title: MNase-seq Input

extract_protocol:
Nuclei of approximately 15 million cells were purified by re-suspending the pellet in Nuc Buffer (15 mM Tris-HCl, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.025% (v/v) NP-40, 1 mM DTT, 0.1 mM PMSF, protease inhibitors) and incubating on ice for 7 minutes. Cells were layered on a sucrose cushion and centrifuged for 20 minutes at 12,000 g to separate the nuclei from the NP-40 detergent. The supernatant was removed, and 10 million purified nuclei were re-suspended in MNase Digestion Buffer (0.32 M sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF) with 100 units of MNase (Worthington) and incubated at 37 ºC for 10 minutes to achieve a digestion efficiency of ~90% mononucleosomes. The reaction was stopped by addition of 60 µl 50 mM EDTA, Nuclei were then sedimented by centrifugation.MNase-digested nuclei were suspended in IP buffer (50 mM HEPES, pH 7.6, 500 mM LiCl, 1 mM EDTA, 0.7% DOC, 1% NP-40, 0.1% SDS, 1x CPI) then rotated for 1 h at 4°C, followed by centrifugation 10,000 g for 10 min. This supernatant is denoted as Input.Proteinase K and SDS (0.5% final concentration) were added and the reaction was incubated for 16 hours at 65 ºC. DNA was purified using Wizard SV gel and PCR cleanup system (Promega) and eluted with 50 µl PBS. RNase A was added and the reaction was incubated for 2 hours at 37 ºC. The reaction was loaded on a 1.5% agarose gel and the ~150-bp mononucleosome band was excised from the gel and purified using Wizard SV gel and PCR cleanup system (Promega).
Deep sequencing libraries were prepared using standard Illumina ChIP-seq library prep kits and 50bp single-end sequencing was performed using an Illumina Genome Analyzer II.


title: MNase-seq SF3B1

status: Public on Apr 22 2015

type: SRA

city: Tel- aviv

first: Gil

last: Ast

state: Israel

address: Ramat Aviv

department: Human Molecular Genetics & Biochemistry

country: Israel

institute: Tel-Aviv University

library_source: genomic

data_processing:
For MNase-seq: Fastq files of each condition were mapped to the human genome (hg19) using Bowtie2 (Langmead and Salzberg, 2012) with default settings. We constructed a perl script that calculates a single score for each over a section of 147 bp from the start of the read, thus creating .wg files containing the marking the position of a nucleosome on a fragmentof 147 bp.
For mRNA-seq: mapped the Fastq files to the human genome (hg19) using Bowtie2 (Langmead and Salzberg, 2012) with default settings.splicing analysis was performed using SpliceTrap (v0.90.5) software with default parameters (Cutoff-M, Junction reads-5) (Wu et al., 2011).
Genome_build: hg19
Supplementary_files_format_and_content: MNase-seq file: a gzip archive of .wg files (one file for each chromosome). Files are tab delimited text with the following format: chr_position, nucleosome score
Supplementary_files_format_and_content: RNA-seq file: contains the results.txt output of the SpliceTrap tool

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal calf serum, 0.29 mg ml–1 L-glutamine, 100 U ml–1 penicillin, 0.1 mg ml–1 streptomycin, and 1 U ml–1 nystatin at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Nuclei of approximately 15 million cells were purified by re-suspending the pellet in Nuc Buffer (15 mM Tris-HCl, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.025% (v/v) NP-40, 1 mM DTT, 0.1 mM PMSF, protease inhibitors) and incubating on ice for 7 minutes. Cells were layered on a sucrose cushion and centrifuged for 20 minutes at 12,000 g to separate the nuclei from the NP-40 detergent. The supernatant was removed, and 10 million purified nuclei were re-suspended in MNase Digestion Buffer (0.32 M sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF) with 100 units of MNase (Worthington) and incubated at 37 ºC for 10 minutes to achieve a digestion efficiency of ~90% mononucleosomes. The reaction was stopped by addition of 60 µl 50 mM EDTA, Nuclei were then sedimented by centrifugation.MNase-digested nuclei were suspended in IP buffer (50 mM HEPES, pH 7.6, 500 mM LiCl, 1 mM EDTA, 0.7% DOC, 1% NP-40, 0.1% SDS, 1x CPI) then rotated for 1 h at 4°C, followed by centrifugation 10,000 g for 10 min. This supernatant is denoted as Input. SF3B1 antibody (4 µg) was added to input sample and rotated overnight at 4°C. Protein A beads (50 µl, Dynabeads Invitrogen) were washed and added to each sample and rotated for 4 h at 4 °C. Beads were washed four times with IP buffer.Proteinase K and SDS (0.5% final concentration) were added and the reaction was incubated for 16 hours at 65 ºC. DNA was purified using Wizard SV gel and PCR cleanup system (Promega) and eluted with 50 µl PBS. RNase A was added and the reaction was incubated for 2 hours at 37 ºC. The reaction was loaded on a 1.5% agarose gel and the ~150-bp mononucleosome band was excised from the gel and purified using Wizard SV gel and PCR cleanup system (Promega).
Deep sequencing libraries were prepared using standard Illumina ChIP-seq library prep kits and 50bp single-end sequencing was performed using an Illumina Genome Analyzer II.

tag: cell line

value: HeLa


title: RNA-seq SF3B1 siRNA

library_source: transcriptomic

molecule: total RNA

extract_protocol:
Total RNA was extracted from the cells using TRI reagent (Sigma)
Deep sequencing libraries were prepared using standard Illumina TruSeq library preparation kits. 2 x 101-bp paired-end sequencing was performed using an Illumina HiSeq 2000.

treatment_protocol: Cells were transfected with 20nM SF3B1 targeting siRNA (Thermo Scientific) using Lipofectamine RNAiMAX (Invitrogen). Following transfection, cells were incubated for 48 hours before RNA extraction.

tag: sirna knock down

value: control Non Targeting


title: S. cerevisiae lin0c

city: Stanford

first: William

middle: J

last: Greenleaf

state: CA

address: 279 Campus Drive West

department: Genetics

country: USA

institute: Stanford University

description:
S. cerevisiae ATAC-seq sample. Four populations of S. cerevisiae strain GSY14744 were used, with three of the four populations (lin2, lin3, and lin6) derived from the first (lin0) and differing only in that they were grown on plates for 200 generations in conditions to minimize selective pressures.
processed data files: lin_all.nucpos.bed, lin_all.nucsig.bw, lin_all.occ.bw, sacCer3.scores.bw, sacCer3.mappable.bed

data_processing:
Library strategy: ATAC-seq

Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag.  Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30, and reads that were not properly paired.

Nucleosome calling was performed in broad open chromatin regions determined using MACS2 and filtered for high mappability.  For the osmotic stress time-course, nucleosome calling was performed in regions around TSS that overlapped with broad open chromatin peaks in at least one time point.

genome build: sacCer3 for S. cerevisiae, ASM294v2.21 for S. pombe, and hg19 for human GM12878

processed data files format and content: *.nucpos.bed.gz files contain nucleosome positions.  Columns are as follows:  1) chromosome 2) dyad position (0-based) 2) dyad position (1-based) 3)

processed data files format and content: *.nucleoatac_signal.bw are BigWig files containing the normalized NucleoATAC signal

processed data files format and content: *.occ.bw are BigWig files contining the nucleosome occupancy

processed data files format and content: *.peaks.final.bed are highly mappable open chromatin regions for which nucleosome calling was performed. For the osmotic stress time course, analyis was performed on regions around tss that overlapped with peaks (osmotic.tss_peak_regions.bed).

processed data files format and content: *.Scores.bw  are BigWig files that contain transposase preference scores used in the sequence bias normalization for nucleosome calling.  These scores represent the log of the relative probability of insertion.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Cells were grown to mid-log phase in YPD

extract_protocol:
5 million cells were washed twice in Sorbitol buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2) before being incubated for 30 min at 30 degrees and shaking at 300 rpm with 0.5 mg/mL 100T zymolyase.  The cells were then washed twice in Sorbitol Buffer before being incubated with 2.5 ml of Nextera Transposase in 47.5 ml of 1x TD buffer at 37 degrees for 30 minutes.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as per Buenrostro et al. (2013).

tag: strain

tag: growth stage

value: mid-log

tag: treatment


title: S. cerevisiae lin0a


title: input_IMR90

city: Paris

first: Jean-François

last: Ouimette

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: Université Paris Diderot

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using the following parameters -t  -q -p 8 -S -n 2 -e 70 -l 50 --maxbts 125 -k 1 -m 1 --phred33-quals
Profiles were discretized using jahmm algorithm(Filion and Cusco, http://arxiv.org/pdf/1405.5467.pdf)
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain signal or peaks

growth_protocol: The female hES H9 cells were cultured in DMEM/F12 medium supplemented with 20% Knock-Out serum, 1mM L-glutamine, 0.1mM Non essential amino acids, 0.4μM β-mercaptoethanol and 12 ng/ml β-FGF on mouse  mitomycin-treated feeders cells. Fetal female fibroblasts IMR90 cells were cultured in DMEM medium supplemented with 10% Serum, 0.1mM NEAA, 2mM L-glutamine and 0.05mM βE mercaptoethanol.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were isolated from an E-gel (Life Technologies, #G661002) . The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: fibroblasts

tag: antibody

value: none (input)


title: input_H9_XaXe

source_name: hESC H9 XIST-

value: hES


title: input_H9_XaXi

source_name: hESC H9 XIST+


title: H3K27me3_IMR90


title: H3K9me3_H9_XaXi


title: HSB male rep2

city: Omaha

first: Ryan

middle: Ying

last: Wong

state: NE

address: 6001 Dodge Street

department: Biology

institute: University of Nebraska at Omaha

data_processing:
Illumina Casava 1.7 software used for basecalling.
Reads were aligned using GSNAP
Reads were quantified with HTSEQ using "union" mode
Reads for each gene was normalized by library size. Counts per million reads (CPM) were calculated with edgeR
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text file include CPM values for each Sample

organism: Danio rerio

source_name: whole brain

extract_protocol:
Brains were removed, placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at -80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit (Qiagen).  We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 (GTGAAA(C)); lsbf2 (GTTTCG(G)); lsbm1 (GTCCGC(A)); lsbm2 (GTGGCC(T)); hsbf1 (CCGTCC(C)); hsbf2 (GGCTAC(A)); hsbm1 (ATGTCA(G)); hsbm2 (TAGCTT(A)); abf1 (ATTCCT(T)); abf2 (GATCAG(A)); abm1 (ACTGAT(A)); abm2 (ACTTGA(A)); shf1 (GAGTGG(A)); shf2 (TTAGGC(A)); shm1 (CGTACG(T)); shm2 (ATCACG(A))

value: High Stationary Behavior

tag: Sex

value: male

tag: age

value: 17 weeks


title: H3K27me3_H9_XaXi


title: H3K9me3_H9_XaXe


title: HSB male rep1


title: HSB female rep2

value: female


title: LSB male rep1

value: Low Stationary Behavior


title: LSB male rep2


title: LSB female rep2


title: HSB female rep1


title: LSB female rep1


title: SH male rep1

value: Scientific Hatcheries


title: SH male rep2


title: SH female rep2


title: SH female rep1


title: AB male rep2

value: AB


title: AB male rep1


title: H3K9me3_IMR90


title: Dry seed

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: dry seeds from dry siliques were collected.

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the Arabidopsis thaliana genome (TAIR 10) obtained from the TAIR website (http://www.arabidopsis.org/) and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls))
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine

organism: Arabidopsis thaliana

source_name: Arabidopsis dry seed

growth_protocol: Arabidopsis thaliana (L.) Heynh, ecotype Wassilewskja (ws-0) plants were grown under standard greenhouse conditions (Belmonte et al., PNAS 2013). Siliques and seed stage were staged according to criteria described in methods of Belmonte et al. Whole seeds were collected for genomic DNA isolation.

extract_protocol:
Collected seeds were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions
Approximately 500 nanogram of genomic DNA isolated from seeds and leaves was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: tissue

value: seed

tag: cultivar


title: Leaf

description: leaves from 4 week plant were collected.

source_name: Arabidopsis leaf

value: leaves


title: Mature green stage seed

description: 13DAP seeds were collected.

source_name: Arabidopsis mature green stage seed

tag: developmental stage

value: 13 DAP


title: H3K27me3_H9_XaXe


title: Post mature green stage seed

description: 18-19 DAP seeds were collected.

source_name: Arabidopsis post mature green stage seed

value: 18 DAP


title: AB female rep2


title: 10% RWC-1

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

country: China

institute: Capital Normal University

data_processing:
Basecalls performed using the Illumina GA Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity (unknown bases are less than 10%) or low-quality sequence (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), then mapped to Bhy_V1.0 (unpublished) whole genome using SOAPaligner/soap2.
The transcript abundance of each gene were normalized by RPKM.
Genome_build: Bhy_V1.0
Supplementary_files_format_and_content: tab-delimited text files include read number for each Sample.

organism: Dorcoceras hygrometricum

extract_protocol:
RNA from hydrated, moderate dehydration (70% RWC) and desiccated (10% RWC) leaf tissues of resurrection plant species B. hygrometrica was harvested using Trizol reagent. Illumina protocols were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plants growing in pots were subjected to hydrated, dehydtrating to 70% RWC and to 10% RWC.

value: leaf tissue


title: 10% RWC-3


title: 70% RWC-2


title: Linear cotyledon stage seed

description: 8DAP seeds were collected.

source_name: Arabidopsis linear cotyledon stage seed

value: 8 DAP


title: 70% RWC-3


title: 70% RWC-1


title: Global stage seed

description: 4DAP seeds were collected.

source_name: Arabidopsis global stage seed

value: 4 DAP


title: 10% RWC-2


title: wild type leaf

description: Leaves from Arabidopsis wild type were collected

source_name: leaves from Arabidopsis wild type 3 week plant

growth_protocol: Arabidopsis thaliana (L.) Heynh, ecotype Columbia (Col) wild type and ddcc mutant plants were grown under standard greenhouse conditions (Belmonte et al., PNAS 2013). Leaves were collected for genomic DNA isolation from 3 week plant.

extract_protocol:
Collected seeds and leaves were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.
Approximately 500 nanogram of genomic DNA isolated from seeds and leaves was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: genotype

value: wild type

value: leaf

value: Col


title: HD-3


title: 221-18hpi

city: Shanghai

first: Hanqi

last: Yin

state: Shanghai

address: libing road 151

institute: shanghai biochip corporation

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
The resulting cleaned reads of each sample was assembled as unigenes using the Trinity package with optimized k-mer length of 25, respectively. The assembled unigenes of all the samples were cleaned by removing redundancies and further assembled as all-unigenes using CD-HIT software. The cleaned reads of each sample were aligned to the assembled all-unigenes using FANSe2 allowing 7 nt mismatch, respectively[26]. The all-unigene with at least 10 mapped reads were considered as reliably assembled unigenes.
Unigene abundance measurements were generationed and normalized using EdgeR ; The normalized standard were counts per million (CPM)
Genome_build: None
Supplementary_files_format_and_content: tab-delimited text files include normalized CPM values and raw fragment counts for each Sample

organism: Spodoptera litura

source_name: SL221 cell

growth_protocol: SL221 cells were cultured in TNM-FH medium supplemented with 10% FBS at 28°C.

extract_protocol:
Total RNA was extracted with Qiagen RNeasy RNA mini kit.Total DNA was extracted with Qiagen AllPrep DNA Kit
Illumina Strand Specific RNA Sequencing.  Illumina sequencing libraries were constructed following a modified strand-specific RNA seq protocol. In brief, 3 μg purified total RNA was used for isolation of coding RNA and non-coding RNA using ribo-zero kit for rRNA depletion, then isolated RNA were simultaneously eluted and fragmented in Elute-Prime-Fragment Mix at 94°C for 8 min. First-strand cDNA synthesis was carried out using SuperScriptII (Invitrogen, Carlsbad, CA) in the presence of hexamer random primer. Second-strand cDNA was synthesized at 16°C for 1 hour. After end-repair and dA-tailing, the DNA fragments were ligated with TruSeq adapter. The sample was amplified with TruSeq PCR primers and sequenced on the Illumina HiSeq2500 platform.

treatment_protocol: SL221 cells infected with wild-type SpltNPV strain. Virus titers were determined by TCID50 (50 % tissue culture infective dose) end-point dilution assay using SL221 cells. SL221 cells were grown to the desired cell density and one million SL221 cells were inculated with SpltNPV (multiplicity of infection (MOI) = 1) in a T25 flask.

tag: infection

value: wild-type baculovirus SpltNPV

tag: time point


title: HD-2


title: 221-12hpi


title: ddcc mutant leaf

description: Leaves from Arabidopsis Col ddcc mutant were collected

source_name: leaves from Arabidopsis ddcc mutant 3 week plant

value: ddcc mutant


title: wild type dry seed

description: Dry seeds from Arabidopsis Col wild type were collected

source_name: dry seeds from Arabidopsis wild type


title: HD-1


title: ddcc mutant dry seed

description: Dry seeds from Arabidopsis Col ddcc mutant were collected

source_name: dry seeds from Arabidopsis ddcc mutant


title: Spli221-6hpi


title: CMCW27

status: Public on Apr 21 2015

city: Dallas

first: James

middle: Francis

last: Amatruda

state: TX

address: 5323 Harry Hines Blvd

department: Pediatrics, Internal Medicine, and Molecular BIology

institute: UT Southwestern

data_processing:
Reads demultiplexed on machine
Analyzed using LifeScope v2.5.1 using default small RNA parameters
filter out SOLiD adapter sequences, rRNA, tRNA
map to hg19 and miRbase, using seed-and-extend algorithm
mapping utilized seed-and-extend algorithm
Genome_build: hg19 and miRbase 16
Supplementary_files_format_and_content: gff file; "group" field contains "ACC" (miRBase accession number) and "ID" (miRBase ID)

source_name: Wilms tumor

extract_protocol:
Small RNAs were prepared from 50 ng of each tumor sample using the mirVana PARIS kit according to the standard manufacturer protocol.
Small RNA libraries were prepared using the protocol for small RNA library preparation in the SOLiD Total RNA-Seq kit from Life Technologies.

tag: mutation status of dicer1 or drosha


title: CMCW59


title: CMCW79

value: DROSHA


title: CMCW7


title: CMCW9


title: CMCW47


title: CMCW23


title: AB female rep1

value: female

value: 17 weeks


title: CMCW15


title: CMCW21


title: CMCW13


title: CMCW1


title: Pulsatile cAMP in suspension, replicate 3, hour 06

city: Houston

first: Gad

last: Shaulsky

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Sample 65
PCrep3_hr06

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names (DDB_G ids) and the second its expression. Files ending with "_raw.txt" contain raw expression values while files ending with "_nor.txt" contain normalized expression values.

molecule: polyA RNA

organism: Dictyostelium discoideum

source_name: Cells in Na+ K+ phosphate buffer shaking suspension

growth_protocol: Dictyostelium discoideum cells were grown in nutrient media (HL-5) to mid-log phase prior to collection for development.

extract_protocol:
TriZol (Life Sciences) -- Cells were scraped (filter) or pelleted (suspension) and disrupted in TriZol. Total RNA was extracted by phenol/chloroform as per manufacturer's instructions.
mRNA was enriched by 2x polyA bead selection (Ambion, Life Sciences). Multiplexed libraries were constructed as outlined in Miranda et al (2013), PMID #23494306.

tag: growth

value: Exogenous cAMP in shaking suspension

tag: time point (hour)

tag: replicate


title: Pulsatile cAMP in suspension, replicate 3, hour 10

description:
Sample 67
PCrep3_hr10

tag: strain


title: Pulsatile cAMP in suspension, replicate 3, hour 05

description:
Sample 64
PCrep3_hr05


title: Pulsatile cAMP in suspension, replicate 3, hour 08

description:
Sample 66
PCrep3_hr08


title: Pulsatile cAMP in suspension, replicate 3, hour 01

description:
Sample 60
PCrep3_hr01


title: 221-mock

value: mock infected SL221 cell

tag: cell line


title: Pulsatile cAMP in suspension, replicate 2, hour 12

description:
Sample 58
PCrep2_hr12

tag: treatment


title: Pulsatile cAMP in suspension, replicate 3, hour 03

description:
Sample 62
PCrep3_hr03


title: Pulsatile cAMP in suspension, replicate 2, hour 10

description:
Sample 57
PCrep2_hr10


title: Pulsatile cAMP in suspension, replicate 3, hour 04

description:
Sample 63
PCrep3_hr04


title: Pulsatile cAMP in suspension, replicate 2, hour 08

description:
Sample 56
PCrep2_hr08


title: Pulsatile cAMP in suspension, replicate 2, hour 04

description:
Sample 53
PCrep2_hr04


title: Pulsatile cAMP in suspension, replicate 2, hour 03

description:
Sample 52
PCrep2_hr03


title: Pulsatile cAMP in suspension, replicate 2, hour 05

description:
Sample 54
PCrep2_hr05


title: Pulsatile cAMP in suspension, replicate 2, hour 02

description:
Sample 51
PCrep2_hr02


title: Pulsatile cAMP in suspension, replicate 1, hour 12

description:
Sample 48
PCrep1_hr12


title: CMCW11


title: Pulsatile cAMP in suspension, replicate 2, hour 01

description:
Sample 50
PCrep2_hr01


title: Pulsatile cAMP in suspension, replicate 2, hour 00

description:
Sample 49
PCrep2_hr00


title: Pulsatile cAMP in suspension, replicate 3, hour 02

description:
Sample 61
PCrep3_hr02


title: Pulsatile cAMP in suspension, replicate 1, hour 03

description:
Sample 42
PCrep1_hr03


title: Pulsatile cAMP in suspension, replicate 1, hour 04

description:
Sample 43
PCrep1_hr04


title: Pulsatile cAMP in suspension, replicate 1, hour 05

description:
Sample 44
PCrep1_hr05


title: Pulsatile cAMP in suspension, replicate 1, hour 00

description:
Sample 39
PCrep1_hr00


title: Pulsatile cAMP in suspension, replicate 1, hour 01

description:
Sample 40
PCrep1_hr01


title: Pulsatile cAMP in suspension, replicate 1, hour 06

description:
Sample 45
PCrep1_hr06


title: Pulsatile cAMP in suspension, replicate 1, hour 10

description:
Sample 47
PCrep1_hr10


title: Pulsatile cAMP in suspension, replicate 3, hour 00

description:
Sample 59
PCrep3_hr00


title: E12.5_290410_FL5_lox_lox_NEG_WT

city: Leuven

first: Petros

last: Papadopoulos

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KU Leuven

data_processing:
The reads were aligned using Tophat version 2.0.8 (Kim, D et al. 2013) against the UCSC mm10 reference genome, using Ensembl genes.gtf annotation version 75 (Ensembl 2014 Nucleic Acids Research 2014)
Read counts on ensemble annotation were computed using the 0.6.0. using -m union -s no -a 20
The differentially expressed genes were called using a generalized linear negative binomial model with controlling the effect of the RNA sample preparation date. The calculations were performed by the DESeq2 R package (Anders and Huber, Genome Biology 2010)
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

organism: Mus musculus

source_name: fetal liver

extract_protocol:
Total RNA was extracted from fetal liver single cell suspension with the standard Trizol reagent protocol. 500ng of total RNA was used for the generation of the library according to the Illumina protocol (TruSeq version 2)
The library was generated under the standard Illumina protocol.

value: WT


title: yak.U.2

city: LYON

first: Mathilde

last: Paris

address: Faculte des sciences de Luminy, case 907

department: IGFL

institute: CNRS

data_processing:
We used the annotation version 5.39 for D. melanogaster and the annotation previously published for D. yakuba, D. pseudoobscura, and D. virilis described in Paris et al. (2013), PLoS Genetics (10.1371/journal.pgen.1003748)
We trimmed all sequenced tags so that their average quality was above 30 and mapped the tags to the transcripts using Bowtie2 [19] with command-line options ‘-a -N 1‘, thereby allowing all possible mappings. We then estimated transcript levels using eXpress [20]. Gene levels were obtained by summing levels over all transcripts of a gene. Gene levels were then normalized to the 95th percentile, log transformed and averaged over replicates. Orthology was assessed from Paris et al. (2013), PLoS Genetics (10.1371/journal.pgen.1003748.
Supplementary_files_format_and_content: six tab-delimited summary tablesincluding normalized and log-transformed FPKM values for all samples. The table is organized as follows: each line corresponds to a particular gene. The corresponding gene ID in the four species and the usual name in D. melanogaster, as well as their genomic localization, and the abundance measurements in all 31 samples. 6 normalizations have been done: simple FPKM (as from eXpress), FPKM+additional median normalization, FPKM + additional 75th percentile normalization, FPKM + additional 95th percentile normalization, FPKM + additional TMM percentile normalization and FPKM + additional quantile normalization.
Supplementary_files_format_and_content: tab table summarizing the maternal/zygotic/maternal-zygotic origin of each gene in each species, according to an SVM classifier. Associated probabilities are indicated.

Gene_abundances_after_p75_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM 75th percentile normalization)
Gene_CLASS_after_p75_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + 75th percentile normalization)
Gene_CLASS_after_FPKM_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM normalization)
Gene_abundances_after_FPKM_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM normalization)
Gene_abundances_after_p50_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + median normalization)
Gene_CLASS_after_p50_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + median normalization)
Gene_abundances_after_p95_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + 95th percentile normalization)
Gene_CLASS_after_p95_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + 95th percentile normalization)
Gene_abundances_after_TMM_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + TMM normalization)
Gene_CLASS_after_TMM_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + TMM normalization)
Gene_abundances_after_Q_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + quantile normalization)
Gene_CLASS_after_Q_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + quantile normalization)

organism: Drosophila yakuba

source_name: D. yakuba_Whole embryo

growth_protocol: Egg laying and development at room temperature, until embryos have reached the blastoderm stage, according to morphological criteria.

extract_protocol:
Trizol extraction (Invitrogen), according to the manufacturer's instructions.
Liraries were made using the standard Illumina Truseq protocol

value: unfertilized egg


title: yak.F.3

source_name: D. yakuba_Whole embryo_female

value: Female

value: Blastoderm

value: Whole embryo


title: E12.5_290410_FL4_wt_ko_EpoCre_het


title: yak.M.3

source_name: D. yakuba_Whole embryo_male

value: Male


title: yak.M.2


title: E12.5_290410_FL2_wt_ko_EpoCre_het


title: E12.5_290410_FL7_lox_lox_EpoCre_KO


title: yak.U.1


title: yak.F.2


title: yak.M.1


title: Pulsatile cAMP in suspension, replicate 2, hour 06

description:
Sample 55
PCrep2_hr06


title: Pulsatile cAMP in suspension, replicate 1, hour 02

description:
Sample 41
PCrep1_hr02


title: Pulsatile cAMP in suspension, replicate 1, hour 08

description:
Sample 46
PCrep1_hr08


title: yak.F.1


title: pse.U.3

organism: Drosophila pseudoobscura

source_name: D. pseudoobscura_Whole embryo


title: E12.5_090410_FL3_lox_wt_EpoCre_het


title: pse.F.3

source_name: D. pseudoobscura_Whole embryo_female


title: E12.5_090410_FL1_lox_lox_EpoCre_KO


title: pse.F.2


title: pse.F.1


title: E12.5_090410_FL7_lox_lox_NEG_WT


title: TAC4wk_PKCde-2KO_2

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC mm10 genes.gtf.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene

source_name: Heart

extract_protocol:
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
non-strand-specific, single-end RNA-Seq

value: Whole heart

tag: age (weeks)

value: F

value: combined knockout


title: pse.M.3

source_name: D. pseudoobscura_Whole embryo_male


title: pse.M.2


title: TAC4wk_PKCde-2KO_4


title: TAC4wk_PKCde-2KO_1


title: pse.M.1


title: TAC4wk_PKCe-KO_4

value: M

value: germline PKCepsilon knockout


title: TAC4wk_PKCd-KO_2

value: postnatal cardiac PKCdelta ablation,


title: TAC4wk_PKCe-KO_2


title: TAC4wk_PKCe-KO_1


title: TAC4wk_PKCd-KO_3


title: TAC4wk_ntg_2

value: wild-type


title: TAC4wk_ntg_3


title: TAC4wk_ntg_1


title: unstressed_PKCde-2KO_4


title: Rec-OE NCCIT total RNA rep2

city: Salt Lake City

first: Edward

last: Grow

state: UT

address: 2000 Circle of Hope Drive

department: Oncology

institute: University of Utah

description: Sample 9

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment to hg19 was performed using Bowtie for HERV-K Rec iCLIP-seq. Tophat/bowtie2 was used for aligning Ribosome profiling (RPF) data. DNAnexus with BWA was used to align Rec siRNA RNA-seq and ELF1 RNA-seq.
For iCLIP-seq data, reads were processed as described in Calo and Flynn, et al, Nature 2014. For RNA-seq reads the GTF file for Refseq genes was used as a transcript model, and RPKM was calculated. Ribosome profiling data was analyzed with CuffLinks/Cuffdiff using default parameters. RNA-seq count data was analyzed using DESeq (version 1), with default parameters. FDR at <0.05 was reported as significant.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file listing score of HERV-K Rec iCLIP-seq data. For Ribosome profiling, a tab-delimted file containing Cufflinks RPKM score is included. For RNA-seq experiments from Rec siRNA and ELF1 samples, a tab-delimited file from DNAnexus reporting RPKM values is included.
Supplementary_files_format_and_content: excel file with Refseq gene ID and FPKM

source_name: Rec-OE-NCCIT hECC

growth_protocol: NCCIT cells were maintained in 10%FBS/RPMI with 1x glutamax, 1x non-essential amino acids, 1x antibiotics/antimycotic

extract_protocol:
Trizol, total RNA, rRNA depletion
Libraries were constructed using NEBnext kit

tag: gender

value: male

tag: cell type

value: NCCIT cells, hECC

tag: molecule subtype

value: total RNA (rRNA depleted)


title: WT control NCCIT total RNA rep1

description: Sample 10

source_name: NCCIT hECC


title: Rec-OE NCCIT total RNA rep1

description: Sample 8


title: unstressed_PKCde-2KO_2

tag: tissue

tag: Sex


title: unstressed_PKCde-2KO_3


title: TAC4wk_PKCde-2KO_3


title: unstressed_PKCde-2KO_1


title: Primed ELF1 hESC

description:
PE-RNA-seq
Poly-A+ RNA in either naïve or primed hESC conditions.
Processed data file: ELF1_RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment to hg19 was performed using Bowtie for HERV-K Rec iCLIP-seq. Tophat/bowtie2 was used for aligning Ribosome profiling (RPF) data. DNAnexus with BWA was used to align Rec siRNA RNA-seq and ELF1 RNA-seq.
For iCLIP-seq data, reads were processed as described in Calo and Flynn, et al., Nature 2014. For RNA-seq reads, the GTF file for RefSeq genes was used as a transcript model, and RPKM was calculated. Ribosome profiling data was analyzed with CuffLinks/Cuffdiff using default parameters. RNA-seq count data was analyzed using DESeq (version 1), with default parameters. FDR at <0.05 was reported as significant.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited file listing score of HERV-K Rec iCLIP-seq data. For ribosome profiling, a tab-delimted file containing Cufflinks RPKM score is included. For RNA-seq experiments from Rec siRNA and ELF1 samples, a tab-delimited file from DNAnexus reporting RPKM values is included.

source_name: ELF1 hESC

growth_protocol: Naïve and primed ELF1 hESC were maintained as described in Ware, et al. PNAS 2014 111(12):4484-9 (PMID 24623855). On MEFs.

extract_protocol:
Trizol, Ambion polyA purification kit.
Libraries were constructed using NEBnext kit.

value: primed hESC

value: female


title: Naïve ELF1 hESC

value: naive hESC


title: unstressed_PKCe-KO_3


title: Control siRNA NCCIT

description:
RNA-seq
Poly-A+ RNA after siRNA knockdown either with HERV-K Rec siRNA pool or control GFP siRNA.
Processed data file: Rec_siRNA_RNA-seq

growth_protocol: NCCIT cells were maintained in 10% FBS/RPMI with 1x glutamax, 1x non-essential amino acids, 1x antibiotics/antimycotic.

treatment_protocol: Cells were transfected with 25nM siRNA for three consecutive days with lipo2000.


title: TAC4wk_PKCe-KO_3


title: HERV-K Rec siRNA NCCIT


title: unstressed_PKCe-KO_2


title: WT control NCCIT Ribosome profiling (RPF)

description:
Ribosome profiling (RNA-seq)
Ribosome-protected fragments from ART-seq kit (RPF).
Processed data file: Rec_ribosome_profiling

extract_protocol:
Ribosome-protected fragments were purified using the ART-seq kit.
Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 2014 65(3):274-87 (PMID 24184352).

treatment_protocol: Cells were treated with cyclohexamide at 37C for 3 minutes, as per ART-seq kit instructions.


title: unstressed_PKCd-KO_3

value: postnatal cardiac PKCdelta ablation


title: unstressed_PKCe-KO_1


title: TAC4wk_ntg_4


title: TAC4wk_PKCd-KO_1


title: unstressed_PKCd-KO_2


title: unstressed_PKCd-KO_1


title: HERV-K Rec iCLIP-seq

description:
ICLIP-seq
FLAG-eGFP tandem purification.
Processed data file: Rec_iCLIP-seq_hits

extract_protocol:
Crosslinked RNAs were purified with tandem FLAG/eGFP immunoprecipitation.
Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 2014 65(3):274-87 (PMID 24184352).

treatment_protocol: UV-crosslinking in a Stratalinker 0.3J/cm2.


title: WT control NCCIT total RNA rep2

description: Sample 11


title: Trastuzumab resistant version of the human BT474 breast cancer cell line

city: Göttingen

first: Silvia

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

country: Germany

institute: University Medical Center Göttingen

description:
BTR50
nexprs_btr50_bt474.xls, nexprs_btr50_btr50T.xls

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.
Quality check was done via FastQC (v0.10.1, Babraham Bioinformatics).
Sequenced reads were hard (first 5 bases) and soft (last bases) trimmed as well as trimmed for adaptor sequences via Flexbar v2.32, then mapped to the human reference genome (GRCh37, Gencode release 14) using STAR v2.3.0 with parameter --outFilterMismatchNmax 3.
Conversion of SAM to BAM files and corresponding sorting was done via SAMtools v0.1.18.
Counting the reads to each gene to the UCSC gtf gene annotation file (March 2012) was done via HTSeq python scripts (0.5.3p9, htseq-count).
Normalization to the library size, estimation of dispersions (method="blind", sharingMode="fit-only") and testing for differentially expressed (DE) genes based on a statistical test assuming negative binomial data distribution was computed via the DESeq (v1.12.1) R package.
Just genes exceeding 20 counts for at least one sample were kept for further analysis.
The numerator and denominator of fold changes (FC) were increased by one to account for zero values.
Significant genes were filtered to a minimum of 2xFC and fdr<0.05 with multiple testing correction according to Benjamini and Hochberg.
Genome_build: hg19
Supplementary_files_format_and_content: xls files include normalized count of reads for each gene and each pair of samples in the related statistical test.

source_name: Cell line

growth_protocol:
The cells were grown in a monolayer and collected as a cell pellet after trypsin treatment. RNA was harvested from cell pellet using the miRNeasy kit (Qiagen).
The human breast cancer cell lines BT474 and HCC1954 were obtained from the American Type Culture Collection (ATCC). The BT474 was cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 0.01 mg/ml of insulin and 1% penicillin/streptomycin.
The human breast cancer cell line HCC1954 was cultured in RPMI media (Gibco) supplemented with 10% fetal bovine serum (Gibco). The medium was supplemented with 1% penicillin/streptomycin (Gibco).
The cells were cultured at 37°C in an atmosphere containing 5% CO2. Cells were harvested with trypsin-ethylenediamine tetraacetic acid (EDTA) (0.5 g/L trypsin; 0.2 g/L EDTA; Sigma).

extract_protocol:
Total RNA was isolated from cell lines BT474, BTR50 and HCC1954 using the Trizol (Invitrogen) method according to the manufacturer's recommendations.
Afterwards, the samples were DNAse I (Sigma) treated in order to remove DNA contamination.
RNA quality was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) microfluidic electrophoresis.
Only samples with comparable RNA integrity numbers were selected for deep sequencing.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 800 ng of total RNA.
Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega).
The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp).
cDNA libraries were amplified and sequenced by using the cBot and HiSeq 2000 from Illumina (SR; 1x51 bp; 6 GB ca. 30-35 million reads per sample).

treatment_protocol:
For treatment experiments, 2x105 cells were seeded in T25 flasks and cultivated as recommended by ATCC.
Cells were treated with 20 μg/ml trastuzumab (Roche Diagnostics GmbH, Penzberg, Germany) or grown in full growth media without inhibitors.
Cell pellets were harvested after 72 h. The cells were incubated in the standard media 24 h before addition of trastuzumab or fresh full growth media.
Resistant cells (BTR50) were developed by culturing parental cells (BT474) in the presence of 20/50 µg trastuzumab (Roche) for around six month.
Parental cells were cultured in parallel to resistant ones without addition of trastuzumab.

tag: drug treatment

value: no drug

value: HER2-positive breast cancer

tag: resistance

value: induced trastuzumab resistance


title: Trastuzumab resistant version of the human BT474 breast cancer cell line under trastuzumab treatment

description:
BTR50 plus trastuzumab
nexprs_btr50_btr50T.xls

value: trastuzumab


title: Human HCC1954 breast cancer cell line under trastuzumab treatment

description:
HCC1954 plus trastuzumab
nexprs_hcc1954_hcc1954T.xls

value: trastuzumab resistance


title: unstressed_ntg_3

value: Whole heart

tag: genotype


title: unstressed_ntg_2

value: M


title: unstressed_ntg_1


title: Human HCC1954 breast cancer cell line

description:
HCC1954
nexprs_hcc1954_bt474.xls, nexprs_hcc1954_hcc1954T.xls


title: Human BT474 breast cancer cell line under trastuzumab treatment

description:
BT474 plus trastuzumab
nexprs_bt474_bt474T.xls

value: no trastuzumab resistance


title: Human BT474 breast cancer cell line

description:
BT474
nexprs_bt474_bt474T.xls, nexprs_btr50_bt474.xls, nexprs_hcc1954_bt474.xls


title: HCT116_miR-155_RNA-seq_rep1

city: Ipswich

first: Guoqiang

last: Zhang

state: Massachusetts

address: 240 County Road

institute: New England Biolabs Inc

description: processed data file: RNA-seq_log2fdc.txt

data_processing:
For RRBS data analysis, adaptor sequences were trimmed from RRBS reads using the trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and reads with a Phred score < 20 were discarded. Reads were mapped to hg19 and methylation at CpG sites was extracted using the Bismark package. Differential methylation analysis was carried out using the logistic regression statistical test in the methylKit package. For calculation of the density CpG in differentially methylated regions, fasta sequences were obtained from hg19 using BEDTools and CpGs were counted.
For RNA-seq data analysis, adaptor and low quality sequences were trimmed and reads mapped to hg19 using the TopHat package. Reads mapped to known genes were counted using the HTseq counting tools against the UCSC know genes table (version March 6, 2013). Differential gene expression was analyzed using the DESeq2 package, which fits raw counts to a negative binomial generalized linear model. Genes with adjusted p value lower than 0.1 (default value in DESeq2) were considered significantly differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: RRBS_CpG_methylation_call.txt: tab-delimited text file including the coordinates of CpG sites, methylation percentage of each sample, differnetial methylation percentage, p-value and q-value;
RNA-seq_log2fdc.txt: baseMean, log2FoldChange, lfcSE, stat, pvalue and padj of each gene

growth_protocol: HCT116 cell were cultured in DMEM and McCoy’s 5A (Gibco) media supplemented with 10% of Fetal Bovine Serum.

extract_protocol:
Genomic DNA were extracted using Easy-DNA™ gDNA Purification Kit (Life Technologies). Total RNA were extracted using TRIZol reagent.
For RRBS library, 1 µg genomic DNA from HCT116 cells transfected with RNAs were digested by MspI, end-repaired, dA-tailed and ligated to methylated loop adaptor using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs). After resolving DNA on 2% agarose gels, the 150 to 400 bp region was excised and DNA was extracted. DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) and amplified using EpiMark Hot Start Taq DNA Polymerase (New England Biolabs). RNA-seq libraries were constructed using 1 μg of total RNA as input with the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs), mRNA were fragmented to 200 bp before library construction.

treatment_protocol: HCT116 cells were transfected with 2 µM miR-155-5p oligonucleotides or random 23-mer oligonucleotide mixtures for a week using Lipofectamine 2000 (Life Technologies).

value: HCT 116

value: Colorectal carcinoma cell line

tag: transfected with

value: miR-155 RNA


title: HCT116_miR-155_RNA-seq_rep2


title: HCT116_Random23mer_RNA-seq_rep3

value: random 23-mer


title: HCT116_Random23mer_RNA-seq_rep2


title: HCT116_miR-155_RNA-seq_rep4


title: HCT116_miR-155_RNA-seq_rep3


title: mel.U.3

organism: Drosophila melanogaster

source_name: D. melanogaster_Whole embryo

value: unfertilized egg


title: mel.U.2


title: HCT116_Random23mer_RNA-seq_rep1


title: Rec-OE NCCIT Ribosome profiling (RPF)

value: NCCIT cells, hECC

value: male


title: mel.F.3

source_name: D. melanogaster_Whole embryo_female

value: Female

tag: developmental stage

value: Blastoderm

value: Whole embryo


title: HCT116_miR-155_RRBS_rep2

description: processed data file: RRBS_CpG_methylation_call.txt


title: HCT116_Random23mer_RRBS_rep2


title: HCT116_Random23mer_RRBS_rep1


title: unstressed_ntg_4

value: wild-type


title: mel.M.3

source_name: D. melanogaster_Whole embryo_male

value: Male


title: mel.F.1


title: mel.M.1


title: vir.U.2

organism: Drosophila virilis

source_name: D. virilis_Whole embryo


title: mel.M.2


title: vir.F.3

source_name: D. virilis_Whole embryo_female


title: vir.F.1


title: vir.M.3

source_name: D. virilis_Whole embryo_male


title: vir.M.2


title: beads_03

status: Public on Apr 20 2015

city: Rotterdam

first: Nicolle

last: Litjens

address: Wytemaweg 80

department: Internal Medicine

country: Netherlands

institute: Erasmus MC

description:
supplementary file name: toptags_CA_edgeRwithBatchEffect.txt
supplementary file name: toptags_CB_edgeRwithBatchEffect.txt

data_processing:
Basecalling: Illumina RTA 1.17.21.3
Demultiplexing: Illumina CASAVA 1.8.4
Alignment: Tophat 1.3.1 with Bowtie 0.12.7
ReadCounting: custom R script, based on IRanges package
Differential expression analysis: R and edgeR package, with model including terms for group and culture batch
Genome_build: hg19
Supplementary_files_format_and_content: tab separated text file, with toptags listing as produced by R/edgeR. 5 columns: logFC, logCPM, LR, Pvalue, FDR. Data lines have geneID as rowIDs. Header line has one column less than data lines, as is customary for R write.table()

source_name: human regulatory T cells obtained from peripheral blood mononuclear cells using flowcytometry-based cell-sorting

growth_protocol: Highly pure cell-sorted human regulatory T cells of one donor were either not or expanded for 11 days in the presence of exogenous recombinant human IL-15 (10 ng/mL; Peprotech Rocky Hill, NJ). Expansion was performed in a polyclonal manner using anti-CD3/anti-CD28 coated beads (aCD3/aCD28 T-cell expander dynabeads, Invitrogen Dynal Oslo, Norway) at a 1:1 ratio or  expanded in an antigen-specific manner using human leukocyte antigen (HLA)-mismatched mature monocyte-derived dendritic cells  at a 1:1 ratio. The beads used were all from one batch and the mature monocyte derived dendritic cells were generated from different donors. Expansion was performed in 96-wells U-bottom plates; 104 or 2.5x104 regulatory T cells were added per well for polyclonal and antigen-specific expansion, respectively. Every 2-3 days, the medium was refreshed or cell-cultures were split and fresh medium (containing double the concentration of IL-15) was added. The samples were obtained in 4 different experiments (batches).

extract_protocol:
Qiagen RNA Easy kit (Qiagen, Valencia, CA, USA)
Illumina Truseq RNA v2

value: regulatory T cells

tag: group

value: C:aCD3/aCD28-coated bead expanded nTreg

tag: cell-culture-batch


title: Tregs_04

description:
supplementary file name: toptags_BA_edgeRwithBatchEffect.txt
supplementary file name: toptags_CA_edgeRwithBatchEffect.txt

value: A:Not-expanded nTregs


title: beads_02


title: vir.M.1


title: Tregs_03


title: Tregs_02


title: HCT116_miR-155_RRBS_rep1


title: Tregs_01


title: DC_03

description:
supplementary file name: toptags_BA_edgeRwithBatchEffect.txt
supplementary file name: toptags_CB_edgeRwithBatchEffect.txt

value: B:Allogeneic mature moDC-expanded nTreg


title: mel.F.2


title: DC_02


title: DC_01


title: DC_04


title: beads_01


title: WT-2_D4(RA)

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

description:
Sample 18
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: GATGTCT
Sample 18

data_processing:
The sequencing company provided "clean reads" (i.e., low quality reads removed).
Basecalls performed using CASAVA version
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
RNA-seq reads were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include FPKM values for wild-type or Haunt KO Samples; ChIRP-seq: bedgraph files were generated using MACS v. 1.4.2, including peaks called by default parameters.

source_name: 46C mES cells (RA, Day4)

growth_protocol: ESCs  were cultured in N2B27 complete "2i" medium including: 100 ml DMEM/F12 basal medium (Life Technologies), 100 ml Neurobasal medium (Life Technologies),  1 ml N2 supplement (Life Technologies), 2 ml B27 supplement (Life Technologies), 1 ml 100 × Glutamax (Life Technologies) and 0.1 mM 2-mercaptoethanol, 1000U/ml recombinant leukemia inhibitory factor (LIF, millipore) and "2i" (1 uM PD03259010, 3 uM CHIR99021)  for one day. The cells were then passaged with N2B27 medium without LIF or "2i", and supplemented with 2 uM retinoic acid (RA), change medium everyday. Cells were harvested at day 4 of RA-induced differentiation

extract_protocol:
Cells were harvested at day 4 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "GATGTCT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.

value: embryonic stem cells

tag: genotype/variation

value: WT

value: LIF withdrawal, 2uM RA-induced differentiation

tag: time


title: vir.U.1


title: KO-j_D2(RA)

description:
Sample 16
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: CAGATGT
Sample 16

source_name: Haunt 58 kb KO mES cells (RA, Day2)

growth_protocol: ESCs  were cultured in N2B27 complete "2i" medium including: 100 ml DMEM/F12 basal medium (Life Technologies), 100 ml Neurobasal medium (Life Technologies),  1 ml N2 supplement (Life Technologies), 2 ml B27 supplement (Life Technologies), 1 ml 100 × Glutamax (Life Technologies) and 0.1 mM 2-mercaptoethanol, 1000U/ml recombinant leukemia inhibitory factor (LIF, millipore) and "2i" (1 uM PD03259010, 3 uM CHIR99021)  for one day. The cells were then passaged with N2B27 medium without LIF or "2i", and supplemented with 2 uM retinoic acid (RA), change medium everyday. Cells were harvested at day 2 of RA-induced differentiation

extract_protocol:
Cells were harvested at day 2 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "CAGATGT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.

tag: cell line

value: Haunt 58 kb KO

tag: strain


title: KO-i_D2(RA)

description:
Sample 15
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: TGCTGAT
Sample 15

extract_protocol:
Cells were harvested at day 2 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "TGCTGAT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.

tag: treatment


title: KO-j_D4(RA)

description:
Sample 20
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: CTGAAGT
Sample 20

source_name: Haunt 58 kb KO mES cells (RA, Day4)

extract_protocol:
Cells were harvested at day 4 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "CTGAAGT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.


title: WT-1_D4(RA)

description:
Sample 17
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: AGCTCAT
Sample 17

extract_protocol:
Cells were harvested at day 4 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "AGCTCAT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.


title: WT-2_D2(RA)

description:
Sample 14
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: GTACCTT
Sample 14

source_name: 46C mES cells (RA, Day2)

extract_protocol:
Cells were harvested at day 2 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "GTACCTT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.


title: WT-1_D2(RA)

description:
Sample 13
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: ACTGACT
Sample 13

extract_protocol:
Cells were harvested at day 2 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "ACTGACT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.


title: MBD2 -/- Input DNA

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
Basecalls performed using Illumina Basecalling Package VN:1.12.4.2
ChIP-seq reads were aligned to the mm9 genome assembly using bwa version 0.5.9 and -q 15
Data were filtered using the following specifications : Only kept reads that mapped to a unique location and as a proper pair. Duplicate reads removed.
Read counts were normalized to “Reads per 10^7 mapped reads” to account for depth of sequencing
Genome_build: mm9; http://www.ncbi.nlm.nih.gov/assembly/165668/
Supplementary_files_format_and_content: bigwig files were created from BAM using bedtools genomeCoverageBed and UCSC wigToBigWig

source_name: Dendritic cells

extract_protocol:
Bone Marrow Dendritic Cells (BMDCs) cells were crosslinked with 1% formaldehyde at room temperature for 10 min, followed by 5 min incubation with 125mM glycine. Chromatin was sheared by sonication and protein-DNA complexes were immunoprecipitated with an anti_H3K9,K14ac antibody (Milipore) and the DNA was subsequently extracted.
ChIP DNA was end repaired by incubation at 20°C for 30 min with 3 U of T4 DNA Polymerase (NEB), 10 U of Polynucleotide Kinase (NEB), 2 U DNA Polymerase I Large (Klenow) fragment (NEB), 1x T4 DNA ligase reaction buffer (NEB) and 400 nM dNTPs. The enzymes were then heat inactivated at 75ºC for 20 min, after which the DNA was ethanol precipitated. A tail of 'A' bases was added to the 3’ ends of the DNA by incubation with 5 U Klenow Fragment (3’-5’ exo-; NEB), 200nM dATP and 1x buffer 2 (NEB) at 37°C for 30 min. The enzymes were heat inactivated and cleaned up as before .Barcoded Ilumina paired end adaptors were then ligated to the processed ChIP DNA by incubation with 300 U of T4 DNA ligase (NEB), 1x T4 DNA ligase buffer (NEB), 7.5% PEG-6000 and 2 pmol of annealed Illumina adaptors for 3 hr at room temperature. Ligated DNA was purified using MinElute PCR columns (Qiagen) and eluted in 10 μl water. Ligated DNA was amplified by 16-18 cycles of PCR with primers complementary to the adaptor sequences and Phusion 2x premix (Finnzymes). The DNA was purified using QIAquick PCR Purification columns (Qiagen).

treatment_protocol: Bone marrow-derived dendritic cells (BMDCs) were generated by culturing bone marrow cells for 10 days of culture in complete medium (RPMI-1640, 10% FCS, 2mM L-Glutamine, 50U/ml penicillin and 50μg/ml strepomycin) containing 20ng/ml rGM-CSF

tag: chip antibody

value: none (input)

value: bone marrow

value: dendritic


title: KO-i_D4(RA)

description:
Sample 19
messenger RNA
processed data file: mRNA profiling_Haunt 58 kb KO_RA differentiation.txt
barcode: TCACGTT
Sample 19

extract_protocol:
Cells were harvested at day 4 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "TCACGTT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.

tag: cell type


title: vir.F.2

extract_protocol:
Trizol extraction (Invitrogen), according to the manufacturer's instructions.
Liraries were made using the standard Illumina Truseq protocol


title: wt H3K9K14ac ChIP-Seq

value: wt

value: Anti H3 Acetyl K9, K14  (Millipore 06-499)


title: wt Input DNA


title: HOXA-a_D4

description: Haunt RA_RNA profiling.xlsx

data_processing:
Basecalls performed using CASAVA version
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
RNA-seq reads were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for wild-type or Haunt KO Samples, bedgraph files were generated using MACS v. 1.4.2, including peaks called by default parameters.

source_name: HOXA KO mES cells

growth_protocol:
ESCs  were cultured in N2B27 complete "2i" medium including: 100 ml DMEM/F12 basal medium (Life Technologies), 100 ml Neurobasal medium (Life Technologies),  1 ml N2 supplement (Life Technologies), 2 ml B27 supplement (Life Technologies), 1 ml 100 × Glutamax (Life Technologies) and 0.1 mM 2-mercaptoethanol, 1000U/ml recombinant leukemia inhibitory factor (LIF, millipore) and "2i" (1 uM PD03259010, 3 uM CHIR99021)  for one day. The cells were then passaged with N2B27 medium without LIF and "2i", and supplemented with 2 uM retinoic acid (RA), change medium everyday. Cells were harvested at day 4 of RA-induced differentiation
Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Cells were harvested at day 4 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 12 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

tag: sample type

value: HOXA knockout in 46C cells (RA, day4)

value: LIF withdrawal, 2uM RA, day4

tag: chirp probes

value: HOXA KO


title: HOXA-b_D4

description: Haunt RA_RNA profiling.xlsx


title: CAG KI-a_D4

description: Haunt RA_RNA profiling.xlsx

source_name: Haunt CAG KI mES cells

value: Haunt CAG promoter knockin in 46C cells (RA, day4)

value: Haunt CAG KI


title: 58 kb KO-a_D4

description: Haunt RA_RNA profiling.xlsx

source_name: Haunt 58 kb KO mES cells

value: Haunt 58 kb knockout in 46C cells (RA, day4)


title: 58 kb KO-b_D4

description: Haunt RA_RNA profiling.xlsx


title: pKO-b_D4

description: Haunt RA_RNA profiling.xlsx

source_name: Haunt pKO mES cells

value: Haunt promoter knockout in 46C cells (RA, day4)

value: Haunt pKO


title: WT-2_D4

description: Haunt RA_RNA profiling.xlsx

source_name: 46C mES cells

value: embryonic stem cells (RA, day4)

value: wild type

value: embryonic stem cells


title: WT-1_D4

description: Haunt RA_RNA profiling.xlsx

source_name: 46C mES cells (pKO control)

value: Haunt pKO control in 46C cells (RA, day4)


title: pKO-a_D4

description: Haunt RA_RNA profiling.xlsx


title: HOXA-a_D2

description: Haunt RA_RNA profiling.xlsx

growth_protocol:
ESCs  were cultured in N2B27 complete "2i" medium including: 100 ml DMEM/F12 basal medium (Life Technologies), 100 ml Neurobasal medium (Life Technologies),  1 ml N2 supplement (Life Technologies), 2 ml B27 supplement (Life Technologies), 1 ml 100 × Glutamax (Life Technologies) and 0.1 mM 2-mercaptoethanol, 1000U/ml recombinant leukemia inhibitory factor (LIF, millipore) and "2i" (1 uM PD03259010, 3 uM CHIR99021)  for one day. The cells were then passaged with N2B27 medium without LIF and "2i", and supplemented with 2 uM retinoic acid (RA), change medium everyday. Cells were harvested at day 2 of RA-induced differentiation
Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Cells were harvested at day 2 of RA-induced differentiation. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, mRNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 5 min. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 12 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: HOXA knockout in 46C cells (RA, day2)

value: LIF withdrawal, 2uM RA, day2


title: HOXA-b_D2

description: Haunt RA_RNA profiling.xlsx


title: CAG KI-a_D2

description: Haunt RA_RNA profiling.xlsx

value: Haunt CAG promoter knockin in 46C cells (RA, day2)


title: CAG KI-b_D2

description: Haunt RA_RNA profiling.xlsx


title: pKO-b_D2

description: Haunt RA_RNA profiling.xlsx

value: Haunt promoter knockout in 46C cells (RA, day2)


title: 58 kb KO-a_D2

description: Haunt RA_RNA profiling.xlsx

value: Haunt 58 kb knockout in 46C cells (RA, day2)

value: Haunt 58 kb KO


title: 58 kb KO-b_D2

description: Haunt RA_RNA profiling.xlsx


title: WT-2_D2

description: Haunt RA_RNA profiling.xlsx

value: 46C mES cells (RA, Day2)


title: pKO-a_D2

description: Haunt RA_RNA profiling.xlsx


title: WT-1_D2

description: Haunt RA_RNA profiling.xlsx


title: WT

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

data_processing:
ChIP-seq: Partek® Flow® (v1.1.1219) and Genomics Suite® (v6.12.0103) softwares (Partek Inc., Copyright ©; 2012)
RNA-seq:Reads were mapped against Ensembl genes using mm9 as a reference genome by TopHat (v2.0.6), and differentially expressed genes between WT and Rad23b-/- or SCC KD cells were determined using Cufflinks (v2.0.2) (Trapnell et al., 2012). Genes with RPKM<1 in both WT and KO/KD samples were not considered for further analysis. For all the other genes, the cutoff for differential expression was set at 1.5-fold change.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: tdf files were generated using igvtools (igvtools count -w 50 -e 200) / txt files are Partek detected enriched regions RAD23B vs. IgG); RNA-seq: text files contain CuffDiff results

source_name: murine JM8.N4 stem cells

extract_protocol:
Total RNA was purified from cell pellets using RNeasy Plus Mini kit (Qiagen) and quantified by spectrophotometer.
ChIP-seq: Libraries were prepared with the Illumina ChIP-seq DNA sample preparation kit according to manufacturer instructions with few modifications.  The material equivalent to 4 normal ChIPs was pooled to a final volume of 50 μl, 30 μl of which were further processed.  Fragments ranging from 150 to 350 bp in size were selected from gel prior to PCR amplification instead of the suggested 200 ±25 bp range.  Size, purity, and concentration of the sample were checked by Agilent Technologies 2100 Bioanalyzer and submitted for sequencing
RNA-seq: 6 μg of total RNA were used to prepare poly-A libraries following the TruSeq™ RNA Sample Preparation Guide (Illumina). Libraries were indexed with the following TruSeq adapters: WT JM8.N4 mESCs: AR005-ACAGTG(A); Rad23b-/- JM8.N4 mESCs: AR006-GCCAAT(A); SCC KD1 JM8.N4 mESCs: AR012-CTTGTA(A); SCC KD2 JM8.N4 mESCs: AR019-GTGAAA(C)  Libraries were checked for quality and concentration by Bioanalyzer (2100 DNA, Agilent Technologies), Qubit (Life Technologies) and qPCR and sequenced in one lane of the HiSeq2000 platform (single-end reads, 50 bp; Illumina).


title: RAD23B-/-

extract_protocol:
Total RNA was purified from cell pellets using RNeasy Plus Mini kit (Qiagen) and quantified by spectrophotometer.6 μg of total RNA were used to prepare poly-A libraries following the TruSeq™ RNA Sample Preparation Guide (Illumina)
ChIP-seq: Libraries were prepared with the Illumina ChIP-seq DNA sample preparation kit according to manufacturer instructions with few modifications.  The material equivalent to 4 normal ChIPs was pooled to a final volume of 50 μl, 30 μl of which were further processed.  Fragments ranging from 150 to 350 bp in size were selected from gel prior to PCR amplification instead of the suggested 200 ±25 bp range.  Size, purity, and concentration of the sample were checked by Agilent Technologies 2100 Bioanalyzer and submitted for sequencing
RNA-seq: 6 μg of total RNA were used to prepare poly-A libraries following the TruSeq™ RNA Sample Preparation Guide (Illumina). Libraries were indexed with the following TruSeq adapters: WT JM8.N4 mESCs: AR005-ACAGTG(A); Rad23b-/- JM8.N4 mESCs: AR006-GCCAAT(A); SCC KD1 JM8.N4 mESCs: AR012-CTTGTA(A); SCC KD2 JM8.N4 mESCs: AR019-GTGAAA(C)  Libraries were checked for quality and concentration by Bioanalyzer (2100 DNA, Agilent Technologies), Qubit (Life Technologies) and qPCR and sequenced in one lane of the HiSeq2000 platform (single-end reads, 50 bp; Illumina).


title: SCC_KD2

value: Rad23b-/-Xpc KD2


title: GuineaPig_IgGs_ChIP3

source_name: murine embryonic stem cells

extract_protocol:
Crosslinked cells were resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40) and incubated for 10' on ice.  Lysates were dounced 10 times using a homogenizer andnuclear pellets were resuspended in sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 1% SDS), incubated on ice for 10', and sonicated to obtain DNA fragments averaging 100 to 300 bp in length (Covaris S-system).
ChIP-seq: Libraries were prepared with the Illumina ChIP-seq DNA sample preparation kit according to manufacturer instructions with few modifications.  The material equivalent to 4 normal ChIPs was pooled to a final volume of 50 μl, 30 μl of which were further processed.  Fragments ranging from 150 to 350 bp in size were selected from gel prior to PCR amplification instead of the suggested 200 ±25 bp range.  Size, purity, and concentration of the sample were checked by Agilent Technologies 2100 Bioanalyzer and submitted for sequencing
RNA-seq: 6 μg of total RNA were used to prepare poly-A libraries following the TruSeq™ RNA Sample Preparation Guide (Illumina). Libraries were indexed with the following TruSeq adapters: WT JM8.N4 mESCs: AR005-ACAGTG(A); Rad23b-/- JM8.N4 mESCs: AR006-GCCAAT(A); SCC KD1 JM8.N4 mESCs: AR012-CTTGTA(A); SCC KD2 JM8.N4 mESCs: AR019-GTGAAA(C)  Libraries were checked for quality and concentration by Bioanalyzer (2100 DNA, Agilent Technologies), Qubit (Life Technologies) and qPCR and sequenced in one lane of the HiSeq2000 platform (single-end reads, 50 bp; Illumina).

tag: antibody

value: IgG

value: Xpc-/-


title: CAG KI-b_D4

description: Haunt RA_RNA profiling.xlsx

value: Haunt CAG promoter knockin in 46C cells (RA, day4)

value: LIF withdrawal, 2uM RA, day4

value: Haunt CAG KI


title: SCC_KD1

value: Rad23b-/-Xpc KD1


title: RAD23B_IgGs_ChIP2

source_name: murine D3 embryonic stem cell line

value: wild type


title: MBD2 -/- H3K9K14ac ChIP-Seq

value: Anti H3 Acetyl K9, K14  (Millipore 06-499)

tag: tissue

value: bone marrow

value: dendritic


title: RAD23B_ChIP1


title: NPC

description:
Sample 12
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 12

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells were derived from 46C (Sox1-GFP knock-in).  46C cells were differentiated for 6 days in N2B27 medium as described before (Conti et al, 2005). GFP positive cells were sorted by fluorescent-activated cell sorting (FACS).

extract_protocol:
RNA was extracted from FACS sorted NPC cells. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: ES-derived neural progenitor cells


title: GuineaPig_IgGs_ChIP1


title: ME

description:
Sample 11
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 11

source_name: Mesendoderm

growth_protocol: Mesendoderm cells were derived from T-GFP ES cells by LIF withdrawal (Fehling et al., 2003; Kubo et al., 2004). T-GFP cells were cultured in differentiation ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for six days. GFP positive cells were sorted out by fluorescent-activated cell sorting (FACS).

extract_protocol:
RNA was extracted from FACS sorted ME cells. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: ES-derived mesendoderm cells


title: NSC

description:
Sample 10
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 10

source_name: Neural stem cells

growth_protocol: 46C cells were differentiated for 6 days in N2B27 medium as described before (Conti et al, 2005). GFP positive cells were sorted by fluorescent-activated cell sorting (FACS). Sorted GFP positive cells were further cultured in N2B27 medium contatining 10 ng/ml EGF and FGF-2.

extract_protocol:
RNA was extracted at passage 15 of NSC culture. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: ES-derived neural stem cells


title: GuineaPig_IgGs_ChIP2


title: WTc-d2

description:
Sample 5
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 5

source_name: CJ7 mES cells (-LIF, day2)

growth_protocol: ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for two days.

extract_protocol:
Differentiated ES cells were harvested at day 2 of LIF withdrawal. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: embryonic stem cells

value: WT

value: LIF withdrawal


title: WTc-d4

description:
Sample 6
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 6

source_name: CJ7 mES cells (-LIF, day4)

growth_protocol: ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for four days.

extract_protocol:
Differentiated ES cells were harvested at day 4 of LIF withdrawal. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.


title: WTc-d6

description:
Sample 9
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 9

source_name: CJ7 mES cells (-LIF, day6)

growth_protocol: ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for six days.

extract_protocol:
Differentiated ES cells were harvested at day 6 of LIF withdrawal. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.


title: WTf-d6

description:
Sample 7
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 7

source_name: JF4 mES cells (-LIF, day6)


title: WTj-d2

description:
Sample 4
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 4

source_name: J1 mES cells (-LIF, day2)


title: WTj-d6

description:
Sample 8
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 8

source_name: J1 mES cells (-LIF, day6)


title: WTc-d0

description:
Sample 1
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 1

source_name: CJ7 mES cells

growth_protocol: Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

treatment_protocol: Cells were washed once with cold PBS, and then add TRIzol for RNA total RNA extraction


title: RAD23B_Xpc-/-_ChIP3


title: WTf-d0

description:
Sample 2
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 2

source_name: JF4 mES cells