title: HT_22

status: Public on Sep 04 2017

city: Garching

first: Carmelo

last: Quarta

address: Parkring 13

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

data_processing:
STAR aligner was used for split-read alignment against the mouse genome assembly mm9 and ENSEBML annotation. To quantify the number of reads mapping to annotated genes we used HTseq-count
Genome_build: mm9
Supplementary_files_format_and_content: tsv files contain raw read count; they have two columns where the first column specifies the gene name and the second the actual read count

source_name: Weight clamped vehicle

extract_protocol:
RNA was extracted using RNeasy Mini Kits (Qiagen). Catalogue number 74106
Prior library preparation RNA integrity was determined with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit. All samples had a RNA integrity number (RIN) value greater than 7. For library preparation, 1 μg of total RNA per sample was used. Library construction was performed as described in the Low Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina) in an automated manner using the Bravo Automated Liquid Handling Platform (Agilent). cDNA libraries were assessed for quality and quantity with the Lab Chip GX (Perkin Elmer) and the Quant-iTPicoGreendsDNA Assay Kit (Life Technologies).

treatment_protocol: Diet-induced obese mice were treated for 5 days with vehicle, GLP-1/Dexa, Dexamethasone (Dexa) or with GLP-1 at the equimolar doses of 100 nmol/kg. A group of calorie restricted mice with body weight matched to that of GLP-1/Dexa-treated mice was included in order to dissect whether the molecular signatures governed by the conjugate are independent from the induced weight loss. Hypothalami were collected at the end of the treatmens (day 5) and snap frozen until the RNA isolation

value: Hypothalamus


title: HT_92

type: SRA

country: Germany

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue


title: HT_91


title: selected strain PM diet muscle biological rep2

status: Public on Sep 05 2017

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

country: USA

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software CASAVA version 1.8.2.
Raw reads were processed for quality control using the Trim Galore! software version 0.4.0. This software was used to trim low-quality ends from reads in addition to Illumina adapter removal. Quality trimming was then specified at phred33.
Sequences after QC were filtered for potential contaminating ribosomal RNAs using the Bowtie2 software version 2.2.5. All Oncorhynchus species rRNAs available in GenBank were used to align against, where unaligned reads were output for further usage. The default Bowtie2 parameters were used.
Bowtie2 version 2.2.5 was used for alignment of reads to the rainbow trout transcriptome using the alignment parameters as recommended by eXpress software version 1.5.1.
Alignment files were piped into the eXpress version  1.5.1 software using the default parameters, but including the strand information, to generate read-counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package in R-Bioconductor Release 3.2.
Genome_build: The rainbow trout transcriptome sequences published from Salem et.al., PLoS One, 2015.
Supplementary_files_format_and_content: tab-delimited text files of effective read counts, rounded to the nearest whole number

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: muscle section dorsal to lateral line

extract_protocol:
Tissue samples were excised, flash-frozen in liquid nitrogen and stored at -80°C until usage. Samples were homogenized using a bead-beater with TRIzol reagent per the manufacturer's recommendation for total RNA isolation.
Total RNA was standardized to 1 µg each sample. DNA was removed using Amplification-grade DNase I from Invitrogen. Ribosomal RNAs were reduced using the Ribo-Zero Gold rRNA Removal Kit from Illumina. Sequencing libraries were then prepared using the ScriptSeq v2 RNA-Seq Library Preparation Kit from Illumina. Barcodes used were Illumina TruSeq indexes 1-12.

tag: strain

value: ARS-KO

value: muscle

tag: diet

value: PM


title: selected strain PM diet liver biological rep1

source_name: section from whole liver

value: liver


title: HT_90

source_name: Dexa


title: HT_31


title: HT_89


title: HT_9


title: HT_32


title: HT_68


title: HT_291


title: HT_38


title: HT_28


title: HT_37


title: HT_67


title: HT_55


title: HT_54


title: HT_70


title: HT_17


title: selected strain PM diet muscle biological rep1


title: HT_69


title: HT_18


title: HT_21


title: HT_12


title: HT_20

source_name: vehicle


title: HT_19


title: Round spermatid, replicate 2

city: Cleveland

first: Ahmad

middle: M

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
FastQC to assess the quality of the reads. Remove adapter sequences using TrimGalore
Read alignment is done using Tophat v2.0.12
The differential gene expression analysis is done using Cuffdiff v2.2.1
FPKM values for mRNAs and lncRNAs
Genome_build: MM10
Supplementary_files_format_and_content: Excel files containing differentially expressed RNAs

source_name: Male mouse germ cells

growth_protocol: Male mice were grown on normal diet

extract_protocol:
RNA was isolated using Qiagen RNA isolation kit
Total RNA (1ug) from each cell type was used to generate next generation RNA-seq libraries using Illumina TruSeq stranded library preparation kit per manufacturer’s protocol;100 bp paired-end, strand-specific

tag: cell type

value: germ cells

tag: cell developmental stage

value: Round spermatid stage

value: Testis

tag: organism developmental stage

value: Adult mice


title: HT_29


title: HT_30


title: Round spermatid, replicate 3


title: HT_1


title: HT_2


title: HT_27


title: Pachytene, replicate 2

value: Pachytene stage


title: Pachytene, replicate 1


title: Spermatogonia (A and B), replicate 1

value: Spermatogonia stage


title: Round spermatid, replicate 1


title: Pachytene, replicate 3


title: Spermatogonia (A and B), replicate 2


title: Spermatogonia (A and B), replicate 3


title: Input_DNA-FOB_ChIPseq_siCHD1

status: Public on Sep 03 2017

city: Göttingen

first: Simon

middle: Joschka

last: Baumgart

state: Lower Saxony

address: Justus-von-Liebig Weg 11

department: Allgemeine und Viszeralchirurgie - Surgery

institute: Göttingen Medical Center

library_source: genomic

data_processing:
Reads were aligned to the human genome (UCSC version hg19) by Bowtie1 (version 1.1.1)(Langmead et al. 2009) and formatted to BAM format via SAMTools (version 1.3.1)(Li et al. 2009).
BAM files were processed to bigwig files via the bamCoverage tool implemented in deeptools2 (Ramirez et al. 2016) and normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC).
Reads were aligned to the human genome (UCSC version hg19) by Bowtie1 (version 1.1.1)(Langmead et al. 2009) and formatted to BAM format via SAMTools (version 1.3.1)(Li et al. 2009).
BAM files were processed to bigwig files via the bamCoverage tool implemented in deeptools2 (Ramirez et al. 2016) and normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC).
Genome_build: hg19 (UCSC)

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal osteoblast

growth_protocol: Bone marrow derived MSC and FOB were cultured at 37 °C and 34 °C, respectively, under 5% CO2 atmosphere and maintained sub-confluent. MSC were grown in alpha modified Eagle's medium (Gibco®) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin and the antifungal agent Fungizone® Antimyotic (25 µg/ml) (growth medium). FOB were cultured in DMEM-F12 (Gibco®) and supplemented as described above. Osteoblast differentiation was induced 36 hours after siRNA transfection by addition of the growth medium supplemented with 10 mM β-glycerophosphate, 0.2 mM ascorbate, 10 nM calcitriol and 100 nM dexamethasone to confluent cells (osteoblast differentiation medium). FOBs were shifted 4 hours before addition of the osteoblast differentiation medium from 34 °C to 39 °C. For adipocyte differentiation confluent cells were cultured in normal growth medium supplemented with 15% FBS and 2 µM insulin, 0.45 mM isobutylmethyl-xanthine, 10 µM troglitazone and 100 nM dexamethasone. The differentiation medium was changed every second day. Cells were differentiated for 5 days.

extract_protocol:
Cells were crosslinked for 10 minutes with 1% Formaldehyde in PBS or 1.42% formaldehyde for CHD1 ChIP. Chromatin extraction and subsequent steps were performed as described in Najafova et al. 2016. Briefly, nuclear extracts were incubated with 1 – 2 µg of antibody over night before precipitation with protein A or G sepharose beads. After washing the immunoprecipitated complexes the DNA was isolated via phenol-chloroform extraction.
ChIP DNA library preparation was performed with the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer's instructions.

treatment_protocol: siRNA treatment was performed 36 hours before differentiation induction. After 2 days of differentiation a second siRNA transfection was performed.

tag: sirna treatment

tag: differentiation-induction

value: Osteoblast differentiation


title: Input_DNA-FOB_ChIPseq_siCON

value: siCon


title: Input_DNA-MSC_ChIPseq_Ad

source_name: Bone marrow derived mesenchymal stem cells

value: Adipocyte differentiation


title: HT_301


title: Input_DNA-MSC_ChIPseq_Ob


title: Input_DNA-MSC_ChIPseq_Und

value: Undifferentiated


title: siCon_RNAseq_MSC_Ob

data_processing:
Reads were aligned by Bowtie2 (version 2.1.0) (Langmead and Salzberg, 2012) to the human genome (UCSC version hg19).
The mapped reads were aggregated to human genes using a custom Ruby script.
Differential gene expression was analyzed by DESeq (Anders and Huber, 2010).
Reads were aligned to the human genome (UCSC version hg19) by Bowtie1 (version 1.1.1)(Langmead et al. 2009) and formatted to BAM format via SAMTools (version 1.3.1)(Li et al. 2009).
BAM files were processed to bigwig files via the bamCoverage tool implemented in deeptools2 (Ramirez et al. 2016) and normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC).
Genome_build: hg19 (UCSC)

extract_protocol:
The total RNA was isolated by QIAzol (Qiagen) according to the manufacturer’s protocol. After measuring the RNA integrity (RNA 6000 nano-kit (Agilent)), 1 µg of RNA of samples with a RIN above 7.5 were used for library preparation.
RNA-seq libraries were prepared with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® after selection for poly(A)-RNA with the NEBNext® Poly(A) mRNA Module.


title: siCon_RNAseq_MSC_Ad


title: siCHD1_RNAseq_MSC_Ob


title: siCHD1_RNAseq_MSC_Ad


title: siCon_RNAseq_MSC_Und


title: siCon_RNAseq_FOB_Ob


title: RNAPII_ChIPseq_FOB_siCHD1

tag: antibody

value: RNA-Polymerase II (N-20, santa cruz)


title: RNAPII_ChIPseq_FOB_siCon


title: siCon_RNAseq_FOB_Und


title: siCHD_RNAseq_MSC_Und


title: H2Bub1_ChIPseq_FOB_siCHD1

value: H2Bub1 D11 (5546, Cell Signaling)


title: siCHD1_RNAseq_FOB_Ob


title: H2Bub1_ChIPseq_FOB_siCon


title: H3.3_ChIPseq_FOB_siCon

value: H3.3 (MerckMilipore, 09-838)


title: H3.3_ChIPseq_FOB_siCHD1


title: H3K27ac_ChIPseq_Und

value: H3K27ac (Diagenode , pAB-196)


title: H2A.Z_ChIPseq_FOB_siCon

value: Gévry et al. 2009


title: H3K27me3_ChIPseq_Ob

value: H3K27me3 (Diagenode ,Mab-003)


title: H2A.Z_ChIPseq_FOB_siCHD1


title: H3K27ac_ChIPseq_Ad


title: Hepatocyte-like cells (HLC) 4

city: Clayton

first: Vijesh

last: Vaghjiani

state: Victoria

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Reaserch

data_processing:
Basecalls performed using Illumina CASAVA pipeline version 1.8.2
The Tophat aligner (v1.3.1) was used to map reads to the genomic sequence of Homo sapiens nenome (Bild version HG19)
The transcripts were assembled uitilising reference based annotation with the Cufflinks tool (V2.2.1)
The analysis was undertaken using two scripts within the cufflinks application, cuffmerge and cuffdiff
The merged sample output from cuffmerge (merged.gtf) was then used as input to cuffdiff which produces the differential expression analysis
Genome_build: HG19
Supplementary_files_format_and_content: counts

source_name: Hepatocyte-like cells (HLC)

growth_protocol: Cells were differrentiated in DMEM F12 with 10% FBS, 10% HepG2 conditioned media, 10ng/ml EGF, 10ng/ml FGF-4, 10ng/ml HGF, 0.1uM insulin and Dexamethasone

extract_protocol:
RNA was extracted using Qiagen RNA mini columns
cDNA libraries were prepared using Illumina TrueSeq stranded mRNA Kit
RNA libraries were sequenced using Illumina HiSeq 2000 (Illumina) with 100 base pair single end reads with 20 million reads per sample

value: HAEC diffrerentiated into HLC


title: Encapsulated hepatocyte-like cells (Enc. HLC) 4

value: Encapsulated HLC


title: Encapsulated hepatocyte-like cells (Enc. HLC) 2


title: H3K27me3_ChIPseq_Ad


title: H3K4me3_ChIPseq_Ad

value: H3K4me3 (Diagenode ,Mab-003)


title: Encapsulated hepatocyte-like cells (Enc. HLC) 3


title: Hepatocyte-like cells (HLC) 3


title: Encapsulated hepatocyte-like cells (Enc. HLC) 1


title: H3K27me3_ChIPseq_Und


title: Hepatocyte-like cells (HLC) 1


title: CHD1_ChIPseq_FOB

value: CHD1 (Bethyl ,A301-218A)


title: H3K27ac_ChIPseq_Ob


title: Hepatocyte-like cells (HLC) 2


title: Human Amnitic Epithelial Cells (HAEC) 3

source_name: Human Amnitic Epithelial Cells (HAEC)

value: Primary cells (controls)


title: Human Amnitic Epithelial Cells (HAEC) 4


title: CHD1_ChIPseq_Ad


title: Human Amnitic Epithelial Cells (HAEC) 2


title: CHD1_ChIPseq_Und


title: Human Amnitic Epithelial Cells (HAEC) 1


title: H3K9me3_T=6d_Ab8898-638466

status: Public on Sep 02 2017

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

data_processing: ChIP DNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, which were subsequently size selected (~300bp). The adapter-modified DNA fragments were subjected to limited PCR amplification (14 cycles). Quality control was made by qPCR and by running the products on a Bioanalyzer (BioRad). Finally, cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse MM9 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Samples were sequenced to a depth of approximately 10-20 million mapped tags per sample. Unless specified otherwise, only the tags uniquely aligning to the genome were considered for further analysis. The 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing, and tags mapping on exact the same genomic locus were discarded to obtain a non-redundant set. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All ChIP-Seqsequence analyses were conducted based on the Mus musculus NCBI m37 genome assembly (MM9) accessed from the Ensembl (release 54; May 2009) or the UCSC (assembly July 2007) Genome Browsers.

source_name: Embryonic Stem cells

growth_protocol: JM8 mouse ES cell lines derived from the C57BL/6N strain were grown on feeder-free gelatinized tissue culture plates. The lines were maintained in Knockout DMEM (500 ml, Gibco) supplemented with 2 mM glutamine, 5 ml 100x beta-mercaptoethanol (360 ul in 500 ml PBS, filter sterilized), 10% fetal calf serum respectively (Invitrogen) and 500 U ml-1 leukaemia-inhibitory factor (ESGRO, Millipore). Trypsin solution was prepared by adding 20 ml of 2.5% trypsin solution (Gibco) and 5 ml chicken serum (Gibco) to 500 ml filter-sterilized PBS containing 0.1 g EDTA (Sigma) and 0.5 g D-glucose (Sigma).

extract_protocol: ChIP experiments were performed using 3.3x106 cells and 3-6 ug antibody per ChIP according to standard protocols with two minor modifications. Crosslinking of the cells was performed on the culture plates for 10 minutes, while ChIP'ed DNA was purified by Qiaquick PCR purification Kit (Qiagen). ChIP enrichment levels were analyzed by qPCR for quality control.

treatment_protocol: Expanded heterozygous tm1a/tm2 ("T=0") ES clones were treated for 48 hours with 0.8 uM 4'hydroxytamoxifen (4'OHT, Sigma) to induce Cre activity and convert the conditional allele (tm1a) into a null allele (tm1c) ("T=2d"). These tm1c/tm2 null ES cells were subsequently cultured without 4'OHT for use in downstream assays ("T=4d"; "T=6d").

value: Agouti C57BL/6N substrain

value: Embryonic Stem cells

tag: source

value: Chromatin IP against H3K9me3

tag: antibody/details

value: Antibody H3K9me3 (Abcam 8898, 638466)

tag: treatment group


title: H3K9me3_T=0_Ab8898-638466


title: H3K4me3_ChIPseq_Ob

value: Osteoblast differentiation


title: H3K9me3_T=0_Ab8898-58206

value: Antibody H3K9me3 (Abcam 8898, 58206)


title: H3K9me3_T=4d_Upstate

value: Antibody H3K9me3 gift from Thomas Jenuwein; similar to H3K9me3 antibody Upstate/ Millipore 07-442 (lot 4861)


title: H3K9me3_T=6d_Upstate


title: H3K9me3_T=0_Upstate


title: CHD1_ChIPseq_Ob


title: H3K4me3_ChIPseq_Und

value: Undifferentiated


title: PARP resistant cell line

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: RNA-seq for PARP resistant cell line

data_processing:
RNA-Seq data analysis was done with rsem(ver. 1.2.3) and Hg19 genome with Ensemble transcriptome used for gene information
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains raw counts and FPKM values for all genes

source_name: CAPAN1 cell line

growth_protocol: Capan-1 was purchased from ATCC and cultured in RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
total RNA isolated using Trizol reagent
Epicentre ScriptSeq strand specific library preparaion was used

treatment_protocol: Capan-1 Olaparib resistant cell line was established by a stepwise exposure to increasing concentrations of Olaparib from 15nM to 128uM

value: breast cancer

tag: phenotype

value: PARP resistant


title: parental CAPAN1 cell line

description: RNA-seq for parental CAPAN1 cell line

value: control


title: H3K9me3_T=2d_Upstate


title: 35S:RPS4-HS eds1-2, no-antibody control, 4h, rep2

city: Koeln

first: Servane

last: Baufume

state: Germany (DEU)

address: Carl-von-Linné-Weg 10

department: Plant Microbe Intreractions

institute: Max Planck Institute for Plant Breeding Research

description: sampled used as normalisation for eds1_HA-2

data_processing:
The adapter sequences were filtered by using the FASTX-Toolkit
Reads were trimmed for quality and retained if the adapter sequence matched after the 10th base of the read. Remaining reads were removed from further analysis.
The mapping program Bowtie (version 0.12.5) was used to map the reads to the Arabidopsis thaliana reference genome (TAIR9)
The peak calling was done using the algorithm of the program QuEST (version 2.4) for each biological replicate separately, using the corresponding 'non-antibody control' to normalize the enrichment fold.
Parameter settings in QuEST: Transcription factor mode. Relaxed (permissive) peak calling parameters.
Genome_build: TAIR9

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves

growth_protocol: Plants were grown for 3,5 weeks at 28°C

extract_protocol:
Chromatin was extracted as described (Gendrel et al., 2005. Nature Methods). DNA was purified by Phenol-Chloroform extraction followed by ethanol precipitation in the presence of 0.3M sodium acetate and glycogen.
For ChIP-seq library preparation, we followed the Illumina ChIP-seq DNA sample preparation kit starting with end repair, A-tailing and adaptor ligation according to the manufacturer’s instructions
The libraries were PCR-amplified prior to agarose gel size selection. A 100-300 bp gel slice was excised and the DNA purified before submitting the libraries to a bioanalyser (Agilent) quality control. Samples were sequenced on an Illumina Genome Analyser IIx

treatment_protocol: Plants were shifted from 28°C to 19°C for 4h before collecting leave samples. Leaves were cross-linkinked under a vacuum using 1% formaldehyde, washed and freezed in liquid nitrogen prior to chromatin extraction.

value: leaves

tag: cultivar/ecotype

tag: genotype

value: 35S:RPS4-HS eds1-2


title: Col-0, no-antibody control, 4h, rep2

description: sampled used as normalisation for Col_HA-2

value: WT


title: 35S:RPS4-HS, no-antibody control, 4h, rep2

description: sampled used as normalisation for RPS4_HA-2


title: 35S:RPS4-HS eds1-2, IP anti-HA, 4h, rep1

value: anti-HA (Abcam ab9110)


title: 35S:RPS4-HS, no-antibody control, 4h, rep1

description: sampled used as normalisation for RPS4_HA-1


title: 35S:RPS4-HS eds1-2, IP anti-HA, 4h, rep2


title: Col-0, no-antibody control, 4h, rep1

description: sampled used as normalisation for Col_HA-1


title: H3K9me3_T=6d_Ab8898-58206


title: 35S:RPS4-HS, IP anti-HA, 4h, rep2


title: EWS

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description: EWS CLIP-seq

data_processing:
For each CLIP-seq read, the 3'-adaptor sequence 'CTCGTATGCCGTCTTCTGCTTG' was removed with program cutadapt (version 1.8.3). The reads with at least 16nt were mapped to the human genome (hg19) by Bowtie2 (version 2.2.5) with default parameters. The mapped reads with same genomic position were kept up to 2.
The mapped reads were used to generate the genomic coverage profiles in bigWig format with programs genomeCoverageBed (bedtools version 2.24) and samtools (version 0.1.19).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig for coverage signal in both strands

source_name: cervical adenocarcinoma

growth_protocol: HeLa cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% newborn bovine serum (Gibico) at 37°C in 5% CO2.

extract_protocol:
The 3' linker labelled by gama-32P-ATP was ligated to RNA-protein complex before SDS-PAGE. After nitrocellulose transfer, the band above EWS was excised and treated with Proteinase K, and the 5' linker was ligated. To isolated RNA, NaOAc, glycogen, 1:1 EtOH:isopropanol was added and precipitated overnight at -20°.
Linker-ligated RNAs were reverse transcribed with Superscript III (Life Technology) and PCR-amplified with Phusion polymerase (ThermoFisher).  The product was fractionated on 4% agarose gel and recovered DNA was quantified for deep sequencing
CLIP-seq

treatment_protocol: HeLa cells were irradiated with UV at 400mJ/cm2 under HL-2000 Hybrilinker.

value: HeLa cell

value: EWS antibody


title: HDMYZ, 0 hour, 1

city: New Haven

first: Mei

last: Zhong

address: 10 Amistad Street

department: Stem Cell Center

institute: Yale University

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Sequence reads were processed by miRDeep2 package, with the following modifications. First, to remove adaptor sequence, we removed both the main adaptor sequence present in the sequencing reads, as well as the second most abundant adaptor variant. In addition, we did not restrict the size of small RNAs during adaptor removal. Second, we used miRBase v18 for mapping the reads. Third, for quantifying miRNA and isoform frequency, we limited reads to more or equal to 15 bases in length with zero mis-match during mapping.
The total number of reads that were mapped to known mature miRNAs was used to normalize read frequencies for each miRNA or each miRNA isoform.
Genome_build: miRBase v18
Supplementary_files_format_and_content: The processed date file is tab-delimited format. Each row in the file indicates a miRNA isoform, each column indicates a kind of information for miRNA isoforms. The first column "Category" indicates the turnover pattern of miRNA isoforms. If left blank, indicates a slow turnover miRNA; "1" means an ultra-fast turnover miRNA whose level goes down more than 90% after 4 hours of ActD treatment; "2" means a fast turnover miRNA whose level goes down more than 50% after 12 hours of ActD treatment. The second column "Precursor" shows the miRNA precursor name for each miRNA isoform. The third column "Mature miRNA" shows the mature miRNA name for each miRNA isoform. The fourth column " Isoform sequence" shows the sequence for each miRNA isoform. The fifth to ninth column show the normalized read frequency for each sample. The tenth column shows the ratio between 4 hour sample versus the average of 0 hour samples. The eleventh column shows the ratio between the average of 12 hour samples versus the average of 0 hour samples. The twelfth column "Detectable" shows the detectability of each miRNA isoform: "1" indicates the average of normalized read frequency for 0 hour is larger than 0.000001; "0" indicates the average of normalized read frequency for 0 hour is less than 0.000001.

source_name: HDMYZ, 0ug/ml Actinomycin D, 0 hour

growth_protocol: HDMYZ cells were cultured in RPMI with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
HDMYZ cells were collected with Trizol reagent (Invitrogen) following manufacturer's protocol. Small RNAs of 15-40 bases were gel-purified from 5 ug total RNA.
Small RNAs of 15-40 bases were gel-purified from 5 ug total RNA with 10% acrylamide gel (American Bioanalytical AB13021). Purified small RNA was subjected to library preparation, similar to Illumina protocol with modification. Briefly, pre-adenylated primer was made following a published protocol (Chen, Y.-R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J. and Fei, Z. (2012) A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods, 8, 41.) using /5Phos/TGGAATTCTCGGGTGCCAAGG/3ddC/. Small RNA was ligated to the pre-adenylated primer with truncated T4 RNA ligase 2 (NEB M0242S). The 35-55 bases product was purified with 10% acrylamide gel and further went through a 5? ligation reaction with primer: dGdTdTdCdAdGdAdGdTdTdCdTdAdCdA GUCCGACGAUC (Dharmacon) with T4 RNA ligase 1 (Fermentas EL0021). The 60-80 bases product was purified with 10% acrylamide gel and reverse transcribed with M-MLV reverse transcriptase (Invitrogen 28025-013) using primer: GCCTTGGCACCCGAGAATTCCA. The RT product was PCR amplified for 18 cycles with Phusion DNA polymerase (NEB M0530) using a universal primer: AATGATACGGCGACCACCGAGATCTACACGTT-CAGAGTTCTACAGTCCGA and a specific primer for each sample. 130-150nt small RNA libraries were purified with 8% acrylamide gel. Barcoded small RNA libraries were sequenced on a HiSeq2000 (Illumina).

treatment_protocol: HDMYZ cells were treated with 2ug/ml ActD for 0 (HDMYZ_0303, HDMYZ_0304), 4 (HDMYZ_4313) and 12 hours (HDMYZ_12311, HDMYZ_12312).

tag: cell line

value: HDMYZ

value: hodgkin's lymphoma

tag: actinomycind treatment

tag: time post treatment

value: 0 hour


title: 35S:RPS4-HS, IP anti-HA, 4h, rep1

tag: tissue


title: HDMYZ, 2ug/ml Actinomycin D, 12 hours, 2

source_name: HDMYZ, 2ug/ml Actinomycin D, 12 hours

value: 12 hours


title: HDMYZ, 0 hour, 2


title: HDMYZ, 2ug/ml Actinomycin D, 12 hours, 1


title: Col-0, IP anti-HA, 4h, rep2


title: HDMYZ, 2ug/ml Actinomycin D, 4 hours

source_name: HDMYZ, 2ug/ml Actinomycin D, 4 hours

value: 4 hours


title: Math1Hoxa5-IRES-GFP_2

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

data_processing:
HCS 2.2.58 was used with default parameters for base calling.
bcl2fastq 1.8.4 (Illumina) was used to generate fastq files
Raw reads were preprocessed using the R/Bioconductor package QuasR: Reads with more than 2Ns were removed with the function preprocessReads(). The remaining reads were aligned to mm10 using the qAlign() with splicedAlignments=TRUE and the following parameters: Rbowtie v1.4.0 (parameters: -max_intron 400000 -min_intron 20000 -max_multi_hit 10 -selectSingleHit TRUE -seed_mismatch 1 -read_mismatch 2 -try_hard yes)
The QuasR function qCount() was used to extract a table with raw read counts per gene for all Entrez genes for each sample.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: table containig raw read counts per gene. First column: ENTREZ gene ID, second column: gene symbol, third column: gene name, fourth column: number of unique, non-masked bases for all exons of the gene

source_name: Pontine nucleus

extract_protocol:
Pontine nuclei neurons were genetically labeled, micro-dissected and dissociated to single cells. 2.000 cells for each replicate were isolated by FACS directly into lysis buffer and RNA was extracted with the Arcturus PicoPure RNA Isolation Kit.
RNA for 1000 cell equivalents was used as template to generate SPIA amplified cDNA using the Ovation RNA-seq System V2 (NuGen). 1 ng amplified cDNA was fragmented and sequencing libraries were prepared with the Illumina TruSeq Nano DNA sample

tag: strain

value: Pontine nucleus

tag: developmental stage


title: Math1Hoxa5-IRES-GFP_3


title: Hoxa5tdTomato_3


title: Hoxa5tdTomato_1


title: Math1tdTomato_4


title: Math1tdTomato_5


title: Math1tdTomato_6


title: Math1Hoxa5-IRES-GFP_1


title: 35S:RPS4-HS eds1-2, no-antibody control, 4h, rep1

description: sampled used as normalisation for eds1_HA-1


title: bcat Ovp rep3

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 320 Yueyang Rd

country: China

institute: Institute of Neuroscience, Chinese Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008)
Supplementary_files_format_and_content: tab-delimited text files include read count for each condition

source_name: primary somatosensory cortex

extract_protocol:
Cortical tissues were dissected, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary somatosensory cortex

tag: age


title: bcat Ovp rep2


title: Math1tdTomato_3


title: bcat Ovp rep1


title: bcat loxP rep3


title: Math1tdTomato_1


title: Math1tdTomato_2


title: Cortex_WT_Hoxb5_1

description:
HoxB5_N/C_Fw
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAAAGACATTGAAGGAACATG

data_processing:
Library strategy: 4C-seq
HCS 2.2.58 was used with default parameters for base calling.
bcl2fastq 1.8.4 (Illumina) was used to generate fastq files
Raw sequence reads were pre-processed by removing the 4C-primer sequence from the 5'-end, and truncated reads were split by sample using the barcode contained in the 4C-primer sequence. Reads whose barcode sequence did not match exactly to a single expected barcode were discarded.
Truncated reads were aligned to the genome using QuasR (Gaidatzis et al., Bioinformatics 2015) with bowtie (Langmead et al., Genome Biology 2009) and default settings (only report uniquely mapped reads)
4C-Fragment coordinates were obtained by "in silico" digestion of the reference genome and the number of alignments per sample and fragment was counted using QuasR. The normalized number of alignments per fragment was obtained by dividing through the total number of alignments on the cis-chromosome (the chromosome containing the viewpoint) and multiplying with one million.
Genome_build: All analyses are based on the mm10 Mus musculus genome assembly obtained from UCSC, corresponding to the Dec. 2011 Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)
Supplementary_files_format_and_content: Fragment coordinates and normalized alignment counts were exported in BedGraph format (http://genome.ucsc.edu/goldenpath/help/bedgraph.html).

source_name: Cortex

extract_protocol: 4C template was prepared as described in (van de Werken et al., 2012) with modifications. Briefly, cells were dissociated (30’ @ 37°C in 0.25% trypsin; 1mg/ml collagenase type II; 5mM EDTA). Cells were fixed using 2% formaldehyde/10%FCS/PBS for 10’ at RT. Cells were lysed for 10’ on ice (50mM Tris-HCl pH 7.5, 150mM NaCl, 5mM EDTA, 0.5% NP40 substitute, 1% Triton-X100, 1X proteinase inhibitors). Chromatin was digested in the context of the nucleus using the restriction enzymes NlaIII, followed by ligation. Ligated chromatin was de-crosslinked in the presence of proteinase K at 65°C O/N and subsequently treated with RNase A. Genomic DNA was extracted by beads purification and subsequently digested O/N using the restriction enzymes Csp6I and ligated under diluted conditions (16°C, O/N) favoring intra-molecular ligations. Genomic DNA was cleaned up using bead purification. The 4C PCR was performed as described in (van de Werken et al., 2012) using the primers indicated for each sample in 'description' field and on the series record.

value: Cortex


title: Col-0, IP anti-HA, 4h, rep1


title: Col-0, 8h, rep3

data_processing:
Illumina CASAVA1.8 software was used for base calling.
Sequenced paired-end reads were separately clipped for adapter sequence and trimmed for low quality retaining reads with average Phred+33 quality/read >= 30 and length >= 50 bases. Reads that did not match these criteria were discarded.
The adapter clipped quality trimmed reads were then balanced for those cases where both the pairs passed filtering. In those cases where only one pair passed filtering, they were written on to a separate single-end file with the idea of mapping them separately in order to consider those reads as they passed filtering.
Reads were mapped on to Arabidopsis thaliana TAIR10 genome using tophat version 2.0.0 with parameters -m 0 -g 1 --genome-read-mismatches 2 --read-mismatches 2 --library-type fr-unstranded.
mean inner distance and standard deviation for paired end reads were estimated separately for each sample using a custom made perl script by first mapping the reads preliminarily to Arabidopsis thaliana genome using BWA version 0.5.9 and then calculating from the bam file mean and standard deviation of inner distance between pairs that fall in the range [Q1 - 2*(Q3-Q1), Q3 + 2*(Q3-Q1)], where Q1 and Q3 are the first and the third quartiles. The junctions.bed file from the paired-end run was converted to a junctions file using bed_to_juncs script that comes with tophat and fed to the SE reads that were generated with the -j parameter for the second run.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab delimited text files of read counts across junctions (introns) with the type of splicing event they fall to - 1) NJ (Normal junction - intron as found in the first transcript), 2) ES (Exon skipping), 3) A3P(Alternative 3prime), 4) A5P(Alternative 5prime), 5) IR(Intron retention), 6) CI(Cryptic intron).

source_name: Col-0, 8h

extract_protocol: Total RNA were extracted using the Qiagen RNeasy kit. RNA were DNaseI-treated and a purification was done using the Qiagen RNeasy MinElute kit. Ribosomal RNAs were depleted from 2.5 µg RNA using the RiboMinus Plant Kit for RNA-seq (Life Technologies). For RNA-seq library preparation, we followed the Illumina "TruSeq RNA Sample Preparation v2 Guide" starting with poly-A enrichment followed by standard cDNA synthesis, end repair, A-tailing, adapter ligation and PCR enrichment (15 cycles). Libraries were quantified by fluorometry (Picogreen, Invitrogen) and equimolar mixtures of libraries were loaded onto the cBot station (Illumina) for cluster generation prior to sequencing on a HiSeq2000.

treatment_protocol: Plants were shifted from 28°C to 19°C for 4 and 8h before collecting and freezing the samples. T0 samples were not shifted.

tag: ecotype/cultivar

value: 3,5 week-old


title: Col-0, T0, rep1

source_name: Col-0, T0


title: Col-0, 4h, rep1

source_name: Col-0, 4h


title: Col-0, 4h, rep2


title: Col-0, 8h, rep1


title: Col-0, T0, rep3


title: Hoxa5tdTomato_2


title: Col-0, 4h, rep3


title: 35S:RPS4, 8h, rep1


title: 35S:RPS4, 8h, rep2


title: Hoxa5 cKO pool 3

city: Louvain-le-Neuve

first: Françoise

last: Gofflot

address: Croix du Sud, 4-5, Bte L7.07.02

department: Institut des Sciences de la Vie

country: Belgium

institute: Université catholique de Louvain

data_processing:
Illumina CASAVA 1.6 was used to generate fastq files with adapters trimmed
Alignment to mouse genome with Tophat 2.0.9 using option --library-type fr-firststrand and -G genes.gtf
Cufflinks 2.2.0 suite was used to quantify transcripts
Alignments were processed with cufflinks, transcriptome assembly was generated with cuffmerge, transcript abundance was evaluated with cuffquant
Cuffdiff was used to assess differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with gene fpkm cuffdiff output files + transcriptome assembly from cuffmerge in gtf format

source_name: 3 brainstems

extract_protocol:
Brainstems were collected after euthanasia of pups at P21. Tissues were  snap frozen in liquid nitrogen, and stored at −80 °C until RNA was extracted. RNA was isolated using TRI Reagent (Sigma Aldrich, T9424) and quantified using a NanoDrop ND-1000 fluorospectrometer (Thermo Scientific, Waltham, MA, USA). RNA from three brainstems was pooled, and three pools were used per genotype.
Illumina truSeq stranded total RNA library prep kit with ribo-zero was used to prepare libraries from 1 µg of total RNA following Illumina’s protocol. Ribosomal RNA was depleted from total RNA. The remaining RNA was purified, fragmented, primed with random hexamers and reverse transcribed into first strand cDNA followed by second strand synthesis. A single A nucleotide was added to the 3’end of the fragments before ligation to multiple indexing adapters. DNA fragments with adapter molecules on both ends were enriched by PCR and purified with Ampure XP magnetic beads. Libraries were validated on Bioanalyser DNA 1000 chip and quantified by qPCR with the KAPA library quantification kit.

treatment_protocol: For tamoxifen treatment, 4 consecutive intragastric injections (50 µl) were performed: we injected the first solution of 1mg/ml at P1, the second of 1,5 mg/ml was injected at P2 and P3, and the last one of 2 mg/ml was injected at P4.

value: brainstem

value: Postnatal day 21

tag: treatment

value: tamoxifen-treated


title: 35S:RPS4, 4h, rep3

value: leaves


title: Hoxa5 cKO pool 1


title: 35S:RPS4, 4h, rep1


title: 35S:RPS4, 4h, rep2


title: 35S:RPS4, 8h, rep3


title: Hoxa5 control pool 3


title: bcat loxP rep2


title: bcat loxP rep1


title: Col-0, 8h, rep2

value: WT


title: 35S:RPS4, T0, rep2


title: Col-0, T0, rep2


title: 35S:RPS4, T0, rep3


title: 35S:RPS4, T0, rep1


title: Hoxa5 control pool 1


title: M202(Sub1) - midnight - rep 6

status: Public on Sep 01 2017

city: Raleigh

first: Anna

last: Locke

state: NC

address: 4112 Williams Hall, 101 Derieux Place

description: Random primed libraries

data_processing:
Library strategy: polyA mRNA-Seq
Base calling and demultiplexing performed with Illumina CASAVA version 1.8. (UC Riverside IIGB Genomics Core)
Adapter sequences were trimmed from reads with Trim Galore (Babraham Bioinformatics)
Reads were aligned to the Oryza sativa cv.Nipponbare genome with Tophat2.  Parameters as follows:  --mate-inner-dist [adjusted for read length] --mate-std-dev 80 --min-intron-length 50 --library-type fr-unstranded --max-intron-length 3000 --max-multihits 1 --coverage-search --segment-mismatches 1 --min-segment-intron 50 --max-segment-intron 3000
Separate .bam alignment files for each sample (6 per sample) were combined and sorted using samtools
Aligned reads per gene were counted for each sample with HTSeq-count.  Parameters as follows:  -s reverse -m intersection-strict -t gene -i ID
Genome_build: Oryza_sativa.IRGSP-1.0.30
Supplementary_files_format_and_content: Spreadsheet (read_counts_ALocke.xls) with H-Seq-count output for every sample.  Gene ID in rows, Sample ID in columns.

organism: Oryza sativa Japonica Group

source_name: 15+ d old whole shoots

growth_protocol: Rice seeds (Oryza sativa L. ssp. japonica) of cultivar M202 and its near-isogenic, Sub1 introgression line, M202(Sub1), were sterilized for 30 min in a solution of 5% (v/v) bleach and 0.01% (v/v) Tween-20, rinsed and soaked overnight in DI water.  After germinating in covered glass dishes on wet paper towels for 5 d, seedlings were transplanted into 10 cm pots in the greenhouse at a planting density of 20 plants per pot.  Plants were grown in the greenhouse for 12 d before beginning the submergence treatment.

extract_protocol:
Total RNA was isolated from frozen shoot tissue with the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).
cDNA libraries for each sample were prepared from purified mRNA according to Wang et al. (2011).

treatment_protocol: Plants were submerged in 121 L bins, in which water was allowed to equilibrate to ambient temperature for 24 h before submergence.  Submergence began at ZT 6:00 and continued for 72 h, at which time plants were placed back on the greenhouse bench for reoxygenation.  Whole shoots were harvested and flash-frozen in liquid N2 immediately upon desubmergence (3d_sub) at midday (ZT9:00), at dusk (ZT15:30), midnight (ZT19:45), dawn (ZT0), and again at midday 24 h following desubmergence (ZT9:00).

tag: time point

value: midnight


title: M202(Sub1) - 3d_sub - rep 6

description: Random primed libraries


title: M202 - midnight - rep 6

description: Random primed libraries


title: M202 - 3d_sub - rep 6

description: Random primed libraries


title: M202 - control - rep 6

description: Random primed libraries

value: control


title: M202(Sub1) - midday - rep 2

description: Random primed libraries

value: midday


title: M202(Sub1) - control - rep 6

description: Random primed libraries


title: Hoxa5 cKO pool 2


title: M202(Sub1) - dusk - rep 6

description: Random primed libraries

value: dusk


title: M202(Sub1) - midday - rep 4

description: Random primed libraries


title: M202(Sub1) - control - rep 4

description: Random primed libraries


title: M202(Sub1) - dawn - rep 2

description: Random primed libraries

value: dawn


title: M202 - dusk - rep 2

description: Random primed libraries


title: M202 - midday - rep 2

description: Random primed libraries


title: M202 - dawn - rep 2

description: Random primed libraries


title: M202(Sub1) - midnight - rep 2

description: Random primed libraries


title: M202(Sub1) - 3d_sub - rep 4

description: Random primed libraries


title: M202 - control - rep 4

description: Random primed libraries


title: M202 - midnight - rep 4

description: Random primed libraries


title: Hoxa5 control pool 2


title: M202 - 3d_sub - rep 4

description: Random primed libraries


title: M202(Sub1) - control - rep 2

description: Random primed libraries


title: M202(Sub1) - dusk - rep 4

description: Random primed libraries


title: M202 - control - rep 2

description: Random primed libraries


title: M202 - midnight - rep 2

description: Random primed libraries


title: M202 - 3d_sub - rep 2

description: Random primed libraries


title: M202 - dusk - rep 4

description: Random primed libraries


title: M202(Sub1) - dawn - rep 4

description: Random primed libraries


title: M202 - midday - rep 4

description: Random primed libraries


title: M202 - dawn - rep 4

description: Random primed libraries


title: M202(Sub1) - dusk - rep 2

description: Random primed libraries


title: TALL-UT-2h-1_S3

city: Melbourne

first: Stephin

last: Vervoort

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Basecalling was performed using CASAVAv1.8.2
Sequenced reads were trimmed using Cutadapt (v1.9) and mapped to the mouse genome (mm10) using hisat2 v2.1.0
Read counting was performed using featureCounts from the subread v1.5.0 package
Normalization and differential gene expression analysis was performed in R using the limma/voom pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Comma Seperated Values containing the Normalised Read Counts fore each sample

growth_protocol: T-ALL cells were cultured with plate-bound anti-CD3 (145-2C11) at 2.5ug/mL (eBioscience) and IL-2 at 100U/mL (R&D Systems).

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
3'mRNA-sequencing libraries were prepared from 100ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturers instruction

treatment_protocol: T-ALL cells were treated with either Panobinostat at 25nM or left untreated as control for 2 hour.

tag: cell type

value: Notch1 T-ALL

value: oncogenic lymphocytes

tag: treated with

value: none (untreated control)


title: M202(Sub1) - midnight - rep 4

description: Random primed libraries


title: M202 - dawn - rep 6

description: Random primed libraries


title: TALL-UT-2h-1_S1


title: M202 - dusk - rep 6

description: Random primed libraries


title: TALL-PANO-2h-1_S6

description: 2 hours treatment

value: 25nM Panobinostat for 2hrs


title: M202 - midday - rep 6

description: Random primed libraries


title: TALL-UT-2h-1_S2


title: TALL-PANO-2h-1_S4

description: 2 hours treatment


title: TALL-PANO-2h-1_S5

description: 2 hours treatment


title: M202(Sub1) - dawn - rep 6

description: Random primed libraries


title: 1_control H3K36me3_ChIPSeq

first: Ni

last: Li

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq  500) were mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis
Tags were extended in silico (using Active Motif software) at their 3´-  ends to a length of 150-250 bp, depending on the average fragment length in the size selected  library (normally 200 bp). To identify the density of fragments (extended tags) along the genome,  the genome was divided into 32-nt bins and the number of fragments in each bin was determined.
Peaks were called using SICER.
Tag Normalization: tag number of all samples was reduced (by random sampling) to the number of tags present in the smallest sample.
"Active Regions" were used when comparing different amples.
Genome_build: mm10
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.

source_name: Intestine

growth_protocol: All mice were maintained in specific-pathogen-free (SPF) facility.

extract_protocol:
The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K36me3(abcam).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

tag: strain background

tag: genotype/variation

value: APCmin

value: post natal 2 months

value: intestine

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot#


title: input.WT.Auxin-0h

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description:
fragmented genomic DNA
Input for 0 h of Auxin treatment in parental cells

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: HCT116 and DLD1 cells were grown in DMEM supplemented with 10% FBS. THP1 cells were grown in RPMI-1640 supplemented with 10% FBS and 55 µM 2-mercaptoethanol.

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit. Total RNA was extracted from cells using RNeasy mini Kit (Qiagen) followed by ribosomal RNA depletion with the RiboZero kit (Epicenter). Poly(A) depleted and Poly(A)-enriched RNA were separated by 3 rounds of Oligo(dT) magnetic beads (Thermo). For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina).
ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq RNA sample Prep Kit using standard protocols.

value: colorectal cancer cell line

tag: cell line

tag: shRNA

value: No shRNA


title: M202(Sub1) - midday - rep 6

description: Random primed libraries

tag: genotype


title: pol2.PAF1-AID.Auxin-4h

description:
fragmented genomic DNA
Chromatin IP of Total Pol II with 4 h of Auxin treatment in PAF1-AID cells


title: pol2.WT.Auxin-4h

description:
fragmented genomic DNA
Chromatin IP of Total Pol II with 4 h of Auxin treatment in parental cells


title: input.PAF1-AID.Auxin-0h

description:
fragmented genomic DNA
Input for 0 h of Auxin treatment in PAF1-AID cells


title: pol2.WT.Auxin-0h

description:
fragmented genomic DNA
Chromatin IP of Total Pol II with 0 h of Auxin treatment in parental cells


title: paf1.43c.abcam_rep1

description:
fragmented genomic DNA
Chromatin IP of PAF1

value: PAF1(Abcam, ab20662)


title: pol2.PAF1-AID.Auxin-1h

description:
fragmented genomic DNA
Chromatin IP of Total Pol II with 1 h of Auxin treatment in PAF1-AID cells


title: pol2.PAF1-AID.Auxin-0h

description:
fragmented genomic DNA
Chromatin IP of Total Pol II with 0 h of Auxin treatment in PAF1-AID cells


title: CD14+ Infected with IBH30656 rep1

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: Zikv 656 set 1

data_processing:
The libraries were run on Illumina Next-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Henomic Workbech 10.0.1 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the human genome database sequence to calculate the RPKM values of cellular gene using CLC Workbench
Relative expressions were calculated with reference of mock infected control cells
Genome_build: NCBI genome build of human genome, Homo sapiens (hg19) sequence
Supplementary_files_format_and_content: .csv file reports RPKMs

source_name: CD14+ Infected with IBH30656

growth_protocol: CD14+ cells were grown in RPMI with 10% FBS

extract_protocol:
Total RNA was extracted from the mock infected control and ZIKV infected cells
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: Cells were infected with ZIKV virus and allowed to grow for 12h

value: purified human CD14+ cells

tag: infection

value: ZIKV virus, IBH30656

tag: time


title: CD14+ Infected with PRVABC59 rep2

description: Zikv 59 set 2

source_name: CD14+ Infected with PRVABC59

value: ZIKV virus, PRVABC59


title: CD14+ Infected with IBH30656 rep2

description: Zikv 656 set 2


title: M202(Sub1) - 3d_sub - rep 2

description: Random primed libraries


title: 3_input DNA

tag: age

tag: tissue


title: CD14+ mock infected control rep1

description: Control set 1

source_name: CD14+ mock infected control

value: Mock infected control

value: control


title: CD14+ mock infected control rep2

description: Control set 2


title: CD14+ Infected with PRVABC59 rep1

description: Zikv 59 set 1


title: 2_Setd2 KO H3K36me3 ChIPSeq

value: APCmin; Setd2IEC-/-


title: rna.WT.shPAF1.rep5

description: total RNA-seq

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
Supplementary_files_format_and_content: The 4Cseqpipe tool was used to map and analyze the 4C-seq experiments.  Using the 4cseqpipe.pl script, fastq files were converted to “raw” format, valid 4C-seq products were mapped to restriction fragments in the genome, aligned data were normalized, and near-cis domainograms were generated. Default options were utilized, and a trend resolution of 10000 was implemented for the domainograms. Output bedgraph files give normalized coverage values across relevant loci corresponding to the published figures.

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit. Total RNA was extracted from cells using RNeasy mini Kit (Qiagen) followed by ribosomal RNA depletion with the RiboZero kit (Epicenter). Poly(A) depleted and Poly(A)-enriched RNA were separated by 3 rounds of Oligo(dT) magnetic beads (Thermo). For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina).
ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq RNA sample Prep Kit using standard protocols. 4C-seq was performed following the protocol published in (van de Werken et al. 2012). In brief, cross-linked chromatin was digested with DpnII, ligated under diluted conditions. Cross-links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions. For each viewpoint approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.

value: Wildtype

value: PAF1 shRNA


title: 26-RBL-Donor-1-P3-D2

city: Boston

first: Sizun

last: Jiang

state: MA

address: 3 Blackfan Circle

institute: BIDMC/Harvard

description: ATAC-seq

data_processing:
Sequencing adapters were trimmed using Trim Galore at default parameters
Paired-end reads were mapped to hg19 using bowtie, with parameters "--chunkmbs 2000 -X 2000", and reads mapping to chrM were removed
Ataqc was used to perform quality control of samples, using default parameters
All reads were subsampled to the lowest sample (13.8 million reads), for sample uniformity
For visualization of the bam files on IGV, igvtools count was used to generate IGV specific TDF visualization files
ngs.plot was used to plot the ATAC reads around EBV Super Enhancers (from Zhou et al 2015) using the following parameters "-N 20 -FL 183 -RB 0.05 -MW 5 -IN 1"
Genome_build: hg19
Supplementary_files_format_and_content: Uniformly sub-sampled bam files, mapped to hg19, for EBV transformed human primary B cells from 1 donor; TDF file

source_name: Primary B cells infected with EBV

growth_protocol: Cells were grown in RPMI media supplemented witth 10% Fetal Bovine Serum, 2 mM glutamine, 1X penicillin and streptomycin.

extract_protocol: ATAC-seq was performed on samples as per described in Buenrostro et al, Nature Methods 2013.

treatment_protocol: Primary B cells were purified from human blood collars using RosetteSep and EasySep B cell kits (StemCell). B cells are infected with EBV virus, titered to ensure >90% of B cells are infected.

value: Primary B cells

tag: ebv strain


title: 29-RBL-Donor-1-WT-D2

description: ATAC-seq


title: 25-RBL-Donor-1-P3-D1

description: ATAC-seq


title: 31-RBL-Donor-1-WT-D7

description: ATAC-seq


title: rna.WT.NONT.rep6

description: total RNA-seq

value: Non-Target shRNA


title: rna.WT.shPAF1.rep6

description: total RNA-seq


title: 28-RBL-Donor-1-WT-D1

description: ATAC-seq


title: rna.WT.NONT.rep5

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO2.shPAF1.rep3

description: total RNA-seq


title: SERPINE2.shPAF1.4C

data_processing:
Library strategy: 4C-Seq
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
Supplementary_files_format_and_content: The 4Cseqpipe tool was used to map and analyze the 4C-seq experiments.  Using the 4cseqpipe.pl script, fastq files were converted to “raw” format, valid 4C-seq products were mapped to restriction fragments in the genome, aligned data were normalized, and near-cis domainograms were generated. Default options were utilized, and a trend resolution of 10000 was implemented for the domainograms. Output bedgraph files give normalized coverage values across relevant loci corresponding to the published figures.


title: 24-RBL-Donor-1-D0

description: ATAC-seq

source_name: Primary B cells


title: 27-RBL-Donor-1-P3-D5

description: ATAC-seq


title: 30-RBL-Donor-1-WT-D5

description: ATAC-seq


title: rna.SERPINE2_enhancer_KO2.NONT.rep3

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO1.shPAF1.rep4

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO1.shPAF1.rep3

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO2.NONT.rep4

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO1.NONT.rep4

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO1.NONT.rep3

description: total RNA-seq


title: rna.IER5_enhancer_KO2.shPAF1.rep4

description: total RNA-seq


title: rna.IER5_enhancer_KO2.shPAF1.rep3

description: total RNA-seq


title: rna.IER5_enhancer_KO2.NONT.rep3

description: total RNA-seq


title: rna.IER5_enhancer_KO2.NONT.rep4

description: total RNA-seq


title: rna.IER5_enhancer_KO1.shPAF1.rep4

description: total RNA-seq


title: rna.IER5_enhancer_KO1.shPAF1.rep3

description: total RNA-seq


title: rna.IER5_enhancer_KO1.NONT.rep3

description: total RNA-seq


title: SERPINE2.NONT.4C


title: rna.SERPINE2_enhancer_KO2.shPAF1.rep4

description: total RNA-seq


title: pol2.shPAF1.43c.rep3

description: Chromatin IP of Total Pol II


title: pol2.NONT.37c.rep3

description: Chromatin IP of Total Pol II


title: pol2.NONT.43c.rep3

description: Chromatin IP of Total Pol II


title: K27ac.shPAF1.37c.rep3

description: Chromatin IP of H3K27ac


title: K27ac.NONT.43c.rep3

description: Chromatin IP of H3K27ac


title: pol2.shPAF1.37c.rep3

description: Chromatin IP of Total Pol II


title: K27ac.NONT.37c.rep3

description: Chromatin IP of H3K27ac


title: total.rna.shPAF1.rep2

description: total RNA-seq


title: total.rna.shPAF1.rep1

description: total RNA-seq


title: rna.WT.NONT.rep1

description: total RNA-seq


title: rna.WT.NONT.rep2

description: total RNA-seq


title: rna.WT.NONT.rep3

description: total RNA-seq


title: rna.WT.NONT.rep4

description: total RNA-seq


title: rna.WT.shPAF1.rep2

description: total RNA-seq


title: total.rna.NONT.rep1

description: total RNA-seq


title: rna.WT.shPAF1.rep4

description: total RNA-seq


title: rna.WT.shPAF1.rep3

description: total RNA-seq


title: total.rna.NONT.rep2

description: total RNA-seq


title: rna.WT.shPAF1.rep1

description: total RNA-seq


title: rna.IER5_enhancer_KO1.NONT.rep4

description: total RNA-seq


title: rna.IER5_enhancer_KO#2.NONT.rep2

description: total RNA-seq


title: rna.IER5_enhancer_KO#2.NONT.rep1

description: total RNA-seq


title: rna.IER5_enhancer_KO#1.shPAF1.rep2

description: total RNA-seq


title: rna.IER5_enhancer_KO#1.shPAF1.rep1

description: total RNA-seq


title: rna.IER5_enhancer_KO#1.NONT.rep1

description: total RNA-seq


title: rna.IER5_enhancer_KO#1.NONT.rep2

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO#2.shPAF1.rep2

description: total RNA-seq


title: K27ac.shPAF1.43c.rep3

description: Chromatin IP of H3K27ac


title: rna.IER5_enhancer_KO#2.shPAF1.rep1

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO#1.shPAF1.rep2

description: total RNA-seq


title: rna.IER5_enhancer_KO#2.shPAF1.rep2

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO#2.NONT.rep1

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO#1.shPAF1.rep1

description: total RNA-seq


title: polyA.enriched.shPAF1.rep2

description: RNA-seq of poly(A)-enriched RNA


title: rna.SERPINE2_enhancer_KO#1.NONT.rep1

description: total RNA-seq


title: polyA.enriched.shPAF1.rep1

description: RNA-seq of poly(A)-enriched RNA


title: polyA.depleted.NONT.rep2

description: RNA-seq of poly(A)-depleted RNA


title: pol2.WT.shPAF1.rep2

description:
fragmented genomic DNA
Chromatin IP of Total Pol II

value: Pol II (CST, catalog# 14958, lot# 1)


title: polyA.depleted.NONT.rep1

description: RNA-seq of poly(A)-depleted RNA


title: polyA.depleted.shPAF1.rep2

description: RNA-seq of poly(A)-depleted RNA


title: polyA.enriched.NONT.rep1

description: RNA-seq of poly(A)-enriched RNA


title: polyA.depleted.shPAF1.rep1

description: RNA-seq of poly(A)-depleted RNA


title: polyA.enriched.NONT.rep2

description: RNA-seq of poly(A)-enriched RNA


title: pol2.shPAF1.37c.rep1


title: pol2.shPAF1.43c.rep2


title: pol2.WT.shPAF1.rep1


title: pol2.WT.NONT.rep1


title: pol2.NONT.42c.rep1


title: pol2.NONT.37c.rep2


title: pol2.shPAF1.42c.rep1


title: pol2.NONT.37c.rep1


title: pol2.WT.NONT.rep2


title: pol2.NONT.43c.rep2


title: pol2.IER5_enhancer_KO#2.shPAF1.rep2


title: rna.SERPINE2_enhancer_KO#1.NONT.rep2

description: total RNA-seq


title: rna.SERPINE2_enhancer_KO#2.NONT.rep2

description: total RNA-seq


title: pol2.IER5_enhancer_KO#2.shPAF1.rep1


title: pol2.IER5_enhancer_KO#1.shPAF1.rep1


title: pol2.IER5_enhancer_KO#2.NONT.rep1


title: pol2.IER5_enhancer_KO#1.shPAF1.rep2


title: pol2.IER5_enhancer_KO#2.NONT.rep2


title: pol2.IER5_enhancer_KO#1.NONT.rep1


title: rna.SERPINE2_enhancer_KO#2.shPAF1.rep1

description: total RNA-seq


title: pol2.IER5_enhancer_KO#1.NONT.rep2


title: pol2.SERPINE2_enhancer_KO#2.shPAF1.rep2


title: pol2.SERPINE2_enhancer_KO#1.shPAF1.rep2


title: pol2.SERPINE2_enhancer_KO#1.shPAF1.rep1


title: pol2.SERPINE2_enhancer_KO#2.NONT.rep2


title: pol2.SERPINE2_enhancer_KO#2.NONT.rep1


title: paf1.santa

value: PAF1 (Santa Cruz, catalog# sc-74797)


title: pol2.SERPINE2_enhancer_KO#1.NONT.rep1


title: paf1.abcam_rep2

value: PAF1 (Abcam, catalog# ab20662, lot# GR243511-1)


title: pol2.SERPINE2_enhancer_KO#1.NONT.rep2


title: k27ac.shPAF1.rep1

description:
fragmented genomic DNA
Chromatin IP of H3K27ac

value: H3K27ac  (CST, catalog# 8173, lot# 1)


title: k27ac.shPAF1.rep2

value: colorectal cancer cell line


title: paf1.37c.abcam_rep1

value: No shRNA


title: pol2.shPAF1.37c.rep2


title: k27ac.NONT.rep1


title: k27ac.NONT.rep2


title: input.shPAF1.42c

description:
fragmented genomic DNA
Input DNA from whole cell extract


title: input.shPAF1.37c


title: input.paf1


title: input.NONT.42c


title: input.NONT.37c


title: THAL_SNS_6h_RNA-seq_replicate2

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
RNA-seq after 6 hr THAL-SNS-032 (250 nM) treatment
THAL_SNS_6h_replicate_1

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

growth_protocol: RPMI with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Prior to RNA isolation, cell were counted and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.
Total RNA was subject to polyA selection and adapter ligation in preparation for next-generation sequencing (Illumina stranded mRNA library prep)

treatment_protocol: See previous section for treatment conditions

value: T-acute lymphoblastic leukemia (T-ALL) cell line

value: 250nM THAL-SNS-032 for 6hrs

tag: barcode

value: AGTTCC


title: SNS_6h_RNA-seq_replicate2

description:
RNA-seq after 6 hr SNS-032 (250 nM) treatment
SNS32_6h_replicate_1

tag: cell type

value: 250nM SNS-032 for 6hrs

value: GGCTAC


title: THAL_SNS_6h_RNA-seq_replicate3

description:
RNA-seq after 6 hr THAL-SNS-032 (250 nM) treatment
THAL_SNS_6h_replicate_2

tag: treated with

value: ATGTCA


title: SNS_6h_RNA-seq_replicate1

description:
RNA-seq after 6 hr SNS-032 (250 nM) treatment
SNS32_6h_replicate_0

value: TAGCTT


title: THAL_SNS_6h_RNA-seq_replicate1

description:
RNA-seq after 6 hr THAL-SNS-032 (250 nM) treatment
THAL_SNS_6h_replicate_0

value: AGTCAA


title: SNS_6h_RNA-seq_replicate3

description:
RNA-seq after 6 hr SNS-032 (250 nM) treatment
SNS32_6h_replicate_2

value: CTTGTA


title: k4m1

description:
fragmented genomic DNA
Chromatin IP of H3K4me1

value: H3K4me1  (homemade)


title: DMSO_6h_RNA-seq_replicate3

description:
RNA-seq after 6hr DMSO (0.1%) treatment
DMSO_6h_replicate_2

value: 0.1% DMSO for 6hrs

value: TTAGGC


title: DMSO_6h_RNA-seq_replicate2

description:
RNA-seq after 6hr DMSO (0.1%) treatment
DMSO_6h_replicate_1

value: CGATGT


title: NVP2_6h_RNA-seq_replicate3

description:
RNA-seq after 6hr NVP-2 (250 nM) treatment
NVP2_6h_replicate_2

value: 250nM NVP-2 for 6 hrs

value: GTGAAA


title: MOLT4_pol2_DMSO_ChIP-seq

description: Chromatin IP against RNA Pol II

data_processing:
For all samples reads were aligned to their indicated build using bowtie2 with parameters -k 1
MACS1.4 with p-value = 1e-9 and default parameters was sued to call peaks and generate wiggles
Genome_build: hg19
Supplementary_files_format_and_content: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: T-ALL

growth_protocol:
cells were cultured in RPMI-10%FCS
cells were cultured in RPMI-10%FCS

extract_protocol:
Standard DNA extraction from MOLT4 cell lines using cell lysis. Probe sonicator 3 minutes total sonication time (1 sec on, 4 sec off, 40% amplitude) on ice
library prep with Rubicon ThruPlex kit

treatment_protocol: See previous section

value: DMSO (0.1%) for 2 hours

value: RNA Pol II

value: Santa Cruz

tag: chip antibody catalog no.

tag: input sample

tag: sequencing barcode

value: ACAGTGGT


title: NVP2_6h_RNA-seq_replicate2

description:
RNA-seq after 6hr NVP-2 (250 nM) treatment
NVP2_6h_replicate_1

value: T-acute lymphoblastic leukemia (T-ALL) cell line

value: GTCCGC


title: MOLT4_pol2_THAL_ChIP-seq

description: Chromatin IP against RNA Pol II

value: THAL-SNS-032 (250 nM) for 2 hours

tag: chip antibody

tag: chip antibody vendor

value: TCGAAGTG


city: Walnut Creek

first: Denis

last: Tolkunov

address: 2800 Mitchell Dr

institute: DOE Joint Genome Institute

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: N.oceanica_IMET1 (http://www.bioenergychina.org/fg/d.wang_genomes/)
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files

organism: Nannochloropsis oceanica

source_name: Nannochloropsis oceanica (IMET1, log phase)_Whole organism

extract_protocol:
N. oceanica IMET1 was cultivated in f/2 liquid medium with 4mM NO3- under continuous light at 50 micromol photons m^(-2)s^(-1) until mid-log phase. Culture was pelleted and nucleic acid was extracted using phenol-chlorophorm and treated with RNase to degrade RNA.
5-10ug of gDNA was sheared to >10kb using g-tube (Covaris). The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of SMRT hairpin adapters using SMRTbell Template Preparation Reagent Kit (Pacific Biosciences). Fragments without adaptors are digested with exonuclease. Libraries were sequenced on Pacific Biosciences RSII sequencer using standard protocols.

tag: strain

tag: growth phase

value: log phase


title: MOLT4_pol2_SNS_ChIP-seq

description: Chromatin IP against RNA Pol II

tag: cell line

value: SNS-032 (250 nM) for 2 hours

value: TTCCATTG


title: MOLT4_SPT5_THAL_ChIP-seq

description: Chromatin IP against SPT5

value: TAGTCTTG


title: DMSO_6h_RNA-seq_replicate1

description:
RNA-seq after 6hr DMSO (0.1%) treatment
DMSO_6h_replicate_0

value: 0.1% DMSO for 6hrs

value: ATCACG


title: MOLT4_SPT5_SNS_ChIP-seq

description: Chromatin IP against SPT5


title: MOLT4_ChIP-seq_input

description: input sample for background measurement

value: ATCACTTT


title: MOLT4_SPT5_NVP2_ChIP-seq

description: Chromatin IP against SPT5

value: NVP-2 (250 nM) for 2 hours

value: TGTGGTTG


title: MOLT4_SPT5_DMSO_ChIP-seq

description: Chromatin IP against SPT5

value: DMSO (0.1%) for 2 hours

value: TCCTCAAT


title: RNASeq_DU_DMSO duplicate 2

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Reads were mapped to hg19 assembly using TopHat version 2.0.6.
DESeq2 was used to calculate the fold change and p-value of differntialy expression.
Genome_build: Hg19
Supplementary_files_format_and_content: DESeq2 output with fold change and p-value of differntialy expression

growth_protocol: Both DU145 and LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI1640 with 10% charcoal-stripped FBS plus 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted using TRIZol Reagent and purified with RNeasy Mini Kit (Qiagen) according to the kit manual.
Libraries were constructed using Illumina True-seq RNA sample preparation kit.

treatment_protocol: Both types of cells were treated with vehicle (DMSO), GSK126 or EPZ-6438 at final concentrations of 5 uM for 60-72 hrs before the RNA samples were collected.

tag: cell types

value: castration resitant prostate cancer cells

tag: cell phenotype

value: AR-negative, EZH2 inhibitor-insensitive

tag: passages

value: vehicle (DMSO)


title: RNASeq_DU_GSK duplicate 1


title: RNASeq_DU_GSK duplicate 2


title: RNASeq_DU_EPZ duplicate 1


title: RNASeq_abl_GSK duplicate 1

value: LNCaP-abl (abl)

value: AR-positive, EZH2 inhibitor-sensitive


title: RNASeq_abl_GSK duplicate 2


title: RNASeq_abl_EPZ duplicate 2


title: RNASeq_abl_EPZ duplicate 1


title: NVP2_6h_RNA-seq_replicate1

description:
RNA-seq after 6hr NVP-2 (250 nM) treatment
NVP2_6h_replicate_0

value: T-acute lymphoblastic leukemia (T-ALL) cell line

value: 250nM NVP-2 for 6 hrs

value: CCGTCC


title: RNASeq_abl_DMSO duplicate 2


title: RNASeq_abl_DMSO duplicate 1


title: H3K27me3 ChIPSeq_DU145_GSK treated

data_processing:
FASTQ files were mapped to hg19 (Homo Sapiens) and dm3 (Drosophila melanogaster) assemblies respectively using BOWTIE (version 0.12.7); duplicated reads were removed.
ChIP-Seq peaks and bigwig files were called and generated using MACS2 (version 2.1.0)
Genome_build: hg19 (human) and dm3 (drosophila)
Supplementary_files_format_and_content: BED files, containging the location of the peaks
Supplementary_files_format_and_content: BigWig files, containing the enrichment information

source_name: DU145_GSK treated

extract_protocol:
Prostate cancer cells were crosslinked with 1% formaldehyde and lysed in RIPA buffer with 0.3 M NaCl. ChIP DNA was purified using PCR Purification Kit (Qiagen) and then quantified by Quant-iTTM dsDNA HS Assay Kit (Invitrogen).
ChIP-Seq libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics) according to the manufacturer's protocol.

treatment_protocol: Both types of cells were treated with vehicle (DMSO), GSK126 or EPZ-6438 at final concentrations of 5 uM for 4-5 days before the cells were crosslinked and collected.

value: H3K27 trimethylation (Cell Signaling, C36B11, #9733S) and H2Av (Active Motif 39715)


title: H3K27me3 ChIPSeq_DU145_EPZ treated

source_name: DU145_EPZ treated


title: H3K27me3 ChIPSeq_DU145_DMSO treated

source_name: DU145_DMSO treated


title: RNASeq_DU_DMSO duplicate 1


title: RNASeq_DU_EPZ duplicate 2


title: MOLT4_pol2_NVP2_ChIP-seq

description: Chromatin IP against RNA Pol II

value: RNA Pol II

value: Santa Cruz

value: GCCAATGT


title: H3K27me3 ChIPSeq_abl_GSK treated

source_name: abl_GSK treated


title: H3K27me3 ChIPSeq_abl_DMSO treated

source_name: abl_DMSO treated


title: pol2.SERPINE2_enhancer_KO#2.shPAF1.rep1

value: colorectal cancer cell line

tag: shRNA

value: PAF1 shRNA

value: Pol II (CST, catalog# 14958, lot# 1)


title: ES-Spt6KD_exp_rep3

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were mapped to the mm9 genome assembly using Bowtie2 version 2.2.4 with the default configurations.
RNA-seq reads were mapped to the mm9 genome assembly using TopHat version 2.0.13 (Trapnell C, et.al 2009) with the default configurations.
peaks were called using SICER version 1.1 ( Zang et al, 2009) with the following setting: redundancy threshold (1), window size (200), fragment size (150), effective genome fraction (0.74), gap size (600),FDR (0.05) .
FPKM(RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample;tab-delimited text files includes FPKM values for each Sample.

growth_protocol: ESCs grow on gelatin-coated dishes in ES medium (DMEM, 15% HyClone FBS, GlutaMAX, MEM nonessential amino acids, sodium pyruvate, leukaemia inhibitory[LIF], β-mercaptoethanol)

extract_protocol:
For ChIPSeq,cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments.  Lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq,  10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with  Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) were used to process RNA-Seq samples following the manufacturer’s protocol.

treatment_protocol: Cells were transfected with control and Spt6 siRNA with RNAiMAX according to manufacturer's protocol.

tag: developmental stage

value: embryonic stem cell and Spt6KD, blastocyst derived

tag: transfection

value: Spt6 siRNA


title: ES_Spt6i_H3K36me3_chip_input_rep2

value: embryonic stem cell, blastocyst derived


title: ES-Ctli_exp_rep2

value: control siRNA


title: ES_Ctli_input_chip


title: ES-Ctli_exp_rep3


title: ES-Ctli_exp_rep1


title: ES_Spt6i_input_chip


title: ES-Spt6KD_exp_rep2


title: ES-Spt6i-H3K27me3_rep1


title: ES_Ctli_H3K36me3_chip_input_rep1


title: ES_Ctli_H3K36me3_chip_input_rep2


title: ES-Spt6i-H3K27me3_rep2


title: ES_Spt6i_H3K36me3_chip_input_rep1


title: ES-Spt6i-H3K36me3_rep2


title: ES-Spt6i-H3K27ac_rep2


title: ES-Spt6KD_exp_rep1


title: ES-Ctli-H3K27me3_rep2


title: ES-Ctli-H3K36me3_rep2


title: ES-Ctli-H3K36me3_rep1


title: ES-Spt6i-H3K27ac_rep1


title: ES-Ctli-H3K27ac_rep2


title: ES-E14-inputDNA_chip_rep2


title: ES-Ctli-H3K27ac_rep1


title: ES-E14-Spt6_rep2


title: ES-E14-inputDNA_chip_rep1


title: ES-E14-Ezh2_rep2


title: wt_2

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Ribo-zero depleted RNA

data_processing:
Base calls were performed using bcl2fastq2 version 2.18
Reads were aligned to UCSC sacCer3 using tophat version 2.0.13 with the -g 1 parameter.
Reads were quantified on genes using the countOverlap function in the Bioconductor package GenomicFeatures.
RPKM values were determined using Bioconductor package edgeR version edgeR_3.14.0 using the count of mapped reads on the intervals for each gene.
Genome_build: sacCer3
Supplementary_files_format_and_content: rpkm.txt text file of expression values per sample in RPKM format.

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Overnight cultures of WT and mutant strains grown in duplicate in appropriate raffinose media.

extract_protocol:
Cells were pelleted, frozen in liq. N2, and stored in -80°C until used. The cell pellet was resuspended in 800ul of cold AE Buffer (50mM NaOAc (pH 5.2), 10mM EDTA in RNase Free water). 80µl of 10% SDS and 800ul acid phenol (pH 4.3) (Ambion# AM9720) were added and incubated for 10min at 65°C. The cell suspension was incubated on ice for 5min and centrifuged for 15min at 14K rpm, 4°C. The supernatant was transferred to a fresh tube, 800ul of Chloroform was added and centrifuged for 15min at 14K rpm, 4°C. Chloroform extraction step was repeated one more time and the supernatant was transferred to a fresh tube. Next 10µg of linear acrylamide, 3M NaOAc, pH 5.2-5.6 (1/10th of total volume) and isopropanol (volume equal to total volume) were added and centrifuged for 15min at 14K rpm, 4°C. The pellet was washed with 1ml 70% Ethanol and resuspended in ~100µl TE buffer (10mM Tris pH8.0, 0.1mM EDTA in RNase Free water). The RNA extract was chilled first on ice for 5 min, then 20 sec at 65° C. It was mixed by gentle vortexing and chilled on ice. RNA integrity was checked following isolation using an Agilent Technologies 2100 Bioanalyzer. The RNA concentration was measured using Qubit 2.0 Fluorometer.
Ribosomal RNA was depleted from 1000 ng total RNA using Ribo-ZeroTM Magnetic Gold Kit (Yeast) (Illumina, MRZY1324) per manufacturer’s instructions. Following depletion, Illumina libraries were generated using the TruSeq Stranded RNA LT kit with Ribo-Zero Gold, 48; Set A (Illumina, RS-122-2301).

treatment_protocol: Overnight cultures were diluted to OD600 of 0.1. After 2h at 30°C, Cse4 overexpression was induced by adding galactose to a final concentration of 4% and cultures were grown at 30°C for 10h.

tag: replicate

tag: genotype

value: WT


title: ES-E14-Ezh2_rep1


title: H3K27me3 ChIPSeq_abl_EPZ treated

source_name: abl_EPZ treated

value: LNCaP-abl (abl)

value: castration resitant prostate cancer cells

tag: treated with


title: wt_1

description: Ribo-zero depleted RNA


title: ES-Spt6i-H3K36me3_rep1


title: psh1_cac2_2

description: Ribo-zero depleted RNA

value: psh1 cac2 mutant


title: EphB1 treated rep 1 (Mm)

city: Edinburgh

first: Christopher

last: Sibley

address: 1 George Square

country: United Kingdom

institute: University of Edinburgh

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using fastx_clipper and converted to reverse complement with fastx_reverse_complement (both fastx_toolkit v0.0.14)
Reads were mapped to mm10 with annotation mm10.GRCm38.gtf using tophat2 (v2.0.11)
Reads were sorted and indexed using samtools (v0.1.19)
Sorted sam files were used as input to ht-seq count against mm10.GRCm38.gtf
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each Sample ...

source_name: EphB1 treated, purified astrocytes

growth_protocol: Purified astrocytes were cultured for 6 weeks (mature astrocytes) in 10% fetal bovine serum, 1mM GlutaMAX in Dulbecco’s modified Eagle medium (DMEM, Life Technologies) to provide cells for in vitro assays

extract_protocol:
RNeasy plus mini kit (Qiagen)
Illumina TruSeq RNA Access library preparation kit

treatment_protocol: One hour serum starvation then 11hrs untreated or 11hrs treatment with either IL-6 or EphB1

tag: cell type

value: Purified astrocytes

tag: agent


title: psh1_cac2_1

description: Ribo-zero depleted RNA


title: IL6 treated rep 2 (Mm)

source_name: IL6 treated, purified astrocytes


title: IL6 treated rep 1 (Mm)


title: psh1_2

description: Ribo-zero depleted RNA

value: psh1 mutant


title: Untreated rep 2 (Mm)

source_name: Untreated, purified astrocytes

value: control


title: psh1_1

description: Ribo-zero depleted RNA


title: Untreated rep 1 (Mm)


title: EphB1 treated rep 2 (Mm)


title: cac2_1

description: Ribo-zero depleted RNA

value: cac2 mutant


title: 6359_C

city: Cambridge

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

data_processing:
Bowtie2 (v. 2.2.2) and Tophat (v2.0.11) used to align reads.
Cufflinks (v2.2.1) used to transform aligned reads into transcripts, and determine FPKM.
Genome_build: Reference genome: GRCm38; Annotation reference: Ensembl_70
Supplementary_files_format_and_content: FPKMs

source_name: Umod+ Cells

extract_protocol:
Total RNA was isolated from whole kidney tissue and Umod+ cells using the RNeasy Plus Mini extraction kit (Qiagen) according to manufacturer's recommendations.
The library preparation was done using TruSeq® Stranded mRNA Sample preparation kit (Illumina inc).

value: C57BL/6 J

tag: genotype (umod)

tag: age

value: Umod+ Cells


title: 6442_C

value: HE


title: 6443_C


title: 6357_C


title: 6763_C


title: 6764_C


title: 6456_C


title: ES-Ctli-H3K27me3_rep1

tag: chip antibody


title: 6723_C

tag: strain


title: 6724_C


title: 6446_C


title: ES-E14-Spt6_rep1


title: 6445_C


title: 6453_C


title: 6458_C


title: 6444_C


title: 6454_C


title: cac2_2

description: Ribo-zero depleted RNA


title: 6470_C


title: 6460_C


title: 6468_C


title: 6462_C


title: 6463_C


title: 6467_C


title: 6469_C


title: 6358_C


title: 6448_C


title: 6437_C


title: 6452_C


title: 6466_C


title: 6449_C


title: 6434_C


title: 6451_C


title: 6440_C


title: 6459_C


title: 6465_C


title: 6461_C


title: 6501_C


title: 6447_C


title: 6431_C


title: 6505_C


title: 6478_C


title: 6504_C


title: 6481_C


title: 6475_C


title: 6353_T

source_name: Kidney

tag: tissue

value: Kidney


title: 6479_C


title: 6352_T


title: 6355_T


title: 6477_C


title: 6474_C


title: 6443_T


title: 6354_T


title: 6441_T


title: 6359_T


title: 6442_T


title: 6473_C


title: 6272_T


title: 6471_C


title: 6349_T


title: 6476_C


title: 6472_C


title: 6348_T


title: 6433_T


title: 6502_C


title: 6503_C


title: 6432_T


title: 6482_C


title: 6358_T


title: 6357_T


title: 6265_T


title: 6350_T


title: 6263_T


title: 6347_T


title: 6465_T


title: 6346_T


title: 6464_T


title: 6271_T


title: 6440_T


title: 6436_T


title: 6264_T


title: 6439_T


title: 6451_T


title: 6461_T


title: 6462_T


title: 6434_T


title: 6449_T


title: 6466_T


title: 6431_T


title: 6504_T


title: 6438_T


title: 6435_T


title: 6448_T


title: 6463_T


title: 6505_T


title: 6437_T


title: 6502_T


title: 6482_T


title: 6479_T


title: 6477_T


title: 6476_T


title: 6472_T


title: 6478_T


title: 6481_T


title: 6459_T


title: 6474_T


title: piggyBac transposon insertion_1_3

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

description: processed data: PCR_sample_annotation1.txt

data_processing:
Basecalls performed by Casava using default settings
Only the reads contained the PB sequences were used for the alignment analysis. And after trimming the PB and adapter sequences by the perl scripts, the reads were aligned to the mouse reference genome (mm9) by the BWA (Li and Durbin, 2009) with default parameters. The alignments with unique genomic location used for the next analysis. As previously described methods (Li et al., 2014), the alignments were used to calculate distribution mode in different genomic regions, such as UTR, CDS, and intergenic regions.
Genome_build: mm9
Supplementary_files_format_and_content: piggyBac read counts on gene; tab-delimited text files including gene name (col 1), the refseq transcripts (col 2), the number of nonredundant reads mapped to gene (col 3) and the number of redundant reads mapped to gene (col 4).

source_name: The mouse haploid NSCLC_piggyBac transposon insertion

growth_protocol: The mouse haploid embryonic stem cells (haESCs) were cultured in suspension for Embryoid body(EB) formation for 3 days. After 3 days the EBs were attached into dished coated with 0.2% gelatin (Sigma), and the medium was changed to NSCLC differentiation medium. The haploid neural stem cell-like cells (NSCLC) differentiation medium consists of N2B27 medium supplemented with 20 ng/ml FGF2, 20 ng/ml EGF, 300 nM LDN193189 (MCE), 10 μM SB431542 (Stemgent) and ROCK inhibitor. The ROCK inhibitor was supplemented as 20 μM Y-27632 (MCE), or 4 μM Thiazovivin (MCE), or 10 μM Y-27632 (MCE) plus 2 μM Thiazovivin (MCE). Five days later when the cells became confluent, they were dissociated into single cells and attached on dishes coated with Poly-D-Lysine (100 μg/ml) and laminin (100 ng/ml), and culture in NSCLC medium for another 4 days. At day 10 after initial induction, the differentiated cells were dissociated DNA content analysis.

extract_protocol:
To identify the trapping sites of piggyBac transposon in a pool of cells, the splinkerette PCR protocol was performed as previously described (Leeb et al., 2014; Li et al., 2014; Potter and Luo, 2010).
In brief, the integration sites in genome were amplified using nested PCR after ligation with Splinkerette adapters. And the PCR products were sequenced with on HiSeq 2500.

treatment_protocol: To generate the mutant library, 10e7 of haploid NSCLCs were transfected using Lipofectamine LTX and PLUS reagents (Invitrogen, 15338100) with 20 μg piggyBac gene trapping plasmid and 10 μg codon optimized PB transposase. G418 was used to select gene trap insertions. An adapted inverse PCR protocol was based on previously reported (Chen et al., 2015a)

tag: strain background

value: mouse haploid neural stem cell-like cells (NSCLC)


title: piggyBac transposon insertion_2_3

description: processed data: PCR_sample_annotation2.txt


title: 6473_T


title: piggyBac transposon insertion_2_5


title: 6475_T


title: piggyBac transposon insertion_1_5


title: 6503_T


title: G17V TMX rep 1

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format and adaptor trimming.
Sequenced reads were aligned to GRCm38 genome usinusing HiSat2 (v2.0.5) and transcript FPKM was computed using Stringtie (v1.2.4).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD4+ T Lymphocytes

extract_protocol:
Total RNA was extracted using TriZol and purified using Rneasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols including Poly A enrichment using oligo-dT selection.

value: CD4+ T Lymphocytes

value: spleen

value: CD4 Cre ERT2 RhoA G17V FLOX/+

tag: treatment

value: Tamoxifen


title: G17V veh rep 1

value: vehicle


title: G17V veh rep 2


title: WT TMX rep 2

value: CD4 Cre ERT2 RhoA +/+


title: WT veh rep 1


title: WT veh rep 2


title: VMH-Fed-6

city: Box 289, Addenbrooke’s Hospital

first: Joseph

last: Polex-Wolf

state: Cambridgeshire

address: Wellcome Trust-MRC Institute of Metabolic Science

department: Metabolic Research Laboratories

institute: University of Cambridge

data_processing:
Basecalls performed using CASAVA 1.7
Reads were aligned to the mouse genome (GRCm38) using Tophat v2.0.11
Counts were determined using Cufflinks v2.2.1
Count normalisation was performed using the edgeR and limma packages in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Reads Per Kilobase of transcript per Million mapped reads (RPKM)

source_name: laser-captured hypothalamic nucleus (region)

extract_protocol:
Hypothalamic nuclei were laser-capture microdissection from cryosections using a P.A.L.M Microlaser system, and RNA extracting using the miRNeasy micro RNA extraction kit (Qiagen).
Total RNA was amplified using an Ovation RNA-Seq System V2 (NuGEN), after which cDNA libraries were prepared using the Encore Rapid DR Multiplex System (NuGEN).

treatment_protocol: Wild-type male C57/BL6 mice were either ad-libitum fed or fasted for 24-hours prior to brain dissection.

tag: nutritional state

value: Ad libitum fed

value: ventromedial nucleus

tag: gender

value: male


title: VMH-Fed-5


title: VMH-Fed-4


title: VMH-Fed-3


title: VMH-Fed-1


title: 6471_T


title: VMH-Fed-2


title: VMH-Fast-6

value: 24 hour fasted


title: VMH-Fast-3


title: VMH-Fast-5


title: VMH-Fast-2


title: G17V TMX rep 2


title: VMH-Fast-4


title: VMH-Fast-1


title: PVN-Fed-6

value: paraventricular nucleus


title: WT TMX rep 1


title: PVN-Fed-5


title: PVN-Fed-4


title: PVN-Fed-1


title: PVN-Fast-5


title: PVN-Fast-4


title: PVN-Fed-2


title: PVN-Fast-3


title: DMH-Fed-4

value: dorsomedial nucleus


title: PVN-Fast-1


title: DMH-Fed-3


title: DMH-Fed-5


title: DMH-Fed-2


title: PVN-Fast-2


title: DMH-Fast-1


title: ARC-Fed-5

value: arcuate nucleus


title: DMH-Fast-2


title: DMH-Fast-3


title: ARC-Fed-4


title: DMH-Fast-4


title: ARC-Fed-2


title: ARC-Fed-3


title: ARC-Fed-1


title: ARC-Fast-1


title: ARC-Fast-5


title: ARC-Fast-2


title: ARC-Fast-4


title: PVN-Fed-3


title: PTC1a

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

institute: Xidian University

description: Sample 3

data_processing:
reads are mapped using the Tophat software using default parameters
only the unique mapped reads are obtained for downstream analysis using samtool
use the cufflink to obtain the expression level of genes (Reads Per Kilobase of exon per Megabase of library size (RPKM) )
use the EdgeR software to obtain the differentially expressed genes
Genome_build: NONCODE v4.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: timepoint-1  2week proximal tubular cells  after STZ injection (Diabetes model)

growth_protocol: Fresh PTCs were isolated by Fluorescence-activated cell sorting (FACS) in animal model during dynamic progression of DN

extract_protocol:
Sorted PTCs were lysed with Trizol-LS immediately (Ambion), and total RNA was prepared using RNeasy Plus Mini Kit (Qiagen) per manufacturers’ instructions. Total RNA concentration was measured by Qubit 2.0 Fluorometer (Invitrogen), and RNA quality was evaluated using Agilent 2100 Bioanalyzer (Agilent).
RNA-seq libraries were prepared with Ovation RNA-Seq System V2 Kit (NuGEN) per manufacturer’s instruction.

treatment_protocol: Diabetes models were constructed by injection of streptozocin(STZ), then mice PTCs were isolated by FACS for direct RNA extraction without extra treatment..

value: Primary cells - proximal tubular cells of kidney


title: PTC2a

description: Sample 5

source_name: timepoint-2  4week proximal tubular cells  after STZ injection (Diabetes model)


title: PTC2b

description: Sample 6


title: PTC3b

description: Sample 8

source_name: timepoint-3  8week proximal tubular cells  after STZ injection (Diabetes model)


title: PTC3a

description: Sample 7


title: PTC0b

description: Sample 2

source_name: timepoint-0  0week proximal tubular cells without STZ injection(Control non-diabetes model)


title: PTC1b

description: Sample 4


title: DMH-Fed-1


title: PTC0a

description: Sample 1


title: BCP

city: Chengdu

first: Wei

last: Liu

address: Wangjiang Road 29

department: college of life sciences

institute: Sichuan university

description: 13-41 nt small RNAs

data_processing:
The adaptor sequences in raw reads and low quality reads were removed using FASTX-Toolkit V0.0.13.
The small RNA reads with length of 13-40 nt were mapped to the genome (MSU 7) and previously predicted tRNA gene using bowtie V1.1.2  with parameters -f -m 1 -t --best --strata.
Genome_build: MSU7
Supplementary_files_format_and_content: counts

organism: Oryza sativa

source_name: Rice bicellular pollen

growth_protocol: Rice grown under Southwest China's natural field conditions

extract_protocol:
Extraction of total RNA was performed using MiR VanaTM RNA Isolation Kit (Ambion), according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tissue samples were collected at sunny noon on July. Collected biological samples were frozen in liquid nitrogen and kept -80 ℃ until RNA extraction.

tag: cultivar

value: Guichao No.2

value: pollen

value: bicellular pollen


title: UNM

description: 13-40 nt small RNAs

source_name: Rice uninucleate microspore

tag: developmental stage

value: uninucleate microspore