title: Organoid scASO n4

description: polyA+ RNA

value: scASO


title: Organoid Mock n4

status: Public on Jan 12 2016

type: SRA

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: polyA+ RNA

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm9 using STAR.
The GENCODE mV1 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Mammary tumor

growth_protocol: Organoids from MMTV-PyMT tumors were prepared as described previously (Ewald AJ et al, Dev. Cell 2008) and cultured in matrigel in the presence of FGF2.

extract_protocol:
Total RNA was extracted using TRIzol reagent from both organoids and homogenized tumor tissue.
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)

treatment_protocol: Tumors: 125 mg/kg/week of ASOs targeting Malat1 or ScASO were injected subcutaneously into MMTV-PyMT mice for several weeks. Organoids: 500 nM of Malat1 ASO1, ASO2 or ScASO were added to the medium and replenished after 3 days. Total treatment time: 6 days.

tag: strain

tag: genotype

value: MMTV-PyMT

tag: tissue

value: Mammary tumor

tag: treatment

value: Mock


title: Organoid scASO n1

description: polyA+ RNA


title: Organoid scASO n2

description: polyA+ RNA


title: Organoid Mock n1

description: polyA+ RNA


title: Organoid ASO2 n3

description: polyA+ RNA

value: Malat1 ASO2


title: Organoid scASO n3

description: polyA+ RNA


title: Organoid ASO1 n4

description: polyA+ RNA

value: Malat1 ASO1


title: Organoid ASO2 n1

description: polyA+ RNA


title: Senes_Untreated_Replicate_3

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

data_processing:
Reads were trimmed using Trim Galore (v0.3.0).
Paired-end reads are aligned to the human genome (hg19) using tophat2. Reference splice junctions were provided by a reference transcriptome (Ensembl build 73).
FPKMs were determined using cufflinks under default settings.
Differentially expressed genes were called using cuffdiff under default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of FPKMs for all samples, as called by cufflinks. Differential gene expression for uninduced vs induced samples, as called by cuffdiff.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MRC5 human fibroblasts were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma, Dorset, UK) supplemented with 10% heat inactivated foetal calf serum (FCS), 100 units/ml penicillin, 100 μgml-1 streptomycin, 2mM glutamine and 50 μgml-1 uridine at 37oC in a humidified atmosphere incubator with 5% CO2

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit according to the manufacturer instructions with on the column DNASE I digestion.
Quality of RNA was assessed on Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit (Agilen Technologis), before creating oligo-dT based cDNA library using Illumina TruSeq RNA Sample Prep Kit,v2.0. kit.
The library was sequenced on a NextSeq500, using a NextSeq500 Mid Output kit 150 cycles flowcell.

treatment_protocol: Parkin-expressing MRC5 fibroblasts were irradiated with 20Gy X-ray and 2 days after were treated with 12.5uM CCCP for 48h (refreshed every 24 hours). At day 4 after irradiation, CCCP was removed and cells were kept in culture with normal serum supplemented medium. Cells were harvested at day 10 after irradiation (6 days after CCCP treatment) for RNA-seq analysis.

tag: cell line

value: Parkin-expressing MRC5 fibroblasts

tag: cell state

value: Senescent

value: untreated


title: Organoid ASO1 n3

description: polyA+ RNA


title: Senes_Treated_Replicate_1

value: Mitochondrial deficient senescent

value: CCCP


title: Organoid ASO2 n2

description: polyA+ RNA


title: Senes_Untreated_Replicate_2


title: Prolif_Replicate_3

source_name: Prolif

value: Proliferating


title: Senes_Untreated_Replicate_1


title: CMP-MN1-L H3K79me2_1

city: Aurora

first: Tobias

last: Neff

state: CO

department: Pediatric Oncology

country: USA

institute: University of Colorado Denver AMC

description: Leukemic cells harvested from a moribund mouse were  briefly cultured in M3234 with FBS, Il3, Il6 and SCF to ensure adequate numbers and good viability.

library_source: genomic

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d mm9 -v snp128_strict_wholeChrs --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Sorted Bam-files were used to generate bedgraph files using 'genomeCoverageBed' (bedtools v2.25.0), and bedGraph files were converted to BigWig using 'bedGraphToBigWig' (UCSC).
Bam files for H3K79me2 were catenated and  Peaks were identified using MACS2 with the parameters  --broad -g mm --broad-cutoff 0.1, using input as control.  Peaks were intersected with Refseq mm9 coordinates (UCSC table browser) using intersectBed.
Genome_build: mm9
Supplementary_files_format_and_content: .bw files are  Chip-seq tracks for visualization as BigWig-file; excel file with H3K79me2 peaks (as determined by MACS2) in bed file format for all three leukemias combined, using all three input files combined as background.

molecule: genomic DNA

source_name: myeloid leukemia

extract_protocol:
DNA was isolated using standard ChIP protocol
Nugen Ovation Ultra low system V2

tag: cell type

value: Bone marrow leukemic blasts sorted from moribund mice that had been transplanted with CMP-cells transformed with MN1

value: Genotype:Dot1l f/f (conditional allele, NOT inactivated)

tag: chip-antibody

value: Abcam anti-H3K79me2 (ab3594)


title: Tumor ASO2 n4

description: polyA+ RNA


title: Tumor scASO n3

description: polyA+ RNA


title: Tumor scASO n1

description: polyA+ RNA


title: Organoid ASO1 n1

description: polyA+ RNA


title: Organoid ASO2 n4

description: polyA+ RNA


title: Tumor ASO2 n2

description: polyA+ RNA


title: Senes_Treated_Replicate_2


title: Prolif_Replicate_2


title: Tumor ASO1 n3

description: polyA+ RNA


title: Tumor ASO1 n1

description: polyA+ RNA


title: HEK_293_E7_2_USC_RNA_43

city: LA

first: Peggy

last: Farnham

state: CA

address: 1450 Biggy St.

department: GMCB

institute: University of Southern California

data_processing:
Illumina Casava (version: BCL2FASTQ Conversion Software 1.8.4)  was used for basecalling.
RNA-seq reads were aligned to hg19 genome assembly using Tophat2 after trimming some raw reads using the quality score in Partek Flow version 3. HTSeq 0.6.1 was used to count aligend sequencing reads (bam file) using htseq-count script ( options: -format=bam -m=intersectio-strict -stranded=no). Also gencodev19 gff file was used for running htseq-count script.
ChIP-seq reads were aligned to hg19 genome assembly using bwa (0.6.2)and bam file was converted to bed file using bedtools. Bed files were converted to sgr files for visualization using a script from Sole-Search program.
4C-seq: Processed files of sequenced 4C-seq reads is from 4Cseqpipe program (http://compgenomics.weizmann.ac.il/tanay/?page_id=367)
hg19
processed data files format and content: RNA-seq: Tab-delimited text files that include counts for each gene
processed data files format and content: ChIP-seq: SGR files which are tab-delimited graph format showing base coordinates and scores.
processed data files format and content: 4C-seq: ID.nearcis.norm.median.scales – Median of normalized contact intensity in 1kb genomic bins.  Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns:  column 1 – the starting coordinate of the 1kb bin  column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin  column 3 – the 80th percentile of values in the window  column 4 – the 20th percentile of values in the window  column 5-145 – as columns 2-4, but with linearly increasing window size, going up to 50kb

source_name: Human embryonic kidney cell-line HEK293

growth_protocol: HCT116 cells and HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin until 80% confluent.

extract_protocol:
For RNA-seq, RNA was prepared using Trizol (Life Technologies, Carlsbad, CA)
For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For 4C-seq, cells were cross linked using 1% formalehyde for 10 minutes and nuclei were isolated, followed by chromatin is digested with a first restriction enzyme (DpnII) and ligated. After reverse cross-linking, DNA is treated with secondary restriction enzyme (Csp6I) followed by second ligation.
RNA-seq:Single-end libraries were prepared using the Illumina TruSeqV2 Sample Prep Kit (Catalog #15596-026), starting with 1 ug total RNA. Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an NextSeq500.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an Illumina HiSeq2000 or NextSeq500
4C-seq: Libraries were made through inverse PCR using primers that anneal to the bait fragment-end, customized barcode and adaptor seqeunces. Libraries were sequenced using an Illumina HiSeq2500

tag: clone

value: HEK293 Deletion Clone 1

tag: time point

value: RNA extracted on day E


title: Organoid ASO1 n2

description: polyA+ RNA


title: C2_USC_RNA_49

source_name: Human colorectal cancer cell-line HCT116

value: Control Conle 2

value: RNA extracted on day D


title: Tumor scASO n2

description: polyA+ RNA

value: MMTV-PyMT

value: Mammary tumor

value: scASO


title: HEK_293_C2_USC_RNA_41

value: HEK293 Control Clone 2


title: HEK_293_C1_USC_RNA_40

value: HEK293 Control Clone 1


title: 18qE_2_USC_RNA_53

value: 18qE Deletion Clone 2


title: Tumor ASO2 n3

description: polyA+ RNA

value: Malat1 ASO2


title: NE3_A_USC_RNA_72

value: 18qNE Deletion Clone 3

value: RNA extracted on day A


title: C1_USC_RNA_48

value: Control Clone 1


title: NE1_A_USC_RNA_68

value: 18qNE Deletion Clone 1


title: NE2_B_USC_RNA_70

value: 18qNE Deletion Clone 2

value: RNA extracted on day B


title: E7_C_USC_RNA_78

value: E7 Deletion Clone

value: RNA extracted on day C


title: E7_A_USC_RNA_76


title: C4_B_USC_RNA_66

value: Control Clone 4


title: E7_B_USC_RNA_77


title: C4_A_USC_RNA_65


title: Tumor ASO2 n1

description: polyA+ RNA


title: C3_C_USC_RNA_64

value: Control Cone 3


title: HEK_293_E7_1_USC_RNA_42

value: HEK293 Deletion Clone 1

value: RNA extracted on day E


title: Tumor ASO1 n2

description: polyA+ RNA

value: MMTV-PyMT

value: Mammary tumor

value: Malat1 ASO1


title: RNAseq control replicate 2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
RNAseq replicate 2
Ctrl2_WT

data_processing:
Lifescope v2.5.1 whole transcriptome pipeline for standard RNAseq and smallRNA pipeline for all translation inhibitors treatment samples. Mapper used was mapreads with standard lifescope default parameters.
Bam files were then merged per samples with MergeSamFiles.jar (picard-tools-1.38) with keeping read group per lane.
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts count table, custom format:  Ensembl transcript ids, open reading frame (ORF) start, ORFend, reads on sequences upstream of the ORF (5’UTR), reads counts on ORF, reads on sequences downstream of the ORF (3’UTR) are given. For annotated coding transcripts the ORF corresponds to the annotated coding sequence. For noncoding RNAs data for all potential ORFs are shown. Custom Java classes and R scripts were used to generate the tables.

source_name: embryonic stem cell line CGR8

growth_protocol: Murine embryonic stem cells (CGR8, passage 17 – 23) were cultured feeder free in gelatin-coated 75cm2 flasks in DMEM, 15% FCS, glutamine, pyruvate, nonessential amino acids, β-mercaptoethanol and leukemia inhibitory factor.

extract_protocol:
After drug treatment, murine ES cells (CGR8) were washed twice with ice cold PBS, 100 µg/ml Cycloheximide, scraped, pelleted and suspended in 200 µl ice cold 50 mM Tris/Cl pH 7.5, 100 mM KCl, 6 mM MgCl2, 5 mM DTT, 100 µg/ml Cycloheximide, 0.25 M Sucrose. Cells were lysed by adding 200 µl of the same buffer with 1% NP40 and 1% Deoxycholate. Nuclei and the bulk of mitochondria were removed by two 7 min 10,000 g centrifugations at 4 °C. 100 µl of the lysate was used directly for preparation of total RNA. To the rest, 40 U RNAseI (Fermentas), 4U DNAseI (Promega, WI) were added and incubated for 1 hr at 30 °C. Monosomes were pelleted by a 2 hr centrifugation at 140,000 g and RNA isolated using a Qiagen small RNA isolation kit.
Ribosomal RNA was depleted with biotinylated antisense cRNA covering the murine 28S and 18S rRNA sequences and biotinylated antisense oligonucleotides complementary to the 5.8S and 5S rRNA.  For non RNAse treated samples, RNA was fragmented in Ambion RNAseIII buffer for 8 min at 95°C. RNA fragments from the heat fragmentation or RNAse I digestion were kinased with polynucleotide kinase. Libraries were prepared with the New England Biolabs NEBnext small RNA library preparation kit for Solid.
stranded RNA-seq , adapter ligation to fragmented RNA ( New England Biolabs NEBnext Small RNA Library prep kit)
SOLiD5500 Wildfire, Life Technology. Sequencing of 50b. with 10b. barcoding sequences.

treatment_protocol: Drug stock solutions were DMDA pateamineA (Jun O. Liu, Texas A&M University), 500µM in DMSO; harringtonine (Santa Cruz Biotechnology, TX), 4 mg/ml in DMSO; puromycin (Sigma, St.Louis, MO) , 20 mg/ml in H2O. Drug concentrations and incubation times were: DMDA-pateamine A, 1µM, 10 min; harringtonin, 2 µg/ml, 10 min; puromycin, 0.2 mg/ml, 20 min. Cells were kept at 37°C after drug addition. The amount of DMSO was adjusted to be equal in all samples Subsequently, cells were cooled rapidly to 0°C with ice cold PBS. Cycloheximide during all subsequent manipulations of the cell extracts which were carried out on ice or at 4°C. Cells were washed twice with ice cold PBS, 100 µg/ml Cycloheximide, scraped, pelleted and suspended in 200 µl ice cold 50 mM Tris/Cl pH 7.5, 100 mM KCl, 6 mM MgCl2, 5 mM DTT, 100 µg/ml Cycloheximide, 0.25 M Sucrose. Cells were lysed by adding 200 µl of the same buffer with 1% NP40 and 1% Deoxycholate. Nuclei and the bulk of mitochondria were removed by two 7 min 10,000 g centrifugations at 4 °C. 100 µl of the lysate was used directly for preparation of total RNA. To the rest, 40 U RNAseI (Fermentas), 4U DNAseI (Promega, WI) were added and incubated for 1 hr at 30 °C. Monosomes were pelleted by a 2 hr centrifugation at 140,000 g and RNA isolated using a Qiagen small RNA isolation kit.

value: ESC line CGR8


title: RNAseq control replicate 1

description:
RNAseq replicate 1
Ctrl1_WT


title: 18qE_1_USC_RNA_52

value: 18qE Deletion Clone 1

value: RNA extracted on day D


title: C3_B_USC_RNA_63


title: Prolif_Replicate_1

value: Parkin-expressing MRC5 fibroblasts

value: Proliferating


description:
library strategy: Ribo-seq
Ribosome Profiling puromycin replicate 1
Puro1_MB7

value: Puromycin 0.2 mg/ml 20 min, RNase


description:
library strategy: Ribo-seq
Ribosome Profiling pateamineA replicate 2
PatA2_MB6

value: DMDA-pateamine A 1µM 10 min, RNase


title: C2_C_USC_RNA_61

value: Control Clone 2


title: C2_B_USC_RNA_60

value: RNA extracted on day B


title: C2_A_USC_RNA_59

value: RNA extracted on day A


title: C1_B_USC_RNA_57

value: Control Clone 1


title: C4_C_USC_RNA_67

value: Control Clone 4

value: RNA extracted on day C


title: C1_A_USC_RNA_56


title: Ribosome Profiling control replicate 2

description:
library strategy: Ribo-seq
Ribosome Profiling control replicate 2
Ctrl2_MB4

value: Rnase


description:
library strategy: Ribo-seq
Ribosome Profiling harringtonine replicate 1
Harr1_MB2

value: harringtonine 2ug/ml 10 min, RNase


title: C1_C_USC_RNA_58


description:
library strategy: Ribo-seq
Ribosome Profiling harringtonine replicate 2
Harr2_MB5

value: harringtonine 2ug/ml 10min, RNase


title: Input_rep2_Control_HCT116_ChIPseq

tag: antibody

value: none, input


title: WT 6 months Male White Adipose (Gonad) mRNA rep3

status: Public on Jan 11 2016

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omnisoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omnisoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl R.75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: White Adipose tissue around Gonad

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: White Adipose tissue around Gonad

value: Wild Type

tag: age

value: 6 months

tag: Sex

value: Male

tag: housing condition

value: housed with Wild Type and Het (Q20) mice


title: WT 6 months Male White Adipose (Gonad) mRNA rep4


title: WT 6 months Male White Adipose (Gonad) mRNA rep2


description:
library strategy: Ribo-seq
Ribosome Profiling puromycin replicate 2
Puro2_MB8

value: ESC line CGR8

value: Puromycin 0.2 mg/ml 20 min, RNase


title: WT 6 months Male White Adipose (Gonad) mRNA rep1


title: WT 6 months Female White Adipose (Gonad) mRNA rep3

value: Female


title: Het (Q92) 6 months Male White Adipose (Gonad) mRNA rep4

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: WT 6 months Female White Adipose (Gonad) mRNA rep2


title: C3_A_USC_RNA_62

value: Control Cone 3

value: RNA extracted on day A


title: WT 6 months Female White Adipose (Gonad) mRNA rep1


title: Het (Q92) 6 months Male White Adipose (Gonad) mRNA rep3


title: Het (Q92) 6 months Male White Adipose (Gonad) mRNA rep1


title: Het (Q92) 6 months Female White Adipose (Gonad) mRNA rep4


title: Het (Q92) 6 months Female White Adipose (Gonad) mRNA rep2


title: Het (Q92) 6 months Male White Adipose (Gonad) mRNA rep2


description:
library strategy: Ribo-seq
Ribosome Profiling pateamineA replicate 1
PatA1_MB3

value: DMDA-pateamine A 1µM 10 min, RNase


title: Het (Q80) 6 months Male White Adipose (Gonad) mRNA rep2

value: Het (Q80) Knock-In

value: housed with Het (Q80) mice


title: Het (Q80) 6 months Male White Adipose (Gonad) mRNA rep1


title: Het (Q80) 6 months Female White Adipose (Gonad) mRNA rep4


title: Het (Q92) 6 months Female White Adipose (Gonad) mRNA rep3


title: Het (Q80) 6 months Female White Adipose (Gonad) mRNA rep2


title: Het (Q20) 6 months Male White Adipose (Gonad) mRNA rep2

value: Het (Q20) Knock-In


title: Het (Q20) 6 months Male White Adipose (Gonad) mRNA rep3


title: Het (Q80) 6 months Male White Adipose (Gonad) mRNA rep4


title: Het (Q92) 6 months Female White Adipose (Gonad) mRNA rep1


title: Het (Q20) 6 months Male White Adipose (Gonad) mRNA rep1


title: Wor4-GFP Opaque Cell 3 (1304C)

city: San Francisco

first: Matthew

last: Lohse

address: 44 Vicksburg Street

institute: BioSynesis, Inc.

data_processing:
Files were indexed and aligned to the C. albicans genome using Bowtie2 with the default parameters
Files were converted to .bam format using samtools
Peak separation distance was determined using the binding characteristics function in the SPP R Bioconductor package
Peaks were called using Macs2
Genome_build: The C. albicans genome A21-s02-m09-r02 was downloaded from the Candida Genome Database on April 6, 2014
Supplementary_files_format_and_content: bedGraph files were converted from bam files using the script genomeCoverageBed

organism: Candida albicans

source_name: opaque cell

growth_protocol: Room temperature SD+aa+Uri overnights were started from 5 to 7 day old colonies. Cultures were diluted back to 200mL at A600= 0.067 in the morning and allowed to regrow at 25°C to an OD600 of ~0.4.

extract_protocol:
Cells were lysed with glass bead vortexing for 2 hours, sonicated for 2 15-minute cycles (30s on, 60s off), and immunoprecipitated at 4˚C overnight (5µL of Living Colors Full-Length GFP Polyclonal Antibody (Clontech 632592), Protein A-Sepharose 4B Fast Flow (Sigma P9424)).
Libraries were prepared using the NEBNext ChIP-Seq library prep kit for Illumina (New England Biolabs)

treatment_protocol: Cells were crosslinked for 15 minutes with Formaldehyde (1% of final volume)

tag: media condition

value: SD+aa+Uri, 25°C

tag: chip antibody

value: Opaque

value: WOR4 / WOR4-GFP


title: Het (Q80) 6 months Male White Adipose (Gonad) mRNA rep3

value: White Adipose tissue around Gonad

value: 6 months


title: Wor4-GFP Opaque Cell 1 (1304A)

value: Living Colors Full-Length GFP Polyclonal


title: Input_4hpf

city: mainz

first: lucas

last: kaaij

address: ackermannweg 4

department: RNA silencing

country: Germany

institute: IMB

data_processing:
data was mapped using bowtie 1.1.1
Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling.
Cisgenome v.2 software package was used for peak-calling (FDR < 0.05).
Genome_build: zv9
Supplementary_files_format_and_content: no processed data is available for this input sample.

organism: Danio rerio

source_name: 4hpf embryo_input

extract_protocol:
phenol/chloroform
Ovation Ultralow Library System V2 Workflow (NuGEN)

value: 4hpf embryos

value: none (input)


title: Het (Q80) 6 months Female White Adipose (Gonad) mRNA rep1

value: Female


title: Het (Q20) 6 months Female White Adipose (Gonad) mRNA rep3

value: housed with Wild Type and Het (Q20) mice


title: Het (Q20) 6 months Female White Adipose (Gonad) mRNA rep4


title: Het (Q20) 6 months Female White Adipose (Gonad) mRNA rep2


title: Het (Q20) 6 months Female White Adipose (Gonad) mRNA rep1


title: Het (Q80) 6 months Female White Adipose (Gonad) mRNA rep3


title: Het (Q175) 6 months Male White Adipose (Gonad) mRNA rep4

value: Het (Q175) Knock-In

value: Male

value: housed with Het (Q175) mice


title: Het (Q175) 6 months Male White Adipose (Gonad) mRNA rep3


title: Wor4-GFP White Cell 1 (1295A)

source_name: white cell

value: White


title: Wor4-GFP White Cell 3 (1295C)


title: Wor4-GFP White Cell 2 (1295B)


title: Untagged Opaque Cell Control 1 (136A)

value: WOR4 / WOR4


title: Het (Q175) 6 months Male White Adipose (Gonad) mRNA rep2


title: Het (Q175) 6 months Male White Adipose (Gonad) mRNA rep1


title: Untagged Opaque Cell Control 3 (136C)


title: Untagged White Cell Control 3 (135C)


title: Untagged Opaque Cell Control 2 (136B)


title: Het (Q175) 6 months Female White Adipose (Gonad) mRNA rep3


title: Untagged White Cell Control 2 (135B)


title: Wor4-GFP Opaque Cell 2 (1304B)


title: Het (Q140) 6 months Male White Adipose (Gonad) mRNA rep4

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q175) 6 months Female White Adipose (Gonad) mRNA rep2


title: Het (Q175) 6 months Female White Adipose (Gonad) mRNA rep4


title: Het (Q140) 6 months Male White Adipose (Gonad) mRNA rep3


title: Het (Q175) 6 months Female White Adipose (Gonad) mRNA rep1


title: Untagged White Cell Control 1 (135A)

value: SD+aa+Uri, 25°C


title: Het (Q140) 6 months Male White Adipose (Gonad) mRNA rep2


title: Het (Q140) 6 months Male White Adipose (Gonad) mRNA rep1


title: Het (Q140) 6 months Female White Adipose (Gonad) mRNA rep2


title: Het (Q140) 6 months Female White Adipose (Gonad) mRNA rep4


title: Het (Q140) 6 months Female White Adipose (Gonad) mRNA rep3


title: Het (Q140) 6 months Female White Adipose (Gonad) mRNA rep1


title: Het (Q111) 6 months Male White Adipose (Gonad) mRNA rep4

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: Het (Q111) 6 months Female White Adipose (Gonad) mRNA rep4

value: White Adipose tissue around Gonad


title: Het (Q111) 6 months Male White Adipose (Gonad) mRNA rep2

value: 6 months


title: Het (Q111) 6 months Female White Adipose (Gonad) mRNA rep3


title: Het (Q111) 6 months Male White Adipose (Gonad) mRNA rep3


title: Het (Q111) 6 months Male White Adipose (Gonad) mRNA rep1


title: Het (Q111) 6 months Female White Adipose (Gonad) mRNA rep1


title: Het (Q111) 6 months Female White Adipose (Gonad) mRNA rep2


title: WT 6 months Male White Adipose (Gonad) Male miRNA rep2

value: Wild Type


title: WT 6 months Male White Adipose (Gonad) Male miRNA rep1


title: WT 6 months Male White Adipose (Gonad) Male miRNA rep4


title: WT 6 months Female White Adipose (Gonad) Female miRNA rep1


title: Het (Q92) 6 months  Male White Adipose (Gonad) miRNA rep1

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: WT 6 months Female White Adipose (Gonad) Female miRNA rep3

value: Female


title: Het (Q92) 6 months  Male White Adipose (Gonad) miRNA rep2


title: Het (Q92) 6 months  Male White Adipose (Gonad) miRNA rep3


title: WT 6 months Female White Adipose (Gonad) Female miRNA rep2

value: housed with Wild Type and Het (Q20) mice


title: Ribosome Profiling control replicate 1

description:
library strategy: Ribo-seq
Ribosome Profiling control replicate 1
Ctrl1_MB1

value: ESC line CGR8

value: Rnase


title: Het (Q92) 6 months  Female White Adipose (Gonad) miRNA rep4


title: Het (Q92) 6 months  Female White Adipose (Gonad) miRNA rep2


title: Het (Q92) 6 months  Female White Adipose (Gonad) miRNA rep3


title: Het (Q92) 6 months  Female White Adipose (Gonad) miRNA rep1


title: Het (Q80) 6 months  Male White Adipose (Gonad) miRNA rep4

value: Het (Q80) Knock-In

value: Male

value: housed with Het (Q80) mice


title: Het (Q80) 6 months  Male White Adipose (Gonad) miRNA rep2


title: Het (Q80) 6 months  Male White Adipose (Gonad) miRNA rep3


title: Het (Q80) 6 months  Male White Adipose (Gonad) miRNA rep1


title: Het (Q80) 6 months  Female White Adipose (Gonad) miRNA rep4


title: Het (Q80) 6 months  Female White Adipose (Gonad) miRNA rep1


title: Het (Q20) 6 months  Male White Adipose (Gonad) miRNA rep4

value: Het (Q20) Knock-In


title: Het (Q80) 6 months  Female White Adipose (Gonad) miRNA rep2


title: Het (Q80) 6 months  Female White Adipose (Gonad) miRNA rep3


title: Het (Q20) 6 months  Male White Adipose (Gonad) miRNA rep2


title: Het (Q20) 6 months  Male White Adipose (Gonad) miRNA rep3


title: Het (Q20) 6 months  Male White Adipose (Gonad) miRNA rep1


title: WT 6 months Male White Adipose (Gonad) Male miRNA rep3


title: Het (Q20) 6 months  Female White Adipose (Gonad) miRNA rep4


title: Het (Q20) 6 months  Female White Adipose (Gonad) miRNA rep1


title: Het (Q20) 6 months  Female White Adipose (Gonad) miRNA rep2


title: Het (Q20) 6 months  Female White Adipose (Gonad) miRNA rep3


title: Het (Q175) 6 months Male White Adipose (Gonad) miRNA rep4

value: Het (Q175) Knock-In

value: housed with Het (Q175) mice


title: Het (Q175) 6 months Female White Adipose (Gonad) miRNA rep3


title: Het (Q175) 6 months Male White Adipose (Gonad) miRNA rep3


title: Het (Q175) 6 months Female White Adipose (Gonad) miRNA rep2


title: H3K27ac Human Brain Putamen HS3

status: Public on Jan 13 2016

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
Mapping Illumina: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S --phred64-quals -q -l 40/45 -n 1
Mapping SOLiD: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S -l 50 -n 3 -C -Q -f
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g hs --nomodel --extsize 400 --llocal 100000
genome build: hg38, rheMac3, panTro4, mm10
processed data files format and content: txt files contain called peaks
processed data files format and content: narrowPeak files contain called peaks in BED format
processed data files format and content: bedGraph files contain treat pileup
processed data files format and content: bw files contain treat pileup read per million (RPM) normalized in bigWig format

source_name: Human female putamen tissue

extract_protocol:
Crosslink, Lyse and Immunoprecipitate
Illumina Truseq DNA library protocol

value: Putamen

tag: gender

tag: Cause of death

value: Uremic coma, brain tumor

tag: postmortem delay

value: 7.0 hrs

tag: experiment type

value: ChIP-Seq

value: H3K27ac (Abcam, ab4729)


title: Het (Q175) 6 months Female White Adipose (Gonad) miRNA rep1

tag: strain

tag: tissue

value: White Adipose tissue around Gonad

tag: genotype

value: 6 months


title: Het (Q140) 6 months  Male White Adipose (Gonad) miRNA rep2

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q140) 6 months  Male White Adipose (Gonad) miRNA rep3


title: Het (Q140) 6 months  Female White Adipose (Gonad) miRNA rep3

value: Female


title: Het (Q140) 6 months  Male White Adipose (Gonad) miRNA rep4


title: Het (Q140) 6 months  Female White Adipose (Gonad) miRNA rep1


title: Het (Q111) 6 months  Male White Adipose (Gonad) miRNA rep4

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: Het (Q111) 6 months  Male White Adipose (Gonad) miRNA rep3

value: Male


title: LY1_CON_NCINP_R3

city: New York

first: Tharu

middle: M

last: Fernando

state: NY

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

description:
Paired_analysis_DE.txt
LY1_4EIP_allreps_counts.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads that passed filter were aligned to hg19 using STAR (Dobin et al., 2012).
Gene expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/ HTSeq/).
Differentially enriched genes were identified with pairwise limma analysis on voom normalized counts (RIP-seq samples).  Genes with a FDR-corrected p-value < 0.05 were considered differentially expressed.
Differentially expressed genes in the PDX samples were identified with the edgeR package (Robinson et al., 2010, PDX samples).  Genes with a FDR-corrected p-value < 0.05 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count and the limma analysis and edgeR outputs are provided as a .txt file.

source_name: OCI-LY1 cells

growth_protocol: IMDM, 10% FBS, pen/strep

extract_protocol:
Inputs for RIP, placed directly in Trizol
Illumina TruSeq Stranded Total RNA sample prep
RIP-seq: Nuclear input samples were taken before 1 mg of nuclear lysate was used for eIF4E RIP. Complexes were eluted by boiling with Tris-EDTA containing 1% SDS and 12% beta-mercaptoethanol. RIP RNA and nuclear input RNA was isolated using Trizol (Life Technologies). mRNA-seq: RNA was isolated using Trizol (Life Technologies).
Genomic DNA was eliminate with Dnase treatment, and total RNA was taken into the Illumina TruSeq Stranded Total RNA library prekit (RIP-seq samples) or  mRNA was isolated using two rounds of poly-T oligo attached magnetics beads and then taken into the Illumina TruSeq RNA sample prep kit (PDX RNAseq).

tag: molecule

value: nuclear RNA

tag: differential expression tool

value: pairwise limma voom


title: Het (Q175) 6 months Female White Adipose (Gonad) miRNA rep4

value: Het (Q175) Knock-In


title: LY1_CON_NCINP_R2


title: Het (Q111) 6 months  Male White Adipose (Gonad) miRNA rep2


title: LY1_CON_4EIP_R3

extract_protocol:
RIP then Trizol
Illumina TruSeq Stranded Total RNA sample prep
RIP-seq: Nuclear input samples were taken before 1 mg of nuclear lysate was used for eIF4E RIP. Complexes were eluted by boiling with Tris-EDTA containing 1% SDS and 12% beta-mercaptoethanol. RIP RNA and nuclear input RNA was isolated using Trizol (Life Technologies). mRNA-seq: RNA was isolated using Trizol (Life Technologies).
Genomic DNA was eliminate with Dnase treatment, and total RNA was taken into the Illumina TruSeq Stranded Total RNA library prekit (RIP-seq samples) or  mRNA was isolated using two rounds of poly-T oligo attached magnetics beads and then taken into the Illumina TruSeq RNA sample prep kit (PDX RNAseq).

value: eIF4E RIP nuclear RNAs


title: Het (Q140) 6 months  Female White Adipose (Gonad) miRNA rep2


title: Het (Q111) 6 months  Female White Adipose (Gonad) miRNA rep1


title: LY1_CON_4EIP_R1


title: Het (Q175) 6 months Male White Adipose (Gonad) miRNA rep2

value: housed with Het (Q175) mice


title: testis 6 week

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

data_processing:
Four random nucleotides were removed from 5'end of read. Adapter sequence were removed from the 3'end of reads by using program fastx_clipper with "-a TGGAATT".  Then reads were mapped to the mouse genome using bowtie 2 (Langmead and Salzberg 2012). Reads with ≥ 2 unaligned Ts at the 5’ end are called poly(A) site-supporting (PASS) reads, which were used to identify pAs. pAs located within 24 nt from each other were clustered together. We used the Significance Analysis of Alternative Polyadenylation (SAAP) method to identify significantly regulated APA events, as previously described. Briefly, for two pAs (or two pA sets) from two comparing samples, a Relative Expression Difference (RED) score was first calculated and was called observed RED. The PASS reads were then sampled based on the assumption that the relative abundance of each pA isoform was the same in two samples. Sampling was preformed 20 times to obtain expected mean and standard deviation of RED, which were then used to convert observed RED to Z score (minus mean and divided by standard deviation). False Discovery Rate (FDR) was calculated by comparing observed Z (Zo) and expected Z (Ze) for a given Z cutoff value (Zc). For 3’UTR-APA, we selected the two most abundant pA isoforms for analysis. For CDS-APA, we combined all isoforms using pAs in upstream regions of the 3’-most exon and compared their expression change with that of isoforms using pAs in the 3’-most exon. Individual intronic pAs were also analyzed by comparing to all other pA isoforms of the gene. For uaRNA analysis, we combined all antisense transcripts using pAs within 2 kb upstream from the transcription start site (TSS), excluding those mapped to other mRNA genes, and compared them to all sense strand transcripts, excluding pAs located within 2 kb downstream of the TSS. We used FDR = 0.05 (SAAP) to select significantly regulated APA events. Global Analysis of Alternative Polyadenylation (GAAP) was previously described. Briefly, for two 3’READS data sets A and B, we sampled by bootstrapping 1.5 M PASS reads from A and B. The number of genes with significant APA changes (based on SAAP analysis) was calculated and called observed value. The data were also randomly permutated (shuffled across samples) to obtain the expected value. The observed value – expected value was normalized number of genes with significant APA regulation. This process was repeated 20 times to obtain standard deviation.
Genome_build: mm9
Supplementary_files_format_and_content: 3READS.pA.read.counts.txt contains information of gene symbol, pA coordinates, read number of pAs in different 3'READS samples. "pA_type" is pA type based on location of a pA.

source_name: testis

growth_protocol: Testis samples were obtained from mice (FVB) by surgical removal according to the approved IACUC protocols.

extract_protocol:
The 3’ region extraction and deep sequencing (3’READS) method was previously described in [10]. Briefly, 25 μg of input RNA was used for each sample, and poly(A)+ RNA was selected using oligo d(T)25 magnetic beads (NEB), followed by on-bead fragmentation using RNase III (NEB).
Poly(A)+ RNA fragments were then selected using the chimeric U5 and T45 (CU5T45) oligo conjugated on streptavidin beads, followed by RNase H (NEB) digestion. Eluted RNA fragments were ligated with 5’ and 3’ adapters, followed by RT and PCR (15x) to obtain cDNA libraries for sequencing on the Illumina platform.

treatment_protocol: RNA were extracted from mouse testes at different developmental time points after birth, namely 1 week (w), 2w, 3w, 4w, 5w and 6w.

value: FVB

value: 6 week

value: testis

tag: library protocol


title: Het (Q175) 6 months Male White Adipose (Gonad) miRNA rep1


title: testis 4 week

value: 4 week


title: Het (Q140) 6 months  Male White Adipose (Gonad) miRNA rep1

value: White Adipose tissue around Gonad


title: testis 5 week

value: 5 week


title: Input-F0

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

source_name: Fetal hematopoietic stem/progenitor cells (HSPCs)

growth_protocol: Human primary fetal liver or adult bone marrow-derived CD34+ HSPCs and ProEs were cultured ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For ChIP-seq analysis using the Illumina HiSeq2500, 10-20 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer’s protocol. Raw ChIP-seq data were processed using the Illumina software pipeline. Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC, hg18) were retained for downstream data analysis.

value: Fetal HSPCs (F0)

tag: developmental stage/tissue

value: fetal liver

tag: cell type

value: primary fetal liver CD34+ HSPCs (F0)


title: GATA2-A5

source_name: Adult erythroid progenitor cells (ProEs)

value: Adult ProEs (A5)

value: adult bone marrow

value: primary adult ProEs (A5)

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: RUNX1-A0

source_name: Adult hematopoietic stem/progenitor cells (HSPCs)

value: Adult HSPCs (A0)

value: primary adult CD34+ HSPCs (A0)


title: testis 2 week

tag: age

value: 2 week


title: testis 1 week

value: 1 week


title: testis 3 week

value: FVB

value: 3 week


title: RUNX1-F0


title: PU1-A0

value: Santa Cruz Biotechnology


title: Het (Q111) 6 months  Male White Adipose (Gonad) miRNA rep1

value: Het (Q111) Knock-In

value: 6 months

tag: Sex

value: Male

tag: housing condition

value: housed with Het (Q111) mice


title: PU1-F0

value: Fetal HSPCs (F0)

value: fetal liver

tag: chip antibody


title: input D1 EpiLCs +Dox for 3h Nanog rep2

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
ChIP-seq reads were aligned with the bwa aligner (bio-bwa.sourceforge.net) to the mouse reference genome (GRCm38/mm10).  Peaks were called with MACS (version 2.1.0 https://github.com/taoliu/MACS).
Unnormalized bedGraph files containing counts per genomic position were generated with the bedtools 'genomeCoverageBed' tool.
Genome_build: GRCm38/UCSC mm10
Supplementary_files_format_and_content: bedGraph format: read counts per genomic position

source_name: D1 epiblast-like cells 3h after Nanog induction +Dox (200ng/ml)

growth_protocol: Embryonic stem cells (mESCs) carrying a Oct4∆PE-GFP reporter and Dox-inducible Nanog transgenes were induced into Epiblast-like cells (EpiLCs) as described previously (Hayashi et. al., 2011). Briefly, For inducing D1 EpiLCs, 1e5 mESCs were cultured in a well of a 12-well plate coated with human plasma fibronectin (Merck Millipore) (16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml), bFGF (12 ng/ml) and KSR (1%). For inducing D2 EpiLCs, the culture medium was changed on next day and the cells were cultured for another day. Then, Day1 and Day2 EpiLCs were dissociated and cultured under floating conditions by plating 1e6 cells/ml on a bacterial dish in GK15 medium with Doxycline (200 ng/ml) to induce Nanog transgene. After 3 hours, cells were collected and fixed for ChIP.

extract_protocol:
ChIPs were performed by using a modified published method (Ng et al., 2013). Briefly, Day (D)1 or D2 EpiLCs were cultured on a bacterial dish for 3h in the presence of 200(ng/ml) of Doxycycline. ESCs and induced EpiLCs were fixed with 1% formaldehyde (room temperature, 10 min), quenched with 1 vol. of 250 mM glycine (room temperature, 5 min), and rinsed with chilled TBSE buffer (20 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA) twice before freezing in liquid nitrogen. After thawing on ice, 3e6 fixed cells were lysed with 1 mL 1% SDS Lysis Buffer (50mMTris-HCl pH8, 10mM EDTA, 1% SDS, Roche protease inhibitor cocktail on ice, 5 min) and then centrifuged (2,000 rpm, 15 min). Nuclear fraction was resuspended in 0.9 mL of dilution buffer (16.7mM Tris-HCl, pH8, 167mM NaCl, 1.2mM EDTA, 1.1% Triton X-100, 0.01% SDS, 0.2mM PMSF, 1X Protease Inhibitors). Samples were sonicated 10 times (30 s pulses with 30 s break interval) using a Bioruptor water bath sonicator (Diagenode). Chromatin extracts were then pre-cleared with Protein G Dynabeads and immunoprecipitated overnight with Protein G Dynabeads coupled with antibodies specific to Nanog (2μg). On the next day, beads were washed for 10 min at 4°C twice in each Low Salt (0.1% SDS, 1%, TritonX-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), High Salt (0.1% SDS, 1%, TritonX-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 300 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP40, 1% Na deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8), and TE buffer. After elution samples were digested with proteinase K and reverse crosslinked for 6 h at 68°C.
12ng of purified DNA from ChIPs was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared, library was size selected and sequenced using HiSeq2000 with single-end 50 nt read length.

treatment_protocol: To induce Nanog expression, Day1 and Day2 EpiLCs were cultured in floating conditions by plating 1e6 cells/ml on a bacterial dish in GK15 medium with Doxycycline (200ng/ml) for 3 hours to induce Nanog transgene.

value: MF1 x MF1

tag: genotype/variation

value: carrying a Oct4{delta}PE-GFP reporter and Dox-inducible Nanog transgenes

value: Day1 epiblast-like cell


title: NFE2-A0

value: adult bone marrow


title: input D1 EpiLCs +Dox for 3h Nanog rep1


title: IRF2-A0

value: Adult HSPCs (A0)

value: Abcam


title: input D2 EpiLCs +Dox for 3h Nanog rep2

source_name: D2 epiblast-like cells 3h after Nanog induction +Dox (200ng/ml)

value: Day2 epiblast-like cell


title: LY1_CON_4EIP_R2

value: eIF4E RIP nuclear RNAs

value: pairwise limma voom


title: Het (Q111) 6 months  Female White Adipose (Gonad) miRNA rep2

value: White Adipose tissue around Gonad

value: Female


title: input mESCs Nanog rep2

source_name: Embryonic stem cells with Dox-inducible Nanog transgene

value: mouse embryonic stem cell


title: input D2 EpiLCs +Dox for 3h Nanog rep1


title: zebrafish-heart_WT_7dpi_#1

city: Utrecht

first: Fabian

middle: Klaus

last: Kruse

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. (2014) Cell.
The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
Genome_build: zv9 (with improved 3' annotation, see Junker et al (2014) Cell)
Supplementary_files_format_and_content: text files: read count matrices in which rows correspond to genes and columns to sections

source_name: cryoinjured ventricle of the heart

extract_protocol:
RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
see: Junker et al., 2014, Cell

treatment_protocol: Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned, and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. (2014) Cell.

value: adult heart

tag: sectioning direction

value: injury area - uninjured, remote myocardium

tag: sectioning thickness

value: 12 µm

tag: embedding strategy

value: extracted heart at 7 days-post-cryoinjury


title: input mESCs Nanog rep1

tag: strain


title: zebrafish-heart_WT_3dpi_#1

tag: tissue

value: extracted heart at 3 days-post-cryoinjury


title: LY1_CON_NCINP_R1

tag: molecule

value: nuclear RNA


title: D1 EpiLCs +Dox for 3h Nanog rep2

value: MF1 x MF1

value: carrying a Oct4{delta}PE-GFP reporter and Dox-inducible Nanog transgenes

value: NANOG (RCAB0001P)


title: D1 EpiLCs +Dox for 3h Nanog rep1

value: Day1 epiblast-like cell


title: NFE2-F5

source_name: Fetal erythroid progenitor cells (ProEs)

value: Fetal ProEs (F5)

value: fetal liver

value: primary fetal liver ProEs (F5)

value: Santa Cruz Biotechnology


title: NFE2-F0

value: Fetal HSPCs (F0)

value: primary fetal liver CD34+ HSPCs (F0)


title: TAL1-A0

value: Adult HSPCs (A0)

value: adult bone marrow

value: primary adult CD34+ HSPCs (A0)


title: TAL1-F5


title: TG133a_TAC_3_RISC (miR-133a)

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description:
RISC (Ago2-immunoprecipitated RNA)
base calling quality score: Phred33

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the mRNA transcriptome, defined by a gtf for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
This gtf is supplied as a 'processed data file'.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: mm10 / UCSC
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each mRNA.

source_name: Mouse

extract_protocol:
Hearts were removed and coronal sections from adult hearts (without right ventricle) were flash frozen in liquid nitrogen. Total RNA was harvested using Trizol reagent (Invitrogen), while cleared lysates were prepared from frozen tissue for Ago2 immunoprecipitation and RISC RNA isolation, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
RISC RNA was isolated from immunoprecipitated Ago2 via direct incubation of immunoprecipitates with Trizol reagent (Invitrogen).  Chemical fragmentation and preparation of single-end RNA-Seq libraries proceeded as for polyadenylated RNA.

value: FVB/N

value: Heart

tag: age (weeks)

value: M

tag: surgery

value: TAC


title: mESCs Nanog rep2

value: MF1 x MF1

value: mouse embryonic stem cell


title: D2 EpiLCs +Dox for 3h Nanog rep1

value: carrying a Oct4{delta}PE-GFP reporter and Dox-inducible Nanog transgenes

value: Day2 epiblast-like cell

value: NANOG (RCAB0001P)


title: mESCs Nanog rep1


title: TG133a_TAC_4_RISC (miR-133a)


title: D2 EpiLCs +Dox for 3h Nanog rep2


title: TAL1-F0

tag: developmental stage/tissue

value: fetal liver


title: TG133a_TAC_2_RISC (miR-133a)


title: GATA1-A0

tag: cell type

value: Abcam


title: H3K27me3-A0

tag: chip antibody vendor

value: Millipore


title: GATA1-F0

value: Fetal HSPCs (F0)

tag: chip antibody cat. #


title: ntg_TAC_3_RISC (miR-133a)


title: ntg_TAC_4_RISC (miR-133a)


title: ntg_TAC_2_RISC (miR-133a)


title: TG133a_TAC_1_RISC (miR-133a)


title: ntg_TAC_1_RISC (miR-133a)


title: H3K27me3-F5

value: Fetal ProEs (F5)

value: primary fetal liver ProEs (F5)


title: Input-A0

value: Adult HSPCs (A0)

value: adult bone marrow


title: Het (Q20) 6 months Male White Adipose (Gonad) mRNA rep4

value: White Adipose tissue around Gonad

tag: genotype

value: Het (Q20) Knock-In

tag: age

value: 6 months

value: Male

value: housed with Wild Type and Het (Q20) mice


title: TG133a_sham_5_RISC (miR-133a)

value: FVB/N

value: Heart

tag: Sex

value: M

value: sham


title: TG133a_sham_4_RISC (miR-133a)


title: TG133a_sham_3_RISC (miR-133a)


title: TG133a_sham_6_RISC (miR-133a)


title: H3K27ac-A5

value: Adult ProEs (A5)

value: primary adult ProEs (A5)

tag: chip antibody


title: TG133a_sham_2_RISC (miR-133a)


title: TG133a_sham_7_RISC (miR-133a)


title: ntg_TAC_5_RISC (miR-133a)

value: TAC


title: H3K27ac-A0

value: primary adult CD34+ HSPCs (A0)

value: Abcam


title: H3K27me3-F0

value: Fetal HSPCs (F0)

value: fetal liver

value: primary fetal liver CD34+ HSPCs (F0)

value: Millipore


title: H3K27ac-F0


title: TG133a_TAC_3_mRNA (miR-133a)

description:
polyadenylated RNA
base calling quality score: Phred33


title: TG133a_TAC_4_mRNA (miR-133a)


title: H3K27ac-F5

value: Fetal ProEs (F5)

value: primary fetal liver ProEs (F5)


title: ntg_sham_1_RISC (miR-133a)


title: ntg_sham_2_RISC (miR-133a)


title: TG133a_sham_1_RISC (miR-133a)


title: TG133a_TAC_2_mRNA (miR-133a)


title: H3K4me3-A0

value: Adult HSPCs (A0)

value: adult bone marrow


title: ntg_sham_3_RISC (miR-133a)

value: FVB/N


title: TG133a_TAC_1_mRNA (miR-133a)

value: Heart


title: H3K4me3-F5


title: ntg_TAC_5_mRNA (miR-133a)

value: M


title: H3K4me3-F0


title: ntg_TAC_3_mRNA (miR-133a)


title: ntg_TAC_4_mRNA (miR-133a)


title: H3K4me1-A5


title: ntg_TAC_2_mRNA (miR-133a)


title: H3K4me1-A0


title: H3K4me1-F0


title: TG133a_sham_3_mRNA (miR-133a)

value: sham


title: TG133a_sham_7_mRNA (miR-133a)


title: TG133a_sham_4_mRNA (miR-133a)


title: TG133a_sham_6_mRNA (miR-133a)


title: TG133a_sham_5_mRNA (miR-133a)


title: ntg_TAC_1_mRNA (miR-133a)


title: H3K4me1-F5


title: TG133a_sham_2_mRNA (miR-133a)


title: ntg_sham_3_mRNA (miR-133a)


title: ntg_sham_2_mRNA (miR-133a)


title: TG133a_sham_1_mRNA (miR-133a)


title: ntg_sham_1_mRNA (miR-133a)


title: poly4_rep2

first: Stephen

middle: N.

last: Floor

address: 513 Parnassus Ave, HSW 740

department: Cell and Tissue Biology

institute: University of California, San Francisco

description:
rRNA-depleted
Polysomal RNA

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters were trimmed using Cutadapt v1.5, reads aligning to the repeatmasker or Illumina iGenomes abundant sequences using Bowtie2 v2.2.4 were discarded. Unaligned reads were then aligned to the Ensembl release 75 transcriptome using Tophat v2.0.13.
Transcript isoform level abundances were calculated using Cuffquant v2.2.1 and normalized between samples with Cuffnorm v2.2.1.
RPKM from Cuffnorm was converted to TPM as in Wagner, Kin & Lynch 2012.
Genome_build: GRCh37
Supplementary_files_format_and_content: CSV files include TPM (transcripts per million) for all Ensembl transcripts and genes in release 75.

source_name: HEK293T cell culture

growth_protocol: HEK293T cells were grown to ~70% confluency in DMEM + 10% FBS and were actively growing when harvested

extract_protocol:
RNA was extracted from pooled technical triplicate sucrose gradient fractions by ethanol precipitation followed by acid phenol:chloroform extraction.  Direct phenol:chloroform extraction was precluded by phase inversion in high sucrose fractions. RNA was then DNase treated, subjected to a second acid phenol:chloroform extraction, and ethanol precipitated. Cytoplasmic RNA was extracted using TRIzol extraction (Life Technologies) and ethanol precipitation. Total RNA integrity was verified using a BioAnalyzer (Agilent).
Ribosomal RNA was then depleted using Ribo-Zero (Illumina) and biological duplicate sequencing libraries were generated using the TruSeq RNA Sample Prep v2 kit (Illumina) without the poly-A selection steps.  An equal mass of rRNA-depleted RNA was used as input to each individual library preparation.

treatment_protocol: Media was aspirated and replaced by PBS + 100 ug/ml cycloheximide and incubated at 37 °C for ten minutes.  The dish was then placed on ice, media aspirated, and replaced by ice cold PBS + 100 ug/ml cycloheximide. Cells were scraped, pelleted at 16,000g for 30 seconds, and resuspended in three pellet-volumes ice cold hypotonic lysis buffer (10 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.5 mM DTT, 1% Triton X-100 and 100 ug/ml cycloheximide) (Folco et al., 2012). After ten minutes, cells were lysed on ice by ten strokes through a 26-gauge needle and nuclei were pelleted at 1,500g for 5 minutes. Lysate from ~15 million cells was layered on top of triplicate 10-50% (w/v) sucrose gradients (20 mM HEPES pH 7.6, 100 mM KCl, 5 mM MgCl2, 1 mM DTT and 100 ug/ml cycloheximide) made using a BioComp gradient master.  Gradients were centrifuged for 2 hours at 36,000 RPM in a SW-41 rotor, punctured, and manually peak fractionated using real-time A260 monitoring with a Brandel gradient fractionator and ISCO UA-6 detector.

tag: cell line

tag: fraction

value: Four ribosomes


title: poly5_rep2

description:
rRNA-depleted
Polysomal RNA

value: Five ribosomes


title: poly6_rep2

description:
rRNA-depleted
Polysomal RNA

value: Six ribosomes


title: LNCaP GIPZ Normal FOXA1 ChIP s7

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Chromatin IP against FoxA1

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: LNCaP GIPZ Normal FOXA1 ChIP s7

growth_protocol: Cell lines were maintained in Normal treatment.

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

treatment_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer.

value: LNCaP

value: prostate tumor

tag: treatment

value: Normal

tag: antibody

value: FoxA1 (abcam, catalog# ab23738, lot# GR44102-1)


title: poly8_rep2

description:
rRNA-depleted
Polysomal RNA

value: Eight+ ribosomes


title: poly3_rep2

description:
rRNA-depleted
Polysomal RNA

value: Three ribosomes


title: poly2_rep2

description:
rRNA-depleted
Polysomal RNA

value: Two ribosomes


title: LNCaP shFOXA1 Normal FOXA1 ChIP s8

description: Chromatin IP against FoxA1

source_name: LNCaP shFOXA1 Normal FOXA1 ChIP s8


title: poly7_rep2

description:
rRNA-depleted
Polysomal RNA

value: Seven ribosomes


title: 80S_rep2

description:
rRNA-depleted
Polysomal RNA

value: Monosome (80S)


title: DU145 pQCXIH Input m139

description: input

source_name: DU145 pQCXIH Input m139

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS.


title: poly8_rep1

description:
rRNA-depleted
Polysomal RNA


title: cyto_rep2

description:
rRNA-depleted
Cytoplasmic RNA

value: Cytoplasm


title: DU145 CMV-AR Ad GATA2 AR ChIP m123

description: Chromatin IP against AR

source_name: DU145 CMV-AR Ad GATA2 AR ChIP m123

value: Ad GATA2

value: AR (millipore, catalog# 06-680 lot# JBC1860890)


title: LNCaP GIPZ Input m136

description:
input
This sample is identical to GSM1501192.

source_name: LNCaP GIPZ Input m136


title: DU145 pLenti Ctrl input m101

description: input

source_name: DU145 pLenti Ctrl input m101


title: poly7_rep1

description:
rRNA-depleted
Polysomal RNA


title: LNCaP shGATA2 EtOH FOXA1 ChIP m81

description: Chromatin IP against FoxA1

source_name: LNCaP shGATA2 EtOH FOXA1 ChIP m81

growth_protocol: Cell lines were maintained in EtOH.

value: EtOH


title: poly6_rep1

description:
rRNA-depleted
Polysomal RNA


title: LNCaP shGATA2 EtOH AR ChIP m80

description: Chromatin IP against AR

source_name: LNCaP shGATA2 EtOH AR ChIP m80


title: poly4_rep1

description:
rRNA-depleted
Polysomal RNA


title: LNCaP GIPZ EtOH GATA2 ChIP m79

description: Chromatin IP against GATA2

source_name: LNCaP GIPZ EtOH GATA2 ChIP m79

value: GATA2 (santa cruz, catalog# sc-9008, lot# H1511)


title: 80S_rep1

description:
rRNA-depleted
Polysomal RNA


title: poly3_rep1

description:
rRNA-depleted
Polysomal RNA


title: poly5_rep1

description:
rRNA-depleted
Polysomal RNA


title: LNCaP GIPZ EtOH FOXA1 ChIP m78

description: Chromatin IP against FoxA1

source_name: LNCaP GIPZ EtOH FOXA1 ChIP m78


title: poly2_rep1

description:
rRNA-depleted
Polysomal RNA


title: cyto_rep1

description:
rRNA-depleted
Cytoplasmic RNA


title: LNCaP GIPZ EtOH AR ChIP m77

description: Chromatin IP against AR

source_name: LNCaP GIPZ EtOHAR ChIP m77


title: LNCaP shGATA2 R1881 (10nM,16h) FOXA1 ChIP m75

description: Chromatin IP against FoxA1

growth_protocol: Cell lines were maintained in R1881 (10nM,16h).


title: LNCaP GIPZ R1881 (10nM,16h) GATA2 ChIP m73

description: Chromatin IP against GATA2


title: LNCaP shGATA2 R1881 (10nM,16h) GATA2 ChIP m76

description: Chromatin IP against GATA2


title: RRBS MLL-AF9 c-kit+ leukemic spleen cells Dnmt3b-knockin MLL-AF9-85-0

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
Illumina CASAVA software was used to demultiplex and export reads in FASTQ format
Illumina paired-end adapter sequences and 3'-MspI-sites were removed with help of Trim Galore! version 0.2.2 using the default settings for RRBS data processing
Reads were mapped using Bismark version 0.7.4
Methylation calls were extracted with the Bismark methylation_extractor script
The extracted methylation data was further analyzed in R using methylKit, the Bioconductor BiSeq package and custom scripts
Genome_build: mm9
Supplementary_files_format_and_content: Extracted CpG methylation call files were generated using custom R scripts. Each processed file contains a column for chromosome, position and extracted methylation data for the respective sample. For each CpG position observed the number of methylated / unmethylated reads is listed.

source_name: leukemic spleen

extract_protocol: 0.3 – 1 µg of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with Illumina TruSeq adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 280 bps insert size were purified from a SYBR gold (Invitrogen) pre-stained agarose gel (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). The libraries were sequenced on an Illumina HiScanSQ instrument with version 3 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.

tag: oncogene


title: PDX4_RIBA2

description:
topTags_Ribavarin-Control.txt
PDX_RIBA-CON_counts

data_processing:
Illumina Casava1.8.0 or 1.8.2 software used for basecalling.
Reads that passed filter were aligned to hg19 using TopHat (Trapnell et al., 2009) or STAR (Dobin et al., 2012).
Gene expression values were estimated with Cufflinks (V1.3.0, Trapnell et al., 2010) or were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/ HTSeq/).
Differentially expressed genes were identified with cuffdiff time series (LY1 samples) or the edgeR package (Robinson et al., 2010, PDX samples).  Genes with a FDR-corrected p-value < 0.05 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: The normalized abundance measurements and differential expression testing given by Cuffdiff are both provided as .txt files. Read counts that map uniquely to the union of all gene exons using HTseq-count and the EdgeR output are provided as a .txt file.

source_name: De-identified patient derived xenograft, passage 4

extract_protocol:
Total RNA was harvested with Trizol reagent (Life Technologies).
Genomic DNA was eliminate with Dnase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.

value: PDX cells

value: 80mg/kg/b.i.d ribavarin IP for 10 days

tag: growth protocol

value: PDX was established in NSG mice for 4 passages

tag: basecalling

value: CASAVA 1.8.2

tag: alignment tool

value: STAR

tag: differential expression tool

value: EdgeR


title: PDX4_CON1

value: Sterile PBS b.i.d. IP for 10 days


title: DU145 CMV-AR Ad LacZ AR ChIP m122

description: Chromatin IP against AR

source_name: DU145 CMV-AR Ad LacZ AR ChIP m122

value: prostate tumor

value: Ad LacZ


title: PDX4_RIBA1


title: PDX4_CON2


title: LNCaP shGATA2 R1881 (10nM,16h) AR ChIP m74

description: Chromatin IP against AR

value: LNCaP


title: RRBS MLL-AF9 c-kit+ leukemic spleen cells Dnmt3b-knockin MLL-AF9-83-0


title: LNCaP shGATA2 EtOH GATA2 ChIP m82

description: Chromatin IP against GATA2

source_name: LNCaP shGATA2 EtOH GATA2 ChIP m82


title: LNCaP GIPZ R1881 (10nM,16h) FOXA1 ChIP m72

description: Chromatin IP against FoxA1

value: FoxA1 (abcam, catalog# ab23738, lot# GR44102-1)


title: RRBS MLL-AF9 c-kit+ leukemic spleen cells Dnmt3b-knockin MLL-AF9-81-0


title: RRBS MLL-AF9 c-kit+ leukemic spleen cells MLL-AF9-79-0

value: MLL-AF9 c-kit+ leukemic spleen cells

value: WT


title: LNCaP shFOXA1 csFCS GATA2 ChIP m28

description: Chromatin IP against GATA2

source_name: LNCaP shFOXA1 csFCS GATA2 ChIP m28

growth_protocol: Cell lines were maintained in phenol free RPMI supplemented with 5% FCS.

value: csFCS


title: LNCaP GIPZ FBS GATA2 ChIP m30

description: Chromatin IP against GATA2

source_name: LNCaP GIPZ FBS GATA2 ChIP m30

value: FBS


title: LNCaP GIPZ csFCS GATA2 ChIP m26

description: Chromatin IP against GATA2

source_name: LNCaP GIPZ csFCS GATA2 ChIP m26


title: LNCaP shFOXA1 phenolfree RPMI+5%FCS AR ChIP m14

description: Chromatin IP against AR

value: phenolfree RPMI+5%FCS

value: AR (millipore, catalog# 06-680 lot# JBC1860890)


title: RRBS MLL-AF9 c-kit+ leukemic spleen cells MLL-AF9-75-0


title: RRBS cMyc-Bcl2 leukemic spleen cells cMyc-Bcl2-13477

value: cMyc-Bcl2 leukemic spleen cells


title: RRBS cMyc-Bcl2 leukemic spleen cells Dnmt3b-knockin cMyc-Bcl2-13473


title: LNCaP GIPZ R1881 (10nM,16h) AR ChIP m71

description: Chromatin IP against AR

source_name: LNCaP GIPZ R1881 (10nM,16h) AR ChIP m71


title: LNCaP shFOXA1 FBS GATA2 ChIP m32

description: Chromatin IP against GATA2

source_name: LNCaP shFOXA1 FBS GATA2 ChIP m32

value: GATA2 (santa cruz, catalog# sc-9008, lot# H1511)


title: LNCaP shFOXA1 RPMI+10%FBS AR ChIP m12

description: Chromatin IP against AR

source_name: LNCaP shFOXA1 RPMI+10%FBS AR ChIP m12


title: RRBS cMyc-Bcl2 leukemic spleen cells cMyc-Bcl2-13439


title: yw embr input 3

status: Public on Jan 10 2016

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: processed data file: ywAB_div_input_profile_in_10000bp_bins_1000bp_shift.wig.gz

data_processing:
The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single. Paired reads were combined.
For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample. Log2 of the ChIP to input ratio was used as a measure of local H3K27me3 enrichment.
To build the whole genome profile, the data were smoothed using a 10kb sliding window, step 1 kb.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig files containing Log2 of the ChIP to input RPM ratio smoothed using a 10kb sliding window with 1000 bp step.

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Flies were raised at 23°C

extract_protocol:
20 ul of 0-4h embryos were used as starting material. Abcam anti-H3K27me3 antibodies (6002) were used for chromatin immunoprecipitation. Chromatin was sheared using BioRuptor instrument (Diagenode).
DNA from precipitated material and input were used for library preparation using Illumina Nextera protocol.

value: yw

tag: tissue

value: 0-4h embryos


title: SuUR embr input 3

description: processed data file: SUUR_AB_div_input_profile_in_10000bp_bins_1000bp_shift.wig.gz

value: SuUR mutant


title: Dam-Pc-SG-SuUR_KO-2

data_processing:
Library strategy: DamID-seq
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.7
The reads obtained were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single
For further analysis, only the reads that started with GATC sequence were retained. The number of reads for each genomic fragment between the neighboring GATC sites (GATC fragments) was summed up.
The data were filtered for reproducibility: all GATC fragments were sorted according to the total read count in two biological samples. This list was binned into groups of 200 fragments having similar read counts. For each GATC fragment, a difference in read counts was calculated between the replicates. Those fragments that showed the difference above 2 standard deviations in the particular group were filtered out.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig files containing scores for each GATC fragment of the genome. Score represents -Log10(P), where P is significance level assessed with exact Fisher’s test for each GATC region in the genome. Positive values were ascribed to GATC fragments enriched in Dam-X sample, while negative values to those enriched in Dam-alone sample.

source_name: salivary glands

growth_protocol: The flies were kept at 23°C

extract_protocol:
50 salivary glands were dissected accurately - fat body was removed completely.
DNA was isolated using phenol-chloroform method. 1ug of genomic DNA was digested by DpnI endonuclease. Digested DNA was ligated with double-stranded DNA adapters and then digested with DpnII endonuclease. Next, methylated fragments were selectively amplified using adapter-specific primer. Before the preparation of libraries for Illumina DamID-seq, the adapters used in DamID procedure were cut with DpnII enzyme. No further fragmentation was performed.

tag: developmental stage


title: SuUR embr AB+ 3

value: Abcam anti-H3K27me3 (6002)


title: Dam-Pc-SG-SuUR_KO-1


title: Dam-SG-SuUR_KO-4

description: control sample for Dam-Pc (SuUR KO)


title: Het (Q111) 6 months  Female White Adipose (Gonad) miRNA rep3

source_name: White Adipose tissue around Gonad

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: White Adipose tissue around Gonad

value: Het (Q111) Knock-In

value: 6 months

value: Female

tag: housing condition

value: housed with Het (Q111) mice


title: Dam-SUUR-SG-1

tag: genotype


title: Dam-SG-SuUR_KO-3

description: control sample for Dam-Pc (SuUR KO)


title: Dam-SG-2

description: control sample for Dam-SUUR


title: Dam-Pc-SG-2


title: Dam-Pc-SG-1


title: LNCaP GIPZ phenolfree RPMI+5%FCS FOXA1 ChIP m17

description: Chromatin IP against FoxA1

value: LNCaP

tag: cell type

value: prostate tumor

value: FoxA1 (abcam, catalog# ab23738, lot# GR44102-1)


title: RRBS cMyc-Bcl2 leukemic spleen cells Dnmt3b-knockin cMyc-Bcl2-13953


title: RRBS MLL-AF9 c-kit+ leukemic spleen cells MLL-AF9-73-0

value: MLL-AF9 c-kit+ leukemic spleen cells

value: WT


title: Dam-SG-6

description: control sample for Dam-Pc


title: Dam-SG-1

description: control sample for Dam-SUUR


title: LNCaP GIPZ phenolfree RPMI+5%FCS AR ChIP m13

description: Chromatin IP against AR

value: phenolfree RPMI+5%FCS

value: AR (millipore, catalog# 06-680 lot# JBC1860890)


title: LNCaP GIPZ RPMI+10%FBS AR ChIP m11

description: Chromatin IP against AR

source_name: LNCaP GIPZ RPMI+10%FBS AR ChIP m11


title: SIN3 220HA_HA_rep2_chipseq

status: Public on Jan 09 2016

city: Detroit

first: Lori

middle: Ann

last: Pile

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the dm3 genome assembly using Bowtie2 with default parameters
Data were filtered using the following specification: 1. Reads mapping to unique region of the Drosophila genome, 2. phred score of reads > 20
peaks were called using MACS 2.1.0 and Irreproducibilty rate analysis was performed to call the final peaks. ChIP peak threshold (IDR 0.1), Enrichment Fold (≥3).
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph files were generated using MACS 2.1.0, Peak files were generated by MACS2.1.0 in bed format. Finally Peaks were called using IDR of 0.1 and FE ≥3

source_name: S2 cells

growth_protocol: Drosophila S2 cells stably transfected with HA-tag constructs of SIN3 187 or SIN3 220 were cultured in Drosophila Schneider's media + L-glutamine supplemented with 10% heat inactivated fetal bovine serum and 0.1 mg/ml of penicillin/streptomycin and 0.1 mg/ml of geneticin. Cells were mainatined at 27oC

extract_protocol:
Chromatin was prepared from cells which were treated with formaldehyde to chross-link protein and DNA. Fragmentation of chromatin to desired size was carried out by MNase treatment and sonication. Chromatin prepared was subjected to immunoprecipitation.
Libraries were prepared according to a previously published protocol (Ford et al.,2014). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, 5 cycles of PCR was carried out using Illumina universal primers to convert all adapter DNA fragments to double stranded DNA. Following the pre_PCR step fragments of approximately 270 - 420 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Purified DNA was PCR amplified with Illumina primers for 12 more cycle cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.

value: Stably transfected HA-tagged SIN3 220 cells

value: Anti-HA-Agarose antibody (Sigma)


title: SIN3 220HA_Input_rep2_chipseq


title: SIN3 187HA_Input_rep2_chipseq

value: Stably transfected HA-tagged SIN3 187 cells


title: SIN3 187HA_Input_rep1_chipseq


title: SIN3 187HA_HA_rep2_chipseq


title: SIN3 220HA_HA_rep1_chipseq


title: Dam-SUUR-SG-2

value: yw


title: yw embr AB+ 3

value: Abcam anti-H3K27me3 (6002)

value: 0-4h embryos


title: SIN3 187HA_HA_rep1_chipseq


title: 500_cell_THS-seq_with_Tn5059_Rep1

city: La Jolla

first: Kun

last: Zhang

address: 9500 Gilman Drive, MC0412, PFBH402

department: Bioengineering

institute: University of California San Diego

description:
THS-seq
downsampled.bed: data downsampled to 8,351,125 reads for analysis

data_processing:
Basecalls performed using Real Time Analysis (RTA) version 1.13
After demultiplexing sequences were aligned to the hg19 genome assembly using default BWA parameters
If needed samples were downsampled to the same number of unique reads with in house scripts before analysis
Peak calling was performed with Dfilter 1.0 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: .bed files of called peaks from Dfilter, with chromosomal locations of each significnatly called peak

source_name: GM12878 B-Lymphocytes

growth_protocol: GM12878 cells were maintained in RPMI 1640. Cells were kept in suspension at 37°C and were harvested when suspensions reached optimal density.

extract_protocol:
GM12878 cells were pelleted at 250 x g, and washed twice then resuspended in PBS before being used for the assay
ATAC-seq with optimized buffer and protease treatment after tagmentation was performed on lysed cells, followed by PCR cycling until curves reach saturation, and after gel size selection libraries are ready for sequencing. THS-seq method used a custom transposon and engineered Tn5 for tagging accessible regions, followed by in vitro transcription. RNA processing consisted of: MMLV first strand synthesis, RNase H digestion, second strand synthesis with Taq polymerase, custom transposon mediated fragmentation, and PCR barcode addition. Then libraries are ready for sequencing.

tag: passage

tag: ethnicity

value: Caucasian

tag: Sex

value: female


title: 6ng_pure_DNA_THS-seq_with_Tn5059

description: THS-seq

tag: cell line


title: 500_cell_THS-seq_with_EzTn5_Rep2


title: 500_cell_THS-seq_with_Tn5059_Rep2


title: 100_cell_THS-seq_with_Tn5059_Rep2


title: 100_cell_THS-seq_with_Tn5059_Rep1


title: S2 rep1

description:
control
replicates 1,2 and 3 combined

data_processing:
Illumina bcl2fastq converter was used to demultiplex samples.
Tuxedo pipeline was used to allign reads to dm3, estimation of  transcripts and analyze differential expression. All steps were performed using default settings.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and expression fold change as determined by Cuffdiff.

growth_protocol: Drosophila Schneider cell line 2 (S2) cells were cultured at 27oC in Schneider's Drosophila medium (1x) + L-glutamine (Life Technologies) with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 mg/ml gentamycin.

extract_protocol:
Total RNA was isolated from treated S2 cells using the EZ1 RNA Universal Kit (Quiagen). Cells were disrupted and homogenized in 750 μl  QIAzol lysis reagent via bead-milling on the TissueLyser II (Qiagen). RNA was collected from the homogenate by chloroform exraction and purified on the EZ1 Advanced (Qiagen) with additional step to remove any residual DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.07 μM CuSO4 and incubated for 48 hr prior to RNA extraction

value: wild type


title: S2 rep2

description: control


title: SIN3 187HA rep3

description: test


title: SIN3 220HA_Input_rep1_chipseq

tag: chip antibody


title: Dam-SG-5

description: control sample for Dam-Pc


title: LID KD + paraquat rep3

description:
test
replicates 1,2 and 3 combined
LID_KD_P_vs_GFP_RNAi.txt

growth_protocol: Drosophila Schneider cell line 2 (S2) cells were cultured at 270C in Schneider's Drosophila medium (1x) + L-glutamine (Life Technologies) with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 mg/ml gentamycin.

treatment_protocol: Cells were treated with dsRNA targeting lid gene for 4 days prior to RNA extraction. In addition cells were treated with 8.3 mM paraquat (1,1′-Dimethyl-4,4′-bipyridinium dichloride (Sigma Aldrich)) for 24 hr prior to RNA extraction.

tag: genotype/variation

tag: dsrna target

value: LID with paraquat


title: S2 rep3

description: control


title: 500_cell_ATAC-seq_with_Tn5059_Rep2

description:
ATAC-seq
downsampled.bed: data downsampled to 8,351,125 reads for analysis


title: SIN3 KD + LID KD + paraquat rep1

description:
test
replicates 1,2 and 3 combined
SIN3_KD_LID_KD_P_vs_GFP_RNAi.txt

treatment_protocol: Cells were treated with dsRNA targeting Sin3A and lid genes for 4 days prior to RNA extraction. In addition cells were treated with 8.3 mM paraquat (1,1′-Dimethyl-4,4′-bipyridinium dichloride (Sigma Aldrich)) for 24 hr prior to RNA extraction.

value: SIN3 and LID with paraquat


title: SIN3 KD + LID KD + paraquat rep3


title: SIN3 KD + LID KD + paraquat rep2


title: SIN3 KD + paraquat rep3

description:
test
replicates 1,2 and 3 combined
SIN3_KD_P_vs_GFP_RNAi.txt

treatment_protocol: Cells were treated with dsRNA targeting Sin3A gene for 4 days prior to RNA extraction. In addition cells were treated with 8.3 mM paraquat (1,1′-Dimethyl-4,4′-bipyridinium dichloride (Sigma Aldrich)) for 24 hr prior to RNA extraction.

value: SIN3 with paraquat


title: LID KD + paraquat rep1


title: SIN3 KD + paraquat rep2


title: SIN3 KD + paraquat rep1


title: GFP RNAi+ paraquat rep3

description:
test
replicates 1,2 and 3 combined
GFP_RNAi_P_vs_GFP_RNAi.txt

treatment_protocol: Cells were treated with dsRNA against the GFP gene as a control for 4 days prior to RNA extraction. In addition cells were treated with 8.3 mM paraquat (1,1′-Dimethyl-4,4′-bipyridinium dichloride (Sigma Aldrich)) for 24 hr prior to RNA extraction.

value: GFP with paraquat


title: 500_cell_THS-seq_with_EzTn5_Rep1


title: GFP RNAi+ paraquat rep2


title: GFP RNAi+ paraquat rep1


title: 500_cell_ATAC-seq_with_Tn5059_Rep1


title: SIN3 KD+LID KD rep2

description:
test
replicates 1,2 and 3 combined
SIN3_KD_LID_KD_vs_GFP_RNAi.txt

treatment_protocol: Cells were treated with dsRNA targeting Sin3A and lid genes for 4 days prior to RNA extraction

value: SIN3 and LID


title: SIN3 187HA rep2

description: test


title: LID KD rep3

description:
test
replicates 1,2 and 3 combined
LID_KD_vs_GFP_RNAi.txt

treatment_protocol: Cells were treated with dsRNA targeting lid gene for 4 days prior to RNA extraction

value: LID


title: LID KD rep1


title: SIN3 KD rep3

description:
test
replicates 1,2 and 3 combined
SIN3_KD_vs_GFP_RNAi.txt

treatment_protocol: Cells were treated with dsRNA targeting Sin3A gene for 4 days prior to RNA extraction


title: SIN3 KD rep1


title: LID KD + paraquat rep2


title: 500_cell_ATAC-seq_with_EzTn5_Rep2


title: SIN3 KD+LID KD rep3


title: 500_cell_ATAC-seq_with_EzTn5_Rep1


title: GFP RNAi rep2

description:
control
replicates 1,2 and 3 combined

treatment_protocol: Cells were treated with dsRNA against the GFP gene as a control for 4 days prior to RNA extraction

value: GFP


title: PAO1_rep2

status: Public on Jan 08 2016

city: Syracuse

first: Christopher

middle: T

last: Nomura

state: New York

address: 1 Forestry Dr.

department: Chemistry

institute: SUNY-ESF

data_processing:
Illumina NextSeq RTAv2 used for base-calling
Sequencing reads were trimmed for adaptor sequences and masked for low-complexity or low-quality sequences, then mapped to P. aeuriginosa PAO1 using CLC Genomics workbench
Reads per kilobase of orf per megabase of library size were calculated using the CLC genomics analysis tool
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: tab delimited text files with RPKM values

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: Each strain was grown in quadruplicate in 50 mL of PB in 500 mL baffled shake flasks at 37 °C and 200 rpm to an OD600 of ~ 0.5.

extract_protocol:
Cultures were stabilized by adding 1 mL of RNAprotect Bacteria reagent (Qiagen) to 0.5 mL of culture.  Cells were then lysed using lysozyme and proteinase K as described in the manufacturer’s protocol. The total RNA from the lysed cells was subsequently purified using the RNeasy mini kit (Qiagen) with an on-column DNAse digestion step.
RNA libraries were prepared for sequencing using protocols recommended by Illumina

value: WT

tag: growth stage

value: exponential phase


title: DNase-seq_W303_S_cerevisiae_Sample1

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

institute: Duke University

description: replicate 1

data_processing:
Single-end sequencing reads were aligned with Bowtie 0.12.7 with the following parameters: -n 2 -l 20 -3 30 -m 1 --best --strata
For each read, the first base pair of the alignment position from the 5' edge was assigned as the DNase cleavage site.  The total number of DNase cuts at each genomic position was tabulated separately for the forward (+) and reverse (-) strands.
Genome_build: UCSC sacCer2 / SGD R61
Supplementary_files_format_and_content: csv files with columns chr, position, forward strand DNase cut count, reverse strand DNase cut count, and total DNase cut count from both strands

organism: Saccharomyces cerevisiae

growth_protocol: Asynchronous population of yeast cells grown in YPD at 37 °C, and assayed in log-phase growth (OD600 of 0.7)

extract_protocol:
Intact nuclei were prepared as before (Henikoff et al., 2011) with some alterations. Unfixed yeast cells (W303 strain, asynchronous cells grown in YPD) grown to OD600 0.7 were centrifuged at 2000 rpm for 5 min, washed with sterile water and resuspended in 20 mL buffer Z (0.56M sorbitol, 7.4pH 50mM Tris,autoclaved). After resuspension, 14  μL β-Mercaptoethanol and 500 μL of 10mg/mL zymolyase dissolved in buffer Z were added. Samples were incubated on the bench top for 30 min and inverted every few minutes.  Cells were then centrifuged at 1500 rpm for 6 min at 4 °C and resuspended in 2.5 mL modified NP buffer (1M sorbitol, 50mM NaCl, 7.4pH 10mM Tris, 5mM MgCl2) supplemented with 0.5 mM spermidine, 0.007% B-Mercaptoethanol, and 0.075% NP-40. Next, dilutions of DNase I were prepared on ice to test the best digestion conditions. In 1.5 mL tubes, 400 μL of cell mixture from above was added to 12 μL of the following DNase I solutions: 0.03, 0.1, 0.3, and 1 U/μL. Samples were inverted once and incubated at 37 °C for 16 min. After incubation, 100 μL of stop buffer (5% SDS, 50mM EDTA) was added to terminate the reaction.  Proteinase K (0.2 mg/mL) was added to each tube, inverted to mix and placed at 65 °C overnight. The next day, DNA was recovered by phenol extraction and isopropanol precipitation and run on a 0.8% agarose gel for 3 hours at 85 volts to check sample digestion.
Sequencing libraries were prepared as previously described (Song and Crawford, 2010)


title: GcsR_rep1

value: deltagcsR PAO1

value: deltagcsR


title: DNase-seq_W303_S_cerevisiae_Sample2

description: replicate 2


title: SIN3 187HA rep1

description:
test
replicates 1,2 and 3 combined


title: GcsR_rep2

value: deltagcsR PAO2


title: GFP RNAi rep1

description:
control
replicates 1,2 and 3 combined


title: PAO1_rep1


title: CNBP knockdown and RNA seq, 2,1

city: Wuerzburg

first: Sanjay

middle: Kumar

last: Gupta

state: Bavaria

address: Biozentrum, Am Hubland

department: Dept of Biochemistry

institute: University of Wuerzburg

data_processing:
Illumina high-seq 2500 platform was used for sequencing
The reads were aligned to the hg19 genome using TopHat
Transcripts were assembled using Cufflinks
Cuffdiff and CummeRbund was further used to find the differentially expressed genes and transcripts and to plot their abundance
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff output

source_name: CNBP knockdown and RNA seq, 2,1

growth_protocol: HEK293 cells were grown and routinely passaged in DMEM with 10% FCS and 1% pen/strip.

extract_protocol: The RNA library was generated using NEB ultradirectional library preparation kit as per manufacturers protocol.

value: FLAG-HA tagged CNBP


title: CNBP knockdown and RNA seq, 1,2

source_name: CNBP knockdown and RNA seq, 1,2


title: SIN3 KD+LID KD rep1


title: CNBP knockdown and RNA seq, 1,1

source_name: CNBP knockdown and RNA seq, 1,1


title: Control knockdown, 3

source_name: Control knockdown, 3


title: CNBP knockdown and RNA seq, 2,2

source_name: CNBP knockdown and RNA seq, 2,2


title: mycPet-1_ChIP

city: Cleveland

first: Evan

last: Deneris

state: OH

address: 2109 Adelbert Rd.

department: Neurosciences

institute: Case Western Reserve University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were filtered for low-quality sequence, then mapped to mm9 whole genome using tophat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks.
Reads were mapped to the Mus musculus genome (UCSC mm10) using the Burroughs-Wheeler Aligner (BWA) and were filtered to select reads that map to a single location (Li and Durbin, 2009). Peak calling was performed with MACS v1.4.2 modified to accept a custom scaling factor of 0.8195945 derived from the Normalization ChIPseq software (NCIS) (Zhang et al., 2008; Liang and Keleş, 2012).
MycPet-1 ChIP peaks were associated to genes using the GREAT web service v3.0 (mm10) with 5kb intervals upstream and downstream of the TSS and TTS of each gene model along with peaks that overlap the gene body.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample in the time-series gene expression trajectory (E11.5, E15.5, PN; Gene_expression_trajectories_E11.5_E15.5_PN.matrix.txt) and WT vs. Pet-1-/- (E15.5_WT vs E15.5_KO) generated by cufflinks. For ChIP-seq, a BED file of mycPet-1 ChIP peaks is provided.

source_name: hindbrain

growth_protocol: Animals were reared in standard housing conditions.

extract_protocol:
EYFP+ 5-HT neurons were sorted using a BD FACSAria into Trizol reagent and extracted RNA was Dnase I treated and purified using the RNA Clean & Concentrator-5 kit (Zymo). Purified total RNA was amplified with the SMARTer Ultra-low mRNA-Seq kit (Clontech) or Ovation RNA-Seq System V2 (NuGEN). Dissected YFP+ tissue between the mid-hindbrain boundary and rhombomere 4 of E12.5 to E15.5 hindbrains from Pet-1-/-; ePet-mycPet-1; ePet-EYFP embryos was quickly flash frozen on dry ice. Chromatin was isolated and immunoprecipitated using a ChIP grade, goat anti-Myc antibody (Abcam ab9132, Cambridge, MA, validation report at abcam.com) with proprietary protocols (Active Motif, Carlsbad, CA).
RNA libraries were prepared for sequencing using either Clontech SMARTer RNA-seq (E11.5, E15.5C_WT, E15.5C_KO, PN) or NuGen Ovation RNA-Seq v2 (E15.5N_WT, E15.5N_KO). ChIP-seq libraries were prepared using standard Illumina ChIP-seq methods.

value: hindbrain


title: Control knockdown, 1

source_name: Control knockdown, 1


title: mycPet-1_Input


title: LID KD rep2


title: GFP RNAi rep3

description:
control
replicates 1,2 and 3 combined


title: Control knockdown, 2

source_name: Control knockdown, 2


title: C1_SM1_C64

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: GSE67835_neurons_vs_AH017_7_filtered_expr_iPSC.counts.gz

data_processing:
Trimmomatic with the arguments “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50”
Tophat2
Rsubread
DESeq adjustment for library size and ERCC counts from 92 ERCC (External RNA Control Consortium) controls
Genome_build: hg19 plus ERCC 92
Supplementary_files_format_and_content: adjusted counts (tsv)

source_name: iPSC-derived cortical neuron

growth_protocol: iPSCs were differentiated into cortical neurons using the Livesey protocol with some modifications (Shi et al. Nat. Protocol. 2012;7(10):1836–1846). In brief, iPSCs were cultured in monolayer on matrigel. Cells were induced using dual SMAD inhibition (1µM dorsomorphin and 10µM SB431542) in neural maintenance media (DMEM/F-12, neurobasal, N-2, B-27, 5µg/ml insulin, 1mM L-glutamine, 100µM non-essential amino acids, 100µM 2-mercaptoethanol, 50 units/ml penicillin and 50mg/ml streptomycin). After the formation of a neuroepithelial sheet, this was passaged into wells plated with L-ornithine and laminin. The subsequent differentiating cells were passaged after different durations in culture to expand cortical neural progenitor stocks. RT-qPCR and immunofluorescence microscopy confirmed the adoption of cortical identity. Cells were treated with 4M cytosine arabinoside for 72 hours prior to single cell analysis.

extract_protocol:
Cells were dissociated as for single cell RT-qPCR at day 72 of neuronal differentiation. 300,000 DAPI negative cells were sorted into 200L of neural maintenance media. These were loaded onto a small C1 chip according to the Smarter-seq protocol detailed by Fluidigm. Cells were co-stained with Hoechst and propidium iodide. Capture chambers were imaged on an Opera Imaging System.
We continued with lysis, reverse transcription, amplification and library prep in accordance with the Fluidigm Smarter-seq protocol.

tag: iPSc

tag: reprogramming vector

value: Sendai virus (SeVdp(KOSM)302L)

tag: time

value: 72 days of neuronal differentiation

value: iPSC-derived cortical neuron


title: C1_SM1_C54


title: C1_SM1_C49


title: C1_SM1_C39


title: C1_SM1_C91


title: C1_SM1_C66


title: C1_SM1_C79


title: C1_SM1_C52


title: C1_SM1_C36


title: C1_SM1_C19


title: C1_SM1_C33


title: C1_SM1_C34


title: C1_SM1_C02


title: C1_SM1_C08


title: C1_SM1_C21


title: C1_SM1_C13


title: L30-3

city: Zheng

first: HONG

last: LI

address: 95 Wenhua Road, Jinshui District

country: China

institute: Henan Agriculture University

data_processing:
Basecalling performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version: 0.0.13.
mRNA-seq reads were aligned to the reference genome ensemble Galgal4 using spliced mapping algorithm in TopHat version: 2.0.9
Fragments per kilo base of exon model per million mapped reads (FPKM) of each gene were calculated  according to the Cufflink (version: V2.1.1)
Differential expression were analysed  using cuffdiff in version 2.3.4
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Gallus gallus

source_name: Liver

extract_protocol:
Liver tissues were moved,snap-frozen in liquid nitrogen,total RNA was harvested with TRIzol® Reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Lushi chicken

tag: age

value: 30 weeks

value: female

tag: tissue

value: liver


title: L30-2


title: Brain_white matter

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description:
Brain_W
SRX381706

data_processing:
Illumina Casava1.7 software used for basecalling
Read mapping: Two reference sequences were prepared based on the HG19 reference
The alignment was performed using the bowtie alignment software version  0.12.8
Methylation calls files for C's in the bowtie alignment files were generated using Bismark software
Genome_build: HG19
Supplementary_files_format_and_content: Methylation calls files; each column contrain chromosome, position, methylatedCounts, unmethylatedCounts values.

source_name: Normal

growth_protocol: Cells were cultured in DMEM at 10% FBS, 5% CO2.

extract_protocol:
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎœltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C. PCR products were sequenced with an Illumina genome analyzer. The reads generated by Illumina sequencing were aligned to the reference genome using SOAPaligner2. The alignment and methylation estimation was performed as described before (Li, Y. et al. PLoS Biol 8, e1000533 (2010)).
100 bases Pair-end reads

treatment_protocol: Untreated

tag: sample type

value: Primary


title: Lung_normali

description:
Lung
SRX381713


title: Colon_normal

description:
Colon
SRX381553


title: Lung_H157

description:
H157
SRX381719

source_name: Squamous cell cancer

value: Cell line


title: Colon_metastasis

description:
Colon_M
SRX381585

source_name: Metastasis


title: L30-1


title: Breast_normal

description:
Breast
SRX381631


title: Colon_cancer

description:
Colon_P
SRX381569

source_name: Cancer


title: Blood_B-cells_CD19

description:
CD19
SRX381725


title: L20-3

value: 20 weeks


title: Lung_H1437

description:
H1437
SRX381716

source_name: Adenocarcinoma


title: L20-1


title: SLJ8666WT-Rep3

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Sequencing data was processed with CASAVA 1.8.2
Data was aligned to yeast genome sacCer3 using tophat 2.0.10 with parameters --segment-mismatches 1 -x 1 -g 1 --no-coverage-search and with a gtf file based on Ensembl 72.
Downstream analysis was done in R 3.0.2. DE genes were called using edgeR 3.4.2.
Genome_build: sacCer3
Supplementary_files_format_and_content: RPM normalized bigWig files separated by strand - pos for forward/plus strand, neg for minus/reverse strand.

source_name: total RNA extract from yeast culture

growth_protocol: yeast cultures were grown to mid-log phase and harvested

extract_protocol:
total RNA was extracted via acid phenol and ethanol precipitated.  QC performed on BioAnalyzer
libraries were prepared according to Illumina instructions, TruSeq universal adapters were ligated and samples were pooled and run on HiSeq 2500 machine.  Single reads, 51 bases.

tag: genotype

value: wild-type


title: SLJ8666WT-Rep2


title: Lung_H1672

description:
H1672
SRX381722

source_name: Small cell lung cancer


title: SLJ8668-sec66del-Rep2

value: sec66 mutant


title: Brain_U87MG

description:
U87MG
SRX381701

source_name: Glioma


title: SLJ8668-sec66del-Rep1