title: IL-1b+IL-6+IL-23+anti-Activin-A Day 2 [pTh17-mAb-Day2-48]

city: Chapel Hill

first: Yisong

last: Wan

state: NC

address: 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill

description:
processed data file:
Th17_Day2b_featureCounts.txt
Th17_Day2b_DESeq2_normalizedCounts.txt

data_processing:
The raw reads were filtered by removing adaptor sequences, contamination and low-quality reads. Cleaned reads were mapped to mm10 using STAR aligner (version 2.5.1.)
Subread featureCounts (version 1.4.6) was applied for gene quantification based on GENCODE annotation (gencode.vM23)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count and log2 transformed DESeq2 normalized counts for each sample

source_name: IL-1b+IL-6+IL-23+anti-Activin-A Day 2

growth_protocol: Cells are grown in X-VIVO medium (Lonza) for indicated time.

extract_protocol:
Live cells were collected, and RNA was harvested using Trizol reagent. Direct-zol RNA Miniprep Kits (Cat#R2050) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol:
A: CD4 T cells from WT mice were activated with IL-6 and transfected with RV-Thy1.1-CA-ALK4 and RV- Thy1.1-CA-ALK5 at day1 post activation. Thy1.1+ cells were sorted by MACS for RNA extraction.
B: Activated WT CD4 T cells were differentiated under various cytokines combinations: IL-1b+IL-6+IL-23, TGFb1+IL-6 and Activin A+IL-6 for 24 and 48hr. Live cells were collected for RNA extraction.
C: Activated WT CD4 T cells were differentiated under various cytokines combinations: IL-1b+IL-6+IL-23, IL-1b+IL-6+IL-23+anti-Activin-A for 24 and 48hr. Live cells were collected for RNA extraction.
D: Activated WT CD4 T cells were differentiated under various cytokines combinations: IL-6, Activin A+IL-6 for 24 and 48hr. Live cells were collected for RNA extraction.

tag: strain

value: 8-12 weeks

tag: genotype

value: Wild-type

value: spleen

tag: cell type

value: Activated T cells

value: IL-1b+IL-6+IL-23+anti-Activin-A Day 2


title: IL-1b+IL-6+IL-23+anti-Activin-A Day 2 [pTh17-mAb-Day2-47]

status: Public on Jan 11 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: age

tag: tissue

tag: treatment


title: 4206

type: RNA

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description: Gene expression data from adults

hyb_protocol: Standard GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: HTA 2.0 chips were scanned at the Cologne Center for Genomics, Cologne, Germany.

data_processing: Raw data scans (.CEL files) were read into the R language and environment for statistical computing (version 3.5.0; R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org/). Pre-processing and quality control was performed by using the Oligo package. The core array data were background corrected by Robust Multi-array Average (RMA) and quantiles-normalized.

label: biotin

organism: Homo sapiens

source_name: blood

label_protocol: 100ng total RNA was labeled using standard GeneChip buffers and reagents (Affymetrix)

growth_protocol: Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.

extract_protocol: Total RNA was isolated in accordance with the PAXgene blood miRNA isolation (QIAGEN) procedure using the QIAcube instrument.

treatment_protocol: PAXgene blood RNA tubes were left at room temperaturee to defrost (approx. 2 hours) while mixing by inversion.

tag: gender

value: female

tag: disease state

value: sepsis

value: blood


title: 5950

description: Gene expression data from adults

value: male


title: 3947374

description: Gene expression data from adults

value: noninfectious


title: 3944817

description: Gene expression data from adults


title: 4109

description: Gene expression data from adults


title: 3356210

description: Gene expression data from adults


title: 5881

description: Gene expression data from adults


title: 3900569

description: Gene expression data from adults


title: 3111443

description: Gene expression data from adults


title: 3583

description: Gene expression data from adults


title: Coronary artery disease [HP19 ]

type: genomic

city: Mumbai

first: TESTER

middle: F

last: ASHAVAID

state: Maharashtra

address: Lalita Girdhar bldg,3rd floor,Biochemistry Dept.,, V.S.Marg, Mahim

department: Lab Medicine

country: India

institute: P.D. HINDUJA HOSPITAL & MRC

description: Genomic DNA extracted from whole blood was genotyped using Illumina Cardiometabo Beadchip Infinium II assay (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation in Illumina Hybridization Oven, single-base extension and allele specific extension was performed.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a  Illumina BeadArray Reader.

data_processing:
Genomic DNA extracted from whole blood was genotyped using Infinium II assay on Illumina Human CardioMetabo-Beadchip.
Image data was analyzed using Beadstudio 3.1.3 with GT module 3.2.33 (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

source_name: Coronary artery disease

label_protocol: A minimum of 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh whole blood sample was performed using modified Miller et al Salting out method.

tag: group

value: case


title: IL-1b+IL-6+IL-23+anti-Activin-A Day 2 [pTh17-mAb-Day2-46]


title: IL-1b+IL-6+IL-23 Day 2 [pTh17-Day2-45]

source_name: IL-1b+IL-6+IL-23 Day 2

value: IL-1b+IL-6+IL-23 Day 2


title: 3499

description: Gene expression data from adults


title: 3008502

description: Gene expression data from adults


title: hv233

description: Gene expression data from adults

value: healthy


title: 3215498

description: Gene expression data from adults


title: IL-1b+IL-6+IL-23 Day 2 [pTh17-Day2-44]


title: IL-1b+IL-6+IL-23 Day 2 [pTh17-Day2-43]


title: IL-6+ActivinA-Day 2 [aTh17-Day2-42]

source_name: IL-6+ActivinA-Day 2

value: IL-6+ActivinA-Day 2


title: IL-6+ActivinA-Day 2 [aTh17-Day2-41]


title: IL-6+ActivinA-Day 2 [aTh17-Day2-40]


title: IL-6-Day 2 [IL-6-Day2-39]

source_name: IL-6-Day 2

value: IL-6-Day 2


title: IL-6-Day 2 [IL-6-Day2-38]


title: IL-6-Day 2 [IL-6-Day2-37]


title: IL-1b+IL-6+IL-23+anti-Activin-A Day 1 [pTh17-mAb-Day1-35]

description:
processed data file:
Th17_Day1b_featureCounts.txt
Th17_Day1b_DESeq2_normalizedCounts.txt

source_name: IL-1b+IL-6+IL-23+anti-Activin-A Day 1

value: IL-1b+IL-6+IL-23+anti-Activin-A Day 1


title: IL-1b+IL-6+IL-23+anti-Activin-A Day 1 [pTh17-mAb-Day1-34]


title: hv232

description: Gene expression data from adults


title: IL-1b+IL-6+IL-23 Day 1 [pTh17-Day1-32]

source_name: IL-1b+IL-6+IL-23 Day 1

value: IL-1b+IL-6+IL-23 Day 1


title: IL-1b+IL-6+IL-23 Day 1 [pTh17-Day1-31]

value: 8-12 weeks


title: hv230

description: Gene expression data from adults


title: IL-6+ActivinA-Day 1 [aTh17-Day1-30]

source_name: IL-6+ActivinA-Day 1

value: Wild-type

value: IL-6+ActivinA-Day 1


title: hv231

description: Gene expression data from adults


title: hv220

description: Gene expression data from adults


title: 3007078

description: Gene expression data from adults


title: hv204

description: Gene expression data from adults


title: hv226

description: Gene expression data from adults


title: hv211

description: Gene expression data from adults


title: IL-1b+IL-6+IL-23 Day 1 [pTh17-Day1-33]

value: spleen

value: Activated T cells


title: hv225

description: Gene expression data from adults


title: hv194

description: Gene expression data from adults


title: hv202

description: Gene expression data from adults

value: female


title: hv203

description: Gene expression data from adults


title: hv201

description: Gene expression data from adults


title: hv192

description: Gene expression data from adults


title: hv183

description: Gene expression data from adults


title: IL-1b+IL-6+IL-23+anti-Activin-A Day 1 [pTh17-mAb-Day1-36]


title: IL-6+ActivinA-Day 1 [aTh17-Day1-28]


title: hv158

description: Gene expression data from adults


title: hv162

description: Gene expression data from adults


title: IL-6-Day 1 [IL-6-Day1-26]

source_name: IL-6-Day 1

value: IL-6-Day 1


title: hv153

description: Gene expression data from adults

value: blood


title: IL-6+ActivinA-Day 1 [aTh17-Day1-29]


title: IL-6-Day 1 [IL-6-Day1-25]


title: IL-1b+IL-6+IL-23 day 2-3

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
pTh17-Day2-18

source_name: Activated T cells

treatment_protocol:
A: CD4 T cells from WT mice were activated with IL-6 and transfected with RV-Thy1.1-CA-ALK4 and RV- Thy1.1-CA-ALK5 at day1 post activation. Thy1.1+ cells were sorted by MACS for RNA extraction.
B: Activated WT CD4 T cells were differentiated under various cytokines combinations: IL-1b+IL-6+IL-23, TGFb1+IL-6 and Activin A+IL-6 for 24 and 48hr. Live cells were collected for RNA extraction.

tag: agent


title: IL-1b+IL-6+IL-23 day 1-2

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
pTh17-Day1-5


title: IL-1b+IL-6+IL-23 day 1-3

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
pTh17-Day1-6


title: hv143

description: Gene expression data from adults


title: hv139

description: Gene expression data from adults


title: hv140

description: Gene expression data from adults


title: hv144

description: Gene expression data from adults


title: TGFb1+IL-6 day 2-2

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
cTh17-Day2-20


title: hv141

description: Gene expression data from adults


title: IL-1b+IL-6+IL-23 day 2-1

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
pTh17-Day2-16


title: IL-6-Day 1 [IL-6-Day1-27]


title: hv113

description: Gene expression data from adults


title: hv119

description: Gene expression data from adults


title: hv111

description: Gene expression data from adults


title: hv136

description: Gene expression data from adults


title: IL-1b+IL-6+IL-23 day 1-1

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
pTh17-Day1-4


title: hv118

description: Gene expression data from adults


title: Coronary artery disease [HP11]

value: male


title: TGFb1+IL-6 day 2-3

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
cTh17-Day2-21


title: TGFb1+IL-6 day 1-1

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
cTh17-Day1-7


title: IL-1b+IL-6+IL-23 day 2-2

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
pTh17-Day2-17


title: TGFb1+IL-6 day 2-1

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
cTh17-Day2-19


title: TGFb1+IL-6 day 1-2

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
cTh17-Day1-8


title: 6636

description: Gene expression data from adults

value: sepsis


title: 6101

description: Gene expression data from adults


title: Activin A+IL-6 day 2-3

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
aTh17-Day2-24

value: Activin A+IL-6


title: Activin A+IL-6 day 2-2

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
aTh17-Day2-23


title: 6413

description: Gene expression data from adults


title: TGFb1+IL-6 day 1-3

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
cTh17-Day1-9


title: CA-ALK5-2

description:
Th17_CA_ALK_featureCounts.txt
Th17_CA_ALK_DESeq2_normalizedCounts.txt
CA-ALK5-29

tag: transduction


title: CA-ALK5-1

description:
Th17_CA_ALK_featureCounts.txt
Th17_CA_ALK_DESeq2_normalizedCounts.txt
CA-ALK5-28


title: Activin A+IL-6 day 2-1

description:
Th17_Day2_featureCounts.txt
Th17_Day2_DESeq2_normalizedCounts.txt
aTh17-Day2-22


title: CA-ALK4-3

description:
Th17_CA_ALK_featureCounts.txt
Th17_CA_ALK_DESeq2_normalizedCounts.txt
CA-ALK4-27


title: 5907

description: Gene expression data from adults

value: noninfectious


title: 4932

description: Gene expression data from adults


title: 5746

description: Gene expression data from adults


title: 4025

description: Gene expression data from adults


title: Activin A+IL-6 day 1-3

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
aTh17-Day1-12


title: 4162

description: Gene expression data from adults


title: Activin A+IL-6 day 1-2

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
aTh17-Day1-11


title: CA-ALK5-3

description:
Th17_CA_ALK_featureCounts.txt
Th17_CA_ALK_DESeq2_normalizedCounts.txt
CA-ALK5-30


title: 4051

description: Gene expression data from adults


title: CA-ALK4-1

description:
Th17_CA_ALK_featureCounts.txt
Th17_CA_ALK_DESeq2_normalizedCounts.txt
CA-ALK4-25


title: 3943

description: Gene expression data from adults


title: CA-ALK4-2

description:
Th17_CA_ALK_featureCounts.txt
Th17_CA_ALK_DESeq2_normalizedCounts.txt
CA-ALK4-26


title: 4218

description: Gene expression data from adults


title: 4027

description: Gene expression data from adults


title: 4771

description: Gene expression data from adults


title: 3938

description: Gene expression data from adults


title: 3755

description: Gene expression data from adults


title: 3880674

description: Gene expression data from adults


title: 3872240

description: Gene expression data from adults


title: 3743873

description: Gene expression data from adults


title: 3730247

description: Gene expression data from adults


title: Activin A+IL-6 day 1-1

description:
Th17_Day1_featureCounts.txt
Th17_Day1_DESeq2_normalizedCounts.txt
aTh17-Day1-10


title: SEHBP-eGFP overexpression – Biological replicate 2

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

data_processing:
Basecalling was performed by BGI
Transcript abundance was estimated using Kallisto
Genome_build: GRCh37.p13 human genome reference assembly

source_name: human embryonic kidney cells

growth_protocol: HEK293T cells were maintained in standard DMEM supplemented with 10%FBS and 1%PenStrep at 37C and 5% CO2

extract_protocol:
The cells were pelleted at 300 × g, and 5 × 10^6 cells were used for total RNA purification using an RNeasy kit (Qiagen). Three biological replicates were submitted for library preparation and sequencing at BGI.
Libraries were constructed using standard protocols at BGI

treatment_protocol: Cells were transfected with Fugene for 24 hr.

tag: transfection

value: SEHBP-eGFP overexpression


title: SEHBP-eGFP overexpression – Biological replicate 1


title: Empty vector control – Biological replicate 3

value: empty vector


title: SEHBP-eGFP overexpression – Biological replicate 3


title: 3651817

description: Gene expression data from adults


title: 4017646

description: Gene expression data from adults

scan_protocol: miRNA-4_1 chips were scanned at the Cologne Center for Genomics, Cologne, Germany.

data_processing: Pre-processing, normalization, probe summarization, and data quality control were executed in Expression Console Software (Affymetrix). Robust Multi-array Average (RMA)  normalization and DABG probe-level detection were specified. All other parameters were default.


title: Empty vector control – Biological replicate 2


title: Empty vector control – Biological replicate 1


title: 3651

description: Gene expression data from adults


title: 3490886

description: Gene expression data from adults


title: 3796

description: Gene expression data from adults

value: patient


title: 3447051

description: Gene expression data from adults


title: 3577539

description: Gene expression data from adults


title: 3453835

description: Gene expression data from adults


title: 3907631

description: Gene expression data from adults


title: 3945035

description: Gene expression data from adults


title: 3483709

description: Gene expression data from adults


title: 3576217

description: Gene expression data from adults


title: 3454267

description: Gene expression data from adults


title: 3944248

description: Gene expression data from adults


title: 3639155

description: Gene expression data from adults


title: 3456820

description: Gene expression data from adults


title: 3419205

description: Gene expression data from adults


title: 3360593

description: Gene expression data from adults


title: 3478108

description: Gene expression data from adults


title: 3805980

description: Gene expression data from adults


title: 3905060

description: Gene expression data from adults


title: 3415746

description: Gene expression data from adults


title: 3292348

description: Gene expression data from adults


title: 3976071

description: Gene expression data from adults


title: 3297275

description: Gene expression data from adults


title: 3623917

description: Gene expression data from adults


title: 5924

description: Gene expression data from adults


title: 3300871

description: Gene expression data from adults


title: 4074160

description: Gene expression data from adults


title: 3273867

description: Gene expression data from adults


title: 3285624

description: Gene expression data from adults


title: 3962538

description: Gene expression data from adults


title: 4078051

description: Gene expression data from adults


title: 3769063

description: Gene expression data from adults


title: 3004993

description: Gene expression data from adults


title: hv210

description: Gene expression data from adults

value: healthy


title: 3783997

description: Gene expression data from adults


title: 3884620

description: Gene expression data from adults


title: hv209

description: Gene expression data from adults


title: 3878294

description: Gene expression data from adults


title: 6482

description: Gene expression data from adults


title: 3835193

description: Gene expression data from adults


title: hv69

description: Gene expression data from adults


title: hv199

description: Gene expression data from adults


title: hv207

description: Gene expression data from adults


title: hv40

description: Gene expression data from adults


title: 3143971

description: Gene expression data from adults


title: hv198

description: Gene expression data from adults


title: hv213

description: Gene expression data from adults


title: hv195

description: Gene expression data from adults


title: 3780832

description: Gene expression data from adults


title: 3891629

description: Gene expression data from adults


title: hv205

description: Gene expression data from adults


title: 3902796

description: Gene expression data from adults


title: 3809140

description: Gene expression data from adults


title: hv190

description: Gene expression data from adults


title: 3605989

description: Gene expression data from adults


title: hv191

description: Gene expression data from adults


title: hv34

description: Gene expression data from adults


title: hv43

description: Gene expression data from adults


title: hv189

description: Gene expression data from adults


title: 6000

description: Gene expression data from adults


title: 3707546

description: Gene expression data from adults


title: hv177

description: Gene expression data from adults


title: hv42

description: Gene expression data from adults


title: hv235

description: Gene expression data from adults


title: 3803936

description: Gene expression data from adults


title: 5433

description: Gene expression data from adults


title: 3257803

description: Gene expression data from adults


title: hv56

description: Gene expression data from adults


title: 5750

description: Gene expression data from adults


title: hv181

description: Gene expression data from adults


title: 5479

description: Gene expression data from adults


title: hv186

description: Gene expression data from adults


title: 5475

description: Gene expression data from adults


title: hv185

description: Gene expression data from adults


title: 3813755

description: Gene expression data from adults


title: 3810998

description: Gene expression data from adults


title: 5726

description: Gene expression data from adults


title: hv182

description: Gene expression data from adults


title: 4731

description: Gene expression data from adults


title: 5164

description: Gene expression data from adults


title: 5752

description: Gene expression data from adults


title: 6604

description: Gene expression data from adults


title: 5377

description: Gene expression data from adults


title: 5235

description: Gene expression data from adults


title: 5260

description: Gene expression data from adults


title: 5273

description: Gene expression data from adults


title: 3485

description: Gene expression data from adults


title: 5317

description: Gene expression data from adults


title: 4938

description: Gene expression data from adults


title: 4982

description: Gene expression data from adults


title: 4831

description: Gene expression data from adults


title: hv215

description: Gene expression data from adults


title: 4829

description: Gene expression data from adults


title: 4951

description: Gene expression data from adults


title: 4923

description: Gene expression data from adults


title: 6019

description: Gene expression data from adults


title: 3150468

description: Gene expression data from adults


title: 4917

description: Gene expression data from adults


title: 5598

description: Gene expression data from adults


title: 3803

description: Gene expression data from adults


title: 4998

description: Gene expression data from adults


title: 6601

description: Gene expression data from adults


title: 4737

description: Gene expression data from adults


title: 4548

description: Gene expression data from adults


title: 5453

description: Gene expression data from adults


title: 6380

description: Gene expression data from adults


title: 5567

description: Gene expression data from adults


title: 4736

description: Gene expression data from adults


title: 3783662

description: Gene expression data from adults


title: 5582

description: Gene expression data from adults


title: hv44

description: Gene expression data from adults


title: 4532

description: Gene expression data from adults


title: 4393

description: Gene expression data from adults


title: 5293

description: Gene expression data from adults


title: 4874

description: Gene expression data from adults


title: 5607

description: Gene expression data from adults


title: 4625

description: Gene expression data from adults


title: 4445

description: Gene expression data from adults


title: 4835

description: Gene expression data from adults


title: 4525

description: Gene expression data from adults


title: 5332

description: Gene expression data from adults


title: 3323

description: Gene expression data from adults


title: 5530

description: Gene expression data from adults


title: 3769

description: Gene expression data from adults


title: 6070

description: Gene expression data from adults


title: 4950

description: Gene expression data from adults


title: 3768367

description: Gene expression data from adults


title: hv35

description: Gene expression data from adults


title: 5651

description: Gene expression data from adults


title: 3018183

description: Gene expression data from adults


title: 5396

description: Gene expression data from adults


title: 4368

description: Gene expression data from adults


title: 3749982

description: Gene expression data from adults


title: 5035

description: Gene expression data from adults


title: 3717

description: Gene expression data from adults


title: 3734523

description: Gene expression data from adults


title: 5261

description: Gene expression data from adults


title: 3647803

description: Gene expression data from adults


title: hv57

description: Gene expression data from adults


title: 6276

description: Gene expression data from adults


title: 5059

description: Gene expression data from adults


title: 5409

description: Gene expression data from adults


title: 3620

description: Gene expression data from adults


title: 3687409

description: Gene expression data from adults


title: 3599379

description: Gene expression data from adults


title: 3601304

description: Gene expression data from adults


title: 4723

description: Gene expression data from adults


title: 3585

description: Gene expression data from adults


title: 3632

description: Gene expression data from adults


title: 3586270

description: Gene expression data from adults


title: 5132

description: Gene expression data from adults


title: 3578493

description: Gene expression data from adults


title: 5873

description: Gene expression data from adults


title: 3547

description: Gene expression data from adults


title: hv53

description: Gene expression data from adults


title: 3528466

description: Gene expression data from adults


title: 4958

description: Gene expression data from adults


title: 3351972

description: Gene expression data from adults


title: 3344784

description: Gene expression data from adults


title: 5189

description: Gene expression data from adults


title: 6418

description: Gene expression data from adults


title: 4745

description: Gene expression data from adults


title: 3365199

description: Gene expression data from adults


title: 6151

description: Gene expression data from adults


title: 4948

description: Gene expression data from adults


title: 4729

description: Gene expression data from adults


title: 3462609

description: Gene expression data from adults


title: 3405860

description: Gene expression data from adults


title: 3428068

description: Gene expression data from adults


title: 4685

description: Gene expression data from adults


title: 3657587

description: Gene expression data from adults


title: 3804157

description: Gene expression data from adults


title: 5381

description: Gene expression data from adults


title: 3270135

description: Gene expression data from adults


title: 3793091

description: Gene expression data from adults


title: 4796

description: Gene expression data from adults


title: hv38

description: Gene expression data from adults


title: 3140433

description: Gene expression data from adults


title: 3211740

description: Gene expression data from adults


title: 3186280

description: Gene expression data from adults


title: 5262

description: Gene expression data from adults


title: 3316840

description: Gene expression data from adults


title: 3159200

description: Gene expression data from adults


title: 3509601

description: Gene expression data from adults


title: 3287179

description: Gene expression data from adults


title: 3261652

description: Gene expression data from adults


title: 3823266

description: Gene expression data from adults


title: 3317184

description: Gene expression data from adults


title: 3284876

description: Gene expression data from adults


title: 3311112

description: Gene expression data from adults


title: 6437

description: Gene expression data from adults


title: hv148

description: Gene expression data from adults


title: hv163

description: Gene expression data from adults


title: hv176

description: Gene expression data from adults


title: 3021476

description: Gene expression data from adults


title: hv156

description: Gene expression data from adults


title: 3585283

description: Gene expression data from adults


title: 3662253

description: Gene expression data from adults


title: hv157

description: Gene expression data from adults


title: hv151

description: Gene expression data from adults


title: hv166

description: Gene expression data from adults


title: hv146

description: Gene expression data from adults


title: hv120

description: Gene expression data from adults


title: hv165

description: Gene expression data from adults


title: hv145

description: Gene expression data from adults


title: hv154

description: Gene expression data from adults


title: hv116

description: Gene expression data from adults


title: hv110

description: Gene expression data from adults


title: hv117

description: Gene expression data from adults


title: hv115

description: Gene expression data from adults


title: 5230

description: Gene expression data from adults


title: hv164

description: Gene expression data from adults


title: 5254

description: Gene expression data from adults


title: 4295

description: Gene expression data from adults


title: 5392

description: Gene expression data from adults


title: 5785

description: Gene expression data from adults


title: 4850

description: Gene expression data from adults


title: 4373

description: Gene expression data from adults


title: hv170

description: Gene expression data from adults


title: 6422

description: Gene expression data from adults


title: hv112

description: Gene expression data from adults


title: 6146

description: Gene expression data from adults


title: 5771

description: Gene expression data from adults


title: hv114

description: Gene expression data from adults


title: 3823

description: Gene expression data from adults


title: 4471

description: Gene expression data from adults


title: 5717

description: Gene expression data from adults


title: 4892

description: Gene expression data from adults


title: 3711

description: Gene expression data from adults


title: 4484

description: Gene expression data from adults


title: 4225

description: Gene expression data from adults


title: 4063351

description: Gene expression data from adults


title: 3910077

description: Gene expression data from adults


title: 3346382

description: Gene expression data from adults


title: 3204833

description: Gene expression data from adults


title: 5853

description: Gene expression data from adults


title: 3192253

description: Gene expression data from adults


title: 3773892

description: Gene expression data from adults


title: 3197090

description: Gene expression data from adults


title: 3328742

description: Gene expression data from adults


title: 3699

description: Gene expression data from adults


title: 3367

description: Gene expression data from adults


title: 4092070

description: Gene expression data from adults


title: 4028693

description: Gene expression data from adults


title: 3880494

description: Gene expression data from adults


title: 3674635

description: Gene expression data from adults


title: 3481233

description: Gene expression data from adults


title: 3529567

description: Gene expression data from adults


title: hv33

description: Gene expression data from adults


title: 3201250

description: Gene expression data from adults


title: 3550595

description: Gene expression data from adults


title: 3606874

description: Gene expression data from adults


title: 3862041

description: Gene expression data from adults


title: 3537939

description: Gene expression data from adults


title: 3179544

description: Gene expression data from adults


title: 3190066

description: Gene expression data from adults


title: 3650

description: Gene expression data from adults


title: 3029442

description: Gene expression data from adults


title: hv48

description: Gene expression data from adults


title: 3019890

description: Gene expression data from adults


title: 3815233

description: Gene expression data from adults


title: 3474652

description: Gene expression data from adults


title: 3457883

description: Gene expression data from adults


title: 3433046

description: Gene expression data from adults


title: 5927

description: Gene expression data from adults


title: 3390

description: Gene expression data from adults


title: 6892

description: Gene expression data from adults


title: 3138950

description: Gene expression data from adults


title: 6890

description: Gene expression data from adults


title: 3272092

description: Gene expression data from adults


title: 3055998

description: Gene expression data from adults


title: 6826

description: Gene expression data from adults


title: 2539

description: Gene expression data from adults


title: 6502

description: Gene expression data from adults


title: hv69

description: Gene expression data from adults


title: hv56

description: Gene expression data from adults


title: 6746

description: Gene expression data from adults


title: hv53

description: Gene expression data from adults


title: hv39

description: Gene expression data from adults


title: hv57

description: Gene expression data from adults


title: 6871

description: Gene expression data from adults


title: hv161

description: Gene expression data from adults


title: 6776

description: Gene expression data from adults


title: 6677

description: Gene expression data from adults


title: 6653

description: Gene expression data from adults


title: 6658

description: Gene expression data from adults


title: hv44

description: Gene expression data from adults


title: 3458598

description: Gene expression data from adults


title: hv43

description: Gene expression data from adults


title: 3386401

description: Gene expression data from adults


title: 6620

description: Gene expression data from adults


title: 6650

description: Gene expression data from adults


title: 4620

description: Gene expression data from adults


title: hv42

description: Gene expression data from adults


title: 4650

description: Gene expression data from adults


title: hv35

description: Gene expression data from adults


title: 4586

description: Gene expression data from adults


title: hv38

description: Gene expression data from adults


title: 6482

description: Gene expression data from adults


title: hv40

description: Gene expression data from adults


title: 4582

description: Gene expression data from adults


title: 6422

description: Gene expression data from adults


title: 4558

description: Gene expression data from adults


title: 5530

description: Gene expression data from adults


title: 4508

description: Gene expression data from adults


title: 4699

description: Gene expression data from adults


title: 4581

description: Gene expression data from adults


title: 5189

description: Gene expression data from adults


title: 4874

description: Gene expression data from adults


title: 4583

description: Gene expression data from adults


title: 6418

description: Gene expression data from adults


title: 4495

description: Gene expression data from adults


title: 6276

description: Gene expression data from adults


title: 5409

description: Gene expression data from adults


title: 4546

description: Gene expression data from adults


title: 4386

description: Gene expression data from adults


title: 4950

description: Gene expression data from adults


title: 5261

description: Gene expression data from adults


title: hv41

description: Gene expression data from adults


title: 4457

description: Gene expression data from adults


title: 3962538

description: Gene expression data from adults


title: 4731

description: Gene expression data from adults


title: 4426

description: Gene expression data from adults


title: 4729

description: Gene expression data from adults


title: 4017646

description: Gene expression data from adults


title: 4328

description: Gene expression data from adults


title: 4231

description: Gene expression data from adults


title: 4321

description: Gene expression data from adults


title: 4232

description: Gene expression data from adults


title: 4288

description: Gene expression data from adults


title: 4078051

description: Gene expression data from adults


title: 4111

description: Gene expression data from adults


title: 3944248

description: Gene expression data from adults


title: 3945035

description: Gene expression data from adults


title: 3823266

description: Gene expression data from adults


title: 3976071

description: Gene expression data from adults


title: 3884620

description: Gene expression data from adults


title: 3815233

description: Gene expression data from adults


title: 4067

description: Gene expression data from adults


title: 3813755

description: Gene expression data from adults


title: 4006

description: Gene expression data from adults


title: 4056

description: Gene expression data from adults


title: 4033

description: Gene expression data from adults


title: 3783662

description: Gene expression data from adults


title: 3605989

description: Gene expression data from adults


title: 3585283

description: Gene expression data from adults


title: hv48

description: Gene expression data from adults


title: 4054

description: Gene expression data from adults


title: 3935

description: Gene expression data from adults


title: 3976

description: Gene expression data from adults


title: 4046

description: Gene expression data from adults


title: 3830

description: Gene expression data from adults


title: 3769063

description: Gene expression data from adults


title: hv41

description: Gene expression data from adults


title: 3861

description: Gene expression data from adults


title: 3546507

description: Gene expression data from adults


title: hv70

description: Gene expression data from adults


title: hv170

description: Gene expression data from adults


title: hv33

description: Gene expression data from adults


title: 3873

description: Gene expression data from adults


title: 3901

description: Gene expression data from adults


title: hv39

description: Gene expression data from adults


title: 3726

description: Gene expression data from adults


title: hv34

description: Gene expression data from adults


title: 6617

description: Gene expression data from adults


title: 3822

description: Gene expression data from adults


title: 3707

description: Gene expression data from adults


title: hv164

description: Gene expression data from adults


title: hv154

description: Gene expression data from adults


title: 3750

description: Gene expression data from adults


title: 3767

description: Gene expression data from adults


title: 3715

description: Gene expression data from adults


title: 3481

description: Gene expression data from adults


title: 3944817

description: Gene expression data from adults


title: hv165

description: Gene expression data from adults


title: 3613

description: Gene expression data from adults


title: hv161

description: Gene expression data from adults


title: 6658

description: Gene expression data from adults


title: hv156

description: Gene expression data from adults


title: hv70

description: Gene expression data from adults


title: 6653

description: Gene expression data from adults


title: 3542

description: Gene expression data from adults


title: hv166

description: Gene expression data from adults


title: 6746

description: Gene expression data from adults


title: 6890

description: Gene expression data from adults


title: 6892

description: Gene expression data from adults


title: 6776

description: Gene expression data from adults


title: 3900569

description: Gene expression data from adults


title: 3424641

description: Gene expression data from adults


title: 3356210

description: Gene expression data from adults


title: 3947374

description: Gene expression data from adults


title: 3471

description: Gene expression data from adults


title: 6620

description: Gene expression data from adults


title: 6617

description: Gene expression data from adults


title: 5254

description: Gene expression data from adults


title: 5230

description: Gene expression data from adults


title: 4850

description: Gene expression data from adults


title: 100262

description: Gene expression data from adults

value: endotoxemia


title: 3763147

description: Gene expression data from adults


title: 100314

description: Gene expression data from adults


title: 4586

description: Gene expression data from adults


title: 4508

description: Gene expression data from adults


title: 100230

description: Gene expression data from adults


title: 4546

description: Gene expression data from adults


title: 4295

description: Gene expression data from adults


title: 4426

description: Gene expression data from adults


title: 3846652

description: Gene expression data from adults


title: 100174

description: Gene expression data from adults


title: 10031B

description: Gene expression data from adults


title: 100316

description: Gene expression data from adults


title: 4373

description: Gene expression data from adults


title: 4471

description: Gene expression data from adults


title: 10026B

description: Gene expression data from adults


title: 4484

description: Gene expression data from adults


title: 4231

description: Gene expression data from adults


title: 1002324

description: Gene expression data from adults


title: 5640_BS

city: Minneapolis

first: Qiyuan

last: Han

state: Minnesota

address: 2231 6th St. Se, Tretyakova lab 2-230

institute: University of Minnesota

library_source: genomic

data_processing:
Reduced representation bisulfite sequencing (RRBS) reads and oxRRBS reads were trimmed of low quality bases and adapter contamination with TrimGalore! 0.4.4_dev (http://www.bioinformatics. babraham.ac.uk/projects/trim_galore/) in paired-end mode, using Cutadapt version 1.8.1. (https://journal.embnet.org/index.php/embnetjournal/article/view/200). Any read pairs where one mate failed quality control were discarded.
Cleaned reads were aligned to the mouse mm10 genome with Bismark version 0.19.0. Resulting alignments were cleaned of PCR duplicates with NuDup (https://github.com/nugentechnologies/nudup), and reads with mapping quality of less than 20 were removed.
Analysis of methylated and hydroxymethylated regions followed the Methpipe analysis pipeline (commit 77d7728e6c52592a71706834d86f5e69183ef082 (Sept 7, 2018))
Genome-wide cytosines were filtered to represent only symmetrically methylated CpG sites. CpG sites that were not covered by at least 10 reads in each sample were discarded. CpG sites were further filtered to exclude sites that occurred within “blacklisted” regions of the mm10 genome assembly (ENCODE file ID ENCFF547MET).
Differentially methylated (DMR) and hydroxymethylated (DhMR) regions were identified by merging consecutive CpGs that crossed the threshold for statistical significance at a false discovery rate of 0.05, and filtering regions with at least three significant CpG sites.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are output from the methcount in the meth pipe analysis, which contains the chromosome location of the CpG sites, fraction numbers of 5mC+5hmC(BS dataset) or 5mC(oxBS dataset) and the corresponding coverage in each CpG site.
Supplementary_files_format_and_content: BS:5mC+5hmC fraction table
Supplementary_files_format_and_content: OXO:5mC fraction table

source_name: proximal colon

growth_protocol: 129S6/SvEvTac-Rag2tm1FwIl10-/- (Rag2-/- / Il10-/-) mice were used and housed in an AAALAC-accredited specific pathogen-free barrier facility. Mice were maintained in polycarbonate microisolator caging (Allentown Caging Equipment Inc., Allentown, NJ) and provided pelleted diet (ProLab 3000, Purina Mills, St. Louis, MO) and filtered water ad libitum.

extract_protocol:
Genomic DNA, total RNA were extracted from approximately 10 mg of proximal colon tissue using AllPrep DNA/RNA mini kit (QIAGEN, Hilden, Germany).
RRBS and oxRRBS libraries were prepared by Ovation® RRBS Methyl-Seq with TrueMethyl® oxBS kit (Tecan, Redwood City, CA) according to the manufacturer’s instructions.

treatment_protocol: Mice aged 6-7 weeks received two doses every other day of 0.2 mL of 2 x 108 fresh inoculums (infected group) or sterile media (control group).

value: Helicobacter. Hepaticus(strain 3B1, ATCC 51449) infection


title: 5639_OXO


title: 10011B

description: Gene expression data from adults


title: 5639_BS


title: 100236

description: Gene expression data from adults


title: 10012B

description: Gene expression data from adults


title: 1000724

description: Gene expression data from adults


title: 100266

description: Gene expression data from adults


title: 100026

description: Gene expression data from adults


title: 1001224

description: Gene expression data from adults


title: 4035

description: Gene expression data from adults


title: MouseSpermONT

city: Rochester

first: Xin

last: Li

state: NY

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

data_processing:
LoRDEC (version 0.5.3, parameters -k 17 -s 3 -a 50000) was used to perform error correction on the long reads (LRs) with short reads (SRs) as input.
The corrected LRs were aligned to the mm10 or hg38 reference genome using GMAP (version 2014-12-24, parameters -t 10 -B 5 -A --nofails -f samse -n1). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The SRs were aligned to the mm10 or hg38 reference genome using HISAT2 (version 2.0.4, parameters --ignore-quals --dta --threads 10 --max-intronlen 150000).
Illumina short reads were quantified using Salmon (v0.8.2), and TPM values were summaized in the processed data table. Sperm samples were further normalized to the renilla spikein number.
SpermPacBio1-6 were combined, and TestisPacBio1-5 were combined.
ONT sequencing reads were aligned to the mouse mm10 reference genome using minimap2 (version 2.11-r797) with parameter "-x splice -a".
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Long reads numbers mapped to each transcript have been summarized into Summary.xlsx table. Transcript TPM values were also summarized in the table.

source_name: sperm

growth_protocol: Mouse sperm samples were acquired from 10-week until 6-month adult male mice. Mice were housed in a temperature (64-79°F) and humidity (30-70%) controlled room with 12 light/12 dark cycle.

extract_protocol:
Before RNA purification, sperm cells were lysed by 1% SDS and 0.1M DTT, with 10 min incubatin on 37 degree. Sperm RNAs were isolated using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina sequencing uses standard RNAseq library construction protocol. Nanopore library was constructed using cDNA-PCR Sequencing Kit (SQK-PCS109, ONT)
PacBio, Illumina RNAseq and Oxford Nanopore Technologies

value: adult

tag: tissue/cell type

value: cauda sperm

tag: molecule subtype

value: full length RNA


title: 4046

description: Gene expression data from adults


title: 10002B

description: Gene expression data from adults


title: 100172

description: Gene expression data from adults


title: 100070

description: Gene expression data from adults


title: 3823

description: Gene expression data from adults


title: 100076

description: Gene expression data from adults


title: 100120

description: Gene expression data from adults


title: 3613

description: Gene expression data from adults


title: MSK-PCa1_pdx_vinblastine-perister_repl_3

city: Boston

first: Eugen

last: Dhimolea

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
prostate cancer PDX tissue
20170714_PrCa1Xeno_Vinbl3_ED4436-2_S12

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Differential gene expression analysis for the RNA-seq data using the bioconductor DEseq2 package
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Prostate cancer PDX

growth_protocol: Cancer cells were grown in 2D cultures or in matrigel alone in either  DMEM/10% FBS (for cell lines) or organoid medium (for patient-derived cells).

extract_protocol:
The gels collected at the end of treatment and were mechanicaly and enzymatically disintegrated. Xenograft/PDX tissues were isolated from harvested tumors at the end of treatment. Next, the RNA was extracted from the tumor cells using RNA extraction kit (Qiagen), The lysates from in vitro samples were also supplemented with ERCC RNA spike-in mix to adjust for the cell number. RNA was sequenced using Illumina NextSeq 500 Next Gen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO, docetaxel (100nM), afatinib (100nM)

tag: cell line

tag: culture setting

value: vinblastine-persister PDX tumors


title: 2539

description: Gene expression data from adults


title: 3976

description: Gene expression data from adults


title: MSK-PCa1_pdx_vinblastine-perister_repl_2

description:
prostate cancer PDX tissue
20170714_PrCa1Xeno_Vinbl2_ED4436-2_S11


title: 10017B

description: Gene expression data from adults


title: MSK-PCa1_pdx_vinblastine-perister_repl_1

description:
prostate cancer PDX tissue
20170720_PrCa1Xeno_Vinbl1_ED4436-3_S1


title: 5640_OXO


title: 100122

description: Gene expression data from adults


title: 5638_OXO


title: 5638_BS


title: MSK-PCa1_pdx_vehicle_repl_3

description:
prostate cancer PDX tissue
20170719_PrCa1Xeno_Veh3_ED4436-3_S1

value: untreated PDX tumors


title: 5626_OXO

value: sterile media


title: 3197090

description: Gene expression data from adults

value: female

value: blood


title: MSK-PCa1_pdx_vehicle_repl_2

description:
prostate cancer PDX tissue
20170714_PrCa1Xeno_Veh2_ED4436-2_S8


title: 100312

description: Gene expression data from adults

value: male


title: 100234

description: Gene expression data from adults


title: MSK-PCa1_pdx_vehicle_repl_1

description:
prostate cancer PDX tissue
20170714_PrCa1Xeno_Veh1_ED4436-2_S7


title: 5626_BS


title: 100310

description: Gene expression data from adults


title: 5625_OXO


title: 1003124

description: Gene expression data from adults


title: 100072

description: Gene expression data from adults


title: HCI003_pdx_afatinib-perister_repl_3

description:
breast cancer PDX tissue
20161113_A5_ED3663_S3

source_name: Breast cancer PDX

value: afatinib-persister PDX tumors


title: 10007B

description: Gene expression data from adults


title: 5625_BS


title: HCI003_pdx_afatinib-perister_repl_2

description:
breast cancer PDX tissue
20161113_A4_ED3663_S2


title: 5624_OXO


title: HCI003_pdx_afatinib-perister_repl_1

description:
breast cancer PDX tissue
20161113_A1_ED3663_S1


title: 5624_BS


title: HCI003_pdx_vehicle_repl_3

description:
breast cancer PDX tissue
20161113_V4_ED3663_S6


title: 100232

description: Gene expression data from adults


title: hv157

description: Gene expression data from adults


title: 3263354

description: Gene expression data from adults


title: 1001724

description: Gene expression data from adults


title: HCI003_pdx_vehicle_repl_1

description:
breast cancer PDX tissue
20161113_V1_ED3663_S4


title: 5746

description: Gene expression data from adults

value: sepsis


title: 3182559

description: Gene expression data from adults


title: 3174398

description: Gene expression data from adults


title: 3215498

description: Gene expression data from adults


title: 3241087

description: Gene expression data from adults


title: 3008502

description: Gene expression data from adults


title: 3111443

description: Gene expression data from adults


title: MDAMB231_xenograft_docetaxel-perister_repl_3

description:
breast cancer xenograft tissue
20181127_MDAMB231_Xeno_Docet_C_ED6344_S18

source_name: Breast cancer xenograft

value: docetaxel-persister xenograft tumors


title: 3082897

description: Gene expression data from adults


title: HCI003_pdx_vehicle_repl_2

description:
breast cancer PDX tissue
20161113_V2_ED3663_S5


title: 4206

description: Gene expression data from adults


title: RH090_NEU_DM

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
D6
Gene expression data from human temporal cortex neurones

hyb_protocol: 12µg of cRNA molecules were heat fragmented and applied to the Human U133 plus 2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the AGCC software package to prepare the .CEL files

data_processing: The data were analyzed with Transcriptome Analysis Console v4.1.1 (Affymetrix) using Robust Multi-Array Average (RMA) as normalization method.

source_name: Diabetic Neurones

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix IVT protocol

extract_protocol:
Immuno directed laser capture microdissection was used to isolate total RNA from neurones, astrocytes and endothelial cells.
RNA was isolated using the Arcturus PicoPure RNA isolation kit according to manufacturer’s protocol.

value: Laser captured cells from human temporal cortex

value: Diabetic material


title: 3007078

description: Gene expression data from adults

source_name: blood


title: MDAMB231_xenograft_docetaxel-perister_repl_2

description:
breast cancer xenograft tissue
20181127_MDAMB231_Xeno_Docet_B_ED6344_S17


title: MDAMB231_xenograft_docetaxel-perister_repl_1

description:
breast cancer xenograft tissue
20181127_MDAMB231_Xeno_Docet_A_ED6344_S16


title: MDAMB231_xenograft_vehicle_repl_3

description:
breast cancer xenograft tissue
20181127_MDAMB231_Xeno_Veh_C_ED6344_S15

value: untreated xenograft tumors


title: 4087

description: Gene expression data from adults

value: patient


title: RH076_NEU_DM

description:
D5
Gene expression data from human temporal cortex neurones


title: 4109

description: Gene expression data from adults


title: MDAMB231_xenograft_vehicle_repl_2

description:
breast cancer xenograft tissue
20181127_MDAMB231_Xeno_Veh_B_ED6344_S14


title: RH001_NEU_DM

description:
D3
Gene expression data from human temporal cortex neurones


title: 3934

description: Gene expression data from adults


title: 3583

description: Gene expression data from adults


title: MDAMB231_xenograft_vehicle_repl_1

description:
breast cancer xenograft tissue
20181127_MDAMB231_Xeno_Veh_A_ED6344_S13


title: 3701

description: Gene expression data from adults


title: RH023_NEU_DM

description:
D4
Gene expression data from human temporal cortex neurones


title: NA041/98_NEU_DM

description:
D2
Gene expression data from human temporal cortex neurones


title: 6582

description: Gene expression data from adults


title: 3676

description: Gene expression data from adults


title: 3499

description: Gene expression data from adults


title: 6497

description: Gene expression data from adults


title: MDAMB231_OR10G3_KO_vehicle_repl_3

description:
breast cancer cells from 2D culture
20181127_MDAMB231_OR42_C_ED6344_S6

source_name: Breast cancer cell line

value: Gene KO in 2D culture


title: RH028_NEU_CTRL

description:
C5
Gene expression data from human temporal cortex neurones

source_name: Control Neurones

value: Normal control material


title: NA263/99_NEU_DM

description:
D1
Gene expression data from human temporal cortex neurones


title: 6556

description: Gene expression data from adults


title: NA047/97_NEU_CTRL

description:
C4
Gene expression data from human temporal cortex neurones


title: 6548

description: Gene expression data from adults


title: 6452

description: Gene expression data from adults


title: 4061994

description: Gene expression data from adults


title: MDAMB231_OR10G3_KO_vehicle_repl_2

description:
breast cancer cells from 2D culture
20181127_MDAMB231_OR42_B_ED6344_S5


title: NA231/93_NEU_CTRL

description:
C3
Gene expression data from human temporal cortex neurones


title: 6537

description: Gene expression data from adults


title: MDAMB231_OR10G3_KO_vehicle_repl_1

description:
breast cancer cells from 2D culture
20181127_MDAMB231_OR42_A_ED6344_S4


title: MDAMB231_MYC_KO_vehicle_repl_2

description:
breast cancer cells from 2D culture
20181127_MDAMB231_MYC1_B_ED6344_S2


title: MDAMB231_MYC_KO_vehicle_repl_3

description:
breast cancer cells from 2D culture
20181127_MDAMB231_MYC1_C_ED6344_S3


title: MDAMB231_MYC_KO_vehicle_repl_1

description:
breast cancer cells from 2D culture
20181127_MDAMB231_MYC1_A_ED6344_S1


title: 6448

description: Gene expression data from adults


title: PM154_org_docetaxel-perister_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20170714_PM154Org_Docetax3_ED4436-2_S18

source_name: Prostate cancer patient-derived organoids

value: docetaxel-persister 3D organoids


title: NA023/94_NEU_CTRL

description:
C2
Gene expression data from human temporal cortex neurones


title: 6489

description: Gene expression data from adults


title: 6430

description: Gene expression data from adults


title: PM154_org_docetaxel-perister_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20170714_PM154Org_Docetax2_ED4436-2_S17


title: 6303

description: Gene expression data from adults


title: 3204833

description: Gene expression data from adults

value: noninfectious


title: 6414

description: Gene expression data from adults


title: 6366

description: Gene expression data from adults


title: 6171

description: Gene expression data from adults


title: 6196

description: Gene expression data from adults


title: 6194

description: Gene expression data from adults


title: NA201/95_NEU_CTRL

description:
C1
Gene expression data from human temporal cortex neurones


title: 6331

description: Gene expression data from adults


title: RH076_BV_DM

description:
D5
Gene expression data from human temporal cortex endothelial cells

source_name: Diabetic Endothelial cells


title: 6200

description: Gene expression data from adults


title: 6429

description: Gene expression data from adults


title: RH090_BV_DM

description:
D6
Gene expression data from human temporal cortex endothelial cells


title: 6110

description: Gene expression data from adults


title: 6268

description: Gene expression data from adults


title: RH001_BV_DM

description:
D3
Gene expression data from human temporal cortex endothelial cells


title: RH023_BV_DM

description:
D4
Gene expression data from human temporal cortex endothelial cells


title: PM154_org_docetaxel-perister_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20170630_PM154Org_Docetax1_ED4436_S16


title: PM154_org_vehicle_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20170714_PM154Org_Veh1_ED4436-2_S13

value: untreated 3D organoids


title: PM154_org_vehicle_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20170714_PM154Org_Veh2_ED4436-2_S14


title: 6057

description: Gene expression data from adults


title: PM154_org_vehicle_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20170714_PM154Org_Veh3_ED4436-2_S15


title: MSK-PCa7_org_docetaxel-perister_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20161004_PrCa7_D_2_ED3476-1_S4


title: RH028_BV_CTRL

description:
C5
Gene expression data from human temporal cortex endothelial cells

source_name: Control Endothelial cells


title: 6086

description: Gene expression data from adults


title: MSK-PCa7_org_docetaxel-perister_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20161004_PrCa7_D_1_ED3476-1_S3


title: NA047/97_BV_CTRL

description:
C4
Gene expression data from human temporal cortex endothelial cells


title: 6048

description: Gene expression data from adults


title: 3195743

description: Gene expression data from adults


title: 6069

description: Gene expression data from adults


title: 3220700

description: Gene expression data from adults


title: NA023/94_BV_CTRL

description:
C2
Gene expression data from human temporal cortex endothelial cells


title: 5950

description: Gene expression data from adults


title: 5894

description: Gene expression data from adults


title: 6018

description: Gene expression data from adults


title: NA41/98_BV_DM

description:
D2
Gene expression data from human temporal cortex endothelial cells


title: RH090_AST_DM

description:
D6
Gene expression data from human temporal cortex astrocytes

source_name: Diabetic Astrocytes


title: NA231/93_BV_CTRL

description:
C3
Gene expression data from human temporal cortex endothelial cells


title: NA201/95_BV_CTRL

description:
C1
Gene expression data from human temporal cortex endothelial cells


title: 5957

description: Gene expression data from adults


title: 3847

description: Gene expression data from adults


title: 5899

description: Gene expression data from adults


title: 5945

description: Gene expression data from adults


title: MSK-PCa7_org_docetaxel-perister_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20161005_PrCa7_D_3_ED3476-2_S2


title: MSK-PCa7_org_vehicle_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20161005_PrCa7_V_3_ED3476-2_S1


title: 6164

description: Gene expression data from adults


title: MSK-PCa7_org_vehicle_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20161004_PrCa7_V_2_ED3476-1_S2


title: 5881

description: Gene expression data from adults


title: MSK-PCa7_org_vehicle_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20161004_PrCa7_V_1_ED3476-1_S1


title: MSK-PCa3_org_docetaxel-perister_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa3Org_Doc3_ED3996-1_S11


title: 5916

description: Gene expression data from adults


title: MSK-PCa3_org_docetaxel-perister_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa3Org_Doc1_ED3996-1_S9


title: 5872

description: Gene expression data from adults


title: RH076_AST_DM

description:
D5
Gene expression data from human temporal cortex astrocytes


title: 6101

description: Gene expression data from adults


title: hv194

description: Gene expression data from adults

value: healthy


title: RH001_AST_DM

description:
D3
Gene expression data from human temporal cortex astrocytes


title: hv203

description: Gene expression data from adults


title: MSK-PCa3_org_vehicle_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa3Org_Veh3_ED3996-1_S8


title: hv231

description: Gene expression data from adults


title: hv230

description: Gene expression data from adults


title: hv111

description: Gene expression data from adults


title: hv162

description: Gene expression data from adults


title: hv201

description: Gene expression data from adults


title: hv119

description: Gene expression data from adults


title: hv158

description: Gene expression data from adults


title: NA047/97_AST_CTRL

description:
C4
Gene expression data from human temporal cortex astrocytes

source_name: Control Astrocytes


title: MSK-PCa3_org_docetaxel-perister_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa3Org_Doc2_ED3996-1_S10


title: RH023_AST_DM

description:
D4
Gene expression data from human temporal cortex astrocytes


title: NA41/98_AST_DM

description:
D2
Gene expression data from human temporal cortex astrocytes


title: MSK-PCa3_org_vehicle_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa3Org_Veh2_ED3996-1_S7


title: 5864

description: Gene expression data from adults


title: 5907

description: Gene expression data from adults


title: 5733

description: Gene expression data from adults


title: NA231/93_AST_CTRL

description:
C3
Gene expression data from human temporal cortex astrocytes


title: MSK-PCa3_org_vehicle_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa3Org_Veh1_ED3996-1_S6


title: NA263/99_AST_DM

description:
D1
Gene expression data from human temporal cortex astrocytes


title: NA023/94_AST_CTRL

description:
C2
Gene expression data from human temporal cortex astrocytes


title: 4554

description: Gene expression data from adults


title: hv232

description: Gene expression data from adults


title: 6594

description: Gene expression data from adults


title: RH028_AST_CTRL

description:
C5
Gene expression data from human temporal cortex astrocytes


title: MSK-PCa1_org_docetaxel-perister_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa1Org_Doc1_ED3996-1_S18


title: MSK-PCa1_org_docetaxel-perister_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa1Org_Doc3_ED3996-1_S5


title: ICI-R_1

first: xianfeng

last: chen

state: MN

address: 1216 2nd St SW

department: Biochem & Molecular Biology

institute: Mayo Clinic

data_processing:
Transcript read quality was assessed using fastqc (v0.11.8), aligned using  bowtie-2 (v2.3.3.1) to grch38, features determined using featureCounts (v2.0.1), comparisons between samples were performed using edgeR (v3.28.1), transcripts were filtered using edgeR filterByExpr(), exact test was performed with doubletail rejection region and dispersion calculated automatically
Genome_build: grch38
Supplementary_files_format_and_content: expression raw count

growth_protocol: Cells were cultured in phenol red-free DMEM/F12 media containing 10% FBS and 1% antibiotic/antimycotic, in a humidified 37°C incubator with 5% CO2

extract_protocol: RNA was harvested from cell pellets using TRIzol reagent and purified using the Qiagen miRNeasy mini kit (Cat# 217004)

treatment_protocol: Cells were chronically treated for 24 months with 0.1% ethanol vehicle, 1uM Z-endoxifen, 1uM 4HT, or 1uM ICI

value: ICI (1microM)

tag: treatment duration

value: 24 months


title: ICI-R_2


title: MSK-PCa1_org_vehicle_repl_3

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa1Org_Veh3_ED3996-1_S3


title: NA263/99_BV_DM

description:
D1
Gene expression data from human temporal cortex endothelial cells


title: ICI-R_3


title: 4HT-R_3

value: 4HT (1microM)


title: MSK-PCa1_org_vehicle_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa1Org_Veh2_ED3996-1_S2


title: 4HT-R_2


title: MSK-PCa1_org_vehicle_repl_1

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa1Org_Veh1_ED3996-1_S1


title: 3178279

description: Gene expression data from adults

value: blood


title: 6413

description: Gene expression data from adults

value: female


title: MSK-PCa1_org_docetaxel-perister_repl_2

description:
prostate cancer cells isolated from 3D mono-culture
20170417_PrCa1Org_Doc2_ED3996-1_S4


title: 3175920

description: Gene expression data from adults


title: 3986

description: Gene expression data from adults

value: male


title: 6597

description: Gene expression data from adults


title: HCI011_org_docetaxel-perister_repl_3

description:
breast cancer cells isolated from 3D co-culture
20161004_HCI011_W_3_ED3476-1_S15

source_name: Breast cancer PDX-derived organoids


title: ENDX-R_3

value: Endoxifen (1microM)


title: NA201/95_AST_CTRL

description:
C1
Gene expression data from human temporal cortex astrocytes

value: Laser captured cells from human temporal cortex


title: 6641

description: Gene expression data from adults


title: 3167665

description: Gene expression data from adults


title: 3305204

description: Gene expression data from adults


title: 6636

description: Gene expression data from adults

value: sepsis


title: 3371213

description: Gene expression data from adults


title: ENDX-R_2


title: 3292348

description: Gene expression data from adults


title: 4771

description: Gene expression data from adults


title: HCI011_org_docetaxel-perister_repl_2

description:
breast cancer cells isolated from 3D co-culture
20161005_HCI011_W_2_ED3476-2_S12


title: ENDX-R_1


title: HCI011_org_docetaxel-perister_repl_1

description:
breast cancer cells isolated from 3D co-culture
20161005_HCI011_W_1_ED3476-2_S11


title: 3478108

description: Gene expression data from adults


title: 3039518

description: Gene expression data from adults


title: HCI011_org_vehicle_repl_3

description:
breast cancer cells isolated from 3D mono-culture
20161005_HCI011_V_3_ED3476-2_S8


title: 4HT-R_1


title: 3302157

description: Gene expression data from adults


title: 3880674

description: Gene expression data from adults


title: 3038669

description: Gene expression data from adults


title: 3050909

description: Gene expression data from adults


title: 3564073

description: Gene expression data from adults


title: Vehicle Control_2

value: Ethanol vehicle


title: HCI011_org_vehicle_repl_2

description:
breast cancer cells isolated from 3D mono-culture
20161005_HCI011_V_2_ED3476-2_S7


title: HCI011_org_vehicle_repl_1

description:
breast cancer cells isolated from 3D mono-culture
20161004_HCI011_V_1_ED3476-1_S13


title: Vehicle Control_1


title: HCI003_org_afatinib-perister_repl_3

description:
breast cancer cells isolated from 3D co-culture
20161115_HCI003_A_3_ED3694_S6

value: afatinib-persister 3D organoids


title: 3097232

description: Gene expression data from adults

value: patient


title: 3086154

description: Gene expression data from adults


title: HCI003_org_afatinib-perister_repl_1

description:
breast cancer cells isolated from 3D co-culture
20161115_HCI003_A_1_ED3694_S4


title: Selex_final

city: Xi’an, Shaanxi

first: Chong

last: Xue

address: 169 Changlexi Road

department: Department of Occupational and Environmental Health

country: China

institute: Fourth Military Medical University

description: affinity-selection of target (motif or molecule) that binds to CIRBP

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2
MiClip (version 1.3) was employed to perform peak calling.Then using ANNOVAR（2012-10-23）to annotate the Peaks.The nucleotides in Peaks region were used for detection of the consensus motif by findMotifsGenome.pl in Homer.
Genome_build: hg19
Supplementary_files_format_and_content: peak_annotation text files
Supplementary_files_format_and_content: tab-delimited text files include results of Kegg, GO and motif analysis.

source_name: purified recombinant human Cirbp (His-tagged) protein

extract_protocol:
Recombinant human Cirbp (His-tagged) protein bound to Ni-NTA magnetic beads (Thermo, USA) was applied to adsorb specifically-bound RNAs. Following several washing with binding buffer, the purified RNAs were eluted by TRIzol extraction, ethanol precipitated and then resuspended in RNase-free water adding DNase for reaction.
The RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®(Life Technologies, USA) and then sequenced on Illumina （Illumina,USA）platformat with single-end 50bp at Ribobio Co. Ltd (Ribobio, China).

value: Ni-NTA magnetic beads (Thermo, USA)

tag: amplification

value: PCR-amplified

tag: library

value: 30-nt random sequences,10^14-10^15


title: 3280677

description: Gene expression data from adults


title: 3147956

description: Gene expression data from adults


title: HCI003_org_docetaxel-perister_repl_3

description:
breast cancer cells isolated from 3D co-culture
20170417_HCI003Org_Doc3_ED3996-2_S11

value: docetaxel-persister 3D organoids


title: HCI003_org_afatinib-perister_repl_2

description:
breast cancer cells isolated from 3D co-culture
20161115_HCI003_A_2_ED3694_S5


title: HCI003_org_docetaxel-perister_repl_2

description:
breast cancer cells isolated from 3D co-culture
20170417_HCI003Org_Doc2_ED3996-2_S9


title: HCI003_org_docetaxel-perister_repl_1

description:
breast cancer cells isolated from 3D co-culture
20170417_HCI003Org_Doc1_ED3996-2_S8


title: 3419205

description: Gene expression data from adults


title: HCI003_org_vehicle_repl_3

description:
breast cancer cells isolated from 3D mono-culture
20161115_HCI003_V_3_ED3694_S3

value: untreated 3D organoids


title: HCI003_org_vehicle_repl_2

description:
breast cancer cells isolated from 3D mono-culture
20161115_HCI003_V_2_ED3694_S2


title: 3415746

description: Gene expression data from adults


title: HCI003_org_vehicle_repl_1

description:
breast cancer cells isolated from 3D mono-culture
20161115_HCI003_V_1_ED3694_S1


title: 3577539

description: Gene expression data from adults


title: 3490886

description: Gene expression data from adults


title: 3623917

description: Gene expression data from adults


title: HCI002_org_docetaxel-perister_repl_2

description:
breast cancer cells isolated from 3D co-culture
20170417_HCI002Org_Doc2_ED3996-2_S7


title: 3363099

description: Gene expression data from adults


title: 3639155

description: Gene expression data from adults


title: 3360593

description: Gene expression data from adults


title: 3456820

description: Gene expression data from adults


title: 3453835

description: Gene expression data from adults


title: 3730247

description: Gene expression data from adults


title: 3651817

description: Gene expression data from adults


title: 3576217

description: Gene expression data from adults


title: 3483709

description: Gene expression data from adults


title: 3743873

description: Gene expression data from adults

value: noninfectious


title: 3150383

description: Gene expression data from adults


title: 3454267

description: Gene expression data from adults


title: HCI002_org_docetaxel-perister_repl_1

description:
breast cancer cells isolated from 3D co-culture
20170417_HCI002Org_Doc1_ED3996-2_S6


title: 3285624

description: Gene expression data from adults


title: 3149638

description: Gene expression data from adults


title: HCI002_org_vehicle_repl_2

description:
breast cancer cells isolated from 3D mono-culture
20170417_HCI002Org_Veh2_ED3996-2_S5


title: 3273867

description: Gene expression data from adults


title: HCI002_org_vehicle_repl_1

description:
breast cancer cells isolated from 3D mono-culture
20170417_HCI002Org_Veh1_ED3996-2_S4


title: 3300871

description: Gene expression data from adults


title: 4088

description: Gene expression data from adults


title: 4932

description: Gene expression data from adults


title: 3755

description: Gene expression data from adults


title: 3447051

description: Gene expression data from adults


title: 4218

description: Gene expression data from adults


title: MDAMB231_org_vehicle_repl_2

description:
breast cancer cells isolated from 3D mono-culture
20170417_MDAMB231Org_Veh2_ED3996-2_S2


title: MDAMB231_org_docetaxel-perister_repl_3

description:
breast cancer cells isolated from 3D co-culture
20170417_MDAMB231Org_Doc3_ED3996-2_S13


title: MDAMB231_org_vehicle_repl_3

description:
breast cancer cells isolated from 3D mono-culture
20170417_MDAMB231Org_Veh3_ED3996-2_S3


title: MDAMB231_org_vehicle_repl_1

description:
breast cancer cells isolated from 3D mono-culture
20170417_MDAMB231Org_Veh1_ED3996-2_S1


title: MDAMB231_org_docetaxel-perister_repl_1

description:
breast cancer cells isolated from 3D co-culture
20170417_MDAMB231Org_Doc1_ED3996-2_S10


title: MDAMB231_org_docetaxel-perister_repl_2

description:
breast cancer cells isolated from 3D co-culture
20170417_MDAMB231Org_Doc2_ED3996-2_S12


title: hv204

description: Gene expression data from adults

value: healthy


title: hv211

description: Gene expression data from adults


title: hv113

description: Gene expression data from adults


title: ChIP-seq WT  HCF1N rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description:
Cre-ERT2, MYC-WT cells; 24 hours +4-OHT
HCF1N-rep3.narrowpeak

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample

source_name: Burkitt lymphoma cell line

growth_protocol: Ramos cells were maintained in RPMI 1640 + 10% FBS + penicillin/streptomycin. Cells carrying Cre-ERT2 were additionally maintained in 100 μg/ml hygromycin, and MYC switchable cells (WT, 4A, VP16 HBM) in 150 ng/ml puromycin.

extract_protocol:
For RNA-seq of tumor-derived samples, extraction was performed by Genewiz. Other RNA-seq extractions were performed using TRIzol. For ChIP-seq experiments, cells crosslinked in 1% formaldehyde were subject to sonication, and the resulting sheared chromatin was combined overnight with antibody.
For RNA-seq of tumor-derived or MYC switchable cells (WT, 4A, VP16 HBM), rRNA depletion and library preparation were performed by Genewiz. For RNA-seq of untagged/HCF1N-tagged samples, library preparation was performed by Vanderbilt Technologies for Advanced Genomics (VANTAGE). ChIP-seq libraries were prepared using NEBnext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina.

treatment_protocol: See individual samples for relevant treatment protocol

tag: cells

value: Ramos cells

tag: engineered genotype

value: Cre-ERT2, MYC-WT

value: 20 nM 4-OHT for 24 hours

tag: antibody


title: hv183

description: Gene expression data from adults

tag: age

value: female

tag: treatment

tag: tissue

value: blood


title: hv144

description: Gene expression data from adults

tag: gender

tag: disease state


title: hv220

description: Gene expression data from adults


title: ChIP-seq WT HCF1N rep1

description:
Cre-ERT2, MYC-WT cells; 24 hours +4-OHT
HCF1N-rep1.narrowpeak


title: hv225

description: Gene expression data from adults

value: male


title: hv118

description: Gene expression data from adults


title: hv226

description: Gene expression data from adults


title: 3872240

description: Gene expression data from adults


title: ChIP-seq parental IgG rep2

description: Cre-ERT2 cells; 24 hours +4-OHT

value: IgG


title: ChIP-seq  parental IgG rep3

description: Cre-ERT2 cells; 24 hours +4-OHT


title: ChIP-seq WT  HCF1N rep2

description:
Cre-ERT2, MYC-WT cells; 24 hours +4-OHT
HCF1N-rep2.narrowpeak


title: hv153

description: Gene expression data from adults


title: hv136

description: Gene expression data from adults


title: hv202

description: Gene expression data from adults


title: hv233

description: Gene expression data from adults


title: hv143

description: Gene expression data from adults


title: ChIP-seq parental IgG rep1

description: Cre-ERT2 cells; 24 hours +4-OHT


title: MYBBP1A replicate 2.BJ fibroblasts

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description:
Mybbp1a-Input.BJ.Pooled.NoBL.bed
Mybbp1a.BJ.Rep2.bw

data_processing:
Alignment: data were aligned using bowtie2 v2.3.4.1 with parameters -p 16 --local -X 1000
Quality filtering: aligned data were subjected to a MAPQ filter of 5 using samtools view (samtools version 1.1)
PCR duplicate removal: data were combined across four NextSeq lanes and sorted by reference (tag ID) using samtools merge and duplicates were removed with PICARD MarkDuplicates with option REMOVE_DUPLICATES=True (PICARD version was 2.21.3-SNAPSHOT)
Track creation: genome maps were created using BEDtools genomeCoverageBed -bg and then samples were adjusted for library size by multiplying each count by the RPM; maps were then subtracted chIP-input, sorted using UCSC Genome Browser tools' bedSort and converted to bigWig format using UCSC Genome Browser tools' bedGraphToBigWig
Peak calling: peaks were called using MACS2 v2.1.0 with parameters -f BAM -g hs -s 37 -q 0.01 and using the input as a control sample; spreadsheets were then filtered at FDR < 1% and BED files of filtered peaks were produced; peaks from two replicates were then merged using UNIX cat and overlapping regions were merged, and finally bedtools intersect -wa -v was used to remove any peaks with overlap with ENCODE blacklist regions as described at https://sites.google.com/site/anshulkundaje/projects/blacklists
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files are library size-adjusted, input-subtracted tracks of Mybbp1a signal; BED files are peak calls for pooled replicates that do not overlap with ENCODE blacklist sites

source_name: Fibroblast cells

growth_protocol: HS766T cells were passaged in DMEM high glucose supplemented with 10% FBS and Penn/strep. Cells were split at 90% confluency into 15cm dish prior to fixation and collection.

extract_protocol:
For isolation of chromatin, cells were lysed with lysis buffer (10 mM HEPES pH 7.4, 10 mM KCl, 0.05% NP-40) with protease inhibitor cocktail (Roche) for 30 minutes and nuclei were collected by centrifugation at 600 g for 10 minutes. Nuclear lysis was performed with low salt buffer (10 mM Tris-HCl pH 7.4, 0.2 mM MgCl2, 1% TritonTM-X100) with protease inhibitor cocktail for 30 minutes and chromatin was collected by centrifugation at 5000 g for 10 minutes. Chromatin was resuspended in NP-40 lysis buffer (50mM Tris-HCl pH 8.0, 150mM NaCl, 1% NP-40) and sonicated with S220 Focused Ultrasonicator (Covaris) with settings: incident peak power: 140, duty cycle: 5%, burst/cycle: 200 for optimal chromatin size of 200 to 500bp in length. Cell debris was then pelleted by centrifugation at 8000 g for 10 minutes at 4°C.
50ng of each biological replicate was used for library preparation using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BiolabsE7370S), and amplified using 10 cycles of PCR using NEBNext Multiplex Oligos for Illumina (New England Biolabs E7335S andE7500S). DNA was size-selected using Agencourt AmpureXP beads (Beckman Coulter A63881), following the protocol in the NEBNext Ultra kit for a 200-bp to 600bp average insert size. Library fragment size distribution was assessed on a Bioanalyzer 2100 instrument (Agilent Technologies), using the DNA 1000 kit (Agilent Technologies 5067-1504). Quantification of libraries was performed using the NEBNext Quant Kit for Illumina® (NEB E7630L).

value: BJ fibroblasts cell line

tag: chip antibody

value: Sigma HPA005466

tag: genetic background

value: WT

tag: replicate


title: 3272140

description: Gene expression data from adults

value: patient


title: hv141

description: Gene expression data from adults


title: 3938

description: Gene expression data from adults

value: sepsis


title: hv139

description: Gene expression data from adults


title: hv192

description: Gene expression data from adults


title: 3898

description: Gene expression data from adults


title: 3004993

description: Gene expression data from adults


title: 3651

description: Gene expression data from adults


title: MYBBP1A replicate 1.BJ fibroblasts

description:
Mybbp1a-Input.BJ.Pooled.NoBL.bed
Mybbp1a.BJ.Rep1.bw


title: hv140

description: Gene expression data from adults


title: 4025

description: Gene expression data from adults


title: Input replicate 2. BJ fibroblasts


title: 3943

description: Gene expression data from adults


title: 4027

description: Gene expression data from adults


title: 4162

description: Gene expression data from adults


title: hv145

description: Gene expression data from adults


title: hv146

description: Gene expression data from adults


title: MYBBP1A replicate 1.BxPC3

description:
Mybbp1a-Input.BxPC3.Pooled.NoBL.bed
Mybbp1a.BxPC3.Rep1.bw

source_name: Pancreatic cancer cells

value: BXPC3 PDAC cell line


title: MYBBP1A replicate 2.BxPC3

description:
Mybbp1a-Input.BxPC3.Pooled.NoBL.bed
Mybbp1a.BxPC3.Rep2.bw


title: Vehicle Control_3

value: Ethanol vehicle

value: 24 months


title: 3297275

description: Gene expression data from adults

value: noninfectious


title: MYBBP1A replicate 2.ASPC1

description:
Mybbp1a-Input.ASPC1.Pooled.NoBL.bed
Mybbp1a.ASPC1.Rep2.bw

value: ASPC1 PDAC cell line


title: MYBBP1A replicate 1.ASPC1

description:
Mybbp1a-Input.ASPC1.Pooled.NoBL.bed
Mybbp1a.ASPC1.Rep1.bw


title: hv112

description: Gene expression data from adults

value: healthy


title: 4051

description: Gene expression data from adults


title: Input replicate 1. BJ fibroblasts


title: hv151

description: Gene expression data from adults


title: hv163

description: Gene expression data from adults


title: Input replicate 2. ASPC1


title: 5039

description: Gene expression data from adults


title: hv148

description: Gene expression data from adults


title: Input replicate 1. ASPC1


title: MYBBP1A replicate 2.PANC1

description:
Mybbp1a-Input.PANC1.Pooled.NoBL.bed
Mybbp1a.PANC1.Rep2.bw

value: PANC1 PDAC cell line


title: hv115

description: Gene expression data from adults


title: hv110

description: Gene expression data from adults


title: hv114

description: Gene expression data from adults


title: hv176

description: Gene expression data from adults


title: 3457883

description: Gene expression data from adults


title: MYBBP1A replicate 1.PANC1

description:
Mybbp1a-Input.PANC1.Pooled.NoBL.bed
Mybbp1a.PANC1.Rep1.bw


title: hv116

description: Gene expression data from adults


title: Input replicate 2. PANC1


title: 5657

description: Gene expression data from adults


title: 3550595

description: Gene expression data from adults


title: 3880494

description: Gene expression data from adults


title: Input replicate 1. PANC1


title: MYBBP1A replicate 2.HS766 WT

description:
Mybbp1a-Input.HS766_WT.Pooled.NoBL.bed
Mybbp1a.HS766T_WT.Rep2.bw

value: HS766T PDAC cell line


title: MYBBP1A replicate 2.HS766T Hemi #2

description:
Mybbp1a-Input.HS766_C4.Pooled.NoBL.bed
Mybbp1a.HS766T_C4.Rep2.bw

value: Mybbp1a Hemizygous #2


title: MYBBP1A replicate 2.HS766T Hemi #1

description:
Mybbp1a-Input.HS766_C3.Pooled.NoBL.bed
Mybbp1a.HS766T_C3.Rep2.bw

value: Mybbp1a Hemizygous #1


title: 3055998

description: Gene expression data from adults

value: female

value: blood


title: Input replicate 2.HS766T Hemi #2


title: Input replicate 2.HS766T WT


title: MYBBP1A replicate 1.HS766T Hemi #1

description:
Mybbp1a-Input.HS766_C3.Pooled.NoBL.bed
Mybbp1a.HS766T_C3.Rep1.bw


title: 4028693

description: Gene expression data from adults


title: MYBBP1A replicate 1.HS766 WT

description:
Mybbp1a-Input.HS766_WT.Pooled.NoBL.bed
Mybbp1a.HS766T_WT.Rep1.bw


title: 3674635

description: Gene expression data from adults

value: male


title: Input replicate 1.HS766T Hemi #1


title: Input replicate 1.HS766T Hemi #2

description:
Mybbp1a-Input.HS766_C4.Pooled.NoBL.bed
Mybbp1a.HS766T_C4.Rep1.bw


title: 4706

description: Gene expression data from adults


title: Input replicate 2.HS766T Hemi #1


title: 3544017

description: Gene expression data from adults


title: Input replicate 1.HS766T WT


title: Input replicate 1. BxPC3


title: 3529567

description: Gene expression data from adults


title: 6913

description: Gene expression data from adults


title: 3481233

description: Gene expression data from adults


title: 3606874

description: Gene expression data from adults


title: 3537939

description: Gene expression data from adults


title: MYBBP1A replicate 1.HS766T Hemi #2

value: Sigma HPA005466


title: 6183

description: Gene expression data from adults


title: Patient 16 brain

city: Seoul

first: Seung Geun

last: Song

address: 101 Daehak-ro, Jongno-gu

department: Department of Pathology

country: South Korea

institute: Seoul National University College of Medicine

scan_protocol: The nCounter platform

data_processing: Raw data (NanoString RCC file) were imported to nSolver Analysis Software version 4.0. and normalized using positive control and housekeeping genes.

label: nanostring

source_name: brain metastasis

label_protocol: The nCounter platform

extract_protocol: RNA was extracted from 100 µm thick formalin-fixed paraffin-embedded tissue

tag: organ

value: brain

tag: age at surgery

tag: histology

value: Other NSCLC

tag: egfr

value: Wild-type

tag: egfr type

tag: Sex

value: Male


title: hHSC_D2_2

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Per-read bead barcodes were parsed and trimmed using UMI-TOOLs (https://github.com/CGATOxford/UMI-tools). Constitutive elements of the bead barcodes were assigned to the closest known sequence allowing for up to 1 mismatch per 6-mer or 7-mer (mean >99% parsing efficiency across experiments).
Paired-end reads were aligned to hg19 using BWA (http://bio-bwa.sourceforge.net) on the Illumina BaseSpace online application.
We used bead-based ATAC-seq processing (BAP) (https://github.com/caleblareau/bap), to identify systematic biases (i.e. reads aligning to an inordinately large number of barcodes), barcode-aware deduplicate reads, and perform merging of multiple bead barcode instances associated with the same cell. Barcode merging is necessary due to the nature of the BioRad SureCell scATAC-seq procedure used in this study, which enables multiple beads per droplet. BAP uses as input an alignment (.bam) file for a given experiment with a bead barcode identifier indicated by a SAM tag.
Aligned reads were combined using samtools merge (http://www.htslib.org)
Subsamples of the data were generated using custom python scripts
Tn5 insertion sites were offset by 4/5 bp and smoothed by 200 bp using custom python scripts
Genome coverage was calculated using bedtools genomecov (https://bedtools.readthedocs.io/en/latest)
Signal tracks were denoised using AtacWorks (https://github.com/clara-genomics/AtacWorks)
Denoised signal tracks were normalized by total coverage using a custom python script
bigWigs were generated using the bedGraphToBigWig utility (https://genome.ucsc.edu/goldenpath/help/bigWig.html)
Genome_build: hg19
Supplementary_files_format_and_content: bigWigs contain non-zero coverage values for every base in the genome

source_name: Hematopoietic stem cells

growth_protocol: Cryopreserved human bone marrow mononuclear cells were purchased from Allcells (catalog number BM, CR, MNC, 10M). Cells were quickly thawed in a 37°C water bath, rinsed with culture medium (RPMI 1640 medium supplemented with 15% FBS) and then treated with 0.2 U/μL DNase I (Thermo Fisher Scientific) in 2 mL of culture medium at room temperature for 15 min. After DNase I treatment, cells were filtered with a 40 μm cell strainer, washed with MACS buffer (1x PBS, 2 mM EDTA and 0.5% BSA), and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter (Bio-Rad). Cell viability was greater than 90% for all samples.

extract_protocol:
For a detailed description of tagmentation protocols and buffer formulations refer to the SureCell ATAC-Seq Library Prep Kit User Guide (17004620, Bio-Rad). Harvested cells and tagmentation related buffers were chilled on ice. Lysis was performed simultaneously with tagmentation. Washed and pelleted cells were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1x PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (ATAC Tagmentation Buffer and Enzyme are both included in the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad)). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator. Single-cell ATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads. Barcoded amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer using the High-Sensitivity DNA kit. Libraries were loaded at 1.5 pM on a NextSeq 550 using the NextSeq High Output Kit and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

treatment_protocol: CD34 positive cells were bead enriched using the CD34 MicroBead Kit UltraPure (Miltenyi Biotec, catalog number 130-100-453) following manufacturer's instructions. The enriched population was then simultaneously stained with CD45, Lineage cocktail, CD34, CD38, CD45RA and CD90 antibodies in MACS buffer for 20 min at 4°C. Stained cells were then washed with MACS buffer and the CD45+ Lin- CD38- CD34+ CD45RA- CD90+ fraction (HSCs) was FACS sorted using a MoFlo Astrios Cell Sorter (Beckman Coulter).

tag: donor

value: Donor 2

value: Hematopoietic stem cells


title: hHSC_D2_1


title: Patient 17 brain

value: Mutant

value: Female


title: hHSC_D1

value: Donor 1


title: hv120

description: Gene expression data from adults

value: healthy


title: 4892

description: Gene expression data from adults

value: sepsis


title: 5707

description: Gene expression data from adults

value: patient


title: 3524625

description: Gene expression data from adults


title: 5771

description: Gene expression data from adults


title: D372_Brus_Nas1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
10xGenomics Cellranger standard analysis.
Genome_build: hg19
Supplementary_files_format_and_content: 10xGenomics Cellranger filtered gene/cellbarcode matrix.

molecule: polyA RNA

source_name: airways

extract_protocol: 10xGenomics 3p single cell rna-seq

value: Nasal epithelium

tag: collection

value: Brushing


title: 6240

description: Gene expression data from adults

value: female

value: blood


title: Patient 14 lung

source_name: primary lung cancer

value: lung

value: Adenocarcinoma


title: D372_Brus_Dis1

value: Lung epithelium


title: Patient 13 lung

value: Wild-type


title: D372_Biop_Pro1

value: Biopsy


title: 6146

description: Gene expression data from adults

source_name: blood

value: male

value: noninfectious


title: D372_Biop_Int2


title: Patient 12 brain

value: brain


title: D372_Biop_Int1


title: Patient 11 brain

value: Other NSCLC

value: Mutant

value: Male


title: 5893

description: Gene expression data from adults


title: 5717

description: Gene expression data from adults

value: sepsis


title: 5799

description: Gene expression data from adults

value: patient


title: Patient 15 brain

value: Female


title: Patient 11 lung


title: D367_Brus_Dis1

value: Brushing


title: D367_Brus_Nas1

value: Nasal epithelium


title: Patient 10 brain


title: Patient 10 lung


title: D367_Biop_Pro1


title: D367_Biop_Int1


title: D363_Brus_Nas1


title: Patient 9 lung


title: D363_Brus_Dis1


title: Patient 8 brain


title: 3964199

description: Gene expression data from adults

value: blood


title: D354_Brus_Dis1


title: Patient 8 lung

value: lung


title: Patient 7 lung

value: Adenocarcinoma


title: Patient 7 brain


title: Patient 6 brain

value: Squamous cell carcinoma


title: 3433046

description: Gene expression data from adults

value: female


title: 3308841

description: Gene expression data from adults


title: 3480292

description: Gene expression data from adults


title: 3596240

description: Gene expression data from adults


title: D354_Biop_Pro1

value: Lung epithelium

value: Biopsy


title: hv117

description: Gene expression data from adults

value: male

value: healthy


title: 3474652

description: Gene expression data from adults


title: 4807

description: Gene expression data from adults


title: 3418907

description: Gene expression data from adults


title: 3420121

description: Gene expression data from adults


title: 3458598

description: Gene expression data from adults


title: Patient 6 lung

value: Wild-type


title: Patient 5 brain

value: brain


title: 3138950

description: Gene expression data from adults


title: D354_Biop_Int2


title: D363_Biop_Int2


title: D353_Brus_Nas1


title: 4100378

description: Gene expression data from adults


title: Patient 5 lung

value: Male


title: Patient 9 brain


title: D353_Brus_Dis1


title: D363_Biop_Pro1


title: D353_Biop_Pro1


title: Patient 4 lung


title: D353_Biop_Int2


title: D344_Brus_Dis1


title: D344_Biop_Pro1


title: Patient 3 brain

value: Mutant


title: 5527

description: Gene expression data from adults

value: patient


title: 3272092

description: Gene expression data from adults

value: sepsis


title: 4007

description: Gene expression data from adults


title: 5392

description: Gene expression data from adults


title: D344_Biop_Nas1


title: 4225

description: Gene expression data from adults


title: Patient 3 lung

value: Female


title: Patient 2 brain


title: D344_Biop_Int1


title: Patient 4 brain


title: D339_Brus_Dis1

value: Brushing


title: Patient 1 brain