title: 0402_Non-responder_ERRBS

description:
ERRBS
13609

value: mutant


title: S2 proximal tubule, replicate #6

status: Public on Mar 31 2015

type: SRA

city: Bethesda

first: Jae Wook

last: Lee

state: MD

address: 10 Center Drive, 6N314

country: USA

institute: National Institutes of Health

description:
mRNA released from cell lysate
S2_6

library_source: transcriptomic

data_processing:
Base-calling was performed using on-instrument real-time analysis (RTA) pipeline provided by Illumina HiSeq 2000.
Individual pair of FASTQ sequences was inspected and nucleotides with phred33 score lower than 30 were trimmed with Trimmomatic 0.32 (http://www.usadellab.org/cms/?page=trimmomatic) using the following command: java -jar trimmomatic-0.32.jar PE -threads 8 -phred33 sample_1.fastq.gz sample_2.fastq.gz sample1_p1.fastq. sample1_up1.fastq sample2_p2.fastq sample2_pup2.fastq TRAILING:30 MINLEN:35
Pairs of FASTQ sequences that survived the trimming process were mapped to rat reference genome (rn5) with STAR 2.3.0-r192 using the following command: STAR --genomeDir <genome directory> --readFilesIn sample_p1.fastq sample_p2.fastq --runThread 8 --outFilterMismatchNmax 3 --genomeLoad LoadAndKeep --outSamstrandField intronMotif --alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
HOMER software package was used to calculate RPKMs.
PA-seq data were mapped to Rn5 using Burrows-Wheeler Aligner. Peaks were called using in-house software written in Python. See Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615.
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: RPKM.without.PAseq.txt is a tab-delimited text file that contains a matrix of reads per kilobase exons per million mapped reads (RPKMs) for RefSeq transcripts without information from PA-seq study. RPKM.with.PAseq.txt is a tab-delimtied text file that contains a matrix of revised RPKMs after including the information on alternative polyadenylation from PA-seq study. Bedgraph files for individual tubule segments, in bedgraph format, contain median read counts at each nucleotide normalized to million uniquely mapped reads. These files can be uploaded onto the UCSC genome browser for visualization. PAseq.peak.rn5 bedgraph files for the forward and reverse strand contain information on polyadenylation peaks in the whole kidney across the rat genome. These files can be uploaded onto the UCSC genome browser to examine the location and intensity of polyadenylation peaks.

molecule: total RNA

organism: Rattus norvegicus

source_name: Microdissected renal tubule segment

growth_protocol: Male Sprague-Dawley rats were grown and maintained in the Animal Facility of the NHLBI. Normal rat chow was fed to the animals. Rats weighing 200-250 g were used for this study.

extract_protocol:
Dissected tubules were lysed in buffer containing RNase inhibitors and universal primers. Reverse transcription was started in this cell lysate. See Tang F. et al. (2010). "RNA-Seq analysis to capture the transcriptome landscape of a single cell" Nature Protocol 5(3):517-35.
We followed an RNA-seq protocol developed for single-cell RNA-seq. See Tang F. et al. (2010). "RNA-Seq analysis to capture the transcriptome landscape of a single cell" Nature Protocol 5(3):517-35. cDNAs were sheared and made into adapter-ligated RNA-seq libraries using NuGen Mondrian machine and Ultralow Library System.
We sequenced from both ends of a cDNA molecule, 50 nucleotides each.

treatment_protocol: The left kidney of a male Sprague-Dawley rat was isolated from the circulation and perfused with 1x dissection solution and collagenase solution. The chunks of the kidney were digested in the same collagenase solution at 37 C for 25 minutes (cortex), 50 minutes (outer medulla), or 90 minutes (inner medulla).

tag: age

value: Adult

tag: Sex

value: male

tag: strain

value: Sprague-Dawley

tag: tissue

value: S2 proximal tubule


title: 0104_Non-responder_ERRBS

city: Miami

first: Maria

middle: E

last: Figueroa

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

description:
ERRBS
13607

library_source: genomic

data_processing:
Reads were created by CASAVA 1.8.2 from the HiSeq 2000, and these are all reads which pass filter.
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR -- flexible adapter remover. FAR project website (2011)) (http://sourceforge.net/projects/theflexibleadap/).
Reads were aligned to the whole genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X and at most 500X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis.
*myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs.
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: myCpG.txt: Methylation calls; tab-delimited text file with the following column headers: chrBase, chr, base, strand, coverage, freqC, freqT

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow mononuclear cells, non-responder

extract_protocol:
Genomic DNA was isolated using the AllPrep DNA/RNA kit from Qiagen (Valencia, CA) according to manufacturer's instructions.
ERRBS libraries were constructed as described in Akalin A et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 2012;8(6):e1002781.

tag: cell type

value: bone marrow mononuclear cells (BM MNC)

tag: response to decitabine

value: non-responder

tag: type of chronic myelomonocytic leukemia

tag: cytogenetics

tag: mutation

tag: gender


title: 0501_Non-responder_ERRBS

description:
ERRBS
13611


title: S2 proximal tubule, replicate #3

description:
mRNA released from cell lysate
S2_3


title: S2 proximal tubule, replicate #4

description:
mRNA released from cell lysate
S2_4


title: S2 proximal tubule, replicate #2

description:
mRNA released from cell lysate
S2_2


title: 0202_Responder_ERRBS

description:
ERRBS
25679

source_name: Bone marrow mononuclear cells, responder

value: responder


title: S2 proximal tubule, replicate #1

description:
mRNA released from cell lysate
S2_1


title: 0107_Non-responder_ERRBS

description:
ERRBS
13605

value: female


title: S1 proximal tubule, replicate #7

description:
mRNA released from cell lysate
S1_7

value: S1 proximal tubule


title: 1002_Non-responder_ERRBS

description:
ERRBS
13603

value: 46 XY, del20q


title: CHIR_SB_Goat_IgG

city: Copenhagen N

first: Karen

last: Schachter

address: Blegdamsvej 3B, building 6.4.24

department: The Danish Stem Cell Center (DanStem)

country: Denmark

institute: University of Copenhagen

data_processing:
High quality reads (Chastity score .= 0.6) were aligned to the mouse genome (mm9) using Bowtie allowing up to two mismatches within the first 32 bases. Reads not aligning uniquely to the mouse genome were removed.
Aligned datasets were filtered for multiple reads at the same position occurring after PCR amplication. Where more than one read mapped to the same position and at the same strand duplicates were removed.
The reads were extended to 250 bp length, and the number of reads at a given position was counted and saved as a fixedStep wig file with 100 bp resolution. Values are denominated in fragments pr. Mreads pr. kbp.
Prior to peak finding the most abundant DNA-fragment size for the sample and IgG control was determined by finding the distance (that as a minimum was two times the read length) between the two strands with most correlation according to the Phantom Peak Coeefficient method (by Anshul Kundaje, akundaje@stanford.edu).
Peaks were identified using ChIP-seq  from unspecific IgG antibodies as a negative control. IgG antibodies were raised in the same species as the antibodies used for the samples. Each dataset was divided into 100 bp windows, and the reads within each window counted genome-wide. The distribution of reads within the windows was fitted to the Poisson distribution with the least root-mean-square deviation. Thresholds were set automatically for both the sample and negative control at the level where the number of expected reads were 0,001 and 0,1 times the observed number of reads or less, respectively. Based on this, the threshold for the sample was set to 20 reads and the threshold for the negative sample was set to 11 reads. The genome was analysed in 100 bp windows, and windows that both had a number of reads in the sample at or above the sample threshold and had fewer reads than the negative threshold were scored positive and their positions saved. This analysis was repeated 4 times - each time the windows were shifted 25 bp. Windows within 100 bp of each other and overlapping windows were merged.- For each region in the resulting the borders were refined by sliding a window of 100 bp from one windowsize upstream to downstream of the temporary border. The exact position where the number of sample reads within the window fell below the sample threshold, or the number of negative reads within the window came above the negative threshold, was defined as new new border of that region.
Genome_build: hg19
Supplementary_files_format_and_content: Txt: tab separated list of peaks from peak-calling, wig: fixedStep Wiggle file containing densities with 100 bp resolution of aligned and filtered reads.

source_name: Human embryonic stem cells

growth_protocol: hESC were culture in DEF-CS media (Cellartis).

extract_protocol:
Cells were fixed for 15 min in culture media containing 1% formaldehyde and were processed for ChIP as in Dietrich  et al. (2007) EMBO J 26: 1637–1648.
DNA from three parallel ChIPs were pooled and 10 ng was used for making ChIP-seq libraries. Libraries were generated according to Illumina recommendations and sequencing was done on a Genome Analyzer II (Illumina).

treatment_protocol: Confluent cultures were treated with with 3mM CHIR99021 (CHIR), or 3mM CHIR99021+ 10mM SB431542 (CHIR+SB) in RPMI-1640 for 6h.

tag: cell line

value: Human embryonic stem cells

tag: treatement

tag: chip antibody

value: goat IgG (DAKO)


title: S1 proximal tubule, replicate #6

description:
mRNA released from cell lysate
S1_6


title: S1 proximal tubule, replicate #5

description:
mRNA released from cell lysate
S1_5


title: S1 proximal tubule, replicate #3

description:
mRNA released from cell lysate
S1_3


title: S1 proximal tubule, replicate #4

description:
mRNA released from cell lysate
S1_4


title: S1 proximal tubule, replicate #2

description:
mRNA released from cell lysate
S1_2


title: CHIR_SB_BetaCatenin

value: anti-Beta-Catenin (R&D systems, AF1329)


title: RPMI_Goat_IgG

value: mock


title: RPMI_BetaCatenin


title: CHIR_BetaCatenin


title: S1 proximal tubule, replicate #1

description:
mRNA released from cell lysate
S1_1


title: CHIR_Goat_IgG


title: DKO_P28

status: Public on Mar 30 2015

city: Cambridge

first: Rahul

last: Karnik

state: MA

address: 419 Broadway

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome (hg19) using MAQ bisulfite alignment mode.
Aligned bam files were processed using custom software (PMID:20852634).
Genome_build: hg19
Supplementary_files_format_and_content: chrom, chromstart, chromend,'number methylated cytosines/number total cytosines',score,strand,number methylated cytosines,number total cytosines

source_name: HUES64 DNMT3A/3B DKO

extract_protocol:
Please see Gu et al., 2011 and Smith et al., 2012
RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010)

value: ES

tag: genotype

value: DMNT3A/3B knockout

tag: passage


title: DKO_P27


title: DKO_P17


title: S2 proximal tubule, replicate #5

description:
mRNA released from cell lysate
S2_5


title: DKO_P13


title: DKO_P8


title: DKO_P11


title: d3

source_name: HUES64 DNMT1 KO

value: DNMT1 knockout


title: d5


title: d6


title: DKO_P6


title: d4


title: d2


title: d1


title: d0


title: DNMT3B_KO_Late

description: original data source: Meissner Lab in house

data_processing:
BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column

source_name: HUES64 DNMT3A KO

extract_protocol:
not provided
Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011)

value: DNMT3A knockout


title: DKO_Late

value: DNMT3A/3B knockout


title: DNMT3A_KO_derived_CD184


title: DKO_Early


title: DNMT3B_KO_Early

source_name: HUES64 DNMT3B KO

value: DNMT3B knockout


title: DNMT3A_KO_Early


title: DNMT3A_KO_Late


title: LSK.H3K9ac

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.1.0 with the default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using UCSC BedTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing the read densities

organism: Mus musculus

source_name: Murine MLL-AF9 leukemic cells

growth_protocol: Murine MLL-AF9 leukemic cells were cultured in IMDM plus 15% FBS supplemented with 20 ng/ml murine SCF, 10 ng/ml murine IL-3 and 10 ng/ml murine IL-6. Lineage(-)Sca1(+)cKit(+) i.e. LSK cells were sorted from fresh isolated wild-type C57BL/6 mouse bone marrow.

extract_protocol:
Samples were crosslinked by 1% formaldehyde for 10 minutes, and the reaction was stopped by addition of glycine to 125 mM final concentration as previously described (Bernt et al. 2011 Cancer Cell).
ChIP was performed as previously described (Bernt et al. 2011 Cancer Cell).  Briefly, cells samples were crosslinked by 1% formaldehyde for 10 minutes, and the reaction was stopped by addition of glycine to 125 mM final concentration.  The fixed cells were lysed in SDS buffer, and the chromatin was fragmented by sonication.  The sheared chromatin was incubated with the indicated antibodies, and recovered by binding to protein A/G agarose (Millipore).  Eluted DNA fragments were used directly for qPCR or subjected to high-throughput sequencing using Illumina HiSeq 2000 platform.

treatment_protocol: Cells were incubated with EPZ4777 (3uM) or DMSO in standard culture medium for 6 days.

value: Lineage(-)Sca1(+)cKit(+) cells

value: anti-H3K9ac (Abcam; ab4441; Lot:GR171767-1)


title: shSirt1-EPZ4777.H3K79me2

value: MLL-AF9 transformed leukemic cells

tag: treatment

value: shSirt1 RNA interference

tag: agent

tag: time


title: shSirt1-EPZ4777.H3K27me3


title: shSirt1-EPZ4777.H3K9me2


title: shSirt1-EPZ4777.H3K9ac


title: shSirt1-EPZ4777.H3K9me3

value: anti-H3K9me3 (Abcam; ab8898; Lot:GR88132-1)


title: shSirt1-DMSO.H3K9me3

value: DMSO


title: d7


title: shSirt1-DMSO.H3K9me2


title: shSirt1-DMSO.H3K79me2


title: shSirt1-DMSO.H3K27me3


title: DKO_P7


title: shLUC-EPZ4777.H3K9me3

value: shLUC RNA interference


title: shLUC-EPZ4777.H3K9ac


title: shLUC-EPZ4777.H3K9me2


title: shLUC-EPZ4777.H3K79me2


title: shLUC-DMSO.H3K9me2


title: HCC_353N

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

country: China

institute: astrazeneca

data_processing:
Illumina HiSeq Control Software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by illumina HiSeq Analysis Software
Raw fastq data was mapped to human genome(Human.B37) and transcriptome(Gene model:RefGene) by ArrayStudiuo V7.0
Sequenced Fragments Per Kilobase of exon per Million fragments mapped to human genome (FPKM) were calculated using ArrayStudiuo V7.0. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Human NCBI genome build 37 and Gene model:RefGene
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample.

source_name: hepatocyte

extract_protocol:
Total RNA were extracted from the snap-frozen HCC or adjacent normal liver tissues.  25 ug total RNA prepared for sequencing for each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tumor status

value: Adjacent Normal tissue

value: liver


title: shLUC-DMSO.H3K9ac


title: shLUC-DMSO.H3K9me3


title: shLUC-EPZ4777.H3K27me3


title: LSK.H3K9me2


title: shLUC-DMSO.H3K79me2


title: shLUC-DMSO.H3K27me3


title: Sirt1-DMSO


title: ATACseq_shSuv39h1_DMSO

description: ATAC-seq

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.1.0 with the default parameters.
To create density files, the read density was normalized to ten million mapped reads and converted to BigWig using UCSC BedTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing the read densities

growth_protocol: Murine MLL-AF9 leukemic cells were cultured in IMDM plus 15% FBS supplemented with 20 ng/ml murine SCF, 10 ng/ml murine IL-3 and 10 ng/ml murine IL-6.

extract_protocol:
Cell nuclei were fresh prepared from 50,000 cells as previously described (Buenrostro et al. 2013 Nature Methods).
ATAC-seq was performed as previously described (Buenrostro et al. 2013 Nature Methods). For each sample, cell nuclei were prepared from 50,000 cells, and incubated with 2.5 uL transposase (Illumina) in a 50 uL reaction for 30 min at 37°C. Following purification of transposase fragmented DNA, the library was amplified by PCR and subjected to high-throughput sequencing using Illumina HiSeq 2000 platform.

treatment_protocol: Cells were incubated with EPZ4777 (1uM) or DMSO in standard culture medium for 6 days.

value: shSuv39h1 RNA interference


title: shSirt1-DMSO.H3K9ac


title: ATACseq_shSuv39h1_EPZ4777

description: ATAC-seq


title: ATACseq_shSirt1_DMSO

description: ATAC-seq


title: Male zebularine-treated replicate 3

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Rat RGSC3.4.64 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: R. norvegicus (RGSC3.4.64)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Male, Brain (preoptic area), Zebularine

extract_protocol:
RNA was extracted with a standard Trizol protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were treated with Vehicle or Zebularine on PN0 and PN1.  Tissue was collected on PN2.

value: Male

value: Brain - preoptic area


title: Male zebularine-treated replicate 2


title: ATACseq_shLUC_DMSO

description: ATAC-seq


title: ATACseq_shLUC_EPZ4777

description: ATAC-seq


title: Male vehicle replicate 3

source_name: Male, Brain (preoptic area), Vehicle


title: Male zebularine-treated replicate 1


title: Female zebularine-treated replicate 3

source_name: Female, Brain (preoptic area), Zebularine

value: Female


title: Male vehicle replicate 1


title: Male vehicle replicate 2


title: Female vehicle replicate 3

source_name: Female, Brain (preoptic area), Vehicle


title: Female zebularine-treated replicate 1


title: Female zebularine-treated replicate 2


title: Female vehicle replicate 2


title: HEK293 cells IgG control ChIP (2514-WPT-26_1)

city: Nashville

first: Qingguo

last: Wang

state: TN

address: 2525 West End AVE Suite 808

department: Biomedical Informatics

institute: Vanderbilt University

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with the following configurations: m(1), -3(1).
Peaks were called using SPP peak caller version 1.10.1 with the following setting: Npeak(300000), x(-500:85).
An IDR threshold of 0.5% was applied to pooled pseudoreplicates to get final sets of peaks.
Peaks that overlap with the blacklisted genomic regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include peaks called in samples.

source_name: cultured cell line

growth_protocol: HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum, 100 Iu/ml penicillin, and 100 ug/ml streptomycin.

extract_protocol:
After crosslinking and quenching of formaldehyde, lysates were prepared, sonicated to give a mean chromatin length of 200 bp, cleared by centrifugation, and cleared lysates subjected to reaction with antibodies (or IgG control) overnight.
ChIP DNA was converted into an Illumina sequencing library using the NEBNext Ultra DNA Library Prep Kit (for Illumina)

value: HEK293 cells

value: Purified rabbit IgG (Bethyl P120-101)


title: HEK293 cells WDR5 ChIP (2514-WPT-27_1)

value: WDR5 antibody (Bethyl A302-430A)


title: HEK293 cells WDR5 ChIP (2514-WPT-25_1)


title: HEK293 cells IgG control ChIP (2514-WPT-28_1)


title: HEK293 cells WDR5 ChIP (2514-WPT-23_1)


title: Sirt1-EPZ6d


title: HEK293 cells IgG control ChIP (2514-WPT-24_1)


title: ATACseq_shSirt1_EPZ4777

description: ATAC-seq


title: vector control cells FLAG ChIP (2514-WPT-13_1)

value: HEK293 cells, retrovirally transduced

value: M2 agarose (Sigma; F1804)


title: WBM-MYC expressing cells FLAG ChIP (2514-WPT-11_1)


title: WT-MYC expressing cells FLAG ChIP (2514-WPT-10_1)


title: WBM-MYC expressing cells FLAG ChIP (2514-WPT-7_1)


title: WT-MYC expressing cells FLAG ChIP (2514-WPT-6_1)


title: WBM-MYC expressing cells FLAG ChIP (2514-WPT-3_1)


title: vector control cells FLAG ChIP (2514-WPT-5_1)


title: WT-MYC expressing cells FLAG ChIP (2514-WPT-2_1)


title: vector control cells FLAG ChIP (2514-WPT-1_1)


title: Female vehicle replicate 1


title: siSetx-GRO-t4

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: GRO-Seq profile of A549 cells treated with siSetx, 4 hours after infection with Influenza PR8ΔNS1

data_processing:
Following adapter trimming and quality filtering, reads were mapped to the human reference genome (GRCh37, hg19) using bowtie v0.12.9 (see PMID: 19261174). Unique best matches were kept and normalized to a total level of 5 million tags per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in wig format and contain normalized mapped GRO-Seq read coverage

source_name: A549 cells

extract_protocol:
At the stipulated times post infection, transcriptionally active nuclei from infected or untreated A549 cells were prepared after swelling for 5 minutes the cells in ice-cold swelling buffer (10mM Tris (pH = 7.5), 2mM MgCl2, 3mM CaCl2). Pelleted cells were re-suspended in 1ml lysis buffer (10mM Tris (pH = 7.5), 2mM MgCl2, 3mM CaCl2, 10% glycerol, 0.5% NP40, 2U/ml−SUPERaseIN (Ambion) and pipetted 20 times with a P1000 tip with the end cut off to reduce shearing. Volume was brought to 10 ml with lysis buffer and nuclei were pelleted at 600g for 5min. Nuclei were washed in 10ml lysis buffer and re-pelleted. A small aliquot was taken for Trypan blue staining to check that lysis occurred and nuclei were still intact. Nuclei were re-suspended in 1ml freezing buffer (50mM Tris-Cl (pH = 8.3), 40% glycerol, 5mM MgCl2, 0.1mM EDTA) using a P1000 tip with the end cut off and re-pelleted and re-suspended in 500μl of freezing buffer and aliquoted into 100μl aliquots and frozen in liquid nitrogen.
Library preparation was done following a previously published protocol (see PMID: 19056941)

value: siSetx

tag: infection

value: Influenza PR8ΔNS1


title: siSetx-GRO-t0

description: GRO-Seq profile of uninfected A549 cells treated with siSetx

value: uninfected


title: ER71 V5-4 ChIP-Seq Rep2

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

description:
Differentiated ES cells on day 3.5
6. iER71 +DOX -V5-4

data_processing:
Sequencing reads were aligned to mouse mm9 genome with BWA
Redundant reads were discard
Aligned results were further processed by methylQA (http://methylqa.sourceforge.net/) to get bigWig files
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Doxycycline treated iER71, ES cell

growth_protocol: Mouse ES cells were maintained on PMEF cells in DMEM with 15% pre-selected fetal calf serum (FCS), 2% LIF, 1% L-glutamine, 1% NEAA and 4.5x 10–4 M MTG. ES cells were differentiated  in IMDM containing 15% differentiation-screened FCS, 1% L-glutamine, 50  g/ml ascorbic acidand 4.5x 10–4 M MTG.

extract_protocol:
Differentiated ES cells were disassociated into single cells and lysed. Chromatin was crosslinked for 10 min at room temperature with 1% formaldehyde, and then sonicated to ~100-250bp using an AFA Focused-ultrasonicator. After sonication, chromatin was immunoprecipitated with V5 or ER71 antibodies at 4C overnight. The reversed ChIP DNA was purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen), and then quantified with Qubit.
ChIP DNA was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs, and underwent amplification for 15 cycles.

treatment_protocol: Doxycycline (1ug/ml) was added in iER71+DOX group from day 2 to 3.5

tag: antibody

tag: differentiation time

value: Day 3.5

tag: tissue

value: embryonic stem cell


title: ER71 pAb-1 ChIP-Seq Rep1

description:
Differentiated ES cells on day 3.5
2. iER71 +DOX -4074-1


title: ER71 IgG Input

description:
Differentiated ES cells on day 3.5
4. iER71 +DOX -IgG

value: IgG


title: ER71 pAb-2 ChIP-Seq Rep2

description:
Differentiated ES cells on day 3.5
3. iER71 +DOX -4074-2


title: siCtrl-GRO-t4

description: GRO-Seq profile of A549 cells treated with control siRNAs, 4 hours after infection with Influenza PR8ΔNS1

value: control siRNAs


title: ER71 pAb-0 ChIP-Seq

description:
Differentiated ES cells on day 3.5
1. iER71 –DOX -4074

source_name: No doxycycline treated iER71, ES cell


title: siCtrl-GRO-t0

description: GRO-Seq profile of uninfected A549 cells treated with control siRNAs


title: dcl3-

status: Public on Mar 28 2015

city: Vienna

first: Manu

last: Dubin

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute, Austrian Academy of Sciences

data_processing:
Casava version 1.7 was used for base-calling
Reads were aligned to the TAIR10 reference genome using NexGenMap version 0.4.3 with the following settings -p -i 0.90 -R 45 --bs-mapping --silent-clip
Methylation and coverage  levels at each cytosine was generated using the methratio.py script from the BSMAP (version 2.73) using the -z and -u flags
Genome_build: TAIR10
Supplementary_files_format_and_content: A TSV (tab separated values) detailing the methylation and coverage levels at each cytosine

organism: Arabidopsis thaliana

source_name: whole rosette_dcl3

growth_protocol: Plants were grown at 20C under long day conditions until the 9 (true) leaf stage

extract_protocol:
DNA was extracted using the NucleoMag 96 Plant kit (Macherey-Nagel)
Libraries were prepared according to Lister et al., 2008 (Cell) with the following modifications:
Bisulfite conversion was preformed using Qiagen epitech kit
PCR amplification was done using KAPA HIFI Uracil plus polymerase together with bar-coded primers (Illumina Tru-seq barcodes 4, 10, 38 and 39) to allow muiltiplexing

treatment_protocol: Rosettes were snap frozen in liquid nitrogen and stored at -80 C

value: Dicer-like-3-5 knockout

tag: genetic backround

value: Columbia 0

tag: line


title: WT

source_name: whole rosette_WT

value: Wild type


title: clone PR107

status: Public on Mar 29 2015

city: Danzhou

first: Jinquan

last: Chao

address: Baodao Xincun

department: Rubber Research Institute

description: Three years old tree and no tapping before

data_processing:
Filter Dirty Raw Reads: Raw reads that only have 3' adaptor fragments should be removed before data analysis
Clean Reads:Reads after filtering dirty raw reads, on which all following analysis are based
Assembly:Transcriptome de novo assembly is carried out with short reads assembling program - SOAPdenovo (Li, Zhu et al. 2009). SOAPdenovo firstly combines reads with certain length of overlap to form longer fragments without N, which are called contigs. Then the reads are mapped back to contigs; with paired-end reads it is able to detect contigs from the same transcript as well as the distances between these contigs. Next, SOAPdenovo connects the contigs using N to represent unknown sequences between each two contigs, and then Scaffolds are made. Paired-end reads are used again for gap filling of scaffolds to get sequences with least Ns and cannot be extended on either end. Such sequences are defined as Unigenes. When multiple samples from a same species are sequenced, Unigenes from each sample's assembly can be taken into further process of sequence splicing and redundancy removing with sequence clustering software to acquire non-redundant Unigenes as long as possible. In the final step, blastx alignment (evalue < 0.00001) between Unigenes and protein databases like nr, Swiss-Prot, KEGG and COG is performed, and the best aligning results are used to decide sequence direction of Unigenes. If results of different databases conflict with each other, a priority order of nr, Swiss-Prot, KEGG and COG should be followed when deciding sequence direction of Unigenes. When a Unigene happens to be unaligned to non of the above databases, a software named ESTScan (Iseli, Jongeneel et al. 1999) will be introduced to predict its coding regions as well as to decide its sequence direction. For Unigenes with sequence directions, we provide their sequences from 5' end to 3' end; for those without any direction we provide their sequences from assembly software.
Genome_build: mm9
Supplementary_files_format_and_content: difference expression unigenes between two clones, with excel format

organism: Hevea brasiliensis

source_name: latex

growth_protocol: Both H. brasiliensis clones RY8-79 and PR107 grown at the Experimental Station of theRubber Research Institute of the Chinese Academy of Tropical Agricultural Sciences

extract_protocol:
Total RNA were isolated latex and leaf according to previously described (Tang et al., 2007). RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies). Beads with Oligo(dT) were used to isolate poly(A) mRNA after total RNA (QIAGEN GmbH, Hilden, Germany). Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature.
Taking these short fragments as templates, the first-strand cDNA was synthesized by using random hexamer-primer and Superscrip (Invitrogen California, USA). The second-strand cDNA was synthesized using buffer, dNTPs, RNaseH and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit (QIAGEN GmbH, Hilden, Germany) and resolved with EB buffer for end reparation and adding poly(A). Then the short fragments were connected with sequencing adapters. After agarose gel electrophoresis, the suitable fragment was selected for the PCR amplification as templates.

treatment_protocol: untreatment

tag: clone

tag: age

value: 3 years old


title: cmt2-_replicate

source_name: whole rosette_cmt2

value: Chromo-methyltransferase-2 knockout


title: methylC-seq F2__111

data_processing:
Casava version 1.7 was used for base-calling
Reads were aligned to the TAIR10 reference genome using using NexGenMap version 0.4.3 with the following settings: -p -i 0.90 -R 45 --bs-mapping --silent-clip
Methylation was called using BisSNP-0.82.2 with the following options -T BisulfiteGenotyper  -out_modes EMIT_VARIANT_AND_CYTOSINES  -stand_call_conf 8 -stand_emit_conf 0 -mmq 30 -mbq 0 -C CG,1 -C CHG,1 -C CHH,1
Genome_build: TAIR10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: CSV file detailing the methylation levels and coverage at each cytosine was generated using the the Bisulfite Genotyper module from BisSNP version 0.82.2

source_name: whole rossete

extract_protocol:
DNA was extracted using the NucleoMag 96 Plant kit (Macherey-Nagel)
Libraries were prepared according to Lister et al., 2008 (Cell) with the following modifications:
Bisulfite conversion was preformed using Qiagen epitech kit
PCR amplification was done using KAPA HIFI Uracil plus polymerase together with bar-coded primers (Illumina Tru-seq barcodes 1-48) to allow muiltiplexing

tag: parent 1

tag: parent 2


title: cmt2-


title: methylC-seq F2__108


title: methylC-seq F2__109


title: clone RY8-79

institute: Chinese Academy of Tropical Agricultural Sciences


title: methylC-seq F2__106


title: methylC-seq F2__110


title: methylC-seq F2__112


title: methylC-seq F2__113


title: methylC-seq F2__107


title: ER71 V5-1 ChIP-Seq Rep1

description:
Differentiated ES cells on day 3.5
5. iER71 +DOX -V5-1


title: methylC-seq F2__101


title: methylC-seq F2__100


title: methylC-seq F2__99


title: methylC-seq F2__98


title: methylC-seq F2__104


title: methylC-seq F2__103


title: methylC-seq F2__97


title: methylC-seq F2__96


title: methylC-seq F2__95


title: methylC-seq F2__93


title: methylC-seq F2__92


title: methylC-seq F2__94


title: methylC-seq F2__91


title: methylC-seq F2__87


title: methylC-seq F2__90


title: methylC-seq F2__89


title: methylC-seq F2__84


title: methylC-seq F2__88


title: methylC-seq F2__82


title: methylC-seq F2__80


title: methylC-seq F2__81


title: methylC-seq F2__105


title: methylC-seq F2__83


title: methylC-seq F2__79


title: methylC-seq F2__85


title: methylC-seq F2__78


title: methylC-seq F2__77


title: methylC-seq F2__76


title: methylC-seq F2__102


title: methylC-seq F2__75


title: methylC-seq F2__74


title: methylC-seq F2__73


title: methylC-seq F2__70


title: methylC-seq F2__72


title: methylC-seq F2__68


title: methylC-seq F2__67


title: methylC-seq F2__66


title: methylC-seq F2__65


title: methylC-seq F2__86


title: methylC-seq F2__64


title: methylC-seq F2__63


title: methylC-seq F2__62


title: methylC-seq F2__61


title: methylC-seq F2__60


title: methylC-seq F2__59


title: methylC-seq F2__55


title: methylC-seq F2__54


title: methylC-seq F2__58


title: methylC-seq F2__53


title: methylC-seq F2__51


title: methylC-seq F2__52


title: methylC-seq F2__50


title: methylC-seq F2__56


title: methylC-seq F2__47


title: methylC-seq F2__71


title: methylC-seq F2__48


title: methylC-seq F2__45


title: methylC-seq F2__43


title: methylC-seq F2__41


title: methylC-seq F2__44


title: methylC-seq F2__42


title: methylC-seq F2__69


title: methylC-seq F2__46


title: methylC-seq F2__40


title: methylC-seq F2__35


title: methylC-seq F2__34


title: methylC-seq F2__37


title: methylC-seq F2__49


title: methylC-seq F2__39


title: methylC-seq F2__36


title: methylC-seq F2__33


title: methylC-seq F2__57


title: methylC-seq F2__31


title: methylC-seq F2__28


title: methylC-seq F2__29


title: methylC-seq F2__25


title: methylC-seq F2__26


title: methylC-seq F2__24


title: methylC-seq F2__23


title: methylC-seq F2__22


title: methylC-seq F2__21


title: methylC-seq F2__27


title: methylC-seq F2__20


title: methylC-seq F2__38


title: methylC-seq F2__18


title: methylC-seq F2__13


title: methylC-seq F2__14


title: methylC-seq F2__15


title: methylC-seq F2__17


title: methylC-seq F2__32


title: methylC-seq F2__10


title: methylC-seq F2__9


title: methylC-seq F2__11


title: methylC-seq F2__30


title: methylC-seq F2__8


title: methylC-seq F2__5


title: methylC-seq F2__6


title: methylC-seq F2__7


title: methylC-seq F2__12


title: methylC-seq F2__4


title: methylC-seq F2__3


title: methylC-seq F2__1


title: methylC-seq F2__2


title: methylC-seq F2__16


title: 9470_16C

data_processing:
base calling and de-muiltiplexing done under contract by Beijing Genomics Institute
Reads were aligned to the pseudo-reference genome (TAIR10 with the SNPs from the relevent accession) using using NexGenMap version 0.4.3 with the following settings -p -i 0.90 -R 45 --bs-mapping --silent-clip
Genome_build: TAIR10 (incorporating relevant SNV's)
Supplementary_files_format_and_content: A TSV (tab separated values) detailing the methylation levels at each cytosine was generated using the methratio.py script from the BSMAP (version 2.73) using the -z  and -u flags

source_name: aerial seedling

growth_protocol: Accessions were sown on soil and stratified for 3 days at 4 C in the dark. They were then transferred to environmentally controlled growth chambers set at 10C or 16C under long day conditions (04:00-20:00) and individual seedlings were transplanted to single pots after one week. When plants attained the 9-true -leaf stage of development, whole rosettes were collected between 15:00 and 16:00 hours and flash frozen in liquid nitrogen.

extract_protocol:
For each sample two individual plants were pooled and total DNA was extracted using CTAB and phenol-chloroform
Approximately two micrograms of genomic DNA was sent for BS-seq library construction and sequencing (preformed under contract by Beijing Genomics Institute)

tag: accession number

tag: accession name

tag: growth temperature

value: whole rosette

tag: developmental stage

value: 9-true -leaf stage


title: 9481_16C


title: 992_16C


title: 992_10C


title: 991_16C


title: 991_10C


title: 9470_10C


title: 9454_16C

value: Ste 3


title: 9454_10C


title: 9437_10C


title: 9452_16C

value: Spro 3


title: 9434_16C

value: Öde 2


title: 9434_10C


title: 9436_10C


title: 9413_10C

value: Kor 4


title: 9427_10C

value: Näs 2


title: 9416_16C


title: 9427_16C


title: 9416_16C_rep


title: methylC-seq F2__19


title: 9413_16C


title: 9412_10C

value: Kor 3


title: 9416_10C


title: 9395_10C


title: 9399_16C


title: 9394_10C


title: 9402_10C


title: 9383_10C

value: Fri 3


title: 9452_10C


title: 9395_16C


title: 9391_10C


title: 9383_16C


title: 9390_10C


title: 9371_16C

value: FäL 1


title: 9380_16C

value: FlyA 3


title: 9382_16C

value: Fri 2


title: 9381_10C

value: Fri 1


title: 9381_16C


title: 9371_10C


title: 9369_10C

value: EkS 2


title: 9399_10C


title: 9356_10C

value: Eden 17


title: 9369_16C


title: 9356_16C


title: 9352_10C

value: Död 2


title: 9353_10C

value: Död 3


title: 9343_16C

value: Dja 1

value: whole rosette


title: 9339_10C_rep

value: Böt 1

value: 9-true -leaf stage


title: 9339_16C


title: 9336_16C

value: Bön 1


title: 9336_10C


title: 9323_16C

value: Ådal 3


title: 9323_16C_rep


title: 9323_10C


title: 9332_16C

value: Bar 1


title: 8426_16C


title: 8426_10C


title: 9058_10C

value: Västervik


title: 9057_16C

value: Vinslöv


title: 9057_10C


title: 9058_16C


title: 8423_10C


title: 9363_16C

value: EdJ 2


title: 9363_10C


title: 8422_10C


title: 8422_16C_rep


title: 8387_16C


title: 9343_10C


title: 8387_10C_rep


title: 8387_10C


title: 8369_16C


title: 8376_16C


title: 8376_10C


title: 8369_10C


title: 9339_10C


title: 8351_16C


title: 9332_10C


title: 8351_10C


title: 8335_10C

value: Lund


title: 8334_10C


title: 8335_16C


title: 8326_10C


title: 8307_16C


title: 8283_10C


title: 8257_16C


title: 8257_10C


title: 8256_16C


title: 8258_16C


title: 8249_16C

value: Vimmerby


title: 8249_10C


title: 8256_10C


title: 8241_16C

value: Liarum


title: 8242_16C


title: 8241_10C


title: 8242_10C


title: 8240_16C


title: 9382_10C

value: Fri 2


title: 8237_10C_rep


title: 8237_16C


title: 8237_10C


title: 8234_16C


title: 8234_10C


title: 8230_10C

value: Algutsrum


title: 8227_16C

value: THÖ 03


title: 8307_10C


title: 8306_10C


title: 8227_10C


title: 7516_10C


title: 8222_10C


title: 7519_10C


title: 8222_16C


title: 7519_16C


title: 6918_16C


title: 6913_10C


title: 6909_16C


title: 6909_16C_rep


title: 6973_16C


title: 6973_10C


title: 6276_10C


title: 6252_16C


title: 6909_10C


title: 6913_16C


title: 8240_10C


title: 6413_10C


title: 6413_16C


title: 6237_16C

value: TOM 03


title: 6235_10C

value: TOM 01


title: 6276_16C

value: whole rosette


title: 6242_10C


title: 6258_10C


title: 6238_10C

value: TOM 04


title: 6242_16C

value: 9-true -leaf stage


title: 6243_10C


title: 6231_10C

value: TNY 04


title: 6252_10C


title: 6237_10C


title: 6231_16C


title: 6209_16C

value: TEDEN 02


title: 6209_10C


title: 6216_16C

value: TFÄ 06


title: 6221_16C

value: TGR 02


title: 6244_10C

value: TRÄ 01


title: 6210_10C

value: TEDEN 03


title: 6221_10C


title: 6216_10C


title: 6244_16C


title: 6202_16C


title: 6235_16C


title: 6197_16C


title: 6189_10C


title: 6193_10C


title: 6192_16C


title: 6189_16C


title: 6191_10C


title: 6188_16C


title: 6193_16C


title: 6180_16C

value: TÄL 07


title: 6188_10C_rep


title: 6192_10C


title: 6180_10C


title: 6184_10C

value: TBÖ 01


title: 6173_16C

value: TÅD 05


title: 6188_10C


title: 6172_10C

value: TÅD 04


title: 6173_10C


title: 6172_16C_rep


title: 6150_16C


title: 6151_10C


title: 6172_16C


title: 6202_10C


title: 6150_10C_rep


title: 6153_16C

value: TAA 03


title: 6197_10C


title: 6153_10C


title: 6151_16C


title: 6149_16C


title: 6149_10C


title: 6142_16C


title: 6150_10C


title: 6134_16C


title: 6131_16C


title: 6132_10C


title: 6128_10C


title: 6126_16C


title: 6129_10C


title: 6136_16C


title: 6134_10C


title: 6136_10C


title: 6129_16C


title: 6127_10C


title: 6126_10C


title: 6122_10C


title: 6118_10C


title: 6125_10C


title: 6122_16C


title: 6124_10C


title: 6118_16C


title: 6115_10C


title: 6114_10C


title: 6114_16C


title: 6112_10C


title: 6113_10C


title: 6112_16C


title: 6105_16C


title: 6131_10C


title: 6109_16C


title: 6109_10C


title: 6104_16C


title: 6102_16C


title: 6104_10C


title: 6105_10C


title: 6100_16C


title: 6102_10C


title: 6098_10C


title: 6124_16C


title: 6098_16C


title: 6094_10C


title: 6092_10C


title: 6100_10C


title: 6090_16C


title: 6090_10C


title: 6088_16C_rep


title: 6074_16C


title: 6076_16C


title: 6088_16C


title: 6085_10C


title: 6076_10C


title: 6071_10C


title: 6071_16C


title: 6070_16C


title: 6069_10C


title: 6046_16C


title: 6043_16C_rep


title: 6046_10C


title: 6043_16C


title: 6092_16C


title: CgxCr rep2

city: Uppsala

first: Clement

last: Lafon-Placette

address: Almas Allé 5

country: Sweden

institute: SLU

data_processing:
excess index clean up: fastq-mcf -L 100 -l 25
additional adapter cleanup: trimmomatic PE ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Sequencing reads were aligned to the C. rubella genome v1.0 (Phytozome) using Stampy v1.0.23: stampy.py -M
Removal of multiple mapped location reads; samtools view -bSq 4
Number of reads for each annotated gene were counted using default option in htseq-count command from HTSeq Python package: python -m HTSeq.scripts.count
Genome_build: C. rubella genome v1.0
Supplementary_files_format_and_content: raw read count

organism: Capsella grandiflora x Capsella rubella

source_name: Capsella grandiflora x Capsella rubella hybrid seed

growth_protocol: All seeds were surface sterilized using 5 % Sodium Hypochloride solution under the fume hood. After sterilization seeds were plated on MS media containing 1% sucrose. After stratification for two days in the dark at 4°C seedlings were grown in a growth room under long-day photoperiod (16 hrs light and 8 hrs darkness) at 22°C light and 20°C darkness temperature and a light intensity of 110 µE. All seedlings were transferred to pots and plants were grown in a growth chamber at 60 % humidity and daily cycles of 16 hrs light at 21°C and 8hrs darkness at 18°C. ts were grown in a growth cabinet under long day photoperiods (16 h light and 8 h dark) at 22°C. After 10 days, seedlings were transferred to soil and plants were grown in a growth chamber at 60% humidity and daily cycles of 16 h light at 22°C and 8 h darkness at 18°C.

extract_protocol:
Two biological replicates with 300-500 seeds per replicate were generated. Seeds were harvested at 6 DAP and stored at -20oC in RNAlater® (Sigma-Aldrich, St Louis, USA). RNA extraction was done using RNAqueous® Kit with Plant RNA Isolation Aid (Life Technologies, Carlsbad, USA).
The RNA-sequencing libraries were prepared using TruSeq® RNA Sample Preparation Kit v2 (Illumina, San Diego, USA) according to the manufacturer's instructions.

treatment_protocol: For all crosses, designated female partners were emasculated, and the pistils were hand-pollinated 2 days after emasculation (same procedure for selfing and outcrossing plants).

value: seed

value: 6 DAP


title: 6043_10C


title: CrxCg rep1

source_name: Capsella rubella x Capsella grandiflora hybrid seed


title: 6042_10C


title: 6040_10C


title: CgxCr rep1


title: 6042_16C


title: 6036_10C


title: 6039_10C


title: 6034_16C


title: 6085_16C


title: CrxCg rep2


title: 6074_10C


title: 6030_16C


title: 6034_10C


title: 6030_10C


title: 6023_10C


title: 6070_10C


title: 6013_10C


title: 6021_10C


title: 6016_10C


title: 6012_10C


title: 6012_16C


title: 5867_16C


title: 6040_16C


title: 5856_16C


title: 5865_10C


title: 5856_10C


title: 5867_10C


title: 6036_16C


title: 5829_16C


title: 5829_10C


title: 1585_10C


title: 1552_16C


title: 5832_10C


title: 5832_16C


title: 1552_10C


title: 1367_10C


title: 1367_16C


title: 1318_16C


title: 1363_10C


title: 1062_16C


title: 1137_16C


title: 1063_10C


title: 1254_10C


title: 6011_10C


title: CrxCr rep2

organism: Capsella rubella

source_name: Capsella rubella seed


title: 1137_10C


title: CrxCr rep1


title: 1062_10C


title: 5835_16C


title: 1061_16C


title: 1061_10C


title: CgxCg rep1

organism: Capsella grandiflora

source_name: Capsella grandiflora seed


title: 1552_16C_rep


title: MCF7_Pol2_N20_ChIP_B

status: Public on Mar 27 2015

city: Grand Forks

first: Tim

last: Casselli

state: ND

address: UND School of Medicine & HS 1301 N Columbia Road Stop 9037

department: Basic Sciences

institute: University of North Dakota

data_processing:
All basecalls performed on Illumina MiSeq using CASAVA v. 1.8
ChIP-seq paired end files (75nt reads) were aligned using bowtie v. 1.0.1 with two allowable mismatches.  Reads with non-unique matches and read pairs with the distance exceeding 700 nt between the R1 and R2 matching coordinates were discarded.
scRNA paired end files (50nt reads) were aligned using bowtie v. 1.0.1 using a 26nt seed length after 24nt trimming from the 3' end of each read, with two allowable mismatches.
ChIP bedgraph files were made by returning the center point positions for each mapped read pair.  Individual replicates were normalized based on the number of uniquely mapped reads in each sample and combined into a single bedgraph file.;  scRNA bedgraph files were generated, separately for each strand, by returning a position of the first nucleotide of R1 reads, which were designated as RNA 5-ends, and of the first nucleotide of R2 reads, which were designated as RNA 3’-ends. Bedgraph files were generated separately from R1 and R2 files.
Genome_build: hg19
Supplementary_files_format_and_content: All processed files are in Bedgraph format. For ChIP-sequencing samples, the bedgraph files contain coordinates of centers of paired end reads, binned in 25-nt intervals, followed by the number of sequencing reads mapping within each bin. MCF7_N20_ChIP_merged_normd.bedgraph file was made by normalizing both individual ChIP bedgraph files after normalization to the number of mappable reads. For scRNA samples, bedgraph files coordinates of the first base of each read: for R1, files, the coordinates represent 5'-ends of RNAs, and for R2 file, the coordinates represent 3'-ends of RNAs. scRNA files are not binned (bin size = 1). For each scRNA replicate, four bedgrapg files are generated: R1_fwd, R1_rev (representing 5'-ends of scRNAs mapping to plus and minus strands, respectively), and R2_fwd and R2_rev (representing 3'-ends of scRNAs mapping to plus and minus strand, respectively). MCF7_scRNA_Rep1and2_merge_norm files were generated by merging individual replicates 1 and 2 after normalization by the number of uniquely mappable reads.

source_name: MCF-7 culture cells

growth_protocol: Cells were grown in DMEM/12 media containing 10% FBS at 37C in 5% CO2 atmosphere

extract_protocol:
Cells were cross-linked with formaldehyde. Chromatin was sheared using Covaris S220 sonicator and immunoprecipitated on magnetic beads containing the antibody. Crosslinks were reversed by heating at 56'C overnight. The precipitated DNA was purified from protein by proteinase K and phenol/chloroform treatments, and used for preparation of a library using Illumina ChIP-seq library preparation kit
All material was extracted from untreated MCF-7 cells
Illumina TruSeq small RNA or ChIP-seq library preparation kits were used to prepare libraries

treatment_protocol: Cells were grown in steady state conditions (not treated) and were collected at +80% confluency

tag: cell line

tag: passages

value: Untreated cells grown in DMEM/F-12  medium +10% FBS

tag: chip antibody

value: N-20, Santa Cruz, sc-899 X

tag: molecule

value: chromatin


title: MCF7_Pol2_N20_ChIP_A


title: MCF7_scRNA_1

extract_protocol:
Total RNA was extracted from nuclei using Trizol reagent. Short RNA (25-70nt size range) was selected using 15% urea-TBE PAGE. Capped RNA was selected using sequential enzymatic treatments using 5'-polyphosphatase, 5'-terminator exonuclease, alkaline phosphatase, and tobacco acid pyrophosphatase. Library was subsequently constructed using Illumina TruSeq SmallRNA kit
All material was extracted from untreated MCF-7 cells
Illumina TruSeq small RNA or ChIP-seq library preparation kits were used to prepare libraries

value: short capped RNA from nuclei


title: 1257_16C

value: whole rosette

value: 9-true -leaf stage


title: Fetal_2nd_2

city: Mainz

first: David

last: Rosenkranz

address: Anselm-Franz-von-Bentzel-Weg 7

department: Institute of Anthropology

country: Germany

institute: Johannes Gutenberg-University Mainz

description:
TRIzol followed my miRVana (Ambion).
Total RNA enriched for molecules <200 nt.
Small RNA-Seq, strand-specific.

data_processing:
Adapter sequences were clipped and the datasets were collapsed to non-identical cloning products (cliplinker_random.pl).
Sequences ranging from 18 to 34 nt were mapped to ncRNA datasets with SeqMap (version: 1.0.12).
Low complexity sequences were removed from the datasets (kill_simples.pl, default settings).
Sequences without annotation were mapped to the genome with piRmapper_1.0.pl (default settings).
Genome_build: Bos taurus: Bos_taurus_UMD_3.1, GenBank assembly accession GCA_000003055.3
Genome_build: Macaca fascicularis: Macaca_fascicularis_5.0, GenBank assembly accession GCA_000364345.1
Genome_build: Homo sapiens: GRCh38, GenBank assembly accession GCA_000001405.15
Supplementary_files_format_and_content: FASTA, sequence headers refer to read counts.

source_name: ovary from 2nd trimester embryos

extract_protocol:
RNA was extracted using TRIzol (Ambion) according to manufacturer’s instruction. NaIO4 treatment was performed on RNA enriched for small RNA (mirVana, Ambion). For oxidation, RNA was exposed to 200mM NaIO4 in borate buffer (29.6mM borax, 29.6mM boric acid, pH6.8) for 10’/RT, then the reaction was stopped by the addition of glycerol. After precipitation with isopropanol and a 75% ethanol wash, libraries were prepared.
Library preparation was based on the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) with modifications. The 3’ and 5' adapters contained 4 random bases at the 5’- and 3’-end, respectively, and were chemically synthesized by BioScientific.

treatment_protocol: Oocytes, embryos and adult tissue were collected and stored at -80 until RNA extraction was performed.

tag: cell type

value: multiple

tag: oxidation


title: MCF7_scRNA_3


title: MCF7_scRNA_2


title: Fetal_2nd_1


title: Fetal_2nd_2_oxidized


title: Fetal_1st_1_oxidized

source_name: ovary from 1st trimester embryos


title: Fetal_1st_2_oxidized


title: Fetal_1st_1


title: Human_ovary_2_oxidized

source_name: adult ovary


title: Fetal_1st_2


title: Human_ovary_1


title: Human_ovary_1_oxidized


title: Bovine_cumulus_GV_b

description:
TRIzol followed my miRVana (Ambion)
total RNA enriched for molecules <200 nt
Small RNA-Seq, strand-specific

data_processing:
Adapter sequences were clipped and the datasets were collapsed to non-identical cloning products (cliplinker_random.pl)
Sequences ranging from 18 to 34 nt were mapped to ncRNA datasets with SeqMap (version: 1.0.12)
Low complexity sequences were removed from the datasets (kill_simples.pl, default settings)
Sequences without annotation were mapped to the genome with piRmapper_1.0.pl (default settings)
Genome_build: Bos taurus: Bos_taurus_UMD_3.1, GenBank assembly accession GCA_000003055.3
Genome_build: Macaca fascicularis: Macaca_fascicularis_5.0, GenBank assembly accession GCA_000364345.1
Genome_build: Homo sapiens: GRCh38, GenBank assembly accession GCA_000001405.15
Supplementary_files_format_and_content: FASTA, sequence headers refer to read counts

organism: Bos taurus

source_name: cumulus cells from GV oocytes

extract_protocol:
RNA was extracted using TRIzol (Ambion) according to manufacturer’s instruction. NaIO4 treatment was performed on RNA enriched for small RNA (mirVana, Ambion). For oxidation, RNA was exposed to 200mM NaIO4 in borate buffer (29.6mM borax, 29.6mM boric acid, pH6.8) for 10’/RT, then the reaction was stopped by the addition of glycerol. After precipitation with isopropanol and a 75% ethanol wash, libraries were prepared.
Library preparation was based on the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) with modifications. The 3’ and 5' adapters contained 4 random bases at the 5’- and 3’-end, respectively, and were chemically synthesized by BiooScientific.

treatment_protocol: oocytes, embryos and adult tissue were collected and stored at -80 until RNA extraction was performed.

value: cumulus cells


title: Bovine_cumulus_GV_a


title: Human_ovary_2


title: Bovine_IVF_1

source_name: IVF embryos in 2-4 cell stage

value: 2-4 cell stage embryonic cells


title: CgxCg rep2

tag: tissue


title: Bovine_oxidized_2_repeat


title: Bovine_IVF_2


title: Bovine_cumulus_MII_1

source_name: cumulus cells from MII oocytes


title: Bovine_cumulus_MI_2

source_name: cumulus cells from MI oocytes


title: Bovine_cumulus_MI_1


title: Bovine_testis_2

source_name: adult testis


title: Bovine_testis_1


title: Fetal_2nd_1_oxidized


title: Bovine_MII_b2

source_name: oocytes at MII stage

value: oocytes


title: Bovine_oxidized_2


title: Bovine_ovary_1


title: Bovine_MII_a2


title: Bovine_oxidized_1


title: Bovine_MII_b1


title: Macaque_testis_1

organism: Macaca fascicularis


title: Bovine_MI_2

source_name: oocytes at MI stage


title: Bovine_MI_1


title: Bovine_GV_b1

source_name: oocytes at GV stage


title: Macaque_oxidized_2


title: Macaque_testis_2


title: Bovine_GV_a


title: Bovine_cumulus_MII_2


title: Bovine_ovary_2


title: Macaque_oxidized_1


title: Macaque_ovary_2


title: Macaque_ovary_1


title: PATZ1-/- MEF rep3

city: Istanbul

first: Batu

last: Erman

address: Orhanli, Tuzla

department: Biological Sciences and Bioengineering Program

country: Turkey

institute: Sabanci University

description: polyA enriched from total RNA

data_processing:
Reads were mapped to the 2012 release of the Mus musculus genome (GRCm38.p2) using Genepattern software (version 3.8.1) and the Bowtie aligner (Bowtie2 version 2.1.0)
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using the RNASeQC module (version 2) in GenePattern.
Read counts were analyzed using the R environment (R 3.0.2) and the DESeq package (version 1.18.0) according to the suggestions in DEseq’s vignette.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: Mouse embryo fibroblasts

growth_protocol: MEF were cultured in DMEM, 10% heat inactivated Fetal Bovine Serum, 100U/ml Penicillin and 100ug/ml Streptomycin, cultured at 37oC with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol (LifeTech 15596018)
RNA libraries were prepared for sequencing using standard protocols following the Illumina TruSeq_RNA_SamplePrep_Guide. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000

value: MEF

tag: genotype

value: PATZ -/-

tag: strain

value: 129Sv and C57Bl/6 mixed background

tag: passage

value: passage three


title: PATZ1-/- MEF rep1

description: polyA enriched from total RNA

tag: age


title: WT MEF rep3

description: polyA enriched from total RNA

value: wild type


title: WT MEF rep1

description: polyA enriched from total RNA


title: WT MEF rep2

description: polyA enriched from total RNA


title: Bovine_MII_a1


title: NoDf_F_w+/w1118_rep_2 [Sample_640002]

status: Public on Mar 26 2015

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
Processed data files:
cufflinks_fpkm_gene_ERCC_249.txt
DESeq2_normalized_read_counts_gene_249.txt
HTSeq_raw_read_counts_gene_ERCC_249.txt
cufflinks_fpkm_gene_235.txt
DESeq2_normalized_read_counts_gene_235.txt
HTSeq_raw_read_counts_gene_ERCC_235.txt

data_processing:
Basecalls were performed using CASAVA-1.8.2/RTA 1.17.21.3/HiSeq Control Software 2.0.10.0 on an Illumina HiSeq 2000 (Illumina Inc., San Diego, CA).
We mapped RNA reads to D. melanogaster genome (release 5, from the FlyBase, excluding “U” or “Uextra”), along with the 96 ERCC spike-in sequences (Zook et al. Plos ONE 2012, 7(7): e41356), with Tophat (v2.0.10) (Kim et al. Genome Biology 2013, 14:R36). We used parameter -g 1 to retain only uniquely mapped reads and provided a GTF format annotation with the -G option. The GTF format annotation includes the annotation for genes on existing chromosomes (derived from FlyBase annotation release 5.57 in GFF format, excluding genes on “U” or “Uextra”), as well as the annotation for 96 exogenous controls.
We measured gene expression levels using cufflinks v2.1.1 (Trapnell et al. Nature Protocols 2012, 7(3):562-78) in Fragments Per Kilobase of transcript per Million mapped reads (FPKM). We also measured the gene expression level in normalized read counts using HT-Seq v0.5.4p1 (Anders et al. Bioinformatics 2015, 31(2):166-9) and R package DESeq2 v1.6.3 (Love et al. Genome Biology 2014, 15(12):550).
There are two sets of processed data. One includes all 249 samples. The other was filtered in two steps (see "flag” for each sample) to make sure every DrosDel deficiency (Df) had at least two reliable replicates in each karyotype/sex combination. First, we checked to see if genes within the reported DrosDel deficiencies (Dfs) had reduced expression, and removed samples without expression reduction at the Dfs; 2) We removed samples without replicates in any one of the three karyotype/sex combinations (XX female, XX female transformed to male and XY male). The remaining 235 samples include 113 samples with 19 Dfs on the X chromosome, 99 samples with 11 Dfs on the autosome 3L, and 23 controls without Dfs.
Genome_build: Drosophila melanogaster Release 5
Supplementary_files_format_and_content: DESeq2_normalized_read_counts_gene_235.txt contains a matrix with read counts of all the genes normalized by DESeq2 for the 235 samples that have replicates and validated deletions. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: DESeq2_normalized_read_counts_gene_249.txt contains a matrix with read counts of all the genes normalized by DESeq2 for all the 249 samples. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: HTSeq_raw_read_counts_gene_ERCC_235.txt contains matrix with raw read counts of all the genes and spike-ins for the 235 samples that have replicates and validated deletions. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID and ERCC ID.
Supplementary_files_format_and_content: HTSeq_raw_read_counts_gene_ERCC_249.txt contains matrix with raw read counts of all the genes and spike-ins for all the 249 samples. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID and ERCC ID.
Supplementary_files_format_and_content: cufflinks_fpkm_gene_235.txt contains matrix with FPKM values of all the genes in the 235 samples that have replicates and validated deletions. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: cufflinks_fpkm_gene_ERCC_249.txt contains matrix with FPKM values of all the genes and spike-ins in all the 249 samples. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID and ERCC ID.

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Flies were grown at 25°C on cornmeal media Fly Food A (LabExpress, Ann Arbor, MI). Adults were aged 5 days before dissection.

extract_protocol:
We used RNeasy 96 Kit (Qiagen, Valencia, CA) to extract total RNA from a pool of 10 dissected heads for each sample. Frozen heads were added to 2ml Axygen 96-well plates (Corning, Life Sciences, Union City, CA) pre-loaded with 200 µL 1mm glass beads (Biospec Products, Inc., Bartlesville, OK) and 200 µL RLT Buffer (Qiagen, Valencia, CA). After covering the plates with Axygen sealing mats, we homogenized the samples with Mini-BeadBeater-96 (Biospec Products Inc., Bartlesville, OK). Manual purification was carried out using QIAvac 96 vacuum manifold (Qiagen, Valencia, CA).
We followed TruSeq RNA Sample Preparation V2 high-throughput protocol (Illumina Inc., San Diego, CA) to construct RNA-seq libraries from polyA+ RNA. For each sample, 100ng of total RNA was used as input in the initial step and 10pg ERCC spike-in RNA (Zook et al. Plos ONE 2012, 7(7): e41356., pool 78A) was added to the Elute, Prime, Fragment Mix in the "Purify and fragment mRNA” step.

tag: drosdel deficiency

value: NoDf

value: Adult

tag: Sex

value: F

tag: x chromosome dose

tag: replicate

tag: flag

value: pass

tag: crosses


title: NoDf_F_w+/w1118_rep_1 [Sample_640001]

tag: developmental stage


title: NoDf_M_w+/Y_rep_3 [Sample_610003]

value: M

value: w+/Y


title: NoDf_M_w+/Y_rep_2 [Sample_610002]


title: NoDf_M_w+/Y_rep_1 [Sample_610001]


title: NoDf_F_w+/w+_rep_3 [Sample_600003]


title: NoDf_M_w1118/Y;tra2/trix_rep_1 [Sample_530001]


title: NoDf_M_w1118/Y;tra2/trix_rep_3 [Sample_530003]


title: NoDf_M_w+/w1118;tra2/trix_rep_1 [Sample_540001]


title: NoDf_F_w+/w+_rep_1 [Sample_600001]


title: NoDf_M_w+/w1118;tra2/trix_rep_3 [Sample_540003]


title: NoDf_M_w+/w1118;tra2/trix_rep_2 [Sample_540002]


title: NoDf_M_w1118/Y;tra2/trix_rep_2 [Sample_530002]


title: NoDf_M_w1118/w1118;tra2/trix_rep_2 [Sample_520002]


title: NoDf_M_w1118/Y_rep_2 [Sample_510002]


title: NoDf_F_w1118/w1118_rep_3 [Sample_500003]


title: NoDf_M_w1118/w1118;tra2/trix_rep_1 [Sample_520001]


title: NoDf_M_w1118/Y_rep_1 [Sample_510001]


title: Df(3L)ED225_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_321303]


title: NoDf_F_w1118/w1118_rep_2 [Sample_500002]


title: NoDf_F_w1118/w1118_rep_1 [Sample_500001]


title: Df(3L)ED4457_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_321103]


title: Df(3L)ED225_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_321301]


title: NoDf_F_w+/w+_rep_2 [Sample_600002]


title: Df(3L)ED4457_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_321101]


title: Df(3L)ED4457_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_321102]


title: Df(3L)ED4543_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_321002]


title: Df(3L)ED225_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_321302]


title: Df(3L)ED4543_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_321003]


title: PATZ1-/- MEF rep2

description: polyA enriched from total RNA


title: NoDf_M_w1118/w1118;tra2/trix_rep_3 [Sample_520003]


title: Df(3L)ED211_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320903]


title: Df(3L)ED4543_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_321001]


title: Df(3L)ED211_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320902]


title: NoDf_M_w1118/Y_rep_3 [Sample_510003]


title: Df(3L)ED4978_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320703]


title: Df(3L)ED4978_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320702]


title: Df(3L)ED4685_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320802]

description:
Processed data files:
cufflinks_fpkm_gene_ERCC_249.txt
DESeq2_normalized_read_counts_gene_249.txt
HTSeq_raw_read_counts_gene_ERCC_249.txt


title: Df(3L)ED4685_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320801]


title: Df(3L)ED4978_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320701]


title: Df(3L)ED217_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320603]


title: Df(3L)ED217_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320602]


title: Df(3L)ED4475_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320503]


title: Df(3L)ED217_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320601]


title: Df(3L)ED4421_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320403]


title: Df(3L)ED4475_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320501]


title: Df(3L)ED4475_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320502]


title: Df(3L)ED210_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320303]


title: Df(3L)ED210_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320302]


title: Df(3L)ED210_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320301]


title: Df(3L)ED230_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320203]


title: Df(3L)ED230_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320202]


title: Df(3L)ED4287_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320103]


title: Df(3L)ED4421_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320401]


title: Df(3L)ED4287_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320102]


title: Df(3L)ED4287_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320101]


title: Df(3L)ED225_M_Df(3L)/+_rep_3 [Sample_311303]


title: Df(3L)ED225_M_Df(3L)/+_rep_2 [Sample_311302]


title: Df(3L)ED225_M_Df(3L)/+_rep_1 [Sample_311301]


title: Df(3L)ED4685_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_3 [Sample_320803]


title: Df(3L)ED4421_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_2 [Sample_320402]


title: Df(3L)ED4457_M_Df(3L)/+_rep_3 [Sample_311103]


title: Df(3L)ED211_M_Df(3L)/+_rep_3 [Sample_310903]


title: Df(3L)ED4543_M_Df(3L)/+_rep_2 [Sample_311002]


title: Df(3L)ED4457_M_Df(3L)/+_rep_2 [Sample_311102]


title: Df(3L)ED4543_M_Df(3L)/+_rep_3 [Sample_311003]


title: Df(3L)ED211_M_Df(3L)/+_rep_2 [Sample_310902]


title: Df(3L)ED4543_M_Df(3L)/+_rep_1 [Sample_311001]


title: Df(3L)ED4457_M_Df(3L)/+_rep_1 [Sample_311101]


title: Df(3L)ED211_M_Df(3L)/+_rep_1 [Sample_310901]


title: Df(3L)ED4685_M_Df(3L)/+_rep_3 [Sample_310803]


title: Df(3L)ED4685_M_Df(3L)/+_rep_2 [Sample_310802]


title: Df(3L)ED4978_M_Df(3L)/+_rep_1 [Sample_310701]


title: Df(3L)ED217_M_Df(3L)/+_rep_3 [Sample_310603]


title: Df(3L)ED4978_M_Df(3L)/+_rep_3 [Sample_310703]


title: Df(3L)ED230_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320201]


title: Df(3L)ED4978_M_Df(3L)/+_rep_2 [Sample_310702]


title: Df(3L)ED217_M_Df(3L)/+_rep_1 [Sample_310601]


title: Df(3L)ED217_M_Df(3L)/+_rep_2 [Sample_310602]


title: Df(3L)ED4475_M_Df(3L)/+_rep_3 [Sample_310503]


title: Df(3L)ED4475_M_Df(3L)/+_rep_2 [Sample_310502]


title: Df(3L)ED4475_M_Df(3L)/+_rep_1 [Sample_310501]


title: Df(3L)ED4421_M_Df(3L)/+_rep_3 [Sample_310403]


title: Df(3L)ED4421_M_Df(3L)/+_rep_2 [Sample_310402]


title: Df(3L)ED210_M_Df(3L)/+_rep_2 [Sample_310302]


title: Df(3L)ED4421_M_Df(3L)/+_rep_1 [Sample_310401]


title: Df(3L)ED210_M_Df(3L)/+_rep_3 [Sample_310303]


title: Df(3L)ED4685_M_Df(3L)/+_rep_1 [Sample_310801]


title: Df(3L)ED230_M_Df(3L)/+_rep_3 [Sample_310203]


title: Df(3L)ED4287_M_Df(3L)/+_rep_2 [Sample_310102]


title: Df(3L)ED230_M_Df(3L)/+_rep_2 [Sample_310202]


title: Df(3L)ED4287_M_Df(3L)/+_rep_3 [Sample_310103]


title: Df(3L)ED230_M_Df(3L)/+_rep_1 [Sample_310201]


title: Df(3L)ED225_F_Df(3L)/+_rep_2 [Sample_301302]


title: Df(3L)ED4457_F_Df(3L)/+_rep_1 [Sample_301101]


title: Df(3L)ED225_F_Df(3L)/+_rep_3 [Sample_301303]


title: Df(3L)ED4457_F_Df(3L)/+_rep_2 [Sample_301102]


title: Df(3L)ED4543_F_Df(3L)/+_rep_3 [Sample_301003]


title: Df(3L)ED4543_F_Df(3L)/+_rep_2 [Sample_301002]


title: Df(3L)ED211_F_Df(3L)/+_rep_3 [Sample_300903]


title: Df(3L)ED211_F_Df(3L)/+_rep_2 [Sample_300902]


title: Df(3L)ED225_F_Df(3L)/+_rep_1 [Sample_301301]


title: Df(3L)ED211_F_Df(3L)/+_rep_1 [Sample_300901]


title: Df(3L)ED4543_F_Df(3L)/+_rep_1 [Sample_301001]


title: Df(3L)ED4685_F_Df(3L)/+_rep_2 [Sample_300802]


title: Df(3L)ED4685_F_Df(3L)/+_rep_1 [Sample_300801]


title: Df(3L)ED4685_F_Df(3L)/+_rep_3 [Sample_300803]


title: Df(3L)ED4978_F_Df(3L)/+_rep_3 [Sample_300703]


title: Df(3L)ED4978_F_Df(3L)/+_rep_1 [Sample_300701]


title: Df(3L)ED4287_M_Df(3L)/+_rep_1 [Sample_310101]


title: Df(3L)ED4475_F_Df(3L)/+_rep_3 [Sample_300503]


title: Df(3L)ED4978_F_Df(3L)/+_rep_2 [Sample_300702]


title: Df(3L)ED217_F_Df(3L)/+_rep_2 [Sample_300602]


title: Df(3L)ED217_F_Df(3L)/+_rep_1 [Sample_300601]


title: Df(3L)ED217_F_Df(3L)/+_rep_3 [Sample_300603]


title: Df(3L)ED4475_F_Df(3L)/+_rep_2 [Sample_300502]


title: Df(3L)ED4421_F_Df(3L)/+_rep_3 [Sample_300403]


title: Df(3L)ED4475_F_Df(3L)/+_rep_1 [Sample_300501]


title: Df(3L)ED210_F_Df(3L)/+_rep_3 [Sample_300303]


title: Df(3L)ED4421_F_Df(3L)/+_rep_2 [Sample_300402]


title: Df(3L)ED210_F_Df(3L)/+_rep_2 [Sample_300302]


title: Df(3L)ED210_F_Df(3L)/+_rep_1 [Sample_300301]


title: Df(3L)ED230_F_Df(3L)/+_rep_2 [Sample_300202]


title: Df(3L)ED4287_F_Df(3L)/+_rep_3 [Sample_300103]


title: Df(3L)ED4287_F_Df(3L)/+_rep_2 [Sample_300102]


title: Df(1)ED6906_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_122402]


title: Df(1)ED6906_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_122403]


title: Df(1)ED6906_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_122401]


title: Df(1)ED6878_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_122302]


title: Df(1)ED6878_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_122303]


title: Df(1)ED6878_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_122301]


title: Df(1)ED409_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_122203]


title: Df(1)ED409_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_122202]


title: Df(1)ED409_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_122201]


title: Df(1)ED7170_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_122102]


title: Df(1)ED7170_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_122101]


title: Df(3L)ED4421_F_Df(3L)/+_rep_1 [Sample_300401]


title: Df(1)ED7170_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_122103]


title: Df(1)ED13478_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_122003]


title: Df(1)ED13478_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_122002]


title: Df(3L)ED230_F_Df(3L)/+_rep_3 [Sample_300203]


title: Df(1)ED13478_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_122001]


title: Df(3L)ED230_F_Df(3L)/+_rep_1 [Sample_300201]


title: Df(1)ED7289_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_121903]


title: Df(1)ED7289_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_121902]


title: Df(3L)ED4287_F_Df(3L)/+_rep_1 [Sample_300101]


title: INPUT_MeCP2_ChIP_CTX1.fastq.gz

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

data_processing:
Base calling was performed using CASAVA software.
Illumina raw reads in .fastq.gz files were aligned to mouse mm9 reference genome with bwa 0.6.2. Uniquely mapped reads  were extended in silico to reflect average fragment size  of the input DNA(~250bp).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of unnormalized histograms for mapped, in silico extended reads

source_name: Cortex

growth_protocol: Brain tissue was taken from wild-type mice maintained under standard housing conditions.

extract_protocol:
total MeCP2 ChIP was performed as described in Cohen et al. Neuron 2012, Ebert et al Nature 2013
Single-end short read sequencing libraires were prepared using standard protocols, following the manufacturers instructions. Libraries were sequenced on the HiSeq 2500

value: 8 weeks


title: Df(3L)ED210_M_Df(3L)/+_rep_1 [Sample_310301]


title: MeCP2IP_MeCP2_ChIP_CTX1.fastq.gz

value: Total MeCP2 antibody (Chen et al. 2003)


title: Df(1)ED7289_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_121901]


title: INPUT_MeCP2_ChIP_FC2.fastq.gz

source_name: Frontal Cortex

value: 6 weeks


title: MeCP2IP_MeCP2_ChIP_FC2.fastq.gz


title: Df(1)ED7147_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_121803]


title: INPUT_MeCP2_ChIP_FC1.fastq.gz


title: Df(1)ED7147_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_121802]


title: MeCP2IP_MeCP2_ChIP_FC1.fastq.gz


title: Df(1)ED6989_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_121703]


title: Df(1)ED6989_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_121701]


title: Df(1)ED6989_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_121702]


title: Df(1)ED7147_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_121801]


title: Df(1)ED7261_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_121603]


title: Df(1)ED7261_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_121601]


title: Df(1)ED7261_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_121602]


title: Df(1)ED6443_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_121401]


title: Df(1)ED6712_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_121203]


title: Cerebellum_cKO_dnmt3a_BS-seq_2

data_processing:
Reads were mapped to the mm9 genome using BS seeker, allowing up to four mismatches. Duplicate reads were removed and only uniquely mapping reads were kept. For Dnmt3a data, reads containing 3 consecutive mCH were discarded in attempt to remove unconverted reads.
Genome_build: mm9
Supplementary_files_format_and_content: text file containing processed data for bisulfite sequencing. One file each CN dinucleotide. Each file summarizes information for the pooled data from 4 replicates for each brain regions. Each line indicates a cytosine in the genome with the following information listed for each column: Chromosome, Base on the plus strand (G or C), nucleotide position, Di or Trinucleotide context (CG, CHH or CHG), specific dinucleotide (CG, CA,CC,CT), fraction of reads non-converted base-calls at this position , number of reads non-converted bases at this position (# of C basecalls), total number of reads for the base at this position (# of C and T base-calls).

source_name: Cerebellum

extract_protocol:
Genomic DNA was isolated from the cerebellum of  dnmt3a flx/flx, or dnmt3a flx/flx Nestin-cre mice at the indicated ages. For bisulfite treatment, 25-100 ng of genomic DNA 0.25-1 ng of unmethylated lambda DNA was added and libraries were generated using the Ovation Ultralow Methyl-Seq Library System (Nugen). Bisulfite treatment was performed using the EpiTect bisulfite conversion kit (Qiagen) following manufacturer’s instructions.
Libraries were constructed using TruSeq reagents (Illumina) and sequenced on the Miseq instrument (Illumina).

value: Dnmt3a flx/flx Tg(Nes-cre)1Kln/J

tag: background

value: 10-11 weeks


title: Df(1)ED6443_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_121403]


title: Df(1)ED6443_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_121402]


title: Cerebellum_cKO_dnmt3a_BS-seq_1


title: Df(1)ED6712_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_121202]


title: Df(1)ED6712_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_121201]


title: Cerebellum_WT_dnmt3a_BS-seq_2

value: Dnmt3a flx/flx


title: Cerebellum_WT_dnmt3a_BS-seq_1


title: Df(1)ED6630_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_121102]


title: Df(1)ED6630_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_121101]


title: Df(1)ED6630_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_121103]


title: Df(1)ED14021_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120903]


title: Df(1)ED14021_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120902]


title: Df(1)ED14021_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120901]


title: Df(1)ED7635_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120803]


title: Df(1)ED7635_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120801]


title: Df(1)ED7635_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120802]


title: Df(1)ED7331_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120602]


title: Df(1)ED7331_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120601]


title: Df(1)ED7161_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120502]


title: Df(1)ED7161_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120501]


title: Df(1)ED6727_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120403]


title: Df(1)ED6727_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120401]


title: Df(1)ED6727_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120402]


title: Df(1)ED7153_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120303]


title: Df(1)ED6829_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120202]


title: Df(1)ED7153_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120301]


title: Df(1)ED6829_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120203]


title: Df(1)ED6829_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120201]


title: Df(1)ED6957_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120103]


title: Df(1)ED6906_F_Df(1)/w1118_rep_2 [Sample_102402]


title: Df(1)ED6957_M_Df(1)/w1118;tra2/trix_rep_1 [Sample_120101]


title: Df(1)ED6957_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120102]


title: Df(1)ED7331_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120603]


title: Df(1)ED6878_F_Df(1)/w1118_rep_1 [Sample_102301]


title: Df(1)ED6878_F_Df(1)/w1118_rep_2 [Sample_102302]


title: Df(1)ED409_F_Df(1)/w1118_rep_3 [Sample_102203]


title: Df(1)ED409_F_Df(1)/w1118_rep_1 [Sample_102201]


title: Df(1)ED7161_M_Df(1)/w1118;tra2/trix_rep_3 [Sample_120503]


title: HeLa-BATF2 Flag

city: Beijing

first: XueJia

last: Bai

state: Beijing

address: 10 You’an Men West

department: Medical Genetics

institute: Capital Medical University

data_processing:
Bowtie2 software was used to perform alignment of clean reads to reference genome with command-line options ‘--no-mixed --no-discordant’
Peaks were called by MACS2 with the options ‘-q 0.05’
Genome_build: GRCh37
Supplementary_files_format_and_content: bed files diaplayed the peak files with quantitative data

source_name: Cervical cancer cells

growth_protocol: The HeLa-BATF2 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% newborn calf serum (NCS) and 150 mg/ml G418

extract_protocol:
HeLa-BATF2 cells were collected, washed with PBS, and treated with 1% formaldehyde for cross-linking reactions. The incubation with glycine for was then performed to quench the excess cross-linking reactants. Samples were exposed to the cold lysis buffer supplemented with mixture protease inhibitors to allow the release of nuclei. The nuclei were collected and resuspended in the nuclear lysis buffer, and then subjected to sonication. Anti-Flag and anti-IgG antibodies of total 5 ug were added to the nucleic supernatant for overnight incubation at 4℃. The protein-DNA complex bound to protein G-agarose was released from protein G-agarose with ChIP elution buffer. To break the cross-linking, NaCl at a final concentration of 0.2 M was added to the supernatant for overnight incubation. Finally, the DNA constituent was isolated by phenol-chloroform extraction; and the concentration was determined using a NanoDrop 2000c nucleic acid spectrophotometer (Thermo Scientific, USA).
The immunoprecipitated DNA was subjected to the library preparation and sequenced on an Illumina platform at Novogene Life Sciences Company, China. The libraries were generated using Illumina TruseqTM DNA Sample Preparation Kit (Illumina, San Diego, USA) following manufacturer’s standard protocol. Indexing codes were added to each sample for identification. The remained overhangs were converted into blunt ends by exonuclease/polymerase treatments. Adenylation of the 3’ ends of DNA fragments was performed and the access enzyme was subsequently removed. Standard Illumina PE adapter oligonucleotides were ligated to the prepared DNA sample for hybridization. To isolate the preferred DNA fragments, agrose electrophoresis was used (120 V, 40 min, 1.5% agarose gel) to separate adapter-ligated constructs derived fragments from 400 bp to 500 bp in size. Following the purification procedures using spin column (QIAGEN, Dusseldorf, Germany), the DNA fragments with ligated adapters at both ends were enriched with Illumina PCR Primer Cocktail by a 10-cycles PCR reaction. The products were retrieved using a AMPure XP system (Beckman Coulter, Beverly, USA) and quantified by Agilent high sensitivity DNA assay on an Agilent Bioanalyzer 2100 equipment.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a designated TruSeq PE Cluster Kit v3-cBot-HS (Illumia, San Diego, USA). After cluster generation, the obtained library was sequenced with an Illumina Hiseq 2000 platform where 100 bp paired-end reads were generated.

treatment_protocol: Native HeLa cells were seeded in 12-well plates at 1×105 per well. Transfection of p3×Flag-CMV-BATF2 was performed at 24 h afterward. Selection with 200 mg/ml G418 was started at 48 h post-transfection and extended for 7 days. The obtained viable cells were then subcloned with limited dilution, and the final diluted cells were maintained in DMEM with 10% NCS with the presence of G418 (200 mg/ml) for additional 3~4 weeks. The subcloned cells were subjected to western blot analyses for detection of FLAG-tagged BATF2/SARI proteins. A cell clone with moderated over-expression of the transgene and normal morphology, which was also able to expand at a normal rate in 150 mg/ml G418-containing medium, was selected and subjected for further analyses.

tag: cell line background

value: HeLa

value: BATF2 over-expressed HeLa cells

tag: transfected with

tag: sorting

tag: passages

tag: chip antibody

value: Mouse monoclonal anti-FLAG M2 antibody

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #


title: Df(1)ED6906_F_Df(1)/w1118_rep_1 [Sample_102401]

city: Bethesda

tag: genotype


title: Df(1)ED7170_F_Df(1)/w1118_rep_3 [Sample_102103]


title: HeLa-BATF2 IgG

tag: cell type

value: Anti-Goat IgG (whole molecule) antibody


title: Df(1)ED7170_F_Df(1)/w1118_rep_2 [Sample_102102]

tag: drosdel deficiency


title: A375R_RPL10a_vivo__SR_vem10d_rep3

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

description:
supplementary file: A375R_RPL10a_vivo_normalized_count_table.txt
RNA isolated using TRAP protocol

data_processing:
All fastq sequencing reads are mapped by STAR 2.3.0e. For data from whole RNA samples, reads are directly mapped to hg19 with standard settings. For data from TRAP protocols, read are mapped to a hybrid genome index containing both hg19 and mm9, and reads that score higher in hg19  are selected for further analysis. This step is designed to avoid potential residual RNA contaminations from mouse stroma tissue in the xenograft tumors during TRAP processing.
HTSeq v0.5.4 is used for feature counting.
DESeq (v1.18.0) is used for the normalization of count table. R3.1.2 is used as the processing platform.
Genome_build: hg19
Supplementary_files_format_and_content: txt files, normalized count tables from each experiment

source_name: melanoma

growth_protocol: A375 were cultured in DMEM containing 10% fetal bovine serum (FBS), 2mM L-Glutamine, 100IU/ml penicillin/streptomycin, and 1µg/ml amphotericin B. Colo800, UACC62, and  H3122 cells were culturd in RPMI containing 10% FBS, 2mM L-Glutamine, 100IU/ml penicillin/streptomycin, and 1µg/ml amphotericin B. All cells were grown in a humidified incubator at 37°C with 5% CO2. Xenograft tumours were established by injecting respective cell lines (A375, A375/A375R, A375R) with matrigel subcutaneously in mice.

extract_protocol:
For direct RNA isolation from cell lines or tissue, PrepEase RNA Extraction kit (USB) is used according to the manufacturer's instructions. For TRAP based RNA extraction, tumor tissues are dissected from mouse and immediately subjected for tissue homogenization. Lysates cleared by centrifugation are used for immunoprecipitation with GFP coated sepharose protein G beads. Ribosome associated RNA is recovered directly from washed beads with RNAqueous-Micro total RNA isolation kit (Ambion).
RNA samples are used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).

treatment_protocol: For in vitro experiments 2*10e5 cells were seeded in a 6-well tissue culture plate in regular growth media with 10% FBS, the next morning media was replaced with media containing 2% FBS including the respective drugs (vehicle; vemurafenib/PLX4032 at 0.1 µM for A375 cells and 1µM for Colo 800 and UACC62 cells; crizotinib at 0.3µM). For in vivo experiments the growth of the tumor was measured using a caliper and the tumor size calculated using the formula: (D*(d*d))/2. When tumours reached a size of 50-150mm3 mice were treated with vemurafenib (75mg/kg/bid) for 5 or 10 doses, the tumor was shock-frozen in liquid nitrogen and stored at -80C until further processing.

tag: cell line

value: melanoma cell line

tag: drug treatment

value: vemurafenib_10 doses_75mg/kg

tag: origin

value: xenograft tumours


title: Df(1)ED13478_F_Df(1)/w1118_rep_3 [Sample_102003]

value: Adult

tag: Sex

value: F

tag: x chromosome dose

tag: replicate

tag: flag

value: pass


title: Df(1)ED7153_M_Df(1)/w1118;tra2/trix_rep_2 [Sample_120302]

tag: developmental stage

value: M

tag: crosses


title: A375R_RPL10a_vivo__SR_vem10d_rep2


title: A375R_RPL10a_vivo__Ronly_vem10d_rep3


title: Df(1)ED6878_F_Df(1)/w1118_rep_3 [Sample_102303]


title: Df(1)ED13478_F_Df(1)/w1118_rep_1 [Sample_102001]


title: A375R_RPL10a_vivo__SR_vem10d_rep1


title: Df(1)ED409_F_Df(1)/w1118_rep_2 [Sample_102202]


title: A375R_RPL10a_vivo__Ronly_vem10d_rep2


title: A375R_RPL10a_vivo__Ronly_vem10d_rep1


title: A375R_RPL10a_vivo__SR_vehicle_rep2

value: vehicle


title: A375R_RPL10a_vivo__SR_vehicle_rep3


title: Df(1)ED7289_F_Df(1)/w1118_rep_3 [Sample_101903]


title: A375R_RPL10a_vivo__SR_vehicle_rep1


title: Df(1)ED7289_F_Df(1)/w1118_rep_2 [Sample_101902]


title: Df(1)ED7289_F_Df(1)/w1118_rep_1 [Sample_101901]


title: A375R_RPL10a_vivo__Ronly_vehicle_rep3


title: Df(1)ED6989_F_Df(1)/w1118_rep_1 [Sample_101701]


title: Df(1)ED7261_F_Df(1)/w1118_rep_3 [Sample_101603]


title: Df(1)ED7170_F_Df(1)/w1118_rep_1 [Sample_102101]


title: A375R_RPL10a_vivo__Ronly_vehicle_rep1


title: A375R_RPL10a_vivo__Ronly_vehicle_rep2


title: Df(1)ED13478_F_Df(1)/w1118_rep_2 [Sample_102002]


title: Df(1)ED7261_F_Df(1)/w1118_rep_1 [Sample_101601]


title: H3122_vitro_crizotinib_48h_rep1

description:
supplementary file: H3122_Crizotinib_normalized_count_table.txt
whole RNA

source_name: lung adenocarcinoma

value: lung adenocarcinoma cell line

value: cells in vitro


title: Df(1)ED6443_F_Df(1)/w1118_rep_3 [Sample_101403]


title: H3122_vitro_crizotinib_48h_rep2


title: H3122_vitro_vehicle_rep2


title: Df(1)ED6989_F_Df(1)/w1118_rep_3 [Sample_101703]


title: Df(1)ED6989_F_Df(1)/w1118_rep_2 [Sample_101702]


title: H3122_vitro_vehicle_rep1


title: UACC62_vitro_vem_48h_rep2

description:
supplementary file: UACC62_Vem_normalized_count_table.txt
whole RNA


title: Df(1)ED6443_F_Df(1)/w1118_rep_1 [Sample_101401]


title: Df(1)ED6712_F_Df(1)/w1118_rep_2 [Sample_101202]


title: Df(1)ED6712_F_Df(1)/w1118_rep_3 [Sample_101203]


title: Df(1)ED6712_F_Df(1)/w1118_rep_1 [Sample_101201]


title: Df(1)ED6630_F_Df(1)/w1118_rep_3 [Sample_101103]


title: UACC62_vitro_vem_48h_rep1


title: Df(1)ED6630_F_Df(1)/w1118_rep_2 [Sample_101102]


title: Colo800_vitro_vem_48h_rep2

description:
supplementary file: Colo800_Vem_normalized_count_table.txt
whole RNA


title: Df(1)ED7261_F_Df(1)/w1118_rep_2 [Sample_101602]


title: UACC62_vitro_vehicle_rep2


title: Df(1)ED6630_F_Df(1)/w1118_rep_1 [Sample_101101]


title: Df(1)ED6906_F_Df(1)/w1118_rep_3 [Sample_102403]


title: Colo800_vitro_vem_48h_rep1


title: Df(1)ED7374_F_Df(1)/w1118_rep_1 [Sample_101001]


title: Colo800_vitro_vehicle_rep1


title: A375_vivo_vem_rep4

description:
supplementary file: A375_RPL10a_vivo_normalized_count_table.txt
RNA isolated using TRAP protocol


title: Df(1)ED6443_F_Df(1)/w1118_rep_2 [Sample_101402]


title: Df(1)ED14021_F_Df(1)/w1118_rep_2 [Sample_100902]


title: Df(1)ED14021_F_Df(1)/w1118_rep_3 [Sample_100903]


title: A375_vivo_vem_rep1


title: A375_vivo_vem_rep2


title: Df(1)ED7635_F_Df(1)/w1118_rep_3 [Sample_100803]


title: Df(1)ED7635_F_Df(1)/w1118_rep_2 [Sample_100802]


title: Df(3L)ED211_M_w1118/w1118;tra2/trix;Df(3L)/+_rep_1 [Sample_320901]


title: A375_vivo_vem_rep3


title: Df(1)ED7635_F_Df(1)/w1118_rep_1 [Sample_100801]


title: Df(1)ED14021_F_Df(1)/w1118_rep_1 [Sample_100901]


title: A375_vivo_vehicle_rep4


title: Colo800_vitro_vehicle_rep2


title: A375_vivo_vehicle_rep3


title: UACC62_vitro_vehicle_rep1


title: Df(1)ED7331_F_Df(1)/w1118_rep_2 [Sample_100602]


title: Df(1)ED7161_F_Df(1)/w1118_rep_3 [Sample_100503]


title: A375_vitro_vem_48h_rep2

description:
supplementary file: A375_in_Vitro_Vem_normalized_count_table.txt
whole RNA


title: Df(1)ED7225_F_Df(1)/w1118_rep_1 [Sample_100701]


title: A375_vivo_vehicle_rep1


title: A375_vitro_vem_48h_rep3


title: Df(1)ED7161_F_Df(1)/w1118_rep_1 [Sample_100501]


title: A375_vitro_vem_6h_rep3


title: Df(1)ED6727_F_Df(1)/w1118_rep_3 [Sample_100403]


title: A375_vitro_vem_48h_rep1


title: A375_vitro_vem_6h_rep2


title: Df(1)ED6727_F_Df(1)/w1118_rep_2 [Sample_100402]


title: A375_vitro_vem_6h_rep1


title: Df(1)ED6727_F_Df(1)/w1118_rep_1 [Sample_100401]


title: Df(1)ED7153_F_Df(1)/w1118_rep_3 [Sample_100303]


title: A375_vitro_vehicle_rep2


title: A375_vitro_vehicle_rep3


title: Df(1)ED7161_F_Df(1)/w1118_rep_2 [Sample_100502]


title: Df(1)ED7153_F_Df(1)/w1118_rep_2 [Sample_100302]


title: A375_vitro_vehicle_rep1


title: Df(1)ED7331_F_Df(1)/w1118_rep_1 [Sample_100601]


title: Df(1)ED6829_F_Df(1)/w1118_rep_3 [Sample_100203]


title: A375_vivo_vehicle_rep2


title: Df(1)ED7153_F_Df(1)/w1118_rep_1 [Sample_100301]


title: Df(1)ED6829_F_Df(1)/w1118_rep_2 [Sample_100202]


title: VC_wild-type_3

description: Total RNA was depleted of rRNA by hybridization (using RiboZero) and heat fragmented. Strand-specific RNA-Seq libraries were prepared using the dUTP method, and sequenced on an Illlumina Hiseq instrument

data_processing:
Base calling was performed using standard approaches.
Illumina raw reads in .fastq files were aligned using bwa 0.6.2.  Target sequences included (1) mm9  autosomal and sex chromosomes plus (2) a read-length-dependent splice library (~3M sequences, each 50-98bp).  The latter comprised all possible minimal intragenic sequences of two or more exons (based on the RefSeq annotation) for which one or more exon-exon junctions could be crossed by reads of the required length.  After bwa-indexing the targets with the bwtsw algorithm, reads were aligned with zero trimming, zero gaps, and allowing up to 5 mismatches. The sam/bam files output by bwa were indexed and sorted and served as input for further processing.
Aligned reads were minimally filtered for QC, removing any reads with uncalled bases or with unmapped or nonuniquely mapped sequences.
Employing "MAPtoFeatures" perl scripts, the loci of uniquely mapped reads were compared to the loci of all genic features (exons, introns, UTRs, CDSs, etc., and all junctions between them) of (1) all genes based on the RefSeq annotation and (2) all rRNA genes based on RepeatMasker, for the alignment target genome. Average exon Density (read coverage per bp) was calculated, equal to rdbp per feature length.  Each sample's Densities were renormalized from total reads not in noncoding genes and not in rRNA to a standard total of 10M reads, and to a standard read length of 35bp.  With these conventions, units of Density always equal RPKM times 0.35.  Quantile normalized exon densities were treated as expression levels comparable among all samples.
Genome_build: For all samples mm9 (NCBI37, Jul7. 2007).
Supplementary_files_format_and_content: Entrez gene ID, refseq gene name, gene length, and exon densities are listed for each of the 14168 genes analyzed across expression platforms in this study.

source_name: Visual Cortex, 8 weeks of age

extract_protocol:
Visual Cortex was dissected from 8-10 week old MeCP2 knockout mice (Mecp2tm1.1Bird) or wild-type littermate controls. RNA was trizol and extracted using Qiagen Rneasy purification with on column DNase steps. ERCC control RNAs were spiked into the samples with equal mass added per visual cortex (note: they were not used in subsequent analysis).
Illumina library construction and sequencing was carried out as follows: total RNA was depleted of ribosomal RNA using the Ribozero rRNA removal kit (Epicentre), heat-fragmented to 200-700 bp in length and cloned using Uricil-N-Glycosylase-based strand-specific cloning. cDNA fragments were sequenced using an Illumina HiSeq 2000
Strand-specific, rRNA depleted total RNA, Single-end 49 bp sequencing

treatment_protocol: Mice were housed under standard conditions in the animal facility and dissected at the same time point in the light-dark cycle for each dissection.

value: wild type

tag: tissue

value: visual cortex


title: Df(1)ED6829_F_Df(1)/w1118_rep_1 [Sample_100201]


title: Donor 2 P13 (Late Passage)

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description: RNA sequencing of MSC cells from a 64 year old donor at passage 13

data_processing:
The RNA-seq reads were mapped to the human genome 19 using Bowtie2 and Tophat2.
We used HTSeq with Ensemble 37 (release 71) annotation for quantification of transcripts.
Normalization and differential expression analysis were done with DESeq2. We chose an FDR of 0.01 and a log2 fold change of 2 to detect genes differentially expressed in early or late passage.
Genome_build: hg19

source_name: bone marrow

growth_protocol: Mesenchymal stromal cells were isolated from the bone marrow of caput femoris upon hip replacement surgery after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (Permit Number EK128/09; RWTH Aachen University) . MSCs were culture expanded in DMEM culture medium (PAA) supplemented with glutamine (PAA), penicillin/streptomycin (PAA), and 10% human platelet lysate (hPL) in a humidified atmosphere at 5% CO2. All cell preparations were characterized with regard to immunophenotype and in vitro differentiation potential towards osteogenic and adipogenic lineages .

extract_protocol:
RNA was isolated from 1,000,000 cells  using the miRNeasy Mini Kit (Qiagen). Quality control and measurement of RNA concentration was done with a NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, USA) and the Agilent 2100 Bioanalyzer (Agilent Technologies).
Multiplexed library preparation of total RNA and deep sequencing with IlluminaHiSeq 2000 technology (IlluminaInc., San Diego, USA) with a read length of 50 bases was performed at EMBL gene core facility (Heidelberg, Germany).

treatment_protocol: Cells were culture expanded until replicative senescence as determined by ultimate growth arrest. Late passages (P13) were within the last three to five passages before entering senescence.

value: Mesenchymal stromal cells

tag: passage

value: Passage 13


title: Donor 1 P13 (Late Passage)

description: RNA sequencing of MSC cells from a 59 year old donor at passage 13


title: Df(1)ED6957_F_Df(1)/w1118_rep_2 [Sample_100102]


title: Donor 3 P13 (Late Passage)

description: RNA sequencing of MSC cells from a 73 year old donor at passage 13


title: VC_wild-type_2


title: Donor 2 P4 (Early Passage)

description: RNA sequencing of MSC cells from a 64 year old donor at passage 4

value: Passage 4


title: Donor 3 P4 (Early Passage)

description: RNA sequencing of MSC cells from a 73 year old donor at passage 4


title: VC_wild-type_1


title: VC_KO_3

value: MeCP2 KO


title: Donor 1 P4 (Early Passage)

description: RNA sequencing of MSC cells from a 59 year old donor at passage 4