh conical tube containing equal volume of DMEM/F12 (Gibco 11039-021) with 10% FBS (Gibco 10082-147) and was centrifuged for 5 minutes at 150xg 4C. The supernatant was removed and discarded, and the cell pellet was resuspended in 2 ml of isolation buffer composed of sterile-filtered Ca2+- and Mg2+-free 1X PBS, 0.1% bovine serum albumin, and 2 mM ethylenediaminetetraacetic acid. 5 μg of EpCAM (Invitrogen 14-5791-81) and Ter119 (Invitrogen 14-5921-82) was added to the cell suspension and incubated at 4°C on a rocker set on low speed for 10 minutes. the cell suspension was washed using isolation buffer and centrifuged at 150xg for 5 minutes at 4C. The supernatant was discarded, and the cell pellet was resuspended in 1 mL of isolation buffer. For depletion of epithelial and red blood cells, 25 μL of sheep anti-rat Dynabeads, which bind to the EpCAM- and Ter119 Ter119-labeled cells, (Invitrogen 11035) were added. The cell suspension was transferred to a 35 mm dish before incubating at 4C for 20 minutes on a rocker set at low speed. The sample was placed on a microcentrifuge magnet for 2 minutes, and the supernatant was collected. One additional epithelial and red blood cell depletion was performed. The sample was then depleted of dead cells using a dead cell removal kit (Miltenyi Biotec 130-090-101), following manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: Mice underwent either a 1, 3, or 7 day ligation surgery, where a metal clip was applied to the main ducts of the submandibular and sublingual glands and remained in place for aforementioned days. Non-surgical mice were used as controls

value: Submandibular Salivary Gland

value: Female

value: Stromal Enriched

value: PdgfraCre+/- Rosa26 tdTomato +/-

value: Tamoxifen Induciton, 7-day ligation

tag: age

value: 12 weeks


title: 7-day ligated sample 2

description:
Library name: 7_day_ligated_2
10X Genomics

tag: Sex


title: R108-LP-3

city: WAGENINGEN

first: Peng

address: Hoevestein 239 12B007

country: Netherlands

institute: Wageningen university

description: Library name: sample 3

data_processing:
Geneious Prime
Assembly: RNA-seq data were aligned and assembled to M. truncatula genome v.5.0 using Geneious Prime software (www.geneious.com)
Supplementary files format and content: Microsoft Excel processed file

organism: Medicago truncatula

source_name: Root

extract_protocol:
The total RNA of R108 and spx1spx3 roots were extracted using TRIzol® Reagent. Three technical replicates were used for each sample.
RNA samples were sequenced at Personal Gene Technology Co. Ltd (Nanjing, China) using the Illumina Novaseq 6000 platform.

value: Root

tag: cultivar

value: WT

value: Low Pi


title: R108-LP-2

description: Library name: sample 2

tag: genotype


title: spx1spx3-LP-3

description: Library name: sample 6

value: Mutant


title: spx1spx3-LP-1

description: Library name: sample 4


title: spx1spx3-LP-2

description: Library name: sample 5


title: R108-LP-1

description: Library name: sample 1


title: Sample_42_BCR Memory B Cell Run5

description:
Library name: Sample_42_BCR
Run5

value: BCR


title: Peripheral whole blood DNA from fILD patient 187

description:
206139120077
206139120077_R03C01

tag: cohort

value: UPitt

tag: smokehx

value: IPF

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 186

description:
206139120077
206139120077_R02C01

value: M

value: Unknown

value: CTD-ILD


title: 3-day ligated sample 2

description:
Library name: 3_day_ligated_2
10X Genomics

value: Submandibular Salivary Gland

value: Tamoxifen Induciton, 3-day ligation


title: 7-day ligated sample 1

description:
Library name: 7_day_ligated_1
10X Genomics

value: Female

value: Stromal Enriched


title: 3-day ligated sample 1

description:
Library name: 3_day_ligated_1
10X Genomics

value: PdgfraCre+/- Rosa26 tdTomato +/-


title: 3-day ligated sample 3

description:
Library name: 3_day_ligated_3
10X Genomics

value: 12 weeks


title: Peripheral whole blood DNA from fILD patient 184

description:
206139120095
206139120095_R08C01

value: Former


title: 1-day ligated sample 2

description:
Library name: 1_day_ligated_2
10X Genomics

value: Tamoxifen Induciton, 1-day ligation


title: Sample_39_BCR Plasmablast Run5

description:
Library name: Sample_39_BCR
Run5

value: pbmc

value: Plasmablast

value: H2 Influenza Vaccination


title: Sample_38_BCR Memory B Cell Run5

description:
Library name: Sample_38_BCR
Run5

value: Memory B Cell

value: BCR


title: 1-day ligated sample 3

description:
Library name: 1_day_ligated_3
10X Genomics


title: Peripheral whole blood DNA from fILD patient 185

description:
206139120077
206139120077_R01C01

value: UPitt

value: Never

value: IPF

value: Whole blood DNA


title: Sample_40_BCR Memory B Cell Run5

description:
Library name: Sample_40_BCR
Run5


title: 1-day ligated sample 1

description:
Library name: 1_day_ligated_1
10X Genomics

value: Submandibular Salivary Gland


title: Peripheral whole blood DNA from fILD patient 183

description:
206139120095
206139120095_R07C01

value: M

value: Unknown

value: CTD-ILD


title: Homeostatic sample 1

description:
Library name: Homeostatic_1
10X Genomics

value: Female

value: Stromal Enriched

value: PdgfraCre+/- Rosa26 tdTomato +/-

value: Tamoxifen Induction, no surgery


title: Homeostatic sample 2

description:
Library name: Homeostatic_2
10X Genomics

value: 12 weeks


title: Sample_37_BCR Plasmablast Run5

description:
Library name: Sample_37_BCR
Run5

value: pbmc

value: Plasmablast


title: Peripheral whole blood DNA from fILD patient 182

description:
206139120095
206139120095_R06C01

value: Former


title: mKO cispaltin

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were using the Cell Ranger software V7.1.0
Assembly: mm10
Supplementary files format and content: 10X hdf5 files with scRNA-seq matrices.

source_name: Kidney

extract_protocol:
Kidneys were perfused by PBS, harvested, minced, and digested for 30 mins at 37℃ using DMEM containing collagenase type I (2mg/ml). The single cells suspension loaded to 10X Chromium System  after filtrating through a 40 μm strainer.
Library was performed according to the manufacter's instructions. (single cell 3' V2 protocol, 10x Genomics)

value: Kidney


title: mKO saline

description: 10x Genomics


title: Peripheral whole blood DNA from fILD patient 181

description:
206139120095
206139120095_R05C01

value: UPitt


title: Sample_36_BCR Memory B Cell Run5

description:
Library name: Sample_36_BCR
Run5

value: Memory B Cell

value: H2 Influenza Vaccination

value: BCR


title: WT saline

description: 10x Genomics


title: WT cisplatin

description: 10x Genomics


title: Sample_41_BCR Memory B Cell Run5

description:
Library name: Sample_41_BCR
Run5


title: Sample_35_BCR Memory B Cell Run5

description:
Library name: Sample_35_BCR
Run5


title: Treated with LGX818 and Cet for 14 Days

city: Guangzhou

first: zhan

last: zhao

state: Guangdong

address: 613 West Huangpu Avenue, Tianhe District

department: department of general surgery

institute: The First Affiliated Hospital of Jinan University

description: Library name: HT-29-LX818-CT

data_processing:
During the CCD scanning of the sequencer, optical signals from the four fluorescence channels are real-time basecalled into BCL data by the built-in software RTA. After sequencing is completed, the Illumina official software Bcl2fastq (v2.17) is used to split the data based on the sample's index sequences and convert it into FASTQ format. The sequencer's HCS software performs the Primary Analysis, where it determines whether a cluster passes the filter (Pass Filter, PF) based on the purity of the fluorescence signals from the first 25 cycles. Specifically, if the Chastity value of the first 25 cycles is less than 0.6 and more than 2 bases do not meet the quality threshold, the sequence is considered to have failed the filter. The PF clusters, after being processed by Bcl2fastq, are stored as FASTQ files, referred to as PF data or raw data. For paired-end sequencing data, the sequence data consists of two FASTQ files, each storing the reads from one end of the sequencing.
Assembly: a lentiviral human CRISPR knockout (hGeCKOv2) library (500× coverage) generated by the Zhang laboratory
Supplementary files format and content: fastq
Library strategy: CRISPR Screen

extract_protocol:
The cells were infected at a multiplicity of infection of 0.3 to ensure that most cells took up only one stable short guide RNA (sgRNA). Puromycin (10 µg/ml) was added to the cells 72 h after infection and maintained in the cultures for 3 days. After effective selection for puromycin resistance, we equally divided these HT-29 cells into four groups: the DMSO (day 0), DMSO (day 14), LGX818 (1 μM/ml) treated for 14 days, or LGX818 (100 nM/ml) + cetuximab (100 ng/ml) treated for 14 days groups. After drug selection, the cells were harvested, and genomic DNA was isolated using a DNA extraction kit (Omega, D3396). The PCR products containing gRNA sequences that were integrated into the genomes of the cells were sequenced by parallel sequencing using a HiSeq 2000 (Illumina).
Resistant genes were identified from sgRNA screen sequencing results using MAGeCK MLE analysis. MAGeCK MLE calculates a “beta score” for each targeted gene to measure the degree of selection upon gene perturbation, similar to the “log fold-change” measurement in differential expression analysis. A positive beta score indicates that the gene is a positively screened gene, whereas a negative value indicates a negatively screened gene.

tag: cell line

value: Human Colorectal Adenocarcinoma Cell Line


title: Homeostatic sample 3

description:
Library name: Homeostatic_3
10X Genomics

value: Submandibular Salivary Gland


title: Treated with LGX818 for 14 Days

description: Library name: HT-29-LX818


title: Peripheral whole blood DNA from fILD patient 180

description:
206139120095
206139120095_R04C01

value: M

value: IPF

value: Whole blood DNA


title: Sample_34_BCR Plasmablast Run5

description:
Library name: Sample_34_BCR
Run5

tag: library type


title: No treatment Day 14

description: Library name: HT-29-D14


title: Sample_33_BCR Memory B Cell Run5

description:
Library name: Sample_33_BCR
Run5


title: Peripheral whole blood DNA from fILD patient 179

description:
206139120095
206139120095_R03C01


title: No treatment Day 0

description: Library name: HT-29-D0


title: Peripheral whole blood DNA from fILD patient 177

description:
206139120095
206139120095_R01C01

value: F

value: Unknown

value: CTD-ILD


title: Peripheral whole blood DNA from fILD patient 178

description:
206139120095
206139120095_R02C01


title: Peripheral whole blood DNA from fILD patient 176

description:
206139120078
206139120078_R08C01


title: Sample_31_BCR Memory B Cell Run4

description:
Library name: Sample_31_BCR
Run4


title: Sample_30_BCR Plasmablast Run4

description:
Library name: Sample_30_BCR
Run4


title: Sample_32_BCR Memory B Cell Run4

description:
Library name: Sample_32_BCR
Run4


title: Peripheral whole blood DNA from fILD patient 175

description:
206139120078
206139120078_R07C01

value: Never


title: Peripheral whole blood DNA from fILD patient 174

description:
206139120078
206139120078_R06C01


title: Sample_28_BCR Plasmablast Run4

description:
Library name: Sample_28_BCR
Run4

value: pbmc


title: Peripheral whole blood DNA from fILD patient 173

description:
206139120078
206139120078_R05C01


title: Peripheral whole blood DNA from fILD patient 172

description:
206139120078
206139120078_R04C01


title: Sample_27_BCR Plasmablast Run4

description:
Library name: Sample_27_BCR
Run4

value: Plasmablast


title: Peripheral whole blood DNA from fILD patient 171

description:
206139120078
206139120078_R03C01


title: Sample_26_BCR Plasmablast Run4

description:
Library name: Sample_26_BCR
Run4


title: Peripheral whole blood DNA from fILD patient 170

description:
206139120078
206139120078_R02C01

value: Former


title: PANC02 cell, shSrebf1-2

city: Hangzhou

first: Mengyi

last: Lao

state: Zhejiang

address: Qingchun 79 road

institute: Zhejiang university

description: Library name: samples11

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files includeFPKM values for each Sample

growth_protocol: KPC and PANC02 pancreatic cancer cells were maintained inDMEM supplemented with10% fetal bovine serum (FBS)and antibiotics in humidified atmosphere with 5%CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The control group and the treatment group cells were transfected with the vector and the shSrebf1 plasmid, respectively.

value: Pancreatic cancer cell

value: lipid metabolism


title: UM

type: RNA

city: Daegu

first: Su Young

last: Oh

address: 2177, Dalgubeol-daero, Jung-gu

country: South Korea

institute: Kyungpook National University

description: OSCC

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 2.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit(900720, Thermo Fisher Scientific) using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Human Gene 2.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

label: biotin

source_name: UMSCC1 (UM)

label_protocol: The GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using GeneChip™ WT PLUS Reagent Kit(902280, Thermo Fisher Scientific).

growth_protocol: OSCC cells were cultured in DMEM medium containing 10% FBS and 1% penicillin/streptomycin solution at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was obtained from UMSCC1 and UM-Cis cells cultured without cisplatin using Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA quality was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, USA), and the quantity was determined using the ND-1000 spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: Cisplatin-resistant UM-Cis cells were derived from original UMSCC1 cells by continuous exposure to stepwise increasing concentrations of cisplatin. Initially, the exponentially growing cells were exposed to 1 μg/ml concentration of cisplatin in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin, and subcultured upon reaching 70 - 80% confluency. At this point, cisplatin concentration was increased gradually and the above process was repeated. Aliquots of cell sublines were cryopreserved at each incremental concentration. The final concentration of cisplatin treated in UM-Cis cells is 5 μg/ml which is the IC50 of the original UMSCC1 cells. This development period was carried out for approximately 12 months.


title: Sample_24_BCR Plasmablast Run4

description:
Library name: Sample_24_BCR
Run4


title: Sample_29_BCR Plasmablast Run4

description:
Library name: Sample_29_BCR
Run4


title: UM-cis

description: cisplatin resistant OSCC

source_name: Cisplatin resistant UMSCC1 (UM-cis)

value: Cisplatin resistance-UMSCC1


title: PANC02 cell, shNC1

description: Library name: samples7

value: shNC


title: PANC02 cell, shNC2

description: Library name: samples8


title: PANC02 cell, shSrebf1-1

description: Library name: samples10


title: UM-1

description: OSCC

source_name: UMSCC1 (UM-1)


title: HSC_NPMc+_rep2

city: Milano

first: Emanuela

last: Colombo

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

description: Gene expression data of LT-HSC purified from a pool of animals expressing the NPMc+ mutant protein

hyb_protocol: Hybridization was performed using the Affymetrix GeneChip® Hybridization, Wash and Stain Kit, according to the Encore® Biotin Module (NuGEN Technologies, Inc)  recommended protocol for Affymetrix GeneChip® Mouse Gene ST 2.0 Arrays. Briefly, Targets were diluted in hybridization buffer at a concentration of 23 ng/ul, denatured at 99 °C for 2 minutes, incubated at 45 °C for 5 minutes  and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip cartridge. A single GeneChip® Mouse Gene ST 2.0 was then hybridized with each biotin-labeled target.   Hybridizations were performed for 18 hours at 45°C in a rotisserie oven. GeneChip® cartridges were washed and stained in the Affymetrix Fluidics Station 450 following the FS450_0002 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.  Partek Genomics Suite v 6.6 was used for analysis of microarray data

data_processing: Probes to Import: Interrogating Probes and Control Probes  Probe filtering: skip  Algorithm: RMA  Background Correction: RMA Background Correction  Normalization: Quantile Normalization+batch effect correction  Log Probes using Base: 2 (scaling parameters)  Probeset Summarization: Median Polish

source_name: LT-HSC sorted 4 months post bone marrow transplatation

label_protocol: Bioin-labeled cDNA targets were synthesized starting from  ≈ 5 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Nugen® Pico WTA Systems V2 (NuGEN Technologies, Inc). With the Encore® Biotin Module (NuGEN Technologies, Inc) was synthesized the fragmented and labeled cDNA. All steps of the labeling protocol were performed according to the manufacturer's recommended protocols.

extract_protocol: total RNA have been extacted from freshly isolated HSC using Rneasy mini kit from Qiagen. The quality of total RNA was first assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA)

value: bone marrow

tag: strain


title: HSC_NPMc+_rep3


title: HSC_NPMc+_rep1


title: Sample_25_BCR Plasmablast Run4

description:
Library name: Sample_25_BCR
Run4

value: H2 Influenza Vaccination

value: BCR


title: UM-cis-2

description: cisplatin resistant OSCC

source_name: Cisplatin resistant UMSCC1 (UM-cis-2)


title: HSC_reference_rep3

description: Gene expression data of LT-HSC purified from a pool of control animals


title: UM-cis-1

description: cisplatin resistant OSCC

source_name: Cisplatin resistant UMSCC1 (UM-cis-1)


title: HSC_reference_rep2