title: Lactimidomycin treated Jurkat cells

city: Gent

first: Petra

last: Van Damme

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB

description: ribosome-associated mRNA

data_processing:
Ribosome profiling (Ribo-Seq) performed in Jurkat cells treated with CHX to study translation elongation and LTM to study translation initiation were analysed using the PROTEOFORMER pipeline (Crappe et al, 2015). PROTEOFORMER was used to perform the quality control, mapping onto a reference genome, identification of TIS and generation of a protein database.
The 3’ adapter sequences were clipped using the fastx_clipper and reads shorter than 26 or longer than 34 nucleotides were discarded for the Ribo-Seq based TIS calling.
The reads were first mapped onto small nuclear RNA, tRNA and rRNA (parameter settings: -snRNA Y -tRNA Y –rRNA Y) sequences to eliminate contaminating reads.
The remaining reads were subsequently mapped onto the human GRCh37 reference genome (Ensembl annotation bundle 75) allowing for a maximum of 2 mismatches along the entire read. Reads mapping to a maximum of 16 locations on the genome were allowed and retained for every loci. All mapping steps were performed using STAR 2.4.0i.
RPF alignments were assigned to a specific P site nucleotide based on the length of the fragment. The offset from the 5’ end of the alignment was +12, +13 and +14 respectively for alignment of less than or equal to 30 bases long, 31–33 bases long, and greater than or equal to 34 bases long.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: read alingments were reduced to single-nucleotide genomic position, based on P-site assignment. Separate BedGraph files were provided for the sense and antisense strand.

source_name: cell line

growth_protocol: For ribosome profiling, Jurkat cells were grown in RPMI medium (Gibco) supplemented with 10% fetal bovine serum, 2 mM alanyl-L-glutamine dipeptide (GlutaMAX, Gibco), 50 units/ml penicillin and 50 µg/ml steptamycin at 37°C and 5% CO2.

extract_protocol:
Cells were collected by centrifugation (5 min at 300g), rinsed with ice-cold PBS and recovered again by centrifugation in the presence of CHX. 108 cells were re-suspended in 1 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 2 mM dithiothreitol (DTT), 100 µg/ml CHX, 1 × complete and EDTA-free protease inhibitor cocktail (Roche)) (Guo et al, 2010). Following 10 min of incubation on ice, samples were passed through QIAshredder spin columns (Qiagen). The flow-through was clarified by centrifugation for 10 min at 16,000 × g and 4°C. 600 µl of the recovered supernatant was subjected to RNase I (Life Technologies) digestion using 1000 U of enzyme. Digestion of polysomes proceeded for 55 min at room temperature and was stopped with SUPERase.In RNase Inhibitor (Life Technologies). Next, monosomes were recovered by ultracentrifugation at 75,000 RPM in a cooled TLA-120.2 rotor over a 1 M sucrose cushion in 20 mM HEPES-KOH pH 7.4, 5 mM MgCl2, 100 mM KCl, 2 mM DTT, 100 µg/ml CHX and 100 U/ml Superase.In. Subsequent steps were performed as described by Ingolia et al. (Ingolia et al, 2011) with some minor adjustments. RNA was extracted from the samples using a heated acid phenol; chloroform; isoamyl alcohol (125:24:1) procedure. 17 µg of RNA was subjected to electrophoresis under denaturing conditions in 15% TBE-Urea polyacrylamide gel (Life Technologies).
Ribosome protected fragments (RPFs) of 28-34 nucleotides were extracted from the gel in RNase-free water for 10 min at 70°C and precipitated with 1/10 volume of 3 M sodium acetate pH 5.2, 1.5 µl GlycoBlue (Life Technologies) and 1 volume of isopropanol overnight at − 80 °C. Following a dephosphorylation reaction (end-repair) with 10 U of T4 polynucleotide kinase (New England Biolabs), the RPFs were depleted of ribosomal RNA contaminants using the Ribo-Zero Magnetic Gold Kit (Illumina) according to the manufacturer’s protocol. Subsequently, fragments were ligated to a 1.5 µg of Universal cloning linker using 200 U of T4 RNA ligase II (both New England Biolabs). The ligated product was size-selected using denaturing gel electrophoresis and purified from gel as described above. Subsequently, reverse transcription (RT) was performed with 200 U of SuperScript III (Life Technologies) according to (Ingolia et al, 2011), followed by a size-selection of the RT product (described above). Next, samples were subjected to circular ligation using 100 U of CircLigase (Illumina) and amplified by PCR using Phusion polymerase (New England Biolabs) for 12 cycles of denaturation (10 s at 98°C), annealing (10 s of 65°C) and elongation (5 s at 72°C) using primer pairs compatible with the Illumina sequencing platform (Ingolia et al, 2011). The resulting ribosome-profiling libraries of LTM- and CHX- treated Jurkat cells were sequenced on a NextSeq 500 instrument (Illumina) to yield 75 bp single-end reads.

treatment_protocol: Cultures were treated with 50 µM lactimidomycin (LTM) (Ju et al, 2005; Schneider-Poetsch et al, 2010) or 100 µg/ml cycloheximide (CHX) (Sigma, USA) for 30 min at 37°C before cell harvest.

value: peripheral blood

value: Jurkat T-lymphocytes

tag: phenotype

value: Lymphoid-like

value: cell culture

value: ATCC

tag: Sex

value: male

value: T Cell/ T Lymphocyte


title: SanbornRao-2015-HIC070

status: Public on Oct 23 2015

type: SRA

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Library strategy: HiC-Seq
The paired end reads were aligned separately using BWA against the b37 human build or the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
Contact matrices were constructed at various resolutions and normalized using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
loops were annotated using HiCCUPS (see Rao, Huntley, et al. Cell 2014), domains were annotated using Arrowhead (see Rao, Huntley, et al. Cell 2014),
genome build: b37 (human), mm9 (mouse)
processed data files format and content: HiCCUPS_looplist.txt files contain loop calls generated via HiCCUPS; first three fields represent the locus participating in the loop closer to the p-end of the chromosome; fields 4-6 represent the locus participating in the loop closer to the q-end of the chromosome; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 represents the observed number of counts at the loop; fields 9-12 represent the expected number of counts at the loop using four different expected models; fields 13-16 are the q-values over each of the expected values; field 17 is the number of enriched pixels that was clustered into a particular loop; field 18-19 are the centroid of the loop; field 20 is the radius of the loop
processed data files format and content: Arrowhead_domainlist.txt files contain domain calls generated via Arrowhead; first 6 fields represent the boundaries of the domain; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 is the corner score for the domain (see Rao, Huntley, et al. Cell 2014); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al. Cell 2014)

molecule: genomic DNA

organism: Homo sapiens

source_name: haploid fibroblast-like

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq/HiSeq2500/HiSeqX following the manufacturer's protocols

tag: cell line

tag: protocol

value: in situ HYbrid Capture Hi-C


title: Cycloheximide treated Jurkat cells

description: ribosome-associated mRNA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: age


title: SanbornRao-2015-HIC072


title: SanbornRao-2015-HIC071


title: SanbornRao-2015-HIC069


title: SanbornRao-2015-HIC068


title: SanbornRao-2015-HIC066


title: SanbornRao-2015-HIC065


title: SanbornRao-2015-HIC067


title: SanbornRao-2015-HIC061


title: SanbornRao-2015-HIC064


title: SanbornRao-2015-HIC062


title: SanbornRao-2015-HIC063


title: SanbornRao-2015-HIC060


title: SanbornRao-2015-HIC059


title: SanbornRao-2015-HIC057


title: SanbornRao-2015-HIC058


title: SanbornRao-2015-HIC056


title: SanbornRao-2015-HIC055


title: SanbornRao-2015-HIC053


title: SanbornRao-2015-HIC051


title: SanbornRao-2015-HIC052


title: SanbornRao-2015-HIC050


title: SanbornRao-2015-HIC049


title: SanbornRao-2015-HIC043


title: SanbornRao-2015-HIC048


title: SanbornRao-2015-HIC042


title: SanbornRao-2015-HIC041


title: SanbornRao-2015-HIC039


title: SanbornRao-2015-HIC040


title: SanbornRao-2015-HIC038


title: SanbornRao-2015-HIC037


title: SanbornRao-2015-HIC036


title: SanbornRao-2015-HIC035


title: SanbornRao-2015-HIC031


title: SanbornRao-2015-HIC054


title: SanbornRao-2015-HIC032


title: SanbornRao-2015-HIC029


title: SanbornRao-2015-HIC028


title: SanbornRao-2015-HIC030


title: SanbornRao-2015-HIC047


title: SanbornRao-2015-HIC027


title: SanbornRao-2015-HIC026


title: SanbornRao-2015-HIC024


title: SanbornRao-2015-HIC022


title: SanbornRao-2015-HIC023


title: SanbornRao-2015-HIC020


title: SanbornRao-2015-HIC033


title: SanbornRao-2015-HIC021


title: SanbornRao-2015-HIC034


title: SanbornRao-2015-HIC019


title: SanbornRao-2015-HIC018


title: SanbornRao-2015-HIC017


title: SanbornRao-2015-HIC025


title: SanbornRao-2015-HIC016


title: SanbornRao-2015-HIC014


title: SanbornRao-2015-HIC013


title: miR10a doxy no1

status: Public on Oct 26 2015

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
Adapter sequences were removed form raw reads using fqtrim (The Center for Computational Biology at Johns Hopkins University, http://ccb.jhu.edu/software/fqtrim/)
Trimmed reads were mapped to the mouse genome using STAR [default settings]
Reads were quantitated using FeatureCounts (SourceForge Subread Package) using RefSeq (hg19) annotation
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain quantitations of reads to refseq.

source_name: Human embryonic stem cells upon 14 days of neural induction. Doxyxyxline was added day11-14 in order to overexpress miR10a

growth_protocol: Expansion and transduction of hESCS: Human ESC H9 (WA09, passage 31-45) (Thomson et al., 1998) was expanded and maintained on γ-irradiated mouse embryonic fibroblasts (MEFs) in DMEM/F12, 20% KSR, 0.05 mM 2-mercaptoethanol, 0.5% Pen/ Strep, 0.5% Glutamate and 10 ng/ml FGF-2 (R&D Systems). The cells were passaged once weekly with dispase (5 mg/ml, Stemcell Tech.) or EDTA (0.5mM).   At the time of lentiviral transduction the ESCs were plated onto Matrigel (1:40, BD Biosciences) without MEFs and infected at a MOI of 50. The infected hESCs were maintained on matrigel for 3 days before plated back onto MEFs for an additional 7 days of expansion prior to differentiation.

extract_protocol:
RNA was exracted using the miRNeasy mini kit form Qiagen
RNA libraries were prepared using Illumina kits.

treatment_protocol: Neural induction, 14days. Patterning towards midbrain with CT0.8 and Shh 200ng/ml: Kirkeby A, Nelander J, Parmar M. Generating regionalized neuronal cells from pluripotency, a step-by-step protocol.  Front Cell Neurosci. 2013 Jan 3;6:64. doi: 10.3389/fncel.2012.00064.  - Kirkeby A, Grealish S, Wolf DA, Nelander J, Wood J, Lundblad M, Lindvall O, Parmar M. Generation of regionally specified neural progenitors and functional neurons from human embryonic stem cells under defined conditions. Cell Rep. 2012 Jun 28;1(6):703-14. doi: 10.1016/j.celrep.2012.04.009. Epub 2012 May 26.

tag: growth

value: 14 days of neural induction

tag: treatment

value: Doxycycline was added day 11-14


title: Rat 712

city: Minneapolis

first: Ann

middle: Margaret

last: Parr

state: MN

address: 2001 6th St SE

department: Department of Neurosurgery

institute: University of Minnesota

data_processing:
Analysis of RNA-seq data was carried out using the Galaxy software platform hosted by the Minnesota Supercomputing Institute. Reads first underwent quality control assessment with the FastQC tool and adapter sequence contamination removal with the CutAdapt tool. Because all base positions had first-quartile Phred scores greater than 20, trimming with FastQ Trimmer was not needed.
Reads were subsequently mapped to the Rattus norvegicus RN4 reference genome with TopHat (version 1.5.0) using an empirically determined insertion size of 210 base pairs.
The mapped reads were assembled into transcripts with Cufflinks (version 0.0.6) using quartile normalization.
Transcriptional datasets for each time point were pooled using CuffMerge.
Differences between strains at each time point were identified with CuffDiff.
Genome_build: RN4
Supplementary_files_format_and_content: Files containing CuffDiff results of gene differential expression testing (between strains, at each time point). In order, the columns indicate (A) tested object identifier (ID; here, equivalent to gene ID), (B) gene ID, (C) Rat Genome Database (RGD) gene ID, (D) genomic locus, (E) sample 1 (Sprague-Dawley, SD), (F) sample 2 (athymic nude, AN), (G) test status (OK = test successful), (H) FPKM for sample 1 (SD), (G) FPKM for sample 2 (AN), (H) log2(fold change) = log2(FPKM(SD)/FPKM(AN)), (I) test statistic, (J) p value, (K) q value, (L) statistically significant (if q<0.05).

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Tissue from spinal cord injury epicenter

growth_protocol: [not applicable]

extract_protocol:
A 1-mm spinal cord segment through the injury site was harvested and flash-frozen in liquid nitrogen. RNA was extracted from tissue samples using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands). RNA quantity and quality were assessed with the Aligent 2100 Bioanalyzer (Aligent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Age-matched adult (16-18 week old) female SD (Hsd:SD, N=15) and AN (Hsd:RH-rnu/rnu, N=15) rats (Charles River, Wilmington, MA) received moderate (200 kdyn) contusion injury using the Infinite Horizon impactor (Precision Systems, Lexington, KY). At 1 or 8 weeks after injury, animals were anesthetized with ketamine (100 mg/kg IP) and xylazine (10 mg/kg IP). Animals underwent transcardial perfusion with phosphate buffered saline (PBS), and a 1-mm spinal cord segment through the injury site was harvested and flash-frozen in liquid nitrogen.

tag: strain

value: athmyic nude (AN)

tag: time point

value: Chronic (8 weeks post-injury)


title: SanbornRao-2015-HIC012


title: mTEC_GFPpos_3

city: San Francisco

first: Mark

middle: S.

last: Anderson

state: CA

address: 513 Parnassus Ave., Box 0540

department: Diabetes Center

institute: UCSF

data_processing:
H3K27ac ChIP-Seq data was mapped against the mouse mm10 reference genome using bowtie v.0.12.7 (-n 2 -m 1).
The obtained sam files were converted and merged into separated bam files using samtools v.0.1.18.
Genome_build: mm10
Supplementary_files_format_and_content: BED format files that contains the peak location generated by MACS package.

organism: Mus musculus

source_name: GFP pos medullary thymic epithelial cells

growth_protocol: mTECs isolated from 4- to 6-wk-old B6 Adig mice (fully backcrossed from MGI:4367724)

extract_protocol:
Fixed cell lysates sonicated, histone-DNA complexes precipitated with anti-H3K27ac antibody (Abcam, Ab4729, lot GR167929-1), washed, eluted, and DNA isolated.
Whole genome amplification performed using WGA-SEQX (Sigma) per its instructions. Sequencing adaptors were ligated and single-end sequencing performed using Illumina Hi-Seq per manufacturer instructions.

treatment_protocol: Thymi from 6-12 mice pooled, diced, enzymatically digested, light fraction isolated by Percoll gradient, stained, and isolated by FACS (DAPI-, CD45-, EpCAM+, Ly51-, MHC-II+, GFP- and DAPI-, CD45-, EpCAM+, Ly51-, MHC-II+, GFP+ subset)

tag: source strain

value: C57BL/6 Adig (Aire GFP reporter)

tag: facs gating

value: DAPI-, CD45-, EpCAM+, Ly51-, MHC-II hi, GFP+

tag: cell type


title: mTEC_GFPneg_3

source_name: GFP neg medullary thymic epithelial cells

value: DAPI-, CD45-, EpCAM+, Ly51-, MHC-II+, GFP-


title: mTEC_GFPneg_2

value: GFP neg medullary thymic epithelial cells


title: mTEC_GFPpos_2

value: GFP pos medullary thymic epithelial cells


title: mTEC_GFPpos_1


title: D10_1

source_name: D10.G4.1 Th2 cell line

value: AKR/J


title: SanbornRao-2015-HIC015


title: mTEC_GFPneg_1


title: FA14dayrep2

city: Boston

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

description: Total RNA from mouse kidney 14 days after folic acid treatment

data_processing:
Adapters and low quality bases were trimmed using Cutadapt with a Phred quality cutoff of 20 and an error rate of 0.1
Trimmed reads were aligned to the NCBIM37 Mus musculus reference genome with Tophat (version 2.07)
Aligned reads were summarized at the gene level against the iGenomes NCBIM37 gene annotations using HTSeq
Summarized read counts were normalized between samples with DESeq
Normalized counts were tested with DESeq in pair-wise comparisons at a p-value of 0.2
Genome_build: NCBIM37
Supplementary_files_format_and_content: Read counts summarized at the gene level in tab-delimited format for both un-normalized (*rawcounts.txt files) and normalized (*.normcounts.txt files) data.

source_name: kidney

extract_protocol:
Total RNA was extracted from frozen kidney tissue using TRIzol reagent (Invitrogen).
The quantity and quality of mRNA were assayed on an Agilent 2200 TapeStation instrument and by SYBR qPCR assay. Libraries were prepared from10 ng total RNA per sample using the IntegenX Apollo 324 system and NuGEN SPIA reagents.

treatment_protocol: Male Balb/c mice (25-29 g) received a single intraperitoneal (ip) injection of 250 mg/kg folic acid (FA) dissolved in a 0.3 M sodium bicarbonate solution. Mice were sacrificed at 1, 2, 3, 7 and 14 days following administration.

value: Folic Acid

value: Balb/c

tag: days post treatment

value: kidney


title: FA7dayrep1

description: Total RNA from mouse kidney 7 days after folic acid treatment


title: FA7dayrep3


title: FA3dayrep3

description: Total RNA from mouse kidney 3 days after folic acid treatment


title: FA7dayrep2


title: FA14dayrep1


title: FA3dayrep1


title: FA14dayrep3


title: FA3dayrep2


title: FA2dayrep3

description: Total RNA from mouse kidney 2 days after folic acid treatment


title: FA2dayrep1


title: FA1dayrep3

description: Total RNA from mouse kidney 1 day after folic acid treatment


title: FA1dayrep2


title: FA1dayrep1


title: Normalrep3

description: Total RNA from untreated mouse kidney


title: Normalrep2

description: Total RNA from untreated mouse kidney


title: FA2dayrep2


title: Normalrep1

description: Total RNA from untreated mouse kidney


title: Sample_WFN2b

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using Bowtie2 v2.1.0 to mm10. Data were conversed and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages.
Candidate genes were filtered to a minimum of 4x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; normalised text file and raw data txt files

source_name: primary microglial cells

extract_protocol:
RNA was isolated using Trizol Reagent according to instructions
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

tag: strain/genotype

value: mouse fibronectin 100 µg/ml

tag: treatment period

value: 3 h


title: Sample_CLL3a

value: Re-LPS 0.1 ng/ml


title: Sample_CME3a

value: untreated


title: Sample_WLL1a


title: Sample_WME2b


title: Sample_WFN3a


title: Sample_WLL2b


title: Sample_WLH1a

value: Re-LPS 10 ng/ml


title: Sample_WLL3a


title: Sample_WME1a


title: Sample_WLH3a


title: Sample_WME3a


title: Sample_CLL2b


title: Sample_CLH3a


title: Sample_CLH2b


title: Sample_CLH1a


title: Sample_WLH2b


title: Sample_WFN1a


title: Sample_CME2b


title: Sample_CFN3a


title: Sample_CLL1a


title: Sample_CFN2b


title: Sample_CME1a


title: SanbornRao-2015-HIC010

source_name: B-lymphoblastoids

value: in situ Hi-C


title: SanbornRao-2015-HIC008


title: SanbornRao-2015-HIC007


title: SanbornRao-2015-HIC009


title: SanbornRao-2015-HIC006


title: SanbornRao-2015-HIC011


title: P3

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

description:
DESeq2_normalized_counts.txt
edgeR_normalized_counts.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
Trimmomatic v0.32 was used to remove adapter sequences, and quality filtering using the following parameters: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36. Reads shorter than 36 bp after trimming were thus removed from the study.
Filtered reads were then aligned to the reference genome using tophat v2.0.11 and the --b2-very-sensitive Bowtie2 (v2.1.0) preset, guided by GTF file. Of note, reads were aligned to the reference genome to which theERCC spike-ins were added.
The number of reads mapping uniquely to each gene was counted by HTSeq-count v0.6.1p1, and processed for statistical analysis using the R Bioconductor packages edgeR (v3.6.7), and DESeq2 (v1.4.5).
Genome_build: Rnor_5.0 Ensembl Release 76 (August 2014)
Supplementary_files_format_and_content: DESeq2_normalized_counts.txt: Tab-delimited text file contain normalized read counts for each sample, as computed by DESeq2.
Supplementary_files_format_and_content: edgeR_normalized_counts.txt: Tab-delimited text file contain normalized read counts for each sample, as computed by edgeR.

source_name: medial prefrontal cortex

extract_protocol:
Brains were dissected out, flash frozen, and stored at -80C until sectioning on a cryostat at -20C for tissue-punching of the medial prefrontal cortex. Total RNA was then extracted using TRI-Reagent according to the manufacturer's protocol (Molecular Research Center, #TR 118), followed by DNAse I treatment to remove any eventual DNA contamination and clean-up (RNA Clean & Concentrator, Zymo Research, Irvine, CA, USA) .
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina with poly(A) mRNA purification from one microgram of total RNA based on magnetic beads, cDNA synthesis using random hexamers, and final amplification using barcoded primers following the manufacturer’s protocol (#E7530, New England Biolabs, Ipswich, MA, USA). In order to determine the lower limit of detection and verify the linearity of quantification during the statistical analysis of the sequencing data, synthetic RNA Spike-Ins (#4456739, ERCC ExFold RNA Spike-In Mixes, Life technologies, Carlsbad, CA) were added to each sample prior to poly(A) mRNA purification following the recommended dilutions (2 µL of a 1:100 dilution). Of note, Mix 1 and Mix 2 of the ERCC ExFold RNA Spike-Ins were equally distributed among samples in an exclusive manner. The resulting barcoded and unstranded libraries were quantified using a KAPA qPCR library quantification kit (KAPA Biosystems, Boston, MA, USA) with three serial dilutions ran in duplicates on a CFX96 real-time PCR instrument (Bio-Rad). Finally, the absence of adapters or primers contamination was verified on a Bioanalyzer using a DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Following five days of habituation and handling under pair-housing, the estrous cycle of female rats was monitored by daily vaginal smearing and subsequent cytological analysis for a minimum of two cycles.

value: Sprague-Dawley

value: medial prefrontal cortex

tag: gender

value: Female

tag: estrous cycle

value: Proestrus


title: P5


title: P1


title: sorghum_cold

status: Public on Oct 25 2015

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

country: China

institute: Shanghai Center for Plant Stress Biology

description:
SbiCOL
small RNA sequencing
Processed data file: SbiCOL_uniq.txt

data_processing: Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor, contain N, or have length less than 17nt were removed. The processed files are named as "prefix"_uniq.txt, where "prefix" is the prefix of the file that contains raw data.  The first column in a processed file contains clean reads, and the second column contains the number of copies of the reads in the library. Data processing performed with in-house scripts.

organism: Sorghum bicolor

source_name: seedlings

growth_protocol: plants grown in a growth chamber with 31°C / 13h light and 22°C /11h dark cycle. Humidity maintained at 50%.

extract_protocol: Total RNA was isolated from seedlings with TRIzol (Invitrogen) and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 18 to 30 nt were excised and ligated to a preadenylated 3' adaptor and a 5’- adaptor using T4 RNA ligase. Ligation products were purified in polyacrylamide gels, followed by RT-PCR. The small RNA libraries were sequenced by the UCR core facility.

treatment_protocol: Four groups of 14-day-old plants are treated as follows: control (untreated), drought (water hold for ~10 days), cold (4 ˚C for 24 hours), and salt (300mM NaCl for 24 hours)

tag: subspecies

value: bicolor

tag: accession

value: seedlings

tag: stress

value: cold


title: D4

tag: tissue

value: Diestrus


title: D5


title: M1

description:
PvM_annotated_regions.csv
DvM_annotated_regions.csv

data_processing:
Illumina Casava1.9 software used for basecalling.
Trimmomatic v0.32 was used to remove adapter sequences, and quality filtering using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Reads shorter than 36 bp after trimming were thus removed from the study.
Filtered reads were then aligned to the reference genome using Bowtie2 (v2.1.0) with the --very-sensitive-local preset. Aligned reads were thus filtered using samtools (v0.1.19) and Picard Tools (v1.84) to retain only reads mapping uniquely, with a mapping quality score above 30, and deduplicated.
Differential ChIP-seq signal was then analyzed using the DiffReps tool (v1.55.4) for each pair-wise comparison, Proestrus vs. Males, Diestrus vs. Males, and Proestrus vs. Diestrus with --nsd 2 --window 500 --step 50, and annotated with the R package ChIPpeakAnno (v2.14.1)
Genome_build: Rnor_5.0 Ensembl Release 76 (August 2014)
Supplementary_files_format_and_content: PvM_annotated_regions.csv: comma-separated file of annotated genomic regions displaying a differential Egr1 binding between Proestrus and Males, as detected by DiffReps
Supplementary_files_format_and_content: DvM_annotated_regions.csv: comma-separated file of annotated genomic regions displaying a differential Egr1 binding between Diestrus and Males, as detected by DiffReps
Supplementary_files_format_and_content: PvD_annotated_regions.csv: comma-separated file of annotated genomic regions displaying a differential Egr1 binding between Proestrus and Diestrus, as detected by DiffReps

extract_protocol:
Brains were dissected out, flash frozen, and stored at -80C until sectioning on a cryostat at -20C for tissue-punching of the medial prefrontal cortex. Chromatin was then crosslinked and sheared to fragments of 200-500 bp using a Bioruptor sonicator (Diagenode, Denville, NJ, USA). Next, pre-cleared chromatin was immunoprecipitated overnight at 4℃ with an antibody directed against Egr1 (sc-110-X, 4 μg, Santa Cruz Biotechnology, Dallas, TX, USA). After washes, elution from beads, and reversal of the cross-link, immunoprecipitated DNA was purified.
ChIP-Seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina and barcoded primers (New England Biolabs) following the manufacturer’s protocol (#E7370). For each biological sample, two libraries were prepared (IP and Input), resulting in a total of 22 barcoded libraries.

value: Male

tag: chip antibody

value: Egr1 (Santa Cruz, catalog# sc-110-X, lot# H1611)


title: M2


title: D2


title: M3


title: F9

description:
DvM_annotated_regions.csv
PvD_annotated_regions.csv


title: F12


title: F4

description:
PvM_annotated_regions.csv
PvD_annotated_regions.csv


title: F11


title: F5


title: M4


title: M2


title: sorghum_salt

description:
SbiSAL
small RNA sequencing
Processed data file: SbiSAL_uniq.txt

value: salt


title: sorghum_control

description:
SbiCRL
small RNA sequencing
Processed data file: SbiCRL_uniq.txt

value: control


title: F3


title: sorghum_drought

description:
SbiDRO
small RNA sequencing
Processed data file: SbiDRO_uniq.txt

value: drought


title: gDNA eGFP(+)

city: Cambridge

first: Shira

last: Weingarten-Gabbay

state: MA

address: 75 Ames St

institute: The Broad Institute

data_processing:
Single-end  reads in the length of 50 or 200nt  were trimmed to 45nt containing the common priming site and the unique 25nt of the oligo’s variable region.
Trimmed reads were mapped to the synthetic library sequences using Novoalign aligner
The number of reads for each designed oligo was counted in each sample.
Genome_build: Synthetic library oligonucleotides
Supplementary_files_format_and_content: Tab delimited file that holds the synthetic oligo id number, sequence, cap-independnet translation activity, promoter activitiy and cDNA/gDNA ratio

organism: synthetic construct

source_name: Designed oligonucleotides

extract_protocol:
none provided by the submitter
Illumina adaptors ligation

tag: functional assay

value: splicing activity

tag: cell line

tag: master plasmid


title: cDNA eGFP(+)


title: Aebp2-WT-Thymus-ChIP-seq

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

description: Aebp2 and Jarid2 ChIP peaks may be over repressented in the the ChIP sequencing pool

data_processing:
Trimming raw sequence reads smaller than 40 bp long out of a fastq file with a custome-made Python script.
Mapping raw sequence reads to the repeat-masked mm9 mouse genome sequence using Bowtie2.
The Bowtie2 result files (sam file) were converted into bed-format file using SamTools.
Peak calling was carried out using MACS2 with two bed files (The peaks of Aebp2-ChIP were subtracted by the peaks of Input).
Genome_build: mm9
Supplementary_files_format_and_content: bed file containing Aebp2-ChIP peak co-ordinates and heights after subtraction from the Input peaks

source_name: Thymus

extract_protocol:
Genomic DNA was isolated from thymus using standard phenol-chloroform extraction protocol, precipitated using standard ethanol precipitation protocol and resuspended in 1X TE buffer.
Thymus tissues of one-month-old C57BL/6N mice (Taconic) were used for ChIP experiments as previously described [Kim et al. 2009. Nucleic Acids Res.].  This particular protocol has one additional step compared to other existing ChIP protocols. The two four base pair (bp) cutter enzymes, AluI and Tsp509, were used to shorten the average length of ChIP DNA right before the elution step from the AEBP2 antibody.  The eluted DNA was further processed for the construction of a library according to the manufacturer’s protocol (NEBNext Fast DNA Library Prep Set for Ion Torrent, NEB cat. No. E6270S). The constructed library was sequenced using a NGS sequencer (Ion Torrent PGM, Life Technologies).

tag: strain

tag: age


title: Aebp2-WT-Thymus-Input


title: Reb1_ChEC_seq_short_linker_5m_(20150213_20)

status: Public on Oct 22 2015

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Reb1 short linker ChEC-seq, 5 minute digestion

data_processing:
Library strategy:  ChEC-Seq
1. We used Novoalign 2.08.03 (http://www.novocraft.com) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC . If a read was mapped to multiple locations, one location was picked at random. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragment ends aligned to it. 4. We normalized base pair counts by dividing by the total number of fragment ends mapped, and then multiplying by the total number of mapped base pairs (Supplementary file .bedgraph).

organism: Saccharomyces cerevisiae

source_name: Reb1 ChEC-seq

extract_protocol: For each ChEC experiment, a 50 mL culture was grown to an OD600 of 0.5-0.7 at 30C in YPD.  Cells were pelleted at 3,000 x g and washed three times with 1 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF), centrifuging as above between washes.  Cells were resuspended in 600 µL Buffer A containing 0.1% digitonin and permeabilized at 30C for 5 min.  CaCl2 was added to 2 mM and ChEC digests were performed at 30C.  At each time point, a 100 µL aliquot of the digest was transferred to a tube containing 100 µL 2X stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA) and 1% SDS.  Protein was then was digested with 80 µg proteinase K at 55C for 30 m.  Nucleic acids were extracted with an equal volume of phenol/chloroform/isoamyl alcohol and precipitated with 2.5 volumes 100% ethanol and 30 µg Glycoblue (Ambion).  Pellets were washed once with 1 mL 100% ethanol, dried, and resuspended in 30 µL 0.1X TE buffer, pH 8.0.  RNA was digested with 10 µg RNase A at 37C for 20 m.  Prior to generating sequencing libraries, ChEC DNA was subjected to size-selection using Ampure XP beads (Agencourt).  A beads:sample ratio of 2.5:1 was used and the unbound fraction, containing small DNA fragments, was extracted to remove RNase and precipitated as above, and used for library preparation.  Sequencing libraries were constructed as described (PMID 22025700, 24144978), except that KAPA polymerase was used for library amplification.

tag: cell part

value: nuclei

tag: mutant

value: WT

value: W1588-4C (congenic to W303-1A except RAD5+)

tag: genotype


title: Reb1_ChEC_seq_N_terminal_5m_(20150213_27)

description: Reb1 N-terminal ChEC-seq, 5 minute digestion


title: Reb1_ChEC_seq_N_terminal_30s_(20150213_22)

description: Reb1 N-terminal ChEC-seq, 30 second digestion


title: Reb1_ChEC_seq_2.5m_(20140731_2)

description: Reb1 ChEC-seq, 2.5 minute digestion


title: Reb1_ChEC_seq_20m_(20140731_5)

description: Reb1 ChEC-seq, 20 minute digestion


title: Reb1_ChEC_seq_40s_(20141114_5)

description: Reb1 ChEC-seq, 40 second digestion


title: Reb1_ChEC_seq_5m_(20140731_3)

description: Reb1 ChEC-seq, 5 minute digestion


title: Sample_CFN1a

tag: strain/genotype

tag: treatment

value: mouse fibronectin 100 µg/ml

value: 3 h


title: Reb1_ChEC_seq_10m_(20140731_4)

description: Reb1 ChEC-seq, 10 minute digestion


title: Reb1_ChEC_seq_60s_(20141114_7)

description: Reb1 ChEC-seq, 60 second digestion


title: Reb1_ChEC_seq_30s_3_(20141219_21)

description: Reb1 ChEC-seq, 30 second digestion, replicate 3


title: Reb1_ChEC_seq_10s_(20141114_2)

description: Reb1 ChEC-seq, 10 second digestion


title: Reb1_ChEC_seq_30s_1_(20141114_4)

description: Reb1 ChEC-seq, 30 second digestion, replicate 1


title: Rap1_ChEC_seq_20m_(20141204_16)

description: Rap1 ChEC-seq, 20 minute digestion

source_name: Rap1 ChEC-seq


title: Reb1_ChEC_seq_20s_(20141114_3)

description: Reb1 ChEC-seq, 20 second digestion


title: Rap1_ChEC_seq_10m_(20141204_12)

description: Rap1 ChEC-seq, 10 minute digestion


title: Reb1_ChEC_seq_no_calcium_(20140731_1)

description: Reb1 ChEC-seq, no calcium


title: Rap1_ChEC_seq_5m_(20141204_11)

description: Rap1 ChEC-seq, 5 minute digestion


title: Reb1_ChEC_seq_short_linker_30s_(20150213_16)

description: Reb1 short linker ChEC-seq, 30 second digestion


title: Rap1_ChEC_seq_2.5m_(20141204_10)

description: Rap1 ChEC-seq, 2.5 minute digestion


title: Rap1_ChEC_seq_50s_(20141219_13)

description: Rap1 ChEC-seq, 50 second digestion


title: Rap1_ChEC_seq_60s_(20141219_14)

description: Rap1 ChEC-seq, 60 second digestion


title: Reb1_ChEC_seq_50s_(20141114_6)

description: Reb1 ChEC-seq, 50 second digestion


title: Rap1_ChEC_seq_40s_(20141219_12)

description: Rap1 ChEC-seq, 40 second digestion


title: Reb1_ChEC_seq_30s_2_(20141219_2)

description: Reb1 ChEC-seq, 30 second digestion, replicate 2


title: Rap1_ChEC_seq_30s_2_(20150213_6)

description: Rap1 ChEC-seq, 30 second digestion, replicate 2


title: Rap1_ChEC_seq_30s_3_(20150213_7)

description: Rap1 ChEC-seq, 30 second digestion, replicate 3


title: Rap1_ChEC_seq_30s_1_(20141219_11)

description: Rap1 ChEC-seq, 30 second digestion, replicate 1


title: Rap1_ChEC_seq_10s_(20141219_9)

description: Rap1 ChEC-seq, 10 second digestion


title: Rap1_ChEC_seq_20s_(20141219_10)

description: Rap1 ChEC-seq, 20 second digestion


title: Abf1_ChEC_seq_short_linker_5m_(20150213_12)

description: Abf1 short linker ChEC-seq, 5 minute digestion

source_name: Abf1 ChEC-seq


title: Abf1_ChEC_seq_10m_(20141204_7)

description: Abf1 ChEC-seq, 10 minute digestion


title: Abf1_ChEC_seq_short_linker_30s_(20150213_9)

description: Abf1 short linker ChEC-seq, 30 second digestion


title: Abf1_ChEC_seq_5m_(20141204_6)

description: Abf1 ChEC-seq, 5 minute digestion


title: Abf1_ChEC_seq_60s_(20141219_8)

description: Abf1 ChEC-seq, 60 second digestion


title: Abf1_ChEC_seq_2.5m_(20141204_5)

description: Abf1 ChEC-seq, 2.5 minute digestion, replicate 1


title: Abf1_ChEC_seq_40s_(20141219_6)

description: Abf1 ChEC-seq, 40 second digestion


title: Abf1_ChEC_seq_30s_3_(20150213_4)

description: Abf1 ChEC-seq, 30 second digestion, replicate 3


title: Abf1_ChEC_seq_50s_(20141219_7)

description: Abf1 ChEC-seq, 50 second digestion


title: Abf1_ChEC_seq_20m_(20141204_8)

description: Abf1 ChEC-seq, 20 minute digestion


title: Abf1_ChEC_seq_30s_2_(20150213_2)

description: Abf1 ChEC-seq, 30 second digestion, replicate 2


title: Abf1_ChEC_seq_10s_(20141219_3)

description: Abf1 ChEC-seq, 10 second digestion


title: Abf1_ChEC_seq_20s_(20141219_4)

description: Abf1 ChEC-seq, 20 second digestion


title: Abf1_ChEC_seq_no_calcium_(20141204_4)

description: Abf1 ChEC-seq, no calcium


title: Free_MNase_ChEC_seq_5m_(20141114_13)

description: Free MNase ChEC-seq, 5 minute digestion

source_name: Free MNase ChEC-seq


title: Free_MNase_ChEC_seq_10m_(20141114_14)

description: Free MNase ChEC-seq, 10 minute digestion


title: Free_MNase_ChEC_seq_2.5m_(20141114_12)

description: Free MNase ChEC-seq, 2.5 minute digestion


title: Free_MNase_ChEC_seq_50s_(20141114_12_2)

description: Free MNase ChEC-seq, 50 second digestion


title: Rap1_ChEC_seq_no_calcium_(20141219_17)

description: Rap1 ChEC-seq, no calcium


title: Free_MNase_ChEC_seq_60s_(20141114_13_2)

description: Free MNase ChEC-seq, 60 second digestion


title: Free_MNase_ChEC_seq_40s_(20141114_11_2)

description: Free MNase ChEC-seq, 40 second digestion


title: Free_MNase_ChEC_seq_10s_(20141114_8)

description: Free MNase ChEC-seq, 10 second digestion


title: Free_MNase_ChEC_seq_30s_(20141114_10)

description: Free MNase ChEC-seq, 30 second digestion


title: Free_MNase_ChEC_seq_20s_(20141114_9)

description: Free MNase ChEC-seq, 20 second digestion


title: Free_MNase_ChEC_seq_20m_(20141114_1)

description: Free MNase ChEC-seq, 20 minute digestion


title: Free_MNase_ChEC_seq_no_calcium_(20141114_11)

description: Free MNase ChEC-seq, no calcium


title: Abf1_ChEC_seq_30s_1_(20141219_5)

description: Abf1 ChEC-seq, 30 second digestion, replicate 1


title: GNF4877_85

city: San Diego

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: 48 hr stimulation

data_processing:
Illumina CASAVA pipeline v.1.8.2 was used for basecalling
Single end sequence reads were mapped to file of Refseq transcripts (NCBI RefSeq snapshot April/2/2013) with bwa v0.5.9 using default parameters
Samtools 0.1.19 was used to make .bam files, sort them, and count reads aligning to each transcript.  RPM was calculated using those counts and the number of mapped reads for each sample.
Genome_build: NCBI RefSeq snapshot April/2/2013
Supplementary_files_format_and_content: text file includes RPM values for each Sample

source_name: islet cell

growth_protocol: Whole islets from Sprague Dawley rats were isolated followed by immediate hand picking to ensure removal of contaminating cell populations

extract_protocol:
Following quantification, dispersed islets were loaded into Fluidigm C1 IFC microfluidic chips according to manufacturer specifications (Fluidigm). Briefly, 60 µL of a 200 cell/µL mixture was combined with 40 µL of C1 suspension reagent. 5 µL was loaded into the 10-17 µm Fluidigm IFC using the mRNA Seq: Cell Load (1771x/1772x/1773x) protocol. After loading, the IFC was manually inspected to ensure single cell capture by phase contrast microscopy. Following inspection, cells were lysed according to Fluidigm's C1 protocol.
Reverse transcription, and PCR amplification were all performed on the IFC using the SMARTer Ultra Low RNA kit (Clontech) with the mRNA Seq: RT & Amp (1771x/1772x/1773x) protocol. cDNA was quantified by Pico Green assay (Life Technologies) and then normalized with C1 DNA dilution buffer to 0.1-0.3ng/µL.  Sequencing libraries were prepared with the Nextera XT DNA Sample Preparation Index Kit, (Illumina, PN FC-131-1002).  Sequencing libraries were run on an Illumina HiSeq 1000 sequencer using single 50 bp reads, one 96-well plate per lane.

treatment_protocol: After isolation, whole islets were cultured in RPMI1640 (Gibco) containing 10% FBS and 5.5mM glucose with either 0.1% DMSO or 3 µM GNF4877. After 48 hrs of culture, islets were trypsinized with 0.05% trypsin for 5 minutes at 37C into a single cell suspension and neutralized with media. Following dispersal, cells were passed through a 40 µm filter and quantified by ViCell (Beckman Coulter).

value: Sprague Dawley

value: pancreas

tag: cell type

value: islet cell

value: 8 week male

value: wild type


title: GNF4877_87

description: 48 hr stimulation


title: GNF4877_94

description: 48 hr stimulation


title: GNF4877_90

description: 48 hr stimulation


title: GNF4877_92

description: 48 hr stimulation


title: GNF4877_8

description: 48 hr stimulation


title: GNF4877_9

description: 48 hr stimulation


title: GNF4877_81

description: 48 hr stimulation


title: GNF4877_79

description: 48 hr stimulation


title: GNF4877_80

description: 48 hr stimulation


title: GNF4877_77

description: 48 hr stimulation


title: GNF4877_93

description: 48 hr stimulation


title: GNF4877_73

description: 48 hr stimulation


title: GNF4877_72

description: 48 hr stimulation


title: GNF4877_74

description: 48 hr stimulation


title: GNF4877_71

description: 48 hr stimulation


title: GNF4877_96

description: 48 hr stimulation


title: GNF4877_7

description: 48 hr stimulation


title: GNF4877_66

description: 48 hr stimulation


title: GNF4877_69

description: 48 hr stimulation


title: GNF4877_65

description: 48 hr stimulation


title: GNF4877_86

description: 48 hr stimulation


title: GNF4877_64

description: 48 hr stimulation


title: GNF4877_95

description: 48 hr stimulation


title: GNF4877_78

description: 48 hr stimulation


title: GNF4877_63

description: 48 hr stimulation


title: GNF4877_62

description: 48 hr stimulation


title: GNF4877_58

description: 48 hr stimulation


title: GNF4877_59

description: 48 hr stimulation


title: GNF4877_55

description: 48 hr stimulation


title: GNF4877_60

description: 48 hr stimulation


title: GNF4877_57

description: 48 hr stimulation


title: GNF4877_52

description: 48 hr stimulation


title: GNF4877_6

description: 48 hr stimulation


title: GNF4877_51

description: 48 hr stimulation


title: GNF4877_50

description: 48 hr stimulation


title: GNF4877_84

description: 48 hr stimulation


title: GNF4877_68

description: 48 hr stimulation


title: GNF4877_49

description: 48 hr stimulation


title: GNF4877_46

description: 48 hr stimulation


title: GNF4877_48

description: 48 hr stimulation


title: GNF4877_45

description: 48 hr stimulation


title: GNF4877_43

description: 48 hr stimulation


title: GNF4877_47

description: 48 hr stimulation


title: GNF4877_56

description: 48 hr stimulation


title: GNF4877_61

description: 48 hr stimulation


title: GNF4877_54

description: 48 hr stimulation


title: GNF4877_40

description: 48 hr stimulation


title: GNF4877_35

description: 48 hr stimulation


title: GNF4877_37

description: 48 hr stimulation


title: GNF4877_39

description: 48 hr stimulation


title: GNF4877_41

description: 48 hr stimulation


title: GNF4877_53

description: 48 hr stimulation


title: GNF4877_33

description: 48 hr stimulation


title: GNF4877_36

description: 48 hr stimulation


title: GNF4877_34

description: 48 hr stimulation


title: GNF4877_30

description: 48 hr stimulation


title: GNF4877_32

description: 48 hr stimulation


title: GNF4877_5

description: 48 hr stimulation


title: GNF4877_44

description: 48 hr stimulation


title: GNF4877_29

description: 48 hr stimulation


title: GNF4877_27

description: 48 hr stimulation


title: GNF4877_42

description: 48 hr stimulation


title: GNF4877_23

description: 48 hr stimulation


title: GNF4877_22

description: 48 hr stimulation


title: GNF4877_20

description: 48 hr stimulation


title: GNF4877_2

description: 48 hr stimulation


title: GNF4877_31

description: 48 hr stimulation


title: GNF4877_19

description: 48 hr stimulation


title: GNF4877_38

description: 48 hr stimulation


title: GNF4877_18

description: 48 hr stimulation


title: GNF4877_15

description: 48 hr stimulation


title: GNF4877_17

description: 48 hr stimulation


title: GNF4877_16

description: 48 hr stimulation


title: GNF4877_13

description: 48 hr stimulation


title: GNF4877_26

description: 48 hr stimulation


title: DMSO_96

description: 48 hr stimulation


title: GNF4877_10

description: 48 hr stimulation


title: GNF4877_24

description: 48 hr stimulation


title: GNF4877_11

description: 48 hr stimulation


title: GNF4877_21

description: 48 hr stimulation


title: DMSO_91

description: 48 hr stimulation


title: GNF4877_1

description: 48 hr stimulation


title: GNF4877_25

description: 48 hr stimulation


title: DMSO_92

description: 48 hr stimulation


title: DMSO_89

description: 48 hr stimulation


title: GNF4877_12

description: 48 hr stimulation


title: DMSO_88

description: 48 hr stimulation


title: DMSO_87

description: 48 hr stimulation


title: DMSO_85

description: 48 hr stimulation


title: DMSO_84

description: 48 hr stimulation


title: DMSO_94

description: 48 hr stimulation


title: DMSO_86

description: 48 hr stimulation


title: DMSO_90

description: 48 hr stimulation


title: DMSO_9

description: 48 hr stimulation


title: DMSO_82

description: 48 hr stimulation


title: DMSO_80

description: 48 hr stimulation


title: DMSO_83

description: 48 hr stimulation


title: DMSO_81

description: 48 hr stimulation


title: DMSO_79

description: 48 hr stimulation


title: DMSO_78

description: 48 hr stimulation


title: DMSO_71

description: 48 hr stimulation


title: DMSO_77

description: 48 hr stimulation


title: DMSO_7

description: 48 hr stimulation


title: GNF4877_14

description: 48 hr stimulation


title: DMSO_76

description: 48 hr stimulation


title: DMSO_95

description: 48 hr stimulation


title: DMSO_74

description: 48 hr stimulation


title: DMSO_8

description: 48 hr stimulation


title: DMSO_75

description: 48 hr stimulation


title: DMSO_73

description: 48 hr stimulation


title: DMSO_64

description: 48 hr stimulation


title: DMSO_63

description: 48 hr stimulation


title: DMSO_65

description: 48 hr stimulation


title: DMSO_62

description: 48 hr stimulation


title: DMSO_59

description: 48 hr stimulation


title: DMSO_66

description: 48 hr stimulation


title: DMSO_69

description: 48 hr stimulation


title: DMSO_72

description: 48 hr stimulation


title: DMSO_6

description: 48 hr stimulation


title: DMSO_54

description: 48 hr stimulation


title: DMSO_55

description: 48 hr stimulation


title: DMSO_52

description: 48 hr stimulation


title: DMSO_67

description: 48 hr stimulation


title: DMSO_57

description: 48 hr stimulation


title: DMSO_49

description: 48 hr stimulation


title: DMSO_61

description: 48 hr stimulation


title: DMSO_43

description: 48 hr stimulation


title: DMSO_42

description: 48 hr stimulation


title: DMSO_47

description: 48 hr stimulation


title: DMSO_41

description: 48 hr stimulation


title: DMSO_60

description: 48 hr stimulation


title: DMSO_45

description: 48 hr stimulation


title: DMSO_46

description: 48 hr stimulation


title: DMSO_5

description: 48 hr stimulation


title: DMSO_58

description: 48 hr stimulation


title: DMSO_37

description: 48 hr stimulation


title: DMSO_39

description: 48 hr stimulation


title: DMSO_36

description: 48 hr stimulation


title: DMSO_68

description: 48 hr stimulation


title: DMSO_35

description: 48 hr stimulation


title: DMSO_34

description: 48 hr stimulation


title: DMSO_33

description: 48 hr stimulation


title: DMSO_38

description: 48 hr stimulation


title: DMSO_31

description: 48 hr stimulation


title: DMSO_32

description: 48 hr stimulation


title: DMSO_30

description: 48 hr stimulation


title: DMSO_3

description: 48 hr stimulation


title: DMSO_28

description: 48 hr stimulation


title: DMSO_48

description: 48 hr stimulation


title: DMSO_29

description: 48 hr stimulation


title: DMSO_24

description: 48 hr stimulation


title: DMSO_4

description: 48 hr stimulation


title: DMSO_26

description: 48 hr stimulation


title: DMSO_20

description: 48 hr stimulation


title: DMSO_22

description: 48 hr stimulation


title: DMSO_2

description: 48 hr stimulation


title: DMSO_21

description: 48 hr stimulation


title: DMSO_23

description: 48 hr stimulation


title: DMSO_27

description: 48 hr stimulation


title: DMSO_51

description: 48 hr stimulation


title: DMSO_19

description: 48 hr stimulation


title: DMSO_17

description: 48 hr stimulation


title: DMSO_15

description: 48 hr stimulation


title: DMSO_16

description: 48 hr stimulation


title: DMSO_14

description: 48 hr stimulation


title: DMSO_11

description: 48 hr stimulation


title: DMSO_12

description: 48 hr stimulation


title: DMSO_10

description: 48 hr stimulation


title: DMSO_1

description: 48 hr stimulation


title: wt A mRNA

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: FPKM and differential expression for mRNA.txt

data_processing:
>> mRNA <<
Reads with Phred scores <20 were trimmed from the ends of the reads.
Reads were aligned to the genome using Tophat
Differential expression was determined using CuffDiff
Genome_build: mm9
Supplementary_files_format_and_content: Text file includes FPKM values and differential expression information for each gene.

source_name: CD8+ T cells

extract_protocol:
100 ng of total RNA was used with the Illumina TruSeq RNA Sample Preparation kit v2. Libraries were sequenced on a Hi-Seq 2000, generating 100 bp reads
Cells were sorted into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.

treatment_protocol: CD8+ T cells were isolated from wt and miR-150-/- mice, then transferred into a recipient mouse which was infected with Listeria. Seven days later, the cells were sorted.

tag: cell state

value: effector

value: wt


title: KO B small RNA

description: Small RNA read counts.txt

data_processing:
>> Small RNA <<
Data that failed Illumina's QC were filtered out.
The first 6 nucleotides of the 3' adapter were searched for (TGGAAT). Reads without the adapter were filtered out, and those with the adapter had the adapter sequence and following nucleotides trimmed from the read.
Any read with >=15 nucleotides after trimming were aligned to the genome using Bowtie.
Genome-matching reads were matched to hairpin sequences from MiRBase (v20)
Reads to each miRNA were normalized by the number of hairpin-matching reads. Anything with <1 read per million in both samples were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: Text file includes the number of reads matching each miRNA.

extract_protocol:
450 ng of total RNA was used with the Illumina TruSeq Small RNA Sample Preparation kit. Libraries were sequenced on a Hi-Seq 2000, generating 50 bp reads
Cells were sorted into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.

value: naïve


title: KO B mRNA


title: KO A mRNA


title: wt B small RNA

description: Small RNA read counts.txt


title: Myocyte-MAPS-WT

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description:
3'-end RNA-seq
processed data file: Myocyte-MAPS-WT123-KO123.xlsx

data_processing:
Sequencing reads were trimmed by using cutadapt program (version 1.2.1). Trimmed reads smaller than 16 nt were discarded.
Reads were mapped to the mouse genome by using Bowtie (version 0.12.7), with parameters "--best --strata -l25 -n2'. Only uniquely mapped reads were kept.
For ChIP-seq, the reads mapped to the same location were kept up to 4.  The heart RBFox2 and input ChIP reads were trimmed 3 bp at 5'-end before mapping because of low sequencing qualities. The genomic coverage signal were counted from reads on both strands and normalized to 1 million total reads. The normalized signal from input samples were subtracted from those corresponding IPed samples and negative values were reset as 0.
For Gro-seq, the replicated samples were combined together. The genomic coverage signal were counted in forward and reverse strands separately and normalized to 1 million total reads.
For CLIP-seq, the reads mapped to the same location with same random barcode sequence (attached to read name) were kept to 1. The genomic coverage signal were counted in forward and reverse strands separately, and then normalized to 1 million total reads.
For 3'-end RNA-seq, the reads mapped to the same location were kept up to 4, and only reads in exons were counted. The counts for different samples were normalized to 10 million total reads.
For RASL-seq, the reads were mapped to targetd exon-exon junctions with up to two mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files are genomic signals for ChIP-seq, Gro-seq and CLIP-seq samples. The Excel file for RASL-seq samples are counts for targeted isoforms.  The Excel file for 3'-end RNA-seq samples are normalized abundance measurements.

source_name: cardiac myocytes from WT mouse hearts

extract_protocol: Qiagen RNA kit and was used For RNA extraction from isolated cardiac myocytes by following manufacturer's instructions. RNA was enriched in two rounds for Poly(A+) RNA with paramagnetic oligo(dT), fragmented into ~200nt in length, converted to cDNA with Superscript III (Invitrogen), and subjected to deep sequencing.

tag: strain background

value: Black Swiss

tag: genotype/variation

value: 9 weeks

value: heart


title: wt B mRNA


title: Myocyte-RASLseq-WT-Week9

description:
RASL-seq
processed data file: Myocyte-RASLseq-WT-Week5-Week9-Week18.xlsx

extract_protocol: Qiagen RNA kit and was used For RNA extraction from isolated cardiac myocytes by following manufacturer's instructions. 1 µg total RNA was mixed with 100 fmol of mouse RASL oligos, 2 pmol of biotinylated-oligo-dT and 5 µl of streptavidin magenetic beads. Followed by one hour of annealing at 45ºC, magnetic beads were washed 3 times by washing buffer. Then ligation was achieved by adding 5U of T4 DNA ligase for 1 hour at 37ºC. After 3 times of wash, ligated oligos were eluted to water by heating at 65ºC for 5 minutes, and then PCR amplified using primers containing sequencing adaptor and barcode sequences. PCR products were purified and sequenced.


title: FTOC WT RANKL+1

city: Fukuoka

first: Toyoshi

last: Yanagihara

state: Fukuoka

address: Maidashi, Higashi-ku

department: Immunobiology and neuroscience

country: Japan

institute: Medical institute of bioregulation, Kyushu University

description: Sample 3

data_processing:
Sequencing was performed in 101-bp paired-end mode using an Illumina HiSeq
Filtered reads were mapped to the UCSC mm10 using the TopHat program(v2.0.10)
The Cufflinks program(V2.1.1) was used to assemble 22448 transcripts and to calculate the fragments per kilobase of exon per million mapped fragments (FPKM) values with the non-default parameters: -u --library-type fr-secondstrand
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each intron (intron-FPKM.xlsx); normalized measurement of gene expression levels (genes-FPKM.txt)

source_name: FTOC WT RANKL+

growth_protocol: 2-DG treated for 4days

extract_protocol:
poly-A containing RNA was purified using poly-T oligo-attached magnetic beads
RNA libraries were prepared for sequencing using standard Illumina protocols.TruSeq RNA Sample Prep Kit c2

treatment_protocol: RANKL stimulated

value: thymus

value: fetal thymus organ culture (FTOC)

tag: stimulated with

value: RANKL


title: FTOC KO RANKL+1

description: Sample 5

source_name: FTOC KO RANKL+

tag: tissue


title: Myocyte-RASLseq-KO-Week18

source_name: cardiac myocytes from RBFox2 KO mouse hearts

value: RBFox2 KO

value: 18 weeks


title: FTOC WT RANKL+2

description: Sample 4


title: Myocyte-MAPS-KO


title: Myocyte-RASLseq-KO-Week5

value: 5 weeks


title: Myocyte-RASLseq-WT-Week18


title: Myocyte-RASLseq-KO-Week9


title: Myocyte-RASLseq-WT-Week5


title: FTOC KO RANKL+2

description: Sample 6


title: KO A small RNA

description: Small RNA read counts.txt


title: wt A small RNA

description: Small RNA read counts.txt


title: MEFs-siSUZ12-GROseq

description: Gro-seq

growth_protocol: DMEM plus 10% FBS

extract_protocol: ~20 million cell nuclei from NC or RNAi cells were extracted and harvested. The global nuclear run-on assay and was carried out and analyzed by deep sequencing using a published protocol (Wang et al., 2011).

treatment_protocol: MEFs were transfected with SUZ12 siRNA for 72 hours before functional studies.

value: MEF cell line

tag: passages

tag: treated with

value: SUZ12 siRNA

tag: molecule subtype

value: nascent RNA


title: MEFs-NC-GROseq

description: Gro-seq

source_name: MEFs-NC-GROseq

treatment_protocol: MEFs were transfected with NC for 72 hours before functional studies.

value: negative control siRNA


title: Heart-KO-GROseq

description: Gro-seq

source_name: RBFox2 KO mouse hearts

extract_protocol: Three isolated hearts was cut into small pieces (~1mm3) and washed with cold PBS to get rid of blood cells. Nuclei were extracted as described (Widnell et al., 1967). The global nuclear run-on assay and was carried out and analyzed by deep sequencing using a published protocol (Wang et al., 2011).


title: Myocyte-Ago2-RBFox2-WT-CLIPseq

description: CLIP-seq

extract_protocol: CLIP-seq library was prepared according to previously published standard protocol (Yeo et al., 2009).

treatment_protocol: Isolated cardiac myocytes were UV-irradiated at 400mj

value: wild type

value: cardiac myocytes

tag: chip antibody

tag: chip antibody vendor

value: Abnova

tag: chip antibody cat. #


title: MEFs-Input-siSUZ12-ChIPseq

description: ChIP-seq

extract_protocol: MEFs were fixed with 1% Formaldehyde at room temperature for 10 min. After the treatment, cross linking was quenched with 0.125 M glycine for 10 min. ~50 million cells were used for each ChIP.


title: FTOC KO RANKL-

description: Sample 2

source_name: FTOC KO RANKL-

value: none (unstimulated control)


title: MEFs-siRBFox2-GROseq

description: Gro-seq

treatment_protocol: MEFs were transfected with RBFox2 siRNA for 72 hours before functional studies.

value: RBFox2 siRNA


title: FTOC WT RANKL-

description: Sample 1

source_name: FTOC WT RANKL-


title: Myocyte-RBFox2-whole-cell-CLIPseq

description: CLIP-seq

value: Black Swiss

tag: age

value: 9 weeks

value: Bethyl


title: Myocyte-Ago2-RBFox2-KO-CLIPseq

description: CLIP-seq

value: heart


title: Myocyte-RBFox2-nulcear-CLIPseq

description: CLIP-seq

extract_protocol: Isolated cardiac myocytes were used to prepare nuclei as described (Widnell et al., 1967). CLIP-seq library was prepared according to previously published standard protocol (Yeo et al., 2009).

value: nuclear RNA


title: Heart-WT-GROseq

description: Gro-seq

source_name: WT mouse hearts


title: MEFs-RBFox2-siSUZ12-ChIPseq

description: ChIP-seq


title: MEFs-SUZ12-DRB-ChIPseq

description: ChIP-seq

treatment_protocol: MEFs were treated with 100μM DRB for 3 hours.

value: DRB

value: Cell Signaling


title: MEFs-Input-NC-ChIPseq

description: ChIP-seq

source_name: MEFs-Input-NC-ChIPseq


title: MEFs-Input-siRBFox2-ChIPseq

description: ChIP-seq


title: MEFs-RBFox2-DRB-ChIPseq

description: ChIP-seq


title: Heart-RBFox2-WT-ChIPseq

description: ChIP-seq

extract_protocol: Four isolated hearts was cut into small pieces (~1mm3) and washed with cold PBS to get rid of blood cells. The heart pieces were fixed with 1.5% Formaldehyde at room temperature for 10 min. After the treatment, cross-linking was quenched with 0.125 M glycine for 10 min. Then the nuclei were extracted as described (Widnell et al., 1967) for ChIP-seq.


title: Heart-SUZ12-WT-ChIPseq

description: ChIP-seq


title: MEFs-H3K27Me3-NC-ChIPseq

description: ChIP-seq

value: Active Motif


title: MEFs-SUZ12-siRBFox2-ChIPseq

description: ChIP-seq

value: MEF cell line


title: Heart-Input-WT-ChIPseq

description: ChIP-seq


title: MEFs-RBFox2-siRBFox2-ChIPseq

description: ChIP-seq


title: T. tenax small RNA #2

city: Marburg

first: Michael

last: Daume

state: Hessen

address: Karl-von-Frisch-Strasse 10

department: Prokaryotic Small RNA Biology

institute: Max Planck Institute for Terrestrial Microbiology

description: small RNAs (<200 nt)

data_processing:
Software: All data processing steps were performed with CLC Genomic Workbench 8.0.1
Raw Data Import: The raw data files were imported using the Illumina Import option (Illumina Pipeline 1.8 and removal of failed reads).
Raw Data Processing: The raw data files were processed by quality score trimming (quality score trimming limit: 0.05; max. number of ambiguities: 2) and by poly-T(60) adapter trimming (strand: minus; action: remove adapter; mismatch cost: 3; gap cost: 3; no internal end matches allowed; minimum end matches score: 3). The processed sequences were filtered by length (15 nt cutoff)
Read Mapping: The trimmed sequences were mapped to the T. tenax reference genome (FN869859) using default settings (mismatch cost set to 4) and saved as a read track file.
Genome_build: T. tenax reference genome (FN869859)
Supplementary_files_format_and_content: The processed data file is in .wig (Wiggle) format. It contains the Mapping Graph track that was created from the coverage plot of the generated read track file. Furthermore, the reference genome (Thermoproteus tenax - FN869859) is included as .fasta (Fasta) file, which is needed for the illustration of the Mapping Graph track.

organism: Thermoproteus tenax

source_name: liquid culture

growth_protocol: Cells were grown heterotrophically in Thermoproteus medium to logarithmic phase.

extract_protocol:
Cells were lysed by homogenization and small RNAs were isolated according to the mirVana miRNA Isolation Kit (Ambion). The extracted small RNAs were used for cDNA library preparation without PNK-treatment.
cDNA libraries were prepared according to the TruSeq Small RNA Library Protocol (Illumina).

tag: strain

tag: developmental stage

value: logarithmic phase


title: WT rep2

city: Philadelphia

first: Christopher

last: Lengner

state: PA

address: 3800 Spruce Street, Room 390EA

institute: University of Pennsylvania

description: CLIP-seq

data_processing:
Basecalls performed with Illumina base calling software [Illumina Real time analysis(RTA) 1.13.48]
Adaptor sequences ('GTGTCAGTCACTTCCAGCG') were removed from the 3' end using the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads were then mapped using Bowtie (-k 100 -n 0) to the mouse genome (mm9)
Peaks were then called using an FDR ≤ 0.05 and motifs were identified using Homer (http://biowhat.ucsd.edu/homer/)
Genome_build: mm9
Supplementary_files_format_and_content: BED format

source_name: intestinal epithelial cells

extract_protocol:
Total intestinal epithelial cells from two individual TRE-Msi1 mice treated with Dox for 24 hours were isolated as above, and wildtype intestinal crypts from two control mice were isolated as above. For crosslinking, cell suspension was exposed to 2 pulses of 265nm UV light at 400mJ/cm 2 in a Stratalinker (Model 2400, Stratagene). Epithelial cells were then lysed using PXL buffer (PBS, 01% SDS, 0.5% deoxycholate, 0.5% NP-40, plus protease inhibitor and RNAsin). The lysates were sequentially treated with DNaseI and RNase, and spun in ultra-microcentrifuge at 40,000g for 20 min. The supernatant was added to protein A Dynabeads (Dynal, 100.02) conjugated with Msi1 antibody (AB5977, Millipore) and incubated for 4 hours at 4 °C. 32P-ATP labeled 3’ RNA (RL-3) linker was ligated to the RNA fragment on beads overnight at 16°C. The beads were re-suspended in 30 µl of Novex loading buffer (without reducing agent), and separated with Novex NuPAGE 10% Bis-Tris gel and transferred to S&S BA-85 nitrocellulose membrane. After overnight exposure, around 50 KD band was visualized and the corresponding membrane was cut to small pieces. The RNA was released by proteinase K digestion and isolated using RNA phenol and CHCl3 solution.
5’ RNA (RL-5) linker was ligated into the RNA fragments. The RNA was transcribed into complementary DNA using RT-PCR and amplified using Re-PCR with Solexa fusion primers.

tag: genotype

value: Wild-type

value: intestine

value: epithelial

tag: dox

value: no

tag: ip


title: TG rep2

description: CLIP-seq

tag: cell type

value: yes


title: primary myoblasts from Barx2 KO mouse 1

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Read alignment and junction mapping was accomplished using TopHat2 v2.0.4 using a 25 bp 5’ segment seed for initial mapping followed by differential gene expression analysis using Cuffdiff v2.0.2 to map reads to the reference genome annotation.
BEDTools was used to generate bedGraphs from the bam files generated from TopHat2.
Bigwig files were generated from bedGraphs using the bedGraph to bigwig command from UCSC.
Genome_build: NCBI mouse build 37.2
Supplementary_files_format_and_content: Bigwig files for UCSC browser viewing

source_name: Barx2 knockout primary myoblasts

extract_protocol:
Total RNA from pooled primary myoblast cultures was isolated using Trizol (Invitrogen) and the RNeasy mini kit with on-column DNase digestion (Qiagen) according to the manufacturers’ instructions.  Biological duplicates were used for each condition.
Sequencing libraries were prepared from 100-500ng total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the manufacturer’s protocol.
Libraries were then validated using the 2100 BioAnalyzer (Agilent), normalized, and pooled for sequencing.  Prepared samples were sequenced on the Illumina HiSeq 2000 using bar-coded multiplexing and either 50 or 100bp read length.

tag: strain background

value: Barx2 knockout

value: skeletal muscle

value: cultured primary myoblasts


title: TG rep1

description: CLIP-seq


title: WT rep1

description: CLIP-seq


title: primary myoblasts from WT mouse 1

source_name: wild-type primary myoblasts

tag: genotype/variation

value: wild type


title: InSPI2 Salmonella RNA-seq

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: RNA from bacteria grown in vitro to mimick intra-macrophage condition.

data_processing:
Reads were de-multiplexed and poly-A tails were removed.
Sequence reads were then mapped against the S. Typhimurium 4/74 reference genome using Segemehl with accuracy set to 100%.
To increase mapping quality, unmapped reads were sequentially truncated by one nucleotide from the end of the read and were mapped again.
This process was iterated until a minimal read length of 20 nucleotides or until a read mapped into a single location on the chromosome.
Genome_build: Bioproject Accession: PRJNA56087; ID: 56087. Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74 [PMID: 21478351]
Supplementary_files_format_and_content: Files in tab-delimited graph (.gr) format are provided showing genomic coverage of uniquely mapped sequence reads, ready to load into Integrated Genome Browser (IGB). Each file consists of two columns showing nucleotide position on the chromosome and number of reads mapped at each location. "plus" and "minus" in the file names refer to the two strands of the Salmonella chromosome.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: in vitro InSPI2 growth condition

growth_protocol: The wild type 4/74 was grown in PCN until OD600 of 0.3. which is the synthetic media mimicking the intra-macrophage condition. The PCN media is a low phosphate, Low Magnesium and Low pH media which mimicks the low-nutrient acidic conditions within the macrophage.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and Dnase I digested.
cDNA libraries were constructed by vertis Biotechnologie AG (Freising, Germany) using an in-house protocol. Total RNA (DNase I digested) was fragmented by ultrasound (4 pulses of 30s at 4°C). The to construct dRNA-seq libraries, these RNA samples were subsequently digested with Terminator Exonuclease (TEX). 3′ ends were subjected to poly(A)-tailing using poly(A) polymerase, pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using an oligo(dT) adapter and M-MLV-RNaseH-reverse transcriptase, following PCR amplification of cDNA using high-fidelity DNA polymerase to ∼20–30 ng/μL. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

tag: growth condition

value: in vitro condition mimicking intra-macrophage condition


title: primary myoblasts from WT mouse 2

tag: tissue


title: Abf1_X_ChIP_seq_(20130118_9)

description: Abf1 MNase-X ChIP-seq

data_processing: 1. We used Novoalign 2.08.03 (http://www.novocraft.com) to map paired-end 25bp reads to release  V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC . If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)

source_name: Abf1 ChEC-seq

extract_protocol: described in PMID 23468649

tag: cell part

value: nuclei

tag: mutant

value: WT

value: W1588-4C (congenic to W303-1A except RAD5+)


title: MEFs-H3K27Me3-siRBFox2-ChIPseq

description: ChIP-seq

tag: passages

tag: treated with

value: RBFox2 siRNA


title: maize_drought_sRNA

status: Public on Oct 21 2015

data_processing: Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor, contain N, or have length less than 17nt were removed. The processed files are named as "prefix"_uniq.txt, where "prefix" is the prefix of the file that contains raw data.  The first column in a processed file contains clean reads, and the second column contains the number of copies of the reads in the library.

organism: Zea mays

growth_protocol: Plants grown in a growth chamber with 28°C / 18h light and 23°C /6h dark cycle. Humility maintained at 90%.

extract_protocol: Total RNA was isolated from seedlings with TRIzol (Invitrogen) and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 18 to 30 nt were excised and ligated to a preadenylated 3' adaptor and a 5’- adaptor using T4 RNA ligase. Ligation products were purified in polyacrylamide gels, followed by RT-PCR. The small RNA libraries were sequenced by the UCR core facility.

tag: subspecies

value: mays

tag: cultivar

value: seedlings

tag: treatment

value: drought


title: MEFs-RBFox2-NC-ChIPseq

description: ChIP-seq

value: MEF cell line

value: negative control siRNA

tag: chip antibody

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat. #


title: maize_cold_sRNA

value: cold


title: primary myoblasts from Barx2 KO mouse 2


title: maize_salt_sRNA

value: salt


title: maize_control_sRNA

value: control


title: MEFs-SUZ12-NC-ChIPseq

description: ChIP-seq

value: Cell Signaling


title: Tribolium castaneum rep3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Library strategy: MethylC-seq
Data were mapped to the Nicrophorus vespilloides and Tribolium castaneum reference genomes.
MethylC-seq analysis was performed as described in Schmitz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: Nicrophorus vespilloides (v1.0, wild type draft assembly, unpublished) reference genome
Genome_build: Tribolium castaneum Tcas_3.0 (v3.0, GA2 strain, see Kim et al., 2010, Nucleic Acids Research (DOI: 10.1093/nar/gkp807)) reference genome
Supplementary_files_format_and_content: Tab-delimited text file. See the supplementary file 'GSE68814_readme.txt' for column definitions.

organism: Tribolium castaneum

source_name: T. castaneum larva

growth_protocol: Nicrophorus vespilloides was kept under standard colony conditions (see Cunningham et al., 2014, Insect Molecular Biology (DOI: 10.1111/imb.12090) for details). Tribolium castaneum was kept using a standard flour/yeast mixture (e.g., wwwuser.gwdg.de/~gbucher1/tribolium-castaneum-beetle-book1.pdf) at 22C with no humidity controls.

extract_protocol:
Genomic DNA (gDNA) was purified from Nicrophorus vespilloides and Tribolium castaneum larva using a Qiagen DNase Plant Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions.
MethylC-seq libraries were constructed according to Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2015) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols.

value: wild-type

tag: developmental stage

value: larva

value: whole body


title: Tribolium castaneum rep2


title: Tribolium castaneum rep1


title: P57B001

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Basecalling was performed by Torrent Suite version 4 software using default settings
Alignment to Drosophila melanogaster genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
Aligned bam files from sequencing runs A, B and C were merged for analysis, and the bam files from run E were analyzed separately.
The total sequencing base pair coverage of all non-redundant exons was summed for all annotated genes in each sample and normalized to total histone RNA sequence coverage using bedtools and custom R programs as described in Wu Y, Gause M, Xu D, Misulovin Z, Schaaf CA et al. Drosophila Nipped-B mutants model Cornelia de Lange syndrome in growth and behavior. PLoS Genetics, in press.
Genome_build: Drosophila melanogaster release 5 (April 2006) with chrU and U_extra sequences removed
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing base pair coverage of all annotated genes, statistical comparisons between P57B wild-type and Nipped-B[407] heterozygous mutants, and gene ontology analysis for genes whose expression is significantly altered by the heterozygous Nipped-B[407] mutation.

organism: Drosophila melanogaster

source_name: third instar wing discs

growth_protocol: Homozygous P57B females and Nipped-B[407]/CyO balanced females were crossed to Oregon R wild-type males at 25 degrees and wing discs were dissected from crawling late third instar female progeny larvae that were P57B/Oregon R and Nipped-B[407]/Oregon R

extract_protocol:
Total RNA was isolated from wing discs using the Zymo Research Quick-RNA MicroPrep Kits with DNaseI treatment following the manufacturer’s protocol.
Ion Torrent IonXpressRNA barcoded sequencing libraries were constructed using Life Technologies Eukaryotic RiboMinus and Ion Total RNA-seq v2 kits according to the manufacturer’s directions. Sample titles indicate the barcode used.

tag: genotype

value: wild-type (P57B/Oregon R)


title: P57B002


title: NIPB005

value: Nipped-B[407]/Oregon R


title: NIPB006


title: NIPB004


title: P57B003


title: Nicrophorus vespilloides rep1

organism: Nicrophorus vespilloides

source_name: N. vespilloides larva


title: Nicrophorus vespilloides rep3


title: Nicrophorus vespilloides rep2


title: AT1 biological replicate

city: Potsdam

first: Alexander

last: Bartholomaeus

address: Telegrafenberg C

department: Department 3 Geochemie

institute: Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences

description: AT1 digested total RNA

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details
Read counts were normalized by million mapped reads for each nucleotide
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C.
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009}

tag: strain

tag: media

value: LB

tag: sample type

value: AT1 digested total RNA


title: AT1

description: AT1 digested total RNA


title: V1

description: V1 digested total RNA

value: V1 digested total RNA


title: V1 biological replicate

description: V1 digested total RNA


title: LB mRNA technical replicate


title: LB mRNA biological replicate


title: LB mRNA


title: Mushroom body 36hr after pupae replicate 2

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters  --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were assigned to genes using HTSeq v0.6.1p1 with parameter -s no -m intersection-nonempty and using iIllumina UCSC/dm3 annotation. FPKM for a gene was calculated by dividing assigned count by the sum of lengths of all exons belonging to the gene and then by total number of reads in million.
Genome_build: dm3
Supplementary_files_format_and_content: tab deliminated files include TPM values, raw count values

source_name: Mshroom body

growth_protocol: Newly hatched Fly larvae were first synchronized with maxiumum 2 hour age difference and then grew at 25C until dissection

extract_protocol:
30 fly larvae brain tissues were dissected at defined ages, digested with a mixture of pronase(1mg/ml) and dispase (1mg/ml) for 30 min at 25C, washed, triturated and 10 GFP labeled cells were sorted with a robotic sorter and stored at -80C in XB buffer from PicoPure kit (life technologies, KIT0204). Total RNA from around 100 pooled cells was extracted using PicoPure kit.
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).

tag: cell type

value: neuroblast

tag: age

value: 36hr after pupae

tag: num_cells (number of neuroblast cells in sample)

tag: ercc_mix (1 or 2)

tag: ercc_5 (10^-5 dilution of ercc in ul)


title: Mushroom body 36hr after pupae replicate 3


title: Mushroom body 36hr after pupae replicate 1


title: LB RPF

description: ribosome protected

value: ribosome protected


title: Mushroom body 84hr after larva hatch replicate 3

value: 84hr after larva hatch


title: Mushroom body 84hr after larva hatch replicate 2


title: Mushroom body 50hr after larva hatch replicate 3

value: 50hr after larva hatch


title: Mushroom body 24hr after larva hatch replicate 2

value: 24hr after larva hatch


title: Mushroom body 50hr after larva hatch replicate 1


title: Antennal lobe 84hr after larva hatch replicate 2

source_name: Antennal lobe


title: Antennal lobe 50hr after larva hatch replicate 3


title: Mushroom body 24hr after larva hatch replicate 1


title: Mushroom body 50hr after larva hatch replicate 2


title: Antennal lobe 50hr after larva hatch replicate 2


title: Antennal lobe 84hr after larva hatch replicate 3


title: Mushroom body 24hr after larva hatch replicate 3


title: LB RPF biological replicate

description: ribosome protected


title: Antennal lobe 36hr after larva hatch replicate 2

value: 36hr after larva hatch


title: Antennal lobe 84hr after larva hatch replicate 1


title: Antennal lobe 36hr after larva hatch replicate 1


title: Antennal lobe 36hr after larva hatch replicate 3


title: Antennal lobe 50hr after larva hatch replicate 1


title: Antennal lobe 24hr after larva hatch replicate 3


title: Mushroom body 84hr after larva hatch replicate 1


title: Antennal lobe 24hr after larva hatch replicate 1


title: Dam P.e. rep2

city: Palo Alto

first: Roel

last: Nusse

address: 265 Campus Drive

department: Developmental biology

institute: Stanford University, School of Medicine

description:
molecule: methylated gDNA
fragmented gDNA digested by Dpn1

data_processing:
Library strategy: DamID-seq
DamID-Seq:Raw reads were mapped to the Drosophlia genome (version 6.02, www.flybase.org) using Bowtie 2 with default setting. After mapping, the uniquely mapped reads were extended 300 base pair (bp) toward 3' prime, and the genome were segmented with a unit of 75 bp window. Then the number of reads falling into each window was quantified. Normalization factors were computed based on the assumption that the mean log ratio between two experiments is equal to 1. The log ratio between treatment and background was observed to follow a normal distribution; the mean and standard deviation were estimated by using the fitdistr function in R (www.r-project.org). The statistical significance of the enrichment was then computed using the estimated mean and standard deviation. Using a sliding window approach, a binding site was called, where at least 4 continuous units (4x75bp windows) had a significant enrichment (p-value<0.01). The false discovery rate of the binding sites was calculated similarly to the previous publication [71].
Genome_build: Dm_r6.02
Supplementary_files_format_and_content: DamID-Seq: tab-delimited text files for peaks

source_name: Midgut progenitor cells

growth_protocol: Crosses were set up and maintained at 18°C, the permissive temperature.

extract_protocol:
DNA extraction: Midguts were homogenized in TENS buffer and gDNA was extracted using phenol-chloroform. gDNA was digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 350bp using Covaris-S2 then digested with Sau3AI to remove the adaptors before processing with Truseq DNA PCR-Free Sample Preparation kit (illumina) as manufacturer's protocols

treatment_protocol: DamID-Seq: 3-7 day old flies were shifted to 29°C for 24 hours to induce Dam or CicDam. For DamID under infection conditions, flies were fed Pseudomonas entomophila (P.e.)  bacteria for 16 hours. Adult flies were dissected in 1×PBS, and the midguts were immediately put into liquid nitrogen.

tag: tissue

value: midgut

value: Pseudomonas entomophila infected Midgut progenitor cells

value: esgts>Dam


title: CicDam P.e. rep1

value: esgts>CicDam


title: CicDam P.e. rep2


title: Dam P.e. rep1


title: CicDam rep2

value: Midgut progenitor cells


title: A5SS_DNA

city: Seattle, WA 98195

middle: B

last: Rosenberg

address: 4000 15th Ave NE

department: Electrical Engineering

institute: University of Washington

description:
Plasmid DNA
synthetic sequences

data_processing:
The fastq files were processed using custom python scripts. All of the analysis is available at https://github.com/Alex-Rosenberg/cell-2015
Genome_build: NA
Supplementary_files_format_and_content: For each library we have a file with all the barcode – intronic sequence associations, as well as a matrix with the number of spliced reads at each position for each library member.
Supplementary_files_format_and_content: [A5SS_seq.txt] Sequences in alternative 5' library

molecule: other

source_name: plasmid prep

growth_protocol: HEK293 cells were cultured in in DMEM (Cellgro) + 10% FBS and L-glutamine/penicillin/streptomycin on coated plates. Plates were coated for 24 hours with 8mL of 100x diluted extracellular matrix gel (Sigma-Aldrich) before HEK293 cells were added to the plates.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) kits 24 hours after transfection. The optional on column DNaseI digest was performed with the RNase-Free DNase Set (Qiagen). Total RNA quality and purity was tested by measuring the A260/A280 ratio on a NanoDrop 1000 Spectrophotometer, and in some cases by measuring the ratio of the 18S and 28S rRNA bands on a native 1% agarose gel. mRNA was separated from 35-48ug total RNA using polyA Spin mRNA Isolation Kits (New England Biolabs). Isolated mRNA was again digested by DNaseI for 30 minutes using the Turbo DNA-free kit (Ambion). cDNA was then synthesized from 109-374ng mRNA using MultiScribe Reverse Transcriptase (Ambion) and Oligo d(T)16 (Ambion). cDNA synthesis was performed by holding reactions at 25°C for 10 min, 42°C for 110 min, and 85°C for 5 min. The quality of cDNA and presence of DNA contamination were checked through qPCR: Citrine, mCherry, and TBP were compared using cDNA, No Reverse Transcription Controls (NRTC) and a No Template Control (NTC). The results indicated that there was no plasmid or genomic DNA carryover into the cDNA reactions.
The resulting cDNA was then amplified by PCR to generate products compatible with the Illumina HiSeq2000 Flow Cell. PCR reactions were performed in 100uL with 2x Phusion HF Master Mix (New England Biolabs), 50pmol forward primer and 50pmol reverse primer with sample specific barcodes and 20% of each cDNA reaction. Cycling was done on a BioRad T100TM Thermal Cycler with the following protocol: 98°C for 5 min, then 7 cycles of 98°C for 10s, 67.5°C for 15s, 72°C for 30s, and a final extension step at 72°C for 5 min. The necessary number of cycles was determined for each sample by first running PCR reactions with EvaGreen in a Biorad CFX and determining when fluorescence began to plateau. Following PCR, 10% of the products were run on a 2% agarose gel to determine if the expected bands were present. The remainder of the PCR products was purified using the QIAquick PCR Purification kit (Qiagen) and eluted into 30uL of EB. Concentrations as well as A260/280 and A260/230 ratios were measured on a NanoDrop 1000 Spectrophotometer.  Illumina compatible PCR products were also generated from the DNA plasmid library with the same protocol as above except the cDNA template was replaced with 10ng of plasmid library DNA and the PCR reaction was performed with 20 cycles.

treatment_protocol: For transfection of a complex pool of plasmids, 1.2 million cells were seeded in a 10cm dish 24 hours before transfection. We mixed 10ug of the plasmid library in 1ml of Opti-MEM Reduced Serum Medium (Life Technologies) with 30ul of Lipofectamine LTX and 10ul of Plus Reagent (Life Technologies), before transfecting into the 10cm dish. The DMEM was was replaced 5 hours after transfection.

value: A5SS_DNA (alternative 5' library)


title: CicDam rep1


title: RNA-Seq Sample rep4

description: Amplified mRNA

data_processing:
RNA-Seq: Raw reads were checked for quality using Fastqc and subsequently aligned using Tophat2, version 2.0.9, against the Flybase genome version 6. Mapped reads were counted using HTSeq-count version 0.5.4p5 with mode „union“. Genes showing a cpm value below 1 in four samples per treatment were considered as poorly expressed and filtered out before conducting differential expression analysis using edgeR, version 3.2.4. Since our replicates were generated independently, we used a paired design and corrected the resulting p-values by the Benjamini-Hochberg method. Subsequently, genes with a fold change of 1.5 and an adjusted p-value lower than 0.1 were considered as significantly deregulated.
Genome_build: Dm_r6.02
Supplementary_files_format_and_content: RNA-Seq: tab-delimited text files include cpm values for each Sample.

extract_protocol:
RNA extraction: Midguts were removed, dissociated and cells were FACS Sorted. RNA was harvested using Arcturus Pico Pure RNA extraction kit and amplified with RiiboAmp HS plus amplification kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-Seq: 3-7 day old flies were shifted to 29°C for 4 days to induce GFP and cic-RNAi. Adult flies were dissected in 1×PBS, then dissociated using colagenase. GFP-positive cells were sorted using FACS Aria III.

value: FACS Sorted midgut progenitor cells

value: esgts>GFP, cic-RNAi


title: Dam rep2


title: RNA-Seq Sample rep3

description: Amplified mRNA


title: Antennal lobe 24hr after larva hatch replicate 2


title: Dam rep1


title: RNA-Seq Sample rep2

description: Amplified mRNA


title: RNA-Seq Control rep3

description: Amplified mRNA

value: esgts>GFP


title: RNA-Seq Control rep2

description: Amplified mRNA


title: RNA-Seq Sample rep1

description: Amplified mRNA


title: RNA-Seq Control rep4

description: Amplified mRNA


title: Control male liver - day 1

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
total RNA pooled from 3 mouse livers
poly-A selected, unstranded library
G88_M10

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along lincRNA gene bodies for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
DESeq (Anders et  al, Genome Biol, 2010) and edgeR (Robinson et al, Bioinformatics, 2010) were used to compute differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel file containing normalizedread  counts of lincRNAs across all samples and differential expression results comparing intact to continuous GH-treated mouse livers is provided. Bigwig files for each sample are also included, where each score represents the normalized gene expression level. Gene models for liver-expressed lincRNAs can be found at GEO series GSE65444.

source_name: liver tissue

growth_protocol: Vehicle (control)-treated and 1 to 7 days continuous GH-treated male CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were extracted.

extract_protocol:
Trizol reagent was used to prepare total liver RNA using standard protocols.
Poly-A-enriched RNA was prepared for Illumina sequencing using a non strand-specific sample preparation protocol

treatment_protocol: Continuous GH treatment was carried out as described in G. Ling et al, Mol. Cell. Biol, 2010 (PMID: 20876297).

value: CD-1 (Charles River)

tag: Sex

value: male

value: 8 weeks old

value: liver


title: Control male liver - day 4

description:
total RNA pooled from 3 mouse livers
poly-A selected, unstranded library
G88_M11


title: Male liver with continuous GH treatment for 4 days - liver 1

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M4


title: RNA-Seq Control rep1

description: Amplified mRNA


title: Male liver with continuous GH treatment for 7 days - liver 1

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M7


title: Male liver with continuous GH treatment for 1 day - liver 2

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M2


title: Male liver with continuous GH treatment for 4 days - liver 3

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M6


title: Male liver with continuous GH treatment for 4 days - liver 2

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M5


title: Male liver with continuous GH treatment for 1 day - liver 3

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M3


title: Male liver with continuous GH treatment for 7 days - liver 2

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M8


title: Male liver with continuous GH treatment for 7 days - liver 3

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M9