title: 48_CON_0_point_1_percent_S43

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

data_processing:
Reads were quantified to Gencode (rel33) using Salmon (v 1.1.0)
Transcript level counts were aggrgated to the gene level using tximport.
Data was analysed using Deseq2
Genome_build: GRCh38, Ensembl release 99
Supplementary_files_format_and_content: txt files with transcript-level counts

source_name: Enteroid monolayer

growth_protocol: Growth in 3D using complete media growth factor positive (high wnt) and after forming confluent 2D monolayers was changed to differentiation media

extract_protocol:
RNA from culture samples was prepared using QIAGEN RNeasy Mini Kit following the manufacturer’s instruction. Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
Total RNA-Seq libraries were prepared for differential gene expression analysis using the SMART-Seq® Stranded Kit [Takara] following manufacturer’s instructions.

value: Inestinal derived organoids

tag: passages

tag: line

value: Preterm


title: oy-0_r2y_ln

status: Public on Jun 30 2021

type: SRA

city: New York

first: Chia-Yi

last: Cheng

state: NY

address: 12 Waverly Place

department: Biology

country: USA

institute: New York University

description: processed data file: NutriNet.Arabidopsis-veg-young.featureCounts.txt

library_source: transcriptomic

data_processing:
Base calling: (Arabidopsis) Picard Tools version 2.17.11 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=false APPLY_EAMSS_FILTER=false. (Maize) bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Removing optical duplicates: Clumpify version 37.24 (Arabidopsis) clumpify.sh -Xmx48g in=in.fq.gz out=out.fq.gz overwrite=t dedupe reorder addcount optical dupedist=40. (Maize) clumpify.sh -Xmx60g in=in.fq.gz out=out.fq.gz overwrite=t dedupe reorder addcount optical dupedist=2500.
Removing adapters: BBDuk version 37.24 (Arabidopsis). (Maize) bbduk.sh in=in.fq.gz out=out.fq.gz overwrite=t ref=~/package/bbmap/resources/adapters.fa ordered=t ktrim=r k=25 mink=11 minlength=35.
Aligning to the genome: BBMap version 37.24 (Arabidopsis). (Maize) bbmap.sh -Xmx56g in=input.fq.gz ordered=t overwrite=t outm=out.sam
Assigning reads: subread v1.5.1 (Arabidopsis) featureCounts -T 1 -s 2 -O -a Araport11.gtf -o out.featureCounts input.sam (Maize) featureCounts -T 1 -R -s 0 -O -a Zea_mays.AGPv4.32.gtf -o out.featureCounts input.sam
Genome_build: (Arabidopsis) TAIR10, (Maize) Zm-B73-REFERENCE-GRAMENE-4.0
Supplementary_files_format_and_content: *.featureCounts.txt: Tab-delimited text files include raw read counts.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
(Arabidopsis) Total RNA was extracted from leaf samples using Direct-zol MiniPrep by Zymo Research.
(Arabidopsis) NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina.
(Maize) RNAs were isolated with a CTAB, acidified phenol-chloroform extraction, and isopropanol precipitation.
(Maize) TruSeq Stranded mRNAseq Sample Prep kit.

tag: tissue

value: Fully-grown adult leaf

tag: age

value: 6 weeks

tag: genotype

tag: treatment

value: Low nitrogen


title: Untreated input replicate 2

city: London

first: Cosetta

last: Bertoli

address: Gower Street

department: MRC Laboratory Molecular Cell Biology

country: United Kingdom

institute: University College London

library_source: genomic

data_processing:
The nf-core/chipseq pipeline (version 1.0.0; https://doi.org/10.5281/zenodo.3240507; Ewels et al., 2020) written in the Nextflow domain specific language (version 0.32.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/chipseq --design design.csv --genome hg19 --singleEnd --narrowPeak --min_reps_consensus 2 -profile crick -r 1.0.0".
All data was processed relative to the human UCSC hg19 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on July 17th 2015.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations, please see the pipeline homepage (https://github.com/nf-core/chipseq).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalised genome-wide bedGraph files were generated from the filtered alignments using the genomeCoverageBed command from BEDTools (version 2.27.1) (Quinlan & Hall, 2010) with parameters "-bg -fs 200 -scale <NORM_FACTOR>". Normalisation factors were generated by scaling the number of mapped reads to 1 million. bedGraph files were converted to bigWig using the bedGraphToBigWig binary available from the UCSC (version 20161115) (Kent et al., 2010).
Supplementary_files_format_and_content: MACS2 narrowPeak files generated using the pipeline command defined above.

molecule: genomic DNA

organism: Homo sapiens

source_name: RPE1 hTERT c-Myc ER

growth_protocol: Cells were cultured in growth medium in 15 cm dishes for 48 hr with or without the addition of 4OH-T.

extract_protocol:
The samples were washed twice in PBS and resuspended in cold ChIP buffer (25 mM Tris/HCl pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton, 0.1% SDS) plus protease inhibitor cocktail (Sigma P8340). The chromatin was sheared with a Bioruptor for 30”on/30”off for 30 minutes using Diagenode tubes.
The DNA library for sequencing was prepared using 2 ng of ChIP’ed DNA for the Kapa Hyper Prep kit according to the manufacturer instructions. QC was performed using the ThermoFisher Qubit and either the Agilent BioAnalyser or TapeStation. The DNA samples were normalised and prepared into Illumina compatible libraries using the KAPA HyperPrep kit according to the manufacturer’s instructions. The libraries were pooled to 4 nM and sequencing was performed on the HiSeq 4000 with at least 75bp reads.

treatment_protocol: Cells were then washed with 1x PBS and crosslinked in 10 ml of 1% formaldehyde at RT for 10 min. Quenching was carried out adding 1 ml of 1.25M glycine for 10 min at RT.

tag: cell type

value: RPE1 hTERT c-Myc ER

tag: timepoint

tag: chip antibody


title: n13_r2y_ln


title: 47_NEC_0_point_1_percent_S37


title: WT 0D-2

city: Shanghai

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

data_processing:
Reads are mapped to mouse genome mm10 with STAR 2.4.1a. Mapping parameters are set as default.
The Rsem v1.2.31 software is then used to align reads to UCSC mouse gene reference. FPKM (fragments per kilobase of exon per million fragments mapped) values of genes’ level from RSEM output are used in the following analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Mus musculus

source_name: C3H10T cells

growth_protocol: All cells were maintained at 37°C in humidified air with 5% CO2. C3H10T1/2  preadipocytes were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (growth medium). Growth medium was replaced every 2 days.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured for an additional day after reaching confluency, and the growth medium was then replaced (day 0) with DMEM supplemented with 10% FBS, 1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine and 10 μg/ml insulin ,1 μM rosiglitazone and 1 nM T3 (differentiation medium, MDI+RT). After 48 h, the differentiation medium was replaced (day 2) with DMEM + 10% FBS containing 5 μg/ ml insulin, and the cells were allowed to accumulate lipid droplets until experimental use. cells were cultured in DMEM + 10% FBS.

value: WT

tag: time point


title: WT 0D-3


title: sakata_r2y_ln

value: Sakata


title: 46_IL16_24h4_media_S32

value: Adult


title: c-Myc activated SMC1 IP replicate 2

description: 4OH-Tamoxifen induced RPE1 hTERT c-Myc ER

value: 4OH-Tamoxifen induced

value: Smc1 (Bethyl laboratories A300-055A rabbit)


title: Untreated input replicate 1


title: akita_r2y_ln

value: Akita


title: c-Myc activated input replicate 1


title: WT 0D-1


title: 44_IL15_24h4_media_S22


title: N21iPSC-Heps Batch 2

city: San Francisco

first: Jacquelyn

middle: J

last: Maher

state: CA

address: 513 Parnassus Avenue

department: Medicine

institute: University of California San Francisco

data_processing:
Reads were mapped to UCSC’s hg19 transcript set using Bowtie 2 version 2.1.0
Gene expression was quantified using RSEM’s (v1.2.15) expectation maximization algorithm
Quantified gene counts were first normalized to counts per million. The counts per million were then further normalized using the Trimmed mean of M-values (TMM) functionality in edgeR
Differential gene expression analysis was performed with treatment type, and batch listed as covariates in a generalized linear model evaluated by a quasi-likelihood F-test.
Genes that were considered differentially expressed contained a cpm count greater than 1 across at least half the replicates in the given comparison in addition to the standard p < .05, |FC| > 1.5 constraints.
Genome_build: hg19

source_name: iPSC-Heps

growth_protocol: iPSC were cultured using standard protocols.

extract_protocol:
Cells were harvested into Trizol and RNA extracted using a Zymo kit.  All samples had RIN > 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iPSC-heps were differentiated using minor modifications of the method of Si-Tayeb et al (PMID 19998274).  Cells were harvested after 22 days.

tag: health status

tag: gender

value: male


title: 43_IL15_24h4_235_S16


title: N20iPSC-Heps Batch 2

value: female


title: mh-1_r2y_ln


title: 42_IL11_24h4_media_S10


title: mr-0_r2y_ln


title: N19iPSC-Heps Batch 2


title: 41_IL11_24h4_235_S4


title: kn-0_r2y_ln


title: N18iPSC-Heps Batch 2


title: mt-0_r2y_ln


title: ge-0_r2y_ln


title: edi-0_r2y_ln


title: N17iPSC-Heps Batch 2


title: shC19orf12-1-3

city: Tianjin

first: Ran

last: Liu

address: Qixiangtai

institute: Tianjin Medical University

data_processing:
Basecalls performed using Illumina Hiseq 4000
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: UCSC hg 19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample.

source_name: human lung adenocarcinoma cell

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using  oligo -dT beads

value: lung

tag: cell line

value: lung adenocarcinoma

value: C19orf12 knockdown


title: shC19orf12-1-2


title: N16iPSC-Heps Batch 2


title: shC19orf12-1-1


title: N15iPSC-Heps Batch 2


title: c-Myc activated SMC1 IP replicate 1


title: ct-1_r1y_ln


title: scramble3

value: sh-scramble (serves as wild type control)


title: 37_IL2_24h4_235_S26

value: Inestinal derived organoids


title: 39_IL3_24h4_235_S36


title: D10 CD34+CD41+CD9- SR1+ cells, Rep1

city: Strasbourg

first: Henri

last: de la Salle

address: 10 rue Spielmann

country: France

institute: EFS Grand-Est

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL13

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10 (EMBnet.journal 17, 10-12, 2011). Reads were mapped to rRNA sequences using bowtie version 2.2.8 (Nat Methods 9, 357-359, 2012), and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped onto the hg38 assembly of Homo sapiens genome using STAR (Bioinformatics 29, 15-21) version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count (Bioinformatics 31, 166-169, 2015) version 0.6.1p1, with annotations from Ensembl version 91 and \union" mode2 (between 16 and 25 106 different non-ribosomal reads/sample). Read counts were normalized across samples with the median-of-ratios method proposed by Anders and Huber (Genome Biol, 11, R106, 2010), to make these counts comparable between samples.
Comparisons of interest were performed using the test for differential expression proposed by Love et al. (Genome Biol 15, 550, 2014) and implemented in the Bioconductor package DESeq2 version 1.16.1. The pValues were adjusted for multiple testing using the Benjamini-Hochberg method. Processed data files provide the log2 values of the normalized read counts divided by the median of the lengths of the ENSEMBL transcripts associated to the respective genes. D0-D7 processed data were generated by the analysis all of the samples, D7-D14 processed data were generated by the analysis of all the samples except D0 ones.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix text files containing raw read counts in each sample (D0-D14 Raw gene counts.txt) or, log2 values of the normalized read counts divided by the median of the lengths of the ENSEMBL transcripts associated to the respective genes and DEseq2  analysis of differential expression (D0-D7 processed data.txt and, D7-D14 processed data.txt).

molecule: polyA RNA

source_name: Peripheral blood cells

growth_protocol: Peripheral blood CD34+ progenitors from adults were purified using Miltenyi technology then, differentiated into MKs in StemSpan™ Megakaryocyte Expansion medium containing Megakaryocyte Expansion Supplement  (containing SCF, IL-6, IL-9, TPO and 20 ng/mL human LDL) from D0 to D7. At D7, cells were placed in StemSpan™ Megakaryocyte Expansion medium supplemented  with 50 ng/mL TPO and, cell differentiation proceeded up to D14. Each cell sample (data file) was generated from a CD34+ cell batch prepared from 5 leukocyte-depletion filters, and thus representing 20 unrelated donors.

extract_protocol:
RNAs were purified from D0 cells (isolated using Miltenyi technology), and of D7 to D14 populations (isolated by flow cell sorting) using RNeasy Plus kit (Qiagen).
RNA-Seq libraries were generated from 500-300 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
Two batches of RNA-seq production were generated (CNSL and VNDT series).

treatment_protocol: When used, SR1 was added at D0 and D7 (1µM).

tag: cell markers

tag: day

tag: rna-seq production

value: CNSL


title: Untreated SMC1 IP replicate 2


title: 38_IL2_24h4_media_S31


title: C16iPSC-Heps Batch 2

value: Healthy control


title: col-0_r1y_ln

value: Fully-grown adult leaf

value: 6 weeks

value: Low nitrogen


title: Untreated SMC1 IP replicate 1

value: RPE1 hTERT c-Myc ER


title: tsu-0_r1y_hn

value: High nitrogen


title: C15iPSC-Heps Batch 1


title: scramble1


title: scramble2


title: 36_Con1_2_24hr_media_S21

value: Preterm


title: 35_Con1_2_24hr_235_S15


title: 40_IL3_24h4_media_S42

value: Adult


title: stw-0_r1y_hn


title: st-0_r1y_hn


title: N20iPSC Batch 2

source_name: iPSC


title: Rashpanjor Biological Rep 2 (Waterlogging)

city: Cuttack

first: Koushik

last: Chakraborty

address: Bidyadharpur

country: India

institute: ICAR-National Rice Research Institute

description:
Replicate 2
RW2

data_processing:
The generated data was aligned to the MSU6 genome using TopHat. The resultant bam were subsequently processed by the Cufflinks pipeline.
Genome_build: MSU6
Supplementary_files_format_and_content: .diff files containing the Expression Analyses from Cuffdiff.

organism: Oryza sativa

source_name: Leaf Sheath

extract_protocol:
Using the standard Trizol Method.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cultivar

value: Rashpanjor

value: Leaf Sheath

tag: developmental stage

value: Max Tillering Stage

value: Waterlogging


title: Rashpanjor Biological Rep 1 (Waterlogging)

description:
Replicate 1
RW1


title: N21iPSC Batch 2

value: male


title: shahdara_r1y_hn

value: Shahdara


title: N19iPSC Batch 2

value: female


title: Varshadhan Biological Rep 2 (Waterlogging)

description:
Replicate 2
VW2

value: Varshadhan


title: 32_Con1_1_8hr_media_S41

value: Inestinal derived organoids

tag: passages

tag: line


title: N18iPSC Batch 2


title: sakata_r1y_hn

tag: tissue

tag: age

value: Sakata


title: 31_Con1_1_8hr_235_S35


title: 30_NEC1_24hr_media_S30


title: Varshadhan Biological Rep 1 (Waterlogging)

description:
Replicate 1
VW1

tag: treatment


title: oy-0_r1y_hn

value: Fully-grown adult leaf

tag: genotype


title: N17iPSC Batch 2


title: bur-0_r1y_ln

value: 6 weeks


title: Rashpanjor Biological Rep 1 (Control)

description:
Replicate 1
RC1

value: Control


title: N15iPSC Batch 2


title: 28_NEC1_8hr_media_S20

tag: cell type


title: Varshadhan Biological Rep 2 (Control)

description:
Replicate 2
VC2


title: N16iPSC Batch 2


title: 27_NEC1_8hr_235_S14


title: 26_NEC2_2_24hr_media_S8


title: 34_Con1_1_24hr_media_S9


title: mt-0_r1y_hn


title: Varshadhan Biological Rep 1 (Control)

description:
Replicate 1
VC1


title: mr-0_r1y_hn


title: C15iPSC Batch 1

value: Healthy control


title: Rashpanjor Biological Rep 2 (Waterlogging + Salinity)

description:
Replicate 2
RWS2

value: Waterlogging + Salinity


title: 22_NEC2_1_24hr_237_S29

value: Preterm


title: mh-1_r1y_hn

value: High nitrogen


title: N14iPSC-Heps Batch 1

value: NAFLD:NAFL not NASH


title: kn-0_r1y_hn


title: N14iPSC Batch 1


title: Rashpanjor Biological Rep 2 (Control)

description:
Replicate 2
RC2

value: Rashpanjor

value: Leaf Sheath


title: Rashpanjor Biological Rep 1 (Waterlogging + Salinity)

description:
Replicate 1
RWS1

value: Max Tillering Stage


title: 21_NEC2_1_24hr_235_S25


title: Varshadhan Biological Rep 2 (Waterlogging + Salinity)

description:
Replicate 2
VWS2


title: n13_r1y_hn


title: 20_NEC2_1_8hr_media_S19


title: 19_NEC2_1_8hr_154_S13


title: edi-0_r1y_hn


title: C16iPSC Batch 2

value: male


title: 18_NEC2_1_8hr_237_S7


title: N12iPSC-Heps Batch 1

description: Duwaerts_iPSC-Heps_all_detectable_genes.xls

data_processing:
Reads were mapped to UCSC’s hg19 transcript set using Bowtie 2 version 2.1.0
Gene expression was quantified using RSEM’s (v1.2.15) expectation maximization algorithm
Quantified gene counts were first normalized to counts per million. The counts per million were then further normalized using the Trimmed mean of M-values (TMM) functionality in edgeR
Differential gene expression between conditions was calculated by fitting a generalized negative binomial log-linear model using edgeR
Genes that were considered differentially expressed contained a cpm count greater than 1 across at least half the replicates in the given comparison in addition to the standard p < .05, |FC| > 1.5 constraints.
Genome_build: hg19

treatment_protocol: iPSC-heps were differentiated using the method of Si-Tayeb et al (PMID 19998274).  Cells were harvested after 21 days.

value: iPSC-Heps


title: ct-1_r1y_hn


title: N13iPSC-Heps Batch 1


title: Total RNA (42 hpf)

city: Pittsburgh

first: Jian Ming

last: Khor

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

data_processing:
Sequence reads (>100 million reads/sample) were subjected to quality control (FastQC)
filtered to remove small numbers of rRNA reads, and mapped to the S. purpuratus genome (v. 3.1) first with BWA (Li and Durbin, 2010) and then using HISAT2 (Kim et al., 2019) to align reads with BWA MAPQ<20.
De novo eRNA peak-calling was carried out as described by Hirabayashi et al., 2019. Briefly, bidirectional enhancers were identified using the FANTOM5 pipeline (FANTOM Consortium, 2014). TSSs were identified according to http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment. and clustered using the decomposition-based peak identification (DPI) software (https://github.com/hkawaji/dpi1/blob/master/identify_tss_peaks.sh). DPI was used with default parameters but without the decomposition parameter. Peaks with at least two supporting CAGE tags were retained and used as input to call bidirectional enhancers using a program available at https://github.com/anderssonrobin/enhancers/blob/master/scripts/bidir_enhancers.
Genome_build: S. purpuratus genome version 3.1 (available on http://www.echinobase.org)
Supplementary_files_format_and_content: peaks
Spurp3.1_eRNA.bed - eRNA peak BED file for S. purpuratus genome version 3.1
Spurp5.0_eRNAliftover.bed - eRNA peak BED file lifted over from S. purpuratus genome version 3.1 to version 5.0
Spurp3.1_eRNA.bw - eRNA peak BigWig file for S. purpuratus genome version 3.1
Spurp5.0_eRNAliftover.bw - eRNA peak BigWig file for S. purpuratus genome version 5.0

organism: Strongylocentrotus purpuratus

source_name: Sea urchin embryos

extract_protocol:
Adult S. purpuratus were obtained from Pat Leahy (Caltech). Gametes were collected by intracoelomic injection of 0.5 M KCl. Fertilization and embryo culture were carried out according to Adams et al. (2019). Embryos were cultured at 15° C in 4-liter plastic beakers fitted with battery powered stirrers. Embryos were harvested at 0, 6, 12, 18, 24, 30, 36, 42, and 48 hr post- fertilization (hpf). The 9 samples were derived from two separate embryo cultures. For the 0 hpf time point, embryos were collected immediately after fertilization. Total RNA (75-100 g/sample) was isolated using the RNeasy Plus Mini kit (Qiagen Cat. No. 74134) and the quality of the preparations was confirmed using an RNA TapeStation (Agilent). RNA integrity numbers (RINs) for all samples were 9.8-10.0. RNA samples were stored at -80°C.
CAGE library preparation, sequencing, mapping, and eRNA identification were performed by DNAFORM (Yokohama, Kanagawa, Japan)

value: Whole embryo

tag: hours post fertilization


title: Total RNA (48 hpf)


title: 24_NEC2_1_24hr_media_S40


title: N11iPSC-Heps Batch 1

value: female


title: col-0_r1y_hn


title: 17_NEC2_1_8hr_235_S3

value: Inestinal derived organoids


title: N10iPSC-Heps Batch 1


title: 16_25_24hr_S39

value: Tissue


title: Total RNA (36 hpf)


title: N9iPSC-Heps Batch 1


title: ge-0_r1y_hn

value: Fully-grown adult leaf


title: bur-0_r1y_hn

value: 6 weeks


title: Varshadhan Biological Rep 1 (Waterlogging + Salinity)

description:
Replicate 1
VWS1

value: Varshadhan


title: 15_25_fresh_S34


title: Total RNA (24 hpf)


title: 14_34_S28


title: bi-1_r1y_ln

value: Low nitrogen


title: N8iPSC-Heps Batch 1


title: Total RNA (30 hpf)


title: bi-1_r1y_hn


title: N7iPSC-Heps Batch 1


title: akita_r1y_hn

value: Akita


title: 13_37_S24


title: N6iPSC-Heps Batch 1


title: 12_27_S18


title: Total RNA (12 hpf)


title: N5iPSC-Heps Batch 1


title: Total RNA (18 hpf)


title: Total RNA (6 hpf)


title: 11_38_S12


title: tsu-0_r1y_ln


title: stw-0_r1y_ln


title: Total RNA (0 hpf)


title: N4iPSC-Heps Batch 1


title: 10_36_S6


title: CTRL_NPC-3

city: montreal

first: stephane

last: Richard

state: Quebec

address: 3755 Cote ste catherine, LDI Room 420

country: Canada

institute: McGill

description: Gene_expression.xlsx; Alternative_splicing.xlsx

data_processing:
Samples were demultiplexed using bcl2fastq v2.20 Conversion Software
Illumina adapter sequences were first removed from the paired-end reads of length 101 through the Trimmomatic v0.39
The reads were then aligned to the human genome (hg19/GRCh37) with STAR v2.7.1a
Gene expression was quantified for all samples through HOMER v4.11.1, employing Gencode v19 gene annotations employing Gencode v19 gene annotations
DESeq2 v1.26.0 was used afterward to normalize the read counts through the regularized logarithm (rlog) transformation and to compute their differential expression relative to the control.
Genome_build: hg19
Supplementary_files_format_and_content: Excel data table including the raw gene counts and FPKM for each sample
Supplementary_files_format_and_content: Excel data table including the alternative splicing events

source_name: Neural progenitor cells

growth_protocol: hiPSCs were cultured under feeder-free condition in TeSR-E8 medium (05990, Stem cell technologies). Neuronal induction was performed using STEMdiff SMADi Neuronal Induction Kit (08581, Stem cell technologies).

extract_protocol:
iPSC and NPC RNA samples were purified using GenElute™ Mammalian Total RNA Miniprep Kit (RTN70, Sigma Aldrich).
RNA sequencing libraries were generated using TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA).

value: iPS-derived neural progenitor cells

tag: mutation

value: wide type


title: N3iPSC-Heps Batch 1

tag: health status


title: st-0_r1y_ln


title: N2iPSC-Heps Batch 1

value: NAFLD:NAFL not NASH

tag: gender


title: shahdara_r1y_ln

value: Shahdara


title: 9_26_S2


title: N1iPSC-Heps Batch 1


title: 8_33_S38


title: 7_22_Marg_S33


title: MUT2: gata1-positive erythroid cells

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
basecalling was done with the Picard module IlluminaBasecallsToFastq
Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired-end reads were mapped using STAR aligner (version 2.4.2a) to the reference genome.
Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM, Cufflinks (version 2.2.1) was used.
Genome_build: GRcz10
Supplementary_files_format_and_content: tab-delimited text file include gene counts for each sample

organism: Danio rerio

source_name: ddx41 mutant

extract_protocol:
gata1-positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep (Zymo).
Libraries were made at BGI following their low-input RNA protocol.

value: 40 hours post fertilization

value: erythroid cells


title: MUT3: gata1-positive erythroid cells


title: C14iPSC-Heps Batch 1

value: Healthy control

value: male


title: 6_29_S27


title: SIB5: gata1-positive erythroid cells

source_name: sibling zebrafish


title: C13iPSC-Heps Batch 1

value: iPSC-Heps


title: n13_r1y_ln


title: SIB4: gata1-positive erythroid cells


title: mt-0_r1y_ln


title: C12iPSC-Heps Batch 1

value: female


title: 5_30_S23


title: SIB1: gata1-positive erythroid cells


title: C11iPSC-Heps Batch 1


title: SIB3: gata1-positive erythroid cells


title: 4_22_NEC_S17


title: akita_r1y_ln


title: Myc_Pi-GFP_IP_rep3

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
Cutadapt, quality trimming (20), read length filtration 18 - 38 nt
Bowtie2 in combination with SAMtools view were used for tRNA and rRNA trimming and potato and P. infestans sRNA filtering to exclude the reads from the other genome for the different datasets, using 0 mismatches allowed per seed against each Fasta filter
SamToFastq converted the files to fastq
Fastx_collapser in the FASTX-toolkit counted the number of St- and Pi-sRNA
ShortStack was used to predict miRNA and summarize sRNA, using strand cutoff 0.5, fold size 1000, dicermin 18 and dicermax 38
Genome_build: Solanom tuberosum genome v4.04
Genome_build: Phytophthora infestans genome (ASM14294v1)
Supplementary_files_format_and_content: Results.txt files from the output of Shortstack including predicted sRNA

organism: Phytophthora infestans

source_name: Ago-RNA co-immunoprecipitation

extract_protocol:
Mycelia and infected leaves were harvested and flash frozen in liquid nitrogen. PiAgo1-GFP and control Pi-GFP immunoprecipitations were performed with anti-GFP antibody (Chromotek, gtm-100).
Barcoded sequencing libraries were constructed using the Ion Total RNA-Seq Kit v2 and Ion Xpress barcode primers. Sequencing was performed on the Ion Proton platform using the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific).

tag: gfp-tagged protein

tag: wild-type background

tag: transformed construct

value: GFP

value: Mycelium

tag: potato line

tag: ip antibody

value: GFP (Chromotek, gtm-100)


title: MUT4: gata1-positive erythroid cells


title: 3_41_S11

value: Tissue


title: mr-0_r1y_ln

value: Fully-grown adult leaf

value: 6 weeks


title: C10iPSC-Heps Batch 1


title: oy-0_r1y_ln

value: Low nitrogen


title: sakata_r1y_ln

value: Sakata


title: C9iPSC-Heps Batch 1


title: mh-1_r1y_ln


title: Myc_Pi-GFP_IP_rep2


title: 1_43_r1_S1


title: 2_43_r2_S5


title: C8iPSC-Heps Batch 1


title: MCF7hypoxia_control3

city: Oxford

first: Adrian

middle: L

last: Harris

address: John Radcliffe Hospital

department: Department of Medical Oncology

institute: University of Oxford

data_processing:
Reads were aligned to the genome using STAR
TPM values were calculated using gene counts and transcript length using custom R script
Genome_build: hg38
Supplementary_files_format_and_content: Matrix containing raw gene counts for MCF7 breast cancer cells in normoxia and hypoxia
Supplementary_files_format_and_content: Matrix containing raw gene counts for J2 immunoprecipitated RNA under normoxia and hypoxia
Supplementary_files_format_and_content: Matrix containing TPM normalised gene counts for J2 immunoprecipiated RNA under normoxia and hypoxia

source_name: MCF7 Cells

growth_protocol: cells were grown in DMEM 5mM glucose supplemented with 10% FBS

extract_protocol:
RNA was extracted using Tri-Reagent following the manufacturer´s instructions
libraries were prepared using Illumina’s instructions

treatment_protocol: normoxia (21% O2) or 0.1% hypoxia was performed for 48h

value: breast cancer cells

tag: cell line

tag: oxygen status

value: hypoxia


title: Myc_Pi-GFP_IP_rep1


title: C7iPSC-Heps Batch 1


title: ge-0_r1y_ln


title: MCF7hypoxia_control2


title: edi-0_r1y_ln


title: C6iPSC-Heps Batch 1


title: Myc_PiAgo1-GFP_IP_rep3


title: MCF7hypoxia_control1


title: Myc_PiAgo1-GFP_IP_rep2


title: C5iPSC-Heps Batch 1


title: Myc_PiAgo1-GFP_IP_rep1


title: C4iPSC-Heps Batch 1


title: MCF7normoxia_control3

value: normoxia


title: C3iPSC-Heps Batch 1


title: MCF7normoxia_control2


title: MCF7normoxia_control1

description: GeneCounts_Normoxia_Hypoxia.csv, GeneCounts_Normoxia_Hypoxia.csv


title: kn-0_r1y_ln


title: j2_ip_hypoxia_rep3

description:
Immunoprecipitated RNA
J2IP_rawcounts_GEO.csv, J2IP_tpmcounts.csv

tag: rip antibody


title: C2iPSC-Heps Batch 1


title: C1iPSC-Heps Batch 1


title: j2_ip_hypoxia_rep2


title: WT_ABA+glucose_rep3

city: Urbana

first: Xueyi

last: Xue

state: Illinois

address: 1201 W. Gregory Dr.

department: Department of Plant Biology

institute: University of Illinois at Urbana-Champaign

data_processing:
Raw reads were trimmed and filtered by removing adapters sequence and bases with low quality score (Q30 score < 15) using Trimmomatic v0.38
Clean reads were mapped to Arabidopsis thaliana (version 11) primary transcript sequences (https://phytozome.jgi.doe.gov) to calculate the gene expression in transcript per million (TPM) using Kallisto v 0.44.0 (Bray, et.al., Nat Biotechnol, 2016).
Candidates with more than 10 counts per million reads in at least 50% samples, and with parameters |b| ≥ 0.2 and q-value < 0.05 were identified differentially expressed genes (DEGs) using Sleuth program (Pimentel, et.al., Nat Methods, 2017).
Genome_build: Arabidopsis thaliana (version 11) primary transcript sequences
Supplementary_files_format_and_content: Matrix table with gene TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: whole seed

growth_protocol: After 3-day imbibition at 4 °C, WT and sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C

extract_protocol:
Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), DNA was removed via Turbo DNA-free kit (AM1907, Invitrogen).
The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche).
The libraries were pooled and sequenced by Hiseq 2500 (Illumina) with paired-end reads.

treatment_protocol: Seeds were transferred at 24 HAI to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment.

tag: strain

tag: tissue

value: germinating seed

value: 30 hours after imbibition

value: wild type

value: ABA+glucose


title: WT_ABA+glucose_rep1

tag: age

tag: treatment


title: WT_ABA+glucose_rep4

tag: genotype


title: WT_ABA+glucose_rep2


title: N13iPSC Batch 1

description: Duwaerts_iPSC_normalized_reads_count_per_million.xls

tag: cell type

value: iPSC

value: male


title: j2_ip_hypoxia_rep1


title: WT_ABA_rep3


title: N12iPSC Batch 1

value: female


title: j2_ip_normoxia_rep2


title: N11iPSC Batch 1


title: j2_ip_normoxia_rep3


title: N10iPSC Batch 1


title: WT_ABA_rep2


title: WT_ABA_rep1


title: j2_ip_normoxia_rep1


title: N9iPSC Batch 1


title: WT_glucose_rep4


title: WT_glucose_rep3


title: KTB34-RasV12

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

data_processing:
CellRanger 2.1.0 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 2.3 was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfificationa.
The CCA function from Seurat 2.3 was used for integrative analysis of the samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered gene-barcode matrices

source_name: HRAS V12 transformed

growth_protocol: DMEM/F12 (1:3) + 5% FBS + Hydrocortisone (0.4 µg/ml) + Insulin (5 µg/ml) + EGF (20 ng/ml) + Adenine phosphate salt (24 µg/ml) + ROCK inhibitor (Y-27632, 1mM)

extract_protocol:
Single cell 3’ RNA-seq experiment was conducted using the Chromium single cell system (10x Genomics, Inc). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA.
10X genomics 3' RNA-seq V2 single cell reagent kit

value: HRAS V12 transformed


title: WT_glucose_rep2


title: KTB6-RasV12


title: KTB34-pLKO

source_name: Vehicle control

value: Vehicle control


title: N6iPSC Batch 1


title: WT_glucose_rep1


title: KTB6-pLKO


title: N5iPSC Batch 1


title: WT_control_rep2

value: control


title: WT_ABA_rep4


title: WT_control_rep3


title: N2iPSC Batch 1

value: NAFLD:NAFL not NASH


title: KTB39-RasV12


title: KTB39-pLKO


title: N4iPSC Batch 1


title: N3iPSC Batch 1


title: KTB22-RasV12


title: N1iPSC Batch 1


title: WT_control_rep1


title: KTB22-pLKO


title: B9_CD8 T cells from cytoplasmic CD101 variant

city: Seattle

first: Jennifer

middle: M

last: Lund

state: WA

address: 1100 Fairview Ave N., E5-110

department: Vaccine and Infectious Disease Division

institute: Fred Hutchinson Cancer Research Center

description:
B9_S18
processed data file:
gene_fragment_counts.txt
CD8.cytoplasmic_vs_no_variant.txt

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4.
Sequencing reads were mapped to human genome build hg38 and GENCODE gene annotation V31 using 2-pass mapping implemented in STAR v2.7.1. Read mates mapped >20Kb apart were excluded.
QC was performed using FastQC v0.11.8 and RSeQC v3.0.0 to examine read quality, insert fragment size, read duplication rates, gene body coverage and read distribution in different genomic regions.
Gene-level expression was quantified by counting unstranded paired-end reads using FeatureCounts in Subread v1.6.5.
Differential gene expression were analyzed between genotype groups using Bioconductor package edgeR v3.26.8. Protein-coding and lncRNA genes with low expression were excluded by requiring at least one count per million in at least N samples (N is equal to the number of samples in the smallest group). The filtered expression matrix was normalized by TMM method and subject to significance testing using GLM LRT method. Genes were deemed differentially expressed if BH-corrected p-values are less than 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of raw fragment counts per gene and sample. The first two columns are ENSEMBL gene ID and length of non-overlapping exonic regions of a gene.
Supplementary_files_format_and_content: tab-delimited text files of edgeR processed data including the following columns: Geneid (ENSEMBL gene ID), Genename (gene name), Genetype (GENCODE annotated gene type), logFC (log2 fold change), logCPM (log2 average CPM), PValue (p-value), FDR (false discovery rate), is.DE (1 for positive fold change and FDR<0.05, -1 for negative fold change and FDR < 0.05, 0 for otherwise), CPM.TMMnormalized.sample_name (TMM-normalized CPM for each sample), FPKM.TMMnormalized.sample_name (TMM-normalized FPKM for each sample).

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies to CD4, CD3, CD8, CD25, and CD127, and CD4 T cells (CD3+CD4+CD25-) and CD8 T cells (CD3+CD8+) were FACS-sorted into individual tubes. RNA was isolated using Qiagen kits.
RNA-seq libraries were prepared from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc., Mountain View, CA, USA) and the Nextera XT DNA Library Preparation Kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).

tag: cd101 genotype

value: cytoplasmic variant

tag: cd101 specific variant

value: peripheral blood mononuclear cells

tag: cell subtype

value: CD8 T cell


title: N8iPSC Batch 1

tag: health status

tag: gender


title: C14iPSC Batch 1

value: Healthy control


title: N7iPSC Batch 1


title: C13iPSC Batch 1


title: WT_control_rep4


title: C11iPSC Batch 1


title: C12iPSC Batch 1


title: E12.0 GFP-1

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

description: mRNA

data_processing:
For 10X Genomics data, reads were processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Cellranger aggr was used to aggregate three cell ranger counts.
For smart-seq2 data, read 2 grouped by barcodes was aligned to corresponding read 1 after removing polyA and TSO sequence. Removing the reads with low quality bases by Cutadat (version 1.18), reads were aligned to mm10 reference genome (Ensembl) by Hisat2. Htseq was used to count uniquely mapped reads to deduplicated genes expression matrix by UMI sequence.
Genome_build: mm10
Supplementary_files_format_and_content: *Raw_gene_counts_matrix.txt files (of tab-delimited text file) with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: 0x_Celltype.txt tab-delimited text file for cell annotation include gene number, count number, mito percentage and celltype for each cell (In column 1, barcode-1 corresponds to placental cells-E10, barcode-2 corresponds to placental cells-E11, barcode-3 corresponds to placental cells-E12).
Supplementary_files_format_and_content: gz file (of tsv file) with 10x data barcodes produced by CellRanger software
Supplementary_files_format_and_content: gz file (of tsv file) with 10x data features produced by CellRanger software
Supplementary_files_format_and_content: gz file (of mtx file) with 10x data matrix produced by CellRanger software

source_name: Placenta

extract_protocol:
Target cells were captured using antibody by fluorescence activated cell sorting (FACS).
For 10X Genomics data, single-cell suspensions were loaded on a Chromium Single Cell Controller (10 × Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 30 Library and Gel Bead Kit V2 (10 × Genomics, 120237). RNAs barcoding were obtained through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads (Invitrogen, 37002D). Single-cell RNA-sequencing (scRNA-seq) libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 (10× Genomics, 120237) following the manufacturer’s introduction. Sequencing was performed on an Illumina HiSeq × Ten with pair end 150 bp (PE150). For smart-seq2 data, the linearized RNA molecules were released in a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with bio-tinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator. Enrich the cDNA fragments by Dynabeads® MyOneTM Streptavi- din C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.

treatment_protocol: Placenta, AGM and yolk sac were dissected from pregnant mice and prepared for single-cell suspensions using collagenase according to previous reports.

value: placenta

value: Hoxa13+ lineage cells

tag: developmental stage

value: embryonic day 12.0


title: E12.0 GFP-2

description: mRNA


title: B7_CD8 T cells from cytoplasmic CD101 variant

description:
B7_S16
processed data file:
gene_fragment_counts.txt
CD8.cytoplasmic_vs_no_variant.txt


title: B6_CD8 T cells from no CD101 variant

description:
B6_S15
processed data file:
gene_fragment_counts.txt
CD8.cytoplasmic_vs_no_variant.txt
CD8.Ig_vs_no_variant.txt

source_name: CD8 T cells from no CD101 variant

value: no variant

value: NoVariant


title: WT IL4 rep 1

city: Amsterdam

first: Menno

last: de Winther

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: Academic Medical Center University of Amsterdam

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2’s analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: matrix of read counts per gene

source_name: Bone marrow-derived macrophages

extract_protocol:
RNA was extracted uisng the Qiagen RNAeasy mini kit
Libraries were constructed using the KAPA HyperPrep mRNA kit

value: WT


title: WT IL4 rep 3


title: B5_CD8 T cells from no CD101 variant

description:
B5_S14
processed data file:
gene_fragment_counts.txt
CD8.cytoplasmic_vs_no_variant.txt
CD8.Ig_vs_no_variant.txt


title: C10iPSC Batch 1

value: iPSC


title: KO IL4 rep 3

value: KO


title: B4_CD8 T cells from no CD101 variant

description:
B4_S13
processed data file:
gene_fragment_counts.txt
CD8.cytoplasmic_vs_no_variant.txt
CD8.Ig_vs_no_variant.txt


title: B3_CD8 T cells from Ig-like CD101 variant

description:
B3_S12
processed data file:
gene_fragment_counts.txt
CD8.Ig_vs_no_variant.txt

source_name: CD8 T cells from Ig-like CD101 variant

value: Ig like variant


title: KO IL4 rep 1


title: KO IL4 rep 2


title: B2_CD8 T cells from Ig-like CD101 variant

description:
B2_S11
processed data file:
gene_fragment_counts.txt
CD8.Ig_vs_no_variant.txt


title: C7iPSC Batch 1

value: male


title: B8_CD8 T cells from Ig-like CD101 variant

description:
B8_S17
processed data file:
gene_fragment_counts.txt
CD8.Ig_vs_no_variant.txt


title: B1_CD8 T cells from cytoplasmic CD101 variant

description:
B1_S10
processed data file:
gene_fragment_counts.txt
CD8.cytoplasmic_vs_no_variant.txt


title: A9_CD4 T cells from cytoplasmic CD101 variant

description:
A9_S9
processed data file:
gene_fragment_counts.txt
CD4.cytoplasmic_vs_no_variant.txt

value: CD4 T cell


title: E13.5 GFP

data_processing:
For 10X Genomics data, reads was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Cellranger aggr was used to aggregate three cell ranger counts
For smart-seq2 data, read 2 grouped by barcodes was aligned to corresbonding read 1 after removing ploya and TSO sequence. Removing the reads with low quality bases by Cutadat(version 1.18), reads were aligned to mm10 reference genome(Ensemble) by Hisat2. Htseq was used to count uniquely mapped reads to deduplicated genes expression matrix by UMI sequence.
Genome_build: mm10
Supplementary_files_format_and_content: tar file (of tab-delimited text file) with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files for cell annotation include gene number, count number, mito percentage and celltype for each cell
Supplementary_files_format_and_content: gz file (of tsv file) with10x data barcodes produced by CellRanger softeware
Supplementary_files_format_and_content: gz file (of tsv file) with10x data features produced by CellRanger softeware
Supplementary_files_format_and_content: gz file (of mtx file) with10x data matrix produced by CellRanger softeware

extract_protocol:
Target cells were captured using antibody by fluorescence activated cell sorting (FACS).
For 10X Genomics data, single-cell suspensions were loaded on a Chromium Single Cell Controller (10 × Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 30 Library and Gel Bead Kit V2 (10 × Genomics, 120237). RNAs barcoding were obtained through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads (Invitrogen, 37002D). Single-cell RNA-sequencing (scRNA-seq) libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 (10× Genomics, 120237) following the manufacture’s introduction. Sequencing was performed on an Illumina HiSeq × Ten with pair end 150 bp (PE150). For smart-seq2 data, the linearized RNA molecules were releasein a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with bio-tinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator.Enrich the cDNA fragments  by Dynabeads® MyOneTM Streptavi- din C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.

value: embryonic day 13.5


title: E11.0 GFP-3

value: embryonic day 11.0


title: WT IL4 rep 2


title: A8_CD4 T cells from Ig-like CD101 variant

description:
A8_S8
processed data file:
gene_fragment_counts.txt
CD4.Ig_vs_no_variant.txt

source_name: CD4 T cells from Ig-like CD101 variant


title: C4iPSC Batch 1

value: female


title: C3iPSC Batch 1


title: E11.0 GFP-1


title: C9iPSC Batch 1


title: E11.0 GFP-2


title: C8iPSC Batch 1


title: C1iPSC Batch 1


title: A5_CD4 T cells from no CD101 variant

description:
A5_S5
processed data file:
gene_fragment_counts.txt
CD4.cytoplasmic_vs_no_variant.txt
CD4.Ig_vs_no_variant.txt

source_name: CD4 T cells from no CD101 variant

value: peripheral blood mononuclear cells


title: A6_CD4 T cells from no CD101 variant

description:
A6_S6
processed data file:
gene_fragment_counts.txt
CD4.cytoplasmic_vs_no_variant.txt
CD4.Ig_vs_no_variant.txt


title: DHTS_rep3

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3' adaptor-trimming and low quality reads removing by fastp software (v0.20.0). The high quality trimmed reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of mRNAs.
Genome_build: MM10
Supplementary_files_format_and_content: FPKM expression values

source_name: vascular endothelial

growth_protocol: An endothelioma cell line (EOMA) was cultured in 1640 medium (Gibco, Gaithersburg, MD, USA) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 mg/L penicillin (Sigma, St. Louis, MO, USA), and 100 mg/mL streptomycin under normoxic conditions (5% CO2 and 21% O2).

extract_protocol:
After 24-h treatment with either DMSO or DHTS, total RNA was extracted from EOMA cells using TRIzol Reagent (15596026; Invitrogen, Carlsbad, CA, USA). A total of 3 µg of RNA per sample was used as input material for RNA sample preparations.
Sequencing libraries were generated using a NEBNext® UltraTM RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s recommendations and library quality was assessed on an Agilent Bioanalyzer 2100 system (Santa Clara, CA, USA). Sequencing was performed on Illumina HiSeq platform at Beijing Novogene (Beijing, China).

treatment_protocol: NC replicates were treated by DMSO for 24 hours.DHTS replicates were treated by 2μM DHTS for 24 hours.

tag: cell line/type

value: endothelioma cell line (EOMA)

value: 2μM DHTS for 24h


title: DHTS_rep2


title: C2iPSC Batch 1

source_name: iPSC

value: Healthy control


title: DHTS_rep1


title: A3_CD4 T cells from Ig-like CD101 variant

description:
A3_S3
processed data file:
gene_fragment_counts.txt
CD4.Ig_vs_no_variant.txt


title: input DNA

city: tianjin

first: yang

middle: wen

last: dong

address: tong yan road

institute: nankai

data_processing:
Using Trim Galore software to dynamically remove low quality and joint sequence fragments from 3'end of sequencing data, and then filter short sequences.
Quality Statistics of Sequencing Data by FastQC
Unique mapping of the original sequence of the sample with reference to the genome sequence by Bowtie2
From Reads alignment to reference genome results, the sequence number of each chromosome is counted, and then the average depth of reference genome is calculated every 5 kb. The density distribution of reference genome is counted, which can be used to detect the distribution of sequence series on reference genome to find whether there is enrichment distribution.
The MACS software is used to locate the enriched regions of reads on the genome.That is peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: ab-delimited text files include genes count for each Sample and bw

growth_protocol: Cells were maintained in DMEM medium (BI company) with 10% FBS and 1% PS

extract_protocol:
Cellular lysates were prepared by incubating the cells in lysis buffer (1%SDS) containing protease inhibitor cocktail (Roche) , The chromatin DNA was precipitated by polyclonal antibodies against Twist1.
The DNA was purified with the Qiagen PCR purification kit. In-depth whole-genome DNA sequencing was performed by the JingNeng Corporation, Beijing. ChIP-seq samples were subjected to quality control by the sequencing company.

tag: tissue origen

value: Liver cancer

tag: chip antibody


title: A4_CD4 T cells from no CD101 variant

description:
A4_S4
processed data file:
gene_fragment_counts.txt
CD4.cytoplasmic_vs_no_variant.txt
CD4.Ig_vs_no_variant.txt


title: E11.0 GFP-4

value: placenta

value: Hoxa13+ lineage cells


title: Twist1_ChIPSeq

value: Twist1 (abcam  ab50887)


title: C6iPSC Batch 1

extract_protocol:
Cells were harvested into Trizol and RNA extracted using a Zymo kit.  All samples had RIN > 7.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: A2_CD4 T cells from Ig-like CD101 variant

description:
A2_S2
processed data file:
gene_fragment_counts.txt
CD4.Ig_vs_no_variant.txt


title: NC_rep2

value: DMSO for 24h


title: C5iPSC Batch 1

description: Duwaerts_iPSC_normalized_reads_count_per_million.xls

value: iPSC


title: A1_CD4 T cells from cytoplasmic CD101 variant

description:
A1_S1
processed data file:
gene_fragment_counts.txt
CD4.cytoplasmic_vs_no_variant.txt

value: cytoplasmic variant


title: SM40

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

country: Germany

institute: Ruhr-University Bochum

description: spt3_M replicate 1

data_processing:
Reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511.
Read counts and expression ratios for annotated gene models were determined with DESeq2 (Anders S, Huber W 2010, Genome Biol 11: R106).
Genome_build: Sordaria macrospora genome version 03, accession number NMPR01000000.
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts and expression ratios DESeq2 for all annotated genes.

organism: Sordaria macrospora

source_name: total sexual mycelium

growth_protocol: Strains were grown for 6d at 25 °C on corn meal medium. For preparation of mycelial RNA, strains were grown in liquid medium, for preparation of perithecial RNA, strains were grown on solid medium.

extract_protocol:
Subsequent RNA preparation for perithecia and mycelia was as described by Yarden et al. (EMBO J 11:2159–2166).
RNA libraries from microdissected RNA as well as total mycelial RNA were prepared for sequencing in a HighSeq4000 using standard Illumina protocols

treatment_protocol: For harvesting perithecia, plates were fixed with ethanol for 10 min, and perithecia were scraped from the plate and broken up using a glass homogenizer.


title: SM41

description: spt3_M replicate 2


title: NC_rep1


title: HeLa cells-ActD-treated-9h-TRIzol_rep3

city: Beijing

first: Tong

address: Life Science Park Road

institute: State Key Laboratory of Proteomics

data_processing:
Casava software used for basecalling
Reference genome (B37) 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 Hisat2 (v2.0.5).
The mapped readscounts of each type of RNA transcripts was counted using FeatureCounts (v1.5.0-p3) according to the gtf file from the Ensemble database.
Genome_build: B37

source_name: HeLa cells

extract_protocol:
The RP-complexes from HeLa cells were captured by PP, proteinase K  was added to digest protein, the eluted RNAs were further purified by TRIzol following the manufacturer’s instructions. For other samples, RNA was harvested using Trizol reagent
RNA was used in each replicate to construct the cDNA library using a NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions.

value: HeLa cells

value: treated with ActD for 9 hours


title: SM39

description: SMAC_03952_P replicate 2

source_name: perithecia


title: A7_CD4 T cells from cytoplasmic CD101 variant

description:
A7_S7
processed data file:
gene_fragment_counts.txt
CD4.cytoplasmic_vs_no_variant.txt

value: CD4 T cell


title: yolk sac ECs

city: Shanghai

description: Smart-seq2_Raw_gene_counts_matrix.txt.tar

data_processing:
For 10X Genomics data, reads was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Cellranger aggr was used to aggregate three cell ranger counts
For smart-seq2 data, read 2 grouped by barcodes was aligned to corresbonding read 1 after removing polyA and TSO sequence. Removing the reads with low quality bases by Cutadat(version 1.18), reads were aligned to mm10 reference genome(Ensemble) by Hisat2. Htseq was used to count uniquely mapped reads to deduplicated genes expression matrix by UMI sequence.
Genome_build: mm10
Supplementary_files_format_and_content: *Raw_gene_counts_matrix.txt files (of tab-delimited text file) with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: 10x_Celltype.txt tab-delimited text file for cell annotation include gene number, count number, mito percentage and celltype for each cell (In column 1, barcode-1 corresponds to placental cells-E10, barcode-2 corresponds to placental cells-E11, barcode-3 corresponds to placental cells-E12.)
Supplementary_files_format_and_content: gz file (of tsv file) with10x data barcodes produced by CellRanger softeware
Supplementary_files_format_and_content: gz file (of tsv file) with10x data features produced by CellRanger softeware
Supplementary_files_format_and_content: gz file (of mtx file) with10x data matrix produced by CellRanger softeware

source_name: Yolk Sac

extract_protocol:
Target cells were captured using antibody by fluorescence activated cell sorting (FACS).
For 10X Genomics data, single-cell suspensions were loaded on a Chromium Single Cell Controller (10 × Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 30 Library and Gel Bead Kit V2 (10 × Genomics, 120237). RNAs barcoding were obtained through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads (Invitrogen, 37002D). Single-cell RNA-sequencing (scRNA-seq) libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 (10× Genomics, 120237) following the manufacture’s introduction. Sequencing was performed on an Illumina HiSeq x Ten with pair end 150 bp (PE150). For smart-seq2 data, the linearized RNA molecules were releasein a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with bio-tinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator.Enrich the cDNA fragments  by Dynabeads® MyOneTM Streptavi- din C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.

value: yolk sac

value: endothelial cells


title: HeLa cells-ActD-treated-9h-TRIzol_rep2


title: AGM non-HE cells

source_name: Embryo

value: embryo

value: non-hemogenic endothelial cells

value: embryonic day 11.0


title: SM37

description: SMAC_03952_M replicate 2


title: HeLa cells-ActD-treated-9h-TRIzol_rep1


title: SM35

description: asm2_P replicate 2


title: HeLa cells-ActD-treated-5h-TRIzol_rep3

value: treated with ActD for 5 hours


title: placental non-HE cells


title: HeLa cells-ActD-treated-5h-TRIzol_rep2


title: SM36

description: SMAC_03952_M replicate 1


title: SM34

description: asm2_P replicate 1


title: placental HE cells

value: hemogenic endothelial cells


title: HeLa cells-ActD-treated-2h-TRIzol_rep3

value: treated with ActD for 2 hours


title: SM33

description: asm2_M replicate 2


title: AGM HE cells


title: HeLa cells-ActD-treated-2h-TRIzol_rep2


title: NC_rep3

value: endothelioma cell line (EOMA)


title: HeLa cells-ActD-treated-5h-TRIzol_rep1


title: MATIP2_4OHT

city: Tokyo

first: Kazutsune

last: Yamagata

address: 5-1-1, Tsukiji, Tyuo-ku

department: Hematological Malignancy

country: Japan

institute: National Cancer Center Research Institute

data_processing:
All steps were performed on Galaxy web site (https://usegalaxy.org).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (Galaxy Version 0.38.0), then aligned to mm10 whole genome using HISAT2 (Galaxy Version 2.1.0+galaxy5)with default settings.
FeatureCount (Galaxy Version 1.6.4+galaxy1) was used to count RNA-seq for genes.
To determine differentially expressed genes from count table, DESeq2 was used with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: differentially expressed genes from count table

source_name: Bone Marrow

growth_protocol: Methocult 3234 supplemeted with 10nM SCF, 10nM IL-3, and 10nM GM-CSF.

extract_protocol:
From 4-OHT-treated MAflox and MATIP cells, total RNA was prepared using Rneasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MAflox and MATIP cells were treated with 100nM 4-OHT or EtOH (control) for 4 days and harveated for total RNA preparations.

value: Bone Marrow

tag: cell line

value: MATIP

value: 4 days of 100nM 4-OHT


title: MATIP1_4OHT


title: HeLa cells-ActD-treated-2h-TRIzol_rep1

last: Liu


title: SM32

description: asm2_M replicate 1


title: MATIP2_non

value: 4 days of EtOH (solvent)


title: MATIP1_non


title: SM30

description: wt_P replicate 1

value: wild type


title: MAflox2_4-OHT

value: MAflox


title: HeLa cells-ActD-treated-0h-TRIzol_rep3

value: HeLa cells

value: treated with ActD for 0 hours


title: SM31

description: wt_P replicate 2


title: HeLa cells-ActD-treated-0h-TRIzol_rep2


title: SM38

description: SMAC_03952_P replicate 1


title: SM29

description: wt_M replicate 2


title: MAflox2_non


title: HeLa cells-ActD-treated-0h-TRIzol_rep1


title: SM28

description: wt_M replicate 1


title: MAflox1_4-OHT


title: TC71_iEF_DOX_8h_Rep3

city: Boston

first: Neekesh

middle: V.

last: Dharia

state: MA

address: 350 Brookline Ave

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Illumina basecalling performed by Novoseq 6000
Sequences were mapped to the GRCh37/hg19 human genome using STAR v2.7.2b with standard parameters --outSAMtype BAM  SortedByCoordinate   --outSAMunmapped Within  --outSAMattributes NH HI NM MD AS XS    --outReadsUnmapped Fastx   --outSAMstrandField intronMotif  --quantMode TranscriptomeSAM GeneCounts   --quantTranscriptomeBan IndelSoftclipSingleend
Gene level reads were summarized by counting the reads that overlapped the gencode v19 annotated gene exons, by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package
Gene-level expression was estimated as log2(1+ transcripts per million (TPM)) using featureCounts.
Gene counts were then used to quantify differentially expressed genes between the experimental and control conditions using DESeq2 v1.24.0 based on  the shrunken log2 fold changes and based on the approximate posterior estimation for GLM coefficients (apeglm v1.6) method for effect size
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files with log2(TPM+1) for each sample; tab-delimited DESeq2 output

source_name: TC71 cell line

extract_protocol:
Cells were harvested and RNA was tracted using Qiagen RNA extraction kit. RNA was sent to Novogene for library preparation and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ewing sarcoma cells


title: TC71_iEF_DOX_8h_Rep2


title: TC71_iEF_DOX_8h_Rep1


title: MATIP2_genome_4-OHT

data_processing:
All steps were performed on Galaxy web site (https://usegalaxy.org).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (Galaxy Version 0.38.0), then aligned to mm10 whole genome using bowtie2 (Galaxy Version 2.3.4.3+galaxy0) with default settings.
peaks were called using MACS2 (Galaxy Version 2.1.1.2016030906) with  "--broad" setting
To generate bigwig files as processed data file from each bam file, bamCoverage (Galaxy Version 3.3.0.0.0) was used with the following settings: normalization to CPM, and paired-end extension.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K27me3-DNA complexes were isolated with anti-H3K27me3 antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: MATIP cells were treated with 100nM 4-OHT or EtOH (control) for 4 days and harveated for chromatin precipitation.

value: 100 nM 4-OHT treatment for 4 days

value: MLL-AF10 (Tip60 delta/delta, Cre-ERT2)


title: Medulloblastoma MYC-Otx2_rep2

city: Trento

first: Luca

last: Tiberi

state: TN

address: via Sommarive, 9

department: Department of Cellular, Computational and Integrative Biology - CIBIO

country: Italy

institute: University of Trento

data_processing:
Reads were aligned to mm10 reference using STAR 2.4.1d
Gene expression counts were computed with htseq-count tool 0.6.1
Quality control was performed with Qualimap v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression counts

source_name: Medulloblastoma

growth_protocol: Cerebellar tumors were isolated from mice and fresh frozen

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Life Technologies) according to manufacturer's instructions
Libraries were prepared from the extracted RNAs using the QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen, Vienna, Austria) using 0.5-1 μg of RNA per library and following the manufacturers’ instructions. We modified the standard protocol adding Unique Molecular Identifiers (UMI) during the second strand synthesis step. Indices from the Lexogen i7 6nt Index Set and i5 6nt Dual Indexing Add-on Kits (Cat. No. 044.96 and 047.96, Lexogen) were used, and 15-19 cycles of library amplification were performed. Libraries were eluted in 30 μL of the kit’s Elution Buffer. The double-stranded DNA concentration was quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher), ranging from 3 to 12 ng/μL. The molar concentration of cDNA molecules in the individual libraries was calculated from the double-stranded DNA concentration and the single library average size (determined on a PerkinElmer Labchip GX). An equal number of cDNA molecules from each library were pooled and the final pool was purified once more in order to remove any free primer and prevent index-hopping.

treatment_protocol: No treatment for isolated cells

value: Medulloblastoma

tag: oncogenes

tag: conditional expression

value: constitutive


title: Medulloblastoma MYC-Gfi1_rep2

tag: strain

tag: tissue


title: Medulloblastoma MYC-Otx2_rep3


title: TC71_iEF_control_8h_Rep2


title: Medulloblastoma MYC-Otx2_rep1


title: MATIP2_H3K27me3_4-OHT

tag: treatment


title: TC71_iEF_control_8h_Rep1


title: Mid_High_Density_3

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

description: Dougherty_MH3_1k_SIC_Index_196_CTTAACACCA_S35

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
For each allelic sequence pair (each allele having up to 10 unique RNA barcodes), mean of the rna/dna ratios from above calculated for each sample --> t-test of sample mean expression values between the alleles of each biallelic sequence
Genome_build: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary_files_format_and_content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

source_name: Cell line

growth_protocol: Cells were grown without changing medium for 72 hours at 37°C, 5% CO2.

extract_protocol:
Cells lifted in 250uL PBS and 750µL Trizol, followed by addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions. Turbo DNAse-free kit was used to remove incidental DNA, followed by a second cleanup using the Zymo kit to achieve a higher final concentration of RNA.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Basal medium (10% FBS in DMEM), with 1% penicillin-streptomycin in the medium before transfection and >6hrs after

value: plasmid-transfected

tag: density


title: MATIP1_genome_4-OHT

tag: genotype


title: MAflox1_non


title: MATIP2_genome_non

value: MLL-AF10 (Tip60 flox/flox, Cre-ERT2)


title: Mid_High_Density_2

description: Dougherty_MH2_1k_SIC_Index_195_ACTCACAACA_S34


title: TC71_iEF_control_8h_Rep3

tag: cell type


title: MATIP1_genome_non


title: High_Density_3

description: Dougherty_HD3_1k_SIC_Index_193_CTTACACTCA_S32


title: MATIP2_H3K27me3_non


title: TC71_dT_T8_dTAGV-1_24h_Rep2


title: TC71_dT_T8_dTAGV-1_24h_Rep1


title: TC71_dT_T8_dTAGV-1_24h_Rep3


title: MATIP1_H3K27me3_non


title: TC71_dT_T8_DMSO_24h_Rep3


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S16_L006

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S16_L006

data_processing:
Sequencing reads were generated using 10X Genomics Cell Ranger software version 2.0 mkfastq command
The same software (count) was used to map reads to the mm10 Mouse genome and to measure the gene abundance
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI counts for each cell are listed in a tab-delimited file

source_name: median eminence of the hypothalamus

extract_protocol:
The median eminence from all animals within the same treatment groups are combined and single cells were dissociated via trituration in papain.
Isolated cells from each treatment group were split into 2 and were encapsulated in droplets and cDNA libraries were made using a 10X Genomics Chromium instrument and 10X Single Cell 3’ V2 Reagent kit.  Paired end sequencing was performed on an Illumina HiSeq 4000.  The first 26bp read contains both a cell barcode and a unique molecular identifier, the next 76bp read contains the cDNA insert.

treatment_protocol: 5 animals were fasted overnight, 5 animals were fasted overnight then refed 1h (normal chow diet)

value: median eminence of the hypothalamus

value: Overnight Fast + Refed

tag: replicate


title: High_Density_2

description: Dougherty_HD2_1k_SIC_Index_192_ACGGGTTCGA_S31


title: TC71_dT_T8_DMSO_24h_Rep2


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S16_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S16_L005


title: Medulloblastoma MYC-Gfi1_rep1


title: High_Density_1

description: Dougherty_HD1_1k_SIC_Index_191_AAGCTATGTA_S30


title: TC71_dT_T8_DMSO_24h_Rep1


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S15_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S15_L006


title: K235R_Input

city: Guangzhou

first: Guang-Rong

last: Yan

state: Guangdong

address: 63 Duobao Road

institute: Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University

description: total RNA

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and  undetermined bases. Then sequence quality was verified using FastQC.
All reads were mapped to human genome by bowtie with default settings.
Mapped reads of m6A fragments and input libraries were provided through R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/).
Called peaks were annotated by intersection with gene architecture using ChIPseeker. Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM.
Genome_build: Version GRCh38.p10

source_name: cervix adenocarcinoma cell line

growth_protocol: These cells were cultured in DMEM medium supplemented with 10% fetal bovine serum at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. mRNA was purified using poly-T oligo attached magnetic beads (Invitrogen). mRNA was then fragmented into ~100nt oligonucleotides using divalent cations under elevated temperature. Fragmented mRNA was incubated with m6A-specific antibody in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630) supplemented with 0.5 μg/μl BSA for 2h at 4 ℃. Immunoprecipitated m6A RNA fragments were used for the construction of m6A-seq libraries (IP). And 1 ug of total RNA was used for the construction of RNA-sequencing libraries (Input).
RNA libraries were prepared for sequencing using standard Illumina protocols.
Immunoprecipitated m6A RNA fragments for m6A-seq (IP), total RNA for RNA-Seq (Input).

value: HeLa

value: cervix adenocarcinoma cell line

value: ALKBH5 KO+lentiviruses expressing ALKBH5 K235R mutant


title: month6_ccl4_rep6

city: Heidelberg

first: Christian

middle: H.

last: Holland

address: Im Neuenheimer Feld 267

department: Institute for Computational Biomedicine

institute: Heidelberg University

data_processing:
Reads were aligned with the using the web application Biojupies (https://amp.pharm.mssm.edu/biojupies/).
Lowly expressed genes were removed using the R/Bioconductor package edgeR (version 3.30.3)
Raw read counts were normalized via TMM methods also using edgeR package followed by logCPM transformation via the R/Bioconductor package limma (version 3.44.3)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: livers

extract_protocol:
RNA was isolated using the TRIzol method. Briefly, 1 ml TRIzol was added to 5 x 106 cells followed by vortexing, a 5-min incubation at room temperature, and the addition of 200 μl chloroform. After mixing, further incubation at room temperature for 2–3 min and centrifugation (12,000 g) at 4 °C for 5 min, the clear supernatant was mixed with 500 μl isopropanol and incubated at room temperature for 10 min. After centrifugation (12,000 g) at 4 °C for 10 min, the supernatant was discarded and the pellet washed with 1 ml cold 75% ethanol followed by vortexing and centrifugation (7,500 g, 4 °C, 5 min). The pellet was dried and dissolved in RNase-free water.
For the preparation of the libraries, rRNA was removed with the Ribo-Zero™ Human/Mouse/Rat rRNA Removal Kit from Biozym Scientific GmbH as described in Cadenas et al. (under review). Briefly, the RNA library was prepared using the TruSeq Stranded totalRNA Sample Prep Kit from Illumina (San Diego, CA) according to the manufacturer’s instructions. All samples were sequenced using an Illumina HiSeq 2500 sequencer v4 (Illumina, San Diego,CA) with 10 transcriptome samples per lane and an average of 25 million paired-end reads (2×125 bp) at IKMB NGS core facilities. Reads were mapped to the corresponding reference genome using Biojupies.

value: CCl4, 1 g/kg b.w. in olive oil

tag: time point

value: 6 months


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S15_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S15_L005


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S14_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S14_L006


title: K235R_IP

description: Immunoprecipiated m6A RNA fragments


title: Mid_High_Density_1

description: Dougherty_MH1_1k_SIC_Index_194_CAGTCACACA_S33


title: month2_oil_rep6

value: olive oil

value: 2 months


title: WT_Input

description: total RNA

value: ALKBH5 KO+lentiviruses expressing wild type ALKBH5


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S14_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S14_L005


title: WT_IP

description: Immunoprecipiated m6A RNA fragments


title: MATIP1_H3K27me3_4-OHT

value: Bone Marrow

value: MATIP


title: NC_Input

description: total RNA

value: lentiviruses expressing blank vector


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S13_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S13_L006


title: A-24-3

first: Deming

last: Jiang

address: No. 500, Dongchuan Road, Minhang District, Shanghai

institute: East China Normal University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  Agrobacterium fabrum str. c58 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
HTSeq software used for calculating RPKM
Genome_build: Agrobacterium fabrum str. c58
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Agrobacterium sp. CGMCC 11546

source_name: Agrobacterium  sp. CGMCC 11546 after 24 h of curdlan fermentation

extract_protocol:
bacterial cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA labrarys were prepared for sequencing using standard Illumina protocols

tag: time


title: month12_oil_rep6

value: 12 months


title: A-24-2


title: month12_ccl4_rep6


title: month0_control_rep5

value: 0 months


title: ScRNA Overnight Fast + Refed Sample 2 data chunk S13_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 2 data chunk S13_L005


title: NC_IP

description: Immunoprecipiated m6A RNA fragments


title: month0_control_rep6


title: A-24-1


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S8_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S8_L006


title: NOMO1.400nM.DAC.d6.n2 [S1-156]

city: Collegeville

first: Shawn

middle: W

last: Foley

address: 1250 S. Collegeville Rd

department: Oncology

institute: GlaxoSmithKline

description: processed data file: DNMT1_AML_fpkm_NOMO1_table.txt

data_processing:
Salmon_v0.12.0 transcript quantification
DEseq2 log2 fold change differential expression and normalized fpkm quantification
fGSEA gene set enrichment analysis
Genome_build: Human hg38
Supplementary_files_format_and_content: fpkm values for all quantifiable genes; log2 fold change values for all quantifiable genes

growth_protocol: Cell lines were obtained from the American Type Culture Collection, the Deutsche Sammlung von Mikroorganismen und Zellbulturen, or AddexBio and maintained in the recommended cell culture media at 37°C in 5% CO2.

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini kit
Libraries were prepared at the NYU Medical Center Genome Technology Center
All 150 PE libraries were sequenced across 6 lanes for a total of 12 fastq samples per sample.

treatment_protocol: Cells were plated 24 hours before treatment with either DMSO, GSK3484862, GSK3685032, DAC, or GSK3510477 then grown for the indicated time before collection.

tag: cell tye

value: AML cell line

value: DAC

tag: dose


title: A-7-3

source_name: Agrobacterium  sp. CGMCC 11546 after 7 h of curdlan fermentation


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S8_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S8_L005

value: median eminence of the hypothalamus


title: NOMO1.400nM.GSK032.d6.n2 [S1-155]


title: month6_ccl4_rep5


title: month2_oil_rep5


title: month2_ccl4_rep6


title: NOMO1.0nM.DMSO.d6.n2 [S1-154]

value: DMSO


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S7_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S7_L006

value: Overnight Fast + Refed


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S7_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S7_L005


title: month12_oil_rep5


title: NOMO1.10000nM.GSK477.d4.n2 [S1-153]


title: WT-3

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  Agrobacterium fabrum str. c58 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq was used to count reads.
Genome_build: Agrobacterium fabrum str. c58
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: wild type strain after 24 h of curdlan fermentation

value: Wild type strain


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S6_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S6_L006


title: NOMO1.1000nM.GSK862.d4.n2 [S1-152]


title: month12_ccl4_rep5


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S6_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S6_L005


title: WT-2


title: NOMO1.10000nM.DAC.d4.n2 [S1-151]


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S5_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S5_L006


title: WT-1


title: month0_control_rep4


title: NOMO1.2000nM.DAC.d4.n2 [S1-150]


title: metZ-3

source_name: metZ deletion mutant after24 h of curdlan fermentation

value: metZ deletion


title: ScRNA Overnight Fast + Refed Sample 1 data chunk S5_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast + Refed replicate 1 data chunk S5_L005


title: NOMO1.400nM.DAC.d4.n2 [S1-149]


title: A-7-2


title: month2_ccl4_rep5

value: CCl4, 1 g/kg b.w. in olive oil


title: NOMO1.80nM.DAC.d4.n2 [S1-148]


title: metZ-2


title: A-7-1


title: month2_ccl4_rep4


title: ScRNA Overnight Fast Sample 2 data chunk S4_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S4_L005

value: Overnight Fast


title: ScRNA Overnight Fast Sample 2 data chunk S4_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S4_L006


title: NOMO1.16nM.DAC.d4.n2 [S1-147]


title: ScRNA Overnight Fast Sample 2 data chunk S3_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S3_L006


title: metH-3

source_name: metH deletion mutant after 24 h of curdlan fermentation

value: metH deletion


title: month12_ccl4_rep4


title: metH-2


title: ScRNA Overnight Fast Sample 2 data chunk S3_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S3_L005


title: NOMO1.3.2nM.DAC.d4.n2 [S1-146]


title: NOMO1.10000nM.GSK032.d4.n2 [S1-145]


title: month0_control_rep3

value: olive oil


title: metH-1


title: month6_ccl4_rep4

value: 6 months


title: NOMO1.2000nM.GSK032.d4.n2 [S1-144]


title: month6_ccl4_rep3


title: ScRNA Overnight Fast Sample 2 data chunk S2_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S2_L005


title: ScRNA Overnight Fast Sample 2 data chunk S2_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S2_L006


title: month2_oil_rep4

value: 2 months


title: month2_oil_rep3


title: NOMO1.400nM.GSK032.d4.n2 [S1-143]


title: metZ-1

source_name: metZ deletion mutant after 24 h of curdlan fermentation


title: NOMO1.80nM.GSK032.d4.n2 [S1-142]


title: month12_oil_rep4


title: ScRNA Overnight Fast Sample 2 data chunk S1_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S1_L006


title: month2_ccl4_rep3


title: ScRNA Overnight Fast Sample 2 data chunk S1_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 2 data chunk S1_L005


title: NOMO1.16nM.GSK032.d4.n2 [S1-141]


title: month12_oil_rep3


title: ScRNA Overnight Fast Sample 1 data chunk S9_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S9_L006


title: NOMO1.3.2nM.GSK032.d4.n2 [S1-140]

description: processed data file: DNMT1_AML_fpkm_NOMO1_table.txt


title: month12_ccl4_rep3


title: ScRNA Overnight Fast Sample 1 data chunk S9_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S9_L005


title: month0_control_rep2


title: NOMO1.0nM.DMSO.d4.n2 [S1-139]


title: NOMO1.10000nM.GSK477.d2.n2 [S1-138]


title: month6_ccl4_rep2


title: ScRNA Overnight Fast Sample 1 data chunk S12_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S12_L006


title: ScRNA Overnight Fast Sample 1 data chunk S12_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S12_L005


title: month2_oil_rep2


title: F1(C24xCol), biological rep 3

type: RNA

city: Tsukuba

first: Naoya

last: sugi

address: 1-1-1 Ten-nodai

institute: Univ. of Tsukuba

description: Gene expression data from  F1 hybrid(C24 x Col) whole rosette at 15DAS

hyb_protocol: Following fragmentation, 200ul of mixture of cRNA and Hybridization coktail loaded into a GeneChip. The chip is hybridised at 45℃ for 16 hours in an oven with a rotating wheel at 60rpm.

scan_protocol: Microarrays were scanned using a Gene Chip scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: arabidopsis F1 hybrid(C24 x Col) whole rosette at 15DAS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds were sown on the MS agar plate. Plate kept in controlled enviromental condition (22℃) under a 12h/12h (day/light) photoperiod.

extract_protocol: Total RNA was isolated from  rosette leaves of 15DAS plants using Rneasy Mini Kit (Qiagen).

value: whole rosette

tag: cultivar

value: F1(C24x Col)

tag: age

value: 15 DAS


title: NOMO1.400nM.DAC.d2.n2 [S1-136]


title: month2_ccl4_rep2


title: NOMO1.1000nM.GSK862.d2.n2 [S1-137]


title: ScRNA Overnight Fast Sample 1 data chunk S11_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S11_L005


title: F1(C24xCol), biological rep 2


title: ScRNA Overnight Fast Sample 1 data chunk S11_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S11_L006


title: month12_oil_rep2

value: 12 months


title: NOMO1.400nM.GSK032.d2.n2 [S1-135]

value: AML cell line


title: NOMO1.0nM.DMSO.d2.n2 [S1-134]


title: month12_ccl4_rep2


title: F1(C24xCol), biological rep 1


title: small intestine Braf p53 off rep2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description:
Ethanol treated control
small_intestine.txt
small_intestine_Braf_p53_off_2

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16   --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: small intestinal organoids

growth_protocol: Organoids were generated and propagated as described before (Sato and Clevers, 2013; Sato et al., 2009; Yui et al., 2012)

extract_protocol:
RNA was isolated according to manufacturer's protocol (Roboklon, Cat#E3598)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cre recombination was induced in vitro with 4-Hydroxytamoxifen (0.5 µM for SI organoids, 3.5 µM for COL organoids) or organoids were treated with ethanol as controls for 24 hours. SI organoid RNA was isolated 8 days, and COL organoid RNA was isolated 3 days after Cre recombination.

value: small intestine

tag: agent

value: Ethanol control


title: ScRNA Overnight Fast Sample 1 data chunk S10_L005

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S10_L005

value: median eminence of the hypothalamus


title: NOMO1.400nM.DAC.d1.n2 [S1-133]

tag: cell line

value: DAC


title: month6_ccl4_rep1


title: month0_control_rep1

value: 0 months


title: NOMO1.400nM.GSK032.d1.n2 [S1-132]


title: NOMO1.0nM.DMSO.d1.n2 [S1-131]

value: DMSO


title: month2_oil_rep1


title: C24, biological rep 2

description: Gene expression data from  C24 whole rosette at 15DAS

source_name: arabidopsis C24 whole rosette at 15DAS


title: C24, biological rep 3


title: ScRNA Overnight Fast Sample 1 data chunk S10_L006

description: scRNASeq sample collected from C57B/L6 mice after Overnight Fast replicate 1 data chunk S10_L006


title: THP1.400nM.DAC.d6.n2 [S1-130]

description: processed data file: DNMT1_AML_fpkm_THP1_table.txt


title: month2_ccl4_rep1

value: CCl4, 1 g/kg b.w. in olive oil


title: small intestine Braf p53 on rep1

description:
4-Hydroytamoxifen treated
small_intestine.txt
small_intestine_Braf_p53_on_1


title: small intestine Braf p53 on rep2

description:
4-Hydroytamoxifen treated
small_intestine.txt
small_intestine_Braf_p53_on_2


title: month12_oil_rep1


title: C24, biological rep 1


title: Col, biological rep 2

description: Gene expression data from  Col-0 whole rosette at 15DAS

source_name: arabidopsis Col-0 whole rosette at 15DAS


title: THP1.400nM.GSK032.d6.n2 [S1-129]


title: Col, biological rep 3


title: small intestine p53 off rep2

description:
Ethanol treated control
small_intestine.txt
small_intestine_p53_off_2


title: month12_ccl4_rep1


title: mPFC_social defeat_susceptible_Right

city: Daejeon

first: Sujin

last: Chae

address: 291 Daehak-ro

country: South Korea

institute: KAIST

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The prepared microarrays were scanned with an Illumina BeadArray reader

data_processing: The prepared microarrays were preprocessed by the Illumina GenomeStudio software (version 1.0.6). Raw signals of at least two biological replicates per condition were transformed to log2 scale and normalized by using the Bioconductor lumi package. Differentially expressed genes (DEGs) were identified by using the Bioconductor limma package with an false discovery rate (FDR) adjusted p-value cutoff of 0.05.

source_name: mouse right mPFC of susceptible of social defeat mice

label_protocol: Illumina

extract_protocol: Total RNA of each 7 representative mice was prepared by Trizol method then further purified by RNAeasy kit (Qiagen, USA). The left and right mPFC RNA of susceptible, resilient and control mice was used for microarray analysis with the MouseRef-8_V2 Expression BeadChip (Illumina).

tag: region

value: medial prefrontal cortex

value: brain


title: small intestine Braf p53 off rep1

description:
Ethanol treated control
small_intestine.txt
small_intestine_Braf_p53_off_1


title: mPFC_social defeat_susceptible_Right_replicate1


title: Col, biological rep 1


title: small intestine p53 off rep1

description:
Ethanol treated control
small_intestine.txt
small_intestine_p53_off_1


title: mPFC_social defeat_susceptible_Left_replicate2

source_name: mouse left mPFC of susceptible of social defeat mice


title: THP1.10000nM.GSK477.d4.n2 [S1-127]