title: H9 IgG

description: IgG background

source_name: Embryonic Stem Cells_IgG

value: Embryonic Stem Cells


title: NT2D1 IgG

status: Public on Nov 05 2014

type: SRA

city: New York

first: Raju

middle: S

last: Chaganti

state: NY

address: 430 East, 67 Street, RRL-337,New York

department: Cell Biology

country: USA

institute: MSKCC

description: IgG background

library_source: genomic

data_processing:
Sequences were mapped to the human genome hg19 using ABI’s Corona Lite Plus genome mapping utility, allowing for up to four mismatches and retaining only unique matches.
We called peaks with MACS (Zhang, et al. 2008), using a band width of 200, model fold 5, and p-value cutoff of 1E-03 against IgG control
MACS identifies peaks on a per-window basis by comparing the number of tags in each genome window to the number of expected tags as calculated by a Poisson distribution and to the distribution of normalized per-window counts in IgG control
Candidate transcription-factor targets were identified based on transcription start site proximity (10Kb, 5Kb and 2Kb) to predicted peaks
Genome_build: HG19
Supplementary_files_format_and_content: text files contain macs output format

molecule: genomic DNA

organism: Homo sapiens

source_name: Human Germ Cell Tumour_IgG

extract_protocol:
Cells were sonicated using Covaris and then the TF-chromatin comples were isolated using magnetic beads linked to specific antibody
SOLiD System 2.0. Fragment Library Preparation protocol was based on size and concentration of ChIP-DNA

tag: cell type

value: Embryonic Carcinoma Cells

tag: cell line


title: NT2D1 NANOG

description: NANOG ChIPseq

source_name: Human Germ Cell Tumour_OCT4


title: 416B_Ctrl_HA

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads aligned to mm10 using Bowtie2
bedGraphs created using bedtools
bedGraphs converted to bigWigs (UCSC program 'bedGraphToBigWig')
Genome_build: mm10
Supplementary_files_format_and_content: bigWig – read density profiles

organism: Mus musculus

source_name: 416B WT control

growth_protocol: Grown in RPMI 1640 plus 10% fetal calf serum plus penicillin and streptomycin

extract_protocol:
As described in Wilson et al., Cell Stem Cell. 2010 Oct 8;7(4):532-44
According to Illumina TruSeq DNA Sample Prep Kit

treatment_protocol: Doxycycline (2 μg/ml) added for 48 hours before fixation to induce T-VP64-PU.1-14 expression

tag: tissue

value: Mouse myeloid progenitor cell line

tag: antibody

value: anti-HA

tag: transfection


title: 416B_HA-T-VP64-PU.1-14_HA

source_name: 416B expressing HA-T-VP64-PU.1-14


title: HUVEC30_n2

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: mononucleosomal DNA

data_processing:
Obtained reads were quality controlled and pre-processed using FastQC (http://www.bioinformatics. babraham.ac.uk/projects/fastqc/) and the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Pre-processed reads were mapped to hg19 using Bowtie.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraphs were generated using the HOMER software package (http://biowhat.ucsd.edu/homer/index.html; Heinz et al, 2009)

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) from pooled donors (Lonza) were grown to 80-90% confluence in Endothelial Basal Medium 2-MV with supplements (EBM; Lonza) and 5% FBS

extract_protocol:
HUVECs stimulated with TNFα for 0-30 min were digested (3 min; at 37°C) with 750 units of micrococcal nuclease (MNase; Sigma-Aldrich ). Mononucleosomal DNA was isolated following separation on 1.3% agarose gels using glass beads (Qiagen) and ethanol precipitation.
Libraries were generated using the NEBNext DNA library prep Master Mix Kit (NEB) according to the manufacturer's instructions and paired-end (2x 50 bp) sequenced on a HiSeq2000 platform (Illumina)

treatment_protocol: Cells were starved for 16-18 h in EBM+0.5% FBS, treated with TNFα (10 ng/ml; Peprotech), and harvested at 0, 10, and 30 min post-stimulation.

value: HUVEC

tag: treatment

value: 30 min TNFα n2

tag: digestion

value: 750 U MNase


title: HUVEC0_n1

description: mononucleosomal DNA

value: untreated control n1


title: HUVEC0_n2

description: mononucleosomal DNA

value: untreated control n2


title: HUVEC30_n1

description: mononucleosomal DNA

value: 30 min TNFα n1


title: HUVEC10_n1

description: mononucleosomal DNA

value: 10 min TNFα n1


title: H3K79me3 CHIP-seq rep1

city: San Francisco

first: Stavros

last: Lomvardas

state: CA

institute: UCSF

description: processed data file: moe_h3k79me3_rep1_q30_rmdup_mean_moe_h3k79me3_rep2_sort_q30_rmdup_sub_moe_d3a_wt_input_q30_rmdup_smooth5_25.wig

data_processing:
2x 50bp sequencing reads were mapped to mm9 using Bowtie2.
ChIP-seq peak calling was done using SICER algorithm.  DNAse hypersensitive footprints were identified as in Hesselberth et al (2009).
WIG: DNase I hypersensitivity WIG values were computed as the number of read ends that aligned to a given position, normalized by total number of reads (10E6) per kilobase, within Seqcap-targeted regions
Genome_build: mm9
Supplementary_files_format_and_content: WIG.  For DHS-seq, WIG file contains dnase cleavage sites

source_name: olfactory epithelium_ChIP-seq

extract_protocol:
For ChIP-seq experiments, nuclei were isolated from mouse olfactory epithelium and native ChIPs were performed using H3K79me3 antibody. For DHS-seq, nuclei were isolated from mouse olfactory epithelium and treated with 20U Dnase (DNAse I, Invitrogen) for 3 min, reactions were stopped with EDTA and proteinase K treated overnight.  Regions 100-500 bp were excised from agarose with Qiagen kit and library was constructed by Nugen Ultralow DR kit and PCR amplified for 25 cycles.  1 microgram library was hybridized to custom designed capture probes (Nimblegen SeqCap Design) targeting olfactory receptor enhancers, and capture was performed per the manufacturer's instructions.  After elution from probes, library was amplified using Truseq adapters for 18 cycles using Phusion DNA Polymerase and sequenced.
ChIP DNA was sonicated for 180 seconds on Covaris S220 and library constructed using Nugen Ultralow DR kit.

tag: strain background

value: mixed

tag: age

value: 6-8 weeks

value: olfactory epithelium

tag: chip antibody

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #


title: Dnase Hypersensitivity sequence capture


title: Dnmt3a +/+ MOE rRNA-depleted RNA am:ac:oc

first: Michael

last: Brainard

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

library_source: transcriptomic

data_processing:
Alignment: DIP, ChIP, and DNase-seq reads were aligned using Bowtie v2.1 with default parameters. RNA-seq reads were aligned using STAR v2.3.0, mapping to the Illumina iGenomes Ensmebl NCBIM37 GTF and mm9 using default parameters.
Filtering: Unmapped reads and those with less than mapping quality (MAPQ) of 30 were removed. For DIP and ChIP samples, PCR duplicates were removed using the Picard v1.64 tool MarkDuplicates.jar
WIG: Tracks were generated consisting of read counts binned into 25 bp normalized by the number of millions of reads and scaled to reflect the average number of reads per 1kb to obtain reads per kilobase per million reads(RPKM, i.e. 1E6 * 1E3 / (window size * total number of reads)). For visualization, tracks were smoothed using a 125 bp moving average window.
RPKM: RNA-seq RPKM matrices were computed by first counting the number of reads aligning to each record within the Illumina iGenomes Ensmebl NCBIM37 GTF using featureCounts. These counts were then normalized across samples using the estimateSizeFactors function in the R package DESeq and by gene length in kilobases.
Genome_build: mm9
Supplementary_files_format_and_content: WIG: Fixed step wig files with a window size of 25 bp. RPKM: Matrices (gene x sample) of RPKM values averaged across biological replicates, with common gene name and ensemblID

molecule: total RNA

source_name: main olfactory epithelium

extract_protocol:
Genomic DNA: Genomic DNA from mOSNs or MOE was isolated using the DNeasy Kit (Qiagen) using the standard protocol for cells and tissues, respectively. RNA: Total RNA was isolated from a given cell population or tissue using TRIzol (Invitrogen), then processed differently for FACS-isolated mOSNs or whole MOE. For mOSN, the aqueous phase of the TRIzol extraction was passed through a Zymo RNA Clean and Concentrator 5 column, DNase-treated on column using 1 unit of TURBO DNase for 15 minutes at 37°C, and eluted twice using 10 μL water. For whiole MOE, total RNA isolation was continued using the standard isopropanol precipitation, resuspension in water, and incubation for 20 minutes at 37°C with 1U TURBO DNase (Ambion). Native chromatin:
Standard: Genomic DNA was sonicated to 200-1000 bp with a mean size of ~400 bp and end repaired (NEBNext End Repair). Adenosine was added to 3' ends (Klenow, 3' to 5' exo-, NEB), and 10:1 Illumina adaptor:samples were ligated onto the 200-500 ng samples. Ribominus/Scriptseq: 200 ng of total RNA was rRNA-depleted using two rounds of RiboMinus (Invitrogen) followed by library construction using ScriptSeq v2 (Epicentre) according to manufacturer protocol and amplification for 15 cycles using Phusion (NEB) and provided primers. Nugen encore complete: 100 ng of total RNA was processed using the Encore Complete RNA-seq system (Nugen) and amplified for 15 cycles using Phusion (NEB) and provided primers. Nugen Ovation Ultralow Input: Post ChIP DNA was sonicated to a mean size of 300 bp and processed using the Ovation Ultralow Input Kit (Nugen)
RNA-seq: Total RNA was isolated as described in extract protocol section and prepared for sequencing as described in library construction protocol section. ChIP-seq: Nuclei were isolated from the MOEs of 3-week old Dnmt3a wildtype and knockout mice and digested with micrococcal nuclease (MNase, Sigma) to yield a population of mono- to tetra- nucleosomes that was, subsequently, used in chromatin immunoprecipitation assays using anti-H3K27ac (Millipore, cma309),  anti-H3K4me1 (Abcam, ab8895), or anti-H3K27me3 (Millipore, 07-449) antibodies. Immunoprecipitated DNA was isolated by phenol-chloroform extraction.  For library preparation, ChIP DNA was sonicated for 120-180 seconds on a Covaris S220 and prepared for sequencing using the Ovation Ultralow Library Kit (Nugen). MeDIP-seq: Genomic DNA was isolated, prepared for paired-end Illumina sequencing as indicated in library construction section. 20-100 ng of adapted genomic DNA was diluted in MB (10 mM phosphate buffer pH 7.0, 140 mM NaCl, 0.05% Triton X-100), denatured at 95°C for 10 minutes, brought to 300 µL MB, and precipitated with 0.5 μg anti-5mC (Active Motif, 39649) or 5hmC (Active Motif, 39791) antibodies overnight at 4°C. Separately, 10 µL per IP of Protein A and G Dynabeads each (Invitrogen) were blocked with 2 mg BSA and 2 mg yeast tRNA in 1 mL MB overnight at 4°C. Beads and IPs were combined the next day and rotated for 3 hours at 4°C. Samples were washed 4 times in MB, eluted twice in 100 µL elution buffer (0.1 M NaHCO3, 1% SDS, 1 mM EDTA) by shaking at 37°C for 15 minutes, phenol:chloroform:isoamyl extracted, ethanol precipitated, and resuspended in 50 µL TE. Samples were then amplified with Illumina TruSeq PCR primers for 15 cycles using Phusion DNA polymerase (NEB). DNase-hypersensitivity: Nuclei from the olfactory epithelium were isolated as described for ChIP-seq and resuspended in nuclease digestion buffer (0.32 M sucrose, 50 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF). 3 million nuclei were brought to 250 μL nuclease digestion buffer, pre-warmed for one minute at 37°C, and incubated with 20 U DNase I (Ambion) for 2 or 5 minutes. Reactions were stopped with the addition of 28 μL 0.5 M EDTA and placement on ice. Reactions were then incubated with 200 μg proteinase K (Ambion) 55°C overnight, extracted using phenol:chloroform:isoamyl (Invitrogen), and ethanol precipitated. Samples were resuspended in TE, incubated with 10 μg RNase A (Roche) at 37°C for 30 minutes, extracted using phenol:chloroform:isoamyl (Invitrogen), and ethanol precipitated. Samples were resuspended in TE, and one half of each reaction was run on a 1% agarose/1x TAE gel. Regions 100-500 bp were excised and purified using Qiagen Gel Extraction Kit. Illumina sequencing libraries were then prepared as described in library construction section and amplified for 9 cycles using Phusion DNA polymerase (NEB) and Illumina TruSeq primers.

treatment_protocol: For odorant induction experiments, mice were divided into two clean cages containing no bedding and placed into separate dark cabinets. After 10 minutes in these cages, a 4 cm x 4 cm piece of Whatman paper with either 80 μL of water or a 1:1:1 mixture of pure amyl acetate:acetophenone:octanal (all purchased from Sigma-Aldrich) was placed at one end of the cage. For RNA-seq experiments, Dnmt3a wildtype, heterozygous-null, homozygous-null mice were treated as above for 60 minutes and euthanized using CO2. Their MOEs were dissected into TRIzol (Invitrogen) and homogenized. RNA was isolated using the standard TRIzol protocol and treated with TURBO DNase (Invitrogen).

tag: mouse age

value: 3 weeks

value: nugen encore complete

tag: antibody info

value: 1:1:1 amyl acetate:acetophenone:octanal


title: Dnmt3a -/- MOE rRNA-depleted RNA H2O


title: Dnmt3a -/- MOE native input

description: native chromatin

value: nugen ovation ultralow input


title: Dnmt3a +/- MOE rRNA-depleted RNA H2O


title: Dnmt3a +/- MOE rRNA-depleted RNA am:ac:oc


title: Dnmt3a +/+ MOE native input

description: native chromatin


title: Nsun_rep1 [do1665_unk_skin_unk_mmuNSUN2#1_CRI01]

status: Public on Nov 06 2014

first: Patrick

last: Lombard

state: Cambridgeshire

address: Tennis Court Road, Cambridge

data_processing:
RNA Methylation profiling by high throughput sequencing
Reads were aligned to the  mouse reference genome (GRCm38/mm9) using Bismark (version 0.7.6). Only the reads uniquely aligning to the genome and aligning without mismatch were considered for further analysis.
small non-coding RNA profiling by high throughput sequencing
Adapters were removed, and the 20-200 nt reads were aligned to the mouse and human reference genomes (UCSC mm9 and GRCh37/hg19) with options m 500 -v2 -best -strataas decribed for PolII ChIP-seq reads. To account for the addition of CCA 3'-ends to mature tRNAs, unaligned reads were trimmed of CCA[CCA] ends and realigned using the same options. Annotations were conducted based on the gene loci predicted by tRNAscan-SE in the mouse and based on predicted tRNA genes from GtRNAdB (http://lowelab.ucsc.edu/GtRNAdb) in human. Fragments that matched at multiple tRNA genes were distributed proportionally to the fraction of uniquely matching fragments at these regions as described (Kutter et al. 2011/2?). Reads with CCA[CCA] ends that covered at least 90% of the tRNA gene were considered mature tRNAs. For fragment aligning at tRNA genes, reads that exceeded the gene start or end by more than 10 % were discarded.  For all mature tRNAs and fragments aligning at tRNA genes, counts were normalized and differential abundance of the fragments was evaluated with the Bioconductor/R package DESeq (Anders and Huber, 2010).
Pol III Chromatin-IP profiling by high throughput sequencing
In the mouse reference genome (UCSC NCBI37/mm9), 3,282 candidate tRNA genes were predicted with tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE) including genes with an 'undetermined' isoacceptor family; loci marked as pseudogenes were discarded. PolIII ChIP-seq reads were aligned to the reference genome using Bowtie (Langmead et al, 2009). Two mismatches and at most 500 multiple matches were tolerated, i.e. specifically the Bowtie options m 500 -v2 -best -strata
Genome_build: mm9
Supplementary_files_format_and_content: GSM1090034..GSM1090041: Tabdeliminated text file methylation report. Columns contain chromosome, start, end, percentage methylation, methylated calls, unmethylated calls.
Supplementary_files_format_and_content: GSM1090042..GSM1090049: Tab deliminated text file containing counts for the tRNA's
Supplementary_files_format_and_content: GSM1090050..GSM1090054: Tab deliminated text file containing counts for the tRNA's

source_name: total mouse skin

growth_protocol: Total mouse back skin from wild-type and NSun2 -/- males in anagen (postnatal day 25) were used. NSun2 -/- mice (GGTC-clone ID: D014D11) were generated by the German Gene Trap Consortium, and bred under a C57Bl6/J CBA F1 background. Wild-type mice were coming from the same breedings as NSun2 -/- mice.

extract_protocol:
Total RNA from mouse skin was prepared using Trizol reagent (Invitrogen) according to the manufacturer's instructions and then treated with DNase (Turbo DNase, Ambion).
Total RNA was extracted as described previously, DNase and Ribo-zero treated. The remaining RNA fraction was bisulfite-converted as followed; about 2 μg of RNA was mixed in 70μl of 40% sodium bisulfite pH 5.0 and DNA protection buffer (EpiTect Bisulfite Kit, Qiagen). The reaction mixture was incubated for four cycles of 5 min at 70ºC followed by 1 hour at 60ºC and then desalted with Micro Bio-spin 6 chromatography columns (Bio-Rad). RNA was desulfonated by adding an equal volume of 1M Tris (pH 9.0) to the reaction mixture and incubated for 1h at 37°C, followed by ethanol precipitation.The bisulfite-converted RNA quality and concentration was then assessed on a Bioanalyzer 2100 RNA nano-chip (Agilent). About 120 ng of bisulfite-converted RNA was used to generate Bisulfite-seq libraries. Bs-Seq libraries were performed according to TruSeq Small RNA preparation kit (Illumina). Since the sample was already sufficiently fragmented by the bisulfite-conversion reaction (about 50-120nt), the size selection step prior to adaptor hybridization and ligation was not performed. First 2’,3’-cyclic phosphate and 5’-hydroxyl termini produced during the bisulfite/desulfonation reaction were end-repaired with T4 PNK and Spermidine (New England Biolabs). RNA adapters suitable for Illumina sequencing were then ligated, reverse-transcribed at 50ºC for 1 hour with SuperScript III and 1mM of each dNTP (SuperScript III cDNA synthesis kit, Invitrogen) followed by 18 cycle-PCR amplification. The amplified product was not size-selected before sequencing.
RNA bisulfite sequencing of RNA from back skin from four wild-type independent biological replicates and four NSun2 -/- independent biological replicates were used. All libraries were sequenced on the Illumina Genome Analyzer II (single-ended and 100 pb read length) and post-processed using the standard GA pipeline software v1.4 (Illumina).

treatment_protocol: Mouse back skin was collected at P25 (postnatal day 25), when hair follicles start the growing phase or anagen phase of the hair cycle. Skin was shaved before collection, and immediately snap-frozen in liquid N2.

tag: background strain

value: C57Bl6/J CBA F1

tag: genotype/variation

value: NSun2 -/-


title: Dnmt3a -/- MOE rRNA-depleted RNA am:ac:oc


title: Dnmt3a +/+ MOE rRNA-depleted RNA H2O


title: Dnmt3a -/- MOE H3K27me3 rep1

description: native chromatin

value: Millipore, 07-449


title: Dnmt3a +/+ MOE H3K27me3 rep1

description: native chromatin


title: Dnmt3a +/+ MOE H3K27me3 rep2

description: native chromatin


title: Dnmt3a +/+ MOE H3K27ac rep2

description: native chromatin

value: Millipore, cma309


title: H3K79me3 CHIP-seq rep2


title: Dnmt3a -/- mOSN rRNA-depleted RNA rep2

source_name: mature olfactory sensory neurons


title: Dnmt3a +/+ MOE H3K27ac rep1

description: native chromatin


title: Dnmt3a +/+ MOE H3K4me1 rep2

description: native chromatin

value: Abcam, ab8895


title: Dnmt3a +/- mOSN rRNA-depleted RNA rep1

value: ribominus/scriptseq


title: Dnmt3a -/- mOSN rRNA-depleted RNA rep1


title: Dnmt3a +/- mOSN rRNA-depleted RNA rep2


title: Dnmt3a +/+ MOE H3K4me1 rep1

description: native chromatin


title: Dnmt3a +/+ mOSN rRNA-depleted RNA rep2


title: Dnmt3a -/- mOSN 5mC rep2

value: standard

value: Active Motif, cat 39649


title: Dnmt3a +/+ mOSN rRNA-depleted RNA rep1


title: Dnmt3a -/- mOSN 5mC rep1


title: Dnmt3a -/- mOSN 5hmC rep2

value: Active Motif, cat 39791


title: Dnmt3a +/- mOSN 5mC rep1


title: Dnmt3a +/- mOSN 5mC rep2


title: Dnmt3a -/- MOE H3K27me3 rep2

description: native chromatin


title: Xing Hua high body weight

city: Guangzhou

first: OuYang

last: Hongjia

state: Guangdong

address: Wushan street 483

department: College of Animal Science

country: China

institute: South China Agricultural University

description: XHh

data_processing:
Illumina Casava1.7 software used for basecalling.
For all generated raw reads, adaptor sequences, low quality reads (Sanger bases quality < 20), and contaminant reads were removed with the Fastx-Toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequenced reads were mapped to chicken genome to annotate the location in the chromosomes using Bowtie (http://bowtie-bio.sourceforge.net /index.shtml).
Genome_build: Gallus_gallus.Galgal4.73
Supplementary_files_format_and_content: fasta files with counts

organism: Gallus gallus

source_name: Breast muscle

growth_protocol: All broilers were reared in cages with a 24-h photoperiod for the first 2 d of age and then changed to a 16-h photoperiod. They were fed with free access to water and fedad libitum with 16.5% CP and 2, 800 kcal of ME/kg.  According to the body weight (BW) records at 7 weeks, three female birds from each of the two-tail groups of WRR and XH were selected, and then four groups including WRRh (the group of Recessive White Rock with high body weight), WRRl (the group of Recessive White Rock with low body weight), XHh (the group of Xinhua Chickens with high body weight) and XHl (the group of Xinhua Chickens with low body weight) were generated. The averages of body weight values were 1,064.0 ± 11.1, 695.0 ± 24.4, 305.8 ± 23.3, and 207.6 ± 11.1 g for WRRh, WRRl, XHh, and XHl group, respectively.

extract_protocol:
Total RNA was extracted from each breast muscle using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions. The quality and concentration of all twelve RNA samples were determined by 1.5% agarose gel electrophoresis and absorbance at A260/280 ratio, and then divided to four mixed RNA pools for WRRh, WRRl, XHh, and XHl.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Breast muscle tissues of the 3 individuals were collected immediately after euthanized, snap frozen in liq nitrogen, then stored at -80°C until RNA extraction.

value: breast muscle

tag: strain

value: Xing Hua Chicken

tag: phenotype

value: slow-growing

value: 7 Weeks

tag: group

value: high body weight


title: Xing Hua low body weight

description: XHl

tag: tissue

value: low body weight


title: Dnmt3a +/+ mOSN 5mC

value: 3 weeks


title: Dnmt3a -/- mOSN 5hmC rep1


title: Dnmt3a +/+ mOSN 5hmC


title: Dnmt3a +/- mOSN 5hmC rep2


title: WSR2

city: Chatujak

first: Piyada

last: Juntawong

state: Bangkok

address: 50 Ngamwongwan rd.

department: Genetics

country: Thailand

institute: Kasetsart University

description: replicate 2

data_processing:
Base calling, adapter trimming and quality filter performed using Torrent Suite software version 3.6.
Reads were aligned to reference genome using TMAP mapping program (https://github.com/iontorrent/TMAP).
Reads aligned to genic region were counted by use of HTseq library (Anders et al. 2014)
Analysis of differentially expressed genes was performed in the R environment  using the edgeR package with GLM (generalized linear model)
Genome_build: JAT 4.5 (ftp://ftp.kazusa.or.jp/pub/jatropha/)
Supplementary_files_format_and_content: Tables with counts for all gene models and results for the differential expression analysis

molecule: polyA RNA

organism: Jatropha curcas

source_name: Whole roots, 24 h waterlogging stress

growth_protocol: Jatropha curcas seeds (originated from Chainat province of Thailand) were germinated in pot soil containing 50% (v/v) peat moss, 25% (v/v) perlite, and 25% (v/v) coconut fiber with daily water supply. Plants were grown under outdoor condition between July and August of 2013 at Kasetsart University, Bang Khen campus.

extract_protocol:
Trizol (Invitrogen) RNA extraction according to manufacturer's protocol. Dnase treatment was performed on column using GF-1 RNA extraction kit (Vivantis)
Poly(A)+ mRNAs were isolated from total RNAs by use of Absolutely mRNA purification kit (Agilent). Two hundred ng of poly(A)+ mRNAs was used for RNA-seq library construction with Ion Total RNA seq kit (Life Technologies).

treatment_protocol: Six-leaf stage plants (~30 d.o) were used in waterlogging treatment. Plant pots were placed in a plastic container filled with tap water. The level of water was set to be at 3 cm above the soil. Waterlogging stress began at mid day and continued for 24 h. For the control, non-treated plants were placed in a container with no water. Tissue was harvested at the end of treatment and immediately placed in liquid nitrogen.

tag: developmental stage

value: ~30 d.o, six-leaf-stage seedlings

value: Whole roots


title: Dnmt3a +/- mOSN 5hmC rep1


title: Recessive White Rocks low body weight

description: WRRl

value: Recessive White Rocks

value: fast-growing


title: NSR2

description: replicate 2

source_name: Whole roots, 24 h nonstress


title: WSR1

description: replicate 1


title: RAW264_RANKL(+)

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

description: Sample 2

data_processing:
Illumina Sequenced reads were mapped to mm9 whole genome using bowtie v2.0.0
MACS2 was used to call peaks and generate bigwiggle file
Motif discovery was performed with SeqPos software.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files report MACS2-called peaks

source_name: RAW264 cell

growth_protocol: Murine macrophage-like cells, RAW264 cells, were obtained from RIKEN cell bank. RAW264 cells were maintained in α-minimum Eagle's medium (Invitrogen) supplemented with 10% CELLect fetal bovine serum (MP Biomedicals), 1% antibiotic-antimycotic solution (Invitrogen), and 1% minimum Eagle's medium non-essential amino acids (Invitrogen).

extract_protocol:
Differentiated and undifferentiated RAW264 cells were collected and pelleted prior to washing and resuspended in buffer A (15 mM Tris-HCl, pH 8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 0.5 mM spermidine, 0.15 mM spermine and protease inhibitors) at 1 × 107 cells/mL. Nuclei were extracted with buffer A containing 0.04% NP-40. The nuclei were washed with buffer A and resuspended in pre-warmed digest buffer (13.5 mM Tris-HCl, pH 8.0, 87 mM NaCl, 54 mM KCl, 6 mM CaCl2, 0.9 mM EDTA, 0.45 mM EGTA), and then digested with 2 U/mL DNase I (Takara Bio, Inc.) for 5 min at 37°C. The digestion was stopped by the addition of an equal amount of stop buffer (50 mM Tris-HCl, pH 8.0, 100 mM NaCl, 0.1% SDS, 100 mM EDTA, pH 8.0) containing 10 μg/mL of RNase A (Roche) and incubated for 15 min at 55°C. Samples were then treated with Proteinase K (Roche; final concentration of 20 μg/mL) for 2 hours at 55°C. DNA was extracted by careful phenol/chloroform purification and DNA fragments between 100 and 500 bp long were purified from an agarose gel. Size-selected DNA fragments were prepared for sequencing according to the manufacturer’s instructions (Illumina). The prepared libraries for DNase-seq were sequenced using the Hiseq2000 system (Illumina).
Using Illumina kit according to manufecturer's instruction

treatment_protocol: RAW264 cells were seeded in 10-cm dishes at a density of 1 × 105 cells/dish and were treated with 234 ng/ml GST-RANKL (Oriental Yeast Co., Ltd.) for 24 hours.

tag: cell line

value: macrophage-like cells RAW264

value: RANKL for 24hours

tag: passage


title: Recessive White Rocks high body weight

description: WRRh


title: RAW264_RANKL(-)

description: Sample 1

tag: treatment

value: without RANKL treatment


title: NSR1

description: replicate 1


title: Sample R

status: Public on Nov 04 2014

city: DeKalb

first: Stuart

middle: A.

last: Hill

state: IL

address: 155 Castle Dr.

department: Department of Biological Sciences

institute: Northern Illinois University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were clipped based on quality and (by default) Illumina adaptor sequences, and mapped to MS11 whole chromosome using SHRiMP v 2.2.3.
Alignments were filtered to retain reads that mapped to a single chromosomal location and SNPs and indels were called using Freebayes v 9.9.2.
Transcripts per million (TPM) were calculated using the method described by Wagner, et al., Theory Biosci., 2012.
Genome_build: MS11 CP003909
Supplementary_files_format_and_content: tab-delimited files include the chromosomal positions mapping the read, the length of the read, and the TPM of the read

organism: Neisseria gonorrhoeae

source_name: ΔrppH cells

growth_protocol: Gonococci were passaged on gonococcal typing medium at 37 ºC in 5% CO2.

extract_protocol:
Neisseria gonorrhoeae strain MS11 and the MS11 ΔrppH strain were grown on solid medium for 12 hrs.  Cells were harvested and small RNA was extracted utilizing the MirVana Mira kit; AM 1560 (Life Technologies, Inc) according to the manufacturer's specifications. Transcripts larger than 250-300 bp were excluded from further analysis by size fractionation.
Two small RNA libraries (wild type and  ΔrppH) were constructed using the "Small RNA v1.5 Sample Prep Kit" (Illumina).

tag: genotype

value: ΔrppH


title: Dnmt3a +/- MOE DNase

description: native chromatin

value: standard


title: LMF small RNA profiling

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

department: Genome Center

institute: UC Davis

description:
Sample22
Kunsenshi male parent of the KK progeny population.
small RNA

data_processing:
Sequence processing: Illumina sequencing reads were processed with custom Python scripts developed in the Comai laboratory and available online (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). In short, sequences were split according to barcode information, trimmed for quality (average Phred sequence quality > 20 over a 5 bp sliding window) and adaptor sequence contamination after which reads shorter than 35-bp were discarded (except for the small RNA reads, for which read length cut-off was reduced to 19 bps). For the smRNA data, a maximum read length of 25 bp was applied as well. After application of those size thresholds, a total of approximately 12.0 M and 9.6 M reads were obtained from the female and male samples, respectively.
Small RNA levels were measured after mapping to the OGI and MeGI reference sequence reads derived from small RNA libraries, which were made from developing buds (Dev. Buds, sampled on June 17th 2013) and developing flowers (Dev. Flower, sampled on April 17th 2014).
This sample was used to measure how many reads mapped to the OGI and MeGI sequences.
Genome_build: Assembled Contigs
Supplementary_files_format_and_content: None

organism: Diospyros lotus

source_name: Parent, developing flowers, male

growth_protocol: Trees from the 57 KK population (T. Akagi et al., J. Japan Soc. Hort. Sci. 76, 214-221 (2014)) (D. lotus) and their parents, planted in Kyoto University (Kyoto, Japan, 35º03’, 135º78’ L/L).

extract_protocol:
Small RNA libraries: Total RNA was extracted using the CTAB method and purified by phenol/chloroform extraction. The small RNA fraction was concentrated from total RNA using the mirVana miRNA Isolation kit (Life Technologies).
Small RNA library: Approximately 150 ng of concentrated small RNA was processed to library construction using the NEBNext Small RNA Library Prep Set (NEB), according to the manufacturer’s instruction. PCR enrichment reactions used 12 cycles of amplifications, followed by DNA cleanup using AMPure (AMPure : reaction = 1.1 : 1 v/v) to remove self-ligated adapter dimers. Library quality and quantity were assessed using the Agilent BioAnalyzer (Agilent Technologies) and Qubit fluorometer (Invitrogen). The constructed libraries were sequenced using Illumina’s HiSeq 2000 sequencer (50-bp single-end reads).

treatment_protocol: Developing flowers were sampled from the male and female parents on April 29, 2014.

tag: cultivar

value: Kunsenshi

value: developing flowers

tag: Sex

value: male


title: LFF small RNA profiling

description:
Sample21
Kunsenshi female parent of the KK progeny population.
small RNA

source_name: Parent, developing flowers, female

value: female


title: LF small RNA profiling

description:
Sample19_2
Kunsenshi female parent of the KK progeny population.
small RNA
Processed data file: AllContigsIMH14_All5.txt

data_processing:
Sequence processing: Illumina sequencing reads were processed with custom Python scripts developed in the Comai laboratory and available online (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). In short, sequences were split according to barcode information, trimmed for quality (average Phred sequence quality > 20 over a 5 bp sliding window) and adaptor sequence contamination after which reads shorter than 35-bp were discarded (except for the small RNA reads, for which read length cut-off was reduced to 19 bps). For the smRNA data, a maximum read length of 25 bp was applied as well. After application of those size thresholds, a total of approximately 12.0 M and 9.6 M reads were obtained from the female and male samples, respectively.
Sex-specific k-mer extraction: To select sex-biased reads, the quality trimmed read files from both male and female samples were processed to identify gender-specific subsequences using custom Python scripts. For the genomic reads, all 35 bp kmers (words) starting with the "AG" dinucleotide were selected from all reads, while keeping track of the number of times each specific subsequence was collected. The use of a dinucleotide trigger sequence allowed us to restrict file size while retaining the ability to compare k-mers between reads by effectively phasing them. For the RNA-Seq data, no trigger sequence was used, resulting in the selection of all possible k-mers. Next, the set of subsequences that met a minimum total (male + female) count threshold of 10 for genomic kmers and 20 for RNA-Seq kmers, and a maximum total count threshold of 200 for genomic kmers and 2000 for RNA-Seq kmers were retained. The k-mer counts were then compared between male and female reads. Finally, fully male specific k-mers (count of 0 in the female set) were identified and used to extract the sex-biased reads from the original quality trimmed read set as follows: all pair-ended reads containing at least one of the selected fully male-specific kmers were retained.
Identification of expressed genes involved in sex determination: RNA-Seq reads from 9 male and 9 female individuals from the KK population and their parents (N = 2 x 10) were subjected to three independent analyses in order to identify candidate genes involved in sex determination in D. lotus. (i) RNA-Seq 150-bp paired-end reads were fragmented to 3 x 50-bp (x 2), and mapped to 796 genomic contigs on the MSY and the 777 corresponding X allelic sequences assembled from the female genomic reads. The original 150-bp PE RNA-Seq reads containing one or more 50-bp kmers mapping to these genomic contigs were used to assemble cDNA contigs. (ii) Male-specific k-mers (MSKs) were isolated directly from the RNA-Seq read sequences (k = 35, ≥ 20X coverage). Next, all reads containing one or more of these MSKs were assembled into cDNA contigs using the CLC assembler. Using the genomic sequence reads obtained from 57 individuals, recombination mapping was performed to define a subset of MSY-linked contigs. The cDNA contigs constructed using approaches (i) and (ii) were used for differential expression analysis by determining reads per kilobase per millions (RPKM) values (> 1.0), and annotated using the TAIR/uniprot databases. The approach followed to integrate all data concerning the putative SD loci is described below. For the third approach, (iii), all male and female full-length RNA-Seq reads were aligned using the CLC assembler to produce approximately 400,000 contigs, including allelic polymorphisms. Selection for contigs that exhibited RPKM values of at least 1.0 reduced that number to approximately 80,000 contigs. The number of RNA-Seq reads from each individual mapping to these contigs, were used for DESeq analysis described below.
Construction of cDNA contigs located in the MSY: To map the RNA-Seq reads to the 796 and 777, respectively, Y- and X genomic contigs, each 150-bp read sequence was first converted to three 50-bp fragments using a custom Python script, to decrease the negative effect of intron sequences on mapping efficiency. Here, each fragmented read from the male and female individuals of the KK population was mapped, respectively, to the 796 putative Y and 777 putative X MSY allelic contigs using BWA and allowing no nucleotide mismatches. The original PE reads for which at least one of the fragmented read was mapped to a genomic contigs, were extracted using custom Python scripts. The mapped PE reads were assembled into contigs using Trinity and CAP3 and default parameters. Next, cDNA contigs exhibiting > 99% nucleotide homology to the 796 Y or 777 X allelic genomic contigs over at least 100-bp, were defined as cDNA contigs located in the sex-determining region. From the Y and X allelic genomic contigs, respectively, 99 and 81 cDNA contigs were retained. Alignment of the genomic and cDNA contigs to each other indicated that these cDNA contigs were derived from 60 of the 796 Y allelic genomic contigs and / or their corresponding X allelic contigs.
Expression profiling: cDNA contigs corresponding to genes expressed in male or female developing bud primordia were assembled with the full-length cDNA reads from all male and female individuals using the CLC assembler and a minimum contig length of 200-bp. Next, the resulting 400,000 cDNA contigs, including some alternative splicing and isoforms, were used as reference sequences for alignment of the reads using BWA with default parameters. The read counts per contig were generated from the aligned SAM files using a custom R script. Differential expression between male and female individuals was analyzed in R (version 3.0.1) using the R package DESeq (version 1.14; http://bioconductor.org/packages/release/bioc/html/DESeq.html) (S. Anders and W. Huber, Genome Biol. 11, R106 (2010)). We conducted DESeq analysis using 10 biological replicates from male and female individuals, with the following parameters: method="per-condition" and sharingMode="gene-est-only". A False discovery rate (FDR) threshold of 0.01 was used to identify differentially expressed genes.
Genome_build: Assembled Contigs
Supplementary_files_format_and_content: .txt: Count file; simple reads mapped per contig. The contig sequences are available in the FASTA file (GSE61386_CLC_MF_All_DeNovo.fasta) that is linked to the GSE61386 record as a supplementary file.

source_name: Parent, early developing bud primordia, female

treatment_protocol: For expression analyses, mixed buds were sampled on June 17th, and July 4th, 2013, corresponding to the early differentiation stages of male/female primordia, respectively.

value: mixed persimmon buds

value: early differentiation of primordia


title: ARCaPM-DR_shGATA2a_R3

middle: Aidan

last: Quinn

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the UCSC hg19 human genome using Tophat 2.0.9 software
Normalized abundance was obtained as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) at the gene level were obtained using Cufflinks version 1.3.0
Genome_build: GRCh37
Supplementary_files_format_and_content: comma separated text files include FPKM values for each Sample

source_name: ARCaPM-DR

extract_protocol:
RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ch-CRPC

tag: induction


title: ARCaPM-DR_shGATA2b_R2


title: ARCaPM-DR_Control_R3

value: shRNA control


title: ARCaPM-DR_Control_R2


title: ARCaPM-DR_shGATA2b_R3


title: ARCaPM-DR_shGATA2a_R2


title: LM small RNA profiling

description:
Sample20_2
Kunsenshi male parent of the KK progeny population.
small RNA
Processed data file: AllContigsIMH14_All5.txt

source_name: Parent, early developing bud primordia, male


title: HF-Y14_4A3

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

description: library strategy: RIP-Seq

data_processing:
PREPROCESSING The fastq files from the immunopurified samples were first processed to remove the presence of sequencing primer using fastx_clipper from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) with the following arguments “-a GTGTCAGTCACTTCCAGCGG -l 15”.
ALIGNMENT The resulting fastq files were then aligned to a database of exon junctions made from 36 nt on each side of all the junctions annotated in the Drosophila melanogaster genome (v 5.22) using bowtie and the following options “-S -a -p6 -m1 -n2 --best –strata” and the resulting alignment files in SAM format where then converted to spliced alignments in genomic coordinates using an in house developed tool. The reads that did not align any exon junction were realigned to the Drosophila melanogaster genome sequence (v. 5.22) using bowtie and the same options as before. The resulting alignments where then merged and converted to binary sorted alignments in BAM format using samtools (Li et al, 2009).
BOUND REGION DETERMINATION: EJC-bound regions were called at all regions having 4 or more "nearby" alignments (withing 50 nt of each other, and on the same DNA strand).

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: 20 X 106 D. melanogaster S2 cells were grown in 150 mm dishes at 24°C in Schneider's medium (Gibco) supplemented with 10% fetal bovine serum. Expression of tagged proteins was induced by supplementing the media with appropriate concentration of CuSO4 (10-50 µM).

extract_protocol:
Cells were washed once with PBS supplemented with 5 mM MgCl2, and resuspended in 800 µl of lysis buffer [10 mM Tris-HCl, pH 8, 100 mM NaCl, 2.5 mM MgCl2, 0.5% Nonidet P40, 0.5% Triton-X100, 10% glycerol and protease inhibitor cocktail (Roche)]. Cells were then sonicated on ice three times at 100% power for 30 sec. The insoluble material was removed by centrifuging for 10 minute at 16,000g, 4°C. The cellular extract was mixed with 50 µl of Flag-M2 affinity gel (Sigma) pre-equilibrated with lysis buffer and incubated 2 hr at 4°C. Beads were washed 5 times with wash buffer (10 mM Tris-HcL, 150 mM NaCl, 1% Nonidet P40, and 2.5 mM MgCl2). The immune-purified RNP complexes were eluted from the beads with 400 µl Flag peptide solution [0.5 mg/ml, 10 mM HEPES (pH 8), 150 mM NaCl, 2.5 mM MgCl2 and 0.05% Nonidet P40]. 50 μl of oligo dT magnetic bead, prepared according to manufacturer’s procedure (Invitrogen) and washed with wash buffer, were added to the RNP complex and mixed for one hour at room temperature. Oligo dT selected complexes were captured on magnet and washed three times with wash buffer. The RNP complexes bound to the magnetic beads were resuspended into 500 μl of Micrococcal Nuclease (MNase) digestion buffer (50 mM Tris-HCl, pH 8, 5 mM CaCl2 and 50 mM NaCl) and digested with 0.5 unit of MNase for the tagged-eIF4A3/Y14 and tagged-Btz/eIF4AIII or 0.3 unit of MNase for the tagged-Y14/eIF4AIII for 15 min at 25° C. The digestion was stopped by adding 20µl of 500 mM EGTA to the reaction. Oligo dT magnetic beads were discarded and nuclease digested RNP complexes were mixed with protein A conjugated magnetic bead preincubated with antibody raised against Drosophila EJC core components (Y14 or eIF4AIII), and mixed gently for two hour at 4°C. RNP complexes were captured on magnet and washed five times with wash buffer.
The affinity purified RNP complexes were treated with 5 units of alkaline phosphatase (Roche) directly on the protein A conjugated beads for 90 minutes at 25°C with agitation. The beads were washed twice with 500 µl of PNK buffer supplemented with EGTA (50 mM tris-HCl, pH 7.5, 10 mM MgCl2, 0.5% Nonidet P40, 20 mM EGTA) and twice with 500 µl of PNK buffer and then ligated to a 3’ RNA linker using 20 units of T4 RNA ligase for 4 hour at 16°C. Beads were washed three times with 500 µl of PNK buffer and the 5’ termini of bound RNA fragments were phosphorylated by 40 units of T4 polynucleotide kinase (NEB). RNP complexes bound to the beads were then deproteinated by Proteinase K (Roche) at final concentration of 4 mg/ml (Roche). The deproteinated RNA was Phenol-chloroform extracted and ethanol precipitated and then ligated to a 5’ RNA linker using 5 units of T4 RNA ligase for 4 hr at 16˚C. The 5’ and 3’ end-ligated RNA was reverse transcribed using SuperScript III and a primer complementary to the 3’ RNA linker following the manufacturer recommendation (Invitrogen). The cDNAs were then amplified by PCR using primers specific to the 5’ and 3’ ligated linkers. The 60-80 nt amplified PCR products were size selected on a 10% denaturing polyacrylamide gel and extracted using QIAEXII (Qiagen). The size-selected amplicons were further amplified by PCR for 10 cycles using primers containing sequence compatible for high-throughput sequencing. Finally, the PCR products were gel purified, using Qiagen gel extraction column, from any contaminating primer-dimers on a 2% NuSieve GTG Agarose gel. The DNA was finally subjected to sequencing on the Illumina GAIIx platform following the manufacturer recommendation (Illumina). The identity of the RNA linkers and PCR primers can be found elsewhere (Licatalosi et al, 2008).

treatment_protocol: After 72 hours of growth, 100 µg/ml cycloheximide was added and the cells were incubated for 2 hr.

tag: cell type

tag: ip

value: tagged Y14 followed by endogenous eIF4AIII


title: HF-Btz_4A3

description: library strategy: RIP-Seq

value: tagged Btz followed by endogenous eIF4AIII


title: ARCaPM-DR_shGATA2b_R1


title: HF-4A3_Y14

description: library strategy: RIP-Seq

value: tagged eIF4AIII followed by endogenous Y14


title: 22Rv1-DR_Control_R3


title: 22Rv1-DR_shGATA2a_R2


title: 22Rv1-DR_shGATA2b_R3


title: 22Rv1-DR_shGATA2b_R2


title: 22Rv1-DR_Control_R2


title: 22Rv1-DR_shGATA2a_R1


title: 22Rv1-DR_shGATA2b_R1


title: Sample W

source_name: wild type cells

value: wild type


title: ARCaPM-DR_Control_R1


title: DU145-DR_shGATA2b_R3


title: 22Rv1-DR_Control_R1


title: SHF2

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
Reads were mapped to the reference genome (Oar_v3.1) using the software package Tophat (v2.0.4).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.1.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.1.1) was used for merging together each of the assemblies with the reference ovine annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty) developed by Simon Anders at EMBL (Heidelberg, Germany).
Genome_build: Sheep genome assembly: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text files including locus, number of mapped reads, gene name, and chromosome location.

organism: Ovis aries

source_name: Subcutaneous adipose depot

extract_protocol:
Total RNA was extracted from samples using the RNeasy Mini kit (QIAGEN, Valencia, CA, USA) and then treated with DNase-free DNase Set (QIAGEN) to avoid genomic DNA amplification.
Libraries were prepared following the Illumina mRNA-Seq protocol. Sequencing libraries were created from 50 ng samples and sequenced with Illumina’s HiSeq 2000 at the University of Wisconsin-Madison Biotechnology Center.

value: Subcutaneous adipose depot

tag: gender

value: Female

value: fetus

tag: maternal diet

value: Hay


title: SHM2

value: Male


title: DU145-DR_shGATA2a_R3


title: DU145-DR_Control_R3


title: SHF1


title: DU145-DR_shGATA2a_R2


title: DU145-DR_shGATA2b_R2


title: DU145-DR_shGATA2a_R1


title: DU145-DR_Control_R2


title: DU145-DR_Control_R1


title: 22Rv1-DR_shGATA2a_R3


title: DU145-DR_shGATA2b_R1


title: SDM1

value: Dried corn distillers grains


title: SDF2


title: SCF2

value: Corn


title: SCM1


title: RHM2

source_name: Perirenal adipose depot

value: Perirenal adipose depot


title: RHM1


title: SDF1


title: SCM2


title: SCF1


title: RDM2


title: RHF1


title: RHF2


title: SHM1


title: RDF1


title: RDM1


title: RCM2


title: SDM2


title: RCF2


title: MHM2

source_name: Longissimus dorsi muscle

value: Longissimus dorsi muscle


title: ARCaPM-DR_shGATA2a_R1


title: MHF1


title: MDM2


title: MDF2


title: MDM1


title: MCM1


title: MDF1


title: BK39

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: reference

data_processing:
At Baseclear FASTQ sequence reads were generated using Illumina Casava pipeline version 1.8.2
Quality assesment was based on data passing the Ilumina Chastity filtering. Subsequently, reads containing adapters and/or PhiX control signal were removed using an in-house (At Baseclear) filtering protocol.
RNA-seq reads were mapped with BWA (version 0.5.9-r16) to CEN.PK113-7D whole genome
samtools (version 0.1.7-r510) was used to convert the BWA sam output to sorted bam format
cuffdiff, from the cufflinks packages (version 1.0.3), was used to calculate the differential expression btween WT ( CEN.PK113-7D; BK37,BK38,BK39) and sample (CEN.PK102-12A; BK34,BK35,BK36)

organism: Saccharomyces cerevisiae

source_name: Aerobic glucose-limited chemostat

growth_protocol: Chemostat cultivations were carried out at 30 °C in 2-L laboratory bioreactors (Applikon, Schiedam, The Netherlands) with working volumes of 1 L. Chemostat cultivation was preceded by a batch phase under the same conditions. When a rapid decrease in CO2 production indicated glucose depletion in the batch cultures, continuous cultivation at a dilution rate of 0.10 h-1 was initiated. Synthetic medium (Verduyn et al., Yeast, 8:501-17) supplemented with 7.5 g∙L-1 glucose was used. Lipoic acid solution in ethanol was prepared separately and added to the medium to a final concentration of 500 ng∙mL-1. Antifoam Pluronic PE 6100 (BASF, Ludwigshafen, Germany) was added to the media before sterilisation to a final concentration of 0.15 g∙L-1.Culture pH was maintained at 5.0 by automatic addition of 2 M KOH. Aerobic bioreactors were sparged with 500 mL∙min-1 air and stirred at 800 rpm to ensure fully aerobic conditions.

extract_protocol:
Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously (Hazelwood et a., Appl. Environ. Microbiol. 76:318-328).
cDNA libraries for the Illumina platform were generated and sequenced at BaseClear BV (Leiden, The Netherlands). cDNA was used as input for library preparation using the Illumina TruSeq DNA library preparation kit (Illumina). Briefly, the DNA was fragmented by nebulization and subjected to end-repair, A-tailing, ligation of adaptors including sample-specific barcodes and size-selection to obtain a library with median insert-size around 200-400 bp. After PCR enrichment, the resultant library was checked on a Bioanalyzer (Agilent) and quantified. The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2500 with paired-end protocol
library with a 350 insert size were prepared and sequenced with an Illumina Hiseq 2500 sequencer.

treatment_protocol: Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously (Hazelwood et a., Appl. Environ. Microbiol. 76:318-328 ).

value: ACS1 ACS2

value: Acs+


title: MCF2


title: MHF2


title: BK38

description: reference


title: RCM1


title: BK37

description: reference


title: BK35

description: mutant with disrupted native pathway of cytosolic acetyl-CoA synthesis, expressing PDH of E. faecalis (pdhA pdhB aceF lpd) and lipoylation genes (lplA lplA2) of E. faecalis from the plasmid

value: acs1Δ  acs2Δ pUDC140:CEN6 ARS4 pdhA pdhB aceF lpd lplA lplA2

value: Acs-  EfPDH


title: MCF1


title: RDF2


title: BK36


title: CFT_073_Urine_rep1

first: Yaara

last: Oren

state: Massachusetts

address: 415 Main street cambridge

institute: Broad institute

data_processing:
Base-calling, alignment, filtering and of normalized abundance measurements were all done using the program "Rockhopper" version 1.3.0 with default parameters. The two reference E. coli used for this study were: NC_000913.2 for E. coli K12 1655 and NC_004431.1 for E. coli CFT073.
genome build: E. coli K12 1655: ASM584v1 and E. coli CFT073: ASM744v1
Supplementary_files_format_and_content: A matrix listing features of the called genes and normalized abundance measurements (upper quartile normalization)

organism: Escherichia coli CFT073

growth_protocol: For RNA preparation, both strains were grown with shaking at 37°C in 12ml MOPS media  supplemented with 0.2% tryptone and 0.2% glucose until the OD600 reached 0.2. Five ml of the bacterial media were then passed through a 0.2m pore size filter and re-suspended with either urine or MOPS. The re-suspended bacteria were grown for 15 additional minutes with shaking at 37°C.

extract_protocol:
To stop bacterial growth, ice was added to the MOPS and urine-grown samples and the cultures were harvested by centrifugation (10 min, 8,000g, 4°C). The supernatant was discarded and 500µl of saline (0.9% NaCl) was added to each sample. Samples were then treated with RNA Protect Bacterial Reagent (QIAGEN) to stabilize RNA according to the manufacturer’s instructions
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kits (Illumina). High RNA quality was confirmed prior to library construction using Agillent’s TapeStation 2200. 50 bp-long single end reads were then sequenced on an Illumina Hi-Seq 2500

tag: condition

value: urine

tag: growth phase


title: CFT_073_Urine_rep3


title: CFT_073_MOPS_rep3

value: MOPS


title: BK34

tag: strain


title: RCF1


title: MHM1


title: CFT_073_Urine_rep2


title: LM mRNA profiling

description:
Sample20
Kunsenshi male parent of the KK progeny population.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt

extract_protocol:
mRNA libraries: Total RNA was extracted using the CTAB method and purified by phenol/chloroform extraction.
mRNA libraries: Fifteen to twenty micrograms of total RNA was processed in preparation for Illumina sequencing, according to the previous report (D. Burkart-Waco et al., Plant Cell 25, 2037-2055 (2013)). Briefly, mRNA was purified using the Dynabeads mRNA purification kit (Life Technologies). Next, cDNA was synthesized via random priming using Superscript III (Life Technologies), followed by heat inactivation for 5 min at 65°C. Second-strand cDNA was synthesized using the second-strand buffer (200 mM Tris-HCl, pH 7.0, 22 mM MgCl2, and 425 mM KCl), DNA polymerase I (NEB) and RNaseH (NEB) with incubation at 16°C for 2.5 h. Double-stranded cDNA was purified using AMPure with a 1.8 : 1 (v/v) AMPure to reaction volume ratio. The resulting double-stranded cDNAs were subjected to fragmentation and following library construction, as follows. Approximately 1.0 μg of cDNA was fragmented using NEBNext dsDNA Fragmentase (New England BioLabs; NEB) for 40-60 min at 37°C and cleaned using Agencourt AMPure XP (Beckman Coulter Genomics) for size-selection. To select fragments ranging between 200 and 600 bp, 25 μl AMPure were added to the initial 50 μl reaction. After a brief incubation, 72 μl of the supernatant was transferred to a new tube, and an additional 12 μl water and 36 μl AMPure were added. After a second brief incubation, the supernatant was discarded and the DNA was eluted from the beads in 20 μl of EB, as recommended. Next, DNA fragments were subjected to end repair using NEB’s End Repair Module Enzyme Mix, and A-base overhangs were added with Klenow (NEB), as recommended by the manufacturer. End repair and A-base addition were both followed by AMPure cleanup using 1.8 : 1 (v/v) AMPure / reaction. Barcoded NEXTflex adaptors (Bioo Scientific) were ligated at room temperature using NEB Quick Ligase (NEB), following the manufacturer’s recommendations. To remove contamination of self-ligated adapter dimers, libraries were size-selected using AMPure in 0.8 : 1 (v/v) AMPure : reaction volume, in order to select for adapter-ligated DNA fragments at least 300-bp long. Half of the eluted DNA was enriched by PCR reaction using Phusion 2X HF master mix (NEB), with the following PCR conditions: 30 s at 95°C; 10 cycles of 10 s at 95°C, 30 s at 65°C, and 30 s at 72°C and a final extension step of 1 min at 72°C. Enriched libraries were purified with AMPure (0.8 : 1 v/v AMPure to reaction), and quality and quantity were assessed using the Agilent BioAnalyzer (Agilent Technologies) and Qubit fluorometer (Invitrogen). The constructed libraries were sequenced on Illumina’s HiSeq 2500 sequencer (150-bp paired-end reads).

value: Kunsenshi

value: mixed persimmon buds

value: early differentiation of primordia

value: male


title: CFT_073_MOPS_rep1


title: 18015_OC_5wk_Control

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description: Processed data file: RNA-seq_JI_diaphysis.txt

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
Reads were mapped to the mm9 genome using TopHat 1.3.2/bowtie 0.12.7.0 with default settings.
RPKM values were calculated using Partek Genomics Suite 6.6.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values.

source_name: 5-week-old diaphysis, wild type

extract_protocol:
Diaphysis and metaphysis for femurs were removed and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain/background

value: mixed

tag: genotype/variation

value: wild type

value: femur diaphysis

tag: age

value: 5 weeks


title: 18018_OC_5wk_Control

tag: tissue


title: L33 mRNA profiling

description:
Sample17
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt

source_name: KK progeny, early developing bud primordia, female

tag: developmental stage

value: female


title: L43 mRNA profiling

description:
Sample18
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt

source_name: KK progeny, early developing bud primordia, male


title: 17791_OC_5wk_Control


title: 17864_OC_5wk_Mutant

source_name: 5-week-old diaphysis, Dlx3Oc-cKO


title: CFT_073_MOPS_rep2


title: 18008_OC_5wk_Mutant


title: L21 mRNA profiling

description:
Sample15
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: 17353_OC_5wk_GP_Mutant

description: Processed data file: RNA-seq_JI_metaphysis.txt

source_name: 5-week-old metaphysis, Dlx3Oc-cKO

value: femur metaphysis


title: L17 mRNA profiling

description:
Sample13
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: 17788_OC_5wk_GP_Control

source_name: 5-week-old metaphysis, wild type


title: 17735_OC_5wk_GP_Control


title: 17365_OC_5wk_GP_Mutant


title: L14 mRNA profiling

description:
Sample11
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L11 mRNA profiling

description:
Sample9
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L13 mRNA profiling

description:
Sample10
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L16 mRNA profiling

description:
Sample12
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: 17695_OC_5wk_GP_Control


title: L10 mRNA profiling

description:
Sample8
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L8 mRNA profiling

description:
Sample7
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: LF mRNA profiling

description:
Sample19
Kunsenshi female parent of the KK progeny population.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L7 mRNA profiling

description:
Sample6
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L32 mRNA profiling

description:
Sample16
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L18 mRNA profiling

description:
Sample14
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L5 mRNA profiling

description:
Sample5
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: L4 mRNA profiling

description:
Sample4
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: MCM2

value: Longissimus dorsi muscle

value: Male

value: fetus

value: Corn


title: MG-1655_Urine_rep3

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


title: Cldn4 KO VILIlow

city: Los Angeles

first: Zea

last: Borok

address: 2011 Zonal Avenue HMR911

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: University of Southern California

description:
Sample 4
processed data file: VILIwtkoloGenes.csv

data_processing:
RNA was sequenced using HiSeq 2000 (Illumina) at the Southern California Genotyping Consortium, University of California Los Angeles (single read, 100 bases).
Reads were trimmed and filtered, then aligned to UCSC mm9 RefSeq Genes using Bowtie (v 1.1.2), all on the Galaxy platform (http://galaxyproject.org/).
A table of read counts was built using the Bioconductor GenomicRanges package, counts were normalized using EDAseq, and differential expression analysis was done using EdgeR in R (version 3.0.1).
Genome_build: mm9
Supplementary_files_format_and_content: .csv files for differential expression analysis between WT no VILI and Cldn4 KO no VILI, WT no VILI vs WT VILI, WT VILI vs Cldn4 KO VILIlow, and WT VILI vs Cldn4 KO VILIhigh

source_name: Cldn4 KO_lung

extract_protocol:
Lungs were homogenized in TRIzol (Life Technologies) using Polytron homogenizer, and total RNA was extracted according to the TRIzol manual.
Libraries were prepared according to instructions, using TruSeq RNA Sample Preparation Kit v3.0 (Illumina)

treatment_protocol: lungs were harvested directly from WT and Cldn4 KO mice, or after 2 hours of VILI experiment

tag: strain background

value: mixed 129S6, C57BL/6, BALB/c

value: Cldn4 KO

tag: exposed to

value: ventilator-induced lung injury (VILI) for 2 h

tag: vili  condition

value: 40 cmH2O

tag: injury level

value: similar injury to WT

value: whole lung


title: Cldn4 KO no VILI

description:
Sample 2
processed data file: Cldn4lungWTvsKOgenes.csv


title: MG-1655_Urine_rep2

value: urine


title: MG-1655_Urine_rep1


title: L2 mRNA profiling

description:
Sample2
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt

tag: cultivar

value: Kunsenshi

value: mixed persimmon buds

value: early differentiation of primordia

tag: Sex

value: male


title: MG-1655_MOPS_rep3

value: MOPS


title: Cldn4 KO VILIhigh

description:
Sample 5
processed data file: VILIwtkohiGenes.csv

value: higher injury than WT


title: WT VILI

description:
Sample 3
processed data file: VILIwtGenes.csv

value: WT


title: L1 mRNA profiling

description:
Sample1
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt


title: MG-1655_MOPS_rep2


title: MG-1655_MOPS_rep1


title: 17859_OC_5wk_GP_Mutant

description: Processed data file: RNA-seq_JI_metaphysis.txt

value: mixed

value: femur metaphysis

value: 5 weeks


title: Ribosome profiling data of E. coli cells treated with the antibiotic erythromycin

status: Public on Nov 03 2014

city: Chicago

first: Krishna

last: Kannan

address: 900 S Ashland Avenue

department: Center for Pharmaceutical Biotechnology

institute: University of Illinois at Chicago

description: mRNA protected by polysomes digested by MNase

data_processing:
Adapter sequences and the untranslated E. coli RNA sequences were removed.
Bowtie was used to align non-redundant reads to the E. coli MG1655 genome (accession number: U00096)
Custom algorithm was used to assign ribosome density to each nucleotide position in the E. coli chromosome. Breifly, in a center-weighted approach, each read was trimmed by 12 positions on each side and the remaining positions were given equal weight of the ribosome density value based on the number of aligned reads.
Genome_build: Reference Sequence: ASM584v2
Supplementary_files_format_and_content: .wig files containing position in the E. coli genome and the corresponding ribosome density value.

organism: Escherichia coli BW25113

growth_protocol: E. coli cells grown until exponential phase in LB medium.

extract_protocol:
Cells were harvested by rapid filtration, frozen imediately and cryo-lyzed using a mixer mill. Cell lysates were fractionated through a 10-55% sucrose gradient and the polysomal fraction was extracted and digested with MNase. mRNA fragments protected by polysomes were size selected.
Polysome protected mRNA fragments were 3' phosphorylated, ligated with a oligo carrying adapter sequences and reverse transcribed. Resulting cDNA was size selected, circularized and PCR amplified for 6-8 cycles.

treatment_protocol: Exponentially growing E. coli cells were treated with the antibiotic erythromycin (100 μg/ml) or telithromycin (50 μg/ml) for 15 minutes. Untreated cells were used as the control.

value: BW25113 ΔtolC

tag: agent

value: erythromycin (100 μg/ml)


title: Batch1_ChIP-seq_PGAL::TOP1rnh1drnh201d

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

description: antibody S9.6 recognises RNA-DNA hybrids independently of their sequence. This antibody was developped by Boguslwaski et al 1986. Mouse Hybridoma cell line was bought from ATCC. IgG 2a antibodies were purified from hybridoma supernatants by Eurogentec

data_processing:
ChIP-seq reads were aligned to the sacCer3 genome assembly using novoalign V2.07 with the option -r Random
Reads mapping to rDNA regions were removed prior to normalisation
bigwig files were created from BAM using the deepTools package: bamCoverage -bs 50 -p 15 --smoothLength 100 -b $i --scaleFactor 1 -f 200 --outFileName $i.bw
A background level of sequencing was attained by calculating the mean read depth of all intergenic regions covered by at least 1 read (regions not annotated by the Saccharomyces gene database). A measure of enrichment for each window is given as the ratio of the windows mean depth vs the intergenic mean: 50 bp window score = (Average read depth in surrounding 100 bp / intergenic mean depth). This method of normalization is mainly adapted from Thurtle and Rhine (Genes Dev, 2014).
Genome_build: sacCer3
Supplementary_files_format_and_content: raw bigwig files created from bam using bedtools genomeCoverageBed and UCSC wigToBigWig. Normalised bigwig files were processed as above.

source_name: asynchronous cells

growth_protocol: For Batch 1: cells were grown at 30°C to OD600 ~0.3–0.4 in complete Kaiser synthetic SGS minimal medium (2% galactose, 2% saccharose) then transferred to the same pre-warmed complete SD minimal medium (2% glucose). The growth was continued for 6 hours and maintained in exponential phase by dilution with pre-warmed SD medium. For batch 2: cells were grown in YPD medium (2% glucose).

extract_protocol:
Sonicated and formaldehyde-crosslinked-chromatin were treated with antibody S9.6 for immunoprecipitation of RNA-DNA hybrids (ChIP).
Libraries were prepared according to Illumina's instructions with modifications. 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 (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 18 cycles and library fragments of ~250-350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced using Illumina MiSeq Benchtop Sequencer following the manufacturer's protocols.
S9.6 CHIP-seq and input chromatin (=control sonicated-crosslinked-DNA)

treatment_protocol: Cells were crosslinked with formaldehyde for 25 minutes at room temperature.

value: Batch 1

value: YAEH275= BY4741 but PGAL1-3HA-TOP1 (KanMx6) rnh201Δ (NatMx6) rnh1Δ (HphMx6)

tag: growth condition

value: Shift from galactose to glucose-containing medium.ChIP at 6 hours in glucose

tag: chip antibody

value: anti-RNA/DNA hybrid (S9.6)


title: Batch2_ChIP-seq_Wild-type

value: Batch 2

value: BY4741:MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: YPD medium


title: WT no VILI

description:
Sample 1
processed data file: Cldn4lungWTvsKOgenes.csv
processed data file: VILIwtGenes.csv
processed data file: VILIwtkoloGenes.csv
processed data file: VILIwtkohiGenes.csv

value: mixed 129S6, C57BL/6, BALB/c

value: whole lung


title: mRNA(+)AZ_rep2

first: Mee-Ngan

middle: F.

last: Yap

address: 320 E Superior St

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

data_processing:
CASAVA-1.8.2 basecalling
Raw FastQ sequencing data were processed on local instance of Galaxy platform..  Sequence libraries were pre-processed by clipping the adaptor sequence (5’CTGTAGGCACCATCAAT3’) and trimming the sequences by discarding the first base and all those extending beyond the 50th base.  The sequencing reads were mapped to the rRNA reference genome with Bowtie2.
The unaligned output files from Bowtie 2 (rRNA-less sequences) were mapped to the S. aureus NCTC 8325 (GeneBank CP000253) with Bowtie v.0.12.0. The alignment .map files were used as inputs for the modified Python scripts to obtain normalized read density in "reads per million mapped reads" (RPM) at each nucleotide positions. Original Python scripts have been published in Ref: Becker et al (2013)Nature Protoc 8: 2212-2239
mRNA abundance were determined by Cufflinks in FPKM (Fragments Per Kilobase of transcript per Million mapped reads)
Differential gene expression was measured by Cuffdiff. Geometric library normalization and pooled dispersion estimation methods were employed with a 0.05 false discovery rate and a minimum alignment count of 10.
Genome_build: GeneBank CP000253
Supplementary_files_format_and_content: Tab-delimited text files include read densities (RPM) at each nucleotide position

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: Bacterial cells_with_azithromycin

growth_protocol: S. aureus cells were grown in 1 liter of  tryptic soy broth until OD600 ~0.45 at 37°C, azithromycin(AZ) was added to a final concentration of 25 μg/ml and incubated for 15 min.  Culture without azithromycin was grown simultaneously.

extract_protocol:
Bacterial cells were disrupted by cryomilling on a Retch MM400 (15 mm grinding balls, 10 ml jars) for 8 set of 3 min cycles at 15 Hz. Ref: Oh et al (2011) Cell 147: 1295-1308
Cell lysates were subjected to micrococcal nuclease digestion, and monosomes were collected by 10-55% sucrose density gradient. Total mRNA and the monosomal mRNAs were isolated by hot-phenol/chloroform method. Total mRNAs were fragmented by alkaline hydrolysis. The fragmented mRNAs and ribosome footprint mRNA (RPF) were ligated to a universal linker. Following rRNA subtraction, PAGE purification, reverse transcription, cDNA circularization, and multiplexing PCR amplification, the cDNA libraries were sequenced on Illumina HiSeq 2000

treatment_protocol: To preserve ribosome occupancy on its mRNA template, 100 μg/ml of chloramphenicol were added to both (-) and (+) AZ S. aureus cultures and incubated for 2 min before harvest.

value: Exponential

value: NCTC 8325

tag: cdna type

value: total fragmented mRNA


title: Batch1_ChIP-seq_Wild-type


title: Batch1_input_chromatin_Wild-type


title: RPF2(-)AZ_rep2

source_name: Bacterial cells_without_azithromycin

tag: growth phase

value: Ribosome protected mRNA fragments


title: RPF2(+)AZ_rep2

tag: strain


title: RPF1(+)AZ_rep2


title: RPF1(-)AZ_rep2


title: 18014_OC_5wk_Mutant

description: Processed data file: RNA-seq_JI_diaphysis.txt

tag: strain/background

value: mixed

value: femur diaphysis

tag: gender

value: male


title: RPF1(+)AZ_rep1


title: Ribosome profiling data of E. coli cells treated with the antibiotic telithromycin

value: BW25113 ΔtolC

value: telithromycin (50 μg/ml)


title: RPF2(+)AZ_rep1


title: mRNA(+)AZ_rep1


title: RPF1(-)AZ_rep1


title: Batch2_input_chromatin_Wild-type


title: Ribosome profiling data of untreated E. coli cells


title: mRNA(-)AZ_rep1


title: mRNA(-)AZ_rep2


title: Batch1_ChIP-seq_rnh1drnh201d

value: Batch 1

value: YAEH255= BY4741 but rnh1Δ (KanMx6) rnh201Δ (NatMx6)


title: FB2456_H3K4me1

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Trimmomatic v0.22  was used for trimming reads for quality (phred33>=30) and length (n>=32)
For ChIP-seq, filtered reads were aligned to hg19 using BWA v0.6.1.
Genome_build: hg19

source_name: Fibroblasts

growth_protocol: Fibroblast primary cell lines were grown on medium containing a-MEM supplemented with 2mmol/l L-glutamine, 100U/ml penicillin, 100mg/ml streptomycin, and 10% fetal bovine serum at 37C with 4% CO2. Cells were harvested at 70-80% confluence and stored at -70C until DNA/RNA extraction

extract_protocol: Libraries were prepared according to the Illumina TruSeq protocol, and quality assessed by Agilent 2100 BioAnalyzer.

tag: cell type

value: Fibroblast primary cell line

value: H3K4me1 (abcam; ab8895)


title: LCL18507_H3K4me3

source_name: Lymphoblastoid cell lines

growth_protocol: Lymphoblastic cell lines were cultured in RPMI 1640 medium supplemented with penicillin/streptomycin, 2 mM L-Glutamine and 15% heat-inactivated fetal bovine serum. The cells were grown at 37°C and 5% CO2. The cell growth was monitored using a hemocytometer and cultures were harvested at a density of 0.8–1.1×106 cells/ml. The cells were lyzed by resuspension in Trizol reagent.

value: lymphoblastic cell line

value: H3K4me3 (Diagenode; #pAb-003-050)


title: MNC491_H3K4me3

source_name: Monocytes

growth_protocol: Circulating monocytes were collected from healthy adult blood donors of European origin. CD14+ magnetic microbeads were used to isolate monocytes from whole blood.

value: monocyte


title: FB2456_H3K4me3


title: LCL18507_H3K4me1


title: lsm5/sad1 rep 2,2

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

data_processing:
basecalling: Basecalling done with Bustard Illumina Pipelline
reference alignment: Sequence reads were mapped to Arabidopsis thaliana TAIR10 genome using TopHat v2.0.9 with default parameters, except of maximum intron length set in 5000
read count summarization: Count tables for different feature levels were obtained from bam files using custom R v3.0.2 scripts.
differential gene expression: Differential gene expression was estimated using edgeR package version 3.4.2 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
differential splicing: The transcriptome was partitioned into subgenic joint features called bins and labeled as exon-bin, intron-bin or alternative-splicing (AS) bins. In addition AS-bins were further classified as exon skipping (ES), 5’ or 3’ alternative (5´alt, 3´alt), intron retention (IR) or multiple. Bins from monoexonic genes and with mean count values lower than 5 reads per condition were discarded.
differential splicing: We used edgeR exactTest for the identification of differential usage of bins corresponding to AS events or introns, and fdr corrected p-values. We also computed read densities in order to have a relationship between the bin and its corresponding gene. A Splicing Index was calculated as bin read density/gene read density, and the Splicing Index Ratio was calculated as Splicing Index in mutants/Splicing Index in WT plants. Only genes with read densities greater than 0.1 in all genotypes, and Splicing Indexes greater than 0.05 in at least one genotype, were used for the analysis. AS events as well as all introns with an absolute Log2 FC (bin read density in the mutant/bin read density in WT) value greater than 0.58, with fdr values lower than 0.15, and an abosolute Log2 Splicing Index Ratio (Splicing Index in the mutant/Splicing Index in WT) greater than 0.58, were deemed as differentially spliced.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comprehensive spreadsheets with the read counts and the results of the analysis of differential expression and differential splicing detailed above

organism: Arabidopsis thaliana

source_name: pool of tissues

growth_protocol: For WT (Col) and lsm4-1 mutant, seeds were grown on Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4 °C, and then grown at 22 °C in continuous light. For WT (C24) and sad1/lsm5 mutant, seeds were grown on soil, stratified for 4 d, and then were grown at 22 °C in continuous light.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate the concentration and quality of samples, NanoDrop 2000c (Thermo Scientific) and gel electrophoresis were used, respectively.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, and first-strand cDNA synthesized by reverse transcriptase (SuperScript II; Invitrogen) and random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies)

treatment_protocol: Whole plants were harvested after 15 d for lsm4-1 and after 30 d (before bolting) for sad1/lsm5.

tag: ecotype

tag: genotype/variation

value: lsm5/sad1 mutant

tag: tissue

value: whole plants


title: lsm5/sad1 rep 3,2


title: lsm5/sad1 rep 3,1


title: MNC491_H3K4me1


title: lsm5/sad1 rep 2,1


title: lsm5/sad1 rep 1,2


title: MNC492_H3K4me3


title: RPF2(-)AZ_rep1

value: Exponential

value: NCTC 8325


title: WT C24 rep 3,1

value: Wild type (control for lsm5/sad1 mutant)


title: MNC492_H3K4me1


title: WT C24 rep 3,2


title: WT C24 rep 2,2


title: FB2555_H3K4me3


title: FB2555_H3K4me1


title: WT C24 rep 1,1


title: WT C24 rep 1,2


title: LCL12892_H3K4me1


title: LCL12892_H3K4me3


title: L3 mRNA profiling

description:
Sample3
KK progeny population of Kunsenshi male and female cross.
mRNA
Processed data file: AllMF-CLC-denovo-count-new08122014-rev_GEO.txt

value: Kunsenshi

value: mixed persimmon buds

tag: developmental stage

value: early differentiation of primordia


title: lsm4 rep 3,2

value: Col

value: lsm4 mutant


title: WT C24 rep 2,1


title: LCL12891_H3K4me3


title: LCL12891_H3K4me1


title: lsm4 rep 3,1


title: lsm5/sad1 rep 1,1


title: lsm4 rep 2,2


title: lsm4 rep 1,2


title: lsm4 rep 2,1


title: LCL19240_H3K4me3


title: LCL19239_H3K4me3


title: LCL12878_H3K4me1


title: LCL19238_H3K4me3


title: lsm4 rep 1,1


title: LCL19239_H3K4me1


title: LCL19240_H3K4me1


title: FB2555_F22_RNAseq

data_processing:
Trimmomatic v0.22  was used for trimming reads for quality (phred33>=30) and length (n>=32)
For RNA-seq, filtered reads were aligned to hg19 using Tophat v1.4.1 and bowtie v0.12.8. Raw read counts were obtained using htseq-count v0.5.3p9. Normalized gene and transcript expression values are obtained using cufflinks v2.1.1
Genome_build: hg19

extract_protocol:
Total RNA was extracted from cell lysates using the miRNeasy Mini Kit including a DNaseI treatment step and quality assessed by Agilent 2100 BioAnalyzer.
Libraries were prepared according to the Illumina TruSeq protocol, and quality assessed by Agilent 2100 BioAnalyzer.


title: LCL12878_H3K4me3


title: WT Col rep 1,2

value: Wild type (control for lsm4 mutant)


title: WT Col rep 2, 1


title: WT Col rep 2,2


title: WT Col rep 1,1


title: FB2456_F22_RNAseq


title: FB2555_F16_RNAseq


title: FB2456_F16_RNAseq


title: FB2317_F16_RNAseq


title: LCL19240_RNAseq


title: FB2316_F16_RNAseq


title: FB2317_F22_RNAseq


title: WT Col rep 3,2


title: MNC773_RNAseq


title: FB2316_F22_RNAseq


title: MNC764_RNAseq


title: LCL19239_RNAseq


title: MNC761_RNAseq


title: LCL19238_H3K4me1


title: eve runt_rep2

status: Public on Nov 02 2014

city: New York

first: Adam

last: Paré

address: 1275 York Avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Data was mapped to the D.melanogaster (dm3 from UCSC) using TopHat (v2.0.9/bowtie2) with a GTF from flybase with transcripts shorter than 150bp removed.
The mapped BAM files were then quantitated on the transcript level using HTSeq; however, the GTF from flybase was modifed so all entries for a gene have the *SAME* GENE-ID
Raw counts were then normalized with DESeq and differential expression was determined again using DESeq (from R/Bioconductor).
Genome_build: UCSC dm3
Supplementary_files_format_and_content: tab delimited text file with a matrix of normalized gene counts for all six samples

source_name: embryos

growth_protocol: Parental flies were raised under standard laboratory conditions (18C-25C). Wild type (OreR) embryos aged 0-1 h were collected on apple juice plates at 25C.

extract_protocol:
Embryos were ground in microfuge tubes in 50 ul Trizol reagent using plastic pestles. An additional 450 ul Trizol was then added and the samples were incubated for 5 min at RT. Next, 100 ul chloroform was added, and the samples were incubated for 3 min at RT. The samples were centrifuged at 12,000 g for 15 min to separate the aqueous and organic phases. At this point the standard Trizol protocols for total RNA extraction were followed.
The standard PolyA TruSeq RNA library preparation protocol

treatment_protocol: Precellularized embryos (0-1 h) were dechorionated, dessicated, covered with halocarbon oil, and injected according to standard protocols. Embryos were injected with either water or a mixture of dsRNAs targetting even-skipped and runt (1 ug/ul each). The embryos were then aged at 18C until just prior to gastrulation (at the onset of pole cell migration but before ventral furrow formation). Embryos of the correct stage were manually removed from the injection slides and stored in 50 ul Trizol reagent. Approximately 50 embryos were collected per replicate.

tag: genotype

value: Oregon R

tag: Stage

value: late blastoderm embryos

tag: injected with

value: eve + runt dsRNA


title: MNC772_RNAseq


title: WT Col rep 3,1


title: MNC775_RNAseq


title: water_rep2

value: water


title: water_rep1


title: eve runt_rep1


title: MRG_plus_rep2_shRNA screen

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

description:
Protocol: shRNA screen
Processed data file: shRNAScreen_rawCounts.txt

data_processing:
For the shRNA screen data analysis, we followed the protocol outlined by Dai et al. 2014 employing the R package limma. First, we extracted and counted the number of times each shRNA was observed in each library using the shRNA sequence as barcode and the R function processHairpinReads().
Supplementary_files_format_and_content: text file with raw counts for hairpin sequences

source_name: neural precursor cell: mid radial glial

growth_protocol: Culturing undifferentiated human ES cells:  HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) (Globalstem). Undifferentiated ES cells were maintained as described previously1 in medium containing DMEM/F12, 20% KSR, 1mM Glutamine, 1% Penicillin/Streptomycin, non essential amino acids and beta-mercaptoethanol.  Undifferentiated ES cells were purified with pluripotency markers Tra-1-60 and PE-conjugated SSEA-3 (BD Pharmingen).   Neural induction and long-term propagation of NPCs:  Neural differentiation of ES cells was performed as described previously1-3. Briefly, neuroectodermal cells were generated either by monolayer induction – with dissociated ES cells plated on Matrigel (BD biosciences), or by co-culture on MS5 stromal cells. In both cases neural fate was directed by dual SMAD inhibition protocol2. Neural rosettes were harvested mechanically beginning on day 8-10 of differentiation. Rosettes were replated on culture dishes pre-coated with 15 μg/mL polyornithine (Sigma), 1 μg/mL Laminin (BD Biosciences) and 1ug/ml Fibronectin (BD Biosciences) (Po/Lam/FN) in N2 medium composed of DMEM/F12 and N2 supplement (Invitrogen). N2 supplement contained Insulin, Apo-transferin, Sodium Selenite, Putrecine and Progesterone. This medium was supplemented with SHH (200 ng/mL), FGF8 (100 ng/mL) and BDNF (20 ng/mL) (all from R&D Systems) to maintain early anterior regionalization of the neural plate. These factors were gradually replaced by FGF2 (20 ng/mL) and EGF (20 ng/mL) in the following two weeks of differentiation in order to maintain a proliferative (FGF and EGF responsive) NPC state. NPCs from all stages were collected at indicated days and FACS purified for HES5::GFP (NE to L-RG) or EGFR for LNPs to purify for the highest NPC state for each stage. Neuroectodermal cells were collected at day 12 of differentiation, Neuroepithelial/early radial glial cells were collected at day 14, mid neurogenesis radial glial cells were collected at day 35, late gliogenic radial glial cells were collected at day 80, and long term NPCs were collected at day 220. At each stage cells were either split for the next passage or subjected to FACS purification for HES5::GFP as described. Cells were replated onto Po/Lam/FN culture dishes. For neuronal, astroglial or oligodendroglial differentiation, NPCs were seeded at high density and subjected to differentiated for 17 days in the presence of AA/BDNF, 5% Fetal Bovine Serum (FBS) (Invitrogen), or AA/BDNF/SHH/FGF8, respectively. For more details, please see Edri et al.3.

extract_protocol:
shRNA screen: We selected 244 transcription factors and epigenetic modifiers that were differentially or continuously highly expressed during our in vitro differentiation time course in an otherwise unbiased fashion (Extended Data Table 4). In addition, we included GFP, RFP, lacZ and luciferase as internal controls.  We then obtained a sub-pool of the human 45K shRNA pool6 distributed by the Broad Institute Genomic Perturbations Platform and the RNAi Consortium (TRC) against these genes. For each gene, 5 distinct shRNAs were included as well as 5 scrambled and 3 empty control vectors, amounting to a total of 1230+8 shRNAs. The plasmid for shRNA expression under the control of the constitutive U6 shRNA promoter was the lentiviral vector pLKO.1. shRNA pool production and infection conditions were performed as previously described6. Subsequently, we performed calibration experiments to determine to optimal combination of MOI and Puromyocin concentration to ensure efficient selection. We identified MOI 0.4 and 1ug/ml of Puromycin as optimal parameters for all stages. We then infected 26 million cells at each stage of NE, ERG and MRG to ensure sufficient shRNA integration events to recover the complexity of the shRNA library. 24h post infection and prior to full expression but after integration of the lentivirus into the genome we collected 3 million cells to determine our baseline shRNA library representation. Subsequently, we subjected the cells to 5 days of Puromycin selection and then FACS sorted the resulting populations into HES5+ and HES5- compartments.
We assessed the representation of the shRNA library in each of the 9 populations by retrieving all shRNA integration events from genomic DNA isolated from each sample using PCR followed by next generation sequencing as previously described (Strezoska, Z. et al 2012). More specifically, we performed two rounds of PCR using the following primers for the primary PCR: Primary R :CTTTAGTTTGTATGTCTGTTGCTATTAT; Primary F: AATGGACTATCATATGCTTACCGTAAC.  For the second, nested PCR we used: Nested F: GGCTTTATATATCTTGTGGAAAGGA; Nested R: GGATGAATACTGCCATTTGTCTC.

value: ES-derived neural progenitor cells

tag: genetic background

tag: treatment

value: GFP positive population after 6 days of shRNA infection


title: MRG_plus_rep3_shRNA screen

value: HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter


title: MRG_rep24h_rep1_shRNA screen

value: Infected cells collected 24h after infection and puero selection


title: MRG_plus_rep4_shRNA screen


title: MRG_rep24h_rep3_shRNA screen


title: MRG_plus_rep1_shRNA screen


title: LCL19238_RNAseq

value: lymphoblastic cell line


title: MRG_rep24h_rep2_shRNA screen


title: MRG_rep24h_rep4_shRNA screen


title: MNC770_RNAseq

value: monocyte


title: MNC758_RNAseq


title: ERG_rep24h_rep3_shRNA screen

source_name: neural precursor cell: early radial glial


title: eve runt_rep3


title: MRG_minus_rep1_shRNA screen

value: GFP negative population after 6 days of shRNA infection


title: ERG_rep24h_rep2_shRNA screen


title: MRG_minus_rep2_shRNA screen


title: ERG_plus_rep2_shRNA screen


title: ERG_plus_rep3_shRNA screen


title: ERG_minus_rep3_shRNA screen


title: ERG_minus_rep1_shRNA screen


title: ERG_minus_rep2_shRNA screen


title: ERG_rep24h_rep1_shRNA screen


title: NE_rep24h_rep4_shRNA screen

source_name: neural precursor cell: neuroepithelial


title: MRG_minus_rep4_shRNA screen


title: MRG_minus_rep3_shRNA screen


title: NE_plus_rep4_shRNA screen


title: NE_rep24h_rep3_shRNA screen


title: NE_plus_rep3_shRNA screen


title: NE_plus_rep2_shRNA screen


title: NE_plus_rep1_shRNA screen


title: NE_minus_rep3_shRNA screen


title: water_rep3


title: NE_minus_rep1_shRNA screen


title: ERG_plus_rep1_shRNA screen


title: strand specific RNA-Seq for LRG derived astrocyte like populations replicate 2

description: Processed data file: AllSamples_geneExpression.fpkm_tracking

data_processing:
For RNA-Seq data processing, reads were trimmed to 80, 60 or 30bp depending on their per-base quality distribution in order to achieve maximum alignment rates. Reads were mapped to the human genome (hg19) using TopHat v2.0 (ref 9) (http://tophat.cbcb.umd.edu) employing the unfiltered gencode.v19.annotation.gtf annotation as the transcriptome reference. TopHat was run with default parameters except for the coverage search being turned off. Transcript expression was estimated with Cuffdiff 2 (ref 10). The workflow used to analyze the data is described in detail in Trapnell et al. (2012) (alternate protocol B)11.
Genome_build: hg19
Supplementary_files_format_and_content: All coordinates are based on hg19. ENCODE narrowPeak Format: chromosome,chromstart,chromend,peak name,macs2 integer score, strand, fold change over background,-log10pvalue,-log10qvalue,relative summit position to peak star  WGBS/RRBS  bed format, each row describes one CpG: chrom,chromstart,chromend,number of reads where CpG was methylated/total number of reads coverging CpG,numeric score for UCSC display,strand-ignore  RNA-Seq txt format: cuffdiff output file: cufflinks  ChIP-Seq bed format containing 1kb tiles above a minimal enrichmend level: chrom,chromstart,chromend

source_name: neural precursor cell derived astrocyte like cells

extract_protocol:
RNA-Seq:RNA was extracted using the miRNeasy kit (Qiagen, 217004). Poly(A) RNA was isolated using Oligo d (T25) beads (NEB, E7490L).
RNA-Seq: The following steps of Illumina library construction (end-repair, addition of A-base, ligation of barcoded adaptors and PCR enrichment) we used a general SPRI cleanup procedure: addition of PEG buffer (20% PEG and 2.5 M NaCl), and extracted and washed as above. The enzymatic reactions were carried as follows: 1. DNA end-repair: T4 PNK and T4 polymerase (New England Biolabs) incubated 12C for 15 min, 25C for 15 min;  2. A-base addition: Klenow (3’->5’ exonuclease; New England Biolabs) incubated at 37C for 30 min. 3. Adaptor ligation: DNA ligase (New England Biolabs) and indexed oligo adaptors and incubated 25C for 15 min, followed by 0.7X SPRI/reaction to remove non-ligated adaptors. 4. PCR enrichment: PCR mastermix (primer set, dNTP mix, Pfu Ultra Buffer (Agilent), Pfu Ultra-II Fusion (Agilent), water), for 20 cycles. The PCR amplified libraries we cleaned up using 0.7X SPRI/reaction (size selection mode) to remove excessive primers. Roughly 5 picomoles of DNA library was then applied to each lane of the flow cell and sequenced on Illumina HiSeq 2000 sequencers according to standard Illumina protocols.


title: strand specific RNA-Seq for LRG derived astrocyte like populations replicate 1

value: neural precursor cell derived astrocyte like cells


title: strand specific RNA-Seq for MRG derived neuronal like populations replicate 2


title: strand specific RNA-Seq for ERG derived neuronal like populations replicate 2

source_name: neural precursor cell derived neuronal like cells


title: NE_rep24h_rep2_shRNA screen


title: strand specific RNA-Seq for MRG derived neuronal like populations replicate 1

value: neural precursor cell derived neuronal like cells


title: strand specific RNA-Seq for NE derived neuronal like populations replicate 2


title: strand specific RNA-Seq for NE derived neuronal like populations replicate 1