title: 14-Daunorubicin-plus ATc

source_name: CRISPRi guide RNA library_Daunorubicin-plus ATc

value: 31.25uM Daunorubicin +ATc

value: GCCGT-GACT


title: HFF_PD74_2

status: Public on Jan 18 2016

type: SRA

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

library_source: transcriptomic

data_processing:
Illumina Casava software was used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.66
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: total RNA extracted from HFF fibroblasts

growth_protocol: Cells were cultured as recommended by ATCC in Dulbeccos modified Eagles low glucose medium (DMEM) with L-glutamine (PAA Laboratories, Pasching, Austria), supplemented with 10% fetal bovine serum (PAA Laboratories). Cells were grown under normal air conditions in a 9.5% CO2 atmosphere at 37°C. For sub-culturing, the remaining medium was discarded and cells were washed in 1 x PBS (pH 7.4) (PAA Laboratories) and detached using trypsine/EDTA (PAA Laboratories). Primary fibroblasts were sub-cultured in a 1:4 (= 2 population doublings (PDs)) or 1:2 (= 1 PD) ratio. For stock purposes, cryo-conservation of the cell lines at various PDs were undertaken in cryo-conserving medium (DMEM + 10% FBS + 5% DMSO). Cells were immediately frozen at -80°C and stored for two to three days. Afterwards, cells were transferred to liquid nitrogen for long time storage. Re-freezing and re-thawing was not performed to avoid premature senescence [Honda et al., 2001]. One vial of each of the five different fibroblast cell lines (MRC-5, HFF, BJ, WI-38 and IMR-90) were obtained and maintained in culture from an early PD. On obtaining enough stock on confluent growth of the fibroblasts in 75 cm2 flasks, cells were sub-cultured into three different 75 cm2 flasks (“triplicates”) and were maintained until they were senescent in culture.

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of around 2.5 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

tag: population doublings

tag: cell type

value: HFF fibroblasts


title: HFF_PD74_3


title: 13-Daunorubicin-uninduced

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

country: USA

institute: Stanford University

library_source: genomic

data_processing:
library strategy: Barcode sequencing (Bar-seq)
created a synthetic reference chromosome sequence for each of the expected amplicons. The synthetic reference included Illumina adaptors, library barcode, PCR amplification priming region, PCR barcode, and the gRNA specificity sequence.
merged forward and reverse reads using PEAR version 0.9.4 with default parameters.
resulting FastQ file was mapped against the created synthetic reference using BWA version 0.6.1-r104 with command line  “bwa index [reference]; bwa aln -n3 -o3 -e1 -l22 [reference] [fastq] > [aln]; bwa samse -f [out] [reference] [aln] [fastq] ”
For each of the expected amplicons, we counted the number of perfect matches (flag NM:i:0) from the resulting alignments (Additional data file 8, column “Count_perfect”) that were used in subsequent analyses.
Supplementary_files_format_and_content: Additional data file 8. An Excel spreadsheet that contains sequence read information and raw counts from MiSeq data.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: CRISPRi guide RNA library_Daunorubicin-uninduced

growth_protocol: Yeast culturing and sample collection was performed using a cell-screening platform that integrates temperature-controlled absorbance plate readers, plate coolers, and a liquid handling robot. Briefly, 700 µl yeast cultures were grown (+/- a drug and +/- ATc) in 48 well plates at 30oC with orbital shaking in Infinite plate readers (Tecan). To maintain cultures in log phase over many doublings, 23 µls of the culture was removed when it reached an OD of 0.76, added to a well containing 700 µl of media, and then allowed to grow further. After three such dilutions, 600 µls of the culture was collected and saved to a 4oC cooling station (Torrey Pines) when it reached an OD of 0.76. This amounted to approximately 20 culture doublings from the beginning of the experiment. Pipetting events were triggered automatically by Pegasus Software and performed by a Freedom EVO workstation (Tecan).

extract_protocol:
After competitive growth of yeast strains and sample collection, yeast plasmids were purified using the Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).
Purified plasmids were used as a template for PCR with barcoded up and down sequencing primers that produce a double index to uniquely identify each sample.  PCR products were confirmed by agarose gel electrophoresis. After PCR, samples were combined and bead cleaned with Thermo ScientificTM Sera-Mag Speed Beads Carboxylate-Modified particles.  Sequencing was performed using Illumina MiSeq.

treatment_protocol: In general, drugs were applied at concentrations that inhibit growth by ~20%

tag: grna libraries

value: gene_tiling_18bp & gene_tiling_20bp

tag: growth condition

value: 31.25uM Daunorubicin

tag: index pair

value: GCCGT-CCAGGT

tag: molecule subtype

value: plasmid DNA


title: HFF_PD74_1


title: HFF_PD16_3


title: 12-DMSO-plus ATc

source_name: CRISPRi guide RNA library_DMSO-plus ATc

value: 1% DMSO +ATc

value: GCCGT-AGGTC


title: H3K27ac.CAPAN1

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: Chromatin IP against H3K27ac

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the human hg19 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters, nomodel and bw=300 (except for the H3K27ac of PDACs for which a bw=100 was used). Each IP was compared to input DNA.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

growth_protocol: RPMI-1640 supplemented with 20% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

extract_protocol: ChIP lysates were generated from 2-5x10^6 cells for histone marks or 20-40x10^6 cells for transcription factors. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

treatment_protocol: No treatment

tag: cell line background

value: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: 12_KT-mTECs_rep3

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

data_processing:
RNA-Seq: Alignment by Tophat (version 2.0.10) to mm9 reference genome.
RNA-Seq: Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
RNA-Seq: Gene expression levels for Refseq genes were summarized as reads per kilobase of exon model per million mapped reads (RPKM) and read counts using custom R scripts
Genome_build: mm9
Supplementary_files_format_and_content: Read counts and RPKM values from RNA sequencing

molecule: polyA RNA

organism: Mus musculus

source_name: Thymic stromal cells

extract_protocol:
cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
For RNA-Seq NEBNext® DNA Library Prep Reagent Set for Illumina®

treatment_protocol: Cell populations isolated by FACS sorting from mouse thymic stroma

tag: tissue

value: Thymus, KitL-tomato- mTECs

tag: strain

value: C57 BL6, KitL-tomato reporter mouse

tag: phenotype

value: Lin- Dapi-EpCAM+ CD31-UEA1+Ly51- td-tomato-


title: 17-ST016598-uninduced

source_name: CRISPRi guide RNA library_ST016598-uninduced

value: TCGT-AGGTC


title: 11-DMSO-uninduced

source_name: CRISPRi guide RNA library_DMSO-uninduced

value: 1% DMSO

value: GCCGT-AACC


title: 10_KT-mTECs_rep1


title: HFF_PD16_2


title: BJ_OLD_2

source_name: total RNA extracted from BJ fibroblasts

value: BJ fibroblasts


title: 9_KT+cTECs_rep3

value: Thymus, KitL-tomato+ cTECs

value: Lin- Dapi-EpCAM+ CD31-UEA1-Ly51+ td-tomato+


title: BJ_OLD_3


title: BJ_OLD_1


title: BJ_Y3


title: 8_KT+cTECs_rep2


title: 15-9150499-uninduced

source_name: CRISPRi guide RNA library_9150499-uninduced

value: gene_tiling_18bp & gene_tiling_20bp

value: GCCGT-GGATT


title: BJ_Y2


title: 8-CBF-666774-plus ATc

source_name: CRISPRi guide RNA library_CBF-666774-plus ATc

value: CGTTGA-CCAGGT


title: 7_KT+cTECs_rep1


title: MRC_5_PD72-3

source_name: total RNA extracted from MRC-5 fibroblasts

value: MRC-5 fibroblasts


title: 7-CBF-666774-uninduced

source_name: CRISPRi guide RNA library_CBF-666774-uninduced

value: CGTTGA-AGGTC

value: plasmid DNA


title: 11_KT-mTECs_rep2


title: 5_KT-VECs_rep2

value: Thymus, KitL-tomato- VECs

value: Lin- Dapi-EpCAM- CD31+td-tomato-


title: BJ_Y1


title: Xbp1 Knock-out (Xbp1KO) rep2, batch 2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained.
Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Ig genes were excluded from the gene-level expression analysis. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 1 in at least one library.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the 'voom' function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include normalized log2-FPKM values for each library. EntrezIDs represent NCBI Entrez Gene IDs.
Supplementary_files_format_and_content: GEO_suppl_raw_counts.txt': Includes raw read counts for each gene in each library. The raw read count is the number of mapped reads (or read pairs for paired-end libraries) assigned to each gene. EntrezIDs represent NCBI Entrez Gene IDs.

source_name: Bone marrow, plasma cells, Xbp1 knockout

extract_protocol:
RNA was isolated from ex-vivo sorted Blimp1-GFP+CD138+ plasma cells using the Qiagen RNeasy Micro kit.
Libraries were generated using the Illumina TruSeq RNA sample preparation kit following manufacturer instructions.

tag: strain/background

tag: genotype/variation

value: bone marrow

value: plasma cells


title: HFF_PD16_1

value: HFF fibroblasts


title: 4-NSC-180973-plus ATc

source_name: CRISPRi guide RNA library_NSC-180973-plus ATc

value: ACTGCT-GACT


title: 4_KT-VECs_rep1

value: C57 BL6, KitL-tomato reporter mouse


title: 3_KT+VECs_rep3

value: Thymus, KitL-tomato+ VECs

value: Lin- Dapi-EpCAM- CD31+td-tomato+


title: 6-DMSO-plus ATc

value: 1% DMSO +ATc

value: CGTTGA-AACC


title: 5-DMSO-uninduced

value: gene_tiling_18bp & gene_tiling_20bp

value: 1% DMSO

value: ACTGCT-GGATT


title: 1_KT+VECs_rep1


title: 6_KT-VECs_rep3


title: 10-Rapamycin-plus ATc

source_name: CRISPRi guide RNA library_Rapamycin-plus ATc

value: 4.375nM Rapamycin +ATc

value: CGTTGA-GGATT


title: Xbp1 Knock-out (Xbp1KO) rep1, batch 2


title: 3-NSC-180973-uninduced

source_name: CRISPRi guide RNA library_NSC-180973-uninduced

value: ACTGCT-CCAGGT

value: plasmid DNA


title: 9-Rapamycin-uninduced

source_name: CRISPRi guide RNA library_Rapamycin-uninduced

value: 4.375nM Rapamycin

value: CGTTGA-GACT


title: 2-9121982-plus ATc

source_name: CRISPRi guide RNA library_9121982-plus ATc

value: ACTGCT-AGGTC


title: 1-9121982-uninduced

source_name: CRISPRi guide RNA library_9121982-uninduced

value: ACTGCT-AACC


title: GAB2_NULL_B

status: Public on Jan 17 2016

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Genomic alignment was performed with Bowtie, using default parameters.
Gene expression levels were estimated and compared using Cufflinks.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FPKM

source_name: GAB2 NULL Mouse Bone Marrow

extract_protocol: RNA (150 ng) from each sample was reverse transcribed into cDNA by using the Illumina TruSeq Stranded mRNA kit. cDNA libraries were size-indexed and validated using an Agilent Bioanalyzer, and their concentrations confirmed by qPCR. Six different libraries (3 WT-Gab2+/+ and 3 Gab2-/-) were normalized to 10 nM and pooled. Pooled libraries (8 pmol each) were loaded onto Illumina cBot for cluster generation, and the flow cell was subjected to 100 cycles of paired-end sequencing on an Illumina HiSeq 2000.

value: bone marrow


title: GAB2_WT_C

source_name: GAB2 WT Mouse Bone Marrow


title: MRC_5_PD72-2

value: MRC-5 fibroblasts


title: GAB2_NULL_A


title: MRC_5_PD72-1


title: GAB2_WT_A


title: GAB2_WT_B


title: IGF2BP3 shRNA RNA-seq 3 [jh126]

status: Public on Jan 16 2016

city: Santa Cruz

first: Jonathan

middle: Michael

last: Howard

state: CA

address: 1154 High Street

department: Molecular, Cell, and Developmental Biology

institute: University of California-Santa Cruz

data_processing:
iCLIP 1: based on random bases of internal barcode positions 1-9 of each read, the readIDs were divided into classes (for later use in duplicate removal). Note: positions 4-7 comprised fixed values for each sample
iCLIP 2: each read was searched for the presence of adaptor sequence TGGAATTC and trimmed from that point on. Reads without the adaptor were discarded. Reads shorter than 30bp after trimming (including internal barcode positions 1-9) were discarded.
iCLIP 3: internal barcode positions 1-9 were trimmed before mapping
iCLIP 4: reads mapping (by bowtie2) to human repeatMasker elements were discarded
iCLIP 5: reads were mapped to hg19 by tophat, aided by a gtf file based on UCSC Knowngenes, and with parameters --no-novel-juncs, --no-coverage-search
iCLIP 6: for each class of internal random barcode bases from step (1), duplicate read mappings of the same length and position were discarded
iCLIP 7: peaks were called on the dup-removed bam files from step (6) by Clipper (Yeo et al) using default parameters for hg19.
RNAseq 1: based on random bases of internal barcode positions 1-8 of both read1 and read2, the readIDs were divided into classes (for later use in duplicate removal).
RNAseq 2: the 151x151bp pairedEnd reads were trimmed to 75x75 by trimming from each read, 10bp from the 5' end (including the internal random barcode) and 66bp from the 3' end
RNAseq 3: reads mapping (by bowtie2) to human repeatMasker elements were discarded
RNAseq 4: reads were mapped by STAR to hg19 with an additional set of junctions derived from Gencode V19 basic with 100bp overlap
RNAseq 5: for each class of internal random barcode bases from step (1), duplicate read mappings of the same start and end position were discarded
RNAseq 6: bam files were converted to coverage using bedtools
RNAseq 7: for each gene in UCSC KnownGenes, the total coverage was calculated over all the coding positions in all potential exons of the gene. UTR positions were excluded.
RNAseq 8: the coverage per gene was divided by 150 to generate an effective count of (75x75bp pairedEnd) reads per gene for input to DESeq
RNAseq 9: DESeq was run to compare the 3 control replicates to the 3 knockdown replicates for all genes with coverage in any sample
Genome_build: hg19
Supplementary_files_format_and_content: iCLIP-seq: peaks.bed.gz these are bed files containing the peaks called by clipper for each sample.
Supplementary_files_format_and_content: RNA-seq: deseq text file: contains the normalized (and averaged over replicates) values in control and knockdown samples for genes with p-adj better than 0.1

source_name: IGF2BP3 shRNA RNA-seq

growth_protocol: For iCLIP protocol, REH and RS4;11 cells were grown in 75cm2 cell culture flasks reaching a density of ~100,000 cells/mL in final volume of 60 mL. For RNA-seq protocol, RS4;11 control and IGF2BP3 KD cell lines were grown in 25 cm2 cell culture flasks to a density of  ~10,000 cells/mL in 25 mL.

extract_protocol:
For iCLIP protocol, cytosolic extracts (detergent lysis) were prepared from REH and RS4;11 cell lines prior to immunoprecipitation.  For RNA-seq, cytosolic extracts (detergent lysis) were prepared from control and IGF2BP3 shRNA RS4;11 cell lines, and RNA isolation from these extracts was performed with TRIreagentLS.
For iCLIP, libraries were constructed as previously described (Huppertz, I., et al. Methods. 2014) with minor changes. 3' Adenylated adapter, AIR ligase, and PCR primers used from NEXTflex™  Illumina Small RNA-Seq Library Prep Kit (Bioo Scientific) and RT primers were adapted for kit reagent use. For RNA-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ Kit was used (Bioo Scientific).
For iCLIP, RNA purification was performed as previously described (Huppertz, I., et al. Methods. 2014). For RNA-seq, PolyA+ selection was performed.

treatment_protocol: RS4;11 control and IGF2BP3 shRNA cells were selected with puromycin treatment at 5µg/mL for 7 days and later used for RNA isolation and library construction.

tag: disease

value: acute lymphoblastic leukemia

value: RS4;11 lymphoblast cells

value: igf2bp3 knockdown


title: IGF2BP3 shRNA RNA-seq 2 [jh125]


title: Wild type (WT) rep4, batch 2

source_name: Bone marrow, plasma cells, WT

value: wild type

value: plasma cells


title: 2_KT+VECs_rep2

source_name: Thymic stromal cells

value: Thymus, KitL-tomato+ VECs

value: C57 BL6, KitL-tomato reporter mouse

value: Lin- Dapi-EpCAM- CD31+td-tomato+


title: control shRNA RNA-seq 1 [jh121]

source_name: control shRNA RNA-seq

value: control


title: Wild type (WT) rep3, batch 2


title: REH IGF2BP3 iCLIP 2 [jh101b]

source_name: REH IGF2BP3 iCLIP

value: acute lymphocytic leukemia (non-T; non-B)

value: REH B-ALL cells


title: control shRNA RNA-seq 2 [jh122]


title: IGF2BP3 shRNA RNA-seq 1 [jh124]


title: REH IGF2BP3 iCLIP 1 [jh101a]


title: REH IGF2BP3 iCLIP 3 [jh101c]


title: DicF rep3

city: Urbana

first: Carin

middle: K.

last: Vanderpool

state: Illinois

address: 601 S. Goodwin Avenue, C226

department: Microbiology

institute: University of Illinois at Urbana-Champaign

data_processing:
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1
Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF.
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Total RNA from bacterial culture

growth_protocol: E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids.

extract_protocol:
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies).

treatment_protocol: E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA.

tag: genotype

value: delta dicF, lacIq

tag: protocol

value: small RNA DicF


title: DicF rep2


title: RS4;11 IGF2BP3 iCLIP 3 [jh099c]

source_name: RS4;11 IGF2BP3 iCLIP

tag: cell type


title: GAB2_NULL_C


title: RS4;11 IGF2BP3 iCLIP 2 [jh099b]


title: vegetative_0

city: Kiel

first: Till

last: Bayer

address: Düsternbrookerweg 20

department: Marine Ecology

institute: GEOMAR Helmholtz Centre for Ocean Research

data_processing:
TopHat v2.0.12 was used for mapping, the options -r 50 --mate-std-dev 73 -I 34000 were set according to insert size and maximum intron length determined from the annotated geome.
Reads were quantified with CuffQuant v2.2.1
Read counts were normalized with CuffNorm v2.2.1
Differential expression was analyzed with CuffDiff v2.2.1
Genome_build: Zostera marina genome v2.1
Supplementary_files_format_and_content: tab delimited text file containing tests for differential expression
Supplementary_files_format_and_content: tab delimited text file containing fpkm values for gene expression
Supplementary_files_format_and_content: tab delimited text file containing count values for genes

organism: Zostera marina

source_name: Leaf tissue

growth_protocol: Shoots were collected from Falkenstein Beach area, Kiel Bight, Germany 54°.41 N, Lon: 10°.19 E on 27 Feb 2014. Within the same day, shoots were planted into flow-through seawater aquaria (15 x 15 x 25 cm) within 600 l tanks. Water temperature was raised 1°C/day from ambient 5°C to 15°C. Light was provided by two halogen metal vapor lamps with a light intensity of ~600 µmol photon sec-1 m-1. In order to mimic summer conditions and induce flowering, the light period was increased from 12 to 16 hours day light in increments of 30 min every third day. Several  marine snails (Littorina sp.) were added to the aquaria to control epiphytic growth on Z. marina leaves.

extract_protocol:
RNA extraction was performed using the InviTrap Spin Plant RNA Mini Kit (Stratek Molecular) following the manufacturer's protocol. RNA  integrity was checked with an automated electrophoresis station, Experion (Bio-RAD), using StdRNA chips and reagents (Bio-RAD). RNA concentrations ranged between 23-182 ng/µl, RQI values were >7.2.
Library preparation involved DNase 1 digestion of total RNA, mRNA isolation by use of oligo(dT) beads, mRNA fragmentation, first and second strand cDNA synthesis, end-repair, A-tailing, bar-coded adapter ligation and PCR amplification. Sequencing libraries were checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) before sequencing. Paired-end (2 x 100 bp) RNA Sequencing (RNASeq) data were generated using standard Illumina protocols and kits (TruSeq SBS KIT-HS v3, FC-401-3001; TruSeq PE Cluster Kit v3, PE-401-3001) and all sequencing was performed using the HiSeq 2000 platforms.

value: Leaf tissue


title: DicF rep1


title: vegetative_4


title: RS4;11 IGF2BP3 iCLIP 1 [jh099a]


title: vegetative_5


title: vegetative_3


title: vegetative_2


title: vegetative_1


title: root_2

source_name: Root tissue

value: Root tissue


title: Vector rep3

value: vector control


title: root_1


title: root_3


title: Vector rep2


title: control shRNA RNA-seq 3 [jh123]


title: root_0


title: Vector rep1


title: male_flower_6

source_name: Male flower tissue

value: Male flower tissue


title: male_flower_5


title: AMOs rep3

city: Beijing

first: Li

last: Gao

address: Qinghuayuan  Street

department: School of Life Sciences

country: China

institute: Tsinghua University

description: processed data file: AMOs.count.txt

data_processing:
Before mapping, low quality(Q<20) reads and adaptor were removed
Clean data were mapped against the X.laevis v7.1 reference by Tophat v2.0.09. Only unique mapped reads were used.
Bedtools v2.16.2 was used to calculate the gene counts and R  Bioconductor /edgeR package v3.8.5 was used to normalize the gene counts with the method of RPKM.
The normalized gene counts were then used to evaluate differential  expression with R Bioconductor/DEGseq package v 1.20.0. The differentially expressed  genes between two conditional samples were determined using the method MARS  (MA-plot-based method with random sampling model), fold change cutoff=0.5, p  value cutoff=0.001 (signature called by DEGseq).
Genome_build: X.laevis v7.1
Supplementary_files_format_and_content: raw count,content[gene name\tgene counts in replicate1\tgene counts  in replicate2\tgene counts  in replicate3]

organism: Xenopus laevis

source_name: Whole embryo_Ascl1 MO knockdown

growth_protocol: Embryos were cultured in 0.1×MMR until st11

extract_protocol:
Two embryos were frozen for each sample and RNA was harvested by phenol chloroform extraction method. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-930-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole embryo

tag: developmental stage


title: male_flower_2


title: male_flower_3


title: male_flower_1


title: AMOs rep2

description: processed data file: AMOs.count.txt


title: male_flower_0


title: cMO rep3

description: processed data file: cMO.count.txt

source_name: Whole embryo_control


title: AMOs rep1

description: processed data file: AMOs.count.txt


title: male_flower_4


title: female_flower_late_0

source_name: Female flower tissue, late flower development


title: female_flower_late_1

value: Female flower tissue, late flower development


title: female_flower_early_3


title: female_flower_early_2

source_name: Female flower tissue, early flower development


title: cMO rep2

description: processed data file: cMO.count.txt


title: female_flower_early_1

value: Female flower tissue, early flower development


title: hMeRIP-Seq S2 (dTet depletion)

status: Public on Jan 15 2016

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

description: dTet CRISPR S2 cells

data_processing:
reads aligned to the dm3 genome using BWA
peaks were called using MACS v1.4
Genome_build: dm3
Supplementary_files_format_and_content: wig and bed files

organism: Drosophila melanogaster

source_name: S2 CRISPR dTet

growth_protocol: S2 cells (Invitrogen) were maintained in serum-free medium (Express Five; Life Technologies) supplemented with 18 mM L-glutamine at 24°C.

extract_protocol: Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina) after reverse transcription of pulled-down RNA and synthesis of a second strand (NEBNext mRNA second strand synthesis module (NEB). The antibody used for RIP was Diagenode rat monoclonal catalog number C15220001.

tag: cell line


title: female_flower_early_0


title: hMeRIP-Seq S2 (Yellow)

description: Yellow CRISPR S2 cells

source_name: S2 CRISPR yellow


title: RNA-Seq dTet KD S2 (r2)

data_processing:
reads aligned to the dm3 genome using BWA
exon quantification was done using FlyBase dm3 transcripts
Genome_build: dm3
Supplementary_files_format_and_content: wig and bed files

source_name: dTet KD S2 cells replicate 2

extract_protocol: Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina) after reverse transcription of pulled-down RNA and synthesis of a second strand (NEBNext mRNA second strand synthesis module (NEB).The antibody used for RIP was Diagenode rat monoclonal catalog number C15220001.


title: hMeRIP-Seq Input S2 (Yellow)

description: Input Yellow CRISPR S2 cells


title: hMeRIP-Seq S2 (#2)

description: hMeRIP S2 cells (#2)

data_processing:
reads aligned to the dm3 genome using BWA
peaks were called using MACS v1.4
exon quantification was done using FlyBase dm3 transcripts
Genome_build: dm3
Supplementary_files_format_and_content: wig file

extract_protocol: Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina) after reverse transcription of pulled-down RNA and synthesis of a second strand (NEBNext mRNA second strand synthesis module (NEB)). The antibody used for RIP was Active Motif 5-Hydroxymethylcytosine (5-hmC) antibody (pAb) (ref 39791).


title: hMeRIP-Seq S2 (#1)

source_name: hMeRIP S2 cells


title: DHBP rep2_RNASeq

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

data_processing:
The sequencing reads were mapped to the S. aureus Newman strain genome by TopHat (version 2.0.0) with two mismatches allowed.
Cutffdiff software (version 2.0.0) was used to perform gene differential expression analysis.
Genes were annotated by BLAST and the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (http://david.abcc.ncifcrf.gov).
Genome_build: Staphylococcus aureus subsp. aureus str. Newman ASM1046v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values calculated by Cuffdiff. Significantly DE genes are labled.

source_name: S. aureus cells

growth_protocol: The Newman wild-type strain, V149A, and D119A mutants were grown at 37 ºC overnight in TSB.

extract_protocol:
Bacteria were collected by centrifugation and washed with PBS. The cells were lysed by a bead beater and the total RNA was extracted by using an RNeasy minikit (Qiagen) with DNase I treatment step. The rRNA was removed by a MICROBExpress kit (Ambion) and the remaining RNA was utilized to construct the cDNA library by a TruSeq RNA sample prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell cultures were then 1:100 diluted into fresh TSB supplemented with 50 μM DHBP when indicated and incubated at 37 ºC for 2 h until the cultures reached an OD600 of ~ 0.6.

value: Newman

value: WT

tag: treatment

value: DHBP treatment


title: RNA-Seq S2 (r1)

source_name: dTet Ctrl S2 cells replicate 1

extract_protocol: Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina) after reverse transcription of pulled-down RNA and synthesis of a second strand (NEBNext mRNA second strand synthesis module (NEB).  The antibody used for RIP was Diagenode rat monoclonal catalog number C15220001.


title: RNA-Seq dTet KD S2 (r1)

source_name: dTet KD S2 cells replicate 1


title: RNA-Seq S2 (r2)

source_name: dTet Ctrl S2 cells replicate 2


title: WalKV149A rep2_RNASeq

organism: Staphylococcus aureus subsp. aureus str. Newman

value: WalKV149A mutant


title: DHBP rep1_RNASeq


title: KPE-3537_2 NA-seq_rep2

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

institute: Max Delbrüch Center

description:
restriction digested DNA
KPE-3537_2

data_processing:
BigWig files (.bw) were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
The input and KPE samples were downsampled using random_lines1 from Galaxy to be comparable with the lower sized ones.
human samples were aligned against hg38, mouse samples were aligned against mm10
bigwig files containing the read density along the chromosomes

source_name: primary lung tumor-drived cells

growth_protocol: NSCLC were grown in F12 medium supplemented with 10% FBS, and 5% penicillin and streptomycin, hydrocortisone, recombinant hEGF, insulin-transferrin selenium; human A549 were propagated in RPMI, 10% FBS, and 5% penicillin and streptomycin

extract_protocol:
AMPure beads
Libraries were prepared as described in detail by Gargiulo et al., 2009 Dev.Cell and Saeed et al., 2012 Blood). Sticky-end DNA were ligated to custom adapters. After adapter ligation DNA, library fragments were amplified by 12 cycle of PCR followed by streptavidin beads purification of amplified/denatured ssDNA. The purified DNA was further PCR amplified and then Libraries were sequenced on the HiSeq2500 Genome Analyzer following the manufacturer's protocols.

treatment_protocol: NA-seq were generated by isolating nuclei from cultured cells and digesting these with NlaIII and HpaII. After isolation, DNA was fractionated with Sau3AI. Input DNA was fractionated with NlaIII and HpaII as well to add non-chromatin cuts.

tag: sample type

value: NlaIII, HpaII, Sau3AI digested chromatin


title: KPE-3563_3 NA-seq_rep3

description:
restriction digested DNA
KPE-3563_3


title: WalKD119A rep2_RNASeq

value: WalKD119A mutant


title: KPE-3537_1 NA-seq_rep1

description:
restriction digested DNA
KPE-3537_1


title: KP141-3537_1 NA-seq_rep1

description:
restriction digested DNA
KP141-3537_1


title: KP141-3563_3 NA-seq_rep3

description:
restriction digested DNA
KP141-3563_3


title: WalKD119A rep1_RNASeq


title: KP141-3537_2 NA-seq_rep2

description:
restriction digested DNA
KP141-3537_2


title: Newman wild-type rep2_RNASeq


title: Input-3537_2 Input sample rep2

description:
restriction digested DNA
Input-3537_2

value: NlaIII, HpaII, Sau3AI digested DNA


title: cMO rep1

description: processed data file: cMO.count.txt


title: A549-3563_3 NA-seq_rep3

description:
restriction digested DNA
A549-3563_3

source_name: human cell line

value: A549 cell line


title: Newman wild-type rep1_RNASeq


title: Input-3537_1 Input sample rep1

description:
restriction digested DNA
Input-3537_1


title: A549-3537_2 NA-seq_rep2

description:
restriction digested DNA
A549-3537_2


title: hMeRIP-Seq Input S2 (dTet depletion)

description: Input dTet CRISPR S2 cells


title: hMeRIP-Seq Input S2

source_name: Input S2 cells


title: 3552_8_KP141_1_2_H3K27ac ChIP sample rep1+2

description:
sheared DNA
3552_8_KP141_1_2_H3K27ac

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3558 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes

growth_protocol: NSCLC were grown in F12 medium supplemented with 10% FBS, and 5% penicillin and streptomycin, hydrocortisone, recombinant hEGF, insulin-transferrin selenium and tail vein inected in Nude mice; human A549 were propagated in RPMI, 10% FBS, and 5% penicillin and streptomycin

extract_protocol:
1% Formaldheyde fixation followed by SDS buffer lysis
Libraries were prepared according to Illumina's instructions. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA, library fragments of ~230 bp (insert plus adaptor and PCR primer sequences) were selected from an agarose gel. The final size-selected lib. was amplified by 15 cycle of PCR followed by column purification of amplified DNA. The purified DNA was captured on an Illumina flow cell for cluster generation. ChIP was performed by cross-linking proteins to DNA using 2mM DSG and 1% formaldehyde solution (Gargiulo et al, 2009). Immunoprecipitated DNA (ChIP-seq) and Input DNA were Libraries were sequenced on the Genome Analyzer of HiSeeq2000 following the manufacturer's protocols.

value: immunoprecipitated DNA


title: Input-3563_3 Input sample A549

description:
restriction digested DNA
Input-3563_3


title: YD65

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
4C-Seq WA01 rep1

data_processing:
Library strategy: 4C-Seq
4C-Seq data were mapped using 4Cseqpipe (van de Werken et al., 2012) with the first cutter set as DpnII and the second cutter set as NlaIII.
Genome_build: hg18

source_name: hESC WA01

growth_protocol: Cells were cultured at 37 celsius degree in 5% CO2, in Essential 8 media (Stemcell Technologies).

extract_protocol:
4C-Seq library was prepared following the protocol described in van de Werken et al. 2012 (PMID: 22961246). DpnII and NlaIII were used as the 4 base cutter in 4C-Seq.
Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).

treatment_protocol: Regular hESC culture without any special treatment.

value: human embryonic stem cell (hESC)


title: A549-3537_1 NA-seq_rep1

description:
restriction digested DNA
A549-3537_1


title: YD66

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
4C-Seq WA01 rep2


title: 3552_5_KPE_1_2_K27me3 ChIP sample rep1+2

description:
sheared DNA
3552_5_KPE_1_2_K27me3

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3557 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes


title: YD87

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
4C-Seq WA01 rep3


title: 3552_2_KP141_2_K27me3 ChIP sample rep2

description:
sheared DNA
3552_2_KP141_2_K27me3

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3556 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes


title: RNA-seq mH2A1.2i_MT_rep1

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

data_processing:
Illumina Casava1.8 software used for basecalling  and demultiplexing.
Sequenced reads were mapped to mm9 whole genome using Bowtie (Langmead et al, 2009), and TopHat(Trapnell C, et.al 2009) for RNA-Seq.
MacroH2A Peaks ,and ATAC-Seq enriched regions were called using MACS2  ( Zhang et al, 2008), with qvalue of 0.05, --gsize mm, with both narrow and broad peak calling options and the rest were defualt setting. Peak summit location, obtaiend through narrow peak calling, were moslty used for overlaping nad colocalization analysis.
FPKM(RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: Peak files and transcript RPKM file. BigWig files generated from aligned reads after removing duplicates.

source_name: C2C12 cell line

growth_protocol: mouse skeletal muscle C2C12 cells  were  grown in high glucose- DMEM (Gibco), 20% fetal bovine serum (FBS, Gibco), Penicillin/streptomycin (1x, Gibco).

extract_protocol:
For ChIPSeq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen). For ATACSeq, 5x104 C2C12 cells were pelleted, washed with 50ul of 1xPBS and lysed in 50ul of Lysis Buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% of IGEPAL CA-630).  To tag and fragment accessible chromatin, nuclei were centrifuged at 500x g for 10min and re-suspended in 40ul of transposition reaction mix with 2ul Tn5 transposase (Illumina Cat# FC-121-1030). The reaction was incubated at 37ºC with shaking at 300rpm for 30min.  DNA-fragments were then purified, and amplified by PCR (12-15 cycles based on the amplification curve).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with anti-histone mH2A1.2 (Cell signaling, 4827S), anti-mH2A1 (Abcam, ab37264), anti-Pbx1 (Abnova, H00005087), anti-histone H3 (acetyl K27) (Abcam, ab4729), anti-trimethyl-histone H3 (Lys27) (Millipore, 07-449). 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. For polyA RNA-Seq, Illumina protocol was followed.  ATACSeq samples were multiplexed using primers Ad2.1-4 paired with Ad1 for final library amplification as described previously (Buenrostro et al., 2013).

treatment_protocol: For differentiation, cells were placed in high-glucose DMEM media (Gibco) with 2% horse serum (Gibco) and Insulin, Frasferrin, Selenium (1x, Gibco).

value: Myotubes


title: RNA-seq mH2A1.2i_MB_Rep2

value: Myoblast


title: AY1653

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq Input_WA01 Set2

data_processing:
ChIP-seq experiments were mapped to human genome build hg18 using Bowtie v0.12.7 with the following options: “-S -t -q -p 4 -m 1 -n 2 -l 32 -e 3001”. Duplicated reads (reads with same strand, mapped to same chromosome, and same starting location) are removed after bam files sorted using samtools. Next, bam files are converted to bed files using bamToBed, and then bed files are extended to up to 300 bp in the direction to the end coordinate: "slopBed -s -l 0 -r 200"; then bed file are converted into BedGragh files using genomeCoverageBed with option "-bg"; Last, BedGraph are converted into bigwig using wigToBigWig files using default parameter.
Genome_build: hg18

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Heintzman et al., 2007). Briefly, 10-20 million of cultured cells and ~0.2 g of frozen tissue samples were cross-linked in 1% formaldehyde at room temperature for 10 and 25 minutes, respectively. Cross-linked samples were sonicated until chromatin fragments were of 200-600 bp in length. Chromatin immunoprecipitation was carried out using 3-5 µg of antibody and 200 µg of chromatin preparation in RIPA buffer at 4 degree overnight. After five washes in RIPA and one wash with 1xTE buffer, chromatins were eluted and reverse cross-linked at 65 C overnight. DNA was purified after phenol extraction.
Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).


title: RNA-seq mH2A1.2i_MB_Rep1


title: AY1661

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq H3K27ac_WA01 set2


title: WalKV149A rep1_RNASeq


title: 3552_1_KP141_1_K27me3 ChIP sample rep1

description:
sheared DNA
3552_1_KP141_1_K27me3

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3555 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes


title: RNA-seq CTL_MT_Rep1


title: RNA-seq CTL_MB_Rep2


title: RNA-seq CTL_MB_Rep1


title: 3552_10_KPE_1-2 H3K27ac ChIP sample rep1+2

description:
sheared DNA
3552_10_KPE_1-2 H3K27ac

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3559 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes


title: AY1660

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq H3K27ac_WA01 set1


title: AY1652

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq Input_WA01 Set1


title: RNA-seq KO HUDEP EDM2 rep2

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description:
RNA-Seq
cDNA
human.count.data.csv

data_processing:
ATAC-seq data: reads were aligned using bowtie2 with -k1 -X 3000 option after adapter tirmming. Duplicates were removed using samtools. Fragment end positions were obtained from the aligned reads, and written out as a smoothed density (using 100bp bandwidth) using spp R package (https://github.com/hms-dbmi/spp).
ChIP-seq: reads were aligned using bowtie2 (either using -k 1 option, or filteirng for uniquely-aligned reads only), and the smoothed enrichment profiles, conservative enrichment profiles as well as peak calls were generated using spp.
RNA-seq data was aligned using tophat2, read counts were quantified with HTSeq. Differential expression analysis was performed using DESeq R pacakge.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: tdf files were generated by converting wig files using igvtools; For RNA-seq data, the HTSeq read counts for each sample were written out into a joint comma-separated text file, separate for mouse and human datasets

source_name: LRF KO HUDEP-2

extract_protocol:
Total RNA was extracted from FACS-sorted splenic erythroblasts (or HUDEP-2 cells) using RNeasy Mini Kit (QIAGEN). 125 ng of purified RNA was used for library construction.
Encore Complete RNA-Seq DR Multiplex System following the manufacturer’s specifications (Nugen).

tag: differentiation stage

value: Late basophilic erythroblasts

tag: culture condition

value: EDM-II doxycycline+ (Day5)

tag: mouse strain


title: Input_MT_rep2

tag: chip antibody

value: none (input)


title: RNA-seq KO HUDEP SFEM rep2

description:
RNA-Seq
cDNA
human.count.data.csv

value: Early basophilic erythroblasts

value: SFEM doxycycline+ (Day0)


title: RNA-seq WT HUDEP EDM2 rep2

description:
RNA-Seq
cDNA
human.count.data.csv

source_name: WT HUDEP-2


title: RNA-seq KO HUDEP EDM2 rep1

description:
RNA-Seq
cDNA
human.count.data.csv


title: IgG_MB

value: Rabbit IgG (Abcam, ab171870)


title: ATAC-seq_MT_Rep2

description: library strategy: ATAC-Seq


title: RNA-seq WT HUDEP SFEM rep2

description:
RNA-Seq
cDNA
human.count.data.csv


title: RNA-seq KO HUDEP SFEM rep1

description:
RNA-Seq
cDNA
human.count.data.csv


title: ATAC-seq_MT_Rep1

description: library strategy: ATAC-Seq


title: ATAC-seq_MB_Rep2

description: library strategy: ATAC-Seq


title: RNA-seq WT HUDEP SFEM rep1

description:
RNA-Seq
cDNA
human.count.data.csv


title: ChIP-seq input hCD34+ derived EBs day 8

description:
ChIP-Seq
chromatin DNA

source_name: G-CSF morbilized CD34+-derived erythrblasts

extract_protocol:
Five million cells were fixed with 1% formaldehyde at RT for 20 min and chromatin was collected using a truChIP High Cell Chromatin Shearing Kit with SDS (Covaris).
ChIP-Seq libraries were generated using a Ovation Ultralow DR Multiplex System 1-8 (NuGEN)

value: EDM-II (Day8)


title: ChIP-seq LRF hCD34+ derived EBs day 8 rep2

description:
ChIP-Seq
chromatin DNA


title: H3K27ac_mH2A1i_MB_Rep1

value: anti-histone H3 (acetyl K27) (Abcam, Cat# ab4729, Lot# GR184332-1)


title: H3K27ac_mH2A1i_MT_Rep1


title: ChIP-seq LRF hCD34+ derived EBs day 8 rep1

description:
ChIP-Seq
chromatin DNA


title: ChIP-seq input HUDEP

description:
ChIP-Seq
chromatin DNA


title: H3K27ac_MB_Rep1


title: mH2A1.2_SiMacro_MB

value: anti-mH2A1 (Abcam, Cat# ab37264, Lot# GR132054-1)


title: Input_MT_rep1


title: mH2A1.2_MT_Rep2


title: mH2A1.2_MT_Rep1

value: mH2A1.2 (Cell signaling, Cat# 4827S, Lot# 1)


title: ATAC-seq KO HUDEP EDM2 rep2

description:
ATAC-Seq
chromatin DNA

extract_protocol:
ATAC-Seq libraries were constructed using 7.5x10^4 HUDEP-2 cells per sample as described in Buenrostro et al. Nat Methods. 2013 Dec;10(12):1213-8
ATAC-Seq libraries were constructed using 7.5x10^4 HUDEP-2 cells per sample as described in Buenrostro et al. Nat Methods. 2013 Dec;10(12):1213-8


title: ChIP-seq LRF HUDEP rep2

description:
ChIP-Seq
chromatin DNA


title: RNA-seq KO mouse EB-S rep3

description:
RNA-Seq
cDNA
mouse.count.data.csv

source_name: LRF KO mouse splenic erythroblasts (Ter119+CD71+CD44mid+FSCmid)

value: Polychromatophilic erythroblasts

value: Not cultured. Directly from spleen.


title: ChIP-seq LRF HUDEP rep1

description:
ChIP-Seq
chromatin DNA


title: mH2A1.2_MB_Rep1

value: mH2A1.2 (Cell signaling,  Cat# 4827S, Lot# 1)


title: ATAC-seq WT HUDEP EDM2 rep2

description:
ATAC-Seq
chromatin DNA


title: mH2A1.2_MB_Rep2


title: ATAC-seq WT HUDEP SFEM rep2

description:
ATAC-Seq
chromatin DNA


title: RNA-seq KO mouse EB-L rep3

description:
RNA-Seq
cDNA
mouse.count.data.csv

source_name: LRF KO mouse splenic erythroblasts (Ter119+CD71+CD44high+FSChigh)

value: Basophilic erythroblasts


title: RNA-seq WT HUDEP EDM2 rep1

description:
RNA-Seq
cDNA
human.count.data.csv


title: ChIP-seq LRF HUDEP rep3

description:
ChIP-Seq
chromatin DNA


title: ATAC-seq KO HUDEP SFEM rep2

description:
ATAC-Seq
chromatin DNA


title: ATAC-seq KO HUDEP EDM2 rep1

description:
ATAC-Seq
chromatin DNA


title: ATAC-seq KO HUDEP SFEM rep1

description:
ATAC-Seq
chromatin DNA


title: RNA-seq WT mouse EB-L rep3

description:
RNA-Seq
cDNA
mouse.count.data.csv

source_name: WT mouse splenic erythroblasts (Ter119+CD71+CD44high+FSChigh)


title: ATAC-seq_MB_Rep1

description: library strategy: ATAC-Seq


title: ATAC-seq WT HUDEP EDM2 rep1

description:
ATAC-Seq
chromatin DNA


title: RNA-seq WT mouse EB-S rep3

description:
RNA-Seq
cDNA
mouse.count.data.csv

source_name: WT mouse splenic erythroblasts (Ter119+CD71+CD44mid+FSCmid)


title: RNA-seq KO mouse EB-S rep2

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: H3K27ac_MT_Rep1


title: RNA-seq WT mouse EB-S rep2

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: RNA-seq KO mouse EB-L rep2

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: 3MWT-Stage5-Rep3

city: Blacksburg

first: M.A. Saghai

last: Maroof

state: VA

address: 220 Ag Quad Ln

department: Crop & Soil Environmental Sciences

institute: Virginia Tech

data_processing:
Sequencing reads were mapped to the reference genome using TopHat, v2.0.8. Sequence mapping data was used to estimate expression values for annotated genes using HTSeq-count ‘Union' mode.
Developmental stage-specific differential gene expression analyses between 3mlpa and 3WMT was performed using DESeq, v1.12.1. The differentially expressed genes significant at 1% false discovery rate (FDR) were identified.
Functional enrichment analyses of differentially expressed genes was performed to identify enriched gene ontology terms significant at 1% FDR using AgriGO tool (parameters: hypergeometric testing and p-value correction using multiple testing with Benjamini-Hochberg method).
Enriched transcription factor families in each seed developmental stage, significant  at 1% FDR  were identified using hypergeometric testing and p-value correction using multiple testing with Benjamini-Hochberg method.
Genome_build: 'Williams 82' soybean reference genome (assembly Glyma.Wm82.a1.0, annotation v1.1)
supplementary file types: abundance measurements, DESeq output, AgriGO enrichment, and Transcription factor family

organism: Glycine max

source_name: Developing seed

extract_protocol:
Whole soybean developing seeds sampled in triplicate from 3mlpa and 3MWT lines at five stages of seed development, were flash frozen, and total RNA was extracted using QIAGEN RNeasy Plant Mini Kit, with on column DNase digestion.
High quality total RNA samples were used to generate 30 mRNA libraries using standard Illumina TruSeq RNA sample preparation kit protocol.

tag: Stage

tag: seed length


title: 3MWT-Stage5-Rep2


title: RNA-seq WT mouse EB-L rep2

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: 3MWT-Stage5-Rep1


title: RNA-seq KO mouse EB-S rep1

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: 3MWT-Stage4-Rep3


title: RNA-seq KO mouse EB-L rep1

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: RNA-seq WT mouse EB-L rep1

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: 3MWT-Stage4-Rep1


title: 3MWT-Stage3-Rep3


title: 3MWT-Stage3-Rep2


title: 3MWT-Stage2-Rep1


title: 3MWT-Stage3-Rep1


title: 3MWT-Stage2-Rep2


title: 3MWT-Stage2-Rep3


title: 3MWT-Stage1-Rep2


title: 3MWT-Stage1-Rep3


title: 3mlpa-Stage5-Rep3


title: 3mlpa-Stage5-Rep2


title: ATAC-seq WT HUDEP SFEM rep1

description:
ATAC-Seq
chromatin DNA


title: 3mlpa-Stage4-Rep1


title: 3mlpa-Stage4-Rep3


title: 3mlpa-Stage4-Rep2


title: 3mlpa-Stage5-Rep1


title: 3mlpa-Stage3-Rep3


title: 3mlpa-Stage3-Rep1


title: AY1704

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq H3K27ac_DHS_37_KO_clone4 Set2

source_name: hESC WA01 DHS_37 KO

value: human embryonic stem cell (hESC)


title: 3mlpa-Stage3-Rep2


title: AY1703

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq H3K27ac_DHS_37_KO_clone4 Set1


title: 3mlpa-Stage2-Rep3


title: 3MWT-Stage4-Rep2


title: RNA-seq WT mouse EB-S rep1

description:
RNA-Seq
cDNA
mouse.count.data.csv


title: 3mlpa-Stage2-Rep2


title: 3mlpa-Stage2-Rep1


title: AY1701

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq H3K27ac_DHS_37_KO_clone3 Set1


title: AY1702

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq H3K27ac_DHS_37_KO_clone3 Set2


title: 3mlpa-Stage1-Rep3


title: AY1697

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq Input_DHS_37_KO_clone4 Set1


title: 3MWT-Stage1-Rep1


title: AY1698

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq Input_DHS_37_KO_clone4 Set2


title: Lentivirus treated, replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina Casava software used for basecalling.
Reads were mapped to the Chlorocebus sabaeus genome version ChiSab1.0 using Tophat2 v2.0.10 with the multithreading option -p 5 and the remaining parameters as the default allowing for two mismatches.  Tophat2 was using bowtie2 v2.1.0.0 as the underlying mapper.
Mapped reads were assembled into transcripts with cufflinks v2.1.1 using the multithreading option -p 5 and the remaining options as the defaults.  The gtf used for transcript construction was the Chlorocebus.sabaeus.Chlsabe.0.pre.gtf downloaded from the Ensembl pre release site ftp://ftp.ensembl.org/pub/pre/gtf/chlorocebus_sabaeus/
Aligned reads were used as inputs for cuffdiff2 to determine gene expression levels (FPKM) and differential expression between conditions using the multithreading option -p 8 and the minimum alignment count of 7 (--min-alignment-count 7).  All other parameters were set to the defaults.
Differential expression was tested for LV treatment  by comparing the combined alignments of samples 4, 5 and 6 (LV) to the combined alignments of samples 1,2 and 3 using cuffdiff2.
Genome_build: ChiSab1.0 GCA 000409795.1
Supplementary_files_format_and_content: Genes_FPKMValues.txt is a tab-delimited text file containing the gene ID, locus, and FPKM values for each gene assembled using cufflinks.  gene_exp.diff is the resulting differential expression results for Lentivirus treated vs. NT.  This file is output by cuffdiff.  A q-value cutoff of 0.05 was used to determine differentially expressed genes.

organism: Chlorocebus sabaeus

source_name: transformed COS-1 cell line

growth_protocol: Cells were grown in DMEM with 10% FBS at 37oC, 5% CO2.

extract_protocol:
Total RNA was extracted using BioRad Total RNA isolation Kits and PureZOL according to the manufacturer’s instruction. The RNA quality was examined using Agilent Bioanalyzer.
Library was constructed in UT Southwestern genomics core using illumina’s mRNA-Seq sample preparation kits to generate full sequence from any poly-A tailed RNA to generate library with single-read, paired-end or multiplexing sequencing on all illumina sequencing systems (Genome Analyzer or HiSeq). The service included mRNA isolation, cDNA synthesize, fragmentation, adding adaptors, size selection, amplification and QC.

treatment_protocol: Cells were serum-starved for 14 h, and then treated with 2ng/ml of epidermal growth factor (EGF) for 90 min.

value: Lentivirus treated


title: Lentivirus treated, replicate 2


title: 3mlpa-Stage1-Rep1


title: AY1696

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq Input_DHS_37_KO_clone3 Set2


title: AY1695

description:
WA01 was hESC line derived from H1 hESC harboring a eGFP reporter for POU5F1 (Zwaka TP et al. 2003)
ChIP-Seq Input_DHS_37_KO_clone3 Set1


title: No treatment, replicate 3

value: Control


title: P_0136

first: Alexandra

last: Dumitriu

address: 72 East Concord Street

department: Neurology

institute: Boston University

description:
mlpd_PCG_DESeq2_norm_counts.txt
mlpd_DESeq2_diffexp_pmi_age_rin_default.txt

data_processing:
RNA-Seq: Bases were called with the Illumina CASAVA 1.7 pipeline
RNA-Seq: mRNA-Seq reads were aligned against UCSC hg19 genome build with tophat 2.0.1, parameters --read-mismatches=3 --read-edit-dist=3 --max-multihits=20 --splice-mismatches=1 --microexon-search --coverage-search --mate-inner-dist=50 --mate-std-dev=50 –num-threads=8
RNA-Seq:  Aligned reads were counted against the Gencode v17 gene annotation using htseq-count in the HTSeq package with –mode=intersection-nonempty
RNA-Seq: Genes that were not protein coding (PCG) were filtered from further analysis
RNA-Seq: Genes were filtered from further analysis that had more than half of both PD and Control samples with zero counts
RNA-Seq: Differential expression between PD and controls was assessed using DESeq2 v1.4.0
genome build: hg19
proteomics: MS/MS and MS/MS/MS spectra were searched against the human IPI database (Version 3.87) from the European Bioinformatics Institute using the SEQUEST algorithm, with modifications permitted to allow the detection of oxidized Met (+16), carboxyamidomethylated Cys (+57), and phosphorylated Ser, Thr and Tyr (+80)
proteomics: The raw proteomics data for 3,558 unique gene symbols were normalized in R using two steps: 1) an intra-experimental (within plex) variation step – for each sample, each protein’s raw signal was normalized to the total ion intensity of the protein within the plex, and 2) an inter-experimental (across plexes) variation step – for each sample, each protein’s normalized value from step 1) was transformed by dividing it to the mean of all normalized values of the protein obtained in step 1) of all 24 samples.
proteomics: The Surrogate Variable Analysis (SVA) method implemented in the sva R package (v3.10.0) was used to eliminate latent noise in the data not explained by the categorical factors, including batch effects. Three significant surrogate variables (SVs) were identified for the proteomics data.
proteomics: The limma R package was used for statistical analysis of differential abundance, using a linear model fit including the 3 SVs for the contrast between the PD and the control groups.
proteomics: The protein abundance p-values were adjusted for multiple comparisons using the q-value method; a gene was considered to be significantly different between PD and control samples if it had an adjusted q-value < 0.05.
processed data files format and content: Processed files contain: normalized counts for all samples (mlpd_PCG_DESeq2_norm_counts.txt) and differential expression values (mlpd_DESeq2_diffexp_pmi_age_rin_default.txt) from DESeq2 for protein-coding genes (PCG), in tab delimited format; normalized protein abundance data for 3,558 gene symbols with information about the proteomics samples included in the four 6-plex experiments (proteomics_dataset.RData - objects contained are "expdata", "genename", and "normdata"; the gene order in "genename" corresponds to the gene order in "normdata")

source_name: BA9 prefrontal cortex

extract_protocol:
QIAzol, Qiagen miRNeasy kit
Illumina TruSeq RNA Sample Prep Kit, mRNA

tag: tissue

value: brain (BA9 prefrontal cortex)

tag: gender

value: male

tag: post-mortem interval (pmi)

tag: rna integrity number (rin)

tag: age at death

tag: proteomics study

value: no

tag: microarray study


title: No treatment, replicate 1


title: No treatment, replicate 2


title: P_0135


title: pregnant mare, ispislateral oviduct, replicate 4

city: Gent

first: Dieter

last: De Coninck

address: J. Plateaustraat 22

department: Applied Ecology and Environmental Biology

institute: Ghent University

data_processing:
Basecalling performed with Illumina CASAVA 1.8 pipeline
Resulting reads were mapped to gene regions of the Ecab2 genome assembly, using Ensemble database built 80 annotations and the CLC Genomics Workbench 7.5.1 software built-in mapping tool with the following specifications: Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.7; Similarity fraction = 0.8; Global alignment = No; Auto-detect paired distances = Yes; Strand specific = Both; Maximum number of hits for a read = 10; Count paired reads as two = No
Uniquely mapping reads per gene regions were counted using a total count filter cutoff equal to = 10.0
Read counts were TMM normalized.
Differential gene-expression analysis was performed with CLC Genomics Workbench's empirical analysis of DGE (EDGE) tool which implements the 'Exact Test' for two-group comparisons developed by Robinson and Smyth (Robinson and Smyth 2008) using standard settings. Genes were considered to be differentially expressed if they had a p-value ≤ 0.05 and an absolute fold change ≥ 2.
Genome_build: Ecab2
Supplementary_files_format_and_content: Tab-delimited text files containing TMM normalized read counts for each sample

organism: Equus caballus

source_name: epithelial cells from the ampullary-isthmic junction of the oviduct

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, US), according to the manufacturers’ protocol, including a DNAse digestion
500 ng of RNA was used to start the library preparation using the 'Truseq stranded Total RNA library prep kit' (Illumina, San Diego, CA, US) with rRNA depletion and according to manufacturer's protocol.

tag: breed

value: Warmblood

tag: pregnancy status

value: pregnant

tag: pregnancy time

value: 4 days after ovulation

tag: oviduct

value: ipsilateral to ovulation side


title: P_0134


title: pregnant mare, ispislateral oviduct, replicate 2


title: pregnant mare, ispislateral oviduct, replicate 1


title: P_0133


title: pregnant mare, contralateral oviduct, replicate 5

value: contralateral to ovulation side


title: P_0132


title: pregnant mare, contralateral oviduct, replicate 4


title: pregnant mare, contralateral oviduct, replicate 3


title: 3mlpa-Stage1-Rep2

tag: genotype


title: pregnant mare, contralateral oviduct, replicate 1


title: P_0130


title: Lentivirus treated, replicate 1

tag: cell line

tag: treatment


title: P_0063


title: pregnant mare, contralateral oviduct, replicate 2


title: cyclic mare, ipsilateral oviduct, replicate 3

value: cyclic


title: cyclic mare, ipsilateral oviduct, replicate 2


title: cyclic mare, contralateral oviduct, replicate 5


title: P_0126


title: cyclic mare, ipsilateral oviduct, replicate 1


title: cyclic mare, ipsilateral oviduct, replicate 4


title: pregnant mare, ispislateral oviduct, replicate 5


title: cyclic mare, contralateral oviduct, replicate 4


title: P_0031

description:
Microarray data in ArrayExpress (E-MTAB-812)
mlpd_PCG_DESeq2_norm_counts.txt
mlpd_DESeq2_diffexp_pmi_age_rin_default.txt
proteomics_dataset.RData

value: yes

tag: proteomics sv1

tag: proteomics sv2

tag: proteomics sv3


title: P_0033

description:
Microarray data in ArrayExpress (E-MTAB-812)
mlpd_PCG_DESeq2_norm_counts.txt
mlpd_DESeq2_diffexp_pmi_age_rin_default.txt

tag: tissue


title: P_0034

tag: gender


title: cyclic mare, ipsilateral oviduct, replicate 5


title: pregnant mare, ispislateral oviduct, replicate 3


title: cyclic mare, contralateral oviduct, replicate 2


title: cyclic mare, contralateral oviduct, replicate 3


title: cyclic mare, contralateral oviduct, replicate 1


title: P_0030

tag: post-mortem interval (pmi)


title: P_0028

tag: rna integrity number (rin)


title: gld-1 +  fasting

city: Frankfurt am Main

first: Devang

middle: Savdas

last: Odedra

state: Hesse

address: Max-von-Laue-Street 15

institute: Buchmann Institute for Molecular Life Sciences

description:
gld-1 RNAi animals transferred to unseeded plates at the second day of adulthood for 48 hours
mRNA

data_processing:
3'-adaptor sequences were trimmed from the RNA sequencing reads using custom-built Perl script.
Read alignment was performed using TopHat
Uniquely mapped reads were quantified by counting the overlap of reads with genes using the HtSeq python package
Count data was variance-stabilized to overcome the influence of bias due to difference in library size.
Differential expression analysis was performed using the DESeq software
Genome_build: Ensembl WS220
Supplementary_files_format_and_content: Comma-separated files containing fold-change values of expression.

organism: Caenorhabditis elegans

source_name: gld-1 +  fasting

growth_protocol: Synchronized L1 larvae were placed on L4440 control or gld-1 RNAi plates and kept at 20°C.

extract_protocol:
A total of ca. 3000 animals pulled from two independent experiments were collected per condition. The animals were washed off the plates with M9, washed four additional times with M9 to remove remaining bacteria and the pellet of worms was frozen in liquid nitrogen.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNAi was performed by feeding according to standard protocols.

tag: RNAi treatment

tag: age

value: Fourth day of adulthood


title: Young adults

description:
Control animals on L4440 plate
mRNA

source_name: Young adults

value: L4440 control

value: First day of adulthood


title: gld-1

description:
Transferred to gld-1 RNAi plate after first day of adulthood and harvested after two days
mRNA

value: Third day of adulthood


title: gld-1 + L4440 feeding

description:
gld-1 RNAi animals were moved to L4440 seeded plates at the second day of adulthood for 48 hours,
mRNA

source_name: gld-1 + L4440 feeding


title: Control

description:
Control animals on L4440 plate
mRNA

source_name: Control


title: P_0029

tag: age at death

tag: proteomics study

tag: microarray study


title: 3105_1_KPE_105 RNA-seq_rep5

data_processing:
Sequencing reads were mapped against the mouse genome build 38 using tophat 2.0.12 with parameters --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were calculated using HTSeq-count with union mode
Genes that have zero expression across all samples are removed from the dataset.
The file readcounts.txt contains the absolute gene expressions values for each of the samples.

source_name: primary lung tumor-drived cells

growth_protocol: NSCLC were grown in F12 medium supplemented with 10% FBS, and 5% penicillin and streptomycin, hydrocortisone, recombinant hEGF, insulin-transferrin selenium and tail vein inected in Nude mice

extract_protocol:
Trypsin/Collegenase/Hyarulonydase/DNaseI digestion
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Sample Prep protocols.

treatment_protocol: Mice received Ad-CMV-Cre between 7-10 weeks and were housed according to standard protocols

tag: cell type

value: primary mouse NSCLC


title: 3105_3_KPE_147 RNA-seq_rep3


title: 3105_2_KPE_108 RNA-seq_rep4


title: P_0027


title: 3105_4_KPE_155 RNA-seq_rep2


title: P_0026


title: 3105_6_KPE_810 RNA-seq_rep1


title: P_0023

value: P_23 - failed QC


title: 3105_8_KP_2 RNA-seq_rep2


title: P_0022


title: 3105_7_KP_1 RNA-seq_rep1


title: 3105_5_KP_141 RNA-seq_rep3


title: 2249_8__61-K27me3 ChIP sample rep4

description:
sheared DNA
2249_8__61-K27me3

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3554 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes

source_name: lung tumors

tag: sample type

value: immunoprecipitated DNA


title: 2249_6__59-K27me3 ChIP sample rep3

description:
sheared DNA
2249_6__59-K27me3

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3553 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes

tag: genotype


title: P_0021

value: brain (BA9 prefrontal cortex)


title: RNA-seq mH2A1.2i_MT_rep2

source_name: C2C12 cell line

tag: strain

tag: cell line

tag: developmental stage

value: Myotubes


title: 2249_9_I58 Input sample rep2

description:
sheared DNA
2249_9_I58

data_processing:
Reads were mapped with BWA against the mouse reference. Samples 2249 are mapped against mm9 and were filtered for Q37 reads. Bigwig files for the 2249 samples were generated using macs
BigWig files (.bw) for the 3552 samples were created as follows: .bam files were converted to .bed with Galaxy (toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0) and sorted with bash (sort -k1,1n -k2,2n -k3,3n). File in .bed format were then converted in BigWig with Galaxy (CONVERTER_bed_gff_or_vcf_to_bigwig_0)
3552 mm10 / 2249 mm9
bigwig files containing the read density along the chromosomes

value: non-immunoprecipitated DNA


title: P_0020

value: male

tag: proteomics sv1

tag: proteomics sv2


title: P_0019

tag: tissue

tag: proteomics sv3


title: RNA-seq mH2A1.2i_MB_Rep3

value: Myoblast


title: RNA-seq CTL_MT_Rep3


title: P_0018

tag: gender

tag: post-mortem interval (pmi)


title: RNA-seq CTL_MT_Rep2


title: Pbx1_mH2A1i_MT

tag: chip antibody


title: H3K27me3_SiMacro_MB

value: anti-trimethyl-histone H3 (Lys27) (Millipore, Cat# 07-449, Lot# 2607758)


title: RNA-seq CTL_MB_Rep3


title: P_0016

tag: rna integrity number (rin)


title: Pbx1_CTLi_MT


title: P_0015

tag: age at death


title: P_0014

tag: proteomics study


title: H3K27me3_MT


title: H3K27me3_MB


title: H3K27ac_mH2A1i_MB_Rep2

value: anti-histone H3 (acetyl K27) (Abcam, Cat# ab4729, Lot# GR184332-1)


title: P_0013

tag: microarray study


title: H3K27ac_mH2A1i_MT_Rep2


title: RNA-seq mH2A1.2i_MT_rep3


title: P_0012

value: no


title: H3K27ac_MB_Rep2


title: P_0006


title: H3K27ac_MT_Rep2


title: ChIP107.H3K4me3_siNS

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

data_processing:
RNA-seq data analysis: Reads were mapped to the mouse genome (mm9) using bowtie2 (local mode). Uniquely mapped reads with MAPQ score>10 were used. Refseq gene model was used to calculate gene expression level. For protein-coding genes, only reads mapped to coding region were used to eliminate the effect of 3’UTR alternative polyadenylation in gene expression calculation. Reads per kilobase per million total uniquely mapped reads (RPKM) value was calculated to reflect gene expression level. Significantly regulated genes were selected based on these criteria: >1.4-fold difference of RPKM between Paf1C siRNA treated cells and siRNA control cells and P value<0.01 (Fisher’s exact test).
3’READS and data analysis.   3’READS reads were mapped to the mouse genome (mm9) using bowtie2 (local mode). Uniquely mapped reads (with MAPQ score > 10) that had at least two additional 5’ Ts not aligned to genome (presumably derived from the poly(A) tail) were named pA site supporting (PASS) reads and were used to calculate pA isoform expression. pA isoforms expressed below 5% of all isoforms of a gene were discarded.  Significantly regulated APA events were identified by the Significance Analysis of Alternative Polyadenylation (SAAP) method [Li et al., 2015].
ChIP-seq data analysis: Reads were mapped to the mouse genome (mm9) using bowtie2. Reads non-uniquely mapped (MAPQ≤10) were discarded. Multiple reads mapped to same genomic loci (defined by chromosome, strand, start and end position) were collapsed to one. To calculate enrichment score of a genomic locus in a meta-gene plot, the first nt at the 5’end of a read was counted for all genes in a group and converted to read per million total reads (RPM) value. The enrichment score was defined by log2 ratio of RPM between IP sample and input sample. The relative genomic location was binned (e.g., every 50 nt relative to TSS or every percent in gene body) before calculating enrichment score and then plotted in R.
Genome_build: mm9
Supplementary_files_format_and_content: 3READS.pA.read.counts.txt contains information of gene symbol, pA coordinates, read number of pAs in different 3'READS samples. "pAtype" is pA type based on location of a pA (I, intron; E, upstream exons; 3, pAs in 3'most exon; UA, pA in upstream antisense of a protein-coding gene.). "RNA-seq.gene.read.counts.txt" contains information of gene symbol, Refseq transcript name, read number and RPKM (read per kb per million total reads) values. Bigwig files: for visualization of ChIP-seq data, all uniquely mapped and collapsed reads were used. Reads were extended from its 5’end mapped position by 250 nts (reflecting the average fragment size in ChIP-seq DNA libraries) and converted to bigwig format files using an in-house perl script and bedGraphToBigWig program from UCSC genome browser.

source_name: H3K4me3 ChIP-seq, siNS

growth_protocol: C2C12 myoblasts (Sigma) were grown and induced to differentiate into myotubes as described [Blais, A., et al. 2007].

extract_protocol: Preparation of solubilized chromatin fraction and immunoprecipitation: Cell pellets were resuspended in buffer A (10 mM HEPES pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 1 mM dithiothreitol (DTT), and protease inhibitors (aprotinin, leupeptin, pepstatin A, and phenylmethyl sulphonyl fluoride)), supplemented with Triton X-100 (0.1%), and incubated on ice for 5 minutes.  The nuclear pellet was separated from the cytoplasmic fraction, washed once with buffer A, and collected by centrifugation.  Nuclei were lysed with buffer B (3 mM EDTA, 0.2 mM EGTA, 1 mM dithiothreitol (DTT), and protease inhibitors (aprotinin, leupeptin, pepstatin A, and phenylmethyl sulphonyl fluoride)). The solubilized chromatin fraction was separated from nucleoplasm by centrifugation at 2250 g for 4 minutes at 4°C, washed once with buffer B, and collected by centrifugation. For immunoprecipitations, the chromatin pellet was resuspended with binding buffer (20 mM Hepes pH7.9, 100 mM potassium chloride, 0.2 mM EDTA, 20% glycerol, 0.5 mM dithiothreitol (DTT), and 0.5mM AEBSF). 1 mg of protein was immunoprecipated, and antibody-protein A sepharose beads were washed three times with buffer (50 mM Hepes pH7.9, 250 mM sodium chloride, 5 mM EDTA, 0.50% NP-40, and 10% glycerol) prior to SDS–PAGE and immuno-blotting.

treatment_protocol: For transient transfection of siRNA, cells were seeded at 104 cells cm−2 for 48 h transfection. 5 μl RNAiMax in 2 ml medium and 50 nM siRNA were applied to cells by using fast-forward method.

tag: cell condition

value: myoblasts

tag: library protocol

value: ChIP-seq


title: ChIP108.H3_siNS

source_name: H3 ChIP-seq, siNS


title: ChIP109.Input_siNS

source_name: Input for ChIP107.H3K4me3_siNS and ChIP108.H3_siNS


title: LF_STR_24h_B3T2

city: Ithaca

first: Neil

middle: Scott

last: Mattson

state: NY

address: 134A Plant Sci Bldg

department: School of Integrative Plant Science

institute: Cornell University

description: Biological Rep 3. Technical Rep 2

data_processing:
Since there is no Petunia genome available we generate a de-novo transcriptome. The 9 processed data files correspond to different de-novo assemblies performed with 3 assemblers (Trinity, Trans-ABySS, SOAPdenovo-trans) for comparison purposes. In some of the software we adjusted K-mer length ("K25", "K47"....) and in other used  default settings to come up with the best  transcriptome. Downstream analysis we performed with the best results  obtained with Trinity de novo assembler. The HP and NH corresponds to the 2 technical reps; HPLC primers and non-HPLC primers, respectively.
Transcriptome is available at ftp://ftp.solgenomics.net/transcript_sequences/by_species/Petunia_hybrida/assemblies/Phybrida_var_Mitchell_mRNA_Villarino2014.fa and is also BLASTABLE (https://solgenomics.net/tools/blast)
Genome_build: de-novo assembly
Supplementary_files_format_and_content: RAW.Matrix.csv: RPKM values including biological replicte (r1,r2,r3), type of primer used (NH: non-HPLC, HP:HPLC), treatment (STR: 150 mM NaCl, CTR: No NaCl)
Supplementary_files_format_and_content: tab-delimited text files include contigs length from each software used. Type of primer used in libtrary preparation NH: non-HPLC, HP:HPLC. K-mer (K) is indicated.
Supplementary_files_format_and_content: NH_TransABySS: Default k-mer; TransABySS
Supplementary_files_format_and_content: HP_TransABySS: Default k-mer; TransABySS
Supplementary_files_format_and_content: ITAG2.3_cds.length: Tomato reference ;
Supplementary_files_format_and_content: HP_Trinity.K25: adjusted k-mer (K) to 25; Trinity
Supplementary_files_format_and_content: NH_Trinity.K25: adjusted k-mer (K) to 25; Trinity
Supplementary_files_format_and_content: HP_SOAP.K25: adjusted k-mer (K) to 25; SOAPdenovo-trans
Supplementary_files_format_and_content: HP_SOAP.K47: adjusted k-mer (K) to 47; SOAPdenovo-trans
Supplementary_files_format_and_content: NH_SOAP.K25: adjusted k-mer (K) to 25; SOAPdenovo-trans
Supplementary_files_format_and_content: NH_SOAP.K47: adjusted k-mer (K) to 47; SOAPdenovo-trans

organism: Petunia x hybrida

source_name: Leaf (LF)

growth_protocol: Growth chamber (200 μmol light 12 h/d, 22°C day/night and 45% relative humidity)

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen, USA) and purified through a Qiagen RNeasy Column (Qiagen, Germany) according to the manufacturer's instructions. A 1% agarose gel buffered by Tris–acetate–EDTA was run to indicate the integrity of the RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 150 mM NaCl (STR), No NaCl (CTR)

tag: genotype

value: Mitchell Diploid

tag: treatment

value: 150 mM NaCl (STR)

tag: time point


title: P_0003

value: yes


title: C_0083 [reanalysis of GSM1580916]

description:
RNA-Seq data in GEO (GSE64977)
mlpd_PCG_DESeq2_norm_counts.txt
mlpd_DESeq2_diffexp_pmi_age_rin_default.txt


title: C_0087 [reanalysis of GSM1580917]


title: LF_STR_24h_B3T1

description: Biological Rep 3. Technical Rep 1


title: ChIP106.Input_siSki8

source_name: Input for ChIP104.H3K4me3_siSki8 and ChIP105.H3_siSki8

tag: cell line


title: C_0081 [reanalysis of GSM1580914]


title: ChIP103.Input_siNS

source_name: Input forChIP102.H3K36me3_siNS


title: C_0075 [reanalysis of GSM1580911]


title: ChIP104.H3K4me3_siSki8

source_name: H3K4me3 ChIP-seq, siSki8


title: H3K27me3_SiMacro_MT

tag: strain

tag: developmental stage

value: anti-trimethyl-histone H3 (Lys27) (Cat# 07-449, Lot# 2607758)


title: C_0082 [reanalysis of GSM1580915]

tag: tissue


title: C_0070 [reanalysis of GSM1580909]


title: C_0069 [reanalysis of GSM1580908]


title: ChIP105.H3_siSki8

source_name: H3 ChIP-seq, siSki8


title: LF_STR_24h_B1T2

description: Biological Rep 1. Technical Rep 2


title: LF_STR_06h_B2T1

description: Biological Rep 2. Technical Rep 1


title: LF_STR_24h_B2T1

description: Biological Rep 2. Technical Rep 1


title: LF_STR_06h_B1T2

description: Biological Rep 1. Technical Rep 2


title: LF_STR_24h_B1T1

description: Biological Rep 1. Technical Rep 1


title: ChIP101.Input_siSki8

source_name: Input for ChIP100.H3K36me3_siSki8


title: LF_STR_06h_B3T1

description: Biological Rep 3. Technical Rep 1


title: LF_STR_06h_B3T2

description: Biological Rep 3. Technical Rep 2


title: ChIP102.H3K36me3_siNS

source_name: H3K36me3 ChIP-seq, siNS


title: ChIP094.PolIICTD_siNS

source_name: PolIICTD ChIP-seq, siNS


title: LF_STR_06h_B2T2

description: Biological Rep 2. Technical Rep 2


title: C_0076 [reanalysis of GSM1580912]

source_name: BA9 prefrontal cortex


title: C_0062 [reanalysis of GSM1580906]


title: LF_STR_06h_B1T1

description: Biological Rep 1. Technical Rep 1


title: ChIP088.H3_siNS


title: ChIP089.Input_siNS

source_name: Input for ChIP087.H3K4me3_siNS and ChIP088.H3_siNS


title: ChIP091.PolIICTD_siSki8

source_name: PolIICTD ChIP-seq, siSki8


title: ChIP095.Input_siNS

source_name: Input for ChIP094.PolIICTD_siNS


title: C_0053 [reanalysis of GSM1580903]


title: LF_STR_00h_B3T0

description: Biological Rep 3. No Technical Rep


title: ChIP100.H3K36me3_siSki8

source_name: H3K36me3 ChIP-seq, siSki8


title: LF_STR_00h_B2T0

description: Biological Rep 2. No Technical Rep


title: C_0050 [reanalysis of GSM1580902]


title: C_0065 [reanalysis of GSM1580907]


title: C_0038 [reanalysis of GSM1580900]


title: ChIP086.Input_siPaf1

source_name: Input for ChIP084.H3K4me3_siPaf1 and ChIP085.H3_siPaf1


title: ChIP087.H3K4me3_siNS

source_name: H3K4me3 ChIP-seq, siNS


title: C_0061 [reanalysis of GSM1580905]


title: LF_CTR_24h_B2T2

description: Biological Rep 2. Technical Rep 2

value: No NaCl (CTR)


title: ChIP092.Input_siSki8

source_name: Input for ChIP091.PolIICTD_siSki8


title: ChIP085.H3_siPaf1

source_name: H3 ChIP-seq, siPaf1


title: LF_CTR_24h_B3T2

description: Biological Rep 3. Technical Rep 2

source_name: Leaf (LF)


title: ChIP083.Input_siNS

source_name: Input for ChIP082.H3K36me3_siNS


title: LF_CTR_24h_B1T2

description: Biological Rep 1. Technical Rep 2


title: LF_CTR_24h_B3T1

description: Biological Rep 3. Technical Rep 1


title: C_0060 [reanalysis of GSM1580904]


title: C_0035 [reanalysis of GSM1580897]


title: LF_STR_00h_B1T0

description: Biological Rep 1. No Technical Rep


title: ChIP082.H3K36me3_siNS


title: C_0032 [reanalysis of GSM1580895]


title: LF_CTR_24h_B2T1

description: Biological Rep 2. Technical Rep 1


title: C_0039 [reanalysis of GSM1580901]


title: C_0031 [reanalysis of GSM1580894]


title: Input_siNS.8

source_name: Input for PolIICTD_siNS


title: PolIICTD_siNS

source_name: PolII ChIP-seq, siNS


title: C_0029 [reanalysis of GSM1580893]

description:
RNA-Seq data in GEO (GSE64977), Microarray data in ArrayExpress (E-MTAB-812)
mlpd_PCG_DESeq2_norm_counts.txt
mlpd_DESeq2_diffexp_pmi_age_rin_default.txt


title: ChIP081.Input_siPaf1

source_name: Input for ChIP080.H3K36me3_siPaf1


title: ChIP080.H3K36me3_siPaf1

source_name: H3K36me3 ChIP-seq, siPaf1


title: C_0024 [reanalysis of GSM1580890]


title: Input_siPaf1.6

source_name: Input for PolIICTD_siPaf1


title: C_0026 [reanalysis of GSM1580892]

description:
RNA-Seq data in GEO (GSE64977), Microarray data in ArrayExpress (E-MTAB-812)
mlpd_PCG_DESeq2_norm_counts.txt
mlpd_DESeq2_diffexp_pmi_age_rin_default.txt
proteomics_dataset.RData

tag: proteomics sv1

tag: proteomics sv2

tag: proteomics sv3


title: LF_CTR_06h_B3T2

description: Biological Rep 3. Technical Rep 2


title: LF_CTR_06h_B1T2

description: Biological Rep 1. Technical Rep 2


title: C_0023 [reanalysis of GSM1580889]

tag: gender

tag: post-mortem interval (pmi)


title: LF_CTR_06h_B3T1

description: Biological Rep 3. Technical Rep 1


title: LF_CTR_24h_B1T1

description: Biological Rep 1. Technical Rep 1


title: C_0025 [reanalysis of GSM1580891]

tag: rna integrity number (rin)

tag: age at death


title: LF_CTR_06h_B2T2

description: Biological Rep 2. Technical Rep 2


title: ChIP084.H3K4me3_siPaf1

source_name: H3K4me3 ChIP-seq, siPaf1


title: LF_CTR_06h_B2T1

description: Biological Rep 2. Technical Rep 1


title: PolIICTD_siPaf1

source_name: PolII ChIP-seq, siPaf1


title: Ski8MT

source_name: ChIP-seq Ski8MT

value: myotubes


title: Ski8MB_Input

source_name: Input for ChIP-seq Ski8MB


title: C_0022 [reanalysis of GSM1580888]

source_name: BA9 prefrontal cortex

tag: proteomics study

tag: microarray study


title: Ski8MT_Input

source_name: Input for ChIP-seq Ski8MT

tag: cell condition

tag: library protocol


title: Ski8MB

source_name: ChIP-seq Ski8MB


title: C_0021 [reanalysis of GSM1580887]


title: LF_CTR_06h_B1T1

description: Biological Rep 1. Technical Rep 1

tag: genotype

tag: treatment


title: C_0017 [reanalysis of GSM1580883]


title: C_0020 [reanalysis of GSM1580886]


title: LF_CTR_00h_B3T2

description: Biological Rep 3. Technical Rep 2

tag: time point


title: C_0019 [reanalysis of GSM1580885]


title: Rtf1MT

source_name: ChIP-seq Rtf1MT

tag: cell line


title: Rtf1MT_Input

source_name: Input for ChIP-seq Rtf1MT


title: LF_CTR_00h_B1T2

description: Biological Rep 1. Technical Rep 2


title: C_0016 [reanalysis of GSM1580882]


title: Rtf1MB_Input

source_name: Input for ChIP-seq Rtf1MB


title: LF_CTR_00h_B3T1

description: Biological Rep 3. Technical Rep 1

source_name: Leaf (LF)


title: C_0018 [reanalysis of GSM1580884]


title: LF_CTR_00h_B2T2

description: Biological Rep 2. Technical Rep 2


title: C_0013 [reanalysis of GSM1580879]


title: C_0012 [reanalysis of GSM1580878]


title: Paf1MT

source_name: ChIP-seq Paf1MT


title: LF_CTR_00h_B2T1

description: Biological Rep 2. Technical Rep 1


title: C_0015 [reanalysis of GSM1580881]

value: C_15 - failed QC


title: LF_CTR_00h_B1T1

description: Biological Rep 1. Technical Rep 1


title: Rtf1MB

source_name: ChIP-seq Rtf1MB


title: Paf1MT_Input

source_name: Input for ChIP-seq Paf1MT


title: C_0011 [reanalysis of GSM1580877]

value: brain (BA9 prefrontal cortex)


title: Leo1MT_Input

source_name: Input for ChIP-seq Leo1MT


title: Paf1MB

source_name: ChIP-seq Paf1MB


title: Leo1MT

source_name: ChIP-seq Leo1MT


title: Leo1MB_Input

source_name: Input for ChIP-seq Leo1MB


title: C_0010 [reanalysis of GSM1580876]


title: C_0006 [reanalysis of GSM1580873]


title: C_0009 [reanalysis of GSM1580875]


title: Leo1MB

source_name: ChIP-seq Leo1MB


title: C_0008 [reanalysis of GSM1580874]


title: C_0005 [reanalysis of GSM1580872]


title: Ctr9MB_Input

source_name: Input for ChIP-seq Ctr9MB


title: Ctr9MT_Input

source_name: Input for ChIP-seq Ctr9MT


title: Ctr9MB

source_name: ChIP-seq Ctr9MB


title: C_0004 [reanalysis of GSM1580871]

source_name: BA9 prefrontal cortex


title: Ctr9MT

source_name: ChIP-seq Ctr9MT


title: C_0003 [reanalysis of GSM1580870]


title: C_0002 [reanalysis of GSM1580869]


title: 10_mut l-leucine rep3 RPF

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Basecalls performed using CASAVA 1.8.2
Reads were clipped of adapter sequence AGATCGGAG. Reads shorter than 25 bases post-clipping and reads that didn't contain the adapter were discarded. Percent of reads retained during clipping varied from 60 to 90%.
Clipped reads were aligned to human rRNA sequences from ensembl 69 biomart using bowtie2 version 2.1.0 with parameters -k 1 -N 1 --local.
Reads that didn't align to rRNA sequences were then aligned to the human genome (hg19) using tophat 2.0.8 with -x 1 -g 1 --segment-mismatches 1 --no-coverage-search.
Downstream analysis was done in R (3.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing reads for separate strands, normalized to reads per million by taking the coverage object in R, and multiplying by 1e6, then dividing by the total alignments for each sample. Minus / C strand normalized coverage multiplied by -1 to allow visualization in positive and negative directions.

source_name: Human fibroblast

growth_protocol: human wild-type fibroblasts, ESCO2-mutant RBS fibroblasts, and ESCO2-corrected RBS fibroblasts were grown on 15-cm plates in DMEM medium supplemented with 10% Fetal Bovine Serum (FBS). At 80% confluence, the cells were washed two times with PBS, and grown for another 24 hrs in DMEM/10% FBS.

extract_protocol:
Prior to lysis, the cells were incubated for 1 minute in DMEM containing 0.1 mg/mL cycloheximide (USBiological, cat. no. C8500-10). After a rinse with ice cold PBS containing 0.1 mg/mL cycloheximide, the cells from up to three plates were collected by scraping into 800 µl chilled Mammalian Lysis Buffer (ART-Seq 1X Mammalian Polysome Buffer, 1% Triton X-100, 0.1% NP-40, 1 mM DTT, 10 U/ml DNase I, 0.1 mg/ml cycloheximide). The cell lysate was triturated 10 times through a 26G needle to insure complete lysis, incubated for 10 minutes on ice with periodic agitation, and clarified by a 10 minute centrifugation at 20,000 x g at 4°C.  The RNA concentration of the supernatant was determined using the Quant-iT RiboGreen RNA Assay Kit (Invitrogen) and a SpectraMax M2 reader (Molecular Devices) according to manufacturer’s instructions.  Aliquots were flash-frozen in liquid nitrogen and stored at -80°C.  Ribosome-protected mRNA fragments (RPFs) and fragmented total RNA depleted for ribosomal RNA were sequenced for each sample.  Footprinting was performed at room temperature for 45 min using ART-Seq Nuclease (Epicentre), then stopped with SUPERase•In™ RNase Inhibitor (Life Technologies).  For the 24 hr timepoint samples, 2.8 units of nuclease was added per µg of RNA.  For the 3 hr timepoint samples, the amount of nuclease was reduced to 0.5 units/µg.  RPFs were isolated from the nuclease/SUPERase•In™ treated lysate using Sephacryl S400 columns (GE Healthcare: MicroSpin S-400 HR, cat. no. 27-5140-01), followed by acid phenol:chloroform extraction and isopropanol precipitation. Total RNA was isolated from untreated lysate by acid phenol:chloroform extraction and isopropanol precipitation.
Ribosomal RNA was removed from 1-5 µg of RPFs and total RNA using either the Ribo-Zero™ Magnetic or the Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre). To purify the Ribo-Zero treated samples, the RNA Clean & Concentrator™-5 Kit (Zymo Research) was used as described in the ART-Seq protocol.  26-34 nt RPFs were further size selected by PAGE purification and the total RNA heat fragmented.  Libraries were constructed as described in the Mammalian ARTseq™ Ribosome Profiling Kit (Epicentre, cat. no. RPHMR12126, protocol version 2012).

treatment_protocol: The cells were supplemented with 10 mM D-Leucine or L-Leucine and incubated for either 3 hrs or 24 hrs.

tag: experiment type

value: Ribosomal profiling

value: esco2 mutant

tag: timepoint after treatment

value: 3 hours

value: l-leucine


title: 11_mut d-leucine rep3 RPF

value: d-leucine


title: 12_mut l-leucine rep3 RPF


title: Paf1MB_Input

source_name: Input for ChIP-seq Paf1MB


title: 8_corr l-leucine rep3 RPF

value: corrected


title: C_0014 [reanalysis of GSM1580880]

tag: tissue

value: male

value: no


title: Cdc73MT_Input

source_name: Input for ChIP-seq Cdc73MT

value: ChIP-seq


title: Cdc73MB_Input

source_name: Input for ChIP-seq Cdc73MB

value: myoblasts


title: Cdc73MT

source_name: ChIP-seq Cdc73MT


title: 9_mut d-leucine rep3 RPF


title: Cdc73MB

source_name: ChIP-seq Cdc73MB


title: RNAseq_siNS_2

description: RNA-seq.gene.read.counts.txt

source_name: siRNA control for RNA-seq, batch 2

value: RNA-seq


title: RNAseq_siPaf1_1

description: RNA-seq.gene.read.counts.txt

source_name: siPaf1 for RNA-seq, batch 1


title: RNAseq_siCdc73_1

description: RNA-seq.gene.read.counts.txt

source_name: siCdc73 for RNA-seq, batch 1


title: siSki8_3READs_2

source_name: siSki8 for 3'READS, batch 2


title: RNAseq_siSki8_2

description: RNA-seq.gene.read.counts.txt

source_name: siSki8 for RNA-seq, batch 2


title: siPaf1_3READs_2

source_name: siPaf1 for 3'READS, batch 2


title: 7_corr d-leucine rep3 RPF


title: RNAseq_siPaf1_2

description: RNA-seq.gene.read.counts.txt

source_name: siPaf1 for RNA-seq, batch 2


title: 10_mut l-leucine rep3 total RNA


title: RNAseq_siCdc73_2

description: RNA-seq.gene.read.counts.txt

source_name: siCdc73 for RNA-seq, batch 2


title: 6_corr l-leucine rep3 RPF


title: 8_corr l-leucine rep3 total RNA


title: 5_corr d-leucine rep3 RPF


title: 11_mut d-leucine rep3 total RNA


title: 12_mut l-leucine rep3 total RNA


title: siCdc73_3READs_1

source_name: siCdc73 for 3'READS, batch 1


title: 7_corr d-leucine rep3 total RNA


title: 6_corr l-leucine rep3 total RNA


title: 12_mut l-leucine rep2 RPF

value: 24 hours


title: RNAseq_siNS_1

description: RNA-seq.gene.read.counts.txt

source_name: siRNA control for RNA-seq, batch 1


title: 11_mut d-leucine rep2 RPF


title: siNS_3READs_2

source_name: siRNA control for 3'READS, batch 2