title: S0um-2

value: control


title: S0um-3

status: Public on Jul 12 2018

type: SRA

city: QingDao

first: Zhang

middle: Rui

last: Qian

state: ShanDong

address: Great Wall Road

country: China

institute: Qingdao Agricultural University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 2.1.0 with default parameters
Count gene expression using htseq with default parameters
Genome_build: ASM130575v1
Supplementary_files_format_and_content: tab-delimited text files include gene expression count for each Sample

molecule: total RNA

organism: Equus asinus africanus

source_name: ovary granulosa cell

growth_protocol: Donkey granulosa cells (dGCs) were aspirated from the antral follicles using a 10 ml syringe

extract_protocol:
Total RNA was extracted from the cultured GCs by the use of an RNAprep pure MicroKit in line with the manufacturer’s instruction (Aidlab, RN07, Beijing, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ZEA was added to the cultured medium at final concentrations of the 10 µM or 30 µM, then the cells were incubated with ZEA for 72 h. The control and 10 μM ZEA group added the same dose of DMSO to 30 μM ZEA group for accuracy.

tag: treatment

tag: cell type

value: Granulosa cell

tag: tissue

value: Ovary


title: S0um-1


title: HUVECs_C5

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

description:
C5_CTTGTA
C5_S12-READs

data_processing:
Qiagen’s Geneglobe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances
Only miRNA with 2 fold changes verus normoxic control in at least one experimental condition were considered
The analyses of the differential expression of small RNAs between the control (normoxia) and the experimental samples were performed with geNorm (Gene Globe Software)
Genome_build: hg19
Supplementary_files_format_and_content: reads per sample; fold-change

organism: Homo sapiens

source_name: HUVECs

growth_protocol: Primary HUVECs (passages 2-6 were used) pooled from 10 independent donors that were obtained from Cellworks (UK, division of Catalog Medsystems Ltd) and maintained until passage five in EGM-2 BulletKit™ medium (Lonza). Cells were split either into 6-well plates or 10 cm dishes and allowed to grow to 70-80% confluence prior to the start of the experiments.

extract_protocol:
Total RNA containing the microRNA fraction was isolated using miRNeasy kit (Qiagen) according to the manufacturer’s protocol.
MiRNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument. Using Qiagen’s Geneglobe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances

treatment_protocol: Hypoxia was induced in a CO2/O2 incubator  for hypoxia research (Tri-gas Binder CB150). Briefly, cells were cultured in 35 mm cm dishes at 0.9% O2 for the time periods specified. Control cells were maintained in normoxic conditions in the same incubator and harvested at the specified times. Cells maintained in cyclic hypoxia were cultured at 0.9% O2 for 1 hour and then in normoxia for 36 minutes for the specified number of cycles (1 h 36 min per cycle).

value: primary endothelial cells 10 donors pool

tag: passages

tag: exposed to

value: 5 cycles of hypoxia (1h hypoxia 0.9% O2 and 36 min reoxygenation)

tag: molecule subtype

value: miRNA


title: BM_CONTROL_REP6

type: RNA

city: Durham

first: Dorothy

last: Sipkins

state: NC

address: 905S La Salle Street

department: Hematological Malignancies and Cell Therapy

country: USA

institute: Duke University

description: NALM6 human ALL cells isolated from SCID mice after control/PI3Kd treatment

hyb_protocol: Hybridization targets were prepared with the Affymetrix WT Plus Kit (Affymetrix, Santa Clara, CA) and Affymetrix GeneChip WT Terminal Labeling Kit (included with Affy WT Plus)  from total RNA, hybridized to GeneChip® Human Clariom D arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20

data_processing: Total RNA isolated from BM and CSF was sent for gene expression profiling using the Clariom D Human microarrays (Affymetrix, Santa Clara, USA) at the Duke Center for Genomic and Computational Biology. Raw cell intensity data was imported in to Expression Console (Affymetrix, Santa Clara, USA) and BM arrays (vehicle and GS-649443 samples), and CSF arrays (vehicle and GS-649443) were normalized using the RMA algorithm. Gene level differential expression analysis was performed using the Transcript Analysis Console (v3.1.0.5: Affymetrix, Santa Clara, USA) and ANOVA statistical analysis performed on the BM and CSF arrays separately. Transcripts identified to be differentially regulated in the BM, or CSF samples by ±1.5-fold with a p-value <0.05 were carried forward for pathway analysis.

label: biotin

source_name: bone marrow, control

label_protocol: Affymetrix WT Plus Kit (PN 902280) and GeneChip WT Terminal Labeling Kit (PN 900670)

growth_protocol: NALM6 cells were engrated in SCID mice, which were treated with control/PI3Kd until animals reached clinical endpoint.

extract_protocol: Mouse femurs were collected and BM cells were aspirated with RPMI1640 containing 10% FBS. Murine spleen tissues were homogenized in RPMI1640 containing 10% FBS. The spine was removed from mice, cut into columns and aspirated with RPMI1640 containing 10% FBS to collect CSF cells. The BM, spleen and CSF cells were passed through 70 μm filters, washed with PBS and treated with ACK lysis buffer.RNA was extracted using RNAeasy kit (Qiagen, Germantown, MD) and total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

treatment_protocol: Mice were dosed twice a day with 2 mg/kg PI3Kd

value: Bone Marrow

value: Control


title: BM_CONTROL_REP5


title: HUVECs_H0

description:
H0_ATCACG
H7_S9-READs

value: normoxia - ctrl


title: Human islets single-cell RNAseq_11

status: Public on Jul 11 2018

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

data_processing:
The Cell Ranger Single-Cell Software Suite (10X Genomics, v1.1.0) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting.
Paired-end reads. Read1 has cell barcode and umi and Read2 is cDNA.
The Human B37.3 Genome assembly and UCSC gene model were used for the alignment.
Genome_build: Human B37.3
Supplementary_files_format_and_content: Genes.tsv/Barcodes.tsv/Matrix.mtx files for each sample

source_name: Pancreatic islets

extract_protocol:
Islets were handpicked and enzymatically digested at 37 ºC for 10 min using TrypLE Express (Life Technologies). Dissociated cells were filtered (30-µm strainer) and recovered by centrifugation. The cell pellet was suspended in 1X PBS containing 0.04% BSA. Single cells suspended in PBS with 0.04% BSA were loaded on a Chromium Single Cell Instrument (10X Genomics).
RNAseq libraries were prepared using Chromium Single Cell 3' Library, Gel Beads & Mutiplex Kit (10X Genomics). Sequencing was performed on the Illumina NextSeq500 using the read lengths: 59-bp read1 for transcript read, 14-bp I7 index for cell barcode read, 8-bp I5 index for sample index read, and 10-bp read2 for UMI (unique molecular identifier) read.

value: Pancreatic islets

tag: individual

tag: ethnicity

value: AA

tag: gender

value: Female


title: Human islets single-cell RNAseq_10

value: C


title: Human islets single-cell RNAseq_9

value: Male


title: Human islets single-cell RNAseq_8


title: BM_CONTROL_REP4


title: Human islets single-cell RNAseq_5


title: Human islets single-cell RNAseq_4


title: Human islets single-cell RNAseq_6

value: H


title: BM_CONTROL_REP2


title: Human islets single-cell RNAseq_7


title: Donor2_GFPBATF_antiGFP

city: San Francisco

first: Ruby

last: Yu

state: CA

address: 513 Parnassus Ave

institute: UCSF

library_source: genomic

data_processing:
We used Bowtie2 2.3.2 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg38 of Homo sapiens genomic sequence obtained from UCSC.
Aligned bam files were converted to bedgraph files and normalized to reads per million using the bedtools v2.26.0 genomecov function function with the "scale" option set to N/10e6, where N = total aligned reads.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

growth_protocol: CD4+ T cells were cultured in XVivo15 medium (STEMCELL) with 5% Fetal Bovine Serum, 50 mM 2-mercaptoethanol, and 10 mM N-Acetyl L-Cystine. Immediately following isolation, T cells were stimulated for 2 days with anti-human CD3/CD28 magnetic dynabeads (ThermoFisher) at a beads to cells concentration of 1:1, along with a cytokine cocktail of IL-2 at 200 U/mL (UCSF Pharmacy), IL-7 at 5 ng/mL (ThermoFisher), and IL-15 at 5 ng/mL (Life Tech).  Following electroporation, T cells were cultured in media with IL-2 at 500 U/mL.  Throughout the culture period T cells were maintained at an approximate density of 1 million cells per mL of media.  Every 2-3 days post-electroporation additional media was added, along with additional fresh IL-2 to bring the final concentration to 500 U/mL, and cells were transferred to larger culture vessels as necessary to maintain a density of 1 million cells/mL.

extract_protocol:
CUT&RUN was performed as described in (https://elifesciences.org/articles/21856), using anti-GFP (ab290), anti-BATF (sc-100974), and rabbit anti-mouse (ab46540) antibodies. Briefly, 6 million cells (30 million cells for anti-GFP CUT&RUN in GFP-BATF-containing cells) were collected and washed. Nuclei were isolated and incubated rotating with primary antibody (GFP or BATF) for 2 hours at 4C. BATF CUT&RUN samples were incubated an additional hour with rabbit anti-mouse antibody. Next, nuclei were incubated with proteinA-micrococcal nuclease (provided by the Henikoff lab) for one hour at 4C. Nuclei were equilibrated to 0C and MNase digestion was allowed to proceed for 30 minutes. Solubilized chromatin CUT&RUN fragments were isolated and purified.
Paired end libraries were generated as described in (https://elifesciences.org/articles/21856). Briefly, purified CUT&RUN DNA underwent end repair followed by ligation to Illumina TruSeq HT dual-indexed adapters. Ligation reactions were followed by two successive Ampure XP bead-based size selections to remove adapter dimers. Libraries were amplified using the KAPA DNA polymerase library preparation kit protocol and amplifying for 14 cycles. Amplified libraries were cleaned up with two successive Ampure XP bead-based size selections to remove adapter dimers.

treatment_protocol: CUT&RUN was performed using epitope-tagged primary human T cells 11 days after electroporation and 4 days after re-stimulation with anti-CD3/anti-CD28 dynabeads (untagged cells were not electroporated). Approximately 20% and 10% of electroporated cells showed GFP-BATF expression as determined by flow cytometry in donor 1 and donor 2 samples, respectively.

value: CD4+ T cells

tag: batf tag

value: GFP-BATF

tag: cut&run antibody

value: anti-GFP (abcam, catalog# ab290-50ul, lot# GR278480-1)


title: BM_CONTROL_REP3


title: Donor2_noelectroporation_antiBATF

value: no tag

value: anti-BATF (Santa Cruz, catalog# sc-100974, lot# F2716)


title: Donor1_GFPBATF_antiGFP


title: decidua_recurrent spontaneous abortion_rep3

type: genomic

city: Nanjing

first: Mingming

address: NO.818 Tianyuan East Road, Jiangning District

department: School of public health

institute: Nanjing Medical University

description:
decidua samples from recurrent spontaneous abortion patients
SAMPLE 5
female, decidua, early pregnancy

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: preprocesQuantile function from minfi R package

label: Cy5 and Cy3

source_name: decidua tissues, recurrent spontaneous abortion

label_protocol: Standard Illumina Protocol

extract_protocol: Human decidua tissues were separated from any products of conception under a dissecting microscope at the time of dilation and curettage and stored at -80°C immediately after being washed thoroughly.

tag: condition

value: recurrent spontaneous abortion

tag: Stage

value: early pregnancy

value: decidua


title: Donor1_GFPBATF_antiBATF


title: Human islets single-cell RNAseq_3


title: Donor2_noelectroporation_antiGFP


title: Donor1_noelectroporation_antiGFP


title: Donor1_noelectroporation_antiBATF


title: decidua_induced abortion_rep2

description:
normal decidua sample
SAMPLE 2
female, decidua, early pregnancy

source_name: decidua tissues, induced abortion

value: induced abortion


title: Human islets single-cell RNAseq_1


title: Donor2_GFPBATF_antiBATF


title: Human islets single-cell RNAseq_2


title: HUVECs_C2

description:
C2_TAGCTT
C2_S11-READs

value: primary endothelial cells 10 donors pool

value: 2 cycles of hypoxia (each 1h hypoxia 0.9% O2 and 36 min reoxygenation)

value: miRNA


title: DMF_batch2_R3

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerwein-Str. 2

country: Germany

institute: Institute of Medical Microbiology

data_processing:
preprocessing according to illumina standart protocol
quality control with FastQC and Qorts
Alignment with STAR aligner 2.4.0b
Genome_build: ENSEMBL Mus_musculus.GRCm38
Supplementary_files_format_and_content: Tab-separated .csv matrix table containing normalized expression values for all genes

organism: Mus musculus

source_name: CD8+ Tcells from Lymph Node and Spleen

growth_protocol: Tc17 cells were primed in RPMI complete media (10% FCS) with plate-bound anti-CD3 mAb (5 µg/ml) in the presence of soluble anti-CD28 (0.5 µg/ml, both produced and purified ‘in house’), recombinant human (rh) IL-2 (50 U/ml, Novartis), rh TGF-β (0.5 ng/ml, Peprotech) recombinant murine (rm) IL-6 (30 ng/ml, Peprotech) and anti-mouse-IFN-g(5 µg/ml, produced and purified ‘in house’)

extract_protocol:
RNA was purified from Trizol according to the manufacturer’s specifications. RNA was quantified with a Qubit 2.0 fluorometer (Invitrogen) and the quality was assessed on a Bioanalyzer 2100 (Agilent) using a RNA 600 Nano chip (Agilent) Samples with an RNA integrity number of > 9 were used for library preparation
Barcoded mRNA-seq cDNA libraries were prepared with 300 ng of total RNA using NEBNext Poly (A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina according to the manual. Quantity was assessed using Invitrogen’s Qubit HS Assay Kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay. Barcoded RNA-Seq libraries were onboard clustered using HiSeq Rapid SR Cluster Kit v2 using 8 pM and 50 bps were sequenced on the Illumina HiSeq2500 using the HiSeq RapidSBS Kit v2 (50 cycle)

treatment_protocol: The 2 day culture was done either in the presence of 0.2 % DMSO alone, with  added DMF(Sigma-Aldrich, 242926, 20 µM) or DMF in combination with GSH(Sigma-Aldrich, G1404, 50 µM)

tag: strain

value: naive CD62L+CD44-CD8+ T cells

tag: sorting antibody

value: anti-CD8 V500 (53-6.7, BD Biosciences)

value: anti-CD44 PE (IM7, eBiosciences)

value: anti-CD62L AF700 (MEL-14, BD Pharmingen)


title: DMSO_batch2_R3


title: DMSO_batch2_R2


title: DMF_batch2_R2


title: DMF_GSH_batch2_R3


title: DMF_batch1_R1


title: DMF_GSH_batch1_R1


title: DMF_GSH_batch2_R2


title: Donor2_noelectroporation_noantibody

value: rabbit anti-mouse (abcam, catalog# ab46540-1mg, lot# GR293833-7)


title: decidua_recurrent spontaneous abortion_rep4

description:
decidua samples from recurrent spontaneous abortion patients
SAMPLE 6
female, decidua, early pregnancy


title: DMSO_batch1_R1


title: WT4

city: New York

first: Stefan

last: Feske

address: 550 First Avenue

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing were performed using the Illumina bcl2fastq software v1.8.4
Sequenced reads were mapped to the mm10 reference genome using bowtie2 v2.1.0 in conjuction with TopHat v2.0.9
Htseq v0.6.1.p.1 was used to generate the matrix of read counts for annotated genomic features
The DESeq2 package (Bioconductor v3.3.0) in the R statistical programming environment was utilized to calculate differential gene statistical comparisons
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing normalized matrix of read counts which includes values for all features and all samples

source_name: FACS sorted GFP+ leukemic cells from BM of mice isolated 21 days after leukemia induction

growth_protocol: ex vivo

extract_protocol:
BM cells were isolated from leukemic mice (3 per cohort) 21 days after disease induction and GFP+ cells were isolated using a cell sorter Moflo XDP. Total RNA was extracted using the RNeasy Micro Kit (Qiagen)
Automated Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat. No. RS-122-2101) was used with 100ng of input RNA for the construction of sequencing libraries

treatment_protocol:
3 doses of poly(I:C) were administered to wild-type or Stim1fl/flStim2fl/fl Mx1-Cre bone marrow donor mice 4 weeks before harvesting CD117+ progenitor cells. Bone marrow progenitor cells were transduced with retroviral supernatant containing ICN1-IRES-GFP. Transduced cells were stained with lineage markers and analyzed by FACS. Leukemia was induced by injecting lethally irradiated C57BL/6 mice with 5x104 GFP+ Lin- cells and 5x105 flreshly isolated bone marrow cells from C57BL/6 donors.
FACS sorted GFP+ cells

tag: genotype

value: wild-type

tag: age

value: 6-8 weeks mice were used as hosts for leukemia induction and BM leukemia cells were isolated 21 days after leukemia induction.

value: Bone marrow


title: DKO4

value: Stim1fl/flStim2fl/fl Mx1-Cre


title: DKO6


title: decidua_recurrent spontaneous abortion_rep2

description:
decidua samples from recurrent spontaneous abortion patients
SAMPLE 4
female, decidua, early pregnancy


title: WT6


title: DKO5


title: decidua_induced abortion_rep1

description:
normal decidua sample
SAMPLE 1
female, decidua, early pregnancy


title: WT5


title: decidua_recurrent spontaneous abortion_rep1

description:
decidua samples from recurrent spontaneous abortion patients
SAMPLE 3
female, decidua, early pregnancy


title: subject_422-Normal-biopsy_864

first: Eric

last: Schadt

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Gene expression were carried out using Affymetrix GeneChip HTHGU133+ (Affymetrix, Santa Clara, CA, USA Cat# 901262) according to the manufacturer’s protocol with the exception that dimethyl sulphoxide replaced the Tetramethylammonium Chloride Solution in the hybridization buffer.

scan_protocol: Arrays were washed and stained on the Affymetrix GeneChip Array Station then scanned on an HTAPS scanner.

data_processing: Array Studio software version 6.0 (OmicSoft Corp., St. Morrisville, NC) was used for data analysis. The microarray data were pre-processed and normalized using RMA. Log2 transformed data was used for statistical analysis.

label: NuGEN Encore Biotin Module

source_name: Normal

label_protocol: RNA samples were amplified by NuGEN Ovation RNA Amplification System V2 Whole Blood Solution (NuGEN, San Carlos, CA) and purified using Agencourt RNAClean magnetic beads.  Labeling was done using the NuGEN Encore Biotin Module (NuGEN). (Agencourt, Beverly, MA) on a Caliper SciClone robot.

extract_protocol: Total RNA including micro ribonucleic acids (miRNA) was isolated with PAXgene Blood RNA MDx Kit plus customized reagent BM3 (Cat#762431, lot 136237127) according to the manufacturer’s instructions (Qiagen Inc., Valencia, CA). Briefly, PAXgene Blood RNA Tubes were incubated at room temperature around 2 hrs before extraction. After centrifugation for 10 min at 3000–5000 x g, the pellet was re-suspended in 290 μl Buffer BR1 with 35 μl proteinase K. The remaining procedures were performed on a BioRobot Universal System using a customized protocol, PAXgene Blood RNA UNIV rcV73_miRNA Centocor.pro (Qiagen).

treatment_protocol: All blood samples were stored at −80 °C until RNA isolation was performed. Blood samples were hybridized by microarray for genome-wide mRNA expression profiling. Ileal, rectal, and colonic biopsies were collected at the screening visits from a sub-group of subjects who consented to this procedure. Biopsies were obtained from selected colonic sections, including the ascending, transverse, and descending colonic regions, and from both inflamed and non-involved areas. The inflamed regions were defined as the colonic segments with the most severe disease activity. Additional biopsies were collected from the terminal ileum and from the rectum (i.e., the distal 10 cm of the colon).

value: blood

value: TRUE

tag: Sex

tag: batch

tag: disease

value: Normal

tag: visit

tag: inflammation


title: subject_424-Normal-biopsy_866

tag: tissue


title: subject_427-Normal-biopsy_869


title: subject_429-Normal-biopsy_871


title: subject_417-Normal-biopsy_859


title: subject_423-Normal-biopsy_865


title: subject_430-Normal-biopsy_872


title: subject_416-Normal-biopsy_858


title: subject_421-Normal-biopsy_863


title: subject_418-Normal-biopsy_860


title: subject_432-Normal-biopsy_874


title: subject_425-Normal-biopsy_867


title: subject_415-Normal-biopsy_857


title: subject_409-Normal-biopsy_851


title: subject_431-Normal-biopsy_873


title: subject_419-Normal-biopsy_861


title: subject_413-Normal-biopsy_855


title: subject_414-Normal-biopsy_856


title: subject_420-Normal-biopsy_862


title: subject_410-Normal-biopsy_852


title: Human islets single-cell RNAseq_12

value: Pancreatic islets

tag: individual

value: C

value: Male


title: subject_407-Normal-biopsy_849


title: subject_306-Descending colon-biopsy_399

source_name: Descending colon

value: Descending colon

value: F

value: Crohn's disease

value: Week 22

value: Inflamed area


title: subject_406-Normal-biopsy_848


title: subject_408-Normal-biopsy_850


title: subject_433-Normal-biopsy_875


title: subject_124-Terminal Ileum-biopsy_396

source_name: Terminal Ileum

value: Terminal Ileum


title: subject_73-Terminal Ileum-biopsy_395

value: Non-involved area


title: subject_39-Ascending colon-biopsy_394

source_name: Ascending colon

value: Ascending colon

value: M


title: subject_84-Transverse colon-biopsy_390

source_name: Transverse colon

value: Transverse colon


title: subject_370-Ascending colon-biopsy_400


title: BM_CONTROL_REP1

value: Bone Marrow

tag: treatment

value: Control


title: subject_84-Rectum-biopsy_391

source_name: Rectum

value: Rectum

value: TRUE


title: subject_284-Transverse colon-biopsy_397


title: subject_39-Descending colon-biopsy_393


title: Donor1_noelectroporation_noantibody

tag: cell type

value: CD4+ T cells

value: no tag

value: rabbit anti-mouse (abcam, catalog# ab46540-1mg, lot# GR293833-7)


title: subject_69-Rectum-biopsy_382


title: subject_12-Descending colon-biopsy_376

value: Descending colon


title: subject_32-Descending colon-biopsy_377

value: F


title: subject_33-Rectum-biopsy_359

value: Crohn's disease

value: Week 6


title: subject_39-Rectum-biopsy_358


title: subject_219-Sigmoid colon-biopsy_369

source_name: Sigmoid colon

value: Sigmoid colon

value: Week 22

value: Inflamed area


title: subject_287-Transverse colon-biopsy_353

value: Non-involved area


title: subject_68-Transverse colon-biopsy_365

value: M


title: subject_74-Descending colon-biopsy_354


title: subject_1-Terminal Ileum-biopsy_374

value: Terminal Ileum


title: subject_68-Terminal Ileum-biopsy_366


title: subject_1-Terminal Ileum-biopsy_356


title: subject_99-Rectum-biopsy_351


title: subject_221-Sigmoid colon-biopsy_370


title: subject_70-Terminal Ileum-biopsy_367


title: subject_37-Ascending colon-biopsy_378

value: Ascending colon


title: subject_40-Descending colon-biopsy_355


title: subject_69-Descending colon-biopsy_383


title: subject_284-Ascending colon-biopsy_398


title: subject_33-Transverse colon-biopsy_349

value: Transverse colon


title: subject_287-Ascending colon-biopsy_348


title: subject_80-Transverse colon-biopsy_345


title: subject_73-Ascending colon-biopsy_337


title: subject_229-Transverse colon-biopsy_342


title: subject_412-Normal-biopsy_854

value: blood

value: FALSE

value: Normal


title: subject_306-Transverse colon-biopsy_338

value: TRUE


title: subject_220-Descending colon-biopsy_330


title: subject_59-Descending colon-biopsy_344


title: subject_181-Ascending colon-biopsy_339


title: subject_99-Terminal Ileum-biopsy_334


title: subject_12-Ascending colon-biopsy_332


title: subject_39-Transverse colon-biopsy_335


title: subject_428-Normal-biopsy_870


title: subject_232-Ascending colon-biopsy_331


title: subject_426-Normal-biopsy_868


title: subject_411-Normal-biopsy_853


title: subject_31-Ascending colon-biopsy_847


title: subject_31-Terminal Ileum-biopsy_844


title: subject_405-Descending colon-biopsy_843


title: subject_16-Transverse colon-biopsy_838


title: subject_405-Rectum-biopsy_841

value: Rectum


title: subject_288-Ascending colon-biopsy_833


title: subject_16-Rectum-biopsy_836


title: subject_288-Rectum-biopsy_830


title: subject_16-Terminal Ileum-biopsy_839


title: subject_66-Rectum-biopsy_822


title: subject_16-Transverse colon-biopsy_835


title: subject_66-Transverse colon-biopsy_823


title: subject_373-Transverse colon-biopsy_827


title: subject_288-Descending colon-biopsy_831

value: Descending colon


title: subject_373-Sigmoid colon-biopsy_826

value: F


title: subject_288-Ascending colon-biopsy_834

value: Crohn's disease


title: subject_405-Sigmoid colon-biopsy_842


title: subject_291-Descending colon-biopsy_819


title: subject_31-Transverse colon-biopsy_846


title: subject_373-Ascending colon-biopsy_828


title: subject_16-Descending colon-biopsy_837


title: subject_31-Rectum-biopsy_845


title: subject_66-Terminal Ileum-biopsy_820


title: subject_373-Rectum-biopsy_825


title: subject_373-Terminal Ileum-biopsy_829


title: subject_405-Terminal Ileum-biopsy_840


title: subject_291-Transverse colon-biopsy_818


title: subject_102-Rectum-biopsy_824


title: subject_291-Ascending colon-biopsy_817


title: subject_288-Transverse colon-biopsy_832


title: subject_66-Ascending colon-biopsy_821


title: subject_76-Sigmoid colon-biopsy_815


title: subject_76-Rectum-biopsy_813


title: subject_404-Transverse colon-biopsy_810


title: subject_101-Transverse colon-biopsy_807


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title: WT_4day_DOX_WCE_reanalyzed

status: Public on Jul 15 2018

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina bcl2fastq version 2.17.1.14 software to generate fastq files.
Reads were aligned to mouse mm10 reference genome using bowtie2 software, with default parameters.
For transcription factors, peaks were identified with MACS version 1.4.2-157. Whole-cell extract was used as control to define a background model. Duplicate reads aligned to the exact same location are excluded by MACS default configuration. Chromatin modification coverage in the promoters was calculated using in-house script. Shortly, promoters were defined as 1Kb region around the TSS, based on mm10 assembly. Each promoter was divided to 50bp size bins, and the coverage in each bin is estimated.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files (bed format) and *prom_500.matrix.txt files.  In the processed matrix file, for each promoter is the coverage in 20 bins, 50bp each.

growth_protocol: ESCs, iPSCs, and 4-8 day DOX induced cells were expaned in N2B27 15% KSR 2i/LIF mouse ESC media; MEF cells in DMEM + 15% FBS

extract_protocol:
Approximately 25*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).
120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

treatment_protocol: DOX induction at day 0 at the relevant plate in final concentration of 2ug/ml

tag: genotype/variation

value: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

tag: stage in reprogramming

value: 8 days after DOX induction

tag: target protein

tag: antibody


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value: Transverse colon


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title: Patient_10_Con

description: CD8+ memory cells from human blood

data_processing:
preprocessing according to illumina standart protocol
quality control with FastQC and Qorts
Alignment with STAR aligner 2.4.0b
Genome_build: ENSEMBL Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Tab-separated .csv matrix table containing normalized expression values for all genes

source_name: human PBMCs

treatment_protocol: PBMCs from MS patients before (n=4) and after one year (n=4) of 240 mg p.o twice a day of DMF (Tecfidera) were enriched by performing Histopaque-1077 (Sigma) density gradient centrifugation and then labelled with anti-CD8a-BV510 (SK1), anti-CD4-Pacifc Blue (RPA-T4), anti-CD14-FITC (HCD14), anti-CD45RA-BV650 (HI100); all from Biolegend. Memory CD8+ T cells were sorted (CD8+CD45RA-) using a FACSAria™ III (BD Biosciences).

value: naive CD62L+CD44-CD8+ T cells

value: anti-CD8a (PRA-T8; BioLegend)

value: anti-CD4 (OKT-4; BioLegend)

value: anti-CD45RA (HI100; BioLegend)


title: subject_61-Rectum-biopsy_506

value: Rectum

value: Crohn's disease

value: Week 6


title: Patient_9_Con

description: CD8+ memory cells from human blood


title: Patient_7_DMF

description: CD8+ memory cells from human blood


title: subject_369-Transverse colon-biopsy_479


title: Patient_5_DMF

description: CD8+ memory cells from human blood


title: subject_232-Terminal Ileum-biopsy_482

value: F


title: Patient_4_DMF

description: CD8+ memory cells from human blood


title: Lu139 siTTF-1

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

country: Japan

institute: Tokyo University

description: Gene expression data from Lu139 cells transfected with siTTF-1

hyb_protocol: Hybridization was processed according to the standard Affymetrix protocol.

scan_protocol: GeneChip® Scanner 3000 7G  (Affymetrix)

data_processing: Affymetrix® Expression Console™ Software  (Affymetrix)

source_name: human small cell lung cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Standard NCI-H209 and Lu139 growth conditions.

extract_protocol: RNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: SCLC cell lines were mixed with siRNAs in an electroporation cuvette and electroporated using Gene Pulser II Electroporation Systems (Bio-Rad) with voltage 200 V and capacitance 950 μF.

tag: cell line

tag: transfection

value: electroporated with siRNAs for TTF-1 (siTTF-1)


title: Lu139 siNTC

description: Gene expression data from Lu139 cells transfected with siNTC

value: electroporated with control siRNAs (siNTC)


title: NCI-H209 siTTF-1

description: Gene expression data from NCI-H209 cells transfected with siTTF-1


title: subject_71-Rectum-biopsy_474


title: Patient_3_Con

description: CD8+ memory cells from human blood

tag: sorting antibody


title: subject_68-Terminal Ileum-biopsy_473

tag: age

value: M


title: subject_371-Ascending colon-biopsy_471

value: Ascending colon

tag: Sex

value: Inflamed area


title: subject_40-Transverse colon-biopsy_472

value: FALSE

tag: batch

value: Non-involved area


title: Patient_2_Con

description: CD8+ memory cells from human blood


title: Patient_1_DMF

description: CD8+ memory cells from human blood


title: NCI-H209 siNTC

description: Gene expression data from NCI-H209 cells transfected with siNTC


title: subject_85-Descending colon-biopsy_469

value: Descending colon

tag: disease


title: subject_43-Rectum-biopsy_467

tag: visit


title: T47D_ESR1E6_E2_RNAseq

city: Houston

first: Jonathan

middle: Thomas

last: Lei

state: TX

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
ChIP-seq:  Reads were aligned to hg19 (GRCh37) reference genome using BWA
ChIP-seq:  Alignment files were converted to BED format using BEDTools
ChIP-seq:  Bed files were used for peak calling by MACS v.1.4.2
ChIP-seq:  MACS derived peaks (p<1e-7) were annotated with GREAT
RNA-seq:  Reads were aligned to hg19 (GRCh37) reference genome using RSEM v1.2.31 and Bowtie 2
RNA-seq:  Differential gene expression was performed using EBseq (FDR < 0.1)
RNA-seq:  Hierarchical clustering was conducted on differentially expressed genes within 1Mb of shared bound sites by ESR1-YAP1, ESR1-PCDH11X, and ESR1-WT identified by ChIP-seq or conducted on differentially expressed genes within 1 Mb of uniquely bound sites by ESR1-YAP1 and ESR1-PCDH11X
RNA-seq:  Heatmaps were created using RSEM generated log2TPM values of intersected genes by ChIP-seq and RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: bed files for ChIPseq data, RSEM tab-delimited output files for RNAseq data include gene id, transcript id, gene length, expected read counts used for differential gene analysis, TPM, and FPKM

growth_protocol: Stable T47D cells expressing HA-tagged ESR1 constructs were maintained in RPMI1640 supplemented with 10% FBS, 4 g/L glucose, 10 mM HEPES,  1 mM sodium pyruvate, and 50 µg/mL gentamycin.

extract_protocol:
Cells were grown hormone-deprived media for 5 days before -/+ E2 for 48h.  RNA was isolated using Qiagen Rneasy kit and subjected to on-column DNaseI digestion before elution in water.
Illumina TruSeq Stranded mRNA-Seq Sample Prep kit was used for library preparation

treatment_protocol: Cells were switched to hormone deprived media (same media compoistion as above except using RPMI1640 without phenol red and 10% charcoal-stripped FBS) for 5-7 days before ChIPseq or RNAseq processing

tag: cell subtype

value: Stable ESR1-e6 truncation expressing model

tag: condition

value: Hormone-deprived media +E2


title: subject_61-Sigmoid colon-biopsy_468

tag: tissue

value: Sigmoid colon

tag: inflammation


title: subject_74-Transverse colon-biopsy_466

value: Transverse colon


title: T47D_ESR1E6_noE2_RNAseq

value: Hormone-deprived media


title: T47D_ESR1NOP2_noE2_RNAseq

value: Stable ESR1-NOP2 fusion expressing model


title: subject_181-Transverse colon-biopsy_470

value: Crohn's disease


title: subject_284-Ascending colon-biopsy_464

value: Week 6


title: subject_306-Descending colon-biopsy_465

value: F


title: T47D_ESR1PCDH11X_E2_RNAseq

value: Stable ESR1-PCDH11X fusion expressing model


title: T47D_ESR1PCDH11X_noE2_RNAseq


title: T47D_ESR1NOP2_E2_RNAseq


title: T47D_ESR1YAP1_noE2_RNAseq

value: Stable ESR1-YAP1 fusion expressing model


title: T47D_YFP_noE2_HA_ChIPseq

extract_protocol:
Cells were grown hormone-deprived media for 7 days before sonicated chromatin extracts were subjected to HA-ChIP, followed by crosslink reversal and chromatin isolation
Wafergen PrepX DNA ChIP library preparation protocol was used.

value: Stable YFP-HA expressing model

tag: chip antibody

value: HA (Santa Cruz, sc-7392)


title: T47D_YFP_E2_RNAseq


title: subject_73-Transverse colon-biopsy_462


title: subject_124-Transverse colon-biopsy_463


title: T47D_YFP_noE2_RNAseq


title: subject_39-Sigmoid colon-biopsy_460

value: M

value: Inflamed area


title: subject_179-Transverse colon-biopsy_459

value: FALSE

value: Non-involved area


title: subject_95-Sigmoid colon-biopsy_456


title: subject_99-Ascending colon-biopsy_458

value: Ascending colon


title: subject_54-Ascending colon-biopsy_461


title: T47D_ESR1PCDH11X_noE2_HA_ChIPseq


title: T47D_ESR1YAP1_E2_RNAseq

value: Hormone-deprived media +E2


title: T47D_ESR1YAP1_noE2_HA_ChIPseq


title: T47D_ESR1WT_noE2_HA_ChIPseq

value: Stable ESR1-WT expressing model


title: subject_98-Sigmoid colon-biopsy_457

value: Sigmoid colon


title: T47D_ESR1NOP2_noE2_HA_ChIPseq

value: Hormone-deprived media


title: subject_94-Terminal Ileum-biopsy_455

value: Terminal Ileum


title: subject_82-Descending colon-biopsy_454

value: Descending colon

value: Crohn's disease


title: subject_55-Terminal Ileum-biopsy_451

value: F

value: Week 6


title: subject_69-Terminal Ileum-biopsy_452


title: Donor 2 Day 14

city: St Louis

first: Farshid

last: Guilak

state: Missouri

address: Couch Building, 3rd Floor, #3213

department: Orthopaedics

institute: Washington University in St Louis

data_processing:
Raw fastq files were processed with Trim Galore! (Babraham Bioinformatics) to eliminate low quality reads and remnant adapter sequences.
After trimming, processed reads were aligned to the human genome (STAR pre-assembled GRCh38 genome) by STAR
The number of aligned reads to each annotated genes or transcripts (GENCODE v21) were counted using HTseq
Normalized counts and differential gene expression analysis was carried out with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for genes for each sample by gene symbol and ENSEMBL ID
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for genes for all samples by gene symbol and ENSEMBL ID

source_name: MSC derived pellets day 14

growth_protocol: At the end of passage 4, MSCs were dissociated from the culture vessels with 0.05% Trypsin-EDTA (Sigma). Trypsin was subsequently inactivated with equal volume of expansion medium. Detached cells were collected by centrifugation (200 x g for 5 min), followed by 3 washes in pre-warmed DMEM-high glucose (Gibco). The resulting cell mixtures were resuspended at 5.0 x 105 cells/mL in chondrogenic medium: DMEM-high glucose (Gibco), 1% Penicillin/streptomycin (Gibco), 1% ITS+ (Corning), 100 nM dexamethasone (Sigma), 50 µg/mL ascorbic acid (Sigma), 40 µg/mL L-proline (Sigma), and 10 ng/mL rhTGF-β3 (R&D Systems). To form pellets, 2.5 x 105 cells (500 µL) was dispended into each 15 mL conical tube, then centrifuged at 200 x g for 5 min. Pellets were cultured for 21 days at 37ºC and 5% CO2 with medium exchange every three days. Pellets were harvested on day 0, day 1, day 3, day 7, day 14, and day 21 for RNA isolation, and on day 3, day 14, and day 21 for histological and biochemical analyses.

extract_protocol:
On day of harvest, pellets were washed once with PBS, snap frozen in liquid nitrogen, and stored at -80ºC until processing. Isolation of RNA was performed following manufacturer’s protocol (Norgen #48500) with the following modifications: for each time point, three pellets were homogenized with a pestle prior to addition of lysis buffer RL; RNA was eluted in 20 µL of DEPC-treated water.
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). Sequencing was performed on a HiSeq2500 (paired end and 100 base-pair reads) with sequencing depth of 100 million reads per samples.

tag: donor

value: Donor 2

tag: day

value: Day 14

tag: source

value: pooled from 3 pellets


title: Donor 3 Day 14

value: Donor 3


title: subject_41-Rectum-biopsy_450

value: Rectum


title: subject_37-Transverse colon-biopsy_449

value: Transverse colon

value: FALSE


title: Donor 3 Day 7

source_name: MSC derived pellets day 7

value: Day 7


title: subject_32-Transverse colon-biopsy_448

value: Inflamed area


title: Donor 1 Day 7

value: Donor 1


title: subject_18-Transverse colon-biopsy_447

value: M


title: subject_5-Ascending colon-biopsy_445

value: Ascending colon


title: Donor 3 Day 3

source_name: MSC derived pellets day 3

value: Day 3


title: subject_12-Transverse colon-biopsy_446

value: Non-involved area


title: subject_1-Transverse colon-biopsy_444

value: Crohn's disease


title: subject_72-Transverse colon-biopsy_453


title: Donor 1 Day 14


title: Donor 1 Day 3


title: Donor 3 Day 1

source_name: MSC derived pellets day 1

value: Day 1


title: Donor 2 Day 7


title: Donor 2 Day 1


title: subject_230-Rectum-biopsy_440

value: Week 6


title: Donor 1 Day 1


title: Donor 2 Day 3

value: Donor 2


title: subject_220-Rectum-biopsy_437

value: F


title: subject_286-Ascending colon-biopsy_443


title: subject_221-Rectum-biopsy_438


title: subject_369-Sigmoid colon-biopsy_439

value: Sigmoid colon


title: Leg.Sp1.ChIP3

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

description:
ChIP with antibody against GFP, chromatin from flies expressing recombineered GFP-tagged Sp1
Leg.Sp1.p2q4.peaks.txt

data_processing:
ChIP-seq reads were aligned to the dm3 genome assembly using Burrows-Wheeler Aligner and replicates were merged.
Peaks were called, with input as control file, using MACS version 2.0.9 with the following setting: (P-value: 10e-2, mfold:2,50).
Peaks passing a more stringent q-value cutoff of 1.00e-04 were used for further analysis.
Genome_build: dm3
Supplementary_files_format_and_content: peak (bed format)

organism: Drosophila melanogaster

source_name: Third instar leg imaginal discs

growth_protocol: Wandering 3rd instar larvae were manually removed from Drosophila culture. Larvae were inverted in PBS to expose imaginal discs and fixed. Imaginal discs dissected off after fixation.

extract_protocol:
Third instar larvae were dissected in PBS and fixed for 20 minutes at room temperature in 1.8% formaldehyde, 50mM HEPES, 1mM EDTA, 0.5mM EGTA, 100mM NaCl. After quenching (0.125M Glycine, 1xPBS, 0.01% Triton) the fixed tissue was washed first in Buffer A (10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF), then in Buffer B (10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF), for 10 minutes at 4C.  Imaginal discs were then dissected off the cuticles in Buffer B.  Discs were sonicated in Buffer C (10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, plus complete protease inhibitor cocktail (Roche)) on ice/EtOH.  Soluble chromatin was transferred to new tubes after centrifugation.  Fresh chromatin, precleared with protein G sepharose beads (Roche), was incubated overnight at 4C with antibody in RIPA buffer (140mM NaCl, 10mM HEPES, 1mM EDTA, 1% Glycerol, 1% Triton X-100, 0.1% DOC, 1mM PMSF).  Antibody-chromatin complexes were pulled down with protein G sepharose beads for 3 hours at 4C.  Bound beads were washed 4-times in RIPA buffer (as above plus 0.1mg/mL ssDNA) and once in TE.  Chromatin was eluted twice in Elution Buffer (1% SDS, 0.1M NaHCO3).  20ug Proteinase K was added, and samples were incubated for 3 hours at 55C, then 65C overnight.  DNA was purified via phenol-chloroform extraction and ethanol precipitation.
DNA samples were prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Preparation Kit.

tag: genotype

value: Sp1-GFP (BAC)

tag: developmental stage

value: leg imaginal disc

tag: antibody

value: ChIP with anti-GFP


title: Leg.Sp1.Input

description:
input
Leg.Sp1.p2q4.peaks.txt

value: input


title: Leg.Sp1.ChIP2


title: subject_232-Rectum-biopsy_442

value: Rectum

value: FALSE


title: subject_231-Sigmoid colon-biopsy_441

value: Inflamed area


title: subject_219-Transverse colon-biopsy_436

value: Transverse colon


title: Leg.Dll.ChIP3

description:
ChIP with antibody against Drosophila Dll transcription factor
Leg.Dll.p2q4.peaks.txt

value: yw

value: ChIP with anti-Dll


title: subject_71-Sigmoid colon-biopsy_435


title: subject_68-Rectum-biopsy_434

value: M

value: Non-involved area


title: subject_40-Ascending colon-biopsy_433

value: Ascending colon

value: Crohn's disease


title: subject_43-Descending colon-biopsy_430

value: Descending colon

value: Week 6


title: subject_85-Ascending colon-biopsy_432

value: F


title: subject_61-Terminal Ileum-biopsy_431

value: Terminal Ileum


title: subject_33-Ascending colon-biopsy_429


title: Leg.Dll.ChIP1

value: leg imaginal disc


title: Leg.Sp1.ChIP1

value: Sp1-GFP (BAC)

value: ChIP with anti-GFP


title: subject_284-Terminal Ileum-biopsy_426


title: Leg.Dll.ChIP2


title: subject_286-Transverse colon-biopsy_483


title: subject_74-Ascending colon-biopsy_428


title: Leg.Dll.Input

description:
input
Leg.Dll.p2q4.peaks.txt

value: input


title: subject_124-Ascending colon-biopsy_425

value: FALSE


title: subject_287-Terminal Ileum-biopsy_427


title: subject_220-Terminal Ileum-biopsy_476

value: Inflamed area


title: subject_94-Rectum-biopsy_423

value: Rectum


title: subject_123-Transverse colon-biopsy_424

value: Transverse colon


title: subject_82-Transverse colon-biopsy_420


title: AEC2-Medium-48h-Rep4

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

data_processing: Data has been log-transformed and normalized (percentile shift) within the Agilent GeneSpring V13 software

source_name: alveolar epithelial cells type 2_untreated

growth_protocol: 48h at 37°C and 5%CO2

extract_protocol: Qiagen Rneasy according to manufacturers instructions

treatment_protocol: Either 5ng/ml TGFB1, 10µM SB431542 or both together

tag: cell type

value: alveolar epithelial cells type 2

tag: donor number


title: subject_80-Ascending colon-biopsy_419

tag: age

tag: Sex

value: M


title: subject_83-Ascending colon-biopsy_421

tag: batch

tag: disease

value: Non-involved area


title: AEC2-TGFB+SB431542-48h-Rep2

scan_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

source_name: alveolar epithelial cells type 2_TGFB+SB31542


title: AEC2-TGFB+SB431542-48h-Rep4

label_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions


title: AEC2-SB431542-48h-Rep3

source_name: alveolar epithelial cells type 2_SB431542


title: AEC2-TGFB-48h-Rep4

source_name: alveolar epithelial cells type 2_TGFB


title: subject_69-Rectum-biopsy_417

tag: visit


title: AEC2-TGFB-48h-Rep2


title: AEC2-SB431542-48h-Rep1


title: AEC2-TGFB+SB431542-48h-Rep1


title: subject_72-Ascending colon-biopsy_418

source_name: Ascending colon

value: Ascending colon


title: AEC2-SB431542-48h-Rep4


title: AEC2-TGFB-48h-Rep3


title: subject_286-Terminal Ileum-biopsy_408

source_name: Terminal Ileum

value: Crohn's disease


title: AEC2-TGFB+SB431542-48h-Rep3


title: subject_59-Transverse colon-biopsy_416

source_name: Transverse colon


title: subject_55-Rectum-biopsy_415

source_name: Rectum


title: subject_84-Ascending colon-biopsy_422


title: subject_41-Transverse colon-biopsy_414


title: AEC2-Medium-48h-Rep2


title: subject_13-Ascending colon-biopsy_410


title: AEC2-Medium-48h-Rep3


title: subject_5-Ascending colon-biopsy_409


title: subject_18-Ascending colon-biopsy_411


title: subject_37-Ascending colon-biopsy_413


title: AEC2-SB431542-48h-Rep2


title: subject_32-Ascending colon-biopsy_412


title: IR72h_IF12_rep1

city: Singapore

first: Joonki

last: Kim

address: 2 Medical drive, Blk MD9

department: Physiology, School Of Medicine

country: Singapore

institute: National University of Singapore

data_processing:
Raw image data file from high-throughput sequencing (Illumina) was transformed to Sequenced Reads (Raw data or Raw reads) by CASAVA base recognition (Base calling).
Low quality reads was trimmed using command-line.
Alignment to reference genome was performed using TopHat2 (Kim et al., 2013).
FPKM (Fragments Per Kilo bases per Million reads) to estimate gene expression levels was performed according to Mortazavi et al. (2008).
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Excel files containing quantified 'FPKM' and 'Readcount' values of all 72 samples.

source_name: Brain

extract_protocol:
Total RNA was extracted from the frozen brain tissue samples using a micro-tube tissue homogenizer and EZ-10 DNAaway RNA extraction mini-prep kit following manufacturer's instruction. Samples with only RIN above 7 were seleted for the rest of the procedures.
Purified mRNA was used for library preparation for sequencing using standard Illumina protocols.

treatment_protocol: Feeding methods: (AD) Ad libitum diet feeding group which had free flow of food pellet 24 h per  day; EOD is every-other-day fasting group which had 24 h of fasting and consecutive 24 h free feeding day loop; IF12 is intermittent fasting 12 h group which had 12 h of fasting time every day. IF16 is intermittent fasting 16 h group which had 16 h of fasting time every  day.

tag: diet

tag: strain

value: Brain

value: 7 months


title: IR72h_IF16_rep3

tag: tissue


title: IR72h_IF12_rep3


title: IR72h_IF16_rep2


title: IR72h_IF16_rep1


title: IR72h_EOD_rep2

value: every-other-day fasting


title: AEC2-Medium-48h-Rep1


title: IR72h_EOD_rep3


title: AEC2-TGFB-48h-Rep1


title: IR72h_EOD_rep1


title: subject_230-Transverse colon-biopsy_406

value: Week 6

tag: inflammation


title: subject_369-Terminal Ileum-biopsy_405

value: Terminal Ileum


title: subject_68-Transverse colon-biopsy_401


title: IR72h_AL_rep3

value: Ad libitum


title: subject_219-Sigmoid colon-biopsy_403

source_name: Sigmoid colon

value: Sigmoid colon

value: F


title: IR72h_AL_rep2


title: subject_71-Descending colon-biopsy_402

source_name: Descending colon

value: Descending colon

value: FALSE


title: subject_94-Sigmoid colon-biopsy_392

value: Week 22


title: IR24h_IF16_rep3


title: IR72h_AL_rep1


title: IR72h_IF12_rep2


title: subject_221-Sigmoid colon-biopsy_404

value: Inflamed area


title: subject_83-Ascending colon-biopsy_389


title: subject_82-Rectum-biopsy_388

value: Rectum


title: subject_80-Ascending colon-biopsy_386

value: M


title: subject_82-Transverse colon-biopsy_387

value: Transverse colon

value: Non-involved area


title: IR24h_IF16_rep2


title: IR24h_IF16_rep1


title: IR24h_IF12_rep2


title: subject_80-Terminal Ileum-biopsy_385

value: Crohn's disease


title: subject_55-Terminal Ileum-biopsy_381


title: subject_72-Transverse colon-biopsy_384


title: IR24h_IF12_rep1

value: Brain


title: IR24h_EOD_rep3

value: 7 months


title: IR24h_IF12_rep3


title: subject_55-Terminal Ileum-biopsy_380


title: IR24h_EOD_rep2

value: every-other-day fasting


title: IR24h_EOD_rep1


title: IR24h_AL_rep3


title: IR12h_IF16_rep3


title: IR24h_AL_rep2


title: IR24h_AL_rep1


title: subject_37-Transverse colon-biopsy_379


title: IR12h_IF16_rep2


title: IR12h_IF16_rep1


title: subject_34-Rectum-biopsy_362

value: Week 6


title: IR12h_IF12_rep3


title: IR12h_IF12_rep2


title: IR12h_IF12_rep1


title: subject_34-Ascending colon-biopsy_363

value: Ascending colon


title: subject_286-Rectum-biopsy_371


title: subject_286-Transverse colon-biopsy_372


title: IR12h_EOD_rep3


title: subject_286-Ascending colon-biopsy_373


title: IR12h_EOD_rep2


title: subject_13-Terminal Ileum-biopsy_360

value: Terminal Ileum


title: subject_83-Terminal Ileum-biopsy_357


title: subject_84-Descending colon-biopsy_347


title: subject_34-Transverse colon-biopsy_364


title: subject_124-Descending colon-biopsy_352


title: subject_71-Terminal Ileum-biopsy_368


title: subject_32-Descending colon-biopsy_350


title: IR12h_AL_rep3

value: Ad libitum


title: subject_371-Rectum-biopsy_361


title: IR12h_EOD_rep1


title: IR12h_AL_rep2


title: subject_83-Transverse colon-biopsy_346

value: F


title: subject_371-Terminal Ileum-biopsy_340


title: subject_13-Transverse colon-biopsy_343


title: subject_70-Terminal Ileum-biopsy_341


title: IR03h_IF16_rep3


title: IR12h_AL_rep1


title: IR03h_IF16_rep1


title: IR03h_IF12_rep3


title: IR03h_IF16_rep2


title: IR03h_IF12_rep1


title: subject_54-Descending colon-biopsy_336

value: Descending colon


title: IR03h_EOD_rep3


title: IR03h_IF12_rep2


title: IR03h_EOD_rep2


title: IR03h_AL_rep3


title: IR03h_AL_rep1


title: IR03h_AL_rep2


title: subject_95-Transverse colon-biopsy_333

value: FALSE


title: ISConly_IF16_rep3


title: ISConly_IF16_rep2


title: subject_5-Terminal Ileum-biopsy_375

value: Week 22


title: ISConly_IF16_rep1


title: ISConly_IF12_rep3


title: ISConly_IF12_rep2


title: 2aECKO_brains

first: Bernice

middle: H

last: Wong

address: 8 College Road, Level 8

department: Cardiovascular and Metabolic Disorders

institute: Duke-NUS Medical School, Singapore

description: Gene expression data from brain

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix GeneChip® Mouse Genome 430 2.0 Array for 16hrs at 45ºC.

scan_protocol: GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). Scanning was done using the GeneChip®  Scanner 3000 7G (Affymetrix)

data_processing: CEL files were processed with Partek Genomics Suite 6.6 according to the gene expression workflow using RMA import settings.

source_name: postnatal day 9 2aECKO brains

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® 3' IVT PLUS Reagent Kit User Manual, Affymetrix)

growth_protocol: All mice were housed in colony cages on a 12hr light/12 hr dark cycle with controlled humidity and temperature at 23ºC. Mice were fed ad libitum on a normal chow diet (Global 18% Protein Rodent Diet from Harlan, Envigo) and have free access to water.  Pups were weaned at 3 weeks of age. Both male and female mice were used in all experiments and no gender differences were observed.

extract_protocol: Tissues were lysed in TRIzol (ThermoFisher Scientific) using a MagNA Lyser Instrument (Roche). Total RNAs were extracted according to protocol described by Untergasser Lab (Untergasser A. “RNAprep - Trizol combined with Columns” Untergasser's Lab. Winter 2008.). RNA concentration was quantified using Nanodrop.

value: brain

value: Mfsd2afl/fl, Tie2-cre

value: postnatal day 9


title: 2afl/fl_brains

description: Gene expression data from brain

source_name: postnatal day 9 Mfsd2afl/fl brains


title: ISConly_IF12_rep1


title: ISConly_EOD_rep3


title: ISConly_EOD_rep2


title: IR03h_EOD_rep1


title: ISConly_AL_rep3