title: 603Pos_G9

description: Recently reactivated latent cell from patient 603 collected by anti-Env antibody capture 36h after PHA activation. Cells were confirmed HIV+ by gag qPCR.


title: 603PosF7

status: Public on Mar 02 2018

type: SRA

city: Sao Paulo

first: Israel

middle: Tojal da

last: Silva

state: SP

address: Tagua, 440

country: Brazil

institute: HOSPITAL A C CAMARGO

library_source: transcriptomic

data_processing:
alignment with STAR 2.4.1d
gene counts with htseq-count 0.6.1p1
Genome_build: hg19
Supplementary_files_format_and_content: plain text gene counts, annotated with UCSC refGene table

molecule: polyA RNA

organism: Homo sapiens

source_name: CD4+ T cell

growth_protocol: CD4+ T cells were isolated from 0.8-1x109 PBMCs by negative selection using the Miltenyi CD4+ T isolation kit. Cells were cultured for 36h at 2x10e6/mL in RPMI supplemented with 10% heat inactivated FCS, 10mM HEPES, 100U/mL PenStrep, and 25% volume conditioned media. 100U/mL IL-2 (Peprotech), 1ug/mL PHA (Sigma), 10uM Z-VAD-FKM (R&D), 10uM Ritonavir, 10uM Dolutegravir, 10uM Emtricitabine, 5uM Tenofovir, and 10uM Maraviroc (all Selleckchem) were added to the media.

extract_protocol:
Single cells were sorted into 96-well plates containing guanidine thiocyanate buffer (Qiagen) supplemented with 1% β-mercaptoethanol. RNA was extracted using Ampure RNAClean SPRI beads.
RNA was converted to full-length cDNA using oligo(dT) priming and SMART template switching technology followed by 24 cycles of PCR preamplification of cDNA. We used the amplified cDNA to construct standard Illumina sequencing libraries Nextera XT library preparation kit. Samples were sequenced by Illumina NextSeq.

treatment_protocol: After 36h in culture, cells were labeled with 5ug/mL each of biotinylated 3BNC117, 10-1074, PG16 followed by Streptavidin PE (1:500, BD) and anti-PE magnetic beads (Miltenyi Biotech). Cells were then passed over a magnetic column and bound cells were eluted for downstream analysis. Cells were gated on live, CD1c, CD8, CD14, CD20, and CD56 negative, CD3 positive and sorted based on Env staining.

tag: condition

value: Gag+Env+

tag: patient


title: 603Pos_E7


title: 603Pos_E1


title: ChIPseq_MV-4-11-B_INPUT_NA_NA_NA_NA_NA_NA_rep1_J2596-J2605

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

library_source: genomic

data_processing:
Base calling was performed using Illumina RTA 1.18.64, afterwards multiplexed samples were converted to FASTQ files using CASAVA 1.8.2 allowing for 1 mismatch in the index sequence. Technical replicates were merged in a single FASTQ files.
ChIP-seq: Reads were mapped to hg19 (canoncial chromosomes) using bowtie2 version 2.2.9, peaks calls were perfomed with MACS2 version 2.1.0. and HOMER HOMER version 4.7 on uniquely mapping reads by using the intersection of calls. Parameters for calling super-enhancers were set as described in the HOMER manual. Note, biological replicates were merged for all analysis reported in the paper.
RNA-seq: Reads were mapped to hg19 (hs37d5) with gsnap version 2012-12-20. The ENSEMBL 70 gene annotation was used for further expression estimations. Raw counts were computed using HTSeq version 0.5.3p9, FPKM expression values were estimated using Cufflinks version 2.0.2. Differential gene expression was computed using DESeq filtering out genes with less than 10 reads across the tested samples.
Quant-seq: Reads were filtered using BBMap version 36.27 and mapped to hg38 (hs38d1) with STAR version 2.5.2b. Raw read counting over genes loci was also performed using STAR. Differential gene expression was computed using DESeq2 filtering out genes with less than 10 reads across the tested samples.
Genome_build: hg19/hg38
Supplementary_files_format_and_content: All processed data files contain tab-separated values. Peaks call files contain positions of all peaks with associated statistics from HOMER. Differential gene expression files list all genes and attach associated statistics from DESeq/DESeq2.

molecule: genomic DNA

source_name: MV-4-11-B cells

growth_protocol: The cell lines were cultured with the media suggested by ATCC at 37 degree Celsius incubators with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 10 ng of ChIP material per sample. NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB #E6240L) and for the quantity measurement KAPA Library Quantification Kit (KapaBiosystems, #KK4824) was used according to the manufacturer’s instructions. 2 nM samples were multiplexed for sequencing.

treatment_protocol: The corresponding compounds (dissolved in DMSO) were added directly into cell culture media, and cells were kept at normal growth conditions for the treatment duration.

tag: method

value: ChIP-seq

tag: chip antibody

tag: treatment

tag: replicate

tag: internal id


title: ChIPseq_MV-4-11-B_H3K27ac_NA_NA_NA_NA_NA_NA_rep1_J3765

description: ChIPseq_MV-4-11-B_H3K27ac_NA_NA_NA_NA_NA_NA_NA_J3765-J2596-J2605_peaks.tsv.gz


title: 603Pre_A12

description: Unselected CD4 T cells from patient 603 collected 36h after PHA activation in vitro.

treatment_protocol: After 36h in culture, cells were labeled with 5ug/mL each of biotinylated 3BNC117, 10-1074, PG16 followed by Streptavidin PE (1:500, BD) and anti-PE magnetic beads (Miltenyi Biotech). Cells were gated on live, CD1c, CD8, CD14, CD20, and CD56 negative and sorted on CD3 positive cells.

value: Control


title: ChIPseq_MV-4-11-B_BRD4_DMSO_NA_NA_NA_NA_NA_rep2_J3764

description: ChIPseq_MV-4-11-B_BRD4_DMSO_NA_NA_NA_NA_NA_NA_J2608-J2778-J3764-J2596-J2605-J3766_peaks.tsv.gz

value: DMSO


title: 603Pos_D10


title: 603PosD5


title: ChIPseq_MV-4-11-B_POLII_DMSO_NA_NA_NA_NA_NA_rep1_J5927

description: ChIPseq_MV-4-11-B_POLII_DMSO_NA_NA_NA_NA_NA_NA_J5927-J2596-J2605-J3766_peaks.tsv.gz

value: RNA Polymerase II (abcam, #ab5095)


title: ChIPseq_MV-4-11-B_BRD4_DMSO_NA_NA_NA_NA_NA_rep1_J2608-J2778


title: 603Pos_C8


title: ChIPseq_MV-4-11-B_BRD4_BI00894999_35nM_4h_NA_NA_NA_rep2_J3760

description: ChIPseq_MV-4-11-B_BRD4_BI00894999_35nM_4h_NA_NA_NA_NA_J2601-J2610-J3760-J2596-J2605-J3766_peaks.tsv.gz


title: ChIPseq_MV-4-11-B_BRD4_BI00894999_35nM_4h_NA_NA_NA_rep1_J2601-J2610


title: 603Pos_E4


title: 603pre6


title: ChIPseq_MV-4-11-B_BRD4_BI00894999_1nM_4h_NA_NA_NA_rep2_J3762

description: ChIPseq_MV-4-11-B_BRD4_BI00894999_1nM_4h_NA_NA_NA_NA_J2600-J2609-J3762-J2596-J2605-J3766_peaks.tsv.gz


title: 603Pos_C7


title: ChIPseq_MV-4-11-B_INPUT_NA_NA_NA_NA_NA_NA_rep2_J3766


title: ChIPseq_MV-4-11-B_BRD4_BI00894999_100nM_4h_NA_NA_NA_rep1_J3758

description: ChIPseq_MV-4-11-B_BRD4_BI00894999_100nM_4h_NA_NA_NA_NA_J3758-J2596-J2605_peaks.tsv.gz


title: 603Pos_3_D12


title: 603Pos_B9


title: ChIPseq_MV-4-11-B_BRD4_BI00894999_1nM_4h_NA_NA_NA_rep1_J2600-J2609


title: 603PosB11


title: Ribo-seq of S2 cells treated with rapamycin

city: Beijing

first: Jian

last: Lu

address: No.5 Yiheyuan Rd, Haidian District

country: China

institute: Peking University

description: ribosome profiling with MNase digestion

data_processing:
The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) was applied to clip the 3'-adaptor sequence from reads that had passed purity filtering.
For mRNA-seq and ribo-seq, The remaining reads were sequentially mapped to the yeast genome (S288C_R64.2.1), the Wolbachia genome (GenBank), 23 species of insect virus (GenBank), transposons (FlyBase), miscRNA (FlyBase), miRNAs (miRBase) and tRNAs using Bowtie version 1.0.1.
For mRNA-seq and ribo-seq, the unmapped reads were subsequently aligned with chromosome arms (FlyBase r6.06) using STAR.
For each the protein-coding gene, the transcript isoform with the longest CDS was used to represent the expression level.  The mRNA-Seq reads and the ribo-Seq reads that were mapped to the CDSes of these transcripts, were summarized with htseq-count.
Genome_build: flybase r6.06
Supplementary_files_format_and_content: For mRNA-seq and ribo-seq, tab-delimited text files include raw counts values for each CDS. For small RNA-seq, tab-delimited text files include raw counts values after adapter trimming

molecule: total RNA

organism: Drosophila melanogaster

source_name: S2 cell

growth_protocol: Drosophila S2 cells were cultured in Schneider’s Insect Medium (Sigma) containing 10% (by volume) heat-inactivated fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher) at 27°C without CO2 for 24 h to reach 2~4×106 cells/mL before further treatments.

extract_protocol:
Total RNA was extracted using the TRIzol reagent and chloroform
For small RNA libraries, 20~50 µg total RNA was analysed on a 15% TBE-Urea gel, and the 18~29-nt band was excised (the ~30-nt 2S rRNA band was avoided with caution).  The resolved RNAs were sequentially ligated with 3’-adaptor and 5’-adaptor, and then reverse-transcribed. For mRNA libraries, 10~20 μg poly(A)+ RNAs were selected on oligo-dT25 DynaBeads and fragmented at 95°C in fragmentation buffer (2 mM EDTA, 12 mM Na2CO3, 88 mM NaHCO3, pH 9.3).  The fragmented RNAs within 40~80 nt were 3’-dephosphorylated, ligated with 3’-adaptor and purified on a 15% TBE-Urea gel.  The 3’-ligated RNAs were subsequently 5’-phosphorylated, ligated with 5’-adaptor, and reverse-transcribed.  All cDNAs were amplified through 12 PCR cycles, and the products within the correct size ranges were collected from 20% TBE gels for quality tests (Fragment Analyzer, Agilent Technologies) and sequencing
RNA-seq,ribo-seq, miRNA-seq

treatment_protocol: For serum starvation assays, the cells were subsequently cultured in serum-containing or serum-free medium for 24 additional hours before harvesting.  For tsRNA transfections, the cells were bathed with the synthetic mimics or the single-stranded negative control RNA (NC) at a final concentration of 100 nM using Lipofectamine 2000 transfection reagent for 32 h. Mock-treated cells were also treated with Lipofectamine 2000 in the same manner, except that no synthetic mimic or NC RNA was used.  For AGO2 knockdown, the cells were bathed with a siRNA duplex that specifically targets the AGO2 mRNA or the double-stranded negative control small RNA (ds-NC) at a final concentration of 30 nM for 24 hours. For rapamycin treatment, rapamycin (Sigma) was diluted with DMSO, and the cells were treated at a final concentration of 274 nM for 2 hours.  As the control in the rapamycin-treatment experiment, we treated S2 cells with DMSO for 2 hours.

tag: cell line

value: S2 cell

value: rapamycin treatment


title: ChIPseq_MOLM-13_INPUT_NA_NA_NA_NA_NA_NA_rep1_J4762

source_name: MOLM-13 cells


title: 603Pos_3_C9


title: 603Pre_B10


title: Ribo-seq of S2 cells transfected with tsRNA mimic T10

description: ribosome profiling with MNase digestion

value: T10 mimic transfection


title: 603Pos_3_C4


title: mRNA-seq of S2 cells transfected with dsNC

description: poly A

value: dsNC transfection


title: Ribo-seq of S2 cells transfected with dsNC

description: ribosome profiling with MNase digestion


title: ChIPseq_MOLM-13_H3K27ac_NA_NA_NA_NA_NA_NA_rep1_J4760

description: ChIPseq_MOLM-13_H3K27ac_NA_NA_NA_NA_NA_NA_NA_J4760-J4762_peaks.tsv.gz


title: mRNA-seq of S2 cells transfected with tsRNA mimic T10

description: poly A


title: 603Pos_3_C12


title: Ribo-seq of S2 cells transfected with tsRNA mimic T6

description: ribosome profiling with MNase digestion

value: T6 mimic transfection


title: 603PosC3


title: 603Pos_3_A3


title: 603Pos_2_H8


title: Ribo-seq of S2 cells transfected with tsRNA mimic T3

description: ribosome profiling with MNase digestion

value: T3 mimic transfection


title: 603Pos_2_G11


title: 603Pos_2_G4


title: mRNA-seq of S2 cells transfected with tsRNA mimic T3

description: poly A


title: Ribo-seq of S2 cells transfected with ssNC

description: ribosome profiling with MNase digestion

value: ssNC transfection


title: mRNA-seq of S2 cells transfected with tsRNA mimic T6

description: poly A


title: ChIPseq_MV-4-11-B_BRD4_BI00894999_1000nM_4h_NA_NA_NA_rep1_J3756

description: ChIPseq_MV-4-11-B_BRD4_BI00894999_1000nM_4h_NA_NA_NA_NA_J3756-J2596-J2605_peaks.tsv.gz


title: mRNA-seq of S2 cells  transfected with ssNC

description: poly A


title: 603Pos_2_D7


title: mRNA-seq of S2 cells treated with rapamycin

description: poly A


title: 603Pos_2_D10


title: 603Pos_2_C7


title: Ribo-seq of S2 cells treated with DMSO

description: ribosome profiling with MNase digestion


title: 603Pos_2_E10


title: mRNA-seq of S2 cells treated with DMSO

description: poly A


title: Ribo-seq of S2 cells under ago2 knock-down and starvation condition

description: ribosome profiling with MNase digestion

value: ago2 knockdown and starvation


title: 603Pos_2_C3


title: 603Pos_3_A8


title: 603Pos_2_B8


title: mRNA-seq of S2 cells under ago2 knock-down and starvation condition

description: poly A


title: 603Pos_1_H2


title: 603Pos_1_H1


title: mRNA-seq of S2 cells under ago2 knock-down condition

description: poly A

value: ago2 knockdown


title: small RNA-seq of S2 cells under starvation condition

description: small RNA

value: starvation


title: 603Pos_1_F9


title: 603Pos_1_D5


title: Ribo-seq of S2 cells under starvation condition

description: ribosome profiling with MNase digestion


title: Ribo-seq of S2 cells under ago2 knock-down condition

description: ribosome profiling with MNase digestion


title: 603Pos_1_G2


title: 603Pos_1_C12


title: mRNA-seq of S2 cells under starvation condition

description: poly A


title: 603Pos_1_B5


title: Ribo-seq of S2 cells under normal condition

description: ribosome profiling with MNase digestion

value: normal


title: mRNA-seq of S2 cells under normal condition

description: poly A


title: NHA_Tun_1

city: Philadelphia

first: Saad

last: Sheikh

state: PA

address: Bldg 421 8-169, 3400 Civic Center Blvd

department: Radiation Oncology

country: USA

institute: University of Pennsylvania, Perelman School of Medicine

data_processing:
Reads were trimmed with bbduk v35.92 using the following parameters, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20, making sure to remove all poly-A and adapter contamination.
Aligned to GRCh38 with STAR v2.5.2a set to the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Read counts for each gene were generated with HTSeq-count v0.6.0, as follows: -m intersection-nonempty -s yes -f bam -r pos
The above data-processing steps were integrated into the Bluebee QuantSeq 3’ mRNA-seq pipeline, on which all of the samples in this experiment were run.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV matrix table with read counts, with genes listed across the rows and the samples across the columns

source_name: human brain tissue_Normal Human Astrocytes

growth_protocol: Glioma derived stem cells were grown in serum free media (Neurobasal A) supplemented with EGF and FGF for 2-3 passages out of liquid nitrogen. U251  and Normal Human Astrocytes were grown in DMEM supplemented with 10% FBS for 4-5 passages out of liquid nitrogen.

extract_protocol:
Total RNA was extracted following twenty-four hours after treatment using the NucleoSpin RNA Extraction Kit (Macherey-Nagel, Duren, Germany) following the manufacturer's protocol
500 ng of total RNA per sample were used to create sequencing libraries according to the Lexogen QuantSeq 3’ mRNA Library Prep Kit FWD protocol.

treatment_protocol: Cells were plated in 6 cm dishes in biologic triplicate. Twenty-four hours after plating, either 0.1% DMSO, 2.5 micromolar NH125 or 1.0 mcg/mL Tunicamycin was added to the growth media. All drug dilutions were performed in each cell lines respective media. Treatment was performed in triplicate

tag: cell type

value: human derived glial cells

tag: passages

value: 1.0 mcg/mL Tunicamycin


title: NHA_Tun_2


title: NHA_NH125_1

value: 2.5 micromolar NH125


title: NHA_NH125_2


title: NHA_NH125_3


title: NHA_DMSO_1

value: 0.1% DMSO (vehicle)


title: 603Pos_1_H12

value: Gag+Env+


title: 603Pos_1_B11


title: NHA_Tun_3


title: NHA_DMSO_3


title: U251_NH125_3

source_name: glioblastoma

value: glioblastoma derived (ATCC)


title: U251_Tun_2


title: U251_Tun_1


title: U251_NH125_2


title: U251_NH125_1


title: U251_DMSO_2


title: U251_DMSO_3


title: T4213_NH125_2

value: glioma derived stem cells


title: T4213_NH125_1


title: T4213_Tun_3


title: T4213_Tun_1


title: tall fescue heat treatment for 12 rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed

organism: Lolium arundinaceum

source_name: leaf

extract_protocol:
The leaves of control and heat treated tall fescue plants were collected for RAN isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: leaf

tag: treatment time

value: 12h after heat treatment

tag: genotype

value: WT


title: NHA_DMSO_2


title: tall fescue heat treatment for 2 rep1

value: 2h after heat treatment


title: RNA.CARM1-KO

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: RNA-seq in CARM1 KO cells

data_processing:
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
edgeR was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: A1847 cell line, CARM1 CRISPR

growth_protocol: A1847 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin  at 37°C supplied with 5% CO2.

extract_protocol:
RNA was extracted with Trizol (Invitrogen) and subsequently cleaned and DNase-treated using RNeasy columns (Qiagen).
Libraries for RNA-seq were prepared with ScriptSeq complete Gold kit (Epicentre) and subjected to a 75 bp paired-end sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions.

treatment_protocol: pLentiCRISPR-CARM1 was constructed by inserting the CARM1 guide RNA (gRNA; 5′-AGCACGGAAAATCTACGCGG-3′). pLentiCRISPR v2 (Addgene) was digested and dephosphorylated with BsmBI restriction enzyme (Fermentas) for 30 min at 37°C. The digested plasmid was run on a 1% agarose gel, cut out, and purified using the Wizard SV Gel and PCR Clean Up kit (Promega). The oligonucleotides were phosphorylated using T4 PNK (M0201S) with T4 Ligation Buffer (New England Biolabs, Inc.). Samples were annealed in a thermocycler at 37°C for 30 min and then at 95°C for 5 min and then were ramped down to 25°C at 5°C/min. Annealed oligonucleotides were diluted 1:200 in RNase/DNase-free water. Ligation of the annealed oligonucleotide and digested pLentiCRISPR v2 plasmid was performed using Quick Ligase (New England Biolabs, Inc.)

tag: genotype/variation

value: CARM1 knockout


title: T4213_DMSO_1


title: T4213_DMSO_2


title: tall fescue  control rep2

value: 0h after heat treatment


title: tall fescue heat treatment for 2 rep2


title: T4213_DMSO_3


title: RNA.CARM1-WT

description: RNA-seq in CARM1 WT cells

source_name: A1847 cell line

value: CARM1 wild type


title: small RNA-seq of S2 cells under normal condition

description: small RNA

value: S2 cell


title: tall fescue heat treatment for 12 rep1


title: WT_mock_rep2

status: Public on Mar 01 2018

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
Quality control was checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). RNA-Seq reads were trimmed using the fastx_trimmer command FASTX-Toolkit (hannonlab.cshl.edu/fastx_toolkit/index.html) with parameter “-f 11 -l 80” before alignment. The trimmed reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2.
Genome_build: TAIR10
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts with parameter " -p -t exon -g gene_id -a tair10_ensembl.gtf "

organism: Arabidopsis thaliana

source_name: 7-day old seedlings

growth_protocol: The seeds were surface sterilized and sown on half Murashige and Skoog (MS) medium containing 1% sucrose and 0.8% agar for 7 days

extract_protocol: The total RNA was isolated with Trizol reagent (Invitrogen) according to the manufacturer’s instruction and RNA-sequencing were carried out by the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China).

treatment_protocol: 7-day old seedlings were immensed in 1/2 MS or 1/2 MS liquid medium containing 50 μM ABA for 3 h

value: seedling

value: wild type


title: WT_ABA_3h_rep3

description: treat with 50 μM ABA for  3 hours


title: WT_mock_rep1


title: WT_ABA_3h_rep2

description: treat with 50 μM ABA for  3 hours


title: WT_ABA_3h_rep1

description: treat with 50 μM ABA for  3 hours


title: T4213_NH125_3


title: nup85_mock_rep2


title: nup85_mock_rep3


title: nup85_ABA_3h_rep2

description: treat with 50 μM ABA for  3 hours


title: nup85_mock_rep1


title: U251_DMSO_1


title: ibm1-3

city: ChongQing

first: Di

last: Fan

address: NO.2 Tiansheng Road

institute: Southwest University

description: WT vs ibm1.txt

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 tair10 whole genome using bowtie2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010.
Differentially expressed genes were analyzed with DEGseq
Genome_build: Arabidopsis thaliana tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: All Arabidopsis were planted in green house in long day condition

extract_protocol:
rosset leaves were removed, and RNA was havested using biospin plant total RNA extraction kit
RNA libraries were prepared for RNA sequencing using standard Illumina protocols and BGI protocols separately

treatment_protocol: 30 days old WT and ibm1-3 Arabidopsis were treated with high light for 48 hours

value: rosset leaf

tag: age

value: 40 days

tag: background ecotype

value: Columbia

tag: protocol

value: low light


title: WT_mock_rep3


title: tall fescue control rep1


title: nup85_ABA_3h_rep1

description: treat with 50 μM ABA for  3 hours


title: WT

description: WT vs ibm1.txt


title: M7_INTS13

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description:
genomic DNA
INTS13 was profiled in in vitro differentiated monocytes (cord blood CD34+ derived)

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (ChIPseq): BWA
alignment (RNAseq, chromatin RNA-seq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: in vitro differentiated monocytes (from fetal liver CD34+ cells)

growth_protocol: Monocytes were differentiated fromCD34+ cells in StemSpan SFEM medium supplemented with 100 ng/ml SCF, 10 ng/ml IL-3 and 50 ng/ml M-SCF, and collected at day 7

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: Monocytes were differentiated from CD34+ cells in StemSpan SFEM medium supplemented with 100 ng/ml SCF, 10 ng/ml IL-3 and 50 ng/ml M-SCF

tag: antibody vendor/catalog#

value: Bethyl A303-575A


title: MONO_day2_chromRNA

description:
ribodepleted RNA
Chromatin RNA-seq was performed in in vitro differentiated monocytes (from fetal liver CD34+ cells)

source_name: in vitro differentiated monocytes (from cord blood CD34+ cells)

growth_protocol: Monocytes were differentiated fromCD34+ cells in StemSpan SFEM medium supplemented with 100 ng/ml SCF, 10 ng/ml IL-3 and 50 ng/ml M-SCF and collected at day2

extract_protocol: NEBNext Ultra Directional Strand specific RNA-Seq  Sample Prep Kit (New England Biolabs, inc.)


title: nup85_ABA_3h_rep3

description: treat with 50 μM ABA for  3 hours


title: granulosa cells_MGCs_M1

city: Groningen

first: Joost

last: Kluiver

address: Hanzeplein 1

country: Netherlands

institute: UMCG

description:
170126_NB501043_0106_AHFLTHBGX2_L*_ACAGTG
4 raw data files are associated with this sample (sample divided over 4 lanes in one run)

data_processing:
3′- and 5′-adaptor sequences were removed using the CLC Genomics Workbench (CLC Bio, Cambridge, MA)
RNA reads were analyzed with miRDeep version 2.0  and annotated against miRBASE version 21 (http://www.mirbase.org) allowing one mismatch
Total read counts were standardized to read counts per million (RPM). Read counts for miRNAs with the same mature sequence were merged.
Genome_build: miRBASE v21
Supplementary_files_format_and_content: All unique miRNAs with at least 20 read counts (RPM) in at least one out of the two conditions were selected.

source_name: granulosa cells_MGCs

growth_protocol: Primary granulosa cells (PrGC) were obtained from pre-ovulatory follicles from three individual healthy women between 18-40 years old undergoing ovum pick-up for in vitro fertilization (IVF) for male factor infertility at the University Medical Centre Groningen, The Netherlands. Patients received human menopauzal gonadotrophin 150-225 IU per day (Menopur®, Ferring Pharmaceuticals, The Netherlands) and a daily subcutaneous GnRH analog, triporeline 0.5mg (Decapeptyl®, Ferring Pharmaceuticals, the Netherlands). 36 hours after 5000 IU human chorionic gonadotropin (hCG) (Pregnyl® Organon, Oss, The Netherlands), oocyte collection was performed. After oocyte collection, cumulus aggregates were obtained by visual inspection and manual separation from the cumulus-oocyte complex and centrifuged in HBSS (Life technologies, USA), for 10 min at 400 g. The pellet was resuspended in trypsin and CCs were cultured in DMEM/F12 medium (Life Technologies, USA) supplemented with 10% FCS (Thermo Scientific, USA), 1% penicillin-streptomycin-amphotericin B (Lonza®, USA) at 37ºC and 5% CO2. For MGCs isolation, the follicular fluid (FF) was centrifuged 5 min at 400 g and 5 min at 500 g, and the pellet was resuspended in HBSS. Blood cells were separated from the MGCs using a PercollTM (GE Healthcare, Sweden) 40% gradient via 10 min centrifugation at 550 g. Cells from the interface were collected and washed in HBSS through 10 min centrifugation at 450 g. The pellet was resuspended in 1 ml trypsin followed by 3-4 minutes incubation at 37ºC to disperse the clustered cells. MGCs from individual patients were plated at a density of 2,5- 3,5 x 105 cells/ml in 12-well plates (Costar, USA) and cultured in DMEM/F12 medium (Life Technologies, USA) supplemented with 10% FCS (Thermo Scientific, USA), 1% penicillin-streptomycin-amphotericin B (Lonza®, USA) at 37ºC and 5% CO2. Cells were washed 2x with HBSS every 2 days of culture.

extract_protocol:
RNA from PrGC was purified using the miRNeasy micro kit (QIAGEN, Germany) according to the manufacturer’s instructions
Small RNA libraries were generated from 200 ng total RNA using NEXTflex Small RNA Sequencing Kit v3 for Illumina Platforms (Bio Scientific, Austin, TX, USA). An extra purification of the libraries was performed with the automated agarose gel separation system Labchip XT (PerkinElmer, Waltham, MA, USA). The obtained cDNA fragment libraries were sequenced on Illumina Nextseq500 (Illumina, San Diego, CA) using default parameters (single read 1x50bp). Briefly, 3′- and 5′-adaptor sequences were removed using the CLC Genomics Workbench (CLC Bio, Cambridge, MA). RNA reads were analyzed with miRDeep version 2.0 (Friedländer et al., 2008) Centre and annotated against miRBASE version 21 (http://www.mirbase.org) allowing one mismatch

treatment_protocol: For the MGCs/CCs sequencing experiment, cells were washed 2x with HBSS and incubated for 24h with serum-free DMEM/F12 suplemented with 1% penicilin-streptomycin and 10 uM androstenedione (AST) (Sigma, USA)

tag: donor id

tag: granulosa cell type

value: mural granulosa cells (MGCs)


title: granulosa cells_MGCs_M2

description:
170126_NB501043_0106_AHFLTHBGX2_L*_ACTTGA
4 raw data files are associated with this sample (sample divided over 4 lanes in one run)


title: granulosa cells_MGCs_M3

description:
170126_NB501043_0106_AHFLTHBGX2_L*_GGCTAC
4 raw data files are associated with this sample (sample divided over 4 lanes in one run)


title: HL-60_shLUC_RNA_PMA_rep2

description:
ribodepleted RNA
RNA-seq was performed in PMA treated HL-60 (48h)  infected with a control shRNA (against luciferase)

source_name: HL-60 cell line

growth_protocol: HL-60 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) of super calf serum (GEMcell) and 2 mM of L-glutamine.

treatment_protocol: HL-60 cells were differentiated with 100 nM Phorbol 12-myristate 13-acetate (PMA) in growing medium

value: PMA treated (48h)

tag: infection

value: control shRNA (against luciferase)


title: granulosa cells_CCs_C3

description:
170126_NB501043_0106_AHFLTHBGX2_L*_AGTCAA
4 raw data files are associated with this sample (sample divided over 4 lanes in one run)

source_name: granulosa cells_CCs

value: cumulus cells (CCs)


title: HL-60_RNA_CTRL_rep2

description:
ribodepleted RNA
chromatin RNA-seq was performed in untreated HL-60

tag: treatment

value: untreated


title: HL-60_RNA_PMA_rep2

description:
ribodepleted RNA
chromatin RNA-seq was performed in PMA treated HL-60 (48h)


title: HL-60_RNA_PMA_rep1


title: granulosa cells_CCs_C1

description:
170126_NB501043_0106_AHFLTHBGX2_L*_CAGATC
4 raw data files are associated with this sample (sample divided over 4 lanes in one run)


title: HL-60_RNA_CTRL_rep1


title: HL-60_POLII_CTRL

description:
genomic DNA
RNAPII was profiled in untreated HL-60

tag: chip antibody

value: Custom, rabbit polyclonal, raised against N terminus of RNAPII


title: HL-60_POLII_PMA

description:
genomic DNA
RNAPII was profiled in PMA treated HL-60 (16h)

value: PMA treated (16h)


title: HL-60_shINTS13_RNA_PMA_rep2

description:
ribodepleted RNA
RNA-seq was performed in PMA treated HL-60 (48h)  infected with an shRNA against INTS13 (INTS13-KD)

value: shRNA against INTS13


title: granulosa cells_CCs_C2

description:
170126_NB501043_0106_AHFLTHBGX2_L*_TAGCTT
4 raw data files are associated with this sample (sample divided over 4 lanes in one run)


title: HL-60_shINTS13_RNA_PMA_rep1_FOR


title: HL-60_PMA16_input

description:
genomic DNA
Input, prepared using 5% of original sample (PMA treated HL-60, 16h)


title: HL-60_NT_input

description:
genomic DNA
Input, prepared using 5% of original sample (untreated HL-60)


title: U251_Tun_3

value: glioblastoma derived (ATCC)

value: 1.0 mcg/mL Tunicamycin


title: HL-60_NAB2_PMA

description:
genomic DNA
NAB2 was profiled in PMA treated HL-60 (16h)

value: ThermoFisher PA5-27925


title: HL-60_INTS13_shEGR1

description:
genomic DNA
INTS13 was profiled in PMA treated HL-60 (16h), infected with an shRNA against EGR1 (EGR1-KD)

value: shRNA against EGR1 (EGR1-KD)


title: HL-60_NAB2_CTRL

description:
genomic DNA
NAB2 was profiled in untreated HL-60


title: HL-60_INTS13_shLUC

description:
genomic DNA
INTS13 was profiled in PMA treated HL-60 (16h), infected with a control shRNA (against LUCIFERASE)

value: control shRNA (against LUCIFERASE)


title: HL-60_INTS13_PMA_rep2

description:
genomic DNA
INTS13 was profiled in PMA treated HL-60 (16h)


title: HL-60_INTS13_PMA_rep1


title: HL-60_shLUC_RNA_PMA_rep1

value: control shRNA


title: HL-60_INTS13_CTRL_rep2

description:
genomic DNA
INTS13 was profiled in untreated HL-60


title: T4213_Tun_2

value: glioma derived stem cells


title: HL-60_INTS11_PMA_rep2

description:
genomic DNA
INTS11 was profiled in PMA treated HL-60 (16h)

value: Bethyl A301-274A


title: HL-60_INTS11_CTRL_rep2

description:
genomic DNA
INTS11 was profiled in untreated HL-60


title: HL-60_INTS11_CTRL_rep1


title: HL-60_H3K4me1_CTRL

description:
genomic DNA
H3K4me1 was profiled in untreated HL-60

value: Abcam ab8895


title: HL-60_H3K27Ac_PMA

description:
genomic DNA
H3K27Ac was profiled in PMA treated HL-60 (16h)

value: Abcam ab4279


title: HL-60_EGR1_PMA

description:
genomic DNA
EGR1 was profiled in PMA treated HL-60 (16h)

value: bethyl A303-390A


title: HL-60_H3K4me1_PMA

description:
genomic DNA
H3K4me1 was profiled in PMA treated HL-60 (16h)


title: CD34_chromRNA

description:
ribodepleted RNA
chromatin RNA-seq was performed in fetal liver derived CD34+ cells, untreated

source_name: fetal liver derived CD34+ cells

growth_protocol: CD34+ cells were maintained and expanded in StemSpan SFEM  medium supplemented with CC100 cytokine cocktail (StemCellTechologies)

value: fetal liver derived CD34+ cells


title: UPS_7715_H3K27Ac

city: Boston

first: Jun

last: Qi

state: Massachusetts

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber

description: ChIP-seq  or input from UPS tumor

data_processing:
FASTQs were aligned to assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1) with parameter '-k 1.'
Wiggles for visualization and peak calling was performed on aligned data using MACS version 1.4.2 using with matched input chromatin as control, with a p-value threshold of 1e-9.
For any genomic region, normalized read density was calculated using Bamliquidator (version 1.0) (https://github.com/BradnerLab/pipeline/wiki/bamliquidator).
Genome_build: hg19
Supplementary_files_format_and_content: wiggle files of tag pileup

extract_protocol:
Samples were homogenized with rotor-stator device. Lysates were sonicated via Bioruptor.
Protein-DNA complexes were isolated via immunoprecipitation and prepared for sequencing with Rubicon Thruplex DNA-seq kit.
ChIP-seq via single-end 75-bp sequencing on Nextseq 500.

value: Undifferentiated Pleomorphic Sarcoma (UPS)

value: H3K27Ac; Abcam ab4729


title: UPS_7715_input

description: ChIP-seq  or input from UPS tumor


title: ups_0712_3

description: RNA-seq from UPS tumor

data_processing:
FASTQs were aligned using Tophat2.
Counts were quantified with RSEM.
Differentially expressed genes found with edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: text

source_name: Undifferentiated Pleomorphic Sarcoma

extract_protocol:
Tissue was homogenized via rotor-stator device and Qiagen Qiashredder column. Total RNA was extracted using Qiagen Rneasy Mini Kit.
Libraries for RNA-seq were constructed using Illumina TruSeq stranded mRNA library prep kit.
RNA-seq libraries were sequenced by single-ended 75-bp sequencing on Illumina NextSeq 500.

value: undifferentiated Pleomorphic Sarcoma


title: ups_0712_1

description: RNA-seq from UPS tumor


title: ups_0712_2

description: RNA-seq from UPS tumor


title: UPS_4e58_input

description: ChIP-seq  or input from UPS tumor


title: UPS_4e58_H3K27Ac

description: ChIP-seq  or input from UPS tumor


title: UPS_0712_H3K27Ac

description: ChIP-seq  or input from UPS tumor


title: UPS_0712_input

description: ChIP-seq  or input from UPS tumor


title: HL-60_INTS13_CTRL_rep1

value: Bethyl A303-575A

value: untreated


title: HL-60_INTS11_PMA_rep1

value: PMA treated (16h)


title: HL-60_H3K27Ac_CTRL

description:
genomic DNA
H3K27Ac was profiled in untreated HL-60


title: icKO_3day_Epi_STAT3i_4

city: Bethesda

first: Maria

middle: Irene

last: Morasso

state: Maryland

address: Bldg 50

institute: NIAMS NIH

data_processing:
Illumina Casava1.8.2 software was used for BCL conversion and demultiplexing
Reads were mapped to mm10 using TopHat 2.1.0 with default settings
RPKM values and ANOVA comparisons were calculated using Partek GS 6.6
Genome_build: mm10

organism: Mus musculus

source_name: Epidermis

extract_protocol: cDNA was prepared using the NEBnext kit and library was generated using the NuGen kit and Mondrian automated system.

tag: strain

value: mixed background

value: Epidermis

value: 3day after Tamoxifen treatment

value: icKO


title: WT_3day_Der_3

source_name: Dermis

value: Dermis

value: WT


title: icKO_3day_Der_2


title: icKO_3day_Der_1


title: WT_3day_Der_2


title: WT_3day_Der_1


title: icKO_3day_Der_3


title: icKO_3day_Epi_STAT3i_3


title: HL-60_EGR1_CTRL

description:
genomic DNA
EGR1 was profiled in untreated HL-60

tag: cell line


title: WT_3day_Epi_STAT3i_3


title: icKO_3day_Epi_STAT3i_1


title: icKO_3day_Epi_STAT3i_2


title: WT_3day_Epi_STAT3i_2


title: WT_3day_Epi_STAT3i_1


title: icKO_Epi_3day_2


title: icKO_Epi_3day_3


title: icKO_Epi_3day_4


title: 603Pos_1_A12

description: Recently reactivated latent cell from patient 603 collected by anti-Env antibody capture 36h after PHA activation. Cells were confirmed HIV+ by gag qPCR.

source_name: CD4+ T cell

tag: condition

value: Gag+Env+

tag: patient


title: WT_3day_Epi_1

tag: tissue


title: WT_3day_Epi_2


title: Dlx4-WT P60#1

source_name: Skin

value: Skin

value: Post-natal day 60


title: Dlx4-KO P60#1


title: Dlx4-WT P60#2


title: Dlx4-KO P1#2

value: Post-natal day 1


title: Dlx4-KO P1#3


title: Dlx4-KO P1#1


title: Dlx4-WT P1#3


title: Dlx4-WT P1#1


title: 3ab Rep 2

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: small RNA

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie -v 0 -S -a --best --strata
Genome_build: TAIR10
Supplementary_files_format_and_content: Space-delimited plain text files: the first column is for MicroRNA gene IDs and the second column for reads counts

source_name: inflorescence

growth_protocol: 16 hour light; 8 hour dark;  at 22 oC

extract_protocol:
Flower inflorescences were collected and total RNA was extracted by Trizol. Illumina TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Illumina small RNA library protocol

value: Columbia (Col)

value: inflorescence


title: icKO_1week_Der_2

value: 1week after Tamoxifen treatment


title: 5a Rep 2

description: small RNA


title: WT Rep2

description: small RNA

value: WT (Col)


title: WT_1week_Epi_2


title: 5a Rep 1

description: small RNA


title: 3ab Rep 1

description: small RNA


title: Dlx4-WT P1#2


title: Dlx4-KO P60#2


title: icKO_1week_Der_1


title: WT_1week_Epi_1


title: WT Rep1

description: small RNA

value: WT  (Col)


title: icKO_1week_Epi_1


title: icKO_1week_Epi_2


title: WT_1week_Der_2


title: WT_3day_Epi_4


title: WT_3day_Epi_3


title: icKO_Epi_3day_1


title: Primary ABC, DKO, replicate 2 (ATAC-Seq)

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

data_processing:
Pair-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500.  Read quality was evaluated using FASTQC.
RNAseq: 50-bp paired reads were mapped to annotated mouse genome (mm10, build 38.75, 41,128 genes and 87,108 transcripts) with CLC Bio Genomic Workbench 7.5 software (Qiagen). Duplicated reads with more than 5 copies were discarded
RNAseq: Read count tables were created using using unique exon read counts and the differential expression was analyzed using EDGER (Bioconductor). Genes with the expression levels less than 1 cpm in at least three conditions were considered non-expressing and removed from further analysis. A negative binomial generalized log-linear model was fit to read counts for each gene. A likelihood ratio tests with the null hypothesis that the pairwise contrasts of the coefficients are equal to zero was used to evaluate the significance of differences in expression between analyzed groups. Benjamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with a FDR)-corrected p-value > 0.01 and less than 2 fold change were filtered out. Genes that passed the filtering were considered to be differentially expressed.
ATAC-seq: We used the makeTagDirectory  followed by findPeaks command from HOMER version 4.7.2 (http://homer. salk.edu/homer/) to  identify peaks of ATAC-seq. A false discovery rate (FDR) threshold of 0.001 was used for all data  sets. The following HOMER command was used: cmd = findPeaks <sample tag directory> -style  factor or histone -o <output file> -i <input tag directory>. The total number of mapped reads in each  sample was normalized to ten million mapped reads
Genome_build: mm10, build 38.75
Supplementary_files_format_and_content: comma-separated values, containing the expression values (log-transformed cpm), nominal and FDR-corrected pavalues and fold changes for all processed samples

source_name: Splenocytes

growth_protocol: C57BL/6 mice and DKO mice were maintained in the Hospital for Special Surgery Animal Facility in full compliance with institutional guidelines approved by the HSS Animal Care and Use Committee.

extract_protocol:
RNA-seq:Total RNA was isolated using QIAGEN RNAeasy plus mini kit from FACS sorted FoB or ABC cells
ATAC-seq:  The nuclei of sorted DKO ABC or DKO Follicular B cells  were prepared by incubation of cells with nuclear preparation buffer (0.30 M sucrose, 10 mM Tris, pH  7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM spermine, 0.5 mM  spermidine and 2 mM 6AA)
RNA-seq: Sequence-compatible libraries were prepared using Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library preparation at the Weil Cornell Epigenomics core. Quality of all RNA and library preparations were evaluated with BioAnalyser 2100 (Agilent)
ATAC-seq: Sequencing libraries were constructed as discribed in PMID: 26083756 :Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang  HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of  regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:  10.1038/nature14590. Epub 2015 Jun 17. PubMed PMID: 26083756; PubMed Central  PMCID: PMC4685948.

tag: strain/genotype

value: > 20 weeks

tag: Sex

value: female

value: spleen

tag: sorting strategy

tag: cell type

value: Primary Age/autoimmune-associated B cells


title: Primary Follicular B cells, DKO, replicate 1 (ATAC-Seq)

tag: age

value: Primary Follicular B cells


title: Primary ABC, DKO, replicate 3


title: Primary ABC, DKO, replicate 2


title: Primary ABC, DKO, replicate 1


title: Primary Follicular B cells, DKO, replicate 3


title: WT_1week_Der_1

value: mixed background

tag: genotype


title: Primary Follicular B cells, DKO, replicate 2


title: Primary Follicular B cells, DKO, replicate 1


title: human_kidney_5hmC

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

description: mapped reads (Hg19) were binned across 150bp windows.

data_processing:
Reads mapped to Hg19 build
Data binned into 150bp windows across the genome
Data converted into wiggle (.wig) file
data normalised by read count
enriched (5hmC) datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: Hg19

source_name: Kidney

extract_protocol:
Sheared gDNA was enriched using antibodies against 5hmC (Active Motif , cat# 39769) prior to enrichment through magnetic IgG beads. Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 15 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

tag: gender

value: Male

value: kidney

tag: genotype/variation

value: wild type

tag: antibody

value: 5-hmC - Active Motif (cat# 39769)


title: Primary Follicular B cells, WT, replicate 2


title: Primary Follicular B cells, WT, replicate 1


title: Primary Follicular B cells, DKO, replicate 2 (ATAC-Seq)


title: B3

data_processing:
The read were trimmed for the Illumina truseq adapter using CLC Bio / Custom script adaptertrimmer.pl using the Illumina Truseq adapter’s 19 bp adjecent to the insert also known as  ‘TGGAATTCTCGGGTGCCAA’. Keeping the > 16 bp long reads.
The data was further processed using commandline tools, custom scripts and the MirDeep2.0.0.5 package (Friedlander et al. 2008, https://www.mdc-berlin.de/38350089/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/older_miRDeep2_versions/mirdeep2_0_0_5.zip)
Genome_build: UCSC hg19 and mirbase version 21 for mirna annotation.
Supplementary_files_format_and_content: Total read counts per sample were normalized to 1 million. Read counts for miRNAs with identical mature sequences were merged. A total of 252 miRNAs were present in at least 3 out of 12 samples with a read count >10 rpm.

source_name: Young_high PD

growth_protocol: T cell clones were generated from phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMC) by limiting dilution in the presence of IL-2 and pooled irradiated PBMC feeder cells as previously described (Pawelec G, Rehbein A, Haehnel K, et al. Human T-cell clones in long-term culture as a model of immunosenescence. Immunol Rev. 1997;160:31-42.).

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands) following the manufacturer’s instructions. Micro Bio-SpinTM chromatography columns, supplied with Bio-Gel P-6 polyacrilyamide gel matrices, were applied to maximize purity of the RNA samples (Bio-Rad laboratories B.V. Veenendaal, The Netherlands).
Small RNA libraries were generated from 2,000ng total RNA using TruSeq Small RNA Sample Preparation Kit and TruSeq small RNA indices (Illumina, San Diego, CA, USA).

tag: donor id

tag: population doublings(pd)

value: T-cell clone

tag: clone id


title: D2

source_name: Old_high PD


title: D1


title: C3

source_name: Old_low PD


title: Primary ABC, DKO, replicate 1 (ATAC-Seq)


title: C2


title: A1

source_name: Young_low PD

value: clone 454-6


title: A3


title: A2


title: human_kidney_5hmC input

value: input


title: B1


title: C1


title: D3


title: B2


title: Day120 rep4

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using tophat2 (version 2.8.0) with default parameters.
Aligned seqeunces were converted relative expression using cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.

source_name: Transplanted islet day 120-4

extract_protocol:
RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns (Qiagen). RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 or Agilent 2200 TapeStation equipment, and 10 ng of total RNA was used with SMARTer Ultra Low Input RNA Kit v3 for Illumina Sequencing (Clontech) for cDNA synthesis.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina.  Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1500 following the manufacturer's protocols.

tag: strain

value: islet

tag: sample type

value: Transplanted islet day 120


title: Day120 rep2

source_name: Transplanted islet day 120-2


title: Day120 rep1

source_name: Transplanted islet day 120-1


title: Day60 rep3

source_name: Transplanted islet day 60-3

value: Transplanted islet day 60


title: Day60 rep4

source_name: Transplanted islet day 60-4


title: Day60 rep2

source_name: Transplanted islet day 60-2


title: Day120 rep3

source_name: Transplanted islet day 120-3


title: Islet rep4

source_name: Isolated islet-4

value: Isolated islet


title: Day60 rep1

source_name: Transplanted islet day 60-1


title: Islet rep2

source_name: Isolated islet-2


title: Islet rep3

source_name: Isolated islet-3


title: hd2bhd2c-RNA-rep1

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.bedtools was used to generate bedGraph file; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
RIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to rRNA sequence first, unmapped reads were mapped to TAIR10 genome by Tophat. Accepcted bam files are converted to bedGraph files by Bedtools; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
RNAseq fpkm were generated by tophat and cufflink by following Trapnell et al.(2012).
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq (txt file: gene fpkm); ChIP-seq(BigWig file)

source_name: seedling

growth_protocol: Arabidopsis plants were grown on soil at 21 degree under continuous light.

extract_protocol:
RNA isolated with Trizol (ThermoFisher, 15596026)
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850; RIP protocols were followed by Bohmdorfer et al., eLife, 5:e19092, 2016; RNA was extracted by Trizol (ThermoFisher, 15596026) following the manufacturer’s instructions.
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330) and Illumina Truseq RNA Library Prep Kit v2 (RS-122-2001), respectivly.

value: seedling

value: hd2b hd2c double mutant

tag: developmental stage

value: 6 day seedling


title: Col-RNA-rep2

value: wild type Columbia-0


title: HD2C-FLAG-CHIP

source_name: Leaf

extract_protocol:
Genomic DNA isolated from immunoprecipitated chromatin using FLAG bedas (Sigma, M8823)
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850; RIP protocols were followed by Bohmdorfer et al., eLife, 5:e19092, 2016; RNA was extracted by Trizol (ThermoFisher, 15596026) following the manufacturer’s instructions.
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330) and Illumina Truseq RNA Library Prep Kit v2 (RS-122-2001), respectivly.

value: Leaf

value: HD2C-FLAG transgenic in hd2c mutant background

value: FLAG bedas (Sigma, M8823)


title: hd2c-H4K16Ac

extract_protocol:
Genomic DNA isolated from immunoprecipitated chromatin using H4K16ac antibody (Millipore, 07-329)
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850; RIP protocols were followed by Bohmdorfer et al., eLife, 5:e19092, 2016; RNA was extracted by Trizol (ThermoFisher, 15596026) following the manufacturer’s instructions.
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330) and Illumina Truseq RNA Library Prep Kit v2 (RS-122-2001), respectivly.

value: hd2c mutant

value: H4K16ac antibody (Millipore, 07-329)


title: Col-H4K16Ac


title: hd2bhd2c-RNA-rep2


title: Col-RNA-rep1


title: Col-0  rosettes  -Fe-Cu Rep2

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie -v 2 -S -a --best --strata
Reads counts for genes were obtained by HTSeq-count
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is for gene IDs and the second column is for reads counts

source_name: Rosettes

growth_protocol: Seeds of Arabidopsis thaliana ecotype Col-0 and mutant spl7 (SALK_109908c) were obtained from the Arabidopsis Biological Resource Center (The Ohio State University). Seeds were imbibed in 0.1% agar at 4°C for 3d. Seeds were planted onto rockwool loosely packed into 1.5ml centrifuge tubes with the bottoms removed. The tubes were inserted in trays in containers of nutrient solution, composed of: 0.8 mM KNO3, 0.4mM Ca(NO3)2, 0.3 mM NH4H2PO4, 0.2 mM MgSO4, 25 μM Fe(III)-EDDHA, 25 μMCaCl2, 25 μM H3BO3, 2 μM MnCl2, 2 μM ZnSO4,0.1 μM CuSO4, 0.5 μM Na2MoO4, and 1 mM MES buffer (pH 5.5). Lighting was provided at a photoperiod of 16h of 150μmol m-2 s-1, 4100K fluorescent light. After 10d, seedlings were transferred to wells in lids of containers containing 0.75 liters of the same nutrient solution (16 plants per container) with constant aeration for an additional 14 days before plants were transferred to treatments.

extract_protocol:
Total RNA was isolated from roots and rosettes using the Plant RNeasy kit (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The pretreatment conditions for growing  Col-0 and spl7 was 25 μM Fe and 0.1 μM Cu, and rescue pretreatment for spl7 was 25 μM Fe and 2.5 μM Cu. In the spl7 RNA-seq experiment, the plants were switched to four treatments: 25 uM Fe, 0.5 uM Cu (control); 25 uM Fe, 0 Cu (-Cu); 0 Fe, 0.5 uM Cu (-Fe); 0 Fe, 0 Cu (-Fe/-Cu); for 3 days. The remaining nutrients were at the same concentrations as described in the growth protocol. Three biological replicates of rosettes and roots were collected after 3 days of treatments and quickly frozen in liquid nitrogen and stored in -80°c.

value: Rosettes

value: Col-0 (WT)

tag: pre-treatment

value: 25 μM Fe, 0.1 μM Cu

tag: treatment

value: -Fe, -Cu


title: spl7  rosettes -Fe-Cu Rep2

tag: tissue

value: 25 μM Fe, 2.5 μM Cu


title: spl7  rosettes -Fe-Cu Rep1


title: HD2C-FLAG-RIP

extract_protocol:
RNA isolated by immunoprecipitation using FLAG bedas (Sigma, M8823)
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850; RIP protocols were followed by Bohmdorfer et al., eLife, 5:e19092, 2016; RNA was extracted by Trizol (ThermoFisher, 15596026) following the manufacturer’s instructions.
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330) and Illumina Truseq RNA Library Prep Kit v2 (RS-122-2001), respectivly.


title: Col-CK-RIP

value: wild type


title: spl7  rosettes  -Fe+Cu Rep2

value: -Fe, +Cu


title: spl7  rosettes  -Fe+Cu Rep1


title: spl7  rosettes  -Fe+Cu Rep3


title: Col-0  rosettes  -Fe-Cu Rep3


title: Col-0  rosettes  -Fe-Cu Rep1


title: Islet rep1

source_name: Isolated islet-1

value: islet

value: Isolated islet


title: spl7  rosettes -Fe-Cu Rep3


title: Col-0  rosettes  -Fe+Cu Rep3


title: Col-0  rosettes  -Fe+Cu Rep2


title: Col-0  rosettes  -Fe+Cu Rep1


title: spl7  rosettes  +Fe-Cu Rep3

value: +Fe, -Cu


title: spl7  rosettes  +Fe-Cu Rep2


title: Col-0   rosettes  +Fe-Cu Rep3


title: spl7  rosettes  +Fe-Cu Rep1


title: Col-0   rosettes  +Fe-Cu Rep2


title: Col-0   rosettes  +Fe-Cu Rep1


title: spl7  rosettes  +Fe+Cu Rep3

value: +Fe, +Cu


title: spl7  rosettes  +Fe+Cu Rep2


title: spl7  rosettes  +Fe+Cu Rep1


title: spl7  rosettes  +Fe+Cu Rep2 Ex


title: spl7  rosettes  +Fe+Cu Rep1 Ex


title: spl7  rosettes  +Fe+Cu Rep3 Ex


title: Col-0  rosettes +Fe+Cu Rep3


title: spl7 root -Fe-Cu Rep2

source_name: Root

value: Root


title: Col-0  rosettes +Fe+Cu Rep1


title: Col-0  rosettes +Fe+Cu Rep2


title: Col-0 root -Fe-Cu Rep2


title: Col-0 root -Fe-Cu Rep3


title: Col-0 root -Fe+Cu Rep3


title: Col-0 root -Fe+Cu Rep1


title: spl7 root +Fe-Cu Rep2


title: spl7 root +Fe-Cu Rep3


title: Col-0 root -Fe+Cu Rep2


title: spl7 root -Fe+Cu Rep2


title: spl7 root -Fe+Cu Rep1


title: spl7 root +Fe-Cu Rep1


title: Col-0  root +Fe-Cu Rep2


title: Col-0  root +Fe-Cu Rep1


title: Col-0  root +Fe-Cu Rep3


title: spl7 root +Fe+Cu Rep3


title: spl7 root +Fe+Cu Rep2


title: spl7 root +Fe+Cu Rep3 Ex


title: spl7 root +Fe+Cu Rep1


title: spl7 root -Fe-Cu Rep3


title: spl7 root -Fe-Cu Rep1


title: spl7 root +Fe+Cu Rep1 Ex


title: spl7 root -Fe+Cu Rep3


title: spl7 root +Fe+Cu Rep2 Ex


title: Col-0  root +Fe+Cu Rep2


title: Col-0 root -Fe-Cu Rep1


title: Col-0  root +Fe+Cu Rep3


title: miR-211-KO rep6

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

data_processing:
Reads were aligned and assigned to Gencode Mouse released M4 transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: Gencode Mouse released M4
Supplementary_files_format_and_content: tab-delimited text files include raw counts and  RPKM values for each Sample

source_name: Whole eye (after removal of the lens and cornea)

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (500 ng) from each sample was prepared using TruSeq RNA sample prep reagents (Illumina, San Diego, CA, USA) according to manufacturer's instructions
The amplified fragmented cDNA of ∼200 bp in size were sequenced in paired-end mode using the HiSeq 1000 (Illumina) with a read length of 2×100 bp

value: whole eye including retina, RPE, Choroid, sclera and ciliary body, whereas the lens and cornea were removed.

tag: background strain


title: Col-0  root +Fe+Cu Rep1


title: miR-211-KO rep2


title: miR-211-KO rep5


title: miR-211-KO rep4


title: WT rep5


title: WT rep4


title: WT rep2


title: miR-211-KO rep1


title: miR-211-KO rep3


title: WT rep3


title: WT rep1


title: MC2_Input

city: Denver

first: Hua

last: Huang

state: CO

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

description:
Input replicate 2 (for H3K27ac IP rep2)
Processed data file: MC2_H3K27ac_VS_Input_q0.001_peaks.xls

data_processing:
Reads were aligned to the mouse mm9 reference genome using Torrent Suite v4.4.6 for the H3K4me1 samples and v5.0.4 for the H3K27ac samples using default parameters.
Peaks were identified by comparison with matched input DNA using MACS version 2.0.10.20130306 (tag:beta) for H3K4me1 and v2.1.1.20160309 for H3K27ac with a q-value threshold of 0.001 (macs2 callpeak -t .. -c .. -f BAM -g mm -n ... -q 0.001 -B --SPMR).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.xls (Excel) files: Peaks from which BED files can be made.
Supplementary_files_format_and_content: *.bedgraph files: Output by MACS2 with parameter settings as described above (macs2 callpeak -t .. -c .. -f BAM -g mm -n ... -q 0.001 -B --SPMR).

source_name: BMMCs, input

growth_protocol: Bone marrow-derived mast cells (BMMCs) were cultured from bone marrow cells collected from tibias and femurs of 6- to 8-week-old mice. Cells were cultured in Iscove's modified Dulbecco's medium supplemented with 10% FBS, 50 uM 2-ME, 100 units/ml penicillin, and 100 ug/ml streptomycin and 20ng/ml of recombinant mIL-3 for 4 weeks. Greater than 99% of BMMCs were mast cells (FcεRI+ c-Kit+) as determined by FACS analysis.

extract_protocol:
Cells were cross-linked with 1% formaldehyde, lysed, and sonicated. Sonicated DNA fragments that bound to H3K4me1 or H3K27ac were immunoprecipitated with anti-H3K4me1 antibody or anti-H3K27ac antibody, respectively.
The immunoprecipitated DNA was repaired, ligated to adapters, and size selected with the Ion Plus Fragment Library Kit (#4471252, Thermo Fisher Scientific, Waltham, MA) according to the Ion ChIP-Seq Library Preparation protocol. Libraries were analyzed for size and quantity using the High Sensitivity Bioanalyzer Kit (#5067-4626, Agilent Technologies, Santa Clara, CA). The ChIP library was sequenced on an Ion Torrent Proton Semiconductor Sequencer.

tag: strain/background

value: Bone marrow-derived mast cells

tag: chip antibody


title: MC5_H3K4me1

description:
H3K4me1 IP replicate 2
Processed data file: MC5_H3K4me1_VS_Input_q0.001_peaks.xls

source_name: BMMCs, H3K4me1 ChIP

tag: cell type

value: anti-H3K4me1 antibody (ab8895, Abcam, Cambridge, MA)


title: MC4_H3K4me1

description:
H3K4me1 IP replicate 1
Processed data file: MC4_H3K4me1_VS_Input_q0.001_peaks.xls


title: MC3_Input

description:
Input replicate 3 (for H3K27ac IP rep3)
Processed data file: MC3_H3K27ac_VS_Input_q0.001_peaks.xls


title: MC4_Input

description:
Input replicate 1 (for H3K4me1 rep 1)
Processed data file: MC4_H3K4me1_VS_Input_q0.001_peaks.xls


title: MC5_Input

description:
Input replicate 2 (for H3K4me1 rep2)
Processed data file: MC5_H3K4me1_VS_Input_q0.001_peaks.xls


title: MC2_H3K27ac

description:
H3K27ac IP replicate 2
Processed data file: MC2_H3K27ac_VS_Input_q0.001_peaks.xls

source_name: BMMCs, H3K27ac ChIP

value: anti-H3K27ac antibody (ab4729, Abcam, Cambridge, MA)


title: MC1_Input

description:
Input replicate 1 (for H3K27ac IP rep 1)
Processed data file: MC1_H3K27ac_VS_Input_q0.001_peaks.xls


title: Patient 17 17T (RNA-seq)

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

description: rRNA depleted, RNAse R treated total RNA

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Quality control was conducted by using fastQC,  after quality control,fastx_trimmer was used to trim adaptor or bad quality sequence (10-120bp was kept), then published find_circ pipeline was used to predict circRNA candidates as the paper described
the function of intersect of bedtools was used to annotate the circRNA to circbase
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include mapped reads count by find_circ for each Sample

source_name: cervical tumor

extract_protocol:
tumor samples and normal tissues were collected from the Oncology Department of the Second Affiliated Hospital of Zhen Zhou University by related surgeons. Plasma samples were isolated by EDTA and centrifuged at 820 ×g for 10 min. The postoperative samples were collected 2 to 34 days after surgery.
RNA libraries were prepared for sequencing using standard Illumina protocols,except rRNA depleted, RNAse R treated before library construction

value: cervical tumor


title: Patient 4 4T (RNA-seq)


title: MC1_H3K27ac

description:
H3K27ac IP replicate 1
Processed data file: MC1_H3K27ac_VS_Input_q0.001_peaks.xls


title: Patient 16 16T (RNA-seq)


title: Patient 16 16N (RNA-seq)

source_name: adjacent normal

value: adjacent normal


title: Patient 17 17N (RNA-seq)


title: Patient 3 3T (RNA-seq)


title: Patient 3 3N (RNA-seq)


title: Patient 4 4N (RNA-seq)


title: Patient 1 1T (RNA-seq)


title: MC3_H3K27ac

description:
H3K27ac IP replicate 3
Processed data file: MC3_H3K27ac_VS_Input_q0.001_peaks.xls


title: Patient 1 1N (RNA-seq)


title: PTL_20_Pax_mRNA

city: Seattle

first: alison

middle: g

last: paquette

state: WA

address: 401 Terry Avenue N

institute: Institute of Systems Biology

description: ProcessedWBFORGEO.txt

data_processing:
Basecalls were performed using bcl2fastq2 v2.17.
Transcript abundances were calculated using the pseudo aligment method Kallisto, without bias, bootstrapping 100 permutations over 16 cores
Transcripts were filtered so that low expressing samples (mean read count <20), or mostly unexpressed (>50% of samples NA) transcripts were removed prior to preprocessing
Relative transcript abundances were calculated using the trimmed mean of M method, implimented within EdgeR, as described by M Robinson, A Oshlack, Genome Biology 2010
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files contain count values generated from Kallisto for each sample

source_name: Whole Blood

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes using microRNA isolation kit (Qiagen) using TRIsol LS (Invitrogen) following manufacturer’s instructions.
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol.400 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94oC and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98oC for 10 seconds, followed by 15 cycles of 98oC for 10 seconds, 60oC for 30 seconds and 72oC for 30 seconds, and finally an extension step for 5 minutes at 72oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).
Libraries were pooled in equimolar quantities and paired-end sequenced on a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 126-bases in length.

tag: condition

value: Preterm Delivery


title: PTL_4_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_3_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_6_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_5_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_19_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_12_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_17_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_13_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_14_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_15_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_11_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_9_Pax_mRNA

description: ProcessedWBFORGEO.txt

value: Term Delivery


title: CON_44_PAX_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_10_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_8_PAX_mRNA

description: ProcessedWBFORGEO.txt


title: CON_33_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_35_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_40_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_31_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_39_PAX_mRNA

description: ProcessedWBFORGEO.txt


title: CON_34_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_26_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_32_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_9_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_24_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_29_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_22_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_18_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_20_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_18_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_17_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_14_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_16_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_19_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_1_PAX_mRNA

description: ProcessedWBFORGEO.txt


title: CON_10_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: PTL_4_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt

source_name: Monocytes

extract_protocol:
RNA was isolated from from peripheral monocytes (separated by Monocyte RosetteSep cocktail) using TRIsol LS (Invitrogen) following manufacturer’s instructions.
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol. Briefly, 400 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94oC and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98oC for 10 seconds, followed by 15 cycles of 98oC for 10 seconds, 60oC for 30 seconds and 72oC for 30 seconds, and finally an extension step for 5 minutes at 72oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).
Libraries were pooled in equimolar quantities and paired-end sequenced on a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 126-bases in length.


title: PTL_20_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_5_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_6_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_9_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_19_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_15_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_11_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_8_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_9_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_17_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_49_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_46_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_39_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_45_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_42_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_44_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_13_Pax_mRNA

description: ProcessedWBFORGEO.txt


title: CON_35_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_41_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_40_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_38_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_32_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_33_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_29_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_31_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_22_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_24_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: PTL_18_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_20_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_10_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_13_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_16_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_1_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_17_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_34_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: LM2 ABL2 shRNA

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Quality control was conducted by using fastQC,  after quality control, only R1 were used, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to hg38 whole genome using tophat
HTSeq v0.6.0 were used to count the reads mapped
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mapped reads count by HTSeq for each Sample ...

source_name: LM2 ABL2 shRNA

growth_protocol: LM2 cells were cultured in DMEM with 10% FBS

extract_protocol:
RNA was harvested using Trizon reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To consturct stable cell lines,LM2 cells were incubated 48 h with lentiviral medium containing Scr, single or double inactivation of ABL1 and ABL2-specific shRNAs in the presence of 8ug/mL Polybrene. To get the compound challenging samples，The LM2 cells were treated with Ponatinib at 1μM for 6h.

tag: cell line

value: Triple negative breast cancer

tag: metastasis

value: Lung specific Metastasis

tag: treated with

value: knockdown ABL2


title: LM2 Scrambled shRNA

source_name: LM2 Scrambled shRNA

value: knockdown Scramble


title: LM2 ABL1/ABL2 shRNA

source_name: LM2 ABL1/ABL2 shRNA

value: knockdown ABL1/2


title: LM2 Ponatinib repeat2

source_name: LM2 Ponatinib

value: Ponatinib


title: LM2 Control repeat1

source_name: LM2 Control

value: DMSO


title: CON_19_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_18_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: CON_26_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: LM2 Control repeat2


title: LM2 Ponatinib repeat1


title: Non-neoplastic liver tissue of P94

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequence reads were aligned to human transcript reference sequences from the ENSEMBLE database (Homo_sapiens.GRCh37.55.cdna.all.fa) for the expression analysis at gene/transcript levels using TopHat and HTSeq softwares
Genome_build: hg19 reference genome for human
Supplementary_files_format_and_content: tab-delimited text file including RPKM values of each gene for each Sample

source_name: Non-neoplastic liver tissue

extract_protocol:
Total RNA (1-3μg/sample) extracted from surgical resection specimens were submitted to the Mount Sinai Genomic Core Facility for quality control analysis. The RNA quality was assessed using the Agilent 2100 Bioanalyzer, and the RNA integrity number for all 21 samples measured 8.2 ± 0.7 (mean ± SD). The poly(A)-RNA was captured using oligo-dT beads and used for cDNA library preparation using the standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Briefly, total RNA was poly-A selected and then fragmented.
The cDNA was synthesized using random hexamers, end-repaired and ligated with appropriate adaptors for sequencing. The library then underwent size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina recommended 6 bp barcode bases are introduced at one end of the adaptors during PCR amplification step. The size and concentration of the RNAseq libraried was measured by Bioanalyzer and Oubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer. The mRNA libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide paired-end reads, according to the standard manufacturer’s protocol (Illumina, CA, USA).

value: Non-neoplastic liver tissue

tag: disease state

value: HBV-HCC


title: Tumor tissue of P94

source_name: Tumor tissue

value: Tumor tissue


title: Non-neoplastic liver tissue of P99


title: Tumor tissue of P75


title: Non-neoplastic liver tissue of P6


title: Non-neoplastic liver tissue of P62


title: Tumor tissue of P6


title: Tumor tissue of P176


title: Non-neoplastic liver tissue of P176


title: Non-neoplastic liver tissue of P49


title: CON_47_Monocyte_mRNA

description: ProcessedMONOFORGEO.txt


title: Tumor tissue of P62


title: Tumor tissue of P179


title: LM2 ABL1 shRNA

source_name: LM2 ABL1 shRNA

value: knockdown ABL1


title: Non-neoplastic liver tissue of P179


title: Non-neoplastic liver tissue of P171


title: Tumor tissue of P171


title: Tumor tissue of P99


title: Tumor tissue of P170


title: Non-neoplastic liver tissue of P170


title: Non-neoplastic liver tissue of P75


title: Non-neoplastic liver tissue of P16


title: ddl-1 Rep 1

description: small RNA

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie -v 0 -S -a --best --strata
In the processed data fles, we report only the high confidence miRNAs.
Genome_build: TAIR10
Supplementary_files_format_and_content: Space-delimited plain text files: the first column is MicroRNA gene IDs and the second column is normalized reads counts

source_name: inflorescence

extract_protocol:
Flower inflorescences were collected and total RNA was extracted by Trizol. Illumina TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Illumina small RNA library protocol

tag: ecotype

value: Wassilewskija (WS)

value: inflorescence

tag: genotype


title: Tumor tissue of P49


title: Ws WT Rep1

description: small RNA

value: WT


title: Ws WT Rep2

description: small RNA


title: Tumor tissue of P161


title: Tumor tissue of P16


title: cdc5-1 Rep 2

description: small RNA

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each miRNA with trimmed mean of M values (TMM) normalization method. Robinson and Oshlack Genome Biology 2010.
As this study examines the function of CDC5 (which is important for the precision of processing of miRNAs), we only consider the high confidence miRNAs.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is MicroRNA gene IDs (for high confidence miRNAs) and the second column is normalized reads counts

value: Columbia (Col)


title: cdc5-1 Rep 1

description: small RNA


title: ddl-1 Rep 2

description: small RNA


title: Non-neoplastic liver tissue of P157


title: Tumor tissue of P157


title: Tumor tissue of P158


title: Col WT Rep1

description: small RNA


title: Col WT Rep2

description: small RNA


title: Non-neoplastic liver tissue of P152


title: Tumor tissue of P140


title: Tumor tissue of P138


title: Non-neoplastic liver tissue of P131


title: Non-neoplastic liver tissue of P112


title: Non-neoplastic liver tissue of P106


title: Tumor tissue of P112


title: Tumor tissue of P106


title: Non-neoplastic liver tissue of P105


title: Non-neoplastic liver tissue of P158


title: Tumor tissue of P105


title: RNA ΔcrRNA3

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Fastq to fasta conversion using FastX version 0.0.13
Poly(A)-trimming from the 3’ end (READemption 0.4.3, Förstner et al., 2014)
Size filtering: discarding reads shorter than 12 nt (READemption 0.4.3, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0 (READemption 0.4.3, Förstner et al., 2014)
Coverage calculation (coverage-raw, READemption  0.4.3, Förstner et al., 2014)
Genome_build: C. jejuni NCTC11168 (NC_002163.1)
Supplementary_files_format_and_content: wiggle

organism: Campylobacter jejuni

source_name: Campylobacter jejuni NCTC11168 cells

growth_protocol: C. jejuni strains were grown to mid-exponential phase (~0.6 OD600) in Brucella Broth. Cells corresponding to 4 or 60 OD600 were collected to extract total RNA or perform  coIP, respectively.

extract_protocol:
Phenol/Chloroform/Isoamyl alcohol RNA extraction (Rieder et. al., RNA Biology 2012)
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina.

treatment_protocol: For the coIP cells were lysed and anti-FLAG antibody (Sigma-Aldrich, #F1804) along with Protein A-sepharose beads (Sigma, #P6649) were used to co-immunoprecipitate Cas9-3xFLAG and bound RNA.

tag: strain

tag: genotype/variation

value: delta crRNA3


title: RNA Δcas9

value: delta cas9


title: Tumor tissue of P152


title: RNA ΔCRISPR-tracrRNA

value: delta CRISPR-tracrRNA


title: coIP CJ Δcr3 Cas9-3xFLAG

description:
Cas9-bound RNA
signal sample

value: delta_cr3 Cas9-3xFLAG


title: RNA WT NCTC11168


title: coIP CJ Δcr3

description:
Unspecifically-bound RNA
background control sample


title: Non-neoplastic liver tissue of P140


title: Tumor tissue of P131


title: Non-neoplastic liver tissue of P138


title: coIP CJ Cas9-3xFLAG

description:
Cas9-bound RNA
signal sample


title: Locked_disc

city: Montreal

first: Karl

middle: JL

last: Fernandes

state: Quebec

address: 900 Rue St-Denis, R09-474

department: Neurosciences

country: Canada

institute: Université de Montréal

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for sequencing adapters and mapped to the reference genome using Tophat 2.0.10
Readcounts were computed using HTSeq-count and the intersection-strict mode of read assignment
Readcounts were then normalized and converted to log2 values using the rlogTransformation implemented in DESeq2 version 1.10.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include normalized log2 readcount values for each sample. Columns are: Gene, log2Readcount.

source_name: Dentate gyrus

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Sample Preparation (Illumina)

tag: age

value: 4 months

value: Wild-type


title: Low_runners


title: PRY-1_mu38_L1_T_RNA_R1

city: boston

first: Ayush

middle: Vasant

last: Ranawade

state: MA

address: 360 Huntington Ave

department: Bioengineering

institute: Northeastern University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.  The sequence reads that passed quality filters were analyzed using ce6 with Burrows–Wheeler Aligner (BWA) with default parameters followed by eXpress to estimate transcript abundances. Differentially-expressed genes were called at a false discovery rate (FDR) of 0.05% using the DESeq package in R.
Genome_build: C elegans ucsc ce6
Supplementary_files_format_and_content: excel file contains list of differentially expressed with fold change that passed false discovery rate of 0.05
Supplementary_files_format_and_content: raw counts for all genes

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Standard NGM growth media condition at 20 degrees

extract_protocol:
Synchronized L1 stage animals were obtained by bleach treatment and RNA was isolated using the Trizol RNA extraction method
RNA libraries were prepared for sequencing using standard Illumina  TruSeq RNA Sample Preparation v2 high-throughput (HT) protocol.
RNA-Seq 100 bp cDNA library

treatment_protocol: Twice bleached synchronized

tag: developmental stage


title: Exercise


title: Complex_Environment


title: N2_L1_T_RNA_R2

value: N2 wildtype


title: N2_L1_T_RNA_R1


title: KLPH/lctl KO [sample 2]

first: Jianguo

last: Fan

state: MD

address: 6 Center Drive Rm 108A

institute: National Eye Institute

data_processing:
Differential mRNA expression between KLPH/lctl  knockout mice and age matched C57bl6/J control mice was quantified by RNA-seq data analysis using the Tuxedo package (i.e. the Tophat-Cufflinks pipeline) on the NIH Biowulf high performance computing platform.
Alignment was performed by use of Tophat version 2.1.1 (Bowtie2) and the mouse10 reference genome (NCBI) with standard parameters. Cufflinks version 2.2.1 was used to assemble the transcriptomes and CuffDiff was used to quantify the levels of gene expression in Reads Per Kilobase of transcript per Million mapped reads (RPKM).
False discovery rate (FDR) value of less than or equal to 0.1 was used as the criteria for “significant” differentially regulated genes.
Output files from Cuffdif was uploaded as the processed data files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene, "1" refers to wild type and "2" refers to KLPH/lctl KO.

growth_protocol: DNA-free total RNA was prepared from a pool of lenses from 5 KLPH/lctl KO or age-matched C57bl6/J control mice, by use of PureLink RNA Mini Kit and TRIzol Reagent (Life Technologies)

extract_protocol:
RNA integrity was evaluated by 2100 Bioanalyzer (Agilent Technologies) with RIN no less than 7. RNA-seq was performed by NIH Intramural Sequencing Center (Bethesda, MD).
One paired end index library from each polyA(+)-selected RNA samples was prepared. Six samples were pooled and loaded on 2 lane(s) of Illumina HiSeq 2000 Sequencer, and run as paired end index 100 base reads with a total of 40 million base read pairs per sample.
Differential mRNA expression between KLPH/lctl  knockout mice and age matched C57bl6/J control mice was quantified by RNA-seq data analysis using the Tuxedo package (i.e. the Tophat-Cufflinks pipeline) on the NIH Biowulf high performance computing platform.

treatment_protocol: and on-column DNase treatment with PureLink Dnase (Life Technologies) according to manufacturer’s instructions.

value: KLPH/lctl KO

value: 6 weeks

value: lens


title: Non-neoplastic liver tissue of P161

value: Non-neoplastic liver tissue

value: HBV-HCC


title: wild type [sample 1]

value: wild type


title: High_runners


title: ZFP36_KO_Th1_3d_1

first: Robert

last: Darnell

address: 1230 York Ave

institute: Rockefeller University

data_processing:
alignment with STAR
feature counts with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: read counts in tabular format (txt) with ensembl gene IDs, gene information, and read counts per sample

source_name: CD4+ T-cells

growth_protocol: CD4+ T-cells were sorted from pooled spleen and lymph nodes of WT or Zfp36 KO mice and activated with anti-CD3 antibody in the presence of formalin-fixed WT bone-marrow-derived dendritic cells, under Th1 polarizing conditions (10U/ml hIL-2 and 5 ng/ml mIL-12).  Cells were harvested at 4 hours or 3 days after activation.  Cells harvested on day 3 were first re-stimulated for 2 hours with PMA (20ng/ml) and ionomycin (1mM).

extract_protocol:
Trizol extraction followed by HiPure RNA column (Roche) with DNAse treatment.
Illumina High-throughput TruSeq RNA Sample preparation after riboZero depletion of rRNA (Illumina)

value: Zfp36 KO

tag: time point

value: 3 days

tag: biol. rep.


title: ZFP36_KO_Th1_3d_2

treatment_protocol: CD4+ T-cells were sorted from pooled spleen and lymph nodes of WT or Zfp36 KO mice and activated with anti-CD3 antibody in the presence of formalin-fixed WT bone-marrow-derived dendritic cells, under Th1 polarizing conditions (10U/ml hIL-2 and 5 ng/ml mIL-12).  Cells were harvested at 4 hours or 3 days after activation.  Cells harvested on day 3 were first re-stimulated for 2 hours with PMA (20ng/ml) and ionomycin (1mM).


title: ZFP36_KO_Th1_3d_3


title: WT_Th1_3d_3

value: WT


title: PRY-1_mu38_L1_T_RNA_R2


title: WT_Th1_3d_1


title: ZFP36_KO_Th1_4h_4

value: 4 hours


title: WT_Th1_3d_2


title: coIP CJ WT


title: ZFP36_KO_Th1_4h_3


title: WT_Th1_4h_4


title: ZFP36_KO_Th1_4h_1


title: ZFP36_KO_Th1_4h_2


title: WT_Th1_4h_3


title: WT_Th1_4h_2


title: WT_Th1_4h_1


title: H3K4me3 replicate 2 Input DNA

city: Bronx

first: Kami

last: Kim

address: 1300 Morris Park Avenue

department: Medicine

institute: Albert Einstein College of Medicine

description: Mnase-digested DNA

data_processing:
Adapter sequences were trimmed using cutadapt (https://cutadapt.readthedocs.io/en/stable/) and aligned to the T. gondii ME49 genome (release 26, ToxoDB.org) using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Aligned BAM files were normalised by library size and converted to bigwig format using deeptools bamCoverage(http://deeptools.readthedocs.io/en/latest/content/tools/bamCoverage.html)
Peaks were called using either HOMER (H2AX, H3.3 samples), MACS2 Callpeak (H3K4me3) or MACS2 Broadpeak (H2AZ, H2BV,CenH3 )
Genome_build: Toxoplasma gondii ME49 release 26
Supplementary_files_format_and_content: bigwig of read coverage, BED files containing called peak regions

organism: Toxoplasma gondii RH

source_name: Intracellular tachyzoites

growth_protocol: Confluent human foreskin fibroblast cells were infected with tachyzoite forms of Toxoplasma gondii (RH_hxgprt) at a ratio of 3-5 parasites per cell.  After around 40hs of infection, cells were harvested and lysed sequentially with 20G/23G/25G needles.

extract_protocol:
Parasites were lysed in lysis buffer to release nuclei. Nuclei were digested with micrococcal nuclease and centrifuged to remove cell debris and harvest digested DNA. Histone-DNA complexes were immunoprecipitated with protein A-conjugated magnetic beads and digested with proteinase K before DNA purification.
Adapters were ligated to DNA using a TruSeq ChIP-seq kit (Illumina). Libraries were sequenced using a Hiseq2500 sequencing machine (Illumina). This involves a first step of cluster generation in situ on the flow cell followed by massively-parallel sequencing using fluorescently-labeled reversible terminator nucleotides. Clustered templates were sequenced base-by- base during each read. Images generated by the Hiseq2500 were processed by Hiseq Sequence Control Software (HCS V2 or latest with RTA v1.17 or latest and CASAVA 1.8 or latest software packages). These software components perform the functions of image analysis (Firecrest) and base-calling (Bustard).

tag: Stage

value: Intracellular tachyzoites


title: CenH3 replicate 1 Input DNA

description: Mnase-digested DNA


title: H2BV replicate 3 Input DNA

description: Mnase-digested DNA


title: H2AZ replicate 1 Input DNA

description: Mnase-digested DNA


title: H2AX replicate 1 Input DNA

description: Mnase-digested DNA


title: RNA ΔtracrRNA

value: delta tracrRNA


title: H3.3 replicate 2 Input DNA

description: Mnase-digested DNA


title: H2AZ replicate 2 Input DNA

description: Mnase-digested DNA (same input used for H2AZ replicate 2 and H3K4me3 replicate 1)


title: H3.3 replicate 1 Input DNA

description: Mnase-digested DNA


title: CenH3 replicate 1

description: Mnase-digested DNA

tag: chip antibody name

value: HA epitope tag

tag: chip antibody source

value: miltenyibiotec

tag: chip antobody catalogue number


title: H2BV replicate 3

description: Mnase-digested DNA

value: myc


title: H3K4me3 replicate 2

description: Mnase-digested DNA

value: Upstate


title: minus replicate 3

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

institute: University of Exeter

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were filtered using the fastq-mcf program from the eautils package (http://code.google.com/p/ea-utils/) applying –x 0.01, –q 20, –p 10, and –u.
Filtered reads were mapped to M. oryzae genome (70-15) using Tophat v 2.1.0
Cufflinks suite of programs was used to calculate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values and to check for differential expression.
Genome_build: 70-15
Supplementary_files_format_and_content: "cds_exp.diff.txt" shows coding sequence differential expression output from Cufflinks. Gene identifiers are those used in M. oryzae genome database at Ensembl (http://fungi.ensembl.org/Magnaporthe_oryzae/Info/Index).

organism: Pyricularia oryzae

source_name: rice sheath infected with M. oryzae

growth_protocol: Rice leaf sheaths (CO39) were inoculated with pmk1AS mutant of Magnaporthe oryzae.

extract_protocol:
At 32 hpi, infected rice sheaths were trimmed manually and total RNA was extracted using QIAGEN RNeasy Plant Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1NA-PP1 added at 26 hpi. Control left untreated.

tag: tissue

value: infected rice sheath

value: 32 hours post infection (hpi)

tag: treatment

value: control

value: Guy11 pmk1AS


title: plus replicate 1

value: 1NA-PP1 added at 26 hpi


title: plus replicate 2


title: minus replicate 1


title: H2AZ replicate 2

description: Mnase-digested DNA

value: Angel laboratory


title: minus replicate 2


title: H2BV replicate 2 Input DNA

description: Mnase-digested DNA


title: H2BV replicate 1

description: Mnase-digested DNA