title: Region_73 - Anterior Medial Frontal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: anterior medial frontal gyrus

value: Female Brain:anterior medial frontal gyrus


title: Region_11 - Pulvinar, Brain1, H3K27ac ChIP

status: Public on Oct 15 2014

type: SRA

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

library_source: genomic

data_processing:
Human: Solexa sequencing: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) as long as the read, allowing 1 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best). SOLiD sequencing: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) of 36bp, allowing 3 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p), a shiftsize of 200 (--nomodel,--shiftsize), and a large lambda of 100000 (--llocal).
Mice: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) as long as the read, allowing 1 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p).
Rat: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) of 36bp, allowing 3 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p), a shiftsize of 200 (--nomodel,--shiftsize), and a large lambda of 100000 (--llocal).
genome build: hg19, mm9, rn4
Supplementary_files_format_and_content: bedgraph: Treat pileup MACS2 bedGraph format.
Supplementary_files_format_and_content: bw: Treat pileup in bigWig format, read per million normalized.
Supplementary_files_format_and_content: peaks.txt: Peaks in MACS2 txt format.
Supplementary_files_format_and_content: peaks.bed: Peaks in MACS2 BED format.

molecule: genomic DNA

organism: Homo sapiens

source_name: Female Brain: pulvinar

extract_protocol: Frozen tissues were dissected at -20ºC, thawed quickly and homogenized. Between 20mm3 and 0.5cm3 was used depending on tissue availability. Tissue was immediately chemically cross-linked by the addition of 2ml one-fifth volume of fresh 11% formaldehyde solution in medium and incubated for 10 minutes while rotating at room temperature. Cells were washed with PBS at 4ºC.Cells were lysed and sonicated. The IP was incubated overnight at 4°C with 50 ul of Dynal Protein G magnetic beads (Invitrogen lot# 90513840) that had been pre-incubated with 5 µg of the appropriate antibody for at least 3 hrs in PBS/0.5% BSA at 4°C. Beads were washed 4 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads in elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and at the same time crosslinking was reversed by overnight incubation at 65°C. After removal of the beads immunoprecipitated DNA was diluted 1:1 with TE and then treated with RNAse A for 2 hours at 37°C, followed by proteinase K treatment for 2 hours at 50°C. DNA was purified using two consecutive phenol:chloroform extractions using MaXtract High Density gel tubes. The resulting DNA was used for analysis either on the solexa sequencer (HiSeq 2000 genome sequencer) or the SOLiD sequencer (5500xl /550xlW). The sample prep was preformed  by using the sequencer  corresponding  ChIP-Seq sample prep kit according  to the manufacturers protocol. HiSeq samples were prepped and run by the MIT BioMicro Center (http://openwetware.org/wiki/BioMicroCenter) using the HiSeq 2000 genome sequencer (10 ChIPs multiplexed per lane). Solexa samples were prepped and run in-house using the SOLiD 5500xl or SOLiD 5500xlW.

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

tag: tissue

value: Female Brain:pulvinar


title: Region_7 - Hippocampus, Brain1, H3K27ac ChIP

source_name: Female Brain: hippocampus

value: Female Brain:hippocampus


title: Region_8 - Superior Temporal Gyrus (planum polare), Brain1, H3K27ac ChIP

source_name: Female Brain: superior temporal gyrus, planum polare

value: Female Brain:superior temporal gyrus, planum polare


title: Region_76 - Superior Frontal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: superior frontal gyrus

value: Female Brain:superior frontal gyrus


title: Region_9 - Subcentral Region, Brain1, H3K27ac ChIP

source_name: Female Brain: subcentral area,

value: Female Brain:subcentral area,


title: Region_6 - Temporal Pole, Brain1, H3K27ac ChIP

source_name: Female Brain: temporal pole

value: Female Brain:temporal pole


title: Starting Material, Normal Liver

city: Philadelphia

first: John

last: Pehrson

state: PA

address: 3800 Spruce Street

country: USA

institute: University of Pennsylvania

description: mononucleosomal DNA

data_processing:
Base-calling was performed using Illumina's CASAVA version 1.8
Raw data was aligned to mm9 genome using bowtie version 0.12.7 with alignment parameters "-k 1 -m 1 --best --strata" to pick unique alignments.
Bigwig profiles were generated by counting number of overlapping unique fragments at every location on the genome and normalizing counts to reads per million (RPM).
Genome_build: mm9
Supplementary_files_format_and_content: Profiles in bigwig format

organism: Mus musculus

source_name: 18.5 d.p.c. fetal mouse liver

growth_protocol: Pregnant mice were maintained on a 12 hr day/night cycle with the lights coming on a 8 AM. They were given water and low fat rodent chow Ad libitum. They were killed mid-morning.

extract_protocol:
Details of procedure for thio-affinity purification of macroH2A nucleosomes are described in: Changolkar, L.N. and J.R. Pehrson, MacroH2A1 histone variants are depleted on active genes but concentrated on the inactive X. Mol Cell Biol, 2006. 26: p. 4410-4420. Briefly, fifty 18.5-d.p.c. fetal mouse livers were very gently homogenized using a Potter Elvehjem tissue homogenizer and nuclei were purified by ultracentrifugation through a sucrose cushion; fetal liver nuclei must be handled with care to avoid aggregation. An H1-stripped chromatin fraction was prepared and digested to mono- and oligonucleosomes. The nucleosomes were first passed through a column of Activated Thiol Sepharose (Amersham Biosciences), which was connected in tandem to a column of Thiopropyl Sepharose (Amersham Biosciences). The columns were disconnected, and washed and eluted as previously described, except in this case we first washed the Activated Thiol Sepharose column with 0.5 M NaCl, 1 mM EDTA, 10 mM Tris pH 7.5 prior to elution with a 100 mM b-mercaptoethanol, 100 mM NaCl, 1 mM EDTA, 10 mM Tris pH 7.5. This elution procedure was also used for the Thiopropyl Sepharose column; the 0.5 M NaCl wash removes nucleosomes bound to the column through cysteine-containing nonhistone proteins.
Mononucleosomal DNA was purified from an agarose gel, and the DNA ends repaired using standard procedures. An A was added to the 3’ ends using Klenow (exo-), and Illumina multiplex adaptors were ligated on following standard procedures. Ligated fragments were gel purified and amplified using standard Illumina multiplex primers.

treatment_protocol: No special treatments.

tag: gender

value: Mixed

tag: strain

value: 129/S6 (Taconic)

value: Fetal Liver

tag: fetal age

value: 18.5 day post coitum

tag: macroh2a genotype

value: Wild-type


title: Activated Thiol Sepharose, Knockout Liver

description: mononucleosomal DNA

value: macroH2A1/2 double knockout


title: Starting Material, Knockout Liver

description: mononucleosomal DNA


title: Activated Thiol Sepharose, Normal Liver

description: mononucleosomal DNA


title: Region_1 - Posterior Precentral Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: posterior precentral gyrus (primary motor cortex)

value: Female Brain:posterior precentral gyrus (primary motor cortex)


title: Region_4 - Superior Temporal Gyrus (Heschl's gyrus), Brain1, H3K27ac ChIP

source_name: Female Brain: Heschl's gyrus, transverse temporal gyrus/superior temporal gyrus  (primary auditory cortex)

value: Female Brain:Heschl's gyrus, transverse temporal gyrus/superior temporal gyrus  (primary auditory cortex)


title: Thiopropyl Sepharose, Normal Liver

description: mononucleosomal DNA


title: Region_2 - Locus Coeruleus, Brain1, H3K27ac ChIP

source_name: Female Brain: locus coeruleus

value: Female Brain:locus coeruleus


title: Region_3 - Occipital Pole, Brain1, H3K27ac ChIP

source_name: Female Brain: occipital pole, Internal calcarine sulcus,  (primary visual cortex V1)

value: Female Brain:occipital pole, Internal calcarine sulcus,  (primary visual cortex V1)


title: P1_Strom_Nes-GFP(-)Pdgfra(+)_Rep2

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S7-2GmPp

library_source: transcriptomic

data_processing:
libraries sequenced usign Illumina GAIIx single end 75nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated from the bcl files using picard tools
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using voom from Limma R package
Genome_build: NCBIM37 Genebuild Ensembl v65
Supplementary_files_format_and_content: tab separated file. Contains normalized counts. Samples in columns, Genes in rows

molecule: total RNA

growth_protocol: Pooled bones (femora, tibiae, scapulae, humeri, radii) were dissected from Nes-Gfp newborn pups, crushed and digested with collagenase (Stem Cell technologies). Bone preps were stained with anti-CD45, CD31, Ter119 and Pdgfra and subjected to FACS sorting (FACS Aria II, BD). 15,000-80,000 cells from each stromal population were sorted into PicoPure Extraction Buffer (Life Technologies).

extract_protocol:
Total RNA from sorted cells was extracted using the Arcturus Picopure RNA isolation kit (Life Technologies), following the manufacturer's instructions.
cDNA has been produced and amplified according to Ovation RNA-Seq System V2 Kit. Amplified cDNA was fragmented by sonication and sequencing adaptors ligated following Illumina protocol from TrueSeq DNA Library Preparation Kit

tag: strain background

tag: genotype/variation

value: Nes-Gfp heterozygous pups

tag: developmental stage

value: P1 (newborn)

value: Bone marrow (collagenase-digested crushed bones)

tag: cell population


title: P1_Strom_Nes-GFP(+)Pdgfra(-)_Rep2

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S6-2GpPm


title: P1_Strom_Nes-GFP(+)Pdgfra(+)_Rep1

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S4-1GpPp


title: KDM3A_HS(-)

city: Beijing

first: Ye

last: Zhang

state: Not applicable

address: 5 Dongdan Santiao

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Illumina  GAIIx system for 80-nt single-end sequencing
ChIP-seq reads were aligned to the hg19 genome assembly using BWA algorithm with the default settings
SICER  V1.1 for peak calling(results were uncorrelated with our data in GEO)
Input control of the HS(-) and HS(+) were added into "input_pool_clean"
Genome_build: hg19
Supplementary_files_format_and_content: .wig files which show our aligned reads in line graphics

source_name: Jurkat cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with KDM3A or p-KDM3A antibody.The sonicated DNA fragments were purified as Input control.
The DNA fragments were end-repaired, adenylated,ligated to adaptors and PCR-amplified for 18 cycles. The PCR products corresponding to bp 250-450 were gel-purified, quantified and stored at -80°C until use for sequencing

treatment_protocol: 1×10^7 Jurkat cells were treated with  or without Heat Shock (42℃ water bath for 1 hour)

tag: cell line

value: Jurkat

tag: cell type

value: Acute T Cell Leukemia T lymphocyte

tag: treatment

tag: antibody manufacturer

value: Millipore Biotech (Billerica, MA, USA)

tag: antibody catalog number


title: P1_Strom_Nes-GFP(-)Pdgfra(-)_Rep2

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S5-2GmPm


title: p-KDM3A_HS(+)

value: customized from Beijing B&M Biotech (Beijing, China)


title: Region_78 - Lingual Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: lingual gyrus

value: H3K27ac (Abcam, ab4729)

value: Female Brain:lingual gyrus


title: P1_Strom_Nes-GFP(+)Pdgfra(-)_Rep1

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S2-1GpPm


title: P1_Strom_Nes-GFP(-)Pdgfra(+)_Rep1

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S3-1GmPp


title: mMCF7 WT

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

data_processing:
Tophat (ver. 2.0.7) and Cufflinks (ver. 2.1.1; https://main.g2.bx.psu.edu/) software suites were used to analyze the RNA deep sequencing data according to Trapnell et al. (2010).
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012) (PMID 22383036).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: breast cancer cell line, MCF7

growth_protocol: Human breast cancer MCF-7 cell line was cultured in Dulbecco’s Modified Eagle’s Medium (Hyclone) containing 10% FBS (Hyclone), 100 U/ml Penicillin (Sigma) and 100 ug/ml streptomycin (Sigma) and maintained in 5% CO2 at 37°C. Mammosphere formation, MCF-7 cells were plated as single cells at 1 X 104 cells/ml density in DMEM/F-12 medium (Hyclone) supplemented with B27 (Gibco), 100 U/ml Penicillin (Sigma), 100 ug/ml streptomycin (Sigma), 10 ng/ml bFGF(Gibco) and 20 ng/ml EGF (Sigma) on 0.5% poly-HEMA (poly[2-hydroxyethyl methacrylate], Sigma) coated dish. Mammospheres were incubated in 5% CO2 at 37°C for 5 days.

extract_protocol:
Total RNA was isolated from the cells [‘monolayer (m) cultured MCF7 wild type (WT) and mMCF7 CD24KD’ and ‘sphere-forming (s) MCF7 WT and sMCF7 CD24KD’] using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated with RNase-free DNase I (Promega, Madison, WI, USA) to eliminate DNA contamination. The RNA concentration and quality were determined using a NanoDrop® ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and the Agilent RNA Integrity number (RIN) (Schroeder et al., 2006) was evaluated using the Agilent 2100 Bioanalyzer and the Agilent RNA 6000 Nano kit (Agilent Technology, Santa Clara, CA, USA). The absorbance ratio at 260:280 nm for all samples was >1.8 and the RIN value was > 9. The integrity of RNA samples was also ascertained by the presence of distinct 28S and 18S ribosomal RNA bands in agarose gels after electrophoretic resolution.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For stable CD24 KD cell line, pSuper-CD24 shRNA plasmid (Ju et al., Carcinogenesis, 2011) was transfected into MCF-7 cell line by using Effectene (QIAGEN) according to manufacturer’s protocol and transfected cells were selected with 1 ug/ml puromycin (Sigma). Selected cells were then plated at clonal density and expanded to obtain single cell-derived subclones.

tag: culture condition

value: monolayer (m) cultured cell

tag: knock down

value: wild type (WT)

tag: type of cd24


title: mMCF7 CD24KD

value: hCD24 knock down (KD)


title: MCF-7_A_2

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

data_processing:
Basecalls was performed using CASAVA version 1.8
Adapter sequence was removed using  cutadapt tools that is part of iMir.
To predict piRNAs, iMir uses piRNABank (tranlib), while miRAnalyzer version 0.3 was used for the identification of miRNAs and other sncRNA.
Differential expression analysis was performed by iMir (p-value ≤ 0.05, Fisher's exact test and absolute fold-change 1.5)
Wicoxon Mann-Whitney test was performed by using MeV version 4.8.1
Biclustering and Principle Component analysis (PCA) was done using DESEQ 1.14.0 package from R Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files represent piRNAs. They were generated using iMir.

source_name: growth-arrested

extract_protocol: Total RNA was extracted from cell lines using the standard RNA Extraction method with TRI Reagent  (Sigma) method. 7.5μg of total RNA was used in a library preparation according to the Illumina TruSeq small RNA sample preparation protocol.

tag: growth

value: growth-arrested

value: Breast cancer cells


title: MCF-7_A_3


title: sMCF7 WT

value: sphere (s) forming cell


title: sMCF7 CD24KD


title: Nt-ERβ_A_2


title: MCF-7_G_2

source_name: Exponetially growing

value: Exponetially growing


title: MCF-7_G_3


title: P1_Strom_Nes-GFP(+)Pdgfra(+)_Rep2

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S8-2GpPp

tag: tissue


title: Nt-ERβ_G_3


title: MCF-7_G_1


title: Nt-ERβ_A_3


title: Nt-ERβ_G_2


title: Nt-ERβ_G_1


title: Ct-ERβ_A_3


title: Input pool

value: two parts with 37 and 42 ℃

tag: chip antibody

value: none (input)


title: p-KDM3A_HS(-)


title: Ct-ERβ_A_2


title: Nt-ERβ_A_1


title: Ct-ERβ_A_1


title: Ct-ERβ_G_3


title: ZR-75.1

source_name: hormone-sensitive, ERα+,

value: hormone-sensitive, ERα+,


title: Ct-ERβ_G_2


title: Ct-ERβ_G_1


title: P1_Strom_Nes-GFP(-)Pdgfra(-)_Rep1

description:
pool of 3x pups; Bone marrow (neonatal) stromal sub-populations from Nes-Gfp mice
S1-1GmPm

value: Nes-Gfp heterozygous pups

value: P1 (newborn)

value: Bone marrow (collagenase-digested crushed bones)


title: MCF-7_A_1


title: MCF10A

source_name: Non-tumorigenic epithelial cells

value: Non-tumorigenic epithelial cells


title: MCF-7


title: primed iPSC-2

status: Public on Oct 14 2014

first: Kang

last: Liu

address: Yiheyuan Road 5

institute: PKU

description:
Sample name: P2
FPKM values in processed data file

data_processing:
Tophat 1.3.0. to align the clean reads to the Macaca_mulatta.MMUL_1.75.gtf/Macaca_mulatta.MMUL_1.75.dna.toplevel.fa.
gene expression was analyzed by the FPKM method。
FDR < 0.01 and the absolute ratio of log2 > 1 as the threshold for the differential expresion of genes.
Genome_build: MMUL 1.0 (Ensembl release 75)
Supplementary_files_format_and_content: The .txt file reports FPKM values and GeneIDs.

organism: Macaca mulatta

source_name: rhesus monkey primed iPSC line

growth_protocol: Rhesus monkey naïve iPSCs were cultured in optimized conversion medium consisting of 85% KnockOut DMEM (KO-DMEM, Invitrogen), 15% KnockOut serum replacement (KSR, Invitrogen), N2 supplement (100X, Invitrogen), 1 mM L-Glutamine, 0.1 mM NEAA, 0.1 mM 2-ME with 4 ng/ml bFGF (R&D systems), 10 ng/ml human LIF (Millipore), CHIR99021 (3 μM; Stemgent), PD0325901 (0.5 μM; Stemgent), SB203580 (10 μM; Tocris) and SP600125 (10 μM; Tocris). Rhesus monkey primed iPSCs were cultured in hESM (D/F12+20%KSR+ bFGF)

extract_protocol:
Total RNA extracted by QIAGEN Rneasy Kit following manufacturer's instructions.
RNA libraries were prepared and sequenced following Illumina protocol

treatment_protocol: feeder cells were removed and colonies were collected for RNA isolution

value: primed pluripotent stem cells

tag: gender

value: male

tag: culture conditions

value: hESM

value: embryo


title: Female naïve iPSC-2_6sm

description:
Sample name: FN2
FPKM values in processed data file

source_name: rhesus monkey naïve iPSC line

value: naïve pluripotent stem cells

value: female


title: naïve iPSC-2_6sm

description:
Sample name: N2
FPKM values in processed data file


title: Female naïve iPSC-1_6sm

description:
Sample name: FN1
FPKM values in processed data file


title: naïve iPSC-1_6sm

description:
Sample name: N1
FPKM values in processed data file


title: TOP1α_2

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing:
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
The raw reads were filtered with Illumina’s quality control pipeline
The reads were mapped to the Arabidopsis Ler genome using SOAP2 v2.21 (M4v0r1); multilocus reads were removed
The nucleosome-calling program NOrMAL (beta2, default parameters) was used to identify nucleosomes and their positions in the genome;
Supplementary_files_format_and_content: nucleosome position txt file (output of NOrMAL: chromosome, Position, Fuzziness, Size, Confidence Score, Forward votes, Reverse votes)

organism: Arabidopsis thaliana

extract_protocol:
1g of inflorescences containing unopened buds from Ler and top1a-2 plants were ground in liquid nitrogen, and the powder was transferred to M1 buffer (10mM phosphate buffer pH7.0, 0.1M NaCl, 10mM mercaptoethanol, 1M hexylene glycol, 1x protease inhibitor cocktail (Roche) and 1mM PMSF). The suspension was filtered through four layers of miracloth. The filtrate was centrifuged at 13,400g for 10 min at 4°C. The pellet (crude nuclei preparation) was resuspended and washed in M2 buffer (M1 buffer plus 10 mM MgCl2 and 0.5%TritonX-100) three times and once in M3 buffer (10mM phosphate buffer pH7.0, 0.1M NaCl, 10mM mercaptoethanol, 1x protease inhibitor cocktail (Roche) and 1mM PMSF). After centrifugation at 16,400g for 1min at 4°C, the nuclei were dissolved in digestion buffer (50mMTris-HCl, 5mM CaCl2, 1xBSA, 20mg/ml RNase A, 1x protease inhibitor cocktail (Roche)) containing 0.4U/ul Micrococcal Nuclease (NEB) and incubated at 37°C for 30min. DNA was extracted using the CTAB method and resolved in a 2% agarose gel. DNA bands corresponding to ~150bp were cut and purified with the Gel Purification Kit (Qiagen).
DNA bands corresponding to ~150bp were cut and purified with the Gel Purification Kit (Qiagen). DNA libraries were constructed with the TruSeq DNA Sample Preparation v2 kit (Illumina) and sequenced with Illumina’s HiSeq2000 platform

tag: ecotype

value: Landsberg erecta (Ler)

value: inflorescences


title: TOP1α_1


title: Ler_2


title: Ler_1


title: WT stranded

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

data_processing:
Basecalls performed using CASAVA
Removal of rRNA reads using alignment to drosophila rRNA reference with bowtie
Detection of circRNA reads using the method described by Memczak et al. (Nature 2013)
Genome_build: dm3
Supplementary_files_format_and_content: Bed files with list of detected circRNA in the samples and number of reads supporting each circRNA.

organism: Drosophila melanogaster

source_name: fly Heads

extract_protocol:
Total RNA was extracted from fly heads or S2 cells  and the ribosomal RNA was removed using the Ribominus kit (Invitrogen). Subsequently the samples were treated for 15 min at 37 °C with 3U per µg RNA with RNase R (Epicentre Biotechnologies) or mock treated.
cDNA libraries were generated using the TruSeq RNA sample preparation kit and protocol (Illumina).

tag: genotype/variation

value: wild type Canton-S

value: fly Heads


title: WT18.rep1_RR

value: RNaseR


title: slow29.rep2_RR

value: C4 mutation Canton-S


title: WT18.rep2


title: WT29.rep1


title: WT29.rep1_RR


title: S2 cells

source_name: S2 cells

value: S2 cells


title: WT29.rep2_RR


title: slow18.rep1


title: slow18.rep1_RR


title: Setd2 ko.1

city: Shanghai

first: Qiuhua

last: Huang

address: 197 ruijin road II

institute: Shanghai Institute of Hematology

data_processing:
Illumina Casava 1.6.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using tophat(version:1.0.13) software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: mESCs

growth_protocol: Setd2 wt and ko mESCs were cultured on feeder cells in standard ES medium,then trypsinized ES cells were transferred on gelatin-coated cell culture dish, cultured for half an hour, then supernatant ES cells were collected and transferred to new gelatin-coated cell culture dish for 1 passage to maximumly remove feeder cells,two days later, mESCs were collected for microarray analysis.

extract_protocol:
QIAGEN RNeasy Kit extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No specific treatment

tag: strain

value: mESCs

tag: age

tag: genotype

value: Setd2 KO


title: WT29.rep2


title: Sted2 wt.1

value: 10-12 passages

value: wild type


title: slow29.rep2


title: WT18.rep2_RR


title: Input DNA

status: Public on Oct 13 2014

city: Pasadena

first: Angelike

last: Stathopoulos

state: CA

address: 1200 E. California Blvd - MC114-96

department: Biology and Biological Engineering

institute: California Institute of Technology

data_processing:
Illumina sequencing reads were aligned to dm3 genome using BWA (0.7.5a)
Peaks were called by SPP and IDR
Signal tracks were generated by SPP
Genome_build: dm3
Supplementary_files_format_and_content: Signal tracks are in wig format

source_name: Whole cell embryonic extract

growth_protocol: Flies were reared in standard cornmeal food at 25°C.

extract_protocol:
Whole embryo cell lysates were clarified by centrifugation from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to standard Illumina's protocols.

tag: developmental stage

value: 2-4 hour embryo

value: yw


title: slow29.rep1


title: WT18.rep1


title: slow18.rep2_RR

tag: treatment


title: Yellow

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences (RAPL)
Size filtering: discarding reads shorter than 12 nt (RAPL)
Read mapping using segemehl version 0.13 (RAPL)
Coverage calculation and normalisation (RAPL)
Genome_build: NC_010063.1, NC_010079.1, NC_012417.1
Supplementary_files_format_and_content: wiggle
Supplementary_files_format_and_content: Unnormalized or normalized read coverages in wiggle format (*_forward.wig = forward strand; *_minus.wig= forward strand)

organism: Staphylococcus aureus subsp. aureus USA300

source_name: bacteria

growth_protocol: overnight on TSB plates

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

tag: subpopulation

value: Yellow


title: slow29.rep1_RR


title: slow18.rep2


title: primed iPSC-1

description:
Sample name: P1
FPKM values in processed data file

tag: cell type

value: primed pluripotent stem cells

value: male

value: hESM

value: embryo


title: Su(H) 2-4 hr rabbit-ab IP rep1

value: Santa cruz rabbit polyclonal #sc-25761


title: White

value: White


title: Su(H) 2-4 hr goat-ab IP rep1

value: Santa cruz goat polyclonal #sc-15813


title: Homeland

value: Homeland


title: Su(H) 2-4 hr goat-ab IP rep2


title: maize_rep6_sec16

status: Public on Oct 12 2014

city: New Haven

first: Timothy

last: Nelson

state: CT

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

description: leaf section 16, replicate 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the reference genome using the software Tophat v2.0.10.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff ( v2.1.1).
Genome_build: Maize AGPv3
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample.

molecule: polyA RNA

organism: Zea mays

source_name: maize leaf section 16

growth_protocol: The seedlings were grown under an 80:20 mix of metal halide, with capsylite halogen lamps at light intensity of 550 μmol/m2/sec, 12:12 l/D, 31 °C L/22 °C D and 50% relative humidity.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, CA) following manufactory’s suggestion.
The libraries were constucted following the protocol described in the article: Wang, L. et al. A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PloS one 6, e26426 (2011).

treatment_protocol: Nine day old third leaves of maize were cut into fifteen 1 cm segments; samples were pooled from an average of seven plants per biological replicate and six biological replicates in total were collected on different dates. 14 day old third leaves of rice were cut into eleven 2 cm segments, samples were pooled from an average of 15 plants per biological replicate and four replicates in total were collected.

tag: cultivar

value: leaf

tag: leaf section

value: 9 days


title: S2 cells_RR

value: RNaseR

value: S2 cells


title: Su(H) 2-4 hr rabbit-ab IP rep2


title: maize_rep6_sec10

description: leaf section 10, replicate 6

source_name: maize leaf section 10


title: maize_rep6_sec15

description: leaf section 15, replicate 6

source_name: maize leaf section 15


title: maize_rep6_sec9

description: leaf section 9, replicate 6

source_name: maize leaf section 9


title: maize_rep6_sec8

description: leaf section 8, replicate 6

source_name: maize leaf section 8


title: maize_rep6_sec4

description: leaf section 4, replicate 6

source_name: maize leaf section 4


title: maize_rep6_sec14

description: leaf section 14, replicate 6

source_name: maize leaf section 14


title: maize_rep6_sec12

description: leaf section 12, replicate 6

source_name: maize leaf section 12


title: maize_rep6_sec2

description: leaf section 2, replicate 6

source_name: maize leaf section 2


title: maize_rep6_sec13

description: leaf section 13, replicate 6

source_name: maize leaf section 13


title: maize_rep6_sec6

description: leaf section 6, replicate 6

source_name: maize leaf section 6


title: maize_rep6_sec3

description: leaf section 3, replicate 6

source_name: maize leaf section 3


title: maize_rep6_sec7

description: leaf section 7, replicate 6

source_name: maize leaf section 7


title: maize_rep4_sec14

description: leaf section 14, replicate 4


title: maize_rep4_sec13

description: leaf section 13, replicate 4


title: maize_rep6_sec1

description: leaf section 1, replicate 6

source_name: maize leaf section 1


title: maize_rep4_sec16

description: leaf section 16, replicate 4


title: maize_rep4_sec15

description: leaf section 15, replicate 4


title: maize_rep4_sec11

description: leaf section 11, replicate 4

source_name: maize leaf section 11


title: maize_rep4_sec12

description: leaf section 12, replicate 4


title: maize_rep4_sec10

description: leaf section 10, replicate 4


title: maize_rep4_sec3

description: leaf section 3, replicate 4


title: maize_rep4_sec6

description: leaf section 6, replicate 4


title: maize_rep4_sec7

description: leaf section 7, replicate 4


title: maize_rep4_sec2

description: leaf section 2, replicate 4


title: maize_rep4_sec1

description: leaf section 1, replicate 4


title: maize_rep6_sec11

description: leaf section 11, replicate 6


title: miR-155-/- Th17

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse whole genome version mm9 using TopHat with option --coverage-search --microexon-search --max-multihits 20
Read counts were performed using in-house codes
Genome_build: mm9

source_name: in vitro polarized CD4+ Th17 cells

growth_protocol: Naïve CD4+CD62LhighCD44lowCD25- T cells were isolated from the lymph nodes of mice and cultured for 4 days under Th17 polarizing conditions that include IL-6, IL-21, IL-1β,TGFβ and blocking for IFNγ, IL-4 and IL-12 (p40). T cells were co-cultured with irradiated splenocytes at a 1:5 T cell to APC ratio and T cell activation was achieved by addition of soluble antibodies for CD3 and CD28. The cells were then harvested and RNA was extracted using the miRVana kit from Applied Biosystems. We then took three biological replicates and pooled them into equal concentrations for library preparation.

extract_protocol: Library preparation was performed starting with 4ug of total RNA using the TruSeq RNA sample prep kit following manufacturer's protocol (Illumina). Briefy, Oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA sythesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors. The resulting cDNA libraries were verified and quantified on Agilent Bioanalyser.

value: primary CD4+ T cells


title: maize_rep3_sec15

description: leaf section 15, replicate 3


title: maize_rep4_sec8

description: leaf section 8, replicate 4


title: maize_rep3_sec14

description: leaf section 14, replicate 3


title: maize_rep3_sec13

description: leaf section 13, replicate 3


title: maize_rep4_sec4

description: leaf section 4, replicate 4


title: maize_rep3_sec11

description: leaf section 11, replicate 3


title: maize_rep3_sec16

description: leaf section 16, replicate 3


title: maize_rep3_sec10

description: leaf section 10, replicate 3


title: maize_rep3_sec8

description: leaf section 8, replicate 3


title: rice_rep4_sec7

description: leaf section 7, replicate 4

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the reference genome using the software Tophat v2.0.10.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff ( v2.1.1).
Genome_build: MSU_osa1r7
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample.

organism: Oryza sativa

source_name: rice leaf section 7

value: Nipponbare

value: 14 days


title: rice_rep4_sec11

description: leaf section 11, replicate 4

source_name: rice leaf section 11


title: rice_rep4_sec10

description: leaf section 10, replicate 4

source_name: rice leaf section 10


title: rice_rep4_sec6

description: leaf section 6, replicate 4

source_name: rice leaf section 6


title: rice_rep4_sec9

description: leaf section 9, replicate 4

source_name: rice leaf section 9


title: rice_rep4_sec5

description: leaf section 5, replicate 4

source_name: rice leaf section 5


title: maize_rep3_sec3

description: leaf section 3, replicate 3


title: maize_rep3_sec7

description: leaf section 7, replicate 3


title: maize_rep2_sec16

description: leaf section 16, replicate 2

source_name: maize leaf section 16


title: maize_rep3_sec2

description: leaf section 2, replicate 3


title: rice_rep4_sec4

description: leaf section 4, replicate 4

source_name: rice leaf section 4


title: maize_rep3_sec4

description: leaf section 4, replicate 3

source_name: maize leaf section 4


title: maize_rep3_sec12

description: leaf section 12, replicate 3

source_name: maize leaf section 12


title: rice_rep4_sec3

description: leaf section 3, replicate 4

source_name: rice leaf section 3


title: maize_rep3_sec6

description: leaf section 6, replicate 3

source_name: maize leaf section 6


title: maize_rep2_sec15

description: leaf section 15, replicate 2

source_name: maize leaf section 15


title: miR-155+/+ Th17


title: maize_rep3_sec9

description: leaf section 9, replicate 3

source_name: maize leaf section 9


title: rice_rep4_sec8

description: leaf section 8, replicate 4

source_name: rice leaf section 8


title: maize_rep2_sec14

description: leaf section 14, replicate 2

source_name: maize leaf section 14


title: rice_rep3_sec11

description: leaf section 11, replicate 3


title: maize_rep2_sec12

description: leaf section 12, replicate 2


title: rice_rep4_sec1

description: leaf section 1, replicate 4

source_name: rice leaf section 1


title: rice_rep4_sec2

description: leaf section 2, replicate 4

source_name: rice leaf section 2


title: maize_rep2_sec13

description: leaf section 13, replicate 2

source_name: maize leaf section 13


title: maize_rep3_sec1

description: leaf section 1, replicate 3

source_name: maize leaf section 1


title: rice_rep3_sec10

description: leaf section 10, replicate 3

source_name: rice leaf section 10


title: rice_rep3_sec8

description: leaf section 8, replicate 3


title: rice_rep3_sec9

description: leaf section 9, replicate 3

source_name: rice leaf section 9


title: maize_rep2_sec9

description: leaf section 9, replicate 2


title: maize_rep2_sec10

description: leaf section 10, replicate 2

source_name: maize leaf section 10


title: maize_rep2_sec8

description: leaf section 8, replicate 2

source_name: maize leaf section 8


title: rice_rep3_sec7

description: leaf section 7, replicate 3

source_name: rice leaf section 7


title: maize_rep2_sec6

description: leaf section 6, replicate 2


title: maize_rep2_sec4

description: leaf section 4, replicate 2

source_name: maize leaf section 4


title: rice_rep3_sec5

description: leaf section 5, replicate 3

source_name: rice leaf section 5


title: maize_rep2_sec11

description: leaf section 11, replicate 2

source_name: maize leaf section 11


title: maize_rep2_sec7

description: leaf section 7, replicate 2

source_name: maize leaf section 7


title: rice_rep3_sec3

description: leaf section 3, replicate 3

source_name: rice leaf section 3


title: rice_rep3_sec2

description: leaf section 2, replicate 3


title: maize_rep2_sec3

description: leaf section 3, replicate 2

source_name: maize leaf section 3


title: maize_rep2_sec2

description: leaf section 2, replicate 2

source_name: maize leaf section 2


title: maize_rep2_sec1

description: leaf section 1, replicate 2


title: rice_rep3_sec1

description: leaf section 1, replicate 3


title: maize_rep1_sec16

description: leaf section 16, replicate 1

source_name: maize leaf section 16


title: maize_rep1_sec15

description: leaf section 15, replicate 1

source_name: maize leaf section 15


title: maize_rep4_sec9

description: leaf section 9, replicate 4

source_name: maize leaf section 9


title: rice_rep2_sec8

description: leaf section 8, replicate 2

source_name: rice leaf section 8


title: rice_rep2_sec10

description: leaf section 10, replicate 2


title: maize_rep1_sec14

description: leaf section 14, replicate 1

source_name: maize leaf section 14


title: rice_rep2_sec11

description: leaf section 11, replicate 2

source_name: rice leaf section 11


title: rice_rep2_sec9

description: leaf section 9, replicate 2

source_name: rice leaf section 9


title: rice_rep3_sec6

description: leaf section 6, replicate 3

source_name: rice leaf section 6


title: maize_rep1_sec13

description: leaf section 13, replicate 1

source_name: maize leaf section 13


title: rice_rep2_sec7

description: leaf section 7, replicate 2

source_name: rice leaf section 7


title: maize_rep1_sec12

description: leaf section 12, replicate 1

source_name: maize leaf section 12


title: rice_rep3_sec4

description: leaf section 4, replicate 3

source_name: rice leaf section 4


title: maize_rep1_sec11

description: leaf section 11, replicate 1

source_name: maize leaf section 11


title: rice_rep2_sec5

description: leaf section 5, replicate 2

source_name: rice leaf section 5


title: maize_rep1_sec10

description: leaf section 10, replicate 1

source_name: maize leaf section 10


title: rice_rep2_sec4

description: leaf section 4, replicate 2


title: rice_rep2_sec2

description: leaf section 2, replicate 2

source_name: rice leaf section 2


title: maize_rep1_sec8

description: leaf section 8, replicate 1

source_name: maize leaf section 8


title: maize_rep1_sec7

description: leaf section 7, replicate 1

source_name: maize leaf section 7


title: rice_rep2_sec3

description: leaf section 3, replicate 2

source_name: rice leaf section 3


title: maize_rep1_sec6

description: leaf section 6, replicate 1

source_name: maize leaf section 6


title: rice_rep2_sec1

description: leaf section 1, replicate 2

source_name: rice leaf section 1


title: maize_rep1_sec4

description: leaf section 4, replicate 1

source_name: maize leaf section 4


title: rice_rep1_sec10

description: leaf section 10, replicate 1

source_name: rice leaf section 10


title: rice_rep1_sec11

description: leaf section 11, replicate 1

source_name: rice leaf section 11


title: maize_rep1_sec3

description: leaf section 3, replicate 1

source_name: maize leaf section 3


title: rice_rep1_sec9

description: leaf section 9, replicate 1

source_name: rice leaf section 9


title: rice_rep2_sec6

description: leaf section 6, replicate 2

source_name: rice leaf section 6


title: rice_rep1_sec8

description: leaf section 8, replicate 1

source_name: rice leaf section 8


title: maize_rep1_sec1

description: leaf section 1, replicate 1

source_name: maize leaf section 1


title: maize_rep1_sec2

description: leaf section 2, replicate 1

source_name: maize leaf section 2


title: rice_rep1_sec6

description: leaf section 6, replicate 1


title: rice_rep1_sec5

description: leaf section 5, replicate 1

source_name: rice leaf section 5


title: rice_rep1_sec7

description: leaf section 7, replicate 1

source_name: rice leaf section 7


title: rice_rep1_sec4

description: leaf section 4, replicate 1

source_name: rice leaf section 4


title: rice_rep1_sec1

description: leaf section 1, replicate 1


title: maize_rep1_sec9

description: leaf section 9, replicate 1

source_name: maize leaf section 9


title: rice_rep1_sec2

description: leaf section 2, replicate 1

source_name: rice leaf section 2


title: F

status: Public on Oct 11 2014

city: Nanjing

first: Xiaolei

last: Ding

address: No.159 Longpan Road

institute: Nanjing Forestry University

data_processing:
Sequence data generated from Illumina genome analyzer wereas filtered by removing low quality reads and adapters. (cutadapt)
Then, we converted all datasion into unique sequence tags with associated numbers. and those tTags annotated as rRNA, tRNA, snRNA, snoRNA, and degraded mRNAs were removed via a Blast search against NCBI and Rfam database.
Repeat sequences were identified also removed using Repeatmasker
Since no records of B. xylophilus miRNAs could be found in the miRBase, The  datasetwere aligned with all known mature miRNAs (miRBase release19.0) using Blast
Cutsom perl script was used to generate all the expression files
Genome_build: GCA_000231135.1
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Bursaphelenchus xylophilus

source_name: Pinus thunbergii

extract_protocol:
Nematode RNAs were collected using the mirVana miRNA Isolation kit (Applied Biosystems, Austin, TX, USA) and the total RNA enrichment procedure was followed. Agilent Technologies 2100 Bio-analyzer (Agilent Technologies, Inc) was used to assess RNA quality, only utilizing samples with RIN (RNA integrity number) greater than eight in downstream experiments.
Four small RNA libraries were constructed according to the standard Illumina Sample Preparation Protocol (Illumina, San Diego, CA, USA).

tag: Stage

value: First stage

value: wild type


title: hybrid of WVa700 and Micro-Tom

status: Public on Oct 10 2014

city: Hangzhou

first: Junxing

last: Li

address: Yuhangtang Road 866

institute: Institute of Vegetable Science, Zhejiang University

data_processing:
The very basic figure from sequencing is converted into sequence data by the base calling step and such sequence data called raw data or raw reads is stored in the *.fq file. Then, we get rid of some contaminant reads from the fq file through the software developed by BGI to deal with the data from HiSeq sequencing and get the final clean reads for the following analysis. And, contaminant reads contain low quality reads, reads with 5' primer contaminants, reads without 3' primer, reads without the insert tag, reads with poly A and reads shorter than 18nt.
Supplementary_files_format_and_content: fasta files in the format of read_id, count followed by read

organism: Solanum lycopersicum x Solanum pimpinellifolium

source_name: leaf

extract_protocol:
Total RNAs of young leaves of Micro-Tom, WVa700, Micro-Tom×WVa700 and WVa700×Micro-Tom were extracted using the Trizol reagent (Invitrogen Inc.) according to the manufacturer’s protocol.
The RNAs were sent to the Beijing Genomics Institute (BGI) for sequencing. Small RNAs were enriched and ligated to a 5’ adaptor and a 3’ adaptor sequentially, then converted to cDNA by RT-PCR, and used for Hiseq high-throuput sequencing directly.

tag: sample group

value: hybrid

value: hybrid of WVa700 and Micro-Tom

tag: molecule subtype

value: small RNA


title: M

value: Middle stage


title: L

value: Last stage


title: rice_rep1_sec3

description: leaf section 3, replicate 1

source_name: rice leaf section 3

tag: tissue


title: Landrace_7 dpi

first: Ning

state: Beijing

address: Yuanmingyuan West Rd. 2,Haidian District

institute: China Agriculture University

description: three pigs total RNA were pooled at equal quantities

data_processing:
Illumina Casava1.7 software used for basecalling.
Trim the bases with low quality (<20) from 5’end
Discard the whole reads with average quality less than 20
Clip adaptor sequence and discard reads less than 18 bp
The clean reads were mapped using BWA-0.6.2 (default set)
TMM was used to measure microRNA expression level and edgeR was used to call for differentially expressed microRNAs.
Genome_build: Ssc3
Supplementary_files_format_and_content: tab-delimited files include TMM values for each sample

organism: Sus scrofa

source_name: lungs

extract_protocol:
Pigs were dissected and the lung tissue samples were stored in liquid nitrogen. The total RNA were extracted using Trizol reagents.
Standard Illumina protocols were used to prepare the RNA libraries

value: 35 days old

tag: breed

value: Landrace

value: WT type

tag: disease state

value: infected with HP-PRRSV

tag: time point

value: 7 dpi


title: C

value: Control stage


title: Tongcheng_7 dpi

value: Tongcheng


title: Landrace_0 dpi

value: 0 dpi


title: Landrace_3 dpi

value: 3 dpi


title: Landrace_5 dpi

value: 5 dpi


title: hybrid of Micro-Tom and WVa700

value: hybrid of Micro-Tom and WVa700

value: leaf


title: Tongcheng_3 dpi


title: Tongcheng_5 dpi


title: Tongcheng_0 dpi


title: 2031770_TimePoint7_BoneMarrow

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v1.13.48) with default parameters.  FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
To quantify gene expression,  RNA-Seq reads were mapped to the listed assembly and annotation using Tophat2 (Trapnell et al, 2013).  Default options were used with the exception that the command --library-type fr-secondstrand was used since reads were generated using a stranded library preparation method from Illumina.  This allowed differentiation between sense and antisense transcripts.  Only reads that map to a single location in the genome were included, to ensure high-confidence mapping.
Several quality control steps were used to verify the reliability of the data: linear correlation of estimated abundance of ERCC spike-in controls with known concentration; confirmation of 99.9% strand-specificity of the controls; less than 0.1% control fusion transcripts; and absence of 3’ bias in the controls was confirmed with RSeqC software (https://code.google.com/p/rseqc).  Transcript abundance levels were inferred using HTSeq v0.5.4 (http://www-huber.embl.de/users/anders/HTSeq/doc/).  HTSeq takes the short-read mapping file (bam) from tophat2 and the gene annotation file which contains the locations of all annotated genes.  Since some libraries were sequenced more deeply than others, the libraries were normalized before determining differential gene expression using the gene level expression files with the default parameters of DESeq version 1.10.1 (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html).
Genome_build: RNA-Seq reads were mapped to an early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, Version 4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under accession  PRJNA214746 ID: 214746.
Supplementary_files_format_and_content: Excel files contain normalized transcript abundances, separately at the gene and exon levels, for each individual.  Abundances are further classified by experimental Time Point (1-7), and Specimen Type (Whole Blood or Bone Marrow).
Supplementary_files_format_and_content: Gene Data Column headers are defined as follows:    'gene_name':  Identifiers of all Genes in the reference annotation.     'gene_symbol': Symbols of all Genes in the reference annotation.    'Sample ID / Raw File 1 / Raw File 2 /Normalized Read Counts':  Sample ID, Raw sequence file names for the sample, and Library size normalized and Log2 transformed read counts of all genes, from the Specimen Type, Individual ID, and Time Point listed directly below.     Notes:  There will be one read count column per specimen per individual per Time Point. So, 2 * 5 * 7 = 70 columns with read counts.    0 as value for read counts of some genes Overlapping genes (sharing exons) were "collapsed" into a single gene for the purposes of RNA-Seq read assignments. So, the read count at such a locus is representative of the cumulative expression of all the genes at that locus. BUT, the entire read count is assigned to only one of the genes and the others in the locus are assigned 0.
Supplementary_files_format_and_content: Exon Data Column headers are defined as follows:    'Exon ID': IDs were generated during analysis.  Each row contains the Exon Identifier of one exon, for which expression data were recorded. IDs are composed of two parts separated by a colon. The first part is the symbol of the gene to which this exon belongs. The second part is a numerical identifier for the order of this exon in the listed gene.    'Start Location of Exon': Each row contains start location of one exon. Note that this location may not match the start location in the original annotation. See Notes section.    'End Location of Exon': Each row contains end location of one exon. Note that this location may not match the end location in the original annotation. See Notes section.    'Strand of Exon': Each row contains strand information of one exon.    'Gene ID':  Each row contains the Gene Identifier of the gene for that exon.  Note that only one gene ID is listed even when the exon is shared among multiple genes. See Notes section.    'Gene Symbol':  Each row contains the Gene Symbol of the gene that the exon belongs to. Note that only one gene Symbol is listed even when the exon is shared among multiple genes. See Notes section.    'Gene and Transcript Membership of Exon':  Each row contains ALL the genes and transcripts that one exon belongs to (has membership in). This column provides the useful information to identify the exons, as they are listed in the reference annotation.    'Sample ID / Raw File 1 / Raw File 2 / Normalized Read Counts': Sample ID, Raw sequence file names for the sample, and Library size normalized and Log2 transformed read counts of all exons. The column header also contains information regarding Specimen Type, Animal ID, and Time Point Each row contains the library size normalized and Log2 transformed read count observed for one exon, in the condition/sample.    Notes:  Number of read counts columns:  There will be one raw read count column per specimen per individual per Time Point. So, 2 * 5 * 7 = 70 columns with read counts    Number of exons listed: For the purpose of RNA-Seq read mapping, the exon boundaries and membership in genes were modified relative to the reference annotation. Essentially, it is ensured that every genomic location (nucleotide base) belonged to only one exon and each exon belonged to one and only one gene. Exons shared by multiple genes are listed only once, and their membership is assigned to only one gene (usually, the largest gene spanning the exon). But, the true membership of this exon, including all transcripts and genes that it is a part of is documented in the column "Gene and Transcript Membership of Exon". In the case of overlapping exons, artificial boundaries are created at the point of overlap so that the nucleotides belong to only one exon. Hence, the number of exons listed, boundaries of exons, and exon IDs are slightly different from the original annotation.    Misc:  Exons of length 1, etc Due to the adjustment of boundaries as described above, some exons are split, resulting in exons that are as small as one base long.

source_name: Bone Marrow

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Bone marrow (1ml) was collected into 1.5 ml tubes with EDTA, and the mononuclear cells were purified by density gradient centrifugation on Lymphoprep (Stem Cell Technologies) solution and preserved in RLT buffer (Qiagen) to stabilize mRNA.  Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted from the BM samples using Qiagen RNEasy Mini-Plus kits following the manufacturer-recommended procedures, and from PB samples using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 96 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate 3-plex sequencing on an Illumina HiSeq2000 at the Yerkes Genomics Core, aiming for 80 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: During the 100-day experiment, pyrimethamine was delivered (1 mg/kg) intramuscularly once on day 20, and for three successive days starting at days 52 and 90 (corresponding to time points 2,4, and 6), corresponding to predicted periods for sub-curative and curative experimental treatment regimens for malaria infection of macaques.

value: Time Point 7

tag: gender

value: Male

tag: mahpic non human primate individual id


title: 2020742_TimePoint7_BoneMarrow


title: 2031756_TimePoint7_BoneMarrow


title: ESC RNA-Seq

city: Singapore

first: Guoliang

address: 60 Biopolis Street, #02-01, Genome

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Reads were filtered to remove sequences such as ribosomal RNA, transfer RNA, mitochondrial RNA and repeat sequences, etc.
The strand-specific (NSC & NPC) reads were mapped on mouse reference genome mm9 with SOLiD whole transcriptome alignment pipeline and analysed by Bioscope (v1.0.1) analysis pipeline. A split-read mapping approach was also applied to map reads that spanned two exons. For strand-specific ESC reads, Tophat (v2.0.9) with Bowtie2 (v2.0.6) were used.
Uniquely mapped reads were used to calculate expression values obtained for all RefSeq genes.
Expression values were determined as RPKM for coding sequences.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files of RPKM values for ESC, NSC and NPC gene locus

source_name: Embryonic stem cells

growth_protocol: Mouse E14 ESCs were cultured under feeder-free conditions in DMEM supplemented with 15% fetal bovine serum (ESC-qualified; Invitrogen), 0.055 mM β-mercaptoethanol (Invitrogen), 2 mM L-glutamine, 0.1 mM nonessential amino acids, 5,000 U ml−1 penicillin/streptomycin and 1,000 U ml−1of leukaemia inhibitory factor (Chemicon) and maintained at 37 °C with 5% CO2. Cells were passaged every 2–3 days using accutase (GIBCO-BRL)

extract_protocol:
Library was created using SOLID Whole Transcriptome Analysis Kit (Life Technologies). Briefly, poly(A) selected RNA was treated with RNAse III. Fragmented RNA were hybridized and ligated with adaptors. This is followed by a reverse transcription. cDNA was purified and subjected to a size selection on a PAGE gel. Fraction 175-250bp was excised and purified. Amplification was performed using PCR primers adapted for Illumina sequencing for 15 cycles.
Trizol RNA extraction

value: WT

tag: passages


title: 2031848_TimePoint7_BoneMarrow


title: 2031845_TimePoint7_BoneMarrow


title: 2010215_TimePoint7_Blood

source_name: Whole Blood


title: 2010111_TimePoint7_Blood


title: 2010303_TimePoint7_Blood


title: 2020553_TimePoint7_Blood


title: B. carinata-B

city: wuhan

first: Qin

last: Zhao

address: luojiashan

institute: wuhan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Brassica rapa genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Brassica rapa genome
Supplementary_files_format_and_content: RPKM

organism: Brassica carinata

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

tag: age

value: 3 mo

tag: genotype

value: parental B. carinata


title: B. rapa-A

organism: Brassica rapa

value: parental B. rapa


title: 2020725_TimePoint6_BoneMarrow

value: Time Point 6


title: 2031713_TimePoint6_BoneMarrow


title: Allohexaploid-C

organism: Brassica carinata x Brassica rapa

value: Brassica allohexaploid


title: 2031844_TimePoint6_BoneMarrow


title: 2020736_TimePoint6_BoneMarrow


title: Parent_Micro-Tom

organism: Solanum lycopersicum

value: parent

value: Micro-Tom

value: small RNA


title: 2010136_TimePoint6_Blood


title: 2031885_TimePoint6_BoneMarrow


title: 2010304_TimePoint6_Blood


title: 2010115_TimePoint6_Blood


title: 2031843_TimePoint5_BoneMarrow

value: Time Point 5


title: 2020536_TimePoint6_Blood


title: 2010210_TimePoint6_Blood


title: 2031883_TimePoint5_BoneMarrow


title: 2031849_TimePoint5_BoneMarrow


title: 2020497_TimePoint5_Blood


title: 2010300_TimePoint7_Blood


title: 2020559_TimePoint5_Blood


title: 2010240_TimePoint5_Blood


title: 2020714_TimePoint5_Blood


title: 2020654_TimePoint5_Blood


title: 2020733_TimePoint4_BoneMarrow

value: Time Point 4


title: 2031887_TimePoint4_BoneMarrow


title: 2031846_TimePoint4_BoneMarrow


title: 2010214_TimePoint4_Blood


title: 2020739_TimePoint4_BoneMarrow


title: 2031796_TimePoint5_BoneMarrow


title: 2010258_TimePoint4_Blood


title: 2020566_TimePoint4_Blood


title: 2020738_TimePoint5_BoneMarrow


title: 2031895_TimePoint4_BoneMarrow


title: NPC RNA-Seq

source_name: Neural progenitor cells

growth_protocol: P0 brain-derived neurosphere cells (NPC) cultures were obtained from dissected telencephalons of four mice, plated in 25-ml flasks and cultured to expand their number in complete medium (2% (vol/vol) B27 in DMEM F12 with Glutamax), supplemented with 10 ng ml−1 EGF, 10 ng ml−1 of basic fibroblast growth factor (FGF) with 0.2% (vol/vol) heparin. Cells were passaged two times, every fourth day (by 0.25% trypsin treatment for 5 min, followed by block with 1 mg ml−1 trypsin inhibitor (Sigma T6522) for 5 min). Neurospheres were then dissociated and cells were seeded at 80,000 per ml in T150 flasks, and expanded by passaging every 4 days in complete medium with EGF, but not FGF and heparin, for 3–5 passages until they reached 1 × 109 in number. To confirm that these cells were telencephalic, we further verified expression of some critical telencephalic markers.

extract_protocol:
Library was created using SOLID Whole Transcriptome Analysis Kit (Life Technologies). Briefly, poly(A) selected RNA was treated with RNAse III. Fragmented RNA were hybridized and ligated with adaptors. This is followed by a reverse transcription. cDNA was purified and subjected to a size selection on a PAGE gel. Fraction 125-200bp was excised and purified. Amplification was performed using SOLiD PCR primers for 15 cycles.
Trizol RNA extraction


title: NSC RNA-Seq

source_name: Neural stem cells

growth_protocol: Mouse neural stem cells NS5 were maintained and passaged with trypsin/EDTA or PBS. The cells were split 1:3 to 1:5 every 2–3 days


title: 2020535_TimePoint4_Blood


title: 2031772_TimePoint3_BoneMarrow

value: Time Point 3


title: 2031714_TimePoint3_BoneMarrow


title: 2031850_TimePoint3_BoneMarrow


title: 2031847_TimePoint3_BoneMarrow


title: 2020741_TimePoint3_BoneMarrow


title: 2010113_TimePoint3_Blood


title: 2010241_TimePoint3_Blood


title: 2010216_TimePoint3_Blood


title: 2010268_TimePoint3_Blood


title: 2020734_TimePoint2_BoneMarrow

value: Time Point 2


title: Parent_WVa700

organism: Solanum pimpinellifolium


title: 2020737_TimePoint2_BoneMarrow


title: 2020740_TimePoint2_BoneMarrow


title: 2031855_TimePoint2_BoneMarrow


title: epiRIL_480

city: PARIS CEDEX 05

first: Vincent

last: Colot

address: 46 rue d'Ulm

country: France

institute: Institut de Biologie de l'Ecole Normale Supérieure (IBENS) Section 3

data_processing:
Methylation calls performed using Bismark v.0.7.8 for WT and ddm1 samples and BSSeeker for epiRILs (060-098-202-260-344-480) .
Quality filtering included trimming of low quality nucleotides.
Bisulfite-seq reads were mapped against the Arabidopsis thaliana reference (TAIR10) using Bowtie choosing unique match allowing one mismatch for WT and ddm1 samples and allowing three mismatches for epiRILs (060-098-202-260-344-480).
Removing of multiple reads which have exactly the same sequence.
Genome_build: Arabidopsis thaliana (TAIR10).
Supplementary_files_format_and_content: Tab-delimited in the following format : chromosome  position   strand   count methylated   count unmethylated  CG, CHH or CHG   exact sequence context

source_name: seedlings

growth_protocol: 12 days-old seedlings grown in liquid media

extract_protocol:
Qiagen DNeasy
Fragment genome DNA to 100-300bp by Sonication, DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors, Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit, Desalting, size selection, PCR amplification and size selection again.

treatment_protocol: no treatment

tag: ecotype

value: 12 days

tag: developmental stage

value: seedlings

tag: genotype/variation


title: 2020669_TimePoint4_Blood


title: epiRIL_344


title: 2010112_TimePoint2_Blood


title: epiRIL_260


title: 2010267_TimePoint2_Blood


title: epiRIL_202


title: 2010213_TimePoint3_Blood


title: 2010302_TimePoint2_Blood


title: 2020545_TimePoint2_Blood


title: 2010269_TimePoint2_Blood


title: epiRIL_098


title: epiRIL_060


title: ddm1_seedlings

value: mutant (ddm1)


title: 2020732_TimePoint1_BoneMarrow

value: Time Point 1

value: Male


title: 2020735_TimePoint1_BoneMarrow


title: 2031771_TimePoint1_BoneMarrow


title: WT_seedlings

value: Wild Type (WT)


title: Control GBM1B

city: Baltimore

first: Mingya

last: Ying

state: MD

address: 707 N Broadway

department: Neurology

institute: Kennedy Krieger Institute

data_processing:
The raw reads were aligned to reference human genome build hg18 using TopHat with default parameters. For each gene, the number of reads aligned to its exons were counted and summarized into gene level counts by R bioconductor package GenomicFeatures based on UCSC refFlat table for hg18. Normalization between samples was carried out by R package edger, which controls sequencing depth and RNA composition effects.
Genome_build: hg18
Supplementary_files_format_and_content: Genes down-and up-regulated following KLF9 Induction

source_name: RNA from glioblastoma stem cells

growth_protocol: The human GBM neurosphere lines GBM1a (0913) and GBM1b (0627) were maintained in serum-free medium containing EGF and FGF.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen).
4 µg total RNA was subjected to library preparation using Illumina TrueSeq RNA Sample Preparation Kit v2 (Illumina). Indexed adapters were used in order to pool 4 cDNA libraries into one sequencing reaction.

treatment_protocol: KLF9-GBM1a and KLF9-GBM1b cells were treated ± Dox for 48 hours after which RNA was isolated and subjected to cDNA library preparation and RNA-Seq.

tag: cell line

tag: cell type

value: glioblastoma cell line


title: KLF9 Induction GBM1B


title: Control GBM1A


title: 2031795_TimePoint2_BoneMarrow


title: 2031798_TimePoint1_BoneMarrow


title: Input DNA GBM1B

data_processing:
The 50 bp long raw KLF9 ChIP-Seq reads were aligned to the reference human genome build hg18 using Bowtie allowing at most two mismatches in the first 28 bp “seed” bases. KLF9 binding sites were called using CisGenome with default settings by comparing the two IP samples against the two control samples.
Genome_build: hg18
Supplementary_files_format_and_content: Genome-wide KLF9 Binding Peaks identified by ChIP-seq

source_name: DNA from glioblastoma stem cells

extract_protocol:
Cells were subjected to ChIP using MAGnify ChIP system (Invitrogen) following manufacturer’s protocol. KLF9 bound DNA was immunoprecipitated using mouse anti-FLAG M2 antibody (Sigma-Aldrich) and Dynabeads Magnetic Beads (Life Technologies).
ChIP-enriched DNA was used for PCR and deep sequencing. ChIP-enriched DNA or input DNA (10ng each) was subjected to library preparation using ChIP-Seq DNA Sample Prep Kit (Illumina) following manufacturer’s protocol.

treatment_protocol: KLF9-GBM1a and KLF9-GBM1b cells were treated ± Dox for 48 hours. Cellular chromatin bound by FLAG-tagged KLF9 was specifically precipitated using anti-FLAG M2 antibody and Dynabeads (Figure 2E) and the specific ChIP-enriched DNAs were further processed to produce libraries for ChIP-Seq.

value: glioblastoma stem cell line


title: 2031773_TimePoint1_BoneMarrow


title: 2010114_TimePoint1_Blood


title: Input DNA GBM1A


title: 2010211_TimePoint1_Blood


title: 2010212_TimePoint1_Blood


title: KLF9 ChIP GBM1B


title: KLF9 ChIP GBM1A


title: 2010301_TimePoint1_Blood


title: 2020519_TimePoint1_Blood


title: cardiomyocyte_rep2

city: Cambridge

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

data_processing:
Illumina Offline BaseCaller1.9.3 software used for basecalling.
Reads were mapped against the hg19 GRCh37_68 version of the human genome using RSEM v. 1.2.3 and bowtie v. 0.12.7  using flags rsem-calculate-expression --phred64-quals -p 4 --output-genome-bam --calc-ci --paired-end --bowtie-chunkmbs 1024, without in-silico polyA addition to the transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files with FPKM values for all protein-coding genes (Ensembl IDs)

source_name: cardiomyocyte cells

growth_protocol: hESCs were differentiated to cardiomyocytes as previously described (Elliott et al. 2011 Nature Methods, PMID: 22020065) and were obtained from David Elliott at Monash University.

extract_protocol:
RNA was extracted using TRIzol reagent according to the manufacturer's instructions.
10 ug RNA was used for library construction according to Illumina RNA-seq library kit with minor modifications. Briefly, mRNA was isolated using Dynabeads mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation. First and second strand synthesis were performed followed by end repair, A-tailing, paired end adaptor ligation and size selection on a Beckman Coulter SPRI TE nucleic acid extractor. 200-400 bp dsDNA was enriched by 15 cycles of PCR with Phusion High-Fidelity DNA Polymerase (NEB) followed by gel purification of 250 bp fragments from the amplified material. Amplified libraries were sequenced on an Illumina GAIIx sequencer.

value: ES-derived cardiomyocyte cells


title: cardiomyocyte_rep1


title: GROSeq_shCTL_E2_Exp3

status: Public on Oct 09 2014

city: La Jolla

first: Daria

last: Merkurjev

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

institute: UCSD

description:
library strategy: GRO-seq
GRO-seq Experiment 3, shCTL, 1hr treatment with 100nM E2

data_processing:
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The begGraph files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

growth_protocol: MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
MCF7 cells were subjected to nuclear run-on for 5minutes at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: Before experiment, the MCF7 cells were hormone-stripped in phenol red free DMEM medium plus 5% charcoal-treated FBS for 3-4 days, followed by treatment of either 100nM 17β-estradiol (E2) or ethanol as vehicle control for 1hr. In some cases, we also treated cells with either 1μgM all-trans Retinoic Acid (RA), or Dimethyl sulfoxide (DMSO) as vehicle control for 1 hour.

tag: cell description

value: beast cancer cell line

tag: treatment

value: shCTL, 1hr treatment with 100nM E2


title: GROSeq_shCTL_Veh_Exp3

description:
library strategy: GRO-seq
GRO-seq Experiment 3, shCTL, 1hr treatment with vehicle control


title: GROSeq_shRARs_RA_Exp2

description:
library strategy: GRO-seq
GRO-seq Experiment 2, shRARs, 1hr treatment with 1μM RA

value: shRARs, 1hr treatment with 1μM RA


title: GROSeq_shRARs_Veh_Exp2

description:
library strategy: GRO-seq
GRO-seq Experiment 2, shRARs, 1hr treatment with vehicle control


title: GROSeq_shAP2g_E2_Exp3

description:
library strategy: GRO-seq
GRO-seq Experiment 3, shAP2g, 1hr treatment with 100nM E2

value: shAP2g, 1hr treatment with 100nM E2


title: GROSeq_shRARs_E2_Exp2

description:
library strategy: GRO-seq
GRO-seq Experiment 2, shRARs, 1hr treatment with 100nM E2

value: shRARs, 1hr treatment with 100nM E2


title: GROSeq_shCTL_Veh_Exp2

description:
library strategy: GRO-seq
GRO-seq Experiment 2, shCTL, 1hr treatment with vehicle control


title: GROSeq_shCTL_E2_Exp2

description:
library strategy: GRO-seq
GRO-seq Experiment 2, shCTL, 1hr treatment with 100nM E2


title: GROSeq_shAP2g_Veh_Exp3

description:
library strategy: GRO-seq
GRO-seq Experiment 3, shAP2g, 1hr treatment with vehicle control


title: ERa_ChIPseq_Veh_Exp1

description: ChIP-seq Experiment 1, 1hr treatment with vehicle control

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The begGraph files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody or by streptavidin magnetic beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors of Truseq system from Illumina, according to the manufacturers instructions.

treatment_protocol: Before experiment, the MCF7 cells were hormone-stripped in phenol red free DMEM medium plus 5% charcoal-treated FBS for 3-4 days, followed by treatment of either 100nM 17β-estradiol (E2) or ethanol as vehicle control for 1hr. In some cases, we also treated cells with either 1uM all-trans Retinoic Acid (RA), or Dimethyl sulfoxide (DMSO) as vehicle control for 1 hour. To perform Biotin-ChIP experiments through Biotin-streptavidin pull-down, we used some BLRP-tagged MCF7 Tet-On inducible stable lines that can in vivo biotinylate BLRP-tagged proteins. To induce BLRP-tagged protein expression, 2μg/ml doxycycline was added into culture media for about 24 hours before hormone treatment and collection.

tag: chip antibody or biotin-streptavidin pulldown of blrp-tagged proteins

value: Santa Cruz Biotech, SC-543

value: 1hr treatment with vehicle control


title: GROSeq_siGATA3_Veh_Exp1

description:
library strategy: GRO-seq
GRO-seq Experiment 1, siGATA3, 1hr treatment with vehicle control


title: GROSeq_siCTL_E2_Exp1

description:
library strategy: GRO-seq
GRO-seq Experiment 1, siCTL, 1hr treatment with 100nM E2

value: siCTL, 1hr treatment with 100nM E2


title: FoxA1_ChIPseq_Veh_Exp18

description: ChIP-seq Experiment 18, 1hr treatment with vehicle control

value: Abcam, ab5089


title: ERa_ChIPseq_siFoxA1_E2_Exp17

description: ChIP-seq Experiment 17, siFoxA1, 1hr treatment with 100nM E2

value: siFoxA1, 1hr treatment with 100nM E2


title: ERa_ChIPseq_siCTL_E2_Exp17

description: ChIP-seq Experiment 17, siCTL, 1hr treatment with 100nM E2


title: GROSeq_siCTL_Veh_Exp1

description:
library strategy: GRO-seq
GRO-seq Experiment 1, siCTL, 1hr treatment with vehicle control


title: FoxA1_ChIPseq_E2_Exp18

description: ChIP-seq Experiment 18, 1hr treatment with 100nM E2

value: 1hr treatment with 100nM E2


title: KLF9 Induction GBM1A


title: ERa_ChIPseq_siGATA3_E2_Exp16

description: ChIP-seq Experiment 16, siGATA3, 1hr treatment with 100nM E2

value: siGATA3, 1hr treatment with 100nM E2


title: Med1_ChIPseq_shRARs_E2_Exp15

description: ChIP-seq Experiment 15, shRARs, 1hr treatment with 100nM E2

value: Bethyl, A300-793A


title: ERa_ChIPseq_siCTL_E2_Exp16

description: ChIP-seq Experiment 16, siCTL, 1hr treatment with 100nM E2


title: Med1_ChIPseq_shCTL_E2_Exp15

description: ChIP-seq Experiment 15, shCTL, 1hr treatment with 100nM E2


title: Med1_ChIPseq_shCTL_Veh_Exp15

description: ChIP-seq Experiment 15, shCTL, 1hr treatment with vehicle control


title: Med1_ChIPseq_shRARs_Veh_Exp15

description: ChIP-seq Experiment 15, shRARs, 1hr treatment with vehicle control


title: P300_ChIPseq_shRARs_E2_Exp14

description: ChIP-seq Experiment 14, shRARs, 1hr treatment with 100nM E2

value: Santa Cruz Biotech, SC-585


title: P300_ChIPseq_shCTL_Veh_Exp14

description: ChIP-seq Experiment 14, shCTL, 1hr treatment with vehicle control


title: P300_ChIPseq_shRARs_Veh_Exp14

description: ChIP-seq Experiment 14, shRARs, 1hr treatment with vehicle control


title: GROSeq_shCTL_RA_Exp2

description:
library strategy: GRO-seq
GRO-seq Experiment 2, shCTL, 1hr treatment with 1μM RA

value: shCTL, 1hr treatment with 1μM RA


title: P300_ChIPseq_shCTL_E2_Exp14

description: ChIP-seq Experiment 14, shCTL, 1hr treatment with 100nM E2


title: ERa_ChIPseq_shRARs_E2_Exp13

description: ChIP-seq Experiment 13, shRARs, 1hr treatment with 100nM E2


title: pERaS118_ChIPseq_shCTL_E2_Exp12

description: ChIP-seq Experiment 12, shCTL, 1hr treatment with 100nM E2

value: Santa Cruz Biotech, SC-12915-R


title: ERa_ChIPseq_shCTL_E2_Exp13

description: ChIP-seq Experiment 13, shCTL, 1hr treatment with 100nM E2


title: GROSeq_siGATA3_E2_Exp1

description:
library strategy: GRO-seq
GRO-seq Experiment 1, siGATA3, 1hr treatment with 100nM E2


title: pERaS118_ChIPseq_shCTL_Veh_Exp12

description: ChIP-seq Experiment 12, shCTL, 1hr treatment with vehicle control


title: DNA-PKcs_ChIPseq_shCTL_Veh_Exp11

description: ChIP-seq Experiment 11, shCTL, 1hr treatment with vehicle control

value: Bethyl, A300-517A


title: DNA-PKcs_ChIPseq_shRARs_Veh_Exp11

description: ChIP-seq Experiment 11, shRARs, 1hr treatment with vehicle control

value: beast cancer cell line


title: DNA-PKcs_ChIPseq_Veh_Exp10

description: ChIP-seq Experiment 10, 1hr treatment with vehicle control


title: Med1_ChIPseq_E2_Exp9

description: ChIP-seq Experiment 9, 1hr treatment with 100nM E2


title: pERaS118_ChIPseq_shRARs_E2_Exp12

description: ChIP-seq Experiment 12, shRARs, 1hr treatment with 100nM E2


title: Med1_ChIPseq_Veh_Exp9

description: ChIP-seq Experiment 9, 1hr treatment with vehicle control


title: GATA3_WT_BiotinChIPseq_Dox_E2_Exp7

description: ChIP-seq Experiment 7, 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with 100nM E2

source_name: MCF7 Tet-On Inducible stable line

value: Biotin-ChIP using Streptavidin Magnetic beads (Solulink)


title: GATA3_C318R_BiotinChIPseq_Dox_E2_Exp7

value: 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with 100nM E2


title: DNA-PKcs_ChIPseq_shCTL_E2_Exp11

description: ChIP-seq Experiment 11, shCTL, 1hr treatment with 100nM E2

value: shCTL, 1hr treatment with 100nM E2


title: GATA3_ChIPseq_E2_Exp6

description: ChIP-seq Experiment 6, 1hr treatment with 100nM E2

value: Santa Cruz Biotech, SC-268


title: GATA3_N320K_BiotinChIPseq_Dox_E2_Exp7


title: RARa_WT_BiotinChIPseq_Dox_E2_Exp4

description: ChIP-seq Experiment 4, 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with 100nM E2


title: GATA3_ChIPseq_Veh_Exp6

description: ChIP-seq Experiment 6, 1hr treatment with vehicle control


title: RARg_WT_BiotinChIPseq_Dox_Veh_Exp5

description: ChIP-seq Experiment 5, 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with vehicle control


title: RARa_WT_BiotinChIPseq_Dox_Veh_Exp4

description: ChIP-seq Experiment 4, 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with vehicle control


title: pERaS118_ChIPseq_shRARs_Veh_Exp12

description: ChIP-seq Experiment 12, shRARs, 1hr treatment with vehicle control


title: DNA-PKcs_ChIPseq_shRARs_E2_Exp11

description: ChIP-seq Experiment 11, shRARs, 1hr treatment with 100nM E2

value: shRARs, 1hr treatment with 100nM E2


title: RARg_ZF_BiotinChIPseq_Dox_RA_E2_Exp3

description: ChIP-seq Experiment 3, 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with 1μM RA and 100nM E2


title: RARg_WT_BiotinChIPseq_Dox_RA_E2_Exp3

value: 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with 1μM RA and 100nM E2


title: RARg_pBox_BiotinChIPseq_Dox_RA_E2_Exp3


title: ERa_ChIPseq_E2_Exp1

description: ChIP-seq Experiment 1, 1hr treatment with 100nM E2

value: Santa Cruz Biotech, SC-543


title: DNA-PKcs_ChIPseq_E2_Exp10

description: ChIP-seq Experiment 10, 1hr treatment with 100nM E2


title: RARa_ZF_BiotinChIPseq_Dox_RA_E2_Exp2

description: ChIP-seq Experiment 2, 24hrs treatment with 2μg/ml doxycycline, 1hr treatment with 1μM RA and 100nM E2


title: HFF-1

city: Nantong

first: Gangcai

last: Xie

state: Jiangsu

address: Number 9, Se Yuan Road

department: Medical school

institute: Nantong University

data_processing:
Image files were preprocessed by illumina software, which generates qseq files
qseq files were converted into fastq files by ruby scripts, and only the ones passing illumina quality controls were retained
Reads were mapped onto human reference genome hg19 by Tophat-1.3.0
Counts on Gencode Genes and RepeatMasker annotated repeat elements were calculated
Differentially expressed repeat elements were calculated by ruby scripts
Genome_build: hg19

extract_protocol:
Total RNA was extracted from embryoid bodies using TRIzol (Invitrogen) following the manufacturer instructions. After extraction a DNAse treatment was applied using TURBO DNA-free™ Kit (Ambion) and a second RNA extraction with TRIzol was performed.
RNA libraries were prepared for sequencing using Illumina TruSeq protocols

value: foreskin fibroblast


title: RARa_pBox_BiotinChIPseq_Dox_RA_E2_Exp2


title: EB

source_name: EB

growth_protocol: For spontaneous differentiation through embryoid body formation, hiPSCs cultured in one well of the geltrex-coated 6-well plate, were dissociated with collogenase IV (1 mg/ml) for 5 min, and then split into small cell clumps. The small cell clumps were transferred into three 10-cm low-attached dishes fed with EB medium (knockout DMEM, 20% knockout serum replacement, 1 mM L-Glutamine, 1% nonessential amino acids, 0.1 mM 2-Mercaptoethanol and primocin). The medium was changed every two days. The embryoid bodies were culture for ten days.

tag: tissue

value: hiPSC-derived embryoid bodies

tag: clone


title: AP2g_ChIPseq_E2_Exp8

description: ChIP-seq Experiment 8, 1hr treatment with 100nM E2

value: Santa Cruz Biotech, SC-8977

value: 1hr treatment with 100nM E2


title: iPS

source_name: iPS

growth_protocol: Human induced pluripotent stem cells (hiPSC) were maintained on Mitomycin C- treated mouse embryonic fibroblasts (MEFs) in hES medium consisting of knockout DMEM, 20% knockout serum supplement, 1 mM L-Glutamine, 1% nonessential amino acids, 0.1 mM 2-Mercaptoethanol, 10 ng/ml bFGF (all of reagents above from Gibeco ) and primocin (invivogen)

value: hiPSCs


title: HEK293_repB_smallRNASeq

city: Berlin

first: Annalisa

last: Marsico

address: Ihnestraße 63-73

department: Computational Biology

institute: Max Planck Institute for Molecular Genetics

description: processed data file contains RPKM for mature miRNA abundance measurements

data_processing:
Sequenced reads were trimmed forthree-prime  adaptor sequence, masked for low-quality and short sequences, then mapped to hg19 whole genome using the short-read aligner Bowtie2. Reads that mapped perfectly to nucleotide position 1 to 18 of each annotated miRNA were used to quantify miRNA expression.
Reads per Kilobase per Milion reads were calculated for each mature miRNA according to the definition in Mortazavi et al., Nat Methods 2008, averaging the two rpkm values from the two replicates for each cell line.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample

source_name: Embryonic kidney derived cells (HEK293 cells)

growth_protocol: Hela, A549 and HEK293 cells were maintained under standard conditions at 37°C and 5% CO2 in DMEM containing 10% FCS and antibiotics.

extract_protocol:
The chromatin fraction was isolated as in Bhatt et al. (Cell 2012), and associated total RNA was isolated using Trizol extraction.
The libraries for sequencing small RNAs were constructed using the Illumina TrueSeq small RNA kit.

treatment_protocol: For Drosha RNAi, 5x10^5 cells were seeded per 10cm dish, transfected after 24h with 60nM siRNA, harvested by trypsinization 72h after transfection.

value: Embryonic kidney derived cells


title: HeLa_Droshasi_smallRNASeq

source_name: HeLa cells_Drosha_si

value: HeLa

value: cervical epithelial


title: A549_repB_smallRNASeq

source_name: Adenocarcinomic human alveolar basal epithelial cells (A549 cells)


title: HeLa_rep1_RNASeq

description: processed data file contains RPKM for primiRNA abundance measurements

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for repeats or low-quality sequence, then mapped to hg19 whole genome using TopHat 2 and default parameters
Reads in the 100 bp regions upstream and downstream of the premiRNA Drosha cutting sites we counted by means of the HTSeq software v0.5.4p2
Reads per Kilobase per Milion reads were calculated for each miRNA primary transcript according to the definition in Mortazavi et al., Nat Methods 2008, averaging the two rpkm values from the regions upstream and downstream of each miRNA precursor.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample

source_name: HeLa cells

extract_protocol:
The chromatin fraction was isolated as in Bhatt et al. (Cell 2012), and associated total RNA was isolated using Trizol.
The library was constructed using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold extraction.


title: A549_repA_smallRNASeq

value: Adenocarcinomic human alveolar basal epithelial cells


title: Hela_repB_smallRNASeq


title: Hela_RASL-seq_si-U2AF65+Flag-U2AF35_rep3

status: Public on Oct 08 2014

city: Wuhan

first: Bo

last: Yang

state: Hubei

address: Luo-jia-shan, Wuchang

department: Biochemistry and Molecular Biology

institute: College of Life Sciences, Wuhan University

description:
RASL-seq library from cells of transfection of U2AF65 siRNA and Flag-U2AF35
Library strategy: RASL-Seq

data_processing:
The sequences were mapped to the oligo pool sequences by Bowtie. The processed data file contain both the genomic location (the first 6 columns) and counts for the short and long isoforms (last 2 columns) of each alternative splicing event.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph and bed files

source_name: Hela Cells

growth_protocol: Hela cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibico) supplemented with 10% fetal bovine serum (FBS) at 37 degress Centigrade and 5% CO2.

extract_protocol:
Total RNAs were extracted by Trizol from treated HeLa cells.
1 µg of Hela total RNA was mixed with 100 fmol of human RASL oligos, 2 pmol of biotinylated-oligo-dT and 5 µl of streptavidin magenetic beads. Followed by one hour of annealing at 45ºC, magnetic beads were washed 3 times by washing buffer. Then ligation was achieved by adding 5U of T4 DNA ligase for 1 hour at 37ºC. After 3 times of wash, ligated oligos were eluted to water by heating at 65ºC for 5 minutes, and then PCR amplified using primers containing sequencing adaptor and barcode sequences. PCR products were purified and sequenced.

treatment_protocol: Transfection of U2AF65 siRNA and Flag-U2AF35

value: Hela

tag: transfection

value: U2AF65 siRNA and Flag-U2AF35


title: HEK293_RNASeq

extract_protocol:
The chromatin fraction was isolated as in Bhatt et al. (Cell 2012), and associated total RNA was isolated using Trizol extraction.
The library was constructed using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold


title: Hela_repA_smallRNASeq


title: A549_RNASeq


title: Hela_RASL-seq_si-U2AF65+pcDNA3.0_rep3

description:
RASL-seq library from cells of transfection of U2AF65 siRNA and pcDNA3.0
Library strategy: RASL-Seq

treatment_protocol: Transfection of U2AF65 siRNA and pcDNA3.0

value: U2AF65 siRNA and pcDNA3.0


title: Hela_RASL-seq_si-U2AF65+Flag-U2AF35_rep1


title: HeLa_Droshasi_RNASeq

description:
Drosha knockdown
processed data file contains RPKM for primiRNA abundance measurements


title: Hela_RASL-seq_si-U2AF65+pcDNA3.0_rep1


title: Hela_RASL-seq_si-NC+pcDNA3.0_rep2

description:
RASL-seq library from cells of transfection of NC siRNA and pcDNA3.0
Library strategy: RASL-Seq

treatment_protocol: Transfection of NC siRNA and pcDNA3.0

value: NC siRNA and pcDNA3.0


title: Hela_RASL-seq_si-NC+pcDNA3.0_rep1


title: Hela_RASL-seq_si-U2AF65+pcDNA3.0_rep2


title: p27 CK- BCR-ABL R10

city: Portland

first: David

last: Ellison

state: OR

address: 3181 SW Sam Jackson Park Rd CR145

institute: Oregon Health and Science University

data_processing:
All reads with adapter contamination were removed. Three bp from the 5’ end and one bp from the 3’ end were trimmed prior to alignment. All samples were aligned to the unmasked mouse genome (mm10) using Subread (Version1.3.6-p1)
Counts for each sample were determined by using the UCSC gtf file and the featureCounts method from Subread.
The biomaRt package used to annotate UCSC Gene ID to Ensembl Gene ID
Differential Expression Analysis was conducted for BCR-ABL and Empty Vector separately: BCR-ABL CK- - versus BCR-ABL KO (BCR-ABL Analysis) and Empty CK- - versus Empty KO (Empty Vector Analysis). The EdgeR generalized linear model was utilized to identify putatively differentially expressed genes. P-values were adjusted for multiple comparison using Benjmani and Hochberg.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited edgeR output for BCR-ABL and Empty Vector analysis. Includes UCSC Gene ID, Gene Name, logFC, logCPM,Pvalue, FDR

source_name: bone marrow

growth_protocol: Bone marrow cells were harvested from p27CK- and p27-/- mice bone marrow and transduced with retrovirus expressing BCR-ABL1 or empty vector control. Cells were cultured for five days and sorted for Lin-GFP+ cells

extract_protocol: RNA-seq libraries were constructed using the TruSeq protocol (Illumina). Poly(A)+ RNA was isolated using oligo-dT bound to magnetic beads. Poly(A)+ RNA was then chemically fragmented. RNA fragments were converted to double stranded cDNA using random hexamer priming. Fragment ends were treated to remove overhanging nucleotides and then a single “A” was added to the 3’ end of each strand to facilitate ligation. Illumina adaptors with barcode sequences was ligated to the fragments. The resulting library was then amplified using polymerase chain reaction with a limited number of round. Unincorporated nucleotides and adaptor dimers were removed using AMPure XP beads (Agencourt). Libraries were combined for multiplexing and sequenced on a HiSeq 2000 sequencer (Illumina). Base call data was assembled into fastq files using the CASAVA suite (Illumina).

tag: transduction


title: Hela_RASL-seq_si-U2AF35_rep3

description:
RASL-seq library from U2AF35 knockdown cells
Library strategy: RASL-Seq

treatment_protocol: Transfection of siRNA against U2AF35

value: U2AF35 siRNA


title: p27 CK- BCR-ABL R6


title: Hela_RASL-seq_si-U2AF35_rep2


title: p27 KO BCR-ABL R4


title: Hela_RASL-seq_si-U2AF65_rep2

description:
RASL-seq library from U2AF65 knockdown cells
Library strategy: RASL-Seq

treatment_protocol: Transfection of siRNA against U2AF65

value: U2AF65 siRNA


title: p27 KO Empty vector R3

value: empty


title: p27 KO BCR-ABL R2


title: Hela_RASL-seq_si-U2AF65_rep1


title: p27 KO Empty vector R1


title: Hela_RASL-seq_si-NC_rep2

description:
RASL-seq library from NC cells
Library strategy: RASL-Seq

treatment_protocol: Transfection of NC siRNA

value: NC siRNA


title: Hela_RASL-seq_si-NC_rep1


title: Hela_RASL-seq_WT_rep1

description:
RASL-seq library from WT cells
Library strategy: RASL-Seq


title: Hela_RASL-seq_WT_rep2


title: Hela_RNA-Seq_si-U2AF65

description: mRNA library from U2AF65 knockdown cells

data_processing:
Paired-end reads were separately mapped into a custom Bowtie index, which was built from UCSC knownGenes (hg18) not including introns. Under the constraint of the insert size, only the paired-end reads whose two ends are about 50 nt apart on the same gene were kept. For each pair, the coordinates of the two end reads were mapped back to the genome based on its gene's genomic location, and then joined together. Only the pair-end reads with one unique genomic location were kept.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph and bed files

extract_protocol:
Total RNAs were extracted by Trizol from treated HeLa cells and polyA RNAs were enriched by oligod(T) selection.
After fragmentation, mRNAs were reversely transcribed to cDNA with Superscript II in the presence of random primer. After RNase H digestion, the second strand cDNA was synthesized by DNA pol I followed by adaptor ligation. Size-selected PCR products were sequenced by Illumila Genome Analyzer II.


title: p27 Ck- Empty vector  R5


title: Hela_U2AF65_CLIP-Seq

description:
library from U2AF65-RNA complex
Library strategy: CLIP-seq

data_processing:
After removing 3' adaptor sequence, the tags longer than 20 nt were mapped to the reference human genome (hg18) with Bowtie2 (version 2.0.0-beta7 with parameters --very-sensitive -rdg 5,2 --score-min L, -0.6, -0.7)
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph and bed files

extract_protocol:
HeLa cells were UV-irradiated at 400 mj and collected by scraping the cells from 15-cm plates. U2AF65 immunoprecipitation was done in 1% NP-40 wash buffer.
5' adaptor was first added to the immunoprecipitated U2AF65 complex on beads, then the eluted protein-RNA complex was subject to 10% Novex NUPAGE gel. After transfering to NC membrane, the corresponding band was cut and RNA was extracted. After 3' adaptor liagtion, RT-PCR was performed by using Super Script III and Ex taq polymerase.

tag: antibody

value: monoclonal anti-U2AF65 antibody, Clone MC3 (Sigma-Aldrich, catalog# U4758, lot# 034K4841)


title: ESREs

city: Rochester

first: Laurie

middle: A

last: Steiner

state: New York

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

data_processing:
Mapping  SHRiMP-2.2.3
FPKM values cuffdiff-2.0.2
Genome_build: NCBI 37.2 build of the Mus musculus genome (mm9)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for both experimental conditions (expansion and maturation)

source_name: ESREs

growth_protocol: ESREs were derived as described in England, S.J., et al., Immature erythroblasts with extensive ex vivo self-renewal capacity emerge from the early mammalian fetus. Blood, 2011. 117(9): p. 2708-17.

extract_protocol:
RNA was obtained using the RNA Easy kit from Qiagen.
The libraries were constructed at the Genomic Reserch Center at the Univeristy of Rochester, using the Nextflex kit from Bioo Scientific.

treatment_protocol: ESREs were matured as described in England, S.J., et al., Immature erythroblasts with extensive ex vivo self-renewal capacity emerge from the early mammalian fetus. Blood, 2011. 117(9): p. 2708-17.

value: Extensively Self Renewing Erythroblasts

value: expansion

tag: genetic background


title: Hela_RASL-seq_si-U2AF35_rep1


title: ESREs after one day of maturation

source_name: ESREs after one day of maturation

value: Extensively Self Renewing Erythroblasts after one day of maturation

value: maturation


title: Input

status: Public on Oct 07 2014

city: ShenZhen

first: Minghui

last: He

state: GuangDong

address: Beishan Industrial Zone, Yantian District

department: Cancer Research Department

institute: BGI-Shenzhen

data_processing:
Base calling was performed using CASAVA version 1.8.2 (illumina).
ChIP-seq reads were trimmed for adaptor sequence and mapped to mouse genome using BWA (v0.5.9) by default parameters.
Peaks were called using MACS (v1.4.2) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated by MACS

source_name: mouse embryonic fibroblasts

growth_protocol:
OG2 MEFs (Silva et al., 2008) were obtained from E13.5 embryos carrying the Oct4-GFP transgene. MEFs were maintained in DMEM/High glucose (Hyclone) containing 10% fetal bovine serum (FBS, PAA), GlutaMax (Invitrogen), non-essential amino acids (Invitrogen) and penicillin/streptomycin (Hyclone).
Mouse ESCs were cultured in mouse ESC medium (DMEM with 15% FBS [Gibco], GlutaMax, nonessential amino acids, sodium pyruvate, 0.1 mM β-mercaptoethanol and 1,000 U ml-1 LIF [Millipore]).
For reprogramming, 15,000 OG2 MEFs in 12-well plates were transduced twice using retroviral supernatants of pMX-Oct4/Sox2/Klf4/c-Myc generated with Plat-E cells. The medium was changed to mouse ESC medium at day 2 post-infection and renewed daily.

extract_protocol:
Harvested cells were lysated and sonicated to 100-500bp. Protein-DNA complexes were isolated with antibody. ChIP complexes were eluted with 1% SDS in 100 mM NaHCO3 and crosslinks were reversed by incubating samples over night at 65C. DNA fragments were purified using phenol-chloroform extraction and ethanol precipitation
Libraries were constructed according to the Illumina ChIP-seq library preparation instructions. Briefly, pull-down DNA was end repaired using a combination of T4 DNA polymerase, T4 PNK and Klenow polymerase. The DNA was then purified and used for A-tailing by adding a dATP to the 3' end. An indexed adaptor with a "T" overhang at the 3' end was then ligated to each DNA sample. The ligated DNA was then subjected to PCR amplification followed by gel purification.

treatment_protocol: Singel cell suspension was crosslinked with 1% formaldehyde for 15 min at room temperature with rotation, then quenched with glycine at a final concentration of 0.125 M. Cells were rinsed twice with cold PBS.

tag: chip antibody

tag: cell stage

value: mouse embryonic fibroblasts

tag: strain


title: Hela_RASL-seq_si-U2AF65_rep3