title: 11B-24h

city: London

first: Esteban

middle: Alberto

last: Gomez Cifuentes

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 36 oil

data_processing:
Illumina NextSeq 500
QIASeq UPX Primary Analysis Tool: Library protocol (poly-A-transcriptome), Read mapping (STAR version 2.5.3a)
Filtering: genes were considered to be expressed at a reasonable level if two or more counts per each million mapped reads were identified per sample, in at least half of the samples.
Differential Gene Expression Analysis between placebo vs oil group: quasi-likelihood method of the Bioconductor R package “edgeR” (adjust p value < 0.1 using BH correction)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample.

source_name: Blood samples

extract_protocol:
Blood samples were thawed and equilibrated to room temperature.  RNA extraction was completed as per the RNeasy MinElute Clean Up Kit (QIAGEN catalog no. 74204) protocol.
1ng of each RNA sample was used to generate a 3’ RNA library using the QIAGEN UPX 3’ Transcriptome kit (QIAGEN catalog no 333088). Libraries were prepared following steps in the manufacturer's handbook for purified RNA samples.

tag: tissue

value: Blood samples

tag: sample info

value: Mineral Oil supplement group

tag: pre-analysis test

value: Quality control check. Not outlier.

tag: sequencing method

value: NextSeq Mid-output kit with R1 = 151bp and R2 = 27bp


title: P01163

status: Public on Dec 13 2019

type: SRA

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

library_source: transcriptomic

data_processing:
Fastq files were align to the hg19 reference genome using STAR and default parameters
Ensembl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using SVA and the 'LIMMA-Voom' method
Genome_build: hg19
Supplementary_files_format_and_content: Voom transformed abundance measurements

molecule: total RNA

organism: Homo sapiens

source_name: Left Ventricle

extract_protocol:
Total RNA was extracted using the miRNeasy Kit (Qiagen) including DNAse treatment. RNA concentration and quality was determined using the NanoVue Plus™ spectrophotometer (GE Healthcare) and the Agilent 2100 RNA Nano Chip (Agilent)
RNA sequencing libraries were prepared using the Illumina TruSeq stranded mRNA kit followed by the Nugen Ovation amplification kit.

treatment_protocol: Explanted myocardium snap frozen in liquid nitrogen.

tag: etiology

value: Dilated cardiomyopathy (DCM)

tag: Sex

value: Male

tag: race

value: Caucasian

tag: age


title: 6D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 32 oil


title: 2C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 35 oil


title: P01146

value: Non-Failing Donor

value: Female


title: GFP-4

city: Santa Cruz

first: Alexis

middle: Marie

last: Thornton

state: CA

address: 1156 High Street

department: Biomolecular Engineering

institute: UC Santa Cruz

data_processing:
kallisto, version 0.45.1
Genome_build: Ensembl release 94 GRCh38 cDNA transcriptome
Supplementary_files_format_and_content: *_abundance.tsv: kallisto transcript abundance estimates.

source_name: GFP overexpression replicate 4

extract_protocol:
Qiagen RNeasy protocol, including DNase I treatment.
NEBNext protocol for Illumina.

tag: cell line

tag: overexpression

value: GFP control


title: 14D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 31 oil


title: P01151


title: 18C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 30 oil


title: 20A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 33 oil


title: P01140


title: 8B-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 28 oil


title: P01137

value: African American


title: 22D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 27 oil


title: 16B-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 26 oil


title: P01134


title: P01127


title: P01135


title: P01124


title: 7C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 24 oil


title: 1D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 25 oil


title: 5A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 34 oil


title: 9D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 22 oil


title: 19B-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 23 oil


title: P01121


title: P01164


title: 13A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 20 oil


title: P01118


title: 10C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 19 oil


title: 6C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 18 placebo

value: Placebo group


title: 13B-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 29 oil


title: P01109


title: P01119


title: P01110


title: 9A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 17 placebo


title: P01117


title: 10D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 14 placebo


title: P01104


title: 22C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 16 placebo


title: 11C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 13 placebo


title: P01116


title: 4B-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 15 placebo


title: 3C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 12 placebo


title: P01100


title: P01106


title: P01122


title: 5D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 11 placebo


title: P01097


title: 4A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 21 oil


title: 14C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 10 placebo


title: P01077


title: 1A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 9 placebo


title: P01076


title: P01095


title: P01071


title: 8A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 8 placebo


title: 20B-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 6 placebo


title: 19C-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 7 placebo


title: P01067


title: P01070


title: P01054


title: 18D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 4 placebo


title: P01052


title: 2D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 3 placebo


title: P01044


title: 7B-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 1 placebo


title: P01032


title: P01027

value: Hypertrophic cardiomyopathy (HCM)


title: P01045


title: C02728


title: D60 hESC-Atrial cell WT and MYL4KO run 2

city: Quechee

middle: J

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

data_processing:
bcbio single-cell RNA-seq pipelinehttps://github.com/bcbio/bcbio-nextgen1.0.6a0-d2b5b522
umis fastqtransform, umis demultiplex_samples, umis cb_filter, umis cb_histogram, rapmap quasiindex, rapmap quasimap, samtools index, umis fasttagcount, umis sparse
Genome_build: GRCh38 (Ensembl 90)
Supplementary_files_format_and_content: Matrix Market Exchange Format (sparse matrix)

molecule: polyA RNA

source_name: hESC-Atrial cell

growth_protocol: Differentiation was initiated 72 hours after plating when the culture was approximately 80% confluent. Step 1: Cells were differentiated with 1.5 μM CHIR99021, 20 ng/mL BMP4 and 20 ng/mL Activin A in RPMI supplemented with B27 minus insulin, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep for 3 days . Step 2: For atrial differentiations, tep 1 was followed by addition of 1 μM retinoic acid in RB27-INS from day 3-6. 5 µM XAV939 was added from day 4-6. From day 6 onward hPSC-atrial differentiation were carried out in RPMI supplemented with B27, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep (RB27+INS).

extract_protocol:
The RT/lysis mix consisted of 25 µL 5X First-Strand buffer (18080-044 Life Technologies), 9 µL 10% (v/v) IGEPAL CA-630 (#18896 Sigma), 6 µL 25 mM dNTPs (Enzymatics N2050L), 10µL 0.1M DTT (#18080-044, Life Technologies), 15 µL 1M TrisHCl [pH 8.0] (51238 Lonza), 10µL Murine RNase inhibitor (M0314, NEB), 15 µL SuperScript III RT enzyme (200 U/µL, #18080-044, Life Technologies) and 60 µL nuclease-free water (AM9937 Ambion), having a total volume 150 µL.
Library preparation was based on the modified CEL-Seq/MARS-Seq protocol (Jaitin DA et al., Science 2014) with minor modifications. The workflow of DNA library preparation can be summarized as follows: RT ® ExoI ® SPRI purification (SPRIP) ® SSS ® SPRIP ® T7 in vitro transcription linear amplification ® SPRIP ® RNA Fragmentation ® SPRIP ® primer ligation ® RT ® library enrichment PCR. The following modifications were made to the protocol (Jaitin DA et al., Science 2014): the RT primer included the P5/PE1 adaptor while the ligation primer includes the P7/PE2 adaptor, a flipped orientation to that in Jaitin DA et al.; prior to ExoI treatment, the aqueous phase from broken droplets was centrifuged at 4°C for 15 minutes at 14krcf to pellet cell debris and gels; during ExoI treatment, 10U HinFI were added to digest primer dimers that may have formed during the RT reaction; the original DNAse digestion step was omitted after linear amplification; after linear amplification the resulting amplified RNA libraries were analyzed on an Agilent BioAnalyzer before proceeding; before primer ligation, the samples were treated with Shrimp Alkaline Phosphatase for 30 minutes. The number of final PCR cycles required for final library enrichment PCR ranged from 10-13 cycles. The remaining steps are otherwise unchanged.
inDrops v3 single-cell RNA-seq  V3 sequencing details (PDF format): https://iccb.med.harvard.edu/files/iccb/files/sequencing_indrops_libraries_02_28_18.pdf

tag: day


title: C02724


title: P01007


title: D60 hESC-Atrial cell WT and MYL4KO run1


title: C02698


title: C02665


title: 16A-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 5 placebo


title: C02660


title: C02645


title: C02592


title: 13D-24h

description:
22 samples were sequencing, but only 18, for quality issues were used for the DGE analysis. Processed data file came from the demultiplex, trimmering, mapping and normalization step from QIASeq UPX Primary Analysis Tool.
Sample 2 placebo


title: C02529


title: P01101


title: C02530


title: C02516


title: C02720


title: SubcutaneousAdiposeTissueFamily26Twin1

type: RNA

city: Helsinki

first: Maheswary

last: Muniandy

address: Tukholmankatu 8

country: Finland

institute: University Helsinki

hyb_protocol: hybridized 250ng to Affymetrix U133 Plus 2.0 microarray

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner

data_processing: GCRMA method used to normalize data

label: biotin

source_name: Subcutaneous Adipose Tissue

label_protocol: biotin

growth_protocol: SAT biopsies via a surgical technique under local anaesthesia

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen) to extract SAT RNA

treatment_protocol: Total RNA extract treated with DNase I (Qiagen)

tag: individual

tag: gender

value: female

tag: bmi category

value: heavy

value: SAT


title: SubcutaneousAdiposeTissueFamily24Twin2

value: lean


title: SubcutaneousAdiposeTissueFamily24Twin1


title: SubcutaneousAdiposeTissueFamily26Twin2

value: male


title: SubcutaneousAdiposeTissueFamily25Twin2


title: SubcutaneousAdiposeTissueFamily22Twin2


title: SubcutaneousAdiposeTissueFamily25Twin1


title: SubcutaneousAdiposeTissueFamily23Twin2


title: SubcutaneousAdiposeTissueFamily23Twin1


title: SubcutaneousAdiposeTissueFamily22Twin1


title: SubcutaneousAdiposeTissueFamily21Twin2


title: C02510


title: SubcutaneousAdiposeTissueFamily21Twin1


title: SubcutaneousAdiposeTissueFamily20Twin1


title: SubcutaneousAdiposeTissueFamily20Twin2


title: SubcutaneousAdiposeTissueFamily18Twin2


title: C02546


title: C02452


title: C02468


title: C02491


title: C02475


title: SubcutaneousAdiposeTissueFamily19Twin1


title: C02496


title: C02464


title: C02458


title: C02397


title: SubcutaneousAdiposeTissueFamily19Twin2


title: C02387


title: SubcutaneousAdiposeTissueFamily18Twin1


title: C02374


title: C02420


title: C02380


title: SubcutaneousAdiposeTissueFamily17Twin1


title: SubcutaneousAdiposeTissueFamily16Twin2


title: C02360


title: SubcutaneousAdiposeTissueFamily16Twin1


title: C02375


title: SubcutaneousAdiposeTissueFamily15Twin2


title: C02356


title: SubcutaneousAdiposeTissueFamily17Twin2


title: SubcutaneousAdiposeTissueFamily14Twin1


title: C02363


title: C02364


title: SubcutaneousAdiposeTissueFamily15Twin1


title: SubcutaneousAdiposeTissueFamily11Twin2


title: C02354


title: C02355


title: C02352


title: C02350


title: C02340


title: C02329


title: C02344


title: SubcutaneousAdiposeTissueFamily12Twin2


title: C02351


title: C02327


title: SubcutaneousAdiposeTissueFamily13Twin2


title: SubcutaneousAdiposeTissueFamily14Twin2


title: C02328


title: C02349


title: C02318


title: SubcutaneousAdiposeTissueFamily10Twin2


title: SubcutaneousAdiposeTissueFamily12Twin1


title: SubcutaneousAdiposeTissueFamily7Twin2


title: C02312


title: SubcutaneousAdiposeTissueFamily6Twin2


title: C02305


title: SubcutaneousAdiposeTissueFamily13Twin1


title: SubcutaneousAdiposeTissueFamily9Twin2


title: SubcutaneousAdiposeTissueFamily10Twin1


title: SubcutaneousAdiposeTissueFamily8Twin1


title: SubcutaneousAdiposeTissueFamily8Twin2


title: SubcutaneousAdiposeTissueFamily11Twin1


title: SubcutaneousAdiposeTissueFamily7Twin1


title: SubcutaneousAdiposeTissueFamily9Twin1


title: C02301


title: SubcutaneousAdiposeTissueFamily4Twin2


title: C02298


title: SubcutaneousAdiposeTissueFamily4Twin1


title: SubcutaneousAdiposeTissueFamily5Twin1


title: C02297


title: C02280


title: SubcutaneousAdiposeTissueFamily6Twin1


title: C02276


title: C02272


title: SubcutaneousAdiposeTissueFamily3Twin2


title: C02242


title: C02303


title: C02233


title: C02210


title: C02205


title: C02190


title: Act2

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

country: China

institute: China Agricultural University

description: domestic pig

data_processing:
bcl2fastq2 v.2.17.1.14 software was used for generating fastq files.
We removed low-quality reads including those with ≥ 5% unidentified nucleotides, > 5 nt aligned to the adapter, and with > 50% of bases with phred quality < 19. Then, high-quality reads of twelve non-strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Stringtie (v.1.3.3).
reads counts of sequence files were obtained using featureCounts(v.1.6.4).
Differentially expressed genes of samples were obtained using DESeq2.
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: Comma-delimited text files include FPKM values for each sample.

organism: Sus scrofa

source_name: Induced pluripotent stem cells

growth_protocol: LCDMV culture system maitain pig iPS selfrenew and growth.

extract_protocol:
The suspended cells were collected for RNA extraction according to the RNA extrac kit, leaving behind the attached cells (primarily consisting of feeders). Total RNA samples (2 µg each) were suspended in 15 µL RNAase-free ddH2O, packed in dry ice, and submitted to Anoroad Gene Technology Corporation (Beijing, China) for RNA sequencing.
Approximately 2 µg total RNA (each sample) and the Oligo(dT) magnetic head were used for generating RNA-Seq cDNA libraries , and then, RNA -seq was conducted following the manufacturer's standard procedures.

treatment_protocol: Before RNA extraction, feeder cells were removed in order to avoid sequencing artifacts. Dissociated pig PC-iPS cells were plated onto six-well plates and cultured for 1 hour.

tag: treatment

value: Activin A

tag: developmental stage

value: adult

value: Induced pluripotent stem cells


title: Act1

description: domestic pig


title: C02172

value: Dilated cardiomyopathy (DCM)


title: SB2

description: domestic pig


title: SB1

description: domestic pig


title: SB3

description: domestic pig


title: SubcutaneousAdiposeTissueFamily3Twin1


title: SubcutaneousAdiposeTissueFamily2Twin1


title: SubcutaneousAdiposeTissueFamily2Twin2


title: SubcutaneousAdiposeTissueFamily1Twin2


title: SubcutaneousAdiposeTissueFamily1Twin1


title: Nanog3

description: domestic pig

value: Nanog knock-in reporter PC-iPS


title: C02164

value: Male


title: C02116

value: Caucasian


title: Nanog2

description: domestic pig


title: C02109


title: Nanog1

description: domestic pig


title: Act3

description: domestic pig


title: PC-ips3

description: domestic pig

value: PC-iPS


title: C02096

value: Female


title: C02108

value: African American


title: PC-ips2

description: domestic pig


title: C02085


title: ST5_83

first: Yi

last: Yu

address: No. 28, Fuxing Road, Haidian District,

department: Nanlou Respiratory Diseases Department

institute: Chinese PLA General Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
In this step, clean reads with high quality were obtained by removing reads containing adapter, reads with an N base rate of raw reads >10% and low quality reads (The Qpred of >50% sequence was less than 20).
At the same time, Q20, Q30 and GC content sequence of the clean reads were calculated.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Genome_build: The genome of T1_13 were served as reference genome in this present study. The FASTA file of transcript sequences and a file with gene information are available on the series record.
Supplementary_files_format_and_content: text file with raw read counts

organism: Escherichia coli

source_name: Feces of patients with severe pneumonia

extract_protocol:
RNA isolation of GT5, ST5 and TOB-resistant ST5 isolates was conducted by using a Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
Sequencing library of each sample was generated by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: isolate id

tag: condition

value: 64 days of space flight


title: ST5_84


title: ST5_82


title: PC-ips1

description: domestic pig

tag: tissue


title: C02069


title: C02081


title: C02080


title: C02101


title: C02067


title: C02095


title: ST5_72


title: ST5_76


title: C02065


title: ST5_56


title: C02058


title: C02056


title: SubcutaneousAdiposeTissueFamily5Twin2


title: C02054


title: ST5_55


title: C02050


title: C02045


title: C02029


title: C02022


title: ST5_48


title: ST5_38


title: ST5_45


title: C02018


title: ST5_31


title: ST5_37


title: ST5_60


title: ST5_30


title: C01997


title: ST5_29


title: C02014


title: ST5_57


title: ST5_28


title: C01960


title: C01957


title: C01952


title: C01931

value: Peripartum cardiomyopathy (PPCM)


title: ST5_27


title: ST5_24


title: C01945


title: ST5_80


title: C01929


title: ST5_22


title: ST5_20


title: C01914


title: ST5_18


title: C01926


title: ST5_16


title: C01910


title: C01912


title: C01904


title: C01905


title: ST5_11


title: ST5_15


title: C01881


title: ST5_8


title: C01895


title: ST5_9


title: ST5_10


title: C01862

value: Hypertrophic cardiomyopathy (HCM)


title: ST5_23


title: C01816


title: C01814


title: C01902


title: ST5_5


title: ST5_4


title: C01875


title: ST5_3


title: C01809


title: ST5_2


title: ST5_6


title: C01794


title: ST5_1


title: C01776


title: ST5_13


title: GT5

value: 64 days at ground laboratory


title: C01631


title: C00202

value: Non-Failing Donor


title: C01413


title: C01418


title: C00198


title: blood137

type: genomic

city: Nanjing

first: Peng

last: Chen

state: Jiangsu

address: China

department: Department of Forensic

institute: Nanjing Medical University

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-886K array
S176

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays and incubated overnight.

scan_protocol: After allele-specific staining, the BeadChip arrays were scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA was genotyped using ASA-750K array (Illumina).
the genotype results were showed directly in nucleotide base (A/T/C/G),  or --(not call)

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: blood

label_protocol: genomic DNA was firstly quantitated and amplified. Prepare MSA1 plate with amplified DNA. After fragment and precip, MSA1 plate with DNA was resuspended with RA1.

extract_protocol: genomic DNA was etracted from blood using TIANamp Genomic DNA kit (cat#DP304)

tag: group

value: Southern Han


title: blood135

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-884K array
26

value: Northern Han


title: blood136

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-885K array
95


title: blood134

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-883K array
29


title: blood133

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-882K array
28


title: blood132

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-881K array
94


title: C00196


title: blood131

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-880K array
106


title: blood130

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-879K array
S137


title: C00195


title: blood129

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-878K array
S82


title: C00193


title: ST5


title: C00197


title: C01783


title: blood127

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-876K array
38


title: C00190


title: blood126

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-875K array
102


title: blood128

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-877K array
101


title: C00188


title: T1_13

value: parental multi-drug resistant E.coli strain


title: blood125

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-874K array
100


title: C00186


title: C00199


title: blood124

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-873K array
40


title: C00168


title: C00158


title: blood123

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-872K array
31


title: C00132


title: blood122

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-871K array
42


title: C00120


title: blood121

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-870K array
112


title: C00192


title: C00105


title: blood119

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-868K array
S133


title: C00074


title: C00055


title: blood117

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-866K array
S179


title: C00085


title: blood116

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-865K array
S162


title: blood114

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-863K array
S51


title: C00039


title: MED8A_Treated

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, Missouri, USA).
Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner.
Aligned reads were combined before quantifying the expression against the ENSEMBL (release 84) database by the Partek Expectation-Maximization algorithm using the counts per million normalization.
Genes with missing values and with a mean expression less than one were filtered out
Genome_build: hg38
Supplementary_files_format_and_content: Partek Expectation-Maximization algorithm using the counts per million normalization.

extract_protocol:
RNA was isolated using Trizol (#15596-018, Thermo Scientific)
500 ng total RNA was processed using the TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San Diego, USA) to prepare the barcoded libraries.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on a Bioanalyzer (Agilent, Böblingen, Germany); 7.5 pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional seven cycles for index reading.

treatment_protocol: Samples were treated with CI-994 IC50 concentration or DMSO for 48 hours

tag: cell type

value: Medulloblastoma

value: CI-994 IC50 concentration for 48hrs


title: D425_Treated


title: blood112

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-861K array
S123


title: MED8A_DMSO

value: DMSO for 48hrs


title: blood113

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-862K array
S75


title: blood111

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-860K array
34


title: D425_DMSO


title: blood118

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-867K array
S178


title: D341_DMSO


title: blood110

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-859K array
S181


title: blood120

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-869K array
S180


title: blood108

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-857K array
44


title: blood109

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-858K array
S31


title: blood107

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-856K array
20


title: HydENseq_YA_2h_rep2

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

library_source: genomic

data_processing:
Library strategy: HydEN-seq
bowtie2 v.2.2.9 was used to align FASTQ files to the S. cerevisiae reference genome (SGD, R64-2-1,). samtools (1.3.1) was used to sort and select reads with MAPQ score ≥40. BEDPE files were generated using bedtools v.2.26.0.
Genome_build: S. cerevisiae S288C, build R64-2-1, released 18 Nov 2014
Supplementary_files_format_and_content: BEDPE files are headerless text files that contain the following tab-delimited columns: mate1 chromosome, mate1 5'-position, mate1 3'-position, mate2 chromosome, mate2 5'-position, mate2 3'-position, mate1 read identifier, MAPQ score, mate1 strand, mate2 strand

organism: Saccharomyces cerevisiae

source_name: POL3AID, POL1YA, rnh202Δ

growth_protocol: Asynchronous cultures were grown to log phase at 30C in YPD and 1.0mM IAA was added for the indicated amount of time before collection.

extract_protocol:
Alkaline hydrolyzed fragments were obtained by treatment of genomic DNA with 300mM KOH as previously described (Orebaugh C.D., Lujan S.A., Burkholder A.B., Clausen A.R., Kunkel T.A. (2018). Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing. Methods Mol Biol. 2018;1672:329-345.)
Libraries were constructed as previously described (Orebaugh C.D., Lujan S.A., Burkholder A.B., Clausen A.R., Kunkel T.A. (2018). Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing. Methods Mol Biol. 2018;1672:329-345.)

tag: lab strain

tag: strain background

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX

tag: genotype/variation

value: 1.0mM IAA, 2 hours

tag: molecule subtype

value: DNA, alkaline hydrolyzed fragments


title: blood105

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-854K array
S124


title: HydENseq_YA_4h_rep2

value: 1.0mM IAA, 4 hours


title: HydENseq_MG_6h_rep2

source_name: POL3AID, POL2MG, rnh202Δ

value: 1.0mM IAA, 6 hours


title: HydENseq_YA_0h_rep2


title: blood104

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-853K array
109


title: blood106

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-855K array
S118


title: HydENseq_MG_4h_rep2


title: blood101

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-850K array
S91


title: HydENseq_MG_2h_rep2


title: HydENseq_MG_0h_rep2


title: blood102

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-851K array
S32


title: blood100

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-849K array
8


title: HydENseq_WT_6h_rep2

source_name: POL3AID, rnh202Δ


title: HydENseq_WT_4h_rep2


title: blood99

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-848K array
46


title: HydENseq_WT_2h_rep2


title: blood98

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-847K array
6


title: HydENseq_YA_6h_rep2


title: HydENseq_YA_6h_rep1


title: blood97

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-846K array
S174


title: HydENseq_YA_4h_rep1


title: blood96

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-845K array
33


title: HydENseq_YA_2h_rep1


title: blood93

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-842K array
S152


title: blood94

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-843K array
9


title: blood103

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-852K array
S134


title: HydENseq_YA_0h_rep1


title: HydENseq_MG_6h_rep1


title: HydENseq_MG_4h_rep1


title: blood92

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-841K array
58


title: HydENseq_MG_2h_rep1


title: blood91

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-840K array
S131


title: ST5_75


title: HydENseq_MG_0h_rep1


title: HydENseq_WT_6h_rep1


title: blood90

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-839K array
17


title: blood89

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-838K array
47


title: blood88

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-837K array
48


title: HydENseq_WT_4h_rep1


title: blood87

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-836K array
27


title: HydENseq_WT_0h_rep1


title: HydENseq_WT_0h_rep2


title: blood85

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-834K array
7


title: HydENseq_1.0_rep2

growth_protocol: Asynchronous cultures were grown to log phase at 30C in YPD before a 2h treatment with IAA..

value: 1.0mM IAA


title: HydENseq_0.6_rep2

value: 0.6mM IAA


title: HydENseq_0.2_rep2

value: 0.2mM IAA


title: blood84

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-833K array
S136


title: blood95

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-844K array
22


title: D341_Treated

tag: cell line


title: blood82

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-831K array
21


title: blood83

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-832K array
5


title: blood81

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-830K array
57


title: blood80

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-829K array
S66


title: HydENseq_1.0_rep1


title: HydENseq_0.6_rep1


title: blood79

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-828K array
S117


title: HydENseq_0_rep2

value: 0mM IAA


title: HydENseq_WT_2h_rep1


title: blood77

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-826K array
16


title: HydENseq_0_rep1


title: blood86

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-835K array
S26


title: blood78

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-827K array
S94


title: blood76

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-825K array
S56


title: OKseq_1.0_80min

description: Okazaki fragment sequencing

data_processing:
bowtie2 v.2.2.9 was used to align FASTQ files to the S. cerevisiae reference genome (SGD, R64-2-1,). samtools (1.3.1) was used to sort and select reads with MAPQ score ≥40. BEDPE files were generated using bedtools v.2.26.0.
Genome_build: S. cerevisiae S288C, build R64-2-1, released 18 Nov 2014
Supplementary_files_format_and_content: BEDPE files are headerless text files that contain the following tab-delimited columns: mate1 chromosome, mate1 5'-position, mate1 3'-position, mate2 chromosome, mate2 5'-position, mate2 3'-position, mate1 read identifier, MAPQ score, mate1 strand, mate2 strand

growth_protocol: Cultures were grown to log phase and arrested with alpha factor at 30C in YPD before a 2h treatment with IAA, followed by a 1h treatment with 1ug/mL rapamycin to deplete DNA ligase before release into media containing IAA and rapamycin at room temperature for the indicated time.

extract_protocol:
Okazaki fragments were enriched by sequential elutions from ion exchange columns as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were constructed as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438) with the following changes: after adaptor ligation, samples were cleaned using a PCR purification kit (GeneJET, ThermoFisher) instead of S-300 columns, and second-strand synthesis was carried out by Taq polymerase (NEB) at 50C. Libraries were purified using magnetic beads (HighPrep PCR Clean-up, MagBio) before and after amplification.

value: 1.0mM IAA, S-phase release 80min

value: DNA, Okazaki fragments


title: blood74

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-823K array
S71

value: Southern Han


title: blood75

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-824K array
36

value: Northern Han


title: blood73

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-822K array
S173


title: OKseq_1.0_75min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 75min


title: OKseq_1.0_70min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 70min


title: OKseq_1.0_65min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 65min


title: blood72

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-821K array
S33


title: blood71

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-820K array
S156


title: OKseq_1.0_60min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 60min


title: OKseq_1.0_55min

description: Okazaki fragment sequencing

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX

value: 1.0mM IAA, S-phase release 55min


title: blood70

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-819K array
37


title: blood69

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-818K array
S175


title: blood68

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-817K array
S90


title: HydENseq_0.2_rep1

value: DNA, alkaline hydrolyzed fragments


title: blood67

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-816K array
51


title: OKseq_1.0_45min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 45min


title: OKseq_0_60min

description: Okazaki fragment sequencing

value: 0mM IAA, S-phase release 60min


title: OKseq_1.0_50min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 50min


title: OKseq_0_55min

description: Okazaki fragment sequencing

value: 0mM IAA, S-phase release 55min


title: OKseq_1.0_90min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 90min


title: OKseq_1.0_85min

description: Okazaki fragment sequencing

value: 1.0mM IAA, S-phase release 85min


title: blood65

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-814K array
S190


title: blood64

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-813K array
S183


title: OKseq_0_45min

description: Okazaki fragment sequencing

value: 0mM IAA, S-phase release 45min


title: blood62

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-811K array
14


title: OKseq_1.0_rep2

description: Okazaki fragment sequencing

growth_protocol: Asynchronous cultures were grown to log phase at 30C in YPD before a 2h treatment with IAA, followed by a 1h treatment with 1ug/mL rapamycin to deplete DNA ligase.

value: 1.0mM IAA

value: DNA, Okazaki fragments


title: OKseq_0.6_rep2

description: Okazaki fragment sequencing

value: 0.6mM IAA


title: OKseq_0.2_rep2

description: Okazaki fragment sequencing

value: 0.2mM IAA


title: blood63

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-812K array
54

value: Northern Han


title: blood60

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-809K array
55


title: OKseq_0_50min

description: Okazaki fragment sequencing

value: 0mM IAA, S-phase release 50min


title: OKseq_0_rep2

description: Okazaki fragment sequencing

value: 0mM IAA


title: blood115

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-864K array
S85

value: Southern Han


title: blood59

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-808K array
S126


title: OKseq_1.0_rep1

description: Okazaki fragment sequencing

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX


title: OKseq_0.6_rep1

description: Okazaki fragment sequencing


title: OKseq_0.2_rep1

description: Okazaki fragment sequencing


title: blood57

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-806K array
3


title: blood66

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-815K array
15


title: blood56

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-805K array
S99


title: blood55

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-804K array
S86


title: 23C

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: Cr79_11.25.3_72 HAF

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using tophat2 -p 32 -g 1
Reads counts for each gene with  htseq-count  -q -f sam -t gene -s no -a 15 -i ID
Genome_build: Oryza sativa japonica reference genome v7
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

organism: Oryza sativa

source_name: seed

growth_protocol: Developing rice seeds without husk were collected at 48 (B) and 72 (C) hours after fertilization.

extract_protocol:
RNeasy Plant mini kit (Qiagen) was used for RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: seed

tag: genotype

tag: time point

value: 72 HAF


title: 23B

description: Cr79_11.25.3_48 HAF

value: 48 HAF


title: blood54

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-803K array
110


title: blood53

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-802K array
S54


title: 19B

description: Cr78_8.22.2_48 HAF


title: 7C

description: OE79-3_72 HAF


title: blood51

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-800K array
87


title: blood61

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-810K array
90


title: blood49

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-798K array
89


title: blood48

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-797K array
60


title: 5B

description: OE78-8_48 HAF


title: 7B

description: OE79-3_48 HAF


title: blood47

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-796K array
98


title: 5C

description: OE78-8_72 HAF


title: 9C-1

description: WT_72 HAF

value: Wild type


title: blood52

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-801K array
S177


title: blood46

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-795K array
49


title: blood45

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-794K array
25


title: blood44

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-793K array
96


title: 9B-1

description: WT_48 HAF


title: blood58

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-807K array
S168


title: OKseq_0_rep1

description: Okazaki fragment sequencing


title: blood43

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-792K array
93


title: cdKO_04_motor neurons_e10.5

city: Brussels

first: Frederic

last: Clotman

address: avenue Hippocrate, 55 boxB1.55.11

department: Institute of Neuroscience

country: Belgium

institute: UCLouvain

description: Gene expression data from mouse embryonic spinal motor neurons at e10.13

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and demultiplexed using Illumina bcl2fastq v 2.17 program. One mismatch was allowed for index sequence identification
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and log2 fold changes. Genes with adjusted P values less than 0.05 and absolute log2 fold changes greater than 1 were called as differentially expressed genes for each comparison
A gene ontology (GO) analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The mgi GO list was used to cluster the set of genes based on their biological process and determine their statistical significance. A PCA analysis was performed using the “plotPCA” function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first 2 principal components. The top 500 genes, selected by highest row variance, were used to generate the plot.
Genome_build: The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and demultiplexed using Illumina bcl2fastq v 2.17 program. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step

organism: Mus musculus

source_name: cdKO mouse embryonic motor neurons

growth_protocol: Mouse embryos were harvested at e10.5

extract_protocol:
RNA was purified with the Rneasy micro kit (QIAGEN #74004) and RNA concentration and quality were assessed using Bioanalyzer (Agilent)
RNA sequencing (RNA-Seq) library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB)
The sequencing libraries were multiplexed and clustered onto a flow cell. After clustering, the flow cell was loaded on the Illumina HiSeq 4000. The samples were sequenced using a 2 × 150 bp paired-end configuration

treatment_protocol: The spinal cords were dissected, dissociated using the neural tissue dissociation kit (MACS; Miltenyi Biotec #130-092-628). Dissociated cells were sorted by FACS to collect YFP-positive cells in TRIzol reagent

value: spinal motor neurons


title: 19C

description: Cr78_8.22.2_72 HAF


title: blood42

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-791K array
23


title: cdKO_02_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.11


title: blood41

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-790K array
S53


title: cdKO_01_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.10


title: control_05_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.9

source_name: Control mouse embryonic motor neurons


title: blood50

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-799K array
24


title: blood40

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-789K array
13


title: blood39

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-788K array
S25


title: blood38

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-787K array
99


title: control_04_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.8


title: control_03_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.7


title: blood37

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-786K array
11


title: blood35

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-784K array
111


title: cdKO_05_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.14


title: blood34

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-783K array
107


title: control_02_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.6


title: control_01_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.5


title: blood33

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-782K array
103


title: blood32

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-781K array
105


title: blood31

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-780K array
88


title: cdKO_03_motor neurons_e10.5

description: Gene expression data from mouse embryonic spinal motor neurons at e10.12


title: blood30

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-779K array
76


title: P_In_rep1

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

description: Input

data_processing:
Basecalls performed using Illumina CASAVA1.7 software.
Peak alignment performed using BWA MEM 0.7.12-r1039, with following parameters, -T 25；-k 18
MACS2-2.1.0.20150420 solfware was used for peak-calling with following parameters, -f AUTO; -q 0.05;--nomodel;--extsize D6IP inserted lengh of Sample fragments;--keep-dup;--call-summits
Recognition of different peaks was performed as following process, first, calculating the RPM of all combined peaks from two groups of experiments, second, calculating foldEnrich value of each group (If there is input, the foldEnrich value = IP_RPM/Input_RPM; otherwise foldEnrich value = IP_RPM/(the lengh of all combined peaks/overall lengh of all exons in whole genome))
Homer findMotifsGenome.pl v4.9.1 was used for Motif analysis with following parameters, -gc;-rna;-len 6,8,10,12;-size given;-hmoer2;-S 25
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using BWA MEM

source_name: cerebral cortex

growth_protocol: Wild-type C57BL/6 mice were purchased from Wushi company (Fujian, China). The mice were mated, and Embryonic day 0.5 (E0.5) was counted from midday of the day of vaginal plug discovery.

extract_protocol:
Total RNAs were extracted from cerebral cortex, and m6A-methylated RNA were isolated with antibody.
Library was constructed with the NEBNext Ultra RNA library Prep kit from Illumina. Library preparation and high-throughput sequencing were performed by Novogene (Beijing, China).

treatment_protocol: No specific treatment on mice.

tag: strain

value: cerebral cortex

tag: chip antibody

tag: age

value: postnatal day 14


title: P_In_rep2

description: Input


title: P_Ip_rep2

description: immunoprecipitation

value: m6A-specific antibody (Synaptic Systems, cat. No. 202 003)


title: P_Ip_rep1

description: immunoprecipitation


title: P_Ip_rep3

description: immunoprecipitation


title: E_Ip_rep3

description: immunoprecipitation

value: embryonic day 13


title: blood28

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-777K array
77


title: E_Ip_rep2

description: immunoprecipitation


title: E_Ip_rep1

description: immunoprecipitation


title: blood29

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-778K array
74


title: blood27

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-776K array
75


title: E_In_rep3

description: Input


title: P_In_rep3

description: Input


title: Spleen LSCe from mice transplanted with shEvi1 (clone #41)-transduced LCLSK-MA9, treated with atRA

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

data_processing:
Adapters were removed and reads were cropped at 65 bp using Trimmomatic (0.36)
Sequencing quality was checked using FASTQC (0.11.5)
Reads were mapped using STAR aligner (2.6.0c) on mouse genome version mm10 (UCSC) with RefSeq gene annotation and index with 100 bp splice junction overhang
HTSeq was used to quantify raw gene counts according to mm10refGene.gtf
Genome_build: mm10
Supplementary_files_format_and_content: raw counts for all samples are summarized as tab delimited txt file

source_name: leukemic stem cell enriched cells (LSCe)

growth_protocol: LSCe (Venus+ RFP+ lineage (CD11b, CD3, Ter119, B220, Gr1) negative, c-Kit+, Sca-1-, CD34+, CD16/CD32+ cells) were isolated from spleen by flow cytometry and allowed to recover for 24 h in IMDM medium containing 10% FBS, 1% L-Glutamine, 50 ng/ml mSCF, 10 ng/ml mIL-3, 10 ng/ml mTPO, 10 ng/ml mFlt3L, and 10 ng/ml mIL-6.

extract_protocol:
Total RNA was isolated using QIAshredder 50 columns (Qiagen) and the RNeasy Mini Kit 50 including DNase treatment (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library concentrations were determined with the Qubit Fluorometric Quantitation system and the size distribution was assessed using the Experion Automated Electrophoresis System. Sequencing libraries were pooled, diluted, and sequenced on an Illumina HiSeq 4000 using 50 bp single read chemistry.

treatment_protocol: LSCe were treated with 1 µM atRA or the corresponding amount of DMSO for another 24 h.

tag: shrn

tag: agent

value: atRA

value: 10-12 weeks

value: Spleen


title: blood26

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-775K array
82

value: Northern Han


title: blood36

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-785K array
S191


title: Spleen LSCe from mice transplanted with shEvi1 (clone #44)-transduced LCLSK-MA9, treated with atRA


title: Spleen LSCe from mice transplanted with shEvi1 (clone #44)-transduced LCLSK-MA9, treated with DMSO

value: DMSO


title: blood25

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-774K array
79


title: E_In_rep2

description: Input


title: Spleen LSCe from mice transplanted with shEvi1 (clone #41)-transduced LCLSK-MA9, treated with DMSO


title: Spleen LSCe from mice transplanted with shCtrl-transduced LCLSK-MA9 (mouse 1), treated with atRA

value: shCtrl


title: blood24

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-773K array
86


title: E_In_rep1

description: Input


title: Spleen LSCe from mice transplanted with shCtrl-transduced LCLSK-MA9 (mouse 3), treated with atRA


title: Spleen LSCe from mice transplanted with shCtrl-transduced LCLSK-MA9 (mouse 2), treated with atRA


title: blood23

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-772K array
81


title: Spleen LSCe from mice transplanted with shCtrl-transduced LCLSK-MA9 (mouse 2), treated with DMSO


title: Gaa KO 5

city: Hershey

first: Nuno

last: Raimundo

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

data_processing:
Partek Flow
Quantified to annotation model Partek E/M
Genome_build: mm10 - Ensembl Transcripts release 95

source_name: cortex

growth_protocol: Mice were maintained under standard pathogen-free conditions with continuous access to food and water

extract_protocol:
Cortices were harvested, flash frozen in liquid nitrogen.Frozen tissues were gronund and RNA was isolated using Trizol reagent. 1 ug of total RNA was used to prepare sequencing libraries using an Illumina Seq RNA prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 12 months

value: Gaa-/-

value: cortex


title: Gaa KO 4


title: blood22

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-771K array
85


title: Gaa KO 2


title: Spleen LSCe from mice transplanted with shCtrl-transduced LCLSK-MA9 (mouse 3), treated with DMSO


title: blood21

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-770K array
80


title: YY1-ChIP Met

city: Tianjin

first: Heng

address: 38 Rd.Tongyan

institute: Nankai University

data_processing:
Fastq Data were filtered using Skewer
Data were analyzed using Fastqc
ChIP-seq clean reads were aligned to the hg19 genome assembly using Bowtie2 with the following configurations…
peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bw

source_name: YY1-ChIP Met

growth_protocol: PLC-PRF-5 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and Twist1-DNA or YY1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: The cell were treated with 600μM metformin for 48h.

tag: treatment

value: 600μM metformin for 48h


title: Gaa KO 3


title: Spleen LSCe from mice transplanted with shCtrl-transduced LCLSK-MA9 (mouse 1), treated with DMSO


title: Twist1-ChIP Control rep2

source_name: Twist1-ChIP Control

value: Twist1 (Abcam, ab50887)


title: Gaa KO 1


title: ATAC-Hex-rep2

data_processing:
Basecalls performed using Basecalling and Illumina Bcl2fastq 2.17
Data were filtered using Cutadapt
Clean reads were aligned to the hg38 genome assembly using Bowtie2 with the following configurations…
peaks were called using MACS2（version 2.1.1）
Genome_build: hg38
Supplementary_files_format_and_content: bw

source_name: ATAC-Hex

extract_protocol:
The open region of DNA was segmented by Tn5 transposase to construct a library for sequencing.
Libraries were prepared according to Illumina's instructions accompanying the ATAC Sample Kit.

treatment_protocol: The cell were treated with 0.5%1,6-hexanediol for 36h.

value: 0.5%1,6-hexanediol for 36h


title: blood19

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-768K array
108


title: Twist1-ChIP Control rep1


title: WT 5

value: wild type


title: ATAC-Hex-rep1


title: blood18

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-767K array
91


title: ATAC-Control-rep2

source_name: ATAC-Control


title: WT 4


title: blood17

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-766K array
84


title: WT 3


title: ATAC-Control-rep1


title: blood16

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-765K array
104


title: WT 2


title: Twist1-ChIP Met

source_name: Twist1-ChIP Met


title: blood15

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-764K array
41


title: blood14

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-763K array
S76

value: Southern Han


title: blood20

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-769K array
83


title: WT 1


title: blood13

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-762K array
32


title: clpp2-2_3

city: Crawley

first: Jakob

last: Petereit

state: WA

address: 35 Stirling Highway

country: Australia

institute: ARC Centre of Excellence in Plant Energy Biology

data_processing:
Fastq datafiles were received from BGI Genomics
Fastq files were quality controlled using FASTQC
The Ensembl Arabidopsis cDNA v34 (Arabidopsis_thaliana.TAIR10.34) database was modified to ensure a proper mapping of mitochondrial transcripts. The nuclear genome of arabidopsis contains a full copy of the mitochondrial DNA arabidopsis. The nuclear copy of the mitochondrial DNA is not expressed, but alignment or pseudoalignment tools cannot distinguish between the two copies. We removed the nuclear copy of the mitochondrial DNA from the database to map all mitochondrial gene transcripts to mitochondrial genes.
Transcripts expression was quantified using Salmon v0.14.0 (release 1st Jun,2019) using the modified Ensembl Arabidopsis cDNA v34 as database.
Transcript quantifications were improted using the R package 'tximport' (2019-06-25 release) using the Annotationhub db AH52247 | TxDb.Athaliana.BioMart.plantsmart28.sqlite.
Imported transcript quantifications were prefiltered and analyzed for differentially expressed genes using Deseq 2 v1.24.0 (Love, M. I., et al. (2014).
Genome_build: modified Arabidopsis cDNA ensembl v34 (Arabidopsis_thaliana.TAIR10.34)
Supplementary_files_format_and_content: output of the 'assay()' function of the R package DEseq2 formatted as .tsv file, containing normalized transcript abundances for all measured genes through all samples.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis (Arabidopsis thaliana) seeds were surface sterilised and dispensed into one-half strength Murashige and Skoog Gamborg B5 liquid media, within enclosed sterilized 100ml polypropylene containers.   The containers were seated on a rotate shaker in the long-day photoperiod (16h light: of 150 µmol m−2 s−1 light intensity, 8 h dark), 22°C at day and 18°C at night. as described above and seedlings were harvested after two weeks.

extract_protocol:
The two week old hydroponically grown Arabidopsis seedlings were used for RNA isolation using the SIGMA Spectrum™ Plant Total RNA Kit according to the instructions.  The RNA quality and quantity was checked using a ThermoFisher nanodrop ND-1000 spectrophotometer (ThermoFisher, USA)
RNA-Seq libraries were prepared by BGI Genomics from total RNA extract, using random hexamer primers. Standard procedure described in BGI Document NO.: SOP-SS-027, library preparation is also described in https://doi.org/10.1186/s13007-018-0337-0

value: whole seedling

value: clpp2-2:KO-2 of mtCLPP2 (AT5g23140)

value: mutant 2

tag: background ecotype


title: clpp2-2_2

tag: tissue


title: blood11

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-760K array
18

tag: group


title: clpp2-2_1


title: blood12

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-761K array
39


title: blood10

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-759K array
S132


title: esg[ts]_ImdD30A gut

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

description: eD

data_processing:
Basecalls performed using Cyberduck(FTP)
Cell Ranger v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) was used to align sequencing reads tothe Drosophila reference transcriptome (FlyBase, r6.30) and generate feature-barcode matrices. These matrices were analyzed using the Seurat R package (version 3.1.1). Cells possessing <500 UMIs or >2500 UMIs were removed to reduce the number of low-quality cells and doublets. Seurat was then used to normalize expression values and perform cell clustering at a resolution of 0.8 with 7 principal components.Clusters were identified based on known markers and previous single-cell analysis of the Drosophila intestine (https://www.flyrnai.org/scRNA/).
Genome_build: dmel-all-transcript-r6.30.fasta.gz
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

organism: Drosophila melanogaster

source_name: Drosophila esg[ts]>ImdD30A guts 10 days post activation

growth_protocol: Flies were raised on regular food ( standard cornmeal food) at 18C befor eclosion. Adult flies were transferred to 29C for 10 days to get ImdD30A expression in gut progenitor cells.

extract_protocol:
After the 10 day heat shift, a total of 27 guts per sample (virgin female) were dissected and  dissociated with elastase(1 mg/ml). The live cells were sorted by OptiprepTM Density Gradient medium.
Library construction performed by Chromium™ Single Cell 3’ Library & Gel Bead Kit.

value: cells from dissected midgut

value: w; esgGal4, tubGAL80[ts], UASGFP/+;UAS-ImdD30A/+


title: clpp2-1_3

value: clpp2-1:KO-1 of mtCLPP2 (AT5g23140)

value: mutant 1


title: clpp2-1_2


title: blood9

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-758K array
45

source_name: blood

value: Northern Han


title: Pooled Hypothalamic RNA from mice with developmental NMDAR antagonism rep3

city: Riyadh

first: Katharine

middle: Sara

last: Collison

state: Riyadh

address: Takhasussi Street

department: Department of Cell Biology

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Centre

hyb_protocol: The labeled and fragmented DNA was hybridized to Mouse Gene 1.0 ST Array for 17 hours at 45°C and 60rpm. Arrays were washed and stained on the Affymetrix fluidics station 450.

scan_protocol: Genechip were scanned using Genechip 7G scanner.

data_processing: The data were analyzed with Partek Genomics Suite using RMA (Robust Multi-Array Average) settings and quantile normalization method was applied. Intensities less than log value of 6 were filtered. Fold change cut-off was ±1.4Significant DEGs were based on criteria of p-value <0.05 and False Discovery Rate<0.05.

label: Biotin

source_name: Hypothalamus

label_protocol: 5.5ug of fragmented cDNA was end labeled according to standard Affymetrix protocol using Affymetrix Genechip WT terminal labeling kit.

growth_protocol: C57Bl/6J mice were housed 3/cage in a controlled environment (pathogen-free conditions of 12 h light/dark cycle, 22 ± 2°C) with standard chow and water available ad libitum. The breeding and care of the animals were in accordance with the protocols approved by the Animal Care and Use Committee of the King Faisal Specialist Hospital & Research Centre

extract_protocol: Total RNA was extracted from snap frozen Hypothalamus using RNeasy Lipid mini kit (Qiagen UK)

treatment_protocol: Maternal administration of NMDA receptor antagonist drug CGP 39551 (5 mg/Kg body weight p.o.) throughout pregnancy and until completion of weaning was used to study its effect on adulthood hypothalamic gene expression in the female offspring. Mice were euthanized at 21 weeks of age and the adrenal glands were harvested and snap frozen for RNA extraction.

tag: gender

value: female


title: esg[ts] gut

source_name: Drosophila esg[ts] guts 10 days post activation

value: w; esgGal4, tubGAL80[ts], UASGFP/+;+/+


title: WT_H4_counts_2

city: Stellenbosch

first: Hugh

last: Patterton

address: Merriman Street

department: Center for Bioinformatics and Computational Biology

country: South Africa

institute: Stellenbosch University

data_processing:
Sequence read files were filtered with Trim Galore with default setting
Filtered reads were aligned to Saccharomyces cerevisiae genome release 64 with RNA STAR using default settings
Aligned *.bam files were counted with featuresCount
Differential gene expression was determined with edgeR using the count tables
Genome_build: S288C_reference_genome_R64-2-1
Supplementary_files_format_and_content: file generated with edgeR using mutant and WT inputs: tabular log2 (mutant/wild-type)
Supplementary_files_format_and_content: individual count files generated by featureCount

source_name: yeast culture

growth_protocol: Yeast cells were cultured in YPD at 30 degrees for the times indicated

extract_protocol:
RNA samples were prepared for sequencing with a TruSeq Stranded Total RNA Sample Prep adaptor kit (Illumina)
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was isolated from 10ml cultures, and purified with an RNeasy kit (Qiagen)

tag: cell type

value: Yeast cells

value: JDY86 H4 WT


title: Pooled Hypothalamic RNA from mice with developmental NMDAR antagonism rep1

value: NMDA receptor antagonist drug CGP 39551 (5 mg/Kg body weight p.o.) throughout pregnancy


title: clpp2-1_1


title: blood8

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-757K array
S93


title: Pooled Hypothalamic RNA from Control mice rep3

value: control


title: Pooled Hypothalamic RNA from Control mice rep2


title: Pooled Hypothalamic RNA from mice with developmental NMDAR antagonism rep2


title: Pooled Hypothalamic RNA from Control mice rep1


title: Pooled Adrenal RNA from mice with developmental NMDAR antagonism rep3

source_name: Adrenal tissue

extract_protocol: Total RNA was extracted from snap frozen Adrenals using RNeasy Lipid mini kit (Qiagen UK)

treatment_protocol: Maternal administration of NMDA receptor antagonist drug CGP 39551 (5 mg/Kg body weight p.o.) throughout pregnancy and until completion of weaning was used to study its effect on adulthood adrenal gene expression in the female offspring. Mice were euthanized at 21 weeks of age and the adrenal glands were harvested and snap frozen for RNA extraction.


title: wt_3

value: control/reference


title: blood7

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-756K array
59


title: Pooled Adrenal RNA from mice with developmental NMDAR antagonism rep1


title: Pooled Adrenal RNA from mice with developmental NMDAR antagonism rep2


title: WT_H4_counts_1


title: wt_2

value: wild type


title: Pooled Adrenal RNA from Control mice rep1


title: UV_B3

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Sequences reads were mapped to the Ginkgo biloba genome database using TopHat2 software with default parameters.
The read counts for each gene was calculated by HTSeq v0.9.1.
Genome_build: GigaScience GigaDB   (http://gigadb.org/dataset/100209, Guan et al. 2016).
Supplementary_files_format_and_content: The tab-delimited text files files include genes read count for each sample (.txt)

organism: Ginkgo biloba

source_name: UV-B

growth_protocol: 25°C/18°C (day/night); photoperiod: 16h/8h (day/night) with photosynthetically active radiation (PAR) in the day photoperiod at about 350 μmol m-2 s-1 provided by fluorescent tubes (Philips Electronics Trading & Services Co Ltd, Shanghai, China)

extract_protocol:
The leaves of control, UV-B treatment were used for RNA isolation. Total RNAs were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, China)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Leaves were treated with a system with three tubular mercury-vapor lamps,and the CK group leaves were grown under UV-B free light.

value: seedling leaves

value: UV-B treatment with the dosage of 21.42 kJ/m2/day for 14 days


title: WT_H3_counts_1

value: JDY86 H3 WT


title: blood6

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-755K array
43

extract_protocol: genomic DNA was etracted from blood using TIANamp Genomic DNA kit (cat#DP304)


title: K16_counts_2

value: JDY86 H3K16Q


title: blood5

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-754K array
19


title: UV_B2


title: wt_1

value: whole seedling


title: blood4

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-753K array
S135

value: Southern Han


title: H18_counts_2

value: JDY86 H3H18A


title: CK3

source_name: Control

value: UV-B free white light for 14 days


title: blood3

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-752K array
10

value: Northern Han


title: Pooled Adrenal RNA from Control mice rep3

value: female


title: H18_counts_1


title: LW_CK

city: Hangzhou

first: Yitao

state: Zhejiang

address: No.548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

hyb_protocol: Array hybridization was carried out according to the NimbleGen`s Expression user`s guide(see manufacture`s user guide)and performed at CapitalBio Corporation(Beijing,China).

scan_protocol: Scanning was carried out according to the NimbleGen`s Expression user`s guide(see manufacture`s user guide)and performed at CapitalBio Corporation(Beijing,China).

data_processing:
Data analysis was carried out according to the NimbleGen`s Expression user`s guide(see manufacture`s user guide)and performed at CapitalBio Corporation(Beijing,China).
Expression data of genes were generated using Robust Multi-Array Analysis (RMA) algorithm as implemented in the NimbleScan Software, version 2.6 (Roche NimbleGen, Inc.).

source_name: MC-4  cells

label_protocol: Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

growth_protocol: The gastric cancer cell lines MC-4 were cultured with RPMI-1640 medium with 5 % (v/v) fetal bovine serum, 100 U/ml penicillin and 100 U/ml streptomycin in a humidified 5 % CO2 atmosphere at 37 ℃.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using NucleoSpin® RNA clean-up（MACHEREY-NAGEL，Germany） according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: When MC-4 cells density reached 80%,the normal group was treated with culture medium.

value: gastric cancer cell line

value: none (control)


title: blood2

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-751K array
S128

data_processing:
Genomic DNA was genotyped using ASA-750K array (Illumina).
the genotype results were showed directly in nucleotide base (A/T/C/G),  or --(not call)


title: CK2


title: LW_HT

treatment_protocol: When MC-4 cells density reached 80%, pPeOp-treated group was treated with 60 µg/ml pPeOp

value: 60 µg/mL pPeOp


title: CK1


title: blood1

description:
geomic DNA extracted from blood and genotyped by Illumina ASA-750K array
92


title: Microglia_rat3.M

status: Public on Dec 12 2019

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: single end protocol R2 used for 7N barcode + 8N UMI in fastq header

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Read count by homer (http://homer.salk.edu/homer/ngs/)
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: text files include mRNA molecule count values for each Sample

organism: Rattus norvegicus

source_name: Total brain

extract_protocol:
10,000 cells from each sample were sorted into lysis/binding buffer (Life Technologies). mRNA was captured with 6.5ul of Dynabeads oligo(dT) (Life Technologies), washed, and eluted at 85C with 10ul of 10 mM Tris-HCl (pH7.5).
We used a derivation of the MARS-seq as described (Jaitin et al. Science 2014), developed for single cell MARS-seq to produce 3' exprssion libraries with a minimum of 3 replicates per sample.

value: Sprague Dawley

value: Brain

tag: selection markers

tag: source

value: BD  Biosciences

tag: catalog #


title: Microglia_rat1.M


title: Microglia_rat2.M


title: K16_counts_1

value: Yeast cells


title: UV_B1

value: seedling leaves


title: Liver from LKO mice fed HFD

city: Hongo, Bunkyo-ku

first: Yuta

last: Shimanaka

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: 24-wk-old liver-specific LPIAT1 KO (LKO) mice (C57BL/6 background) were housed in climate-controlled (25 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard diet (CE2; CLEA Japan) or high fat diet (HFD-60; Oriental Yeast) and water. ）

extract_protocol: Total RNA was purified using a GenElute Mammalian Total RNA Miniprep kit (Sigma-Aldrich) , and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Lpiat1F/F and LKO mice (Alb-Cre; Lpiat1F/F) were fed high fat diet (HFD) or chow for 18 weeks from 6 weels old.

tag: diet

value: high fat diet

value: liver-specific LPIAT1 KO

value: male

value: C57BL/6 background


title: AB6894

description: paired-end (read2 used to read cell and molecule barcodes only)

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Single-cell libraries were prepared as previously described (Keren-Shaul, Nature Protocols, 2019). In brief, mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier (Keren-Shaul, Nature Protocols, 2019).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

value: Immune cells

tag: selection marker

tag: catalog#


title: AB6893

tag: strain


title: AB6892


title: AB6895


title: Pooled Adrenal RNA from Control mice rep2

value: control


title: AB6891


title: Liver from Lpiat1 F/F mice fed HFD

tag: genotype


title: AB6890

tag: age


title: Liver from LKO mice fed chow

value: chow


title: E50_counts_1

value: JDY86 H3E50A


title: Tumor endothelial cells, Tax2689

city: Nice

first: Kay-Dietrich

last: Wagner

address: 28 Avenue Valombrose

department: Institute of Biology Valrose

country: France

institute: INSERM

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Genome_build: mm8
Supplementary_files_format_and_content: Excel file containing read counts, FPKM, annotation, p values and fold-change

source_name: tumor endothelial cells

extract_protocol:
Endothelial cells were isolated using CD31 beads (Miltenyi) and the RNA extracted using Trizol
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s instructions

treatment_protocol: control mice were injected with sunflower oil, overexpression mice with Tamoxifen

value: Ppard overexpression

value: tumor endothelial cells


title: Tumor endothelial cells, Tax2382


title: Tumor endothelial cells, Tax2455


title: Tumor endothelial cells, Tax2604


title: Tumor endothelial cells, oil2368

value: wild-type


title: Tumor endothelial cells, oil2315


title: Tumor endothelial cells, oil2653


title: Tumor endothelial cells, oil2453


title: EyeBank_cultured_human_corneal_epithelial_cells_+i3T3_008

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

institute: CUO-Recherche

description: Gene expression of passage 3 cells cultivated 6 days with i3T3 (80% confluence)

hyb_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

scan_protocol: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: gPixNormIQR : The normalized Inter-quartile range of all of the inlier pixels per feature. The range is computed independently in each channel.

source_name: primary human epithelial corneal cell population

label_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

growth_protocol:
Once the Descement membrane has been peeled, remaining corneas (stromas with their attached epithelial cells) are then incubated with dispase (2.5 mg/ml) overnight at 4°C. Using forceps, the epithelium is mechanically separated from the underlying stroma and treated with trypsin, which allows the human corneal epithelial cells (hCECs) to dissociate one from another. Once isolated, hCECs are seeded in tissues culture flasks together with feeder layer for expansion.
Cells are grown in DH medium (Dulbecco–Vogt modification of Eagle's medium with Ham's F12 in a 3:1 ratio supplemented with 5% FetalClone II serum, 5 μg/ml of insulin, 0.4 μg/ml of hydrocortisone, 10 ng/ml of epidermal growth factor, 10−10 M of cholera toxin, 100 IU/ml of penicillin, and 25 μg/ml of gentamycin) until they reach 75-95% confluence.

extract_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

treatment_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

tag: Sex

value: female

tag: protocol

value: cultivated 6 days with i3T3


title: Bisulfite-Seq: P1120_DN

city: Beijing

first: Sijin

last: Cheng

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

institute: Peking University

description: processed data file: DN.filt.DMR.bed.gz

data_processing:
kallisto was used to quantify the abundances of transcripts.
DESeq2 was used to conduct differential gene expression analysis
Bismark was used to align sequencing data from Bisulfite-Seq data to human reference genome.
MethPipe was used to quantify the methylation level.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts calculated by kallisto; differentially methylated region (DMR) for each CD8 T cell subset

source_name: CD103- CD39- (DN) T cells isolated from colorectal cancer patient

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using HISTOPAQUE-1077 (Sigma-Aldrich) solution according to the manufacturer’s instructions. Briefly, 3 mL of fresh peripheral blood was collected prior to surgery in EDTA anticoagulant tubes and subsequently layered onto HISTOPAQUE-1077. After centrifugation, lymphocyte cells remained at the plasma-HISTOPAQUE-1077 interface and were carefully transferred to a new tube and washed twice with 1x PBS (Invitrogen). These lymphocytes were re-suspended with FACS buffer (PBS supplemented with 1% fetal bovine serum (FBS, Invitrogen)). Tumors and adjacent normal tissues were cut into approximately 1-mm3 pieces in the RPMI-1640 medium (Invitrogen), and mechanically dissociated and enzymatically digested with MACS Tumor Dissociation Kit (Miltenyi Biotec) for 30 min on a rotor at 37 °C, according to the manufacturer’s instruction. The dissociated cells were subsequently passed through a 70-µm cell-strainer (BD) and centrifuged at 400g for 10 min. The cell pellets were suspended in red blood cell lysis buffer (Solarbio) and incubated on ice for 2 min to lyse red blood cells. After washing twice with PBS (Invitrogen), the cell pellets were re-suspended in FACS buffer. The following fluorescent-labeled antibodies were used: BV711 anti-CD3 (BC96; 1:100—#300450), APC anti-CD8 (RPA-T8; 1:100—#301048), BV421 anti-CD45RA (HI100; 1:100—#47-0458-42), BV421 anti-CD45RO (HI100; 1:100—#47-0458-42), BV421 anti-CCR7 (HI100; 1:100—#47-0458-42), PE anti-CD39 (eBioA1; 1:100—#17-0399-42), FITC anti-CD103 (B-Ly7 and Ber-ACT8; 1:100—#12-1038-42) (all from eBioscience). Cell surface staining was performed in FACS buffer. Stained cells were acquired on the FACS AriaII (all BD Biosciences) for cell sorting. Data were analyzed with FlowJo software (Treestar).  1000 cells of different subtypes including naïve and TEM CD8+ T cells from PBMC, tumor-reactive CD8+ T cells, two clusters of tumor bystander CD8+ T cells were enriched by gating 7AAD−CD3+CD8+CD45RO-CD45RA+CCR7+, 7AAD−CD3+CD8+CD45RO+CD45RA-CCR7-, 7AAD−CD3+CD8+CD103+CD39+, 7AAD−CD3+CD8+CD103+CD39-, and 7AAD−CD3+CD8+CD103-CD39-, respectively, and sorted into 0.2 ml tubes(Axygen) chilled to 4 °C, prepared with lysis buffer with 1 μl 10 mM dNTP mix (Invitrogen), 1 μl 10 μM Oligo dT primer, 1.9 μl 1% Triton X-100 (Sigma), and 0.1 μl 40 U μl−1 RNase Inhibitor (Takara).
Transcriptome amplifications were performed according to Smart-Seq2 protocol with modification of reagent amount and PCR cycle numbers. The amplified cDNA products were purified with Agencourt XP DNA beads, and the concentration of each sample was quantified by Qubit HsDNA kits. Libraries were constructed and amplified using the TruePrep DNA Library Prep Kit V2 for Illumina. The libraries were then purified with Agencourt XP DNA beads and anaylsed by fragment analyser for quality assessment. Purified libraries were analysed by an Illumina Hiseq 4000 sequencer with 150-bp pair-end reads. Whole-genome bisulfite-seq was performed according to a previously published protocol (45). Briefly, 1000 cells were sorted into lysis buffer by FACS; DNA was released after proteinase treatment at 50?°C and then subjected to bisulfite conversion. After bead-based purification, DNA was complemented with the biotinylated random primer Bio-P5-N9 (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 100 units of Klenow polymerase (3’ to 5’ exo-). This random priming was repeated seven times in total. Second strands were synthesized using another random primer, P7-N9 (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’), and final libraries were generated after 7 to 9 cycles of PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

tag: subject status/id

value: colorectal cancer patient P1120

tag: tissue/position

value: Rectum

value: CD103- CD39- (DN) T cells


title: Bisulfite-Seq: P0117_DP

description: processed data file: DP.filt.DMR.bed.gz

source_name: CD103+ CD39+ (DP) T cells isolated from colorectal cancer patient

value: colorectal cancer patient P0117

value: Right colon

value: CD103+ CD39+ (DP) T cells


title: Bisulfite-Seq: P1120_SP

description: processed data file: SP.filt.DMR.bed.gz

source_name: CD103+ CD39- (SP) T cells isolated from colorectal cancer patient

value: male

value: CD103+ CD39- (SP) T cells


title: Bisulfite-Seq: P0117_DN

description: processed data file: DN.filt.DMR.bed.gz


title: Bisulfite-Seq: P0117_SP

description: processed data file: SP.filt.DMR.bed.gz


title: Bisulfite-Seq: P1120_EM

description: processed data file: EM.filt.DMR.bed.gz

source_name: Effector Memory (EM) T cells isolated from colorectal cancer patient

value: Effector Memory (EM) T cells


title: EyeBank_cultured_human_corneal_epithelial_cells_+iHFL_007

description: Gene expression of passage 3 cells cultivated 5 days with iHFL (80% confluence)

value: cultivated 5 days with iHFL


title: Bisulfite-Seq: P1113_SP

description: processed data file: SP.filt.DMR.bed.gz

value: colorectal cancer patient P1113

value: Colon sigmoideum


title: Bisulfite-Seq: P1113_DN

description: processed data file: DN.filt.DMR.bed.gz


title: Liver from Lpiat1 F/F mice fed chow

value: chow

value: C57BL/6 background


title: Bisulfite-Seq: P1113_EM

description: processed data file: EM.filt.DMR.bed.gz


title: EyeBank_cultured_human_corneal_epithelial_cells_+iHFL_004

description: Gene expression of passage 3 cells cultivated 7 days with iHFL (80% confluence)

value: cultivated 7 days with iHFL


title: EyeBank_cultured_human_corneal_epithelial_cells_+i3T3_005

description: Gene expression of passage 3 cells cultivated 7 days with i3T3 (80% confluence)

value: female

value: cultivated 7 days with i3T3


title: EyeBank_cultured_human_corneal_epithelial_cells_003

description: Gene expression of passage 3 cells cultivated 21 days without feeder layer (80% confluence)

value: cultivated 21 days without feeder layer


title: Bisulfite-Seq: P1113_DP

description: processed data file: DP.filt.DMR.bed.gz