title: RNAseq_T10_rep2

city: Austin

first: Sibum

last: Sung

state: Texas

address: 2506 SPEEDWAY, Stop A5000

department: Molecular Biosciences

institute: University fo Texas at Austin

description: RNAseq_normalized_average_transcript_counts.xlsx

data_processing:
ChIP-seq and RNA-seq reads were aligned to Arabidopsis TAIR10 genome using Bowtie2 and Tophat, respectively.
Aligned RNA-seq reads were transformed to digital counts using Rsubread, and following statistical analysis were done in edgeR.
ChIP-seq peaks were called by MACS2

source_name: seedling

growth_protocol: The Arabidopsis Col-0 with a functional FRI allele was used as the wild-type strain. Standard growth conditions were 22 ˚C with a 16-h light/8-h dark (long day) photoperiodic cycle under white fluorescent light.

extract_protocol:
Harvested samples were flash-frozen in liquid nitrogen. Total RNA was extracted using the Trizol/chloroform method.
Ribosomal RNAs were depleted from the extracted RNA using RiboMinus Plant Kit (Thermo Fisher). The polyA-enrichment procedure was omitted in order to capture the total RNA. Library construction was done using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions.

tag: ecotype

tag: treatment

value: 40 day cold followed by 10 day normal


title: ASD 32

status: Public on Aug 01 2020

type: genomic

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

country: Japan

institute: Hirosaki University Graduate School of Medicine

description: Genome-Wide Human SNP Array 6.0

hyb_protocol: Hybridization were carried out using the SNP 6 Core Reagent Kit and a GeneAmp® PCR System 9700 in accordance with manufacture's instructions. Samples were loaded onto  the arrays to rotate in the hybridization oven (GeneChip® Hybridization Oven 645) for 18 hours at 50℃ and 60 rpm. After hybridization, the arrays were washed and stained using GenomeWideSNP6_450 protocol for the Fluidics Station 450.

scan_protocol: GeneChips® were scanned using the GeneChip® Scanner 3000 7G controlled by Affymetrix GeneChip® Command Console® software.

data_processing:
Generated CEL files were conducted to normalize signal intensities using Genotyping Console. Copy number states were derived from a Hidden Markov Model based algorithm implemented Birdseed v2.
Copy number state: 0, 1, 2, 3, 4

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from peripheral blood

label_protocol: Fragmented DNA were subjected to 3' terminal labeling with TdT enzyme.

extract_protocol: Genomic DNA from peripheral blood were extracted using QIAamp DNA Blood Mini kit (QIAGEN, Hilden, Germany) in accordance with manufacturer's instructions. 500 ng of genomic DNA was carried out to digestion by Sty and Nsp.

tag: disease

value: Autism spectrum disorder (ASD)

tag: race

value: Japanese

tag: gender

value: female


title: SKNAS cells treated with 1 µM CYC065 for 1 hr (S6)

type: RNA

city: Belmont

first: Evon

last: Poon

state: Surrey

address: 15, Cotswold Road, Godstone Road

department: Clinical Studies

country: United Kingdom

institute: Institute of Cancer Research

hyb_protocol: Following fragmentation, 5.5 ug of ss c-DNA were hybridized for 16 hr at 45C on Gene Chip® human or mouse transcriptome expression array. GeneChips were washed and stained in the Gene Chip®  Fluidics station 450

scan_protocol: GeneChips were scanned using the Gene Chip® Scanner

data_processing: Samples were RMA normalized using the “limma” package from R and differentially expressed genes were called using a linear model and empirical Bayes statistics from the “affy” package

molecule: total RNA

label_protocol: cRNA were prepared according to the standard Affymetrix GeneChip® WT PLUS Reagent Kit protocol from 100 ng total RNA and labeled (Gene Chip® human or mouse transcriptome expression array)

growth_protocol: Kelly, SKNAS, BE(2)C AND SH-SY-5Y cell lines were maintained in DMEM as recommended by the suppliers, supplemented with 10% fetal calf serum (FCS) (Gibco), and were maintained at 37°C under 5% CO2 in air.

extract_protocol: Cells or tissue were harvested using Qiagen mRNeasy Plus Kit

treatment_protocol: Kelly, BE(2)C AND SH-SY-5Y were treated with 1 µM CYC065 for 1 hour and SKNAS was treated with 5 µM CYC065 for 1 hour.  Mice were treated with CYC065 50 mg/kg or vehicle for 6 hours.

tag: cell line

value: SKNAS neuroblastoma cell line

value: 1 µM CYC065 for 1 hr


title: SKNAS cells treated with 1 µM CYC065 for 1 hr (S5)


title: BE2C in vitro CYC065 C1

description: Untreated BE(2)C cells

data_processing:
Samples were RMA normalized using the “limma” package from R and differentially expressed genes were called using a linear model and empirical Bayes statistics from the “affy” package
The file GSE89197_DE_BE2C_and_SHSY5Y.xls contains fold changes and statistics for the BE(2)C and SHSY5Y cell line data.

label: biotin and DNA Labeling Reagent

source_name: Untreated

value: BE(2)C neuroblastoma cell line

value: Untreated


title: SKNAS cells treated with 1 µM CYC065 for 1 hr (S4)


title: ASD 31

description: Genome-Wide Human SNP Array 6.0


title: RNAseq_V20d_rep2

type: SRA

country: USA

library_source: transcriptomic

organism: Arabidopsis thaliana

value: 20 day cold


title: RNAseq_V10d_rep2

value: 10 day cold


title: ASD 30

description: Genome-Wide Human SNP Array 6.0


title: ASD 29

description: Genome-Wide Human SNP Array 6.0

value: male


title: RNAseq_V1d_rep2

value: 1 day cold


title: Takara_G1

city: København Ø

first: Victoria

last: Probst

address: Genomic Medicine, Blegdamsvej 9

country: Denmark

institute: Rigshospitalet, state hospital

description:
HT_G1
single cell RNA-seq
HT_merged_counts.txt

data_processing:
Fastq files were processed on a bash shell. Two rounds of trimming was performed using TrimGalore!. First trimming removed Nextera XT adaptors. Second trimming removed cDNA amplification adaptors.
Quality assessment of sequencing output was performed by two rounds of FastQC after each trim.
Trimmed sequences were aligned using pseudoaligner ’Spliced Transcripts Alignment to a Reference’ (STAR).
Files comprising reads per gene for each sample, which were merged in a single tab-delimited file imported into R studios as a count matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: *counts.txt: Count matrices.

source_name: T47D cell line

growth_protocol: Cells were cultured in 15 ml Complete growth medium in Nunclon Delta coated flasks with 75 cm2 culture area. Cells were grown in an incubator at 37 Cand 5% CO2. Cells had a doubling time of 32 h, and were passaged twice a week at dilution 1 : 4 using TrypLETM Express Enzyme (1 X)(Cat. nr. 12604013, GIBCOTM, NY, USA). Cell line was maintained in cell culture flasks with 75 cm2 culture area.

extract_protocol: NEBNext Single Cell/ Low Input RNA Library Prep Kit (NEB), SMART-seq HT kit (Takara), and non-commercially available protocol Genome & transcriptome sequencing (G&T).

treatment_protocol: T47D single cell suspension was prepared by removal of growth medium and subsequent washing of cell layer using 10 ml PBS. Cells were disaggregated with 2 ml TrypLETM Express Enzyme (1X) (cat nr. 12604013, GibcoTM, USA) for approximately 2 min in an incubator at 37 C. Reaction was stopped adding full growth media (RPMI-1640+GlutaMAXTM (cat nr. 61870-010, GibcoTM, UK) + 10% Fetal Bovine Serum (FBS) + 5% Penicillin/ Streptamycin) in double the amount of TrypLETM. Suspension was spun down 3 min 1200 rpm. Cells were washed once in PBS, resuspended in FACS buffer (PBS + 0.04 % bovine serum albumin (BSA)), and filtered using a 100 μm strainer.

tag: cell type

value: Breast cancer cell line

tag: passages


title: RNAseq_V40d_rep2

value: 40 day cold


title: Takara_F1

description:
HT_F1
single cell RNA-seq
HT_merged_counts.txt


title: Takara_H1

description:
HT_H1
single cell RNA-seq
HT_merged_counts.txt


title: Takara_E2

description:
HT_E2
single cell RNA-seq
HT_merged_counts.txt


title: [exon] aCD3-aCD28 diagnosis-CD subject-243 biological rep-6

city: Indianapolis

first: Boyd

last: Steere

state: IN

address: Lilly Corporate Center

department: Immunology

institute: Lilly

description:
subject-ID_243
@52084400978711110317428272788209

hyb_protocol: 5 μg of biotin-labeled cDNA per HTA2 platform standard procedure

scan_protocol: Scanning performed with Affymetrix GeneChip station under default settings followed by CEL file derivation from Affymetrix GeneChip Command Console (AGCC)

data_processing:
Background correction and quantile normalization of the gene expression data obtained from the Affymetrix Human Transcriptome Array 2.0 (HTA2) platform were performed by the RMA method while controlling for batch.  Summarization was performed with RLM.  Annotations were defined by the Affymetrix NetAffx(TM) NA35 release, which is based on the GRCh37 human reference genome. Differential expression at the gene-level was performed using the empirical Bayes method implemented in LIMMA{Ritchie:ef}controlling for donor in the model.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

label_protocol: Minimum RNA input was 100ng with a concentration range of 10 ng/μl to 50 ng ng/μl.  Label molecule was biotin.  Amplification performed using standard protocol from Affymetrix WT Express Kit.

growth_protocol: Whole blood was collected into EDTA-containing tubes. PBMC were purified using Ficoll-Paque density gradient purification. The absolute number of cells was determined using a haemocytometer (Marienfeld).

extract_protocol: Total RNA was extracted from cultured cells, using the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s protocol. The RNA yield was determined by quantifying the samples on an Agilent Bioanalyzer.  Only samples with a 28S/18S ratio of 0.8 to 3.0 and a RIN Score of >= 6.0 passed QC metrics and were accepted for analysis.

treatment_protocol: For stimulation assays, 0.5×10^6 to 1×10^6 PBMC were cultured in 200 μl medium in duplicates in round bottom 96-well plates and exposed to ultrapure 200 ng/ml LPS (Enzo Life Sciences; Cat.# ALX-581-008), 200 ng/ml L18MDP (Invivogen) 10 μg/ml anti-IL-10R (Biolegend; clone: 3F9), and/or anti-CD3/anti-CD28 beads (Invitrogen) for 16 hours in complete RPMI with L-glutamine (Sigma) supplemented with 10 % human serum (Sigma; Cat.# H4522), non-essential amino acids (Gibco); 1 mM Sodium-Pyruvate (Gibco) and 100 U/ml penicillin and 10 μg/ml streptomycin (Sigma).

tag: stimulation

tag: diagnosis

value: CD

tag: Sex

value: M

tag: batch

tag: tissue

value: peripheral PBMC


title: ASD 28

description: Genome-Wide Human SNP Array 6.0


title: G&T_C2

description:
GT_C2
single cell RNA-seq
GT_merged_counts.txt


title: RNAseq_V1h_rep2

value: 1 hour cold


title: Takara_E1

description:
HT_E1
single cell RNA-seq
HT_merged_counts.txt


title: ASD 27

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)


title: [exon] aCD3-aCD28 diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978708110317428272788044

value: F


title: Takara_D2

description:
HT_D2
single cell RNA-seq
HT_merged_counts.txt


title: ASD 26

description: Genome-Wide Human SNP Array 6.0

value: Japanese


title: Untreated SKNAS cells (S2)

source_name: Untreated SKNAS cells

value: SKNAS neuroblastoma cell line


title: RNAseq_NV_rep2

value: normal


title: Untreated SKNAS cells (S1)


title: Kelly cells treated with 1 µM CYC065 for 1 hr (K6)

value: Kelly neuroblastoma cell line

value: 1 µM CYC065 for 1 hr


title: Kelly cells treated with 1 µM CYC065 for 1 hr (K5)


title: Untreated Kelly cells (K3)

source_name: Untreated Kelly cells

value: Untreated


title: ASD 44

description: Genome-Wide Human SNP Array 6.0


title: Kelly cells treated with 1 µM CYC065 for 1 hr (K4)


title: G&T_F1

description:
GT_F1
single cell RNA-seq
GT_merged_counts.txt


title: ASD 25

description: Genome-Wide Human SNP Array 6.0

value: female


title: RNAseq_T10_rep1

value: 40 day cold followed by 10 day normal


title: ASD 24

description: Genome-Wide Human SNP Array 6.0


title: ASD 36

description: Genome-Wide Human SNP Array 6.0

value: male


title: RNAseq_V40d_rep1


title: RNAseq_V20d_rep1

value: 20 day cold


title: Takara_D1

description:
HT_D1
single cell RNA-seq
HT_merged_counts.txt

value: Breast cancer cell line


title: ASD 23

description: Genome-Wide Human SNP Array 6.0


title: ASD 39

description: Genome-Wide Human SNP Array 6.0


title: Takara_C1

description:
HT_C1
single cell RNA-seq
HT_merged_counts.txt


title: RNAseq_V10d_rep1

value: 10 day cold


title: Takara_B2

description:
HT_B2
single cell RNA-seq
HT_merged_counts.txt


title: Untreated Kelly cells (K1)


title: Untreated Kelly cells (K2)


title: ASD 22

description: Genome-Wide Human SNP Array 6.0


title: RNAseq_V1d_rep1

value: 1 day cold


title: ASD 21

description: Genome-Wide Human SNP Array 6.0


title: Untreated SKNAS cells (S3)


title: Takara_B1

description:
HT_B1
single cell RNA-seq
HT_merged_counts.txt


title: RNAseq_V1h_rep1


title: ASD 20

description: Genome-Wide Human SNP Array 6.0


title: Takara_A2

description:
HT_A2
single cell RNA-seq
HT_merged_counts.txt


title: RNAseq_NV_rep1


title: ASD 19

description: Genome-Wide Human SNP Array 6.0


title: Takara_A1

description:
HT_A1
single cell RNA-seq
HT_merged_counts.txt


title: NEB_H2

description:
NEB_H2
single cell RNA-seq
NEB_merged_counts.txt


title: NEB_G2

description:
NEB_G2
single cell RNA-seq
NEB_merged_counts.txt


title: forearm, ulcer nonhealer, X215_s

city: Boston

first: Aristidis

last: Veves

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

data_processing:
FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was utilized for initial quality metrics on raw FASTQ files. Reads were trimmed and had adapters removed using cutadapt at Phred score 10 and minimum read length 17. Processed reads were mapped to Ensembl 91 using STAR in 2-pass mode
Aligned BAM files were sorted and indexed using sambamba. Read quantification to exonic and genic regions was performed using featureCounts in both stranded and unstranded mode. Duplicate alignments were marked using Picard (http://broadinstitute.github.io/picard/).
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: gene count matrix

source_name: forearm whole skin

extract_protocol:
Total RNA was isolated from snap frozen forearm punch biopsies using the miRNeasy Mini Kit (Qiagen). 1ug of total RNA was used for library construction.
Sequencing libraries of ribosomal RNA depleted RNA were generated using the NEBNext® Ultra™ II RNA Library Prep kit, per the manufacturer’s instructions.

tag: disease state

value: Diabetes

tag: group

value: Diabetes - Ulcer - Non Healer

tag: age

value: forearm whole skin


title: 40V_H3K36me3_rep2

library_source: genomic

extract_protocol:
Seedlings were crosslinked at 4 ˚C with 1% formaldehyde solution under vacuum for 25 min. The reaction was terminated by addition of 0.125 M glycine. Crosslinked seedlings were rinsed in distilled water and then flash frozen in liquid nitrogen. ChIP was performed following the Abcam ChIP protocol (https://www.abcam.com/protocols/chip-using-plant-samples---arabidopsis)
Library construction was done using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® (NEB) following the manufacturer’s instructions.

tag: antibody

value: 40 day cold


title: ASD 17

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)

value: Japanese


title: Min6 cells overexpressing EGFP_NS

city: Changsha

first: Yan-Shan

last: Dai

state: Hunan

address: Furong District People's road, No. 139

country: China

institute: Central South University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Mus musculus

source_name: Min6 cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetr ix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Min6 cells were originally purchased from ATCC and were cultured in DMEM containing 15% FBS, 25 mM Glucose and 50 μM β-mercaptoethanol.  Min6 cells were seeded in a six-well plate and allowed to attach overnight. Min6 cells were incubated for 24 hours before collection and analysis.

extract_protocol: Min6 cells were collected.  Total RNA was extracted using  TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Min6 cells were infected with adenovirus AdV-EGFP or AdV-SPARC for 48 hours.

value: pancreatic β cell line

tag: genotype

value: overexpressing EGFP-control adenovirus


title: forearm, ulcer nonhealer, X213_s

value: M


title: NV_H3K36me3_rep2

tag: ecotype

tag: treatment

value: normal


title: Min6 cells overexpressing sparc_NS

value: overexpressing SPARC adenovirus


title: 6w TAC ko, rep3

city: Hannover

first: Christian

last: Bär

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hannover Medical School

description: H19 KO mus musculus after 6 weeks transverse aortic constriction

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 700 ng of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’ (gProcessedSignal_QuantileNormalized_Surrogate20Used)

source_name: cardiomyocytes of cardiac tissue

label_protocol: Synthesis of cRNA was performed with the ‘Quick Amp Labeling kit, no color’ (#5190-0447, Agilent Technologies), except that contained NTP-mix (to be used in the T7 reaction) was exchanged by a mix composed of 15 mM of each ATP, CTP, GTP, 11.25 mM of UTP, and 3.75 mM of aaUTP (final concentration of each nucleotide was 1.875 mM). The labeling of aaUTP-cRNA was performed by use of the Amino Allyl MessageAmp™ II Kit (#AM1753; Life Technologies) and Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies).

extract_protocol: 6weeks after TAC cardiomyocytes were isolated accoridng to retrograde perfusion method, total RNA was isolated form the cardiomyocytes using the MiRNeasy Mini Kit (Qiagen)

treatment_protocol: Adult H19 KO mice and wt littermates underwent transverse aortic constriction (TAC)

value: H19 KO

value: 6 weeks transverse aortic constriction (TAC)

value: cardiomyocytes


title: 6w TAC ko, rep2


title: 6w TAC wt, rep3

description: wildtype mus musculus after 6 weeks transverse aortic constriction

value: wildtype


title: T10_H3K4me3_rep2

value: 40 day cold followed by 10 day normal


title: 6w TAC ko, rep1


title: ASD 15

description: Genome-Wide Human SNP Array 6.0

tag: disease

tag: race

value: male


title: NEB_F1

description:
NEB_F1
single cell RNA-seq
NEB_merged_counts.txt

tag: cell line

value: Breast cancer cell line


title: forearm, ulcer nonhealer, X212_s

value: Diabetes

value: Diabetes - Ulcer - Non Healer


title: 40V_H3K4me3_rep2

value: 40 day cold


title: ASD 18

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)

tag: gender

value: female


title: T10_H3K36me3_rep2


title: 6w TAC wt, rep2

tag: cell type


title: ASD 14

description: Genome-Wide Human SNP Array 6.0

value: Japanese


title: NEB_E2

description:
NEB_E2
single cell RNA-seq
NEB_merged_counts.txt

tag: passages


title: NV_H3K4me3_rep2


title: forearm, ulcer nonhealer, X211_s

value: forearm whole skin


title: forearm, ulcer healer, X210_s

value: Diabetes - Ulcer - Healer

value: F


title: forearm, ulcer healer, X209_s

value: M


title: ASD 16

description: Genome-Wide Human SNP Array 6.0


title: 6w TAC wt, rep1


title: NEB_E1

description:
NEB_E1
single cell RNA-seq
NEB_merged_counts.txt


title: 40V_H3K27me3_rep2


title: ASD 12

description: Genome-Wide Human SNP Array 6.0


title: T10_H3K27me3_rep2


title: NEB_F2

description:
NEB_F2
single cell RNA-seq
NEB_merged_counts.txt


title: NEB_D1

description:
NEB_D1
single cell RNA-seq
NEB_merged_counts.txt


title: forearm, ulcer healer, X208_s


title: ASD 13

description: Genome-Wide Human SNP Array 6.0


title: ASD 11

description: Genome-Wide Human SNP Array 6.0


title: NEB_C2

description:
NEB_C2
single cell RNA-seq
NEB_merged_counts.txt


title: ASD 10

description: Genome-Wide Human SNP Array 6.0


title: forearm, ulcer healer, X207_s


title: T10_H3K36me3_rep1


title: NV_H3K27me3_rep2

value: normal


title: ASD 9

description: Genome-Wide Human SNP Array 6.0


title: NEB_B2

description:
NEB_B2
single cell RNA-seq
NEB_merged_counts.txt


title: forearm, ulcer healer, X206_s


title: ASD 8

description: Genome-Wide Human SNP Array 6.0


title: NV_H3K36me3_rep1


title: forearm, no ulcer, X204_s

value: Diabetes - No Ulcer


title: 40V_H3K36me3_rep1


title: forearm, no ulcer, X203_s


title: NEB_B1

description:
NEB_B1
single cell RNA-seq
NEB_merged_counts.txt


title: NEB_D2

description:
NEB_D2
single cell RNA-seq
NEB_merged_counts.txt


title: ASD 7

description: Genome-Wide Human SNP Array 6.0


title: 40V_H3K4me3_rep1


title: forearm, no ulcer, X202_s


title: NEB_A2

description:
NEB_A2
single cell RNA-seq
NEB_merged_counts.txt


title: NEB_A1

description:
NEB_A1
single cell RNA-seq
NEB_merged_counts.txt


title: ASD 5

description: Genome-Wide Human SNP Array 6.0


title: ASD 6

description: Genome-Wide Human SNP Array 6.0


title: forearm, no ulcer, X201_s


title: NEB_C1

description:
NEB_C1
single cell RNA-seq
NEB_merged_counts.txt


title: T10_H3K27me3_rep1


title: ASD 3

description: Genome-Wide Human SNP Array 6.0


title: 40V_H3K27me3_rep1


title: DKP162

city: Hamburg

first: Maksims

last: Fiosins

address: Falkenried 94

department: Center for Molecular Neurobiology

institute: University Medical Center Hamburg-Eppendorf

data_processing:
sRNA-seq analysis: We used Oasis 2 for sRNA detection, differential expression and classification analysis. Oasis 2 https://oasis.ims.bio/
Genome_build: Hg38
Supplementary_files_format_and_content: Count files: Expression of sRNAs

source_name: Peripheral blood

extract_protocol:
Isolation of total RNA from peripheral blood sample: Peripheral blood samples were collected into PAXgene Blood RNA tube (PreAnalytiX) from consenting patients and healthy controls, the tubes were gently inverted for multiple times, incubated for 20-24 hours under room temperature and stored under -80 °C until processing. Total RNA was isolated using the PAXgene Blood RNA kit (PreAnalytiX) according to the manufacturer’s protocol. The purity and concentration of isolated RNA were measured with NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific). The RNA integrity was determined by Agilent RNA 6000 Nanochip (Agilent Technologies) using the 2100 Bioanalyzer (Agilent Technologies).
Small RNA libraries were prepared using 1 ug high-quality RNA following the protocol of Illumina TrueSeq small RNA library kit (Illumina). In brief, 3’adapter was denatured for 2 minutes under 70°C, and ligated to the RNA with T4 RNA Ligase 2 deletion mutant for 1 hour at 28°C. Then the reaction was stopped with stop solution for 15 minutes under 28°C. Subsequently, 5’ adapter was denatured for 2 minutes at 70°C , then added to the RNA with ATP and T4 DNA ligase for 1 hour under 28°C . After adaptors ligation, the RNA was reverse transcribed to complement DNA (cDNA) by using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) and dNTPs for 1 hour at 50°C. Then, the cDNA was indexed and amplified with PCR mix and primers supplied in the kit for 12 cycles (denaturing at 98°C for 30 s, annealing at 60°C for 30 s, extension at 72°C for 15 s, with a final extension at 72°C for 10 min). Amplified and indexed cDNAs were then pooled together, mixed with DNA loading dye and loaded on a 5% TBE acrylamide gels (Bio-Rad). After 57 minutes electrophoresis under 145 V, the gel was stained with Midori Green for 5 minutes and viewed under the UV transilluminator, fragments between Illumina’s custom ladder 145 bp to 160 bp were cut out for library preparation. The gel was centrifuged at 20,000 x g for 2 minutes through a Gel Breaker tube (Bio-Cat). Then cDNA was eluted from the homogenized gel by adding 300ul UltraPure water and shaking under 800 x rpm for 2 hours. Then the gel was transferred on a 5 um filter tube (Bio-Cat) and centrifuged for 10 seconds under 600 x g and the gel debris was separated. Afterward, 2ul Glycoblue, 30ul of 3M sodium acetate and 975ul 100% ethanol (pre-chilled under -20°C) were added and well mixed to the sample, following an immediate centrifuge at 20,000 x g for 20 minutes under 4°C. After  remove and discard the supernatant, the pellet was washed with 500ul 70% pre-chilled ethanol. The supernatant was discarded after sample being centrifuged at 20,000 x g for 2 minutes under room temperature, and the pellet was dried in a 37°C heat block for 10 minutes with open lid. Finally, the pellet was resuspended in 10ul 10mM Tris-HCL (pH 8.5) and the sample quality was checked using Agilent High Sensitivity DNA chip (Agilent Technologies) using the 2100 Bioanalyzer (Agilent Technologies). All high quality libraries were then sequenced on Illumina HiSeq 2000 Sequencer.

value: Peripheral blood

value: Parkinson’s disease


title: DKP161


title: Takara_C2

description:
HT_C2
single cell RNA-seq
HT_merged_counts.txt


title: ASD 2

description: Genome-Wide Human SNP Array 6.0


title: DKP160


title: T10_H3K4me3_rep1

value: 40 day cold followed by 10 day normal


title: ASD 1

description: Genome-Wide Human SNP Array 6.0

value: male


title: T10_input


title: control 124

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: NV_H3K4me3_rep1


title: DKP156


title: 40V_input


title: DKP155


title: ASD 4

description: Genome-Wide Human SNP Array 6.0


title: NV_input


title: control 123

description: Genome-Wide Human SNP Array 6.0


title: control 122

description: Genome-Wide Human SNP Array 6.0


title: DKP154


title: DKP153


title: NV_H3K27me3_rep1


title: DKP157


title: E14 ESCs, Day 4 (+OHT) -LIF REP1

city: LEICESTER

first: RICHARD

middle: DAVID WILLIAM

last: KELLY

address: LANCASTER ROAD

department: BIOCHEMISTRY

institute: UNIVERSITY OF LEICESTER

description:
Day 4 (+OHT) -LIF
SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Genome Studio

label: Biotin

source_name: E14 embryonic stem cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: ES cell lines were maintained on gelatinized plates in standard ES cell medium consisting of Knockout DMEM (Invitrogen), 15% fetal calf serum (FCS), 1_ glutamine/penicillin/streptomycin (Invitrogen), 100 _M _-mercaptoethanol (Sigma-Aldrich), and Leukemia inhibitory factor (LIF) under feeder free conditions. To induce Hdac1/2 deletion (HDAC1-/-; HDAC2-/wt), cells were cultured for 16 hours in the presence of 4-hydyoxytamoxifen (OHT, 1_M), to activate the CreER fusion protein. Spontaneous differentiation was induced by the removal of Leukemia inhibitory factor (-LIF) for 4 days.

extract_protocol: Total RNA was isolated from ES cells using Trizol (Invitrogen) and RNeasy MinElute Cleanup Kit.

treatment_protocol: To induce Hdac1/2 deletion, cells were cultured for 16 hours in the presence of 4-hydyoxytamoxifen (OHT, 1uM), to activate the CreER fusion protein. To induced spontaneous differentiation cells were culture in media without LIF (-LIF).

tag: strain

value: ESCs

value: Male

value: HDAC1-/-; HDAC2-/wt

tag: culture conditions

value: cultured without LIF

tag: agent

value: OHT

tag: time

value: Day 4


title: Rat 71

city: Maastricht

first: Zita

last: Soons

state: Netherlands

address: Postbus 616

department: General Surgery

country: Netherlands

institute: Maastricht University

data_processing:
Isoform expression was quantified using RSEM v1.1.15. As a reference, we used the gene definitions from the University of California Santa Cruz for genome build rn5. RSEM was run with default parameters.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include the following values for each sample: transcriptCount, transcriptExpression, TPM, FPKM, transcriptCountPosteriorEstimate, transcriptExpressionPosteriorEstimate, transcriptExpressionLowerBound, transcriptExpressionUpperBound, TPM_PosteriorEstimate FPKM_PosteriorEstimate

organism: Rattus norvegicus

source_name: Kidney tissue

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) was used with 100–1000 ng of total RNA for the construction of sequencing libraries. In short, total RNA samples were poly(A)-selected and subsequently reverser transcribed into double-stranded cDNA. The following steps were cDNA fragmentation, end-repair, and polyadenylation before ligation of the TruSeq adapters containing the index for multiplexing. We checked the quality and quantity of the libraries with a Qubit (1.0) fluorometer and the Caliper LabChip® GX (Caliper Life Sciences, Inc.). The product had an average fragment size of ∼260bp. We normalized the libraries to 10 nm in 10 mm Tris-Cl, pH 8.5 with 0.1% Tween 20.
Total RNA samples were poly(A)-selected and subsequently reverser transcribed into double-stranded cDNA. The following steps were cDNA fragmentation, end-repair, and polyadenylation before ligation of the TruSeq adapters containing the index for multiplexing. We checked the quality and quantity of the libraries with a Qubit (1.0) fluorometer and the Caliper LabChip® GX (Caliper Life Sciences, Inc.). The product had an average fragment size of ∼260bp. We normalized the libraries to 10 nm in 10 mm Tris-Cl, pH 8.5 with 0.1% Tween 20.
The TruSeq SR Cluster kit v3-cBot-HS (Illumina, Inc.) was used for cluster generation. Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS kit v3-HS (Illumina, Inc.).

treatment_protocol: The animals were randomized for hyperammonemic diet or ad libitum standard laboratory chow.

value: Sprague Dawley

tag: diet

value: normal diet

tag: Sex


title: E14 ESCs, Day 0 (+OHT) -LIF REP3

description:
Day 0 (+OHT) -LIF
SAMPLE 9

value: wild type

value: Day 0


title: Rat 88


title: E14 ESCs, Day 4 (+OHT) -LIF REP3

description:
Day 4 (+OHT) -LIF
SAMPLE 12


title: E14 ESCs, Day 0 (+OHT) -LIF REP2

description:
Day 0 (+OHT) -LIF
SAMPLE 8


title: control 120

description: Genome-Wide Human SNP Array 6.0

value: Japanese


title: E14 ESCs, Day 4 (+OHT) +LIF REP3

description:
Day 4 (+OHT) +LIF
SAMPLE 6

value: cultured with LIF


title: Rat 69

value: hyperammonemic diet


title: E14 ESCs, Day 0 (+OHT) -LIF REP1

description:
Day 0 (+OHT) -LIF
SAMPLE 7


title: DKP152

tag: tissue

value: Peripheral blood

tag: age

value: Parkinson’s disease


title: DKP149

value: male


title: control 119

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: control 118

description: Genome-Wide Human SNP Array 6.0

value: female


title: E14 ESCs, Day 4 (+OHT) +LIF REP2

description:
Day 4 (+OHT) +LIF
SAMPLE 5

value: ESCs

value: Male

tag: genotype


title: DKP145


title: Rat 67


title: DKP144


title: control 117

description: Genome-Wide Human SNP Array 6.0


title: Rat 61


title: E14 ESCs, Day 4 (+OHT) -LIF REP2

description:
Day 4 (+OHT) -LIF
SAMPLE 11

value: HDAC1-/-; HDAC2-/wt

value: cultured without LIF


title: control 121

description: Genome-Wide Human SNP Array 6.0


title: DKP142


title: control 116

description: Genome-Wide Human SNP Array 6.0


title: E14 ESCs, Day 4 (+OHT) +LIF REP1

description:
Day 4 (+OHT) +LIF
SAMPLE 4

value: OHT

value: Day 4


title: E14 ESCs, Day 0 (+OHT) +LIF REP1

description:
Day 0 (+OHT) +LIF
SAMPLE 1


title: control 114

description: Genome-Wide Human SNP Array 6.0


title: E14 ESCs, Day 0 (+OHT) +LIF REP2

description:
Day 0 (+OHT) +LIF
SAMPLE 2


title: E14 ESCs, Day 0 (+OHT) +LIF REP3

description:
Day 0 (+OHT) +LIF
SAMPLE 3


title: DKP135


title: E14 ESCs, LBH589_18hr REP3

description:
LBH589_18hr REP3
SAMPLE 12

growth_protocol: ES cell lines were maintained on gelatinized plates in standard ES cell medium consisting of Knockout DMEM (Invitrogen), 15% fetal calf serum (FCS), 1_ glutamine/penicillin/streptomycin (Invitrogen), 100 _M _-mercaptoethanol (Sigma-Aldrich), and Leukemia inhibitory factor (LIF) under feeder free conditions. wild type (Ctrl/0hr) E14 ESC were compared to ESC treate with Panobinostat/LBH589 (50nM) for 2hr, 6hr and 18hr.  Each time points were analyzed in triplicate.

treatment_protocol: To inhibit HDAC activity , E14 ESC were treated with Panobinostat/LBH589 (50nM) for 2hr, 6hr and 18hr.


title: DKP133


title: EC62-SLUG - D2

city: Irvine

first: Christopher

last: Hughes

state: CA

address: 2400 Biological Sciences III, Hughes Lab

institute: University of California, Irvine

data_processing:
Quality control was performed on data using FASTQC(v. 0.11.2)
Reads were trimmed using Trimmomatic(v.0.32) with Illumina TruSeq adapter sequences using a PHRED quality score 15 and minimum length 20 bases.
Trimmed reads were then aligned to the human hg19 reference genome using the Ensembl GRCh37 annotations and post processed using Tophat2(v.2.0.12), Bowtie2(v.2.2.3) and Samtools(v.0.1.19).
Expression levels were quantified both with FPKM (Fragment per kilobase per million mapped reads) using Cufflinks(v. 2.1.1) and with raw counts using HTSeq(v.0.6.1p1.).
Genome_build: human hg19 reference genome, Ensembl GRCh37 annotations
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample ...

growth_protocol: The 3D Fibrin bead assay was performed using either control GFP or Slug overexpressing GFP (SlugOE) HUVEC with three biological replicates each. The EC were harvested at day 2 and day 6 post-embedding

extract_protocol:
The monolayer of Human Lung Fibroblasts seeded on top of the gel were first completely removed and the angiogenic EC were extracted from fibrin-gel using serial trypsinization using 5% trypsin. Cells were then released from the cytodex beads using Collagenase IV. Individual EC were separated from the beads using 100µm cell strainer and centrifugation. The EC were then lysed in RNA lysis buffer and incubated at 55ºC with Protease K (Qiagen 19131) for 15 minutes. The RNA was then isolated following the manufacturer’s protocol using a Qiagen RNA Mini Kit (Qiagen 74104).
RNA integrity (RIN) was measured for all samples using a Bioanalzyer Agilent 2100. All sequencing libraries analyzed were generated from RNA samples with a RIN score ≥ 9. The Illumina TruSeq mRNA stranded protocol was used to obtain poly-A mRNA from all samples. A total of 200ng of isolated mRNA was used to construct RNA-seq libraries, and these were quantified and normalized using the Library Quantification Kit from Kapa Biosystems

value: HUVEC

tag: cell line number

tag: tissue/cell type

value: human umbilical vein/vascular endothelium

tag: time point

value: Angiogensis Day 2

tag: genotype/variation

value: Slug OE


title: EC62-GFP - D2

value: GFP Ctrl


title: EC62-GFP - D6

value: Angiogensis Day 6


title: EC61-SLUG - D6


title: EC61-GFP - D6


title: control 111

description: Genome-Wide Human SNP Array 6.0

tag: disease

tag: race

value: Japanese


title: control 112

description: Genome-Wide Human SNP Array 6.0

tag: gender


title: control 115

description: Genome-Wide Human SNP Array 6.0


title: DKP130

value: Peripheral blood

value: Parkinson’s disease


title: DKP136

value: male


title: control 110

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: DKP128


title: EC61-SLUG - D2

tag: cell type


title: control 113

description: Genome-Wide Human SNP Array 6.0

value: female


title: E14 ESCs, LBH589_18hr REP1

description:
LBH589_18hr REP1
SAMPLE 10

tag: strain

tag: cell line

value: ESCs

value: Male

value: wild type


title: control 109

description: Genome-Wide Human SNP Array 6.0


title: E14 ESCs, LBH589_6hr REP1

description:
LBH589_6hr REP1
SAMPLE 7

tag: agent


title: DKP126


title: E14 ESCs, LBH589_6hr REP3

description:
LBH589_6hr REP3
SAMPLE 9

tag: time


title: E14 ESCs, LBH589_18hr REP2

description:
LBH589_18hr REP2
SAMPLE 11


title: E14 ESCs, LBH589_2hr REP3

description:
LBH589_2hr REP3
SAMPLE 6


title: E14 ESCs, LBH589_6hr REP2

description:
LBH589_6hr REP2
SAMPLE 8


title: EC61-GFP - D2


title: DKP131


title: control 108

description: Genome-Wide Human SNP Array 6.0


title: control 107

description: Genome-Wide Human SNP Array 6.0


title: control 106

description: Genome-Wide Human SNP Array 6.0


title: DKP123


title: EC64-GFP - D6


title: DKP122


title: E14 ESCs, LBH589_2hr REP2

description:
LBH589_2hr REP2
SAMPLE 5


title: EC64-SLUG - D2


title: EC64-SLUG - D6


title: DKP115


title: DKP117


title: control 105

description: Genome-Wide Human SNP Array 6.0


title: E14 ESCs, Ctrl/0hr (LBH589) REP2

description:
Ctrl/0hr (LBH589) REP2
SAMPLE 2


title: E14 ESCs, LBH589_2hr REP1

description:
LBH589_2hr REP1
SAMPLE 4


title: EC64-GFP - D2


title: EC62-SLUG - D6


title: CAF-2

city: HONGKONG

first: LIYI

last: ZHANG

state: HONGKONG

address: 21 SASSOON ROAD

department: CLINICAL ONCOLOGY

institute: THE UNIVERSITY OF HONGKONG

data_processing:
Sequencing reads were mapped to human genome assembly (NCBI Build GRCh37.1) using CLC GenomicsWorkbench. Only sequencing reads with at most 2 mismatches and a maximum of 10 mappable locations were retained for calculation of gene expression. The gene expression level is measured by RPKM (number of exon reads mapped per kilobase per million mapped reads).
Genome_build: human NCBI genome build 37.1
Supplementary_files_format_and_content: tab-delimited text files include COUNT and RPKM values for each Sample

source_name: Primary FGFR2+ Cancer associated fibroblasts

growth_protocol: FGFR2+ CAFs were isolated from ESCC specimens. In short, freshly collected tissues were cut into as small pieces as possible in sterile PBS, followed by collagenase digestion. The suspension was filtered through 20 µm stainless steel wire mesh to collect a single cell suspension. The filtrate was centrifuged and washed before being finally plated on 6 cm tissue culture dishes in 5 ml DMEM medium supplemented with 10% FBS. After culturing for 30 minutes at 37ºC, unadherent cells (mainly tumour cells) were removed to obtain pure fibroblasts.

extract_protocol:
Total RNA of fibrocytes and CAFs was isolated using the mirVana miRNA Isolation Kit. Extracted total RNA were treated with the DNA-free Kit. Large 18S and 28S ribosomal RNAs (rRNAs) were removed from total RNA with the RiboMinus Transcriptome Isolation Kit. The rRNA-depleted RNA was precipitated with Pellet Paint (Novagen Inc, Madison, WI) and checked on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). The rRNA depleted RNA was fragmented by incubation for 5 minutes at 94°C in 5× Array Fragmentation Buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary fibroblasts

value: Esophageal Squamous Cell Carcinoma (ESCC)

tag: patient id

value: ESCC patients #6-9


title: control 103

description: Genome-Wide Human SNP Array 6.0


title: control 104

description: Genome-Wide Human SNP Array 6.0


title: Fbc-2

source_name: Primary FGFR2+ fibrocytes

growth_protocol: FGFR2+ fibrocytes were purified from peripheral blood of ESCC patients. Briefly, PBMCs were isolated by centrifugation over Ficoll following the protocol of manufacturer and cultured on Fibronectin pre-coated tissue culture plates in DMEM supplemented with 10% FBS. After 2 days, the nonadherent cells (largely lymphocytes) were aspirated off, and the remaining adherent cells cultivated for 14 days. Over time, the contaminating monocytes died off, and fibrocytes appeared as spindle shaped cells. The crude fibrocytes were lifted by incubation in trypsin-EDTA 0.05% and purified by immunomagnetic selection using anti-Col I microbeads.

value: Primary fibrocytes


title: control 102

description: Genome-Wide Human SNP Array 6.0


title: DKP102

tag: Sex


title: DKP069

tag: tissue


title: CAF-1

value: ESCC patients #1-5


title: K562_S6

city: Pittsburgh

first: Yuchuan

last: Wang

state: PA

address: 5000 Forbes Ave

institute: Carnegie Mellon University

description: K562 Repli-Seq S6 fraction

data_processing:
Pipeline for processing multi-fraction Repli-Seq data can be found at https://github.com/ma-compbio/MFRT
Adapters were removed using FASTX-Toolkit with parameters fastx_clipper -Q 33 -v -n -l 10. Reads were mapped to hg38 with bwa.
The bam file was then sorted and deplicated reads were removed.
The read counts were calculated on 10kb sliding windows with 1kb step size. The total number of mapped reads were then normalized to 1 million read counts per fraction.
The raw signals of each window were normalized by the signals from G1. Genomic bins with 0 mapped reads in G1 were considered as unmappable regions.
For each 1kb bin, the replication timing signal was calculated as the percentage of the total signal over the seven fractions.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: K562 lymphoblast cell line

treatment_protocol: Exponentially growing K562 cells (ATCC CCL-243) cultured in IMDM-10% FBS were pulse-labeled with 200 μM BrdU for 60 minutes, then fixed in 70% ethanol and stained with propidium iodide as previously described (PMID: 29599440) for sorting by DNA content. FACS sorting window was defined in a similar way as previously published (PMID:19966280). Briefly, the area between G1 and G2 peaks were divided into 6 windows evenly (S1-S6). Then the same width of window (S7) was added immediately on the right of S6 to pick the cells which were at the end of S phase at the beginning of 60-minute BrdU pulse labeling and moved into G2 by the end of the pulse. Another same width of window (G1) was added immediately on the left of S1 to collect non-replicating cells. At least 120,000 cells were collected from each fraction, then using 120,000 cells each, sequencing libraries were made. From G1 fraction, the total genome library was made as the control.  From S1-S7 fraction, libraries that represent nascent DNA were made by incorporating anti-BrdU immunoprecipitation as described (PMID: 29599440). These libraries were sequenced on HiSeq 2500 with 50SE chemistry aiming to obtain 20-40 million reads each.

value: lymphoblast cell line from 53-yr-old human female with chronic myelogenous leukemia


title: K562_G2

description: K562 Repli-Seq G2 fraction


title: DKP073

tag: age


title: K562_S5

description: K562 Repli-Seq S5 fraction


title: K562_S4

description: K562 Repli-Seq S4 fraction


title: DKP067


title: Fbc-1


title: K562_S3

description: K562 Repli-Seq S3 fraction


title: E14 ESCs, Ctrl/0hr (LBH589) REP1

description:
Ctrl/0hr (LBH589) REP1
SAMPLE 1

tag: genotype


title: control 100

description: Genome-Wide Human SNP Array 6.0


title: E14 ESCs, Ctrl/0hr (LBH589) REP3

description:
Ctrl/0hr (LBH589) REP3
SAMPLE 3


title: control 101

description: Genome-Wide Human SNP Array 6.0


title: DKP066


title: DKP062B


title: 2 WT gWAT

city: St Louis

first: Irfan

middle: J

last: Lodhi

state: MO

address: 660 S Euclid Ave Campus box 8127

institute: Washington University School of Medicine in St. Louis

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were then aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.52. Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.133.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.34
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights7.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Genome_build: Aligned to m_musculus reference build Ensembl_R76

molecule: polyA RNA

source_name: Gonadal white adipose tissue

growth_protocol: Female Med19-iAKO and control mice were grown to 12-weeks of age.

extract_protocol:
Total RNA was isolated using a combination of TRIzol reagent (Invitrogen 15596026) and PureLink RNA Mini Kit (Invitrogen 12183018A).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12-week old MED19-iAKO mice were injected with 100mg/kg of tamoxifen for 5 days. 14 days post tamoxifen gWAT was harvested for RNA isolation

value: Gonadal white adipose tissue

value: 12 weeks

value: WT


title: 1 KO gWAT

value: Med19 KO


title: control 99

description: Genome-Wide Human SNP Array 6.0

value: Japanese


title: K562_S2

description: K562 Repli-Seq S2 fraction


title: DKP062A

value: Peripheral blood

value: Parkinson’s disease


title: 4 KO gWAT

value: female


title: control 98

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: K562_S1

description: K562 Repli-Seq S1 fraction


title: 7 KO gWAT


title: DKP049

value: male


title: K562_G1

description: K562 Repli-Seq G1 fraction


title: control 97

description: Genome-Wide Human SNP Array 6.0


title: control 96

description: Genome-Wide Human SNP Array 6.0


title: 9 WT gWAT


title: DKP048


title: DKP046


title: DKP044


title: DKP045


title: control 94

description: Genome-Wide Human SNP Array 6.0


title: control 93

description: Genome-Wide Human SNP Array 6.0


title: DKP043


title: 19 WT gWAT


title: 17 KO gWAT


title: WT-VAD-biol-rep3__RNAseq

city: New York

first: Johannes

middle: C.

last: van der Mijn

state: NY

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description:
WT-VAD-3
K15_S14_L006

data_processing:
Differential expression of genes was determined by the DESeq package (version 1.32, Bioconductor) in R.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: wild type_vitamin A deficient_kidney

extract_protocol:
Pieces of organ tissue were snap-frozen in liquid nitrogen; microdissected kidney cortex pieces were stored in RNAlater; Total RNA was extracted from four kidney cortices of four mice from each of the four cohorts using RNeasy spin columns (#74134, Qiagen). All samples passed the RNA quality control that was performed with a Bioanalyzer 2100 prior to further processing. The complete transcriptomes were sequenced using an Illumina HiSeq2000 Sequencer with 51bp single-end reads and 4 samples per lane as previously described
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After weaning for 2 weeks all mice were randomized to a Vitamin A (VA) sufficient regular chow (#88406, Harlan, Madison, WI) or VA-deficient diet (#88407, Harlan). Mice were sacrificed by cervical dislocation after 24 weeks to harvest the organs.

tag: strain background

value: wild type

tag: diet

value: vitamin A deficient

value: kidney


title: 89 WT gWAT


title: control 92

description: Genome-Wide Human SNP Array 6.0


title: control 91

description: Genome-Wide Human SNP Array 6.0


title: DKP042


title: DKP041


title: control 89

description: Genome-Wide Human SNP Array 6.0


title: 8 KO gWAT


title: OCI-LY7 ChromRNA Control rep2

middle: C

last: Hellmuth

state: New York

address: 413 E 69th Street

data_processing:
Casava 1.8.2 was used for basecalling.
Reads were aligned to hg38 using STAR 2.5 with default parameters.
Bam files for each condition were merged with samtools and merged bam files were converted to bigWigs using deeptools bamCoverage. Separate bigWig files were generated for each strand.
Genome_build: hg38
Supplementary_files_format_and_content: strand-specific bigWig files representing ChromRNA read coverage

source_name: DLBCL cell line

growth_protocol: Human DLBCL cell lines were grown in Iscove’s Modified Dulbecco’s Medium with 20% FBS supplemented with 1% glutamine, and 1% penicillin/streptomycin

extract_protocol:
ChromRNA-seq was performed as previously described (Bhatt et al., 2012; Lai et al., 2015) with minor changes. Nuclei were isolated using the PURE Prep Nuclei Isolation Kit (Sigma, Cat No NUC-201). 20 million LY7 cells were lysed in 800µl cold PURE Lysis Buffer containing 0.12% TritonX. The lysate was layered on 600µl of a 1.8M sucrose cushion and centrifuged at 20000g for 15min at 4C. The nuclear pellet was was resuspended in 250µl cold glycerol buffer (20mM Tris pH 7.9, 75mM NaCl, 0.5mM EDTA, 50% glycerol, 0.85 mM DTT) and then lysed with 250µl nuclear lysis buffer (20mM HEPES pH7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3M NaCl, 1M urea, 1% NP-40, 1mM DTT). Chromatin was pelleted at 14000g for 2min at 4C. RNAse inhibitor (recombinant RNAsin, Promega N2511) was added to all buffers at 100U/ml. RNA was isolated from the Chromatin-fraction using TRIzol reagent (Invitrogen).
TruSeq total RNA, stranded

value: Diffuse Large B Cell Lymphoma (DLBCL) cell line

tag: grna

value: control / non-targeting, SG93

tag: overexpression

value: CRISPRi / dCas9-KRAB

tag: molecule subtype

value: Chromatin-bound RNA


title: control 95

description: Genome-Wide Human SNP Array 6.0

data_processing:
Generated CEL files were conducted to normalize signal intensities using Genotyping Console. Copy number states were derived from a Hidden Markov Model based algorithm implemented Birdseed v2.
Copy number state: 0, 1, 2, 3, 4

source_name: genomic DNA from peripheral blood

tag: disease

tag: race


title: WT-VAD-biol-rep1__RNAseq

description:
WT-VAD-1
K13_S12_L006

tag: genotype/variation


title: DKP039


title: control 88

description: Genome-Wide Human SNP Array 6.0

tag: gender


title: OCI-LY7 ChromRNA Control rep1

tag: cell line

tag: cell type


title: TRACK-VAD-biol-rep4__RNAseq

description:
TRACK-VAD-4
K12_S11_L006

source_name: GGT-HIF1A_M3 ("TRACK")_vitamin A deficient_kidney

value: GGT-HIF1A_M3 ("TRACK")


title: DKP037


title: control 86

description: Genome-Wide Human SNP Array 6.0


title: TRACK-VAD-biol-rep3__RNAseq

description:
TRACK-VAD-3
K11_S10_L005


title: TRACK-VAD-biol-rep2__RNAseq

description:
TRACK-VAD-2
K10_S9_L005


title: DKP030


title: TRACK-VAD-biol-rep1__RNAseq

description:
TRACK-VAD-1
K9_S8_L005


title: control 84

description: Genome-Wide Human SNP Array 6.0


title: control 85

description: Genome-Wide Human SNP Array 6.0


title: DKP018


title: OCI-LY7 ChromRNA Control rep3


title: control 90

description: Genome-Wide Human SNP Array 6.0


title: WT-VAD-biol-rep2__RNAseq

description:
WT-VAD-2
K14_S13_L006


title: TRACK-biol-rep4__RNAseq

description:
TRACK-4
K8_S7_L005

value: regular chow


title: DKP040


title: DKP015


title: TRACK-biol-rep3__RNAseq

description:
TRACK-3
K7_S6_L005


title: DKP006


title: control 82

description: Genome-Wide Human SNP Array 6.0


title: DKK110

value: Control


title: control 81

description: Genome-Wide Human SNP Array 6.0


title: TRACK-biol-rep1__RNAseq

description:
TRACK-1
K5_S4_L005


title: control 87

description: Genome-Wide Human SNP Array 6.0


title: WT-biol-rep3__RNAseq

description:
WT-3
K3_S3_L005

source_name: wild type_regular chow_kidney


title: DKP031


title: control 80

description: Genome-Wide Human SNP Array 6.0


title: control 79

description: Genome-Wide Human SNP Array 6.0


title: DKK107


title: WT-biol-rep2__RNAseq

description:
WT-2
K2_S2_L005


title: control 78

description: Genome-Wide Human SNP Array 6.0


title: control 83

description: Genome-Wide Human SNP Array 6.0


title: DKK106


title: control 77

description: Genome-Wide Human SNP Array 6.0


title: control 76

description: Genome-Wide Human SNP Array 6.0


title: DKK105


title: control 75

description: Genome-Wide Human SNP Array 6.0


title: DKK102


title: TRACK-biol-rep2__RNAseq

description:
TRACK-2
K6_S5_L005


title: AML37-Fx1-3

first: Cem

last: Meydan

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

description: Frozen clinical samples, CD34-selected

data_processing:
RNAseq fastq files were trimmed using Trim Galore and cutadapt to remove adapter sequences.
Trimmed fastq files were aligned using STAR (version 2.5.1b) to the human genome (hg19) using Gencode (version v19) transcriptome assembly.
Coding genes were quantified using subread featureCounts (v1.4.5-p1) using paired and strand-specific mode to annotate uniquely mapped reads to Gencode annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts and transcripts per million (TPM)

source_name: AML37, primary cell-FX1

extract_protocol:
Total RNA from ex vivo treatments was lysed with Trizol. After adding chloroform, lysates were centrifuged at 13000 G for 30minutes, and intermediate layer was harvested as DNA/ Protein-free RNA samples. They were cleaned up using  RNeasy mini columns.
Illumina TruSeq stranded mRNA strand-specific library sequenced paired-end 50bp

treatment_protocol: Cells were treated for 12 hours using EC50 concentration for the same primary cell.

tag: treatment

value: FX1 treated

value: Acute Myeloid Leukemia primary cells


title: DKK109

value: Peripheral blood


title: DKK099


title: AML37-Fx1-2

description: Frozen clinical samples, CD34-selected


title: control 73

last: Shimoyama

address: 5 Zaifu-cho

description: Genome-Wide Human SNP Array 6.0

extract_protocol: Genomic DNA from peripheral blood were extracted using QIAamp DNA Blood Mini kit (QIAGEN, Hilden, Germany) in accordance with manufacturer's instructions. 500 ng of genomic DNA was carried out to digestion by Sty and Nsp.

value: Japanese


title: control 74

description: Genome-Wide Human SNP Array 6.0

value: female


title: DKK096


title: AML37-Fx1-1

description: Frozen clinical samples, CD34-selected


title: DKK095


title: Rat 64

tag: strain

value: Sprague Dawley

value: hyperammonemic diet

value: Male


title: control 72

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: WT-biol-rep1__RNAseq

description:
WT-1
K1_S1_L005

value: wild type

value: kidney


title: AML37-DMSO-3

description: Frozen clinical samples, CD34-selected

source_name: AML37, primary cell-DMSO

value: DMSO treated


title: control 71

description: Genome-Wide Human SNP Array 6.0


title: DKK101

tag: Sex

value: male


title: DKK094

tag: tissue


title: AML37-DMSO-2

description: Frozen clinical samples, CD34-selected


title: control 70

description: Genome-Wide Human SNP Array 6.0


title: DKK086

tag: age


title: DKK079


title: AML37-DMSO-1

description: Frozen clinical samples, CD34-selected

tag: genotype


title: control 69

description: Genome-Wide Human SNP Array 6.0


title: AML37-Minus-3

description: Frozen clinical samples, CD34-selected

source_name: AML37, primary cell-Untreated

value: Untreated


title: AML37-Minus-2

description: Frozen clinical samples, CD34-selected


title: DKK077


title: DKK070


title: AML37-Minus-1

description: Frozen clinical samples, CD34-selected


title: control 68

description: Genome-Wide Human SNP Array 6.0


title: control 67

description: Genome-Wide Human SNP Array 6.0


title: Day 7 XX male [XXM #10]

city: Cleveland

first: Kuan-Hui

middle: Ethan

last: Chen

state: MS

address: 1003 W Sunflower Rd

institute: Delta State University

description: Gene expression data from day7 thymic epithelium/stroma

hyb_protocol: Analysis used probe sets present on an Affymetrix mouse GeneChip 1.0 ST array

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files

data_processing:
These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
affymetrix-algorithm-name = plier-gene-default
affymetrix-algorithm-version = 2.0
affymetrix-array-type = MoGene-1_0-st-v1
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: Day 7 XX male

label_protocol: cRNA labelling was performed by the DNA & Protein MicroArray Facility, University of California, Irvine

growth_protocol: Mice were bred in vivarium following procedures approved by the Institutional Animal Care and Use Committee in accordance with NIH guidelines

extract_protocol: RNA was extracted from the epithelium/stroma using a Qiagen RNeasy mini for Microarray Analysis kit as per the manufacturer instructions. An on-column DNAse digestion step was performed.

treatment_protocol: Thymic epithelium/stroma was collected from day 7 pups

tag: sex/genotype

value: XX male

value: Day 7

value: Thymic epithelium


title: Day 7 XX female [XXF #11]

source_name: Day 7 XX female

value: XX female


title: Day 7 XY female [XYF #12]

source_name: Day 7 XY female

value: XY female


title: Day 7 XY female [XYF #8]


title: control 66

first: Shuji

institute: Hirosaki University Graduate School of Medicine

description: Genome-Wide Human SNP Array 6.0


title: Day 7 XY male [XYM #9]

source_name: Day 7 XY male

value: XY male


title: DKK069

source_name: Peripheral blood

value: Peripheral blood

value: Control


title: Day 7 XX male [XXM #6]


title: control 65

description: Genome-Wide Human SNP Array 6.0

value: Japanese

value: female


title: DKK068


title: Day 7 XX female [XXF #7]


title: Day 7 XY female [XYF #4]


title: shIR_rep1

city: Cambridge

first: William

last: Mallard

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: CHB8 treated with INSR-targeting shRNA

data_processing:
Reads were mapped to the human reference genome using TopHat v2.0.10 with the following options: --no-coverage-search; --transcriptome-index with a TopHat transcript index built from Gencode v19.
Gene expression was estimated using Cuffdiff v2.2.0 with default options against a reference transcriptome based on Gencode v19.
Genome_build: hg19
Supplementary_files_format_and_content: gene_exp.diff contains raw Cuffdiff output, including: gene-level expression estimates (in FPKM), log2 fold change between control and knockdown conditions, and associated p-values.

source_name: CHB8 hESCs_shIR

growth_protocol: Cells were cultured in mTeSR1 feeder-free media supplemented with 1 μg/ml puromycin as described previously (Teo et al., 2011).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit according to the manufacturer's protocol. Total RNA was quantified using the Quant-iT RiboGreen RNA Assay Kit and normalized.
Libraries were prepared with an automated variant of the Illumina TruSeq mRNA Sample Preparation Kit that preserves strand orientation of the RNA transcript. This method uses oligo-dT beads to select mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis from the RNA template. The resulting cDNA then goes through library preparation (end repair, base 'A' addition, adapter ligation, and enrichment) using indexed adapters for multiplexing. After enrichment, the libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then equimolar pooled.
Pooled libraries were normalized and denatured using 0.2 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer's protocols on an Illumina HiSeq 2500 at the Broad Institute Specialized Service Facility. Each run generated 76bp paired-end reads with 8bp barcodes. Two biological replicates were sequenced for shScr- and shIR-CHB8 hESCs.

treatment_protocol: shIR and shScr lentiviral plasmids were purchased from Open Biosystems and transfected into hESCs with Lipofectamine 2000 as described previously (Teo et al., 2011).

value: human embryonic stem cells

tag: tranfected with

value: specific INSR-targeting shRNA


title: shIR_rep2

description: CHB8 treated with INSR-targeting shRNA


title: DKK067


title: control 64

city: Hirosaki

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: shScr_rep2

description: CHB8 treated with non-targeting scrambled shRNA

source_name: CHB8 hESCs_shScr

value: non-targeting scrambled shRNA


title: control 63

description: Genome-Wide Human SNP Array 6.0


title: Day 7 XX male [XXM #5]


title: DKK066


title: Day 7 XX female [XXF #3]


title: Day 7 XY male [XYM #1]


title: Day 7 XX male [XXM #2]


title: shScr_rep1


title: DKK056


title: control 61

description: Genome-Wide Human SNP Array 6.0


title: Wildtype mouse, overload, biological rep 6

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

description: Gene expression data from overloaded plantaris muscle

hyb_protocol: 50 ng in hybridization buffer were loaded onto the GeneChip array

scan_protocol: The arrays were scanned with the Affymetrix 428 Scanner

data_processing: Data were processed with the Affymetrix GeneChip Command Console Software (AGCC) to produce the CEL files that could be uploaded to the GenePattern platform (PMID: 18551415) for further downstream analysis and visualization. Normalization of raw data with RMA, quantile normalization, background correction, no present/absent calls calculated, median scaling.

source_name: Wildtype mouse

label_protocol: Random priming of 1000 ng total RNA after rRNA removal (RiboMinus procedure), in vitro transcription-based linear amplification using the Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay. Following random incorporation of of dUTP during second-cycle, first-strand reverse transcription, strands are fragmented by treatment with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the unnatural dUTP residues and breaks the DNA strand. DNA is labeled by terminal deoxynucleotidyl ransferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

extract_protocol: Animals were sacificed and the plantaris muscles were immediately removed. Total RNA was extracted after homogenization of the muscle with an Ultraturrax® with the TRIzol® protocol. The muscle of only one side was used for this experiment.

treatment_protocol: Mice at the age of 3 months (n=6 per experimental group) were anesthetized with pentobarbitone (ip, 50 mg/kg body weight) and the plantaris muscles of both legs from each mouse were mechanically overloaded by the surgical removal of the soleus muscles and a major portion of the gastrocnemius muscles as described in PMID 6460726, 22511986). Control animals remained untreated.

tag: muscle

value: plantaris muscle

value: wt

tag: experimental condition

value: overlaod of plantaris muscle


title: DKK055


title: Wildtype mouse, overload, biological rep 5


title: control 60

description: Genome-Wide Human SNP Array 6.0


title: DKK054

value: male


title: control 59

description: Genome-Wide Human SNP Array 6.0


title: Wildtype mouse, overload, biological rep 4


title: control 58

description: Genome-Wide Human SNP Array 6.0


title: DKK052


title: control 57

description: Genome-Wide Human SNP Array 6.0


title: control 62

description: Genome-Wide Human SNP Array 6.0


title: DKK051


title: DKK043


title: control 55

description: Genome-Wide Human SNP Array 6.0


title: DKK042


title: Wildtype mouse, overload, biological rep 3


title: CB2008050-S-57_sensitive

city: Beijing

first: Haizhao

last: Yi

address: No. 52 Fucheng Rd., Haidian District

institute: Peking University Cancer Hospital & Institute

description: Gene expression data from rectal cancer tissue

hyb_protocol: The labeled cRNA targets were then hybridized on the slides

scan_protocol: After hybridization, slides were scanned by GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, US).

data_processing: Data were extracted with Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US). Raw data were normalized by the MAS 5.0 algorithm, and Gene Spring Software v12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: RECTAL CANCER

label_protocol: RNA samples of each group were subsequently used to generate fluorescence-labeled cRNA targets for the Affymetrix Human U133 Plus 2 arrays .

growth_protocol: All the tumor tissues were stored at -80°C before extraction

extract_protocol: Total RNA was  isolated using TRIzol reagent (Life technologies, Carlsbad, CA, US), according to the manufacturer’s instructions, and purified by using the RNeasy Mini Kit (Qiagen, GmBH, Germany)

treatment_protocol: Pre-treatment tumor staging was performed in all patients using endorectal ultrasonography, pelvic magnetic resonance imaging, or computed tomography. The radiotherapy regimen consisted of a 50.6 Gy dose delivered in 22 fractions with concurrent capecitabine treatment for 5 weeks

tag: disease state

value: rectal cancer

value: rectal cancer biopsy

tag: sensitivity

value: sensitive

tag: patient age

tag: tumor stage


title: Wildtype mouse, overload, biological rep 2


title: control 54

description: Genome-Wide Human SNP Array 6.0

tag: disease

tag: race

tag: gender


title: CB2008050-S-54_sensitive


title: DKK041


title: Wildtype mouse, no overload, biological rep 6

description: Gene expression data from control plantaris muscle

value: no overload


title: CB2008050-S-55_sensitive


title: Wildtype mouse, no overload, biological rep 5


title: DKK040


title: Wildtype mouse, overload, biological rep 1


title: control 53

description: Genome-Wide Human SNP Array 6.0


title: Wildtype mouse, no overload, biological rep 4


title: CB2008050-R-10_resistant

value: resistant


title: CB2008050-S-52_resistant


title: control 56

description: Genome-Wide Human SNP Array 6.0


title: DKK039

value: Peripheral blood


title: CB2008050-R-09_resistant


title: CB2008050-S-53_sensitive

value: unknown


title: control 52

description: Genome-Wide Human SNP Array 6.0

value: Japanese


title: Wildtype mouse, no overload, biological rep 3


title: DKK038

value: female

value: Control


title: control 51

description: Genome-Wide Human SNP Array 6.0


title: control 50

description: Genome-Wide Human SNP Array 6.0


title: CB2008050-R-08_resistant


title: control 49

description: Genome-Wide Human SNP Array 6.0


title: Wildtype mouse, no overload, biological rep 1


title: DKK036


title: Myostatin knock out, overload, biological rep 6

source_name: Myostatin knock out mouse,

value: Mstn-/-


title: DKK034


title: DKK057


title: CB2008050-R-05_resistant


title: control 47

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: CB2008050-R-04_resistant


title: CB2008050-R-03_resistant


title: Wildtype mouse, no overload, biological rep 2


title: DKK037


title: Myostatin knock out, overload, biological rep 5


title: CB2008050-R-02_resistant


title: Myostatin knock out, overload, biological rep 4


title: CB2008050-R-01_resistant


title: CB2009639_2_PRT_154_sensitive


title: Myostatin knock out, overload, biological rep 2


title: CB2008050-R-07_resistant


title: control 48

description: Genome-Wide Human SNP Array 6.0


title: Myostatin knock out, no overload, biological rep 6


title: control 45

description: Genome-Wide Human SNP Array 6.0


title: DKK031


title: Myostatin knock out, overload, biological rep 3


title: DKK032


title: Myostatin knock out, overload, biological rep 1


title: CB2009639_2_PRT_153_resistant


title: DKK026


title: DKK033


title: control 44

description: Genome-Wide Human SNP Array 6.0


title: CB2009639_2_PRT_152_unknown


title: Myostatin knock out, no overload, biological rep 5


title: control 43

description: Genome-Wide Human SNP Array 6.0


title: control 46

description: Genome-Wide Human SNP Array 6.0


title: CB2009639_2_PRT_150_unknown


title: Myostatin knock out, no overload, biological rep 4


title: Myostatin knock out, no overload, biological rep 3


title: DKK019


title: DKK017


title: control 38

description: Genome-Wide Human SNP Array 6.0


title: control 40

description: Genome-Wide Human SNP Array 6.0


title: DKK021


title: NPC48h_EPZ_RNA-seq_rep2

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: RNA-Seq

data_processing:
fastq files were demultiplexed on RELACS barcodes and aligned to the mm10 genome assembly using snakePipes (v1.1.1 and v1.2.2). QC metrix and further downstream files were also generated using snakepipes (Bhardwaj at al, 2018).
We use gencode M18 as reference gene model annotation
ChIP-Seq BW files were generated on filtered bam files (mapq>=5, UMI-deduplicated) using a bin size of 25bp, and sequencing depth normalized (for normalization, MT and scaffold chromosmes were excluded). RNA-Seq BW were RPKM normalized. ATAC-Seq BW were normalized using Deseq2 scaling factors computed on the locally enriched locy (identified using MACS2)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig, normalized coverage

source_name: neural progenitor cells

growth_protocol: mESC were cultured on inactivated MEFs up to p3, and in feeder-free condition from p4 onwards, in ESC complete medium + LIF (leukemia inhibitor factor) (1/1000) + beta-Mercapto-EtOH (1/500). Cells were splitted every 2-3 days upon reach of ~ 70% confluence. NPC were derived from mESC following Bibel et al. (2007)

extract_protocol:
formaldehyde fixed chromatin was preprocessed following RELACS high-thoughput ChIP-seq protocol (Arrigoni et al., 2019) using Covaris sonicator. For end repair, a-tailing, barcoding, and adaptor ligation we use reagents from the NEBNext Ultra II kit. RNA was extracted using RNeasy Mini Kit and processed using TrueSeq Stranded mRNA kit.  ATAC-seq was generated following the protocol of Buerostro et al. 2015.
Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After illumina adapter ligation, library was PCR amplified (15 cycles). Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on HiSeq3000 (RELACS ChIP-Seq, ATAC-Seq) and NextSeq HIGH (RNA-Seq) following manufacturer's protocols.

treatment_protocol: mESC growing in feeder-free plates were treated with either DMSO or EPZ5676 for 48 hours. NPC were treated  with either DMSO or EPZ5676 for 48 hours immediately after embryoid bodies disaggregation in complete N2 medium

tag: cell type

value: Dot1l-HA-FLAG ES-derived neural progenitor cells

tag: treatment

tag: passage

tag: chip ab / kit

value: TrueSeq stranded mRNA


title: control 41

description: Genome-Wide Human SNP Array 6.0

source_name: genomic DNA from peripheral blood


title: DKK020

tag: tissue

tag: age

tag: Sex


title: NPC48h_EPZ_RNA-seq_rep1

description: RNA-Seq


title: control 42

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_EPZ_RNA-seq_rep3

description: RNA-Seq


title: control 37

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_DMSO_RNA-seq_rep3

description: RNA-Seq

value: DMSO


title: NPC48h_DMSO_RNA-seq_rep2

description: RNA-Seq


title: DKK015


title: CB2009639_2_PRT_146_unknown


title: Myostatin knock out, no overload, biological rep 1

value: plantaris muscle

tag: genotype


title: CB2009639_2_PRT_148_unknown


title: CB2009376-143_unknown


title: CB2009639_2_PRT_145_resistant


title: Myostatin knock out, no overload, biological rep 2

tag: muscle


title: CB2009639_2_PRT_147_resistant


title: CB2009376-142_unknown


title: DKK018

value: male


title: CB2009639_2_PRT_149_sensitive

value: rectal cancer


title: control 39

description: Genome-Wide Human SNP Array 6.0


title: control 36

description: Genome-Wide Human SNP Array 6.0


title: DKK016


title: control 35

description: Genome-Wide Human SNP Array 6.0


title: DKK014


title: NPC48h_DMSO_RNA-seq_rep1

description: RNA-Seq


title: mESC_EPZ_RNA-seq_rep3

description: RNA-Seq

source_name: mouse embryionic stem cells

value: Dot1l-HA-FLAG C57BL/6 mouse embryonic stem cells


title: DKK012


title: control 33

description: Genome-Wide Human SNP Array 6.0


title: DKK011


title: mESC_EPZ_RNA-seq_rep2

description: RNA-Seq


title: CB2009376-141_unknown

value: rectal cancer biopsy


title: mESC_EPZ_RNA-seq_rep1

description: RNA-Seq


title: CB2009376-140_resistant


title: CB2009376-139_resistant


title: CB2009376-138_sensitive

value: sensitive


title: mESC_DMSO_RNA-seq_rep2

description: RNA-Seq


title: mESC_DMSO_RNA-seq_rep3

description: RNA-Seq


title: control 31

description: Genome-Wide Human SNP Array 6.0


title: control 32

description: Genome-Wide Human SNP Array 6.0


title: DKK008


title: DKK009


title: DKK007


title: control 30

description: Genome-Wide Human SNP Array 6.0


title: control 29

description: Genome-Wide Human SNP Array 6.0


title: mESC_DMSO_RNA-seq_rep1

description: RNA-Seq


title: control 34

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_EPZ_ATAC_rep2

description: ATAC-Seq


title: DKK002


title: control 28

description: Genome-Wide Human SNP Array 6.0


title: str_astros

city: Stockholm

first: Jens

middle: Peter

last: Magnusson

address: Alfred Nobels Allé 8

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
bcl files were converted to fastq files using cellranger mkfastq (v2.0.1)
Alignment to the mouse genome (mm10) supplemented with tdTomato sequence was performed with cellranger count (v2.0.1)
Normalisation, filtering of low quality cells, tSNE or UMAP visualizations and clustering were performed with Seurat (v2.3.4)
Further filtering of cells was performed to remove cells that are not implicated in the astroglial neurogenic program.
Genome_build: mm10 supplemented with tdTomato DNA sequence
Supplementary_files_format_and_content: csv files contain raw gene expression matrices and metadata containing clustering information and cell cycle score

source_name: striatal Rbpj-K -/- astrocytes

extract_protocol:
Brains were extracted and dissected to isolate the portion of striatum subjected to the virus injection. Tissue was digested with Miltenyi's Brain Dissociation Kit and tdTomato+ cells were sorted on a BD FACS Influx sorter.
Libraries were prepared using Chromium Single Cell 3' Library and Gel Bead Kit (v3, 10X Genomics)

tag: strain

value: Adult (>2 months old)

tag: experimental genotype

value: Rbpj-K -/-

value: Striatum

value: Astrocytes

tag: sorting

value: FACS (tdTomato+)


title: 83_VijaySeq1_2_SoZa06_04MAY17_N728S521

city: La Jolla

last: Riffelmacher

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Ltbrfl/fl Cre- (Ctrl) stim

growth_protocol: Neutrophils were isolated from the blood of 8 week old LTβRΔN, and littermate controls, using a magnetic bead negative selection kit (Stem Cell Technologies).

extract_protocol:
Cells were lysed in Trizol LS (Thermo Fisher). RNA extraction, reverse transcription, cDNA amplification, fragmentation, additional PCR amplification, final library purification, and quality control were performed as described (methodology section).
Sequencing was performed according to a single-end strategy using the HiSeq2500 sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

treatment_protocol: Following isolation, cells were stimulated for 2 hours with recombinant, colitis associated, cytokines (TNF [100ng/ml], IL-6 [50ng/ml] and GM-CSF [100ng/ml]) in the presence or absence of soluble LIGHT stimulation [500ng/ml].

value: Ltbrfl/fl Cre- (Ctrl)

value: stimulated

value: Blood

value: Neutrophil


title: NPC48h_EPZ_ATAC_rep1

description: ATAC-Seq

value: Dot1l-HA-FLAG ES-derived neural progenitor cells


title: control 27

description: Genome-Wide Human SNP Array 6.0

value: healthy control

value: Japanese


title: CB2009376-134_resistant

tag: disease state

tag: sensitivity

value: resistant

tag: patient age


title: CB2009376-136_resistant

value: rectal cancer

tag: tumor stage


title: CB2009376-137_unknown

value: unknown


title: NPC48h_DMSO_ATAC_rep2

description: ATAC-Seq

value: DMSO


title: CB2009639_2_PRT_151_resistant

value: rectal cancer biopsy


title: CB2009376-133_resistant


title: CB2009376-135_unknown


title: 82_VijaySeq1_2_SoZa06_04MAY17_N727S521


title: control 26

description: Genome-Wide Human SNP Array 6.0

tag: disease

tag: race

tag: gender

value: female


title: control 25

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_DMSO_ATAC_rep1

description: ATAC-Seq

tag: cell type

tag: treatment

tag: passage


title: 80_VijaySeq1_2_SoZa06_04MAY17_N724S521

tag: tissue


title: 81_VijaySeq1_2_SoZa06_04MAY17_N726S521


title: control 24

description: Genome-Wide Human SNP Array 6.0


title: CB2009030-PRT-132_resistant


title: control 23

description: Genome-Wide Human SNP Array 6.0

value: male


title: NPC48h_EPZ_Input_rep1

description: RELACS ChIP-Seq

tag: chip ab / kit


title: NPC48h_EPZ_H3K9me3_rep2

description: RELACS ChIP-Seq


title: 78_VijaySeq1_2_SoZa06_04MAY17_N722S521

source_name: Ltbrfl/fl x Mrp8-Cre (LTβRΔN) stim

tag: genotype

value: Ltbrfl/fl x Mrp8-Cre (LT{beta}R{delta}N)


title: 79_VijaySeq1_2_SoZa06_04MAY17_N723S521


title: control 22

description: Genome-Wide Human SNP Array 6.0


title: 77_VijaySeq1_2_SoZa06_04MAY17_N721S521


title: NPC48h_EPZ_H3K9me3_rep1

description: RELACS ChIP-Seq


title: NPC48h_EPZ_H3K79me2_rep2

description: RELACS ChIP-Seq

value: H3K79me2 (abcam, ab3594)


title: control 21

description: Genome-Wide Human SNP Array 6.0


title: 76_VijaySeq1_2_SoZa06_04MAY17_N720S521


title: CB2009030-PRT-130_resistant


title: CB2009030-PRT-131_resistant


title: control 20

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_EPZ_Input_rep2

description: RELACS ChIP-Seq


title: NPC48h_EPZ_H3K79me2_rep1

description: RELACS ChIP-Seq


title: 75_VijaySeq1_2_SoZa06_04MAY17_N719S521


title: 73_VijaySeq1_2_SoZa06_04MAY17_N716S521

source_name: Ltbrfl/fl Cre- (Ctrl) unstim

value: unstimulated


title: NPC48h_EPZ_H3K4me3_rep2

description: RELACS ChIP-Seq


title: DKK023

last: Fiosins

address: Falkenried 94

institute: University Medical Center Hamburg-Eppendorf

data_processing:
sRNA-seq analysis: We used Oasis 2 for sRNA detection, differential expression and classification analysis. Oasis 2 https://oasis.ims.bio/
Genome_build: Hg38
Supplementary_files_format_and_content: Count files: Expression of sRNAs

extract_protocol:
Isolation of total RNA from peripheral blood sample: Peripheral blood samples were collected into PAXgene Blood RNA tube (PreAnalytiX) from consenting patients and healthy controls, the tubes were gently inverted for multiple times, incubated for 20-24 hours under room temperature and stored under -80 °C until processing. Total RNA was isolated using the PAXgene Blood RNA kit (PreAnalytiX) according to the manufacturer’s protocol. The purity and concentration of isolated RNA were measured with NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific). The RNA integrity was determined by Agilent RNA 6000 Nanochip (Agilent Technologies) using the 2100 Bioanalyzer (Agilent Technologies).
Small RNA libraries were prepared using 1 ug high-quality RNA following the protocol of Illumina TrueSeq small RNA library kit (Illumina). In brief, 3’adapter was denatured for 2 minutes under 70°C, and ligated to the RNA with T4 RNA Ligase 2 deletion mutant for 1 hour at 28°C. Then the reaction was stopped with stop solution for 15 minutes under 28°C. Subsequently, 5’ adapter was denatured for 2 minutes at 70°C , then added to the RNA with ATP and T4 DNA ligase for 1 hour under 28°C . After adaptors ligation, the RNA was reverse transcribed to complement DNA (cDNA) by using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) and dNTPs for 1 hour at 50°C. Then, the cDNA was indexed and amplified with PCR mix and primers supplied in the kit for 12 cycles (denaturing at 98°C for 30 s, annealing at 60°C for 30 s, extension at 72°C for 15 s, with a final extension at 72°C for 10 min). Amplified and indexed cDNAs were then pooled together, mixed with DNA loading dye and loaded on a 5% TBE acrylamide gels (Bio-Rad). After 57 minutes electrophoresis under 145 V, the gel was stained with Midori Green for 5 minutes and viewed under the UV transilluminator, fragments between Illumina’s custom ladder 145 bp to 160 bp were cut out for library preparation. The gel was centrifuged at 20,000 x g for 2 minutes through a Gel Breaker tube (Bio-Cat). Then cDNA was eluted from the homogenized gel by adding 300ul UltraPure water and shaking under 800 x rpm for 2 hours. Then the gel was transferred on a 5 um filter tube (Bio-Cat) and centrifuged for 10 seconds under 600 x g and the gel debris was separated. Afterward, 2ul Glycoblue, 30ul of 3M sodium acetate and 975ul 100% ethanol (pre-chilled under -20°C) were added and well mixed to the sample, following an immediate centrifuge at 20,000 x g for 20 minutes under 4°C. After  remove and discard the supernatant, the pellet was washed with 500ul 70% pre-chilled ethanol. The supernatant was discarded after sample being centrifuged at 20,000 x g for 2 minutes under room temperature, and the pellet was dried in a 37°C heat block for 10 minutes with open lid. Finally, the pellet was resuspended in 10ul 10mM Tris-HCL (pH 8.5) and the sample quality was checked using Agilent High Sensitivity DNA chip (Agilent Technologies) using the 2100 Bioanalyzer (Agilent Technologies). All high quality libraries were then sequenced on Illumina HiSeq 2000 Sequencer.

value: Peripheral blood

tag: age

tag: Sex

value: Control


title: CB2009030-PRT-128_resistant


title: control 18

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_EPZ_H3K4me3_rep1

description: RELACS ChIP-Seq


title: CB2009030-PRT-129_resistant


title: control 17

description: Genome-Wide Human SNP Array 6.0


title: 71_VijaySeq1_2_SoZa06_04MAY17_N728S520

value: Ltbrfl/fl Cre- (Ctrl)

value: Blood

tag: strain


title: 72_VijaySeq1_2_SoZa06_04MAY17_N729S520

value: Neutrophil


title: CB2009030-PRT-125_resistant


title: CB2009030-PRT-127_resistant


title: control 15

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: NPC48h_EPZ_H3K4me1_rep2

description: RELACS ChIP-Seq

value: Dot1l-HA-FLAG ES-derived neural progenitor cells


title: 70_VijaySeq1_2_SoZa06_04MAY17_N727S520

source_name: Ltbrfl/fl x Mrp8-Cre (LTβRΔN) unstim


title: CB2009030-PRT-124_resistant

value: resistant


title: control 19

description: Genome-Wide Human SNP Array 6.0

value: Japanese


title: 69_VijaySeq1_2_SoZa06_04MAY17_N726S520


title: control 14

description: Genome-Wide Human SNP Array 6.0


title: CB2009030-PRT-123_resistant

value: rectal cancer


title: CB2009030-PRT-122_sensitive

value: sensitive


title: NPC48h_EPZ_H3K36me3_rep2

description: RELACS ChIP-Seq


title: NPC48h_EPZ_H3K36me3_rep1

description: RELACS ChIP-Seq


title: control 13

description: Genome-Wide Human SNP Array 6.0


title: CB2009030-PRT-126_resistant

value: rectal cancer biopsy


title: 68_VijaySeq1_2_SoZa06_04MAY17_N724S520


title: CB2009030-PRT-121_sensitive


title: NPC48h_EPZ_H3K27me3_rep2

description: RELACS ChIP-Seq


title: control 16

description: Genome-Wide Human SNP Array 6.0

value: female


title: 67_VijaySeq1_2_SoZa06_04MAY17_N723S520


title: ZCWPW1 Homozygous KO

city: Oxford

first: Simon

last: Myers

address: Roosevelt Drive

department: Wellcome Center for Human Genetics

institute: University of Oxford

description: processed data file:

data_processing:
For the HEK293T experiments, reads were mapped to either hg38 (NCBI’s GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz) using bwa mem (version 0.7.17-r1188) (Li, 2013).
Duplicates were removed using picard’s markDuplicates (version 2.20.4-SNAPSHOT).
Unmapped, mate unmapped, non primary alignment, failing platform, and low MAPQ reads were removed using samtools with parameters “-q 30 -F 3852 -f 2 -u” (version 1.9 (using htslib 1.9)).
Other unmapped reads and secondary alignments were removed using samtools fixmate.
Fragment position bed files were created using bedtools bamtobed (v2.28.0).
For the DMC1 mouse experimental data, we processed the data following the algorithm provided by (Khil et al., 2012) to map the reads to the mouse mm10 reference genome (Lunter and Goodson, 2011), and obtain type I reads.
We called DMC1 peaks, as described previously (Davies et al., 2016).
For the HEK293T experiments, peaks for ZCWPW1, PRDM9, H3K4me3, and H3K36me3 were called using a peak caller previously described (Davies et al., 2016) and available at https://github.com/MyersGroup/PeakCaller.
Single base peaks were called with parameters pthresh 10−6 and peakminsep 250 on 22 autosomes.
Code can be found at github.com/MyersGroup/Zcwpw1 (archived at doi.org/10.5281/zenodo.3559758)
Genome_build: mm10 for SSDS DMC1 ChIP-seq and hg38 for HEK293T cell experiments
Supplementary_files_format_and_content: SingeBasePeaks and ForceCalledPeak files are BED format like files with positions of the peaks in first three columns, followed by fragment coverage of the sample replicates and the input, followed by enrichement value, likelihood, and pvalue
Supplementary_files_format_and_content: Frament Position files are BED format files for the locations of each DNA fragment pulled down in the ChIP (each fragment derived from two paired reads)
Supplementary_files_format_and_content: bigWigs contain the fragment depth in binary format for e.g. IGV visualisation, or creating a average profiles using bwtools
Supplementary_files_format_and_content: bedgraphs contain coverage for the single stranded DNA type 1 reads for 5 prime and 3 prime reads for DMC1 SSDS in ZCWPW1 KO mice

source_name: Testis of B6 mouse

extract_protocol:
ssDNA libraries were prepared as described in (Khil et al, 2012) using the TruSeq DNA Library Prep Kit according to Illumina's instructions, with the addition of a kinetic enrichment step before ligation of adapters by denaturing the DNA at 95°C for 3 min and cooling down to room temperature for 2 min
Protein-DNA immunocomplexes were isolated from sonicates using antibodies against the relevant proteins

treatment_protocol: Frozen tissue was crosslinked, sonicated, and processed for ChIP with the relevant antibody

tag: strain background

tag: developmental stage

value: adult (10 weeks)

value: Testis

tag: genotype/variation

value: ZCWPW1 KO

tag: chip antibody

tag: molecule subtype

value: single stranded DNA


title: NPC48h_EPZ_H3K4me1_rep1

description: RELACS ChIP-Seq


title: control 11

description: Genome-Wide Human SNP Array 6.0

tag: disease

value: male


title: NPC48h_EPZ_H3K27me3_rep1

description: RELACS ChIP-Seq


title: NPC48h_EPZ_H3K27ac_rep2

description: RELACS ChIP-Seq


title: control 12

description: Genome-Wide Human SNP Array 6.0

tag: race


title: control 10

description: Genome-Wide Human SNP Array 6.0

tag: gender


title: HomIP_Cochlea3

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller.
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner.
Reads counts were calculated for each sample.
Differential expression of genes were computed between wild type and mutant samples.
Genome_build: M. musculus GRCm38
Supplementary_files_format_and_content: *.cpm.txt: Tab-delimited text files include counts per million reads (CPM) for each sample.

growth_protocol: Room temperature 18-23°C, 12 hour light/dark cycle.

extract_protocol:
The hair cell translatome was enriched for by ribosome immunoprecipitation using an HA antibody (see protocol outlined in Sanz et al., 2009).
Gfi1Cre;RiboTag IP RNA-seq libraries were prepared in biological triplicates from cochlear tissues using the Ovation® Ultralow Library Preparation Kit (NuGEN), and vestibular tissues using the NEBNext® Ultra™ Directional RNA Library Prep Kit (New England BioLabs) per manufacturers' instructions.

value: Cochlea

tag: cell type

value: hair cells (enriched)

tag: antibody

value: HA


title: HomIP_Cochlea2


title: CB2008096-PRT115_sensitive

tag: disease state

tag: sensitivity

tag: patient age

tag: tumor stage


title: CB2008096-PRT114_resistant

tag: tissue


title: NPC48h_EPZ_H3K27ac_rep1

description: RELACS ChIP-Seq

tag: treatment

tag: passage

tag: chip ab / kit


title: control 9

description: Genome-Wide Human SNP Array 6.0


title: CB2008096-PRT112_sensitive


title: CB2008096-PRT110_resistant


title: control 8

description: Genome-Wide Human SNP Array 6.0


title: HomIP_Cochlea1

tag: age


title: NPC48h_DMSO_Input_rep2

description: RELACS ChIP-Seq

value: DMSO


title: CB2008096-PRT108_resistant


title: control 7

description: Genome-Wide Human SNP Array 6.0

value: healthy control


title: CB2008096-PRT107_resistant


title: NPC48h_DMSO_Input_rep1

description: RELACS ChIP-Seq

value: Dot1l-HA-FLAG ES-derived neural progenitor cells


title: NPC48h_DMSO_H3K9me3_rep2

description: RELACS ChIP-Seq


title: HetIP_Cochlea2

tag: genotype/variation


title: control 6

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_DMSO_H3K9me3_rep1

description: RELACS ChIP-Seq


title: control 5

description: Genome-Wide Human SNP Array 6.0


title: CB2008096-PRT106_sensitive


title: HetIP_Cochlea3


title: control 4

description: Genome-Wide Human SNP Array 6.0


title: NPC48h_DMSO_H3K79me2_rep1

description: RELACS ChIP-Seq

value: H3K79me2 (abcam, ab3594)


title: Mesothelium_3

first: Thaddeus

last: Stappnbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Cleveland Clinic, Lerner Research Institute

data_processing:
Pooled libraries were sequenced on an Illumina HiSeq 2500 using 1x50 single end sequencing.
Transcript abundance was estimated using Kallisto (v0.43.1) using the GRCm38.p5 assembly.
Transcript abundances were summarized at the gene-level using the R package tximport (v1.10.1) with argument countsFromAbundance="lengthScaledTPM". The resulting count matix was used as the input for edgeR and deposited as the processed file to the NCBI GEO archive.
Preprocessing and normalization was performed using packages edgeR (v3.24.3) and the voom function from Limma (v3.38.3).
Genome_build: Gencode M14 annotation (GRCm38.p5 assembly)
Supplementary_files_format_and_content: Transcript abundance estimate

source_name: primary peritoneal mesothelial cells

extract_protocol:
10 week old C57BL/6 mice were sacrificed.  The peritoneal cavities were washed by injecting 10 ml of 1x PBS (Sigma) via a syringe equipped with a 25G×5/8″ needle (BD). After gently shaking for 30 seconds, the fluid was removed and discarded. The peritoneum was filled with 5 ml of 0.25% Trypsin/EDTA solution (Gibco). The corpse was then maintained at 37°C for 20 min in a tissue-culture incubator before removal of the fluid. The detached cells were pelleted by centrifugation at 300×g for 10 min and resuspended in FACS buffer. The mesothelial cells were sorted from the cell suspension as CD45- PDPN+ GPM6a+ cells into DMEM + 10% FBS on a FACS Aria II flow cytometers (BD). Total RNA was extracted from the sorted mesothelial cells using the NucleoSpin RNA kit (Macherey-Nagel).
rRNA was depleted using Ribo-Zero kit. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: primary peritoneal mesothelial cells

value: 10 week old

tag: time point

value: fresh isolated


title: Mesothelium_4


title: NPC48h_DMSO_H3K4me3_rep2

description: RELACS ChIP-Seq


title: CB2008096-PRT103_resistant

value: rectal cancer

value: rectal cancer biopsy

value: resistant


title: CB2008096-PRT104_resistant


title: control 2

description: Genome-Wide Human SNP Array 6.0

tag: disease

value: Japanese

value: female


title: Mesothelium_2


title: NPC48h_DMSO_H3K4me3_rep1

description: RELACS ChIP-Seq


title: CB2008096-PRT101_resistant


title: Mesothelium_1


title: control 1

description: Genome-Wide Human SNP Array 6.0

tag: race


title: CB2008096-PRT105_resistant


title: CB2008096-PRT102_resistant


title: NPC48h_DMSO_H3K4me1_rep2

description: RELACS ChIP-Seq


title: NPC48h_DMSO_H3K79me2_rep2

description: RELACS ChIP-Seq


title: control 3

description: Genome-Wide Human SNP Array 6.0

tag: gender


title: LSO-4

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: ARS1

organism: Capra hircus

extract_protocol:
Goat oocyte cells samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: breed

value: Ji'ning grey goat

value: Oocyte

value: LSO


title: LSO-5


title: NPC48h_DMSO_H3K4me1_rep1

description: RELACS ChIP-Seq

tag: cell type