title: mES HiChIRP 7SK odd

description: RNA-enriched long-range contact

data_processing:
Library strategy: HiChIRP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

value: ESC


title: BMDM EPSWT HiChIP SMC1a biological replicate 2

status: Public on Dec 04 2018

type: SRA

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

description:
Protein-enriched long-range contact
BMDM_EPSWT_HiChIP_SMC1a.hic

library_source: genomic

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

molecule: genomic DNA

organism: Mus musculus

source_name: Bone-marrow derived macrophages

growth_protocol: Grown in DMEM with 15% FBS and supplemented with L929

extract_protocol: Protein enrichment of 3C library

treatment_protocol: Crosslinked with 1% formaldehyde

tag: cell type

value: Primary macrophage cells

tag: gender

value: male


title: BMDM EPSWT HiChIP SMC1a biological replicate 1

extract_protocol:
Protein enrichment of 3C library
Nextera


title: mES HiChIRP 7SK even

description: RNA-enriched long-range contact

source_name: v6.5 embryonic stem cell line

growth_protocol: Grown on gelatin-coated plates with KO DMEM supplemented with LIF

extract_protocol:
RNA enrichment of 3C library
Nextera

treatment_protocol: Crosslinked with 1% glutaraldehyde

tag: cell line


title: BMDM EPSKO HiChIP H3K4me3 biological replicate 2

description:
Protein-enriched long-range contact
BMDM_EPSKO_HiChIP_H3K4me3.hic


title: BMDM EPSKO HiChIP H3K4me3 biological replicate 1


title: BMDM EPSKO HiChIP SMC1a biological replicate 1

description:
Protein-enriched long-range contact
BMDM_EPSKO_HiChIP_SMC1a.hic


title: BMDM EPSWT HiChIP H3K4me3 biological replicate 2

description:
Protein-enriched long-range contact
BMDM_EPSWT_HiChIP_H3K4me3.hic


title: sc_Day15_CD49f_30

city: New York

first: Betty

state: NY

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
For single cell mRNA-seq, alignment to GRCh38 using Gencode v25 gene annotation Reads were aligned with STAR version 020201 and gene level read counts were calculated using featureCounts Version 1.5.1 from the Subread packag. Raw counts were log2 transformed and quantile normalized using R library preprocessCore.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF single cell experiment raw count table derived from R preprocessCore.

molecule: total RNA

organism: Homo sapiens

source_name: adult human dermal fibroblast

extract_protocol:
Single cells were sorted by FACS and single cells were isolated using C1 Single-Cell Auto Prep System by Fluidigm.
Illumina TruSeq RNA Sample Prep Kit was used with up to 1 ug of total RNA for the construction of sequencing libraries Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage. For single cell, Illumina Nextera XT Kit was used with 0.1-0.3ng of cDNA for the construction of sequencing libraries Illumina protocols.

value: HDFa

value: adult human dermal fibroblast

tag: genotype/variation

value: wildtype

tag: cell population


title: BMDM EPSWT HiChIP H3K4me3 biological replicate 1


title: BMDM HiChIRP lincRNA-EPS biological replicate 2

description:
RNA-enriched long-range contact
BMDM_HiChIRP_EPS.hic


title: BMDM HiChIRP lincRNA-EPS biological replicate 1


title: mES HiChIP Oct4 biological replicate 1

description:
Protein-enriched long-range DNA contact
mES_HiChIP_Oct4.hic

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: bigwig: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

value: ES cell


title: mES HiChIRP 7SK biological replicate 2

description:
RNA-enriched long-range contact
mES_HiChIRP_7SK.hic


title: BMDM Hi-C biological replicate 2

description:
Long-range contact
BMDM_HiC.hic

data_processing:
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

extract_protocol:
3C library
Nextera


title: mES HiChIRP 7SK biological replicate 1


title: mES HiChIRP RNase 7SK biological replicate 2

description:
Negative control long-range DNA contact
mES_HiChIRP_RNase_7SK.hic

data_processing:
Library strategy: HiChIRP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: bigwig: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

extract_protocol:
Rnase negative control of RNA enrichment of 3C library
Nextera


title: BMDM Hi-C biological replicate 1

description:
Long-range contact
BMDM_HiC.hic


title: Zc3h13KO_Input

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

data_processing:
Reads were aligned to the mm10 mouse genome assembly using Bowtie with the parameters ‘-m 1 --best --strata’. SAM files were converted to BAM format, sorted and indexed using SAMtools.
MACS2 was used to call peaks of m6A enrichment for WT IP vs input samples, using the default parameters.
BigWig files for each sample were created using the qExportWig function from the QuasR package in R (Gaidatzis et al. 2014) with 50-bp bins.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: scores represent normalized counts in 50-bp bins. narrowPeak: BED6+4 format representing peak locations. Columns 5-10 are defined by MACS2 (https://github.com/taoliu/MACS).

source_name: ES cells

growth_protocol: All samples: Mouse embryonic stem cells were cultured on gelatin-coated dishes in mES medium (DMEM (Gibco 21969-035), supplemented with 15% fetal bovine serum (Gibco), 1x non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 2 mM L-glutamine (Gibco), 0.1mM 2-mercaptoethanol (Sigma), 50mg/ml penicillin, 80mg/ml streptomycin and LIF conditioned medium) at 37°C in 5% CO2.

extract_protocol:
Total RNA from mESCs was isolated using Absolutely RNA Microprep Kit (Stratagene), followed by mRNA selection using double Oligo d(T)23 (NEB) purification.
Libraries were prepared with 30 ng of m6A-IPs and duplicate input samples (200ng mRNA) using NEB-Next RNA Directional Library Preparation Kit

tag: background

value: Rosa26:CRE, Bir ligase

value: ES cells

tag: genotype

tag: rip antibody


title: Zc3h13KO_IP_rep2

value: anti-m6A (Synaptic Systems; polyclonal Rabbit , Cat. No. 202 003)


title: Mettl3KO_IP_rep2


title: WT_Input

value: WT


title: Mettl3KO_IP_rep1


title: Zc3h13KO_IP_rep1


title: WT_IP_rep2


title: Mettl3KO_Input


title: mp clv3 rep2 (2)

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 cDNA using BWA with parameters -e 60 -i 15 -q 10 -t 4
Reads Per Kilobase of transcript per Megabase of library size (RPKM) were calculated.
Genome_build: TAIR10
Supplementary_files_format_and_content: spreadsheet include numbers of mapped reads,RPKM values for each Sample as well as log2 RPKM ratios, p-values and FDR for multipairwise comparisons

organism: Arabidopsis thaliana

source_name: plant

growth_protocol: Seeds pretreated with stratification for 2 days at 4°C were transferring the seedlings to the soil in the greenhouse for another 6-weeks (22°C, 16 h/8 h photoperiod).Shoot apices from 6-week inflorescence of Col-0 or mp319 clv3-7 plants were collected and removing older flowers.

extract_protocol:
Plant tissues were flash frozen in liquid nitrogen, and Total RNA from apices were isolated using the mirVana™ miRNA Isolation Kit (lifetechnology). 10 μg of totalRNA were subject to DNase I treatment and mRNA was purified by Dynabeads® mRNA DIRECT™ Purification Kit(lifetechnology). The strand-specific RNA-seq libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions and subjected to Illumina HiseqTM2500 for 2x100bp pair end sequencing.
library source: transcriptomic; library selection: cDNA; instrument model: Illumina HiSeq 2500

tag: developmental stage

value: 6-week adult plant

tag: tissue

value: Shoot apices

value: mp clv3


title: mp clv3 rep1 (2)


title: WT_IP_rep1


title: clv3 rep1


title: CG7358_rep1

data_processing:
The libraries were sequenced on NextSeq500 with 85 bp paired end
The data was mapped agains Ensembl release 90 using STAR (v.2.5.1b).
Counts per gene were derived using featureCounts (v1.5.1)
Genome_build: BDGP6
Supplementary_files_format_and_content: counts per gene as tab separated file (tsv), read depth normalised bigwig tracks (bw)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: S2R+ cells

growth_protocol: S2R+ cells are maintained in Schenider Medium at room temperature

extract_protocol:
Cells were pelleted and RNA was isolated with Trizol using standart protocol
Librariesfor sequencing were prepared according to the NEBNext® Ultra™ Directional RNA Library Prep Kit protocol.

treatment_protocol: 3 dsRNA treatments (6 days total)

tag: treatment

value: 10 ug of dsRNA against CG7358

tag: replicate

tag: passages


title: CG7358_rep3


title: CG7358_rep2


title: Nito_rep1

value: 10 ug of dsRNA against Nito


title: Nito_rep3


title: Nito_rep2


title: Vir_rep3

value: 10 ug of dsRNA against Vir


title: Vir_rep1


title: Fl2d_rep3

value: 10 ug of dsRNA against Fl(2)d


title: Fl2d_rep2


title: Fl2d_rep1


title: Ime4_dMetll14_rep3

value: 10 ug of dsRNA against Ime4 and dMettl14


title: Ime4_dMetll14_rep2


title: Ime4_dMetll14_rep1


title: clv3 rep2


title: cImmortPL_Temp33_S1

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

data_processing:
Fastq files were generated using the bcl to fastQ converter 2.17.
Transcript level counts were estimated using Salmon v0.8.2, using the ENSEMBL GRCh38 version of the human transcriptome.
Transcript level counts were converted to gene level counts using the Bioconductor R package tximport v1.3.13.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with ensemble gene id and the averaged gene length across all 9 samples in the first two columns, followed by 9 columns containing counts for each sample

source_name: Undifferentiated conditionally immortalised podocytes

growth_protocol: Conditionally immortalised temperative sensitive human podocytes were cultured in defined podocyte media (RPMI 1640, 10% FCS, 1% ITS, 1% L-Glutamine) under permissive conditions at 33 degrees celsius (5% carbon dioxide).

extract_protocol:
RNA were extracted using QIAGEN RNeasy micro kit.
TruSeq stranded total RNA with RiboZero rRNA depletion

tag: clone

value: SV40 conditionally immortalised podocyte line

tag: temperature

value: 33 degrees celsius


title: cImmortPL_Temp37_S5

source_name: Differentiated conditionally immortalised podocytes

growth_protocol: Conditionally immortalised temperative sensitive human podocytes were cultured in defined podocyte media (RPMI 1640, 10% FCS, 1% ITS, 1% L-Glutamine) under permissive conditions at 33 degrees celsius (5% carbon dioxide). Upon reaching 60-70% confluency cells were thermo-switched to 37 degrees celsius (5% carbon dioxide) to inactivate the SV40 T antigen and allow podocyte differentiation for 14 days.

value: 37 degrees celsius


title: cImmortPL_Temp33_S2

value: Undifferentiated conditionally immortalised podocytes


title: cImmortPL_Temp37_S4

value: Differentiated conditionally immortalised podocytes


title: Glomeruli_S9

source_name: Day 25 kidney organoid derived glomeruli

growth_protocol: Human iPSCs were cultured in a differentiation medium (8 uM CHIR99021 in APEL medium) for 4 days, followed by FGF9 (200 ng/mL) and Heparin (1 ug/mL) for 3days. Then, cells were dissociated into single cells and spun down at 400xg for 2min to form a pellet and then transferred onto a Transwell 0.4mm pore polyester membrane. Pellets were treated with 5 uM CHIR99021 in APEL for 1 h, and then cultured with FGF9 (200ng/mL) and heparin (1ug/mL) for 5 days, followed by another 13 days in APEL basal medium. iPSC-derived kidney organoids were dissociated by incubation with TrypLE select enzyme (Thermo Fisher Scientific) for 10 minutes at 37°C, with gentle pipetting every 2 minutes to aid dissociation. Cells were then passed through a series of cell strainers with sequentially smaller mesh sizes, ranging from 100µM to 40µM (pluriSelect), to isolate individual glomeruli.

value: human iPSC line CRL1502 (clone C32)

value: Glomeruli from hiPSCs-derived kidney organoid (25 days differentiation)


title: R2

city: Wuhan

first: Heshan

last: Zhang

state: Hubei

address: Southern Lake Street, Hongshan District, Wuhan city, China

department: Institute of Animal Husbandry and Veterinary science

institute: Hubei Academy of Agricultural Sciences

data_processing:
Data filtering,SOAPnuke,v1.5.2,default parameters with '-l 15 -q 0.5 -n 0.05 --seqType 0'
Transcriptome assembly,Trinity,v2.0.6,default parameters with '--min_contig_length 150  --CPU 10 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stderr'
Gene functional annotation,Blast,v2.2.23,default parameters with evalue =1e-5
Quantification of gene expression levels,RSEM,v1.2.12,default parameters
CDS predict,ESTscan,v3.0.2,default parameters
GO enrichment,Blast2GO,v2.5.0,default parameters
KEGG enrichment,Blast2GO,v2.5.0,default parameters
SSR ,MISA,v1.0,default parameters with '1-12,2-6,3-5,4-5,5-4,6-4 100 150'
Differential expression analysis,DESeq R package,(1.10.1)
Transcription factor predict,Hmmsearch,v3.0,default parameters
Genome_build: de novo assembly; FASTA file is available on the series record.
Supplementary_files_format_and_content: text format files including FPKM values for each Sample

organism: Trifolium repens

source_name: Red-flowered mutant

growth_protocol: The experimental materials grew under natural conditians in the field until squaring stage.

extract_protocol:
Total RNA of each sample was extracted with the column plant RNAout kit (Tiandz Technology, Beijing, China).The RNA quality was detected by 1.5% agarose gels, and these bands that have not been degraded and contaminated were used to later test. The RNA concentration was quantified using the Nano Photometer® spectrophotometer (IMPLEN, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the pre-flowering stage, the plants with many flower buds were divided into two groups, a control group and treatment group. The plants from the control group were placed in the field for growth, and the plants from the treatment group  grew under shaded conditions, which were created by covering the top of plants with a cubic shading net to prevent sunlight from irradiating the flowers.

tag: strain

value: Red-flowered mutant

value: Petal

tag: flower color

value: Red


title: TW1

source_name: Red-flower mutant grown under shaded conditions

value: White


title: Glomeruli_S8

tag: cell type


title: cImmortPL_Temp33_S3


title: Glomeruli_S7


title: cImmortPL_Temp37_S6


title: TW2


title: TW3


title: R3


title: R1


title: CMP [CAGRF9188-1373]

status: Public on Dec 03 2018

first: Matthew

last: Ritchie

state: Victoria

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina software was used for basecalling.
Sequenced reads were mapped using the align function in the Rsubread package (Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package using the Ensembl mouse annotation (Ens84, GRCm38).
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with combined observational and sample-level weights (Liu et al. Nucleic Acids Research 2015) were fitted to summarise the values from replicates samples using functionality from the limma package (Ritchie et al. Nucleic Acids Research, 2015).
Genome_build: Ens84, GRCm38
Supplementary_files_format_and_content: a tab-delimited text file with columns representing Ensembl Gene ID, total gene length (total base count of all exons), Gene Symbol and the number of reads mapping to that gene for each sample.

source_name: Multi Potential Progenitor

extract_protocol:
FACS sorted cell pellets were lysed and RNA prepared on same day using QIAGEN RNeasy plus mini or micro kit with B-mercaptoethanol added to inhibit RNAses.
RNA was submitted to the Australian Genome Research Facility (AGRF) for high throughput mRNA sequencing. Messenger RNA libraries were synthesized using Illumina’s TruSeq Stranded mRNA sample preparation protocol, and 100 bp single or paired end reads were generated by high-throughput sequencing with an Illumina HiSeq 2500 (Illumina). 2-5 independent RNA samples (biological replicates) per cell type were sequenced.

value: Bone marrow

tag: monoclonal antibody

tag: batch


title: Eo [CAGRF9188-1422]

source_name: Eosinophil Lineage


title: CMP [CAGRF9188-1371]


title: EoP [CAGRF7126-1376]


title: GMP [CAGRF7126-1379]


title: Eo [CAGRF7126-1260]

value: IL-5:lo, Ly6G:-, Siglec-F+


title: GMP [CAGRF7126-1377]


title: Eo [CAGRF9188-1423]


title: EoP [CAGRF7126-1375]


title: SiglecFside BL/6 [CAGRF11700-1635]

source_name: SiglecFside

value: PI:- CD4:- CD8:- CD19:- B220:- Ter119:- Ly6C:+/- SiglecF:+ Ly6G:- SSC-A:v.lo FSC-A:In


title: SiglecFside BL/6 [CAGRF11700-1631]


title: SiglecFside Plt4 [CAGRF11700-1573]

value: Myb Plt4/Plt4

value: PI:- CD4:- CD8:- CD19:- B220:- Ter119- SiglecF:+ Ly6C:+/- Ly6G:- SSC-A:Lo FSC-A:In


title: SiglecFside Plt4 [CAGRF11700-1578]


title: Vir_rep2

value: 10 ug of dsRNA against Vir


title: SiglecFside Plt4 [CAGRF11700-1563]


title: SiglecFside BL/6 [CAGRF11700-1559]


title: SiglecFside BL/6 [CAGRF11700-1555]

value: PI:- CD4:- CD8:- CD19:- B220:- Ter119- SiglecF:+ Ly6C:+ Ly6G:- SSC-A:Lo FSC-A:Hi


title: SiglecFside BL/6 [CAGRF11700-1570]


title: 4-week-old mouse islets rep2

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: 4-week-old mouse islets rep2

data_processing:
The single-end 50 base pair reads were mapped to the UCSC mouse transcriptome (mm9) by STAR, allowing for up to 10 mismatches.
Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflink
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated

extract_protocol:
Pancreatic islets were isolated from mice and flash frozen. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) per manufacturer’s instructions.
TruSeq stranded mRNA libraries were prepared by the UCSD Institute for Genomic Medicine Genomics Center using standard protocols and sequenced using HiSeq2500 Highoutput Run V4 (Illumina).

tag: age

value: 4 weeks old

value: primary pancreatic islets


title: 4-week-old mouse islets rep3

description: 4-week-old mouse islets rep3


title: KS12

description:
Shh-Cre;Grhl2f/- #1
KS12_C80FPANXX_CGATGT_L008

data_processing:
Demultiplexing and BCL conversion was performed using bcl2fastq v2.17.1.14.
Sequenced reads were mapped using the align function in the Rsubread package (version 1.20.6, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.16.5, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with combined observational and sample-level weights (Liu et al. Nucleic Acids Research 2015) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.30.12, Ritchie et al. Nucleic Acids Research, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: a tab-delimited text file with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene for each sample.

growth_protocol: E16.5 lungs were subjected to enzymatic digest to generate single cell suspensions. EpCAM+ cells were subsequently purified from cell suspensions using FACS

extract_protocol:
FACS sorted cell pellets were snap frozen prior to lysis and RNA preparation using QIAGEN RNeasy plus mini kit
RNA libraries were prepared using Illumina TruSeq Stranded mRNA-seq Sample Preparation Kit (cat# RS-122-2101 and RS-122-2102) following the manufacture’s protocol. The RNA libraries were sequenced on a HiSeq 2500. Cluster generation was performed on a cBot with HiSeq PE Cluster Kit v4 - cBot – HS (cat # PE-401-4001) and sequenced with the HiSeq SBS Kit v4 (200 cycles, cat# FC-401-4003). The Hiseq 2500 was operating with HiSeq Control Software v2.2.68 and base-calling was performed with RTA v1.18.66.3. The average insert size (as assessed by electrophoresis) was 216 bp (+/- 4%).

value: Grhl2 conditional knockout

tag: epcam status

value: Positive

tag: Sex

value: Female

value: murine lung epithelium


title: 4-week-old mouse islets rep1

description: 4-week-old mouse islets rep1


title: KS8

description:
Shh-Cre;Grhl2f/- #5
KS8_C80FPANXX_GAGTGG_L008

tag: genotype

value: Male


title: KS10

description:
Shh-Cre;Grhl2f/+ #3
KS10_C80FPANXX_ATTCCT_L008

value: Grhl2 control


title: KS6

description:
Shh-Cre;Grhl2f/+ #7
KS6_C80FPANXX_GTTTCG_L008


title: KS1

description:
Shh-Cre;Grhl2f/+ #1
KS1_C80FPANXX_ATGTCA_L008


title: KS3

description:
Shh-Cre;Grhl2f/- #10
KS3_C80FPANXX_GTCCGC_L008


title: 1-year-old mouse islets rep2

description: 1-year-old mouse islets rep2

value: 1 year old


title: G01T1

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: Ribo and Globin depleted library

data_processing:
Basecalls performed using CASAVA version 1.8.2
Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15
Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).
Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 58906 genes (rows) [counts matrix]

source_name: Not Responder T1 patient9

extract_protocol:
Peripheral blood was collected in EDTA tubes at T1 and T2 and stored at -20°C after adding 400µl of 2X Denaturing solution (Ambion, USA).Total RNA was extracted from 800 µl of blood with MirVana Paris Kit and treated with Turbo DNA-free Kit (Ambion, USA). RNA Quality was assessed on Agilent Bioanalyzer with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and samples were considered suitable for processing if RNA Integrity Number was greater than 7.5
Sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina, San Diego, CA) using 800 ng of total RNA

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

tag: clinical classification

value: NR


title: G07T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient4

tag: tissue

value: R


title: G07T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient4


title: G47T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient14


title: G45T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient15


title: G44T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient14


title: G47T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient14


title: G49T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient16


title: G49T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient16


title: G44T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient14


title: G45T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient15


title: G43T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient13


title: SiglecFside Plt4 [CAGRF11700-1562]

value: Bone marrow


title: G43T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient13


title: G42T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient13


title: 1-year-old mouse islets rep3

description: 1-year-old mouse islets rep3


title: G35T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient12


title: G35T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient12


title: 1-year-old mouse islets rep1

description: 1-year-old mouse islets rep1


title: G29T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient8


title: G33T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient9


title: G33T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient9


title: G28T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient7


title: G12T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient11


title: G42T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient13


title: G01T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient9


title: Sperm Donor Pool H3.3 ChIP-seq

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

data_processing:
Basecalls were performed using CASAVA version 1.7.
Reads for H3K9me3 and H3.3 ChIP-seq were aligned using Novoalign V2.07.03 with parameters -rRandom -oSAM to an index containing the hg18 genome (UCSC), Lambda, PhiX, and Illumina Adapter sequences. Reads for H3K36me3, H3K4me1, H3K14ac, and H3K27ac ChIP-seq datasets were aligned with ELAND using the default parameters (Illumina).
Alignments were parsed using NovoalignParser (USeq) or ElandParser (USeq).
ChIP-seq data processing and analysis were performed as previously described in Hammoud et al., 2009. Briefly, differential enrichment between histone ChIP-seq datasets and mononucleosomal control datasets (from GSE15690) were determined with ScanSeqs (USeq), and statistically enriched peaks were called with EnrichedRegionMaker (USeq).
The GSM* numbers for the mononucleosomal controls used were GSM392708-GSM392713, GSM392717-GSM392720 plus approximately 5 million mapped filtered reads randomly subsampled from GSM392701-GSM392707, GSM392714-GSM392716.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files contain ChIP-seq peaks. The files are linked to the Series record as supplementary files.

source_name: Sperm donor pool, H3F3B ChIP

growth_protocol: The four sperm donor samples were obtained from men of known fertility attending the University of Utah Andrology laboratory, consented for research. Samples were collected after 2-5 days abstinence, subjected to a density gradient to purify viable, motile, mature sperm, and pooled.

extract_protocol: Histone isolation and chromatin immunoprecipitation experiments were performed with sperm pooled from four fertile donors as previously described (Hammoud et al., 2009). For each immunoprecipitation, 10 µL of antibody was coupled to 100 µL of Dynabeads (Invitrogen). Following the ChIP procedure and library preparation (Illumina TrueSeq DNA sample Preparation Protocol), DNA lengths corresponding to mononucleosomes (+ adapters) were gel purified and subjected to sequencing.

value: sperm

tag: chip antibody

tag: antibody vendor

value: Abnova

tag: antibody catalog #

tag: antibody lot #


title: Sperm Donor Pool H3K9me3 ChIP-seq, rep2

source_name: Sperm donor pool, H3K9me3 ChIP

value: Active Motif


title: Sperm Donor Pool H3K27ac ChIP-seq, rep1

source_name: Sperm donor pool, H3K27ac ChIP


title: Sperm Donor Pool H3K4me1 ChIP-seq, rep1

source_name: Sperm donor pool, H3K4me1 ChIP

value: Abcam


title: Sperm Donor Pool H3K14ac ChIP-seq, rep1

source_name: Sperm donor pool, H3K14ac ChIP

value: Upstate


title: G11T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient5


title: Sperm Donor Pool H3K4me1 ChIP-seq, rep2


title: Sperm Donor Pool H3K36me3 ChIP-seq

source_name: Sperm donor pool, H3K36me3 ChIP


title: E41T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient8


title: Sperm Donor Pool H3K14ac ChIP-seq, rep2


title: Sperm Donor Pool H3K9me3 ChIP-seq, rep1

data_processing:
Basecalls were performed using CASAVA version 1.7.
Reads for H3K9me3 and H3.3 ChIP-seq were aligned using Novoalign V2.07.03 with parameters -rRandom -oSAM to an index containing the hg18 genome (UCSC), Lambda, PhiX, and Illumina Adapter sequences. Reads for H3K36me3, H3K4me1, H3K14ac, and H3K27ac ChIP-seq datasets were aligned with ELAND using the default parameters (Illumina).
Alignments were parsed using NovoalignParser (USeq) or ElandParser (USeq).
ChIP-seq data processing and analysis were performed as previously described in Hammoud et al., 2009. Briefly, differential enrichment between histone ChIP-seq datasets and mononucleosomal control datasets (from GSE15690) were determined with ScanSeqs (USeq), and statistically enriched peaks were called with EnrichedRegionMaker (USeq).
The GSM* numbers for the mononucleosomal controls used were GSM392708-GSM392713, GSM392717-GSM392720 plus approximately 5 million mapped filtered reads randomly subsampled from GSM392701-GSM392707, GSM392714-GSM392716.
The GSM* numbers for the mononucleosomal controls used were GSM392708-GSM392713, GSM392717-GSM392720 plus approximately 5 million mapped filtered reads randomly subsampled from GSM392701-GSM392707, GSM392714-GSM392716.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files contain ChIP-seq peaks. The files are linked to the Series record as supplementary files.


title: G11T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient5


title: Sperm Donor Pool H3K27ac ChIP-seq, rep2


title: G28T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient7


title: E41T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient8


title: Sperm Donor2 smRNA-seq

description:
7397X2
Directional RNA-Seq.

data_processing:
Basecalls were performed using CASAVA version 1.7.
Reads were aligned to hg18 using Novoalign V2.07.09 allowing up to 10 alignments per read, using these parameters for mRNA-seq alignments: -FILMFQ -o SAM -m -l17 -t60 -rA 10 -a and these settings for smRNA-seq alignments: -FILMFQ -o SAM -m -l17 -h90 -t30 -rA 10 -a. The novoalign index was made by combining hg18 fasta files (UCSC), Illumina adapter sequences, and splice junction fasta files made using MakeSpliceJunctionFasta (USeq version 6.0) with -s 34 as input radius and merged ensGene and knownGene table (from genome.ucsc.edu) as annotation.
Alignment (SAM format) files were fixed using SamFixer (USeq 8.3.3). For each donor sample, smRNA and mRNA alignment files were merged and sorted with SortSam (picard 1.40), then converted to binary PointData with SamParser (USeq 8.3.3) using parameters -m 0 -a 1000 to retain all reads. Counts for Refseq genes, piRNAs, and miRNAs were determined with DefinedRegionScanSeqs (USeq 8.3.3) using parameters -p 0 -o.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files contain RPKM expression values for RefSeq genes, piRNAs, and miRNAs. Files are linked to the Series record as supplementary files.

source_name: Sperm Donor 2, smRNA

growth_protocol: The two sperm donor samples were obtained from men of known fertility attending the University of Utah Andrology laboratory, consented for research. Samples were collected after 2-5 days abstinence and subjected to a density gradient to purify viable, motile, mature sperm.

extract_protocol: Total RNA was extracted from fertile donors (Donor1 and Donor2) using Trizol. The RNA was treated with DNase and submitted for long and small RNA-seq directional library preparation using the standard Illumina protocol.

tag: library prep method

value: smRNA directional


title: Sperm Donor1 smRNA-seq

description:
7397X1
Directional RNA-Seq.

source_name: Sperm Donor 1, smRNA


title: Sperm Donor2 mRNA-seq

description:
7396X2
Directional RNA-Seq.

source_name: Sperm Donor 2, mRNA

value: mRNA directional


title: Sperm Donor1 mRNA-seq

description:
7396X1
Directional RNA-Seq.

source_name: Sperm Donor 1, mRNA


title: E17T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient4


title: E17T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient4


title: E40T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient7


title: E32T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient3


title: E32T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient3


title: G12T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient11


title: E16T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient3


title: E07T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient1


title: E07T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient1


title: E16T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient3


title: E40T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient7


title: hrr25is_CMK_rep1 [RNA-seq]

status: Public on Dec 02 2018

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

description: processed data file: hrr25is_rep1_rep2_DESeq.csv

data_processing:
Base calls were performed with CASAVA-1.8.2
Reads were clipped of 3' adapters and aligned to SacCer3 from SGD with STAR 2.3.0 using default settings
Read counts for genes were obtained using HTSeq 0.6.0 using default paramaters
Genome_build: SacCer3
Supplementary_files_format_and_content: bam files

organism: Saccharomyces cerevisiae

source_name: Total RNA from hrr25is cells treated with CMK

growth_protocol: Yeast were grown in YPD media at 30°C to an OD600 of 0.3.

extract_protocol:
Total RNA was extracted using hot phenol as in Gasch, AP. Methods Enzymol. 2002.
Total RNA was rRNA-depleted and prepared for sequencing using the Yeast ScriptSeq Complete Gold Kit (Epicentre). DNA was sequenced on an illumina HiSeq 2500 generating single-end reads of 100 bp length using standard Illumina protocols.

treatment_protocol: Cells were split and treated with either DMSO or CMK for 1 hour.

tag: strain info

value: his3Δ leu2Δ ura3Δ Hrr25Δ::kanMX4 pRS315-hrr25-I82G,I23C

tag: treated with

value: CMK


title: hrr25is_DMSO_rep1 [RNA-seq]

source_name: Total RNA from hrr25is cells treated with DMSO

value: DMSO


title: hrr25is_CMK_rep2 [RNA-seq]


title: hrr25is_DMSO_rep2 [RNA-seq]


title: WT_CMK_rep1 [RNA-seq]

description: processed data file: WT_rep3_rep4_DESeq.csv

source_name: Total RNA from WT cells treated with CMK

value: his3Δ leu2Δ ura3Δ Hrr25Δ::kanMX4 pRS316-HRR25


title: Sperm Donor2 Bisulfite Sequencing

data_processing:
Basecalls were performed using CASAVA version 1.7.
Reads were aligned using Novoalign V2.07.03 with parameters -rRandom -t120 -h120 -b2 to an index containing the hg18 genome (UCSC), Lambda, PhiX, and Illumina Adapter sequences. The index was made using novoindex with parameter -b.
Alignments were filtered and converted to binary PointData with NovoalignBisulfiteParser (USeq package, version 7.6.4) using the default thresholds for quality score and alignment score and the option -u to get unique alignments.
Filtered alignments (PointData) were analyzed to determine methylation statistics, summary plots, and to determine differentially methylated regions with BisStat and BisSeq (USeq) using the default parameters.
Genome_build: hg18
Supplementary_files_format_and_content: Bed files contain hypermethylated or hypomethylated regions in merged sperm donor data.
'GSE40178_D1D2_HypermethylatedLoci_FractionMethylation>0.8%_SerializedWindowObjectsMin0.8Max1.0.bed' and 'GSE40178_D1D2_HypomethylatedLoci_Less20%FractionMethylation_SerializedWindowObjectsMin1.0E-4Max0.2.bed' are linked to the Series record as supplementary files.
Supplementary_files_format_and_content: Bar files contain tracks for visualization of methylation data in the Integrated Genome Browser (IGB) genome browser.
'GSE40178_BisStatFullCoverageGraphs.tar', 'GSE40178_BisStat_GCContexts.tar', and 'GSE40178_NBP.tar' are linked to the Series record as supplementary files.

source_name: Sperm Donor 2

extract_protocol: Sperm DNA was extracted as previously described (Hossain et al., 1997; Bahnak et al., 1998). Three micrograms of genomic DNA were sheared using a COVARIS Adaptive Focused Accoustics S-series system (Woburn, Massachusetts 01801-1721). Sheared DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA 91355). DNA concentration was measured and unmethylated lambda DNA was added at a concentration to represent 1% of the DNA mass of each sample. The lambda DNA served as an internal control for conversion efficiency. (Promega Madison, WI 53711). Fully methylated paired-end adapters from the TruSeq DNA Sample Prep Kit were ligated to sheared DNA (following the Illumina library preparation protocol). After the adapter addition, samples were cleaned using a QIAquick PCR purification kit (Qiagen, Valencia, CA 91355) and subjected to sodium bisulfite conversion. Sodium bisulfite treatment was done using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA 91355) with modified PCR conditions to ensure ~99.98% conversion efficiency: 98°C 10 min, 60°C 25 min, 98°C 10 min, 60°C 85 min, 98°C 10 min, 60°C 175 min, 98°C 10 min, 60°C 120 min, 20°C storage for the next step in library prep. Following cleanup of bisulfite-treated DNA, sequencing libraries were enriched by 16 cycles of PCR amplification using Agilent PfuTurbo Cx HotStart DNA Polymerase (Agilent, Santa Clara, CA 95051) to complete the library construction process. DNA fragments in the size range of 200-300bp were gel purified. Libraries were quality controlled by running the final library on an Agilent DNA 1000 Bioanalyzer chip DNA Chip and by qPCR using the KapaBiosystems KAPA Library Quant Kit for Illumina sequencing libraries. Libraries were sequenced on a 101 cycle paired-end sequencing run on an Illumina HiSeq 2000.

treatment_protocol: Sperm pellet samples were washed in 1X PBS and centrifuged at 10,000 G for 3 min.

tag: cell type


title: WT_DMSO_rep4 [RNA-seq]

source_name: Total RNA from WT cells treated with DMSO


title: hrr25as_3MBPP1_rep2 [RNA-seq]

description: processed data file: hrr25as_rep1_rep2_DESeq.csv

source_name: Total RNA from hrr25as cells treated with 3MBPP1

value: his3Δ leu2Δ ura3Δ Hrr25Δ::kanMX4 pRS315-hrr25-I82G


title: hrr25as_DMSO_rep1 [RNA-seq]

source_name: Total RNA from hrr25as cells treated with DMSO


title: H2BP1me-2

city: Beer-Sheva

first: Eitan

last: Rubin

address: Building 39 room 005

country: Israel

institute: Ben Gurion University of the Negev

data_processing:
Each sample was sequenced in a single lane to achieve maximal sequence depth (number of reads per lane) and  resulted in an average of 200 million reads with reads length of 2X 50 bp (paired-end 50) and mapped to the human reference genome (NCBI Build 36, hg19) using bowtie2 with default parameters
A table of potentially overlapping genomic features (position and type) was extracted from the hg19 human genome annotation files included in the Homer package (Heinz et al., 2010). The Basic and Repeats files were combined, and short (<200bp) features were filtered out. For repetitive elements, some features types were merged into groups to improve the clarity and statistical power of the analysis. The complete details of feature type conversions are provided in the supplemntary material of the accompanying publication (Table S1). Only the 5’ ends (the first 100bp) of each feature were subsequently retained for the enrichment analysis to avoid complications due to difficulties in aligning repetitive DNA.
A fold-change value between ChIP and input was calculated for every feature. The number of tag pairs that overlap with each feature was counted using FindOlp.pl, a tool developed for this purpose (available upon request), looking for overlaps of at least 25bp from either side of the feature. Tag pairs were extracted from the original BAM-formatted files, filtering for proper pairing and for tag size of 100-750 bases. Features overlapping with less than 3 reads were discarded. Raw tag-pair counts were converted to reads-per-kbp-per-million reads (RPKM), and the per-feature fold change was calculated for each experiment as log(base 2) of the ratio between the RPKM values from the ChIP experiment and its corresponding input experiment. Features with the highest and lowest 1% fold-change values were then clipped to remove artifacts from poorly sequenced centromeric regions resulting in artificially high coverage (Pickrell et al., 2011). To simplify subsequent analysis, any feature type occurring less than 100 times in the genome (after discarding low-coverage features and the clipping of extreme values) was discarded.
Enrichment analysis. Enrichment of a feature type was defined as log(base 2) of the ratio between the number of times a feature type occurs in the top decile of fold-change values, O, and the expected number of occurrences of that features type in the top decile, E.  Under the null hypothesis that repeat types are randomly distributed relative to fold-change values, the expected number is taken as E=0.1xN, where N is the total number of times features of a given type occur in the genome (after filtration). A binomial test was used to evaluate the significance of the enrichment by calculating the probability to observe O features of a given type in the top 10% tier under the null hypothesis of p=0.1.
Genome_build: hg19

source_name: MCF-7 Breast cancer

growth_protocol: Human breast MCF-7 cells were obtained from the IGBMC cell line collection. Cells were grown in 7% CO2 at 37°C in DMEM-high glucose media supplemented with 10% FBS, 20 U/ml penicillin/streptomycin, and 0.4mM glutamine (GIBCO)

extract_protocol: ChIP-seq libraries were prepared from 10ng fragmented DNA using the NEBNext ChIP-Seq Library Prep Master Mix Kit (NEB-E6240S). Accordingly, after end-repair and A-tailing sequencing, adaptors were ligated and size selection of adaptor-ligated DNA using AMPure XP Beads (Beckman Coulter) performed. Libraries were enriched with 12 PCR cycles and sequenced according to manufacturer’s protocol on an Illumina HiSeq2000 instrument

treatment_protocol: ChIPwas preforend with Cross-linking Chromatin Immunoprecipitation (X-ChIP) protocol in (Tropberger et al., 2013) was followed with minor changes. Briefly, cells were cross-linked with 1% formaldehyde and sonicated with a Bioruptor (Diagenode) for 10min at density of 1X106 cells per 100μL of lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and approximately 20μg of sheared chromatin were used for each chip experiment. Protein A Sepharose fast flow beads (GE Healthcare) were blocked with 2μg BSA (per 100μL slurry beads) for 3h, washed with 3X ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, 167mM NaCl pH 8.1) and added to the reaction after overnight incubation with the designated antibody. After 2h incubation, the beads were washed with 1X low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, 150mM NaCl pH 8.1), high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, 500mM NaCl pH 8.1), LiCl wash buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1) and 3X TE buffer (10mM Tris-HCl, 1mM EDTA, pH 8.0) at 40C. DNA was eluted 2X by 15min incubation with freshly made ChIP elution buffer (1% SDS, 0.1M NaHCO3). Protein–DNA cross-linking was reversed by incubating at 65ºC for 4h in the presence of 10μL 0.5M EDTA, 10μL of 1M Tris-HCl pH 6.5, 2μL of 10mg/mL proteinase K (Roche), and DNAse free RNaseA (Roche). ChIP DNA was purified using the PCR purification kit (Qiagen).

tag: cell line

value: H2BP1me-1 Rabbit polyclonal


title: H2BP1me-1


title: WT_DMSO_rep3 [RNA-seq]


title: hrr25as_DMSO_rep2 [RNA-seq]


title: Input DNA me-2


title: WT_3MBPP1_rep1 [RNA-seq]

description: processed data file: WT_rep1_rep2_DESeq.csv

source_name: Total RNA from WT cells treated with 3MBPP1


title: hrr25as_3MBPP1_rep1 [RNA-seq]


title: WT_DMSO_rep1 [RNA-seq]


title: WT_3MBPP1_rep2 [RNA-seq]


title: WT_DMSO_rep2 [RNA-seq]


title: Postnatal day 7, replicate 4

status: Public on Dec 01 2018

city: Helsinki

first: Matti

last: Kankainen

address: PL0056 (Viikinkaari 5)

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
Basecalls performed using standard Illumina base-caller
The bioinformatic analysis of RNA-seq data was carried out by Exiqon A/S and included alignment of reads to the mouse reference genome (GRCm38; annotation reference: Ensembl_70), quality analysis, feature summation, and normalization of expression estimates. The normalized expression values for each transcript were calculated as Fragments per Kilobase per Million Mapped Reads (FPKM).
Genome_build: GRCm38 genome assembly, EnsEMBL v70
Supplementary_files_format_and_content: Tab-delimited text file (.txt). Columns: 1)  tracking ID, 2) gene name, 3) transcript ID, 4) locus, 5) FPKM value

source_name: Whole heart

extract_protocol:
Hearts of postnatal day 1 (P1) and day 7 (P7) Hsd:ICR(CD-1®) male mice were harvested. The atrial appendages were removed, hearts were flash frozen in liquid nitrogen and stored until processing at -80 °C.
1.5 µg of total RNA was collected, ribodepleted and further prepared to RNA-seq library by using ScriptSeq v2™ Complete kit . RNA libraries were otherwise prepared for sequencing using standard Illumina protocols

value: Heart

tag: individual id

tag: strain

tag: age

value: Postnatal day 7

value: male


title: Postnatal day 7, replicate 3

tag: Sex


title: G29T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient8

value: Whole blood cells collected from patient after septic shock

tag: patient

value: R


title: Input DNA me-1


title: WT_CMK_rep2 [RNA-seq]


title: Postnatal day 7, replicate 1


title: Postnatal day 1, replicate 4

value: Postnatal day 1


title: Postnatal day 7, replicate 2


title: Postnatal day 1, replicate 2


title: Sperm Donor1 Bisulfite Sequencing

source_name: Sperm Donor 1

value: sperm


title: Postnatal day 1, replicate 3


title: Postnatal day 1, replicate 1


title: pineal_rep1_08

first: Steven

middle: L.

last: Coon

address: 10 Center Dr; Room 8S261A

department: NICHD

institute: National Institutes of Health

data_processing:
Trim low quality reads and adapters using Trimmomatic software
Mapping trimmed reads to human reference genome using TopHat software
Transcript assembly and quantification using Cufflinks software
Genome_build: Ensembl WASHUC2.0
Supplementary_files_format_and_content: Pineal_retina_36_samples_23352_transcripts_count.txt
Supplementary_files_format_and_content: Pineal_retina_36_samples_23352_transcripts_FPKM.txt

organism: Gallus gallus

source_name: 08 time piont

extract_protocol:
Total RNA was extracted using TRIzol, followed by clean-up with an RNeasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One-day-old (Gallus domesticus) were obtained from Hyline International, Inc. and entrained to a 12 h light : 12 h dark cycle of illumination for 9 days. The light cycle was switched to L:D 0: 24 (constant darkness) on day 10. Sampling was initiated immediately at the beginning of the subjective day.

tag: time point

value: pineal


title: pineal_rep1_00

source_name: 00 time point

growth_protocol: One-day-old (Gallus domesticus) were obtained from Hyline International, Inc. and entrained to a 12 h light : 12 h dark cycle of illumination for 9 days. The light cycle was switched to L:D 0: 24 (constant darkness) on day 10.


title: pineal_rep1_04

source_name: 04 time piont


title: WT_H3K4me3

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Illumina Casava1.7 was used for base calling and FASTQ generation
ChIP-seq reads (FASTQ) were aligned to the mm9 genome assembly using bowtie (v0.12.7) with the following configurations (-S -k 5 --best --strata -p 2)
Peaks were called using HOMER (v4.7) using findPeaks function with the following parameters: FDR < 0.001, F (=fold enrichment over control tag count) > 4, P (poisson p-value threshold relative to control tag count) < 0.001.
Enriched motifs were predicted using the same HOMER's findMotifsGenome function with regional size of 200 (for TF) and 1000 (for H3K4me3).
BedGraph file were made using makeUCSCfile program. PeakCalling and bedGraph files are provided as processed data.
Genome_build: mm9

source_name: BM LSK

extract_protocol:
Bone marrow cells were harvested from WT and Mll-PTD knock-in heterozygous mice. For autoMACS Pro Separation, HSPCs were concentrated using anti-mouse CD117 microBeads, stained with biotin-conjugated anti-Sca1 (D7) monoclonal antibody, and purified using anti-biotin microBeads.The ChIP-enriched DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen)
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Illumina)

tag: genotype/variation

value: Wild-type

value: H3K4me3, Abcam, ab8580


title: exp6 double negative replicate

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Raw output BAMs were converted back to FASTQ using PICARD Sam2Fastq. Reads were then mapped to the human genome using rnaStar. The genome used was HG19 with junctions from ENSEMBL (GRCh37.69_ENSEMBL) and a read overhang of 49. Gene level counts were computed using htseq-count and the same gene models as used in the mapping step.
HTSeq v0.5.4 is used for feature counting.
Counts were normalized and rescaled into log2 counts using the limma R package
Genome_build: mm9
Supplementary_files_format_and_content: txt files, normalized count tables from each experiment

source_name: CD4+PD-1-GFP(Foxp3)- T cells

extract_protocol:
T cell samples were homogenized in Trizol and processed according to instructions with reagent.
Follow Ion Torrent protocol, start with 100ng RNA using Ambion Low Input RiboMinus Eukaryote System v2 kit +  LifeTech Ion Total RNA seq kit V2

value: CD4+PD-1-GFP(Foxp3)- T cells


title: Mll-PTD_H3K4me3

value: Mll-PTD knock-in heterozygous


title: exp5 GFP

source_name: CD4+PD-1-GFP(Foxp3)+ T cells

value: CD4+PD-1-GFP(Foxp3)+ T cells


title: exp6 GFP


title: exp5 PD1

source_name: CD4+PD1hiGFP(Foxp3)- T cells

value: CD4+PD1hiGFP(Foxp3)- T cells


title: exp5 double negative replicate


title: exp6 PD1


title: exp3 double negative


title: exp6 double negative


title: exp3 GFP


title: exp6 GFP replicate


title: exp3 PD1


title: G_BU_8

city: Guangzhou

first: Wenwu

address: Wushan street, Tianhe District, Guangzhou 510642, Guangdong, China

institute: South China Agricultural University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Gallus gallus (galgal4) whole genome using bowtie 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Gallus gallus genome (galgal4)
Supplementary_files_format_and_content: text file for each sample with RPKM values. The file "rpkm.txt" contains the RPKM values for all samples and is available on the series record.

source_name: bursa of Fabricius

extract_protocol:
Spleen and bursa of Fabricius were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (reorder-no 5065-4401) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: bursa of Fabricius

tag: treatment

value: immunized and heat-stressed

tag: breed

value: white leghorn chickens


title: G_BU_10


title: hen1-8 heso1-1 AGO1-IP Rep1

city: Nashville

first: Yongchao

last: Dou

state: Tennessee

address: 2525 west end

institute: vanderbilt medical center

description: AGO1-associated RNA

data_processing:
Adapters from the 3’ ends of reads were trimmed using Cutadpt (Version 1.12) with a maximum allowed error rate of 0.1. Reads shorter than 13 and longer than 31 nucleotides in length were excluded from further analysis.
 Reads were mapped to tair10 genome by Bowtie (version 1.1.0) with those exactly mapped to t/r/sn/sno RNAs discarded.
Remaining reads were mapped to Arabidopsis hairpin sequences from miRbase v21 with no mismatch allowed.
Unmapped reads were mapped to the tair10 genome with no more than one mismatch and mappable reads were removed. The remaining reads were trimmed 1 bp a time from the 3’ end and remapped to hairpin sequences with no mismatch allowed.
The remapping process was repeated 10 times and mapped reads with 5' GMC longer than 12nt were retained.
Genome_build: Tair10
Supplementary_files_format_and_content: mirna read counts table in text format

source_name: inflorescence

growth_protocol: Plants were grown at 22±1 ℃ at a light intensity of approximately 120 μmol m-2 sec-1 and 16 hours light/8 hours dark photoperiod.

extract_protocol:
Total RNAs (samples 1-12) or AGO1 immunoprecipitated (samples 13-16) small RNAs were extracted from inflorescence tissues using trizol reagent
Small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

tag: genotype

value: hen1-8 heso1-1

tag: rip-antibody

value: Rabbit anti-AGO1


title: hen1-8 heso1-1 atrm2-1 AGO1-IP Rep1

description: AGO1-associated RNA

value: hen1-8 heso1-1 atrm2-1


title: hen1-8 heso1-1 AGO1-IP Rep2

description: AGO1-associated RNA


title: exp5 double negative


title: exp3 GFP replicate


title: hen1-8 heso1-1 atrm2-1 AGO1-IP Rep2

description: AGO1-associated RNA


title: atrm2-1 Rep2


title: atrm2-1 Rep1


title: G_BU_5

value: immunized and non-heat-stressed

value: male


title: G_BU_4


title: hen1-8 atrm2-1 Rep2

value: hen1-8 atrm2-1


title: hen1-8 atrm2-1 Rep1


title: hen1-8 heso1-1 atrm2-1 Rep2


title: G_BU_1

value: non-immunized and non-heat-stressed


title: hen1-8 heso1-1 atrm2-1 Rep1


title: G_SP_8

source_name: spleen

value: spleen


title: hen1-8 heso1-1 Rep2


title: G_BU_3


title: G_BU_2


title: hen1-8 heso1-1 Rep1


title: hen1-8  Rep2


title: G_SP_7


title: G_SP_6


title: hen1-8  Rep1


title: G_SP_5


title: G_BU_6


title: Col-0 Rep1

value: wild type


title: G_BU_7


title: Col-0 Rep2


title: G_SP_4


title: G_SP_2


title: G_SP_3


title: cycloheximide for 2 hours 2

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

data_processing:
FastaQ files of each sample was aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Expression level of each TU are presented by Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: Arabidopsis Genome Annotation TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample produced by Cufflinks,Cuffcompare and Cuffdiff.

source_name: Inflorescences

growth_protocol: Arabidopsis plant  materials were grown under long day conditions at 22℃. Inflorenscences were collected from five-week old plants that grew in soil.

extract_protocol: All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq RNA sample Prep V2 kit according to the instructions (Illumina). Sequences were determined by HiSeq 2500 sequencing system in the genomic center in Rockefeller University.

value: cycloheximide for 2 hours

tag: replicate

value: Biological repliate 2

value: 35S:AP1-GR ap1,cal


title: cycloheximide for 2 hours 3

value: Biological repliate 3


title: non-treatment 3

value: non-treatment


title: dexamethasone + cycloheximide for 2 hours 3


title: non-treatment 2


title: dexamethasone + cycloheximide for 2 hours 1

value: Biological repliate 1


title: cycloheximide for 2 hours 1


title: non-treatment 1


title: dexamethasone + cycloheximide for 2 hours 2


title: G_SP_1


title: G_SP_10

value: immunized and heat-stressed


title: 24N

city: Daegu

first: Keun Soo

last: Ahn

address: 56 Dalseong ro, Junggu

department: Surgery

country: South Korea

institute: Keimyung University Dongsan Medical Center

data_processing:
The RNA sequencing samples were analyzed with the use of the MAP-R Seq pipeline
Paired-end reads were aligned by TopHatv2 against the hg19 build of the human reference genome using the bowtie1 aligner option.
FeatureCounts software was used to quantify gene expression. Each sample’s mapped reads were aligned to ENSEMBL’s GRCh37.75 RNA features reference gene definition file and then quantified.
The number of raw reads aligning to each RNA feature was then normalized to RPKM
Genome_build: hg19
Supplementary_files_format_and_content: raw read count and RPKM

source_name: Adjacent normal liver for control (control of 24T)

growth_protocol: Fresh tissue samples of primary tumor and matched surrounding normal liver tissues were obtained and saved in the frozen status (-80C).

extract_protocol:
Total RNA was extracted using TRIzol® RNA Isolation Reagents.
The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol to have single 8bp indices for multiplexing. Quality and size of libraries were assessed using Agilent 2100 bioanalyzer DNA kit (Agilent, Santa Clara, CA, USA). All libraries were quantified by qPCR using CFX96 Real Time System (Biorad, Hercules, CA, USA)

value: Liver (adjacent tumor tissue for control)


title: 26N

source_name: Adjacent normal liver for control (control of 26T)


title: 27N

source_name: Adjacent normal liver for control (control of 27T)


title: 25N

source_name: Adjacent normal liver for control (control of 25T)


title: 30N

source_name: Adjacent normal liver for control (control of 30T)


title: 28N

source_name: Adjacent normal liver for control (control of 28T)


title: 23N

source_name: Adjacent normal liver for control (control of 23T)


title: 29N

source_name: Adjacent normal liver for control (control of 29T)


title: 19N

source_name: Adjacent normal liver for control (control of 19T)


title: 17N

source_name: Adjacent normal liver for control (control of 17T)


title: 16N

source_name: Adjacent normal liver for control (control of 16T)


title: 14N

source_name: Adjacent normal liver for control (control of 14T)


title: 15N

source_name: Adjacent normal liver for control (control of 15T)


title: 12N

source_name: Adjacent normal liver for control (control of 12T)


title: 13N

source_name: Adjacent normal liver for control (control of 13T)


title: 10N

source_name: Adjacent normal liver for control (control of 10T)


title: 8N

source_name: Adjacent normal liver for control (control of 8T)


title: 7N

source_name: Adjacent normal liver for control (control of 7T)


title: 6N

source_name: Adjacent normal liver for control (control of 6T)


title: 5N

source_name: Adjacent normal liver for control (control of 5T)


title: 3N

source_name: Adjacent normal liver for control (control of 3T)


title: 4N

source_name: Adjacent normal liver for control (control of 4T)


title: 2N

source_name: Adjacent normal liver for control (control of 2T)


title: 1N

source_name: Adjacent normal liver for control (control of 1T)


title: 22N

source_name: Adjacent normal liver for control (control of 22T)


title: 31T

source_name: Tumor (Intrahepatic cholangiocarcinoma)

value: Tumor (Intrahepatic cholangiocarcinoma)

tag: recurr

tag: dsfree(mo)

tag: death

tag: survival(mo)

tag: cea

tag: diff

tag: pathologic type

value: bileduct

tag: class

value: B

tag: stageajcc

value: I

tag: size(cm)

tag: hepatitis b


title: 29T

tag: tissue

tag: Sex

value: female

tag: age

value: Mod

value: A


title: 30T

value: male

value: Poor

value: IVB


title: 24T

value: cholangiolar


title: 28T

value: II


title: 18N

source_name: Adjacent normal liver for control (control of 18T)


title: 22T


title: 21T


title: 23T


title: 26T


title: 25T

value: IVA


title: 27T

value: III


title: 17T


title: 14T


title: 18T


title: 12T


title: 13T


title: 20T


title: 15T


title: 31N

source_name: Adjacent normal liver for control (control of 31T)


title: 11T


title: 6T


title: 7T


title: 10T


title: 5T


title: 4T


title: 3T


title: 2T


title: 19T


title: 1T


title: 16T


title: exp6 BC double neg

data_processing:
Raw output BAMs were converted back to FASTQ using PICARD Sam2Fastq. Reads were then mapped to the human genome using rnaStar. The genome used was HG19 with junctions from ENSEMBL (GRCh37.69_ENSEMBL) and a read overhang of 49. Gene level counts were computed using htseq-count and the same gene models as used in the mapping step.
HTSeq v0.5.4 is used for feature counting.
Counts were normalized and rescaled into log2 counts using the limma R package
Genome_build: hg19
Supplementary_files_format_and_content: txt files, normalized count tables from each experiment

source_name: CD4+PD-1-CD25- T cells

tag: cell type

value: CD4+PD-1-CD25- T cells


title: exp7 BCA double neg


title: exp7 BC0 CD25

source_name: CD4+CD25hi T cells

value: CD4+CD25hi T cells


title: exp8 BC009 CD25


title: exp7 BC0 double neg


title: exp8 BC009 PD1

source_name: CD4+PD-1hiCD25- T cells

value: CD4+PD-1hiCD25- T cells


title: exp7 BCA PD1


title: exp8 BC005 PD1


title: exp8 BC009 double neg


title: exp7 BC0 PD1


title: exp6 BC PD1


title: 8T

value: Tumor (Intrahepatic cholangiocarcinoma)


title: TERT+ OCT4-GFP+ gonocytes from P6 Rep 4

city: Stanford

middle: E

last: Artandi

address: CCSR Room 1150, 259 Campus Drive

department: Hematology

institute: Stanford University

description:
gonocytes that express both TERT and OCT4
FinalSampleCountTable.txt

data_processing:
Paired-end 101bp RNA-seq reads were quality trimmed using Trim_Galore in paired mode with a Phred cutoff of 15 and a length cutoff of 50bp.
Trimmed paired reads were aligned to the mm9 mouse genome build using command line versions of TopHat v2.0.4 and Bowtie2 v2.0.0-6 (Trapnell et al., 2012). Multi-hit mapping was restricted to five genome locations at most (-g 5) with a segment length of 45bp, discordant pairs were filtered out, and de novo junction discovery was disabled. All other mapping options were set to default values.
Subsequent data processing and analysis from the transcriptomes was performed in the R software (http://www.r-project.org/). For analysis in DESeq2, .bam files output from Bowtie were used to generate a matrix of genomic features and read counts using the GenomicRanges and GenomicFeatures packages available from Bioconductor. A transcript annotation file was generated from the UCSC database and counts for each gene were summed from reads aligning to gene exons
Genome_build: mm9
Supplementary_files_format_and_content: tab-deliminated matrix of raw read counts per gene feature used for analysis in DeSeq

source_name: testis

extract_protocol:
Testes were dissociated based on standard two-step protocols (Brinster and Zimmermann, 1994). Briefly, testes were removed and detunicated using sharp forceps, and placed into HBSS (137mM NaCl, 5.4mM KCL, 0.44mM KH2PO4, 0.25mM Na2HPO4, 4.2mM NaHC03, 1G/L glucose, 9mM HEPES ph7.4) + 2% fetal bovine serum. Tubules were placed into 5ml/testis of 1mg/ml collagenase IV (Worthington) for 5 min at room-temperature for the removal of interstitial cells. Detangling was assisted using sharp forceps as well as trituration with a bulb pipette. The tubules were collected in a 100um filter basket, washed with HBSS, and incubated for 15min at 32C in 5ml/testis of 0.25% trypsin (Invitrogen; EDTA-free) + 1mg/ml collagenase IV + Dnase1 (Invitrogen), with frequent trituration with a bulb pipette. The cell preparation was filtered through a 40um basket, and in some experiments untrypsinized cell were subjected to additional 10min room-temperature incubation in HBSS/FBS + 5mM EDTA.  The two dissociation fractions were washed and pooled.
Cells were sorted directly into Trizol LS (Invitrogen), and RNA extracted following the manufacturer’s recommendation. RNA was further purified on Rneasy Micro columns (Qiagen). cDNA was prepared and amplified using the Nugen Ovation V2 kit, starting from 5 to 10ng of total RNA. The cDNA was sonicated to 200bp size using a Covaris S2 machine, and 25ng of cDNA was used to make the libraries, following standard Illumina Truseq V2 protocols. Samples were sequenced on an Illumina Hiseq2500 machine, with paired-end 101bp reads.

tag: strain

value: B6/J X B6/N mixed background

tag: developmental stage

value: day 6 neonate

tag: genotype

value: Tert-Tomato/+


title: TERT+ OCT4-GFP+ gonocytes from P6 Rep 3


title: TERT+ OCT4-GFP+ gonocytes from P6 Rep 2


title: TERT-High Kit+ Rep 5

description:
single cell suspension of differentiated spermatogonia fractionated by expression of TERT and Kit.
FinalSampleCountTable.txt

value: adult


title: TERT+ OCT4-GFP+ gonocytes from P6 Rep 1


title: TERT-High Kit+ Rep 4


title: TERT-High Kit+ Rep 3


title: TERT-High Kit+ Rep 1


title: GFRa1- TERT-High Kit- Rep4

description:
single cell suspension of undifferentiated spermatogonia fractionated by expression of TERT, GFRa1, and Kit.
FinalSampleCountTable.txt


title: GFRa1- TERT-High Kit- Rep2


title: exp8 BC005 CD25

city: New York


title: GFRa1- TERT-High Kit- Rep3


title: exp8 BC005 double neg


title: exp6 BC CD25


title: GFRa1- TERT-High Kit- Rep1


title: TERT-High Kit+ Rep 2


title: exp7 BCA CD25


title: 10178

city: Salt Lake City

first: Sheri

last: Holmen

state: UT

address: 2000 Circle of Hope Dr.

institute: University of Utah

data_processing:
Reads were aligned with STAR (version 2.5.2b) to the mouse genome (GRCm38) using Ensembl (release 87) annotation as a splice reference.
Alignments were counted over gene annotation use Subread featureCounts (version 1.5.1) with Ensembl GRCm38 (release 87) annotation.
Differential expression was performed using DESeq2 (version 1.16.1). Regularized log2 (rlog) expression values after normalization was saved and used for heat map visualization.
Genome_build: GRCm38
Supplementary_files_format_and_content: Compressed text files representing the raw counts and processed regularized log2 expression values.

source_name: Mouse brain tumor (FFPE)

extract_protocol: RNA was extracted from FFPE tissue using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE.

treatment_protocol: Tissues were formalin fixed and paraffin embedded.

value: brain tumor

tag: tumor genotype

value: PDGFA

tag: mouse genotype


title: 10176


title: 7773

source_name: Normal mouse brain (FFPE)

value: normal brain


title: 10789


title: 7774


title: 10173


title: 10794


title: 10793


title: GFRa1+ TERT-High Kit- Rep2


title: GFRa1+ TERT-High Kit- Rep4


title: GFRa1+ TERT-High Kit- Rep3


title: 11770


title: IWT-PDGFA

description:
IDH1WT (exogenous) astrocyte
14323X8_IWT-PDGFA
IWT-PDGFA expresses exogenous WT IDH1

data_processing:
Paired reads were aligned to the genome with Novocraft Novoalign v3.7.1 with options -b 2 -t 360 -h 120 -r random.
Reads were de-duplicated with Picard MarkDuplicates v2.9.0.
Alignments were processed with USeq (v9.0.8) NovoalignBisulfiteParser. Point data was filtered for CpG contexts using USeq ParsePointDataContexts. Base fraction CpG methylation tracks were generated with USeq BisStat with a minimum read coverage of 10.
Genome_build: mm10
Supplementary_files_format_and_content: tar bundle of bar.zip point data representing Converted and NonConverted CpG observations from NovoalignBisulfiteParser.
Supplementary_files_format_and_content: bigWig file representation of the fraction methylation at CpG sites
Supplementary_files_format_and_content: bed file of the covered regions with a mean depth of 10 bp across samples used in differential methylation analysis

source_name: IDH1WT (exogenous) astrocyte

growth_protocol: DMEM, 10% FBS.

extract_protocol:
Qiagen DNeasy DNA extraction kit.
Genomic DNA was processed with the Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations.

value: astrocyte

tag: idh genotype

value: IDH wildtype

value: Immortalized astrocyte cell line

tag: background strain

value: C57Bl/6, 129, and FVB/n


title: PDGFA

description:
IDH1WT astrocyte
14323X7_PDGFA

source_name: IDH1WT astrocyte


title: 9322


title: 10015


title: 932S

description:
IDH1WT tumor line (RAS glioma)
14323X6_932S

source_name: IDH1WT tumor line (RAS glioma)

value: cell line derived from tumor

value: N::TVA; Cdkn2alox/lox

value: Cell line derived from brain tumor


title: 139B

description:
IDH1WT tumor line (RAS glioma)
14323X5_139B


title: 13029

description:
Mutant IDH tumor line
14323X3_13029

source_name: Mutant IDH tumor line

value: IDH mutant


title: 13033

description:
Mutant IDH tumor line
14323X2_13033


title: GFRa1+ TERT-High Kit- Rep1


title: 13027

description:
Mutant IDH tumor line
14323X4_13027


title: 11955


title: 13036

description:
Mutant IDH tumor line
14323X1_13036


title: WT772

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

data_processing:
Paired end fastq files were pseudoaligned to Ensemble v82 transcritps using kallisto (VN: 0.43.1)
Transcript level expression and estimated counts were summarized to gene level using tximport Bioconductor package.
Differential expression analysis was performed with DESeq2 bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited output files - abundance.tsv generated by kallisto

source_name: Lin-Sca1+Kit+ bone marrow cells

extract_protocol:
RNA extracted using Qiagen RNeasy Micro Kit
SMART-Seq v4 Ultra Low Input RNA Kit (Clontech)

tag: genotype/variation

value: young Asxl2 WT

tag: batch

tag: littermate

value: young


title: WT711


title: KO771

value: young Asxl2 KO


title: WT335

value: Asxl2 WT

value: old (>1-year old)


title: WT363


title: KO709


title: Mut3-ASXL2

source_name: Lin-Kit+ bone marrow cells

growth_protocol: Cells were grown in IMDM medium supplemented with 15% FBS and recombinant mouse IL3, IL6 and SCF

extract_protocol:
GFP+ cells were sorted, expanded and RNA was extracted using Qiagen Rneasy Kit
TruSeq sample preparation kit (Illumina)

value: Mutant3 Asxl2 over-expression


title: Mut-3-ASXL2-2


title: Mut2-ASXL2

value: Mutant2 Asxl2 over-expression


title: WT-ASXL2-2

value: WT (full-length) Asxl2 over-expression


title: Mut-1-ASXL2-2

value: Mutant1 Asxl2 over-expression


title: Mut-2-ASXL2-2


title: WT-ASXL2


title: EV-2

value: Empty vector


title: Mut1-ASXL2


title: EV


title: HTT ChIPseq Q111/+ Rep 4

city: Seattle

first: Jocelynn

middle: Renee

last: Pearl

state: Washington

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Heterozygous knock-in HD mutant mouse striatum (Q111/+)  ChIP with HTT antibody

data_processing:
We used Bowtie2 (v2.2.5) to align paired-end 25bp reads to release mm9 of the M.musculus genomic sequence obtained from UCSC
We extracted properly paired reads (Supplementary file .bed)
Peak-calling on each sample was performed with MACS v2.1, scaling each library to the size of the input DNA sequence library to improve comparability between samples
Genome_build: mm9
Supplementary_files_format_and_content: MACS .narrowPeak file

source_name: Mouse striatum

growth_protocol: Cohorts of heterozygote and wild-type littermate mice were generated by crossing B6.HttQ111/+ and B6.Htt+/+ mice. Male mice were sacrificed at 122 ± 2 days of age (or 16 weeks) via a sodium phenobarbital based euthanasia solution (Fatal Plus, Henry Schein).

extract_protocol:
striatal tissue was homogenized in glass dounce and fixed with formaldehyde for 10 min at room temperature.  Chromatin was fragmented using MNase digestion followed by sonication. HTT-DNA complexes were isolated using Abcam EPR5526 antibody.
library strategy: Modified ChIP-seq (see PMID 22025700)

treatment_protocol: Both hemispheres of each animal’s brain was microdissected on ice into striatum, cortex, and remaining brain regions. These tissues were snap frozen and stored in -80°C.

tag: tissue type

value: striatum

value: 4 months

tag: htt genotype

tag: chip antibody

value: Anti-HTT antibody (Abcam #ab109115,  Lot # GR155234-1)


title: HTT ChIPseq WT Rep 3

description: Wildtype mouse striatum ChIP with HTT antibody

value: WT


title: Input Control DNA WT Rep 4

description: Wildtype mouse striatum ChIP input control (no antibody selection)


title: HTT ChIPseq WT Rep 2

description: Wildtype mouse striatum  ChIP with HTT antibody


title: HTT ChIPseq Q111/+ Rep 3


title: 4W12-OE-3

city: Wuhan

first: langlang

last: zhang

state: HuBei

address: Cross road of Jiufeng 1 and Guanggu 7 road

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

data_processing:
Samples were sequenced on Hiseq X10 sequencer (illumina).
Raw sequencing data was first filtered by Trimmomatic
Clean reads from each sample were mapped to the reference genome of vitis vinifera (Vitis_vinifera.IGGP_12x; http://plants.ensembl.org/Vitis_vinifera/Info/Index), using Hisat2 v.2.0.5 (https://ccb.jhu.edu/software/hisat2/index.shtml) with default parameters
Reads mapped to the exon regions of each gene were counted by featurecouts (Rsubread) and RPKMs were calculated
Genes differential expressed between groups (3 biological replicates per group) were identified using the edgeR package
Genome_build: Vitis_vinifera.IGGP_12x; http://plants.ensembl.org/Vitis_vinifera/Info/Index
Supplementary_files_format_and_content: A matrix table file of differential expressed genes between two groups include RPKM values for each sample

organism: Vitis amurensis

source_name: cold stressed VaWRKY12 overexpression callus

growth_protocol: The transformation of EV and VaWRKY12 was performed based on the petiole segments culture method to generate the transgenic callus on B5 solid medium  with 20 mg L-1 Kanamycin (NPTII)  for selection, both the transformation and the transgenic callus were maintain at plates under a dark environmental conditions at 25 °C .

extract_protocol:
Total RNA was extracted from collected samples using TIANDZ Column Plant RNAout 2.0 Kit (Tiandz, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 15 days after transferred on new B5 medium, the transgenic callus lines were treated at 4 °C for 24 hours

tag: tissue

value: calus

value: VaWRKY12 overexpression


title: HTT ChIPseq WT Rep 1


title: Input Control DNA Q111/+ Rep 3

description: Heterozygous knock-in HD mutant mouse striatum (Q111/+)  ChIP input control (no antibody selection)


title: HTT ChIPseq Q111/+ Rep 2


title: 4W12-OE-2


title: 4W12-OE-1


title: 4EV-2

source_name: cold stressed EV callus

value: callus

value: Envelope


title: 4EV-3


title: Input Control DNA WT Rep 2

description: Wildtype mouse striatum  ChIP input control (no antibody selection)


title: Input Control DNA Q111/+ Rep 1


title: KO336

value: Asxl2 KO


title: HTT ChIPseq Q111/+ Rep 1


title: KO365


title: K11_foxo1

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat v2.1.0 with default parameters.
Raw reads number of genes was calculated by HTSeq. cufflinks v2.2.1 was run for relative quantitation of genes expression and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hepatic tissue

extract_protocol:
Total RNA were isolated by Trizol reagent , digested with DNase  and purified with RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: hepatic FOXO1 knockout


title: K10_foxo1


title: 4EV-1


title: C3_wildtype

value: wildtype control


title: K3_foxo1


title: C10_wildtype


title: C1_wildtype


title: C12_wildtype


title: K9_foxo1


title: K12

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat v2.1.0 with default parameters.
Raw reads number of genes was calculated by HTSeq. cufflinks v2.2.1 was run for relative quantitation of genes expression and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Total RNA were isolated by Trizol reagent, digested with DNase  and purified with RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatic tissue

value: hepatic FTO knockout


title: K11


title: K7


title: C42


title: C38


title: C34


title: LaminB1_ChIPSeq_Heart_E12.5_1

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: ChIP protocol as previously described (PMID:23934658)

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq Reads were aligned to mouse reference genome (mm9) using bowtie with the followingparameters '-k 1 -m 1 --best –strata'
Genome_build: mm9
Supplementary_files_format_and_content: BED: LADs called by custom peak software
Supplementary_files_format_and_content: WIG: A signal .wig file is computed with an input file and a laminB file with  an adjustment parameter.  The name gives the embryonic stage (e12.5 or e9.5),  then the adjustment (between 0.12 and 0.17) and the indication which input  and which ChIP files were used

source_name: Heart

growth_protocol: Timed pregnant CD1 females purchased from Charles River.

extract_protocol:
Protocol as previously described (PMID: 23934658). Briefly, whole hearts microdissected on ice, fixed in 1.1% formaldehyde x 10 min, pooled in lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 1% NP-40, 1% SDS, 0.5% DOC), sheared with Diagenode Bioruptor, IP overnight with Protein G Dynabeads, 2ug antibody, washed 5x in RIPA, eluted into TE, incubated at 65°C x 16hr and DNA purified by phenol-chloroform extraction.
Library prepared with NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer instructions

value: Embryonic day 12.5

value: Whole Heart, pooled 6 embryos

value: Lamin B1 (Abcam, ab16048, Lot GB95643-1)


title: LaminB1_ChIPSeq_Heart_E12.5_Input


title: LaminB1_ChIPSeq_Heart_E12.5_2


title: LaminB1_ChIPSeq_Heart_E12.5_3


title: LaminB1_ChIPSeq_Heart_E9.5_3

value: Embryonic day 9.5

value: Whole Heart, pooled 3 litters


title: LaminB1_ChIPSeq_Heart_E9.5_4


title: LaminB1_ChIPSeq_Heart_E9.5_Input


title: LaminB1_ChIPSeq_Heart_E9.5_1


title: Exo-AT1

city: cheng du

first: Yan

last: Zhang

address: No. 14, 3rd Sec., Ren Min Nan Road, Chengdu 610041, Sichuan Province, P.R. China

institute: West China School of Stomatology, Sichuan University

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. The numbers of mapped tags that were defined as the raw expression levels of that miRNA.
To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned. When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs. Differentially expressed miRNAs between two samples were filtered through Fold change. Hierarchical clustering was performed.
miRNA target prediction was performed by targetscan and other popular method, then the GO and KEGG pathway analysis were performed based on the top 20 differentially expressed miRNAs.
Genome_build: rn6
Supplementary_files_format_and_content: txt files including the reads of miRNAs in Exo-AT and Exo-ADSCs

organism: Rattus norvegicus

source_name: adipose tissue

growth_protocol: To obtain Exo  from adipose tissue (Exo-AT), adipose tissue harvested from 4-week-old SD rats was minced into pieces. Adipose tissue explants were added into the Celstir Spinner Flask (Wheaton, USA) supplemented with 75mL α-minimal essential medium (α-MEM, Hyclone), 100 U/mL penicillin, and 100 μg/mL streptomycin and cultured with speed at 100r/min for 3 days. To obtain exosomes from ADSCs (Exo-ADSC), prior to culture medium collection, ADSCs were washed twice with PBS, and the medium was switched to serum-free medium (α-MEM, 100 U/mL penicillin, and 100 μg/mL streptomycin) and cultured for 3 days. Finally, the culture medium was centrifuged at 1,200rpm for 10min to remove the debris of cells.

extract_protocol:
Total RNA from Exo-ADSC and Exo-AT was isolated using TRIzol reagent (Invitrogen, USA)
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:1) 3'-adaptor ligation;2) 5'-adaptor ligation;3) cDNA synthesis;4) PCR  amplification;5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 36 cycles on Illumina HiSeq per the manufacturer's instructions.

value: adipose tissue

value: 4 weeks


title: heart_E12.5_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
The RNA-seq data were aligned to the hg19 reference genome using GSNAP 2012-7-20
Alignments were filtered for concordant pair-end reads using Bamfilter.
Ensembl (v67) transcripts/genes were quantified using cuffquant and cuffnorm programs from the cufflinks software package using default options and reported as FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM file: Expression values as FPKMs were calculated suing Cufflinks and Ensembl gene annotations. Columns are Ensembl Gene ID,Official gene symbol,Chrom,Start coord,End Coord,strand,Biotype, FPKM expression value

extract_protocol:
Trizol extraction of total RNA was performed to the manufacturer's instructions
Illumina TruSeq® RNA Sample Preparation v2 with the final product size selected between 350 and 650 bp

value: embryonic day 12.5

value: Mixed C57BL/6 x 129S6

value: heart


title: Exo-ADSCs1

source_name: adipose stem cells

value: adipose derived stem cells

value: passage 3


title: Exo-ADSCs2


title: heart_E12.5_rep1


title: HMGA2 transduced 4

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

institute: University of Technology Sydney

data_processing:
Alignments were all made against hg19 using Tophat with default parameters.
Quantification of coding genes was done using HOMER with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts and RPKM normalized expression levels.

extract_protocol:
RNA was isolated from cells using an RNeasy kit (Qiagen) and amplified using an Ovation RNA-Seq System V2 kit (Nugen).
Library construction protocol – RNAseq (Transcriptome) protocol from BGI

tag: cell markers

value: HMGA2 overexpression


title: Exo-AT2

tag: age


title: 6pre

city: Essen

first: Susanne

last: Horn

address: Hufelandstr. 55

department: Klinik für Dermatologie

country: Germany

institute: Universitätsklinikum Essen

description: Poly-dT enriched mRNA

data_processing:
Illumina Casava1.8.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences and read mapping was performed using Gsnap and the diploid amphibian reference genome of Xenopus tropicalis (November 2009 draft assembly GCA_000004195.1).
Transcript quantification was performed creating a matrix of read counts per transcript and differential gene expression was analyzed using the DESeq2 package in R.
Genome_build: Xenopus tropicalis GCA_000004195.1 xenTro3
Supplementary_files_format_and_content: DESeq normalized read counts in tab separated file format

organism: Ambystoma mexicanum

source_name: Jaw bone

growth_protocol: Individuals of Ambystoma mexicanum (axolotls) albino type were obtained from the colony of the Center for Regenerative Therapies TU Dresden (CRTD). Animals were kept in 18°C Dresden tap water and were fed with Artemia and fish pellets. For surgery animals were anesthetized in 0.01% ethyl-p-aminobenzoate (SIGMA).

extract_protocol:
Samples were disrupted and homogenized using the TissueLyser (Qiagen), lysed in 600ul RLT Buffer and DTT (RNeasy Kit, Qiagen). Per sample one sterilized steel ball (Qiagen) was used in a 2 ml LoBind Tube (Eppendorf) at 30 Hz for 2 x 3 min. After homogenization and a short centrifugation the mix was transferred to a new tube and processed according to the RNeasy Kit (Qiagen) protocol for Animal Tissue (Handbook 06/2012).
RNA sequencing libraries were prepared using mRNA Library Prep for Illumina RNA-Seq (Beckman Coulter) with an estimated fragment size of 300bp. SeraMag Poly-dT mRNA (GE health care life sciences) enrichment of mRNA was performed before sequencing 75bp single end reads on an Hiseq 2000 (Illumina).

treatment_protocol: All surgeries were performed in 5 cm long juvenile axolotls (snout to tail). Axolotls were placed in agar dishes filled with 0.01% ethyl- p- aminobenzoat (SIGMA). Anesthetized individuals were fixed with needles and jaw was removed at a length of 5mm from the midline. The amputated jaws were incubated in RNA- later (SIGMA) and freezed to -80°C. After surgery the weight of the individuals was controlled all 3 days. After five weeks of regeneration the regenerated jaw was removed, incubated in RNA- later (SIGMA) and freezed to -80°C.

value: Normal jaw tissue

tag: animal size

value: 5cm (snout to tail)

tag: library

tag: library idex

tag: library index sequence

value: AGGTTT


title: 2pre

description: Poly-dT enriched mRNA

value: GCTCCA


title: 2post

description: Poly-dT enriched mRNA

value: jaw tissue after five weeks of regeneration

value: CATGGC


title: 3post

description: Poly-dT enriched mRNA

value: CTATAC


title: 6post

description: Poly-dT enriched mRNA

value: CTCAGA


title: HMGA2 transduced 2

tag: genotype


title: 11post

description: Poly-dT enriched mRNA

value: GCAAGG


title: Control 4

value: control


title: Control 2


title: Control 3


title: Control 1


title: FR (Folate Repletion) Repl2

city: Heidelberg

first: Thorsten

last: Zenz

address: Im Neuenheimer Feld 460

department: Department of Translational Oncology

institute: German Cancer Research Center (DKFZ)

description: Cells were grown in Medium containing 0,002 µM for 15 weeks after which were grown for additional 17 weeeks in medium containing 4,5 µM folate

data_processing:
Bcl2fastq 2.17.1.14 for base calling
Sequenced reads were trimmed for adaptor sequence and polyA tails, low quality reads removed, then STAR version 2.3.0e with human_genome38 was used for mapping (default parameters)
The mapped reads were counted using HTSeq-Count v0.5.3p7 (unstranded reads, union mode) and gencode.v22 annotation,
Compared the read counts of the different groups with DESeq2 (version 1.2.9) using the DESeq2 normalization and standard protocol
Genome_build: human_genome38
Supplementary_files_format_and_content: Tab-delimited text file with raw counts to genes of all samples, 3 DESeq2 output files (tab-delimited text files) of the comparisons of the different groups

source_name: Human foreskin keratinocytes

growth_protocol: Growth in tissue culture, Folate modulation (see SAMPLE characteristics) in medium

extract_protocol:
Total RNA extraction by RNAeasy Kit protocol, Qiagen
cDNA library for sequencing with Illumina HiSeq 2000 v4 platform, following standard Illumina protocol

treatment_protocol: Either Medium containing 4.5 µM folate continously (FC) or Medium containing 0.002 µM folate continously (FD) or Medium for 15 weeks containing 0.002 µM folate, then for 17 weeks 4.5 µM folate (FR)

tag: cell type

value: Human Foreskin Keratinocytes immortalized by HPV 16 E6 and E7

tag: folate concentration in culture medium

value: First 0.002 µM, then 4.5 µM

tag: time (week) in folate condition

value: 17 weeks in FR condition after 15 weeks of FD condition


title: FR (Folate Repletion) Repl3


title: TE5_Input

data_processing:
Raw fastq files were aligned to human gneome using bowtie (VN:1.1.2) and duplicates were removed using picard.
Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01
Bedgraph files generated by MACS2 were converted to bigWig files using ucsc bedGraphToBigWig tool.
pipeline: https://github.com/PoisonAlien/chiptk
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million. NarrowPeak files indicating peaks detected by MACS2

source_name: Esophageal squamous carcinoma cells

growth_protocol: cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol

tag: cell line

tag: antibody (catalog)


title: TT_H3K27Ac

value: TT


title: TE7_Input


title: FR (Folate Repletion) Repl1


title: 3pre

description: Poly-dT enriched mRNA

value: TCCCGA


title: TE5_H3K27Ac


title: GR_chipseq_supb15_dex

city: Iowa City

first: Miles

middle: A

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

department: Biochemistry

institute: University of Iowa

data_processing:
Mapped to genome with Bowtie2
Called peaks with dex over vehicle using MACS2
Genome_build: hg19

growth_protocol: Grew SUP-B15 cells (DSMZ) in RPMI + 10%FBS at 37˚C, 5% CO2

extract_protocol:
Cels were crosslinked with formaldehyde, quenched, sheared with a Covaris sonicator, and IP'd with an antibody specific for GR (N499, a gift from K. Yamamoto).
Standard protocllusing NuGen Ovation low DNA kit.

treatment_protocol: Treated cells for 90' with 0.02% ethanol or 1µM dexamethasone in 0.02% ethanol

tag: treatment

value: dexamethasone

value: B-cell acute lymphoblastic leukemia line

tag: translocation

tag: antibody

value: Glucocorticoid receptor N499


title: TT_Input


title: TE7_H3K27Ac


title: HMGA2 transduced 3

value: HMGA2 overexpression


title: FC (Folate Control) Repl3

description: Cells were grown in Medium containing 4,5 µM folate continously


title: HMGA2 transduced 1


title: KYSE70_Input


title: KYSE70_H3K27Ac


title: FD (Folate Deficiency) Repl2

description: Cells were grown in Medium containing 0,002 µM continously


title: KYSE510_Input


title: FD (Folate Deficiency) Repl1


title: FC (Folate Control) Repl2


title: FC (Folate Control) Repl1


title: GR_chipseq_supb15_vehicle

value: vehicle


title: KYSE510_H3K27Ac


title: KYSE140_H3K27Ac


title: FD (Folate Deficiency) Repl3


title: E2_R2

data_processing:
The long-range genomic interaction regions generated by the 4C-Seq experiment were analyzed by using the R package r3CSeq v1.22.0 (Thongjuea et al., Nucleic Acids Res., 2013). Briefly, for each replicate the raw reads were aligned to the masked version of the reference human genome (masked for the gap, repetitive and ambiguous sequences) downloaded from the R Bioconductor repository (BSgenome.Hsapiens.UCSC.hg19.masked). The chromosome 9 was selected as the viewpoint chromosome and HindIII was used as the restriction enzyme to digest the genome. A non-overlapping window size of 2 kb was selected to identify the interaction regions. The number of mapped reads for each window were counted and then normalized to obtain RPM (the reads per million per window) values to perform the statistical analysis. The interaction regions were then plotted based on the significance level and visualized on the UCSC Genome Browser as custom tracks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include interactions regions with associated statistical values and genes

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol
4C-Seq