title: 604R

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
RTAVersion 1.13.48 used to create .bcl files and bcl2fastq version 1.8.4 used to generate fastq files
We checked the quality of the raw reads data for each sample using FastQC [1] (version 0.10.0) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference transcriptome (UCSC rn5) [5] using TopHat (version 2.0.9) and Bowtie (version 2.1.0.0). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation and differential expression analysis, using UCSC rn5.fa as the reference genome sequence and UCSC rn5.gtf as the reference transcriptome annotation. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
Genome_build: RN5
Supplementary_files_format_and_content: text file of raw rmapped read counts

source_name: supraspinatus muscle

extract_protocol:
RNA was extracted using the QIAGEN miRNeasy kit and RNA was delivered to the University of Michigan sequencing core for library preparation
Used Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002) (Illumina, San Diego, CA) using manufacturer's recommended protocols

value: Sprague Dawley

tag: stress

value: bilateral full-thickness supraspinatus tear and suprascapular neurectomy

tag: time

value: 60 days

value: supraspinatus muscle


title: SC-NES cells rep 3

status: Public on Aug 29 2018

type: SRA

city: New Haven

first: Stephen

last: Strittmatter

state: CT

address: 295 Congress avenue

department: Neurology

country: USA

institute: Yale University

description:
maria_teresa.gene.RPKM.2ndRun.txt
maria_teresa.gene.count.2ndRun.txt

library_source: transcriptomic

data_processing:
The sequenced reads were clipped one nucleotide in both ends, leaving 74 nucleotide long reads for sequence alignment to human reference genome (GRCh38/hg38) by using the STAR software. Beyond default parameters in the alignment procedure, human gene annotation retrieved from the GENCODE project (version 21, http://www.gencodegenes.org/releases/21.html) was additionally provided to improve exon-exon junction mapping. To quantify accurately the origin of the genomic locus of short sequenced reads, only the uniquely mapped reads were used for downstream analyses. FeatureCounts was used  to quantify expression profiles of each type of annotation entry retrieved from GENCODE v21. Additional quality control measures were introduced to assess potential issues including reads classification, mitochondrial contamination, and gene coverage uniformity.  R package DESeq2 was used to identify DEX genes. We generated two types of gene expression value, read counts and RPKM (reads per kilobase of exon model per million mapped reads). The reads count per gene served as the input for DESeq2. When performing the comparisons, DESeq2 first gets the mean expression level as a joint estimate for both groups, and then calculates the difference as well as the P value for the statistical significance of this change. The adjusted P value was calculated based on multiple testing with the Benjamini-Hochberg procedure, estimating the false discovery rate (FDR). To detect statistically significant DEX genes, FDR was set to be minor than 0.01.
R package DESeq2 was used to identify DEX genes. We generated two types of gene expression value, read counts and RPKM (reads per kilobase of exon model per million mapped reads). The reads count per gene served as the input for DESeq2. When performing the comparisons, DESeq2 first gets the mean expression level as a joint estimate for both groups, and then calculates the difference as well as the P value for the statistical significance of this change. The adjusted P value was calculated based on multiple testing with the Benjamini-Hochberg procedure, estimating the false discovery rate (FDR). To detect statistically significant DEX genes, FDR was set to be minor than 0.01.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and read count values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Human spinal cord

growth_protocol: NES cells were kept in proliferation in T25 flasks coated  with poly-L-ornithine (0.01%), laminin (5 μg/ml) and fibronectin (1 μg/ml). Cells were expanded in NES medium  and split 1:2 approximately every 7 days with 0.25% trypsin. For cryopreservation, cells were trypsinized and ~  2 X 106 cells were pelleted (200 x g for 3 minutes) and resuspended in cryopreservation medium containing  10% DMSO and 90% NES medium. For resuscitation, cells were rapidly thawed at 37 ºC, resuspended in prewarmed  culture media, centrifuged for 3 minutes at 200 x g, resuspended in NES medium, and replated on  coated plates. Neuronal differentiation of NES cells was performed in two steps. For the pre-differentiation step  NES cells were seeded at a density of 0.5 x 105 cells/cm2 in a T25 coated flask in NES medium without EGF  and FGF2. After 7 days, cells were dissociated and replated at a density of 0.8-1 x 105 cells/cm2 in BrainPhys  Medium (Stem Cell Technologies, Cambridge, MA, #05790) supplemented with B27 (2%), N2 (1%) and BDNF  (20 ng/ml). Half volume of the medium was changed every 2-3 days and neurons were differentiated up to 3  months.

extract_protocol:
In vitro samples were collected using RNA later and frozen at -80 C. Spinal cords containing the grafts were dissected and the portion containing the cells was isolated and kept in RNA later at -80 C.Total RNA was extracted using the RNeasy plus minikit (Quiagen, #74134) according to manufacturer’s instruction.  mRNA libraries were prepared according to the TruSeq RNA Illumina kit protocol and sequenced using a  HighSeq 2500 sequencing system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 6 weeks post conception

tag: status

value: undifferentiated, in proliferation.


title: SC-NES cells rep 2


title: shLB_8h_2

status: Public on Aug 30 2018

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description:
RNAseq experiment
FPKMs_0CT1_0CT2_0shLB1_0shLB2-8CT1_8CT2_8shLB1_8shLB2-24CT1_24CT2_24shLB1_24shLB2.txt

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Cufflinks (PubMed ID 22383036) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq. ATACseq analysis:  Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq and ATACseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP_LB1_0h_11732_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_8h_11733_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_24h_11734_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_0h_11864.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_8h_11865.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_24h_11866.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_0h_11732_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_LB1_8h_11733_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_LB1_24h_11734_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_0h_11864.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_8h_11865.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_24h_11866.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: FPKM_0h-8h-24h.txt (FPKM values)
Supplementary_files_format_and_content: FPKMs_0CT1_0CT2_0shLB1_0shLB2-8CT1_8CT2_8shLB1_8shLB2-24CT1_24CT2_24shLB1_24shLB2.txt (FPKM values)

organism: Mus musculus

source_name: mouse mammary epithelial cells

growth_protocol: NMuMG cells were maintained in Dubelcco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Invitrogen) supplemented with 10μg/ml of insulin (Sigma) at 37ºC in 5% CO2.

extract_protocol:
ChIP experiments were performed as previously described (Herranz et al., 2008, PubmedID: 18519590). RNA extraction was performed with GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich). ATAC experiments were performed as previously described (Buenrostro et al., 2013, PubmedID: 24097267).
Libraries were prepared according to Illumina instructions.

treatment_protocol: TGFβ was added at a final concentration of 1-5 ng/ml to induce EMT in NMuMG cells.

tag: cell line

value: NMuMG

tag: chip antibody


title: 602R

organism: Rattus norvegicus

tag: strain

tag: tissue


title: 305L

value: 30 days


title: 603R


title: SC-Graft rep 1

value: differentiated in vivo for two months upon transplantation in the lesioned spinal cord.


title: TAP CLIP-seq 2

city: Madrid

first: Begona

last: Aguado

state: Madrid

address: Nicolas Cabrera 1

department: Genomics and NGS Service

institute: CBMSO

description: RNA isolation from tandem affinity purified RNP complexes bound to TAP peptide (IgG sepharose resin, calmodulin agarose resin)

data_processing:
For the TAP sample, the peaks of both replicate 1 and 2 were combined and used as a single TAP control.
CLIP analysis software: pyicoclip. Default parameters.
Peaks in each replicate of RBS1 and RBS2 that appear in the TAP reads were removed.
The overlapping peaks of the RBS1 or RBS2 replicates were considered as the final set of peaks using fjoin.py.
Addition of 20 flanking nts.
Peaks annotation.
Peaks assumed to be in intergenic regions were removed.
Genome_build: hg19
Supplementary_files_format_and_content: Tabular files containing peaks. Column1=chromosome; column2=start; column3=end; column4=number of reads in hit after filtering; column5=strand; column6=hit sequence; column7=ENSEMBL gene id; column8=gene short name; column9=ENSEMBL transcript id;  column10=feature; column11=feature type

source_name: HEK293 transfected cells

growth_protocol: HEK293 cells, grown in Dulbecco’s Modified Eagle Medium (DMEM), were transfected with the plasmids pcDNA3-CTAP, pcDNA3-RBS1-CTAP and pcDNA3-RBS2-CTAP using lipofectamine (Thermo Scientific) according to the manufacturer instructions. 24 h post-transfection, monolayers were washed with ice-cold PBS prior to UV irradiation (150 mJ/cm2 at 254 nm).

extract_protocol:
The RNA-protein complexes associated to RBS1, RBS2 or the TAP polypeptide were isolated as in the tandem affinity purification procedure  (IgG sepharose resin, calmodulin agarose resin) until the second purification step. After washing the calmodulin resin with the associated complexes, beads were incubated with 500 µl of Proteinase K Buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 0.5% SDS, 2 mM EGTA, 1 mM EDTA, proteinase K 0.2 mg/ml) at 65°C, during 2 h with gentle rocking. The elution products are recovered by gravity flow. RNAs were then extracted with phenol-chloroform, ethanol precipitated and resuspended in 20 µl of H20. Each RNA preparation was monitored using the Agilent 2100 Bioanalyzer (Agilent technologies).
RNA (about 100 ng) obtained from two independent biological replicates of each sample (RBS1, RBS2 and TAP) were used to generate cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit v2 (Illumina) according to the manufacturer's protocol, but omitting the polyA+ selection step. All purifications steps were done using AMPure XP beads (Beckman Coulter). cDNA libraries were subjected to Illumina adapter ligation with TruSeq Universal Adapter 5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3’ and TruSeq Adapter, Index 5’GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCTCGTATGCCGTCTTCTGCTTG3’ and were sequenced in an Illumina HiSeq2000 sequencer. Reads length were 50 bp in a single-read run cycle.
CLIP-Seq

tag: cell type

value: human embryonic kidney cells


title: 304L


title: SC-NES cells rep 1


title: 105R

value: 10 days


title: 104R


title: 302R


title: 102R


title: 303L


title: 05L

value: control

value: 0 days (control)


title: 01L


title: 03R


title: 101L


title: SU58xZI418N_2

city: Planegg

first: John

last: Parsch

state: BY

address: Grosshaderner Str. 2

department: Biology II

country: Germany

institute: University of Munich (LMU)

data_processing:
Illumina HiSeq2500 software used for basecalling.
Illumina sequence reads were mapped to the reference D. melanogaster transcriptome (FlyBase release 6.09) using NextGenMap (version 0.4.12) with default parameters
Expression was quantified on a “per gene” basis. For this, if a sequence read mapped to one or more transcripts of the same gene, it was counted as one “hit” for that gene.
Genome_build: dmel_r6.09
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene/sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Malpighian tubule

growth_protocol: All flies were maintained on standard cornmeal-molasses medium at 20° with a 14 h light:10 h dark cycle

extract_protocol:
Total RNA extraction was performed using the MasterPure RNA Purification Kit (Epicentre)
Poly-A mRNA was purified and fragmented by sonication. First strand single end cDNA was synthesized using random primers. Tagged libraries were run on a HiSeq 2500 sequencer (Illumina) to generate paired-end reads of 125 bases.

treatment_protocol: Adult flies aged 6 days were anesthetized on ice and tubules were dissected in 1xPBS (phosphate buffered saline) and stored in RNAlater to prevent RNA degradation

tag: Sex

value: female

value: 6 days (adult)

value: S58 x Z418 hybrid


title: SU58xZI418N_1


title: SU26xZI418N_1

value: S26 x Z418 hybrid


title: HUVEC_UT_Notch1

city: OSLO

first: Guttorm

last: Haraldsen

state: OSLO

address: Sognsvannsveien 20

department: Department for Pathology

country: Norway

institute: Oslo University Hospital

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.2.6
Duplicate reads were removed using samtools rmdup
Peak calling was done using macs2 version 2.1.1.20160226
Genome_build: hg19
Supplementary_files_format_and_content: bigWig for viewing in genome browser; bed with for peaks (five columns: chromosome, start, end, peak name, peak summit position)

molecule: genomic DNA

source_name: Human umbilical vein endothelial cells (HUVECs)

growth_protocol: Pools of HUVECs from 13 donors were grown on 15 cm culture dishes coated with 0.1% gelatin in MCBD 131 medium supplemended with 7.5% fetal calf serum, 10 ng/ml EGF, 1 ng/ml bFGF, 1 μg/ml hyrdocortisone, 50 μg/ml gentamicin, 250 ng/ml fungizone, and 1% L-glutamine. HUVECs that reached compact, high-density monolyer. We define the superconfluent state as described earlier in Küchler et al. Am J Pathol. 2008 Oct;173(4):1229-42.

extract_protocol:
For Notch1, RBPJ, and NF-κB/RelA ChIP-seq experiments, cells were crosslinked in a two-step crosslinking procedure: 45 min in 2 mM disuccinimidyl glutarate (DSG) followed by 10 min incubation with 1% formaldehyde (FA) before quenching with 125 mM glycine. For H3K27ac ChIP-seq, only FA crosslinking was applied. For each 15 cm dish, cells were lysed in 1.6 mL lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH 8), removed with a cell scraper, and kept at 4°C before sonication (material used for NF-κB/RelA and H3K27ac ChIP-seq was stored at -80°C). DSG/FA and FA samples were sonicated for 40 and 16 cycles, respectively, on a Bioruptor Twin set to 30 sec ON/OFF and high intensity. To remove cell debris, samples were subjected to centrifugation at 10,000g for 1 min and supernatants were collected. ChIP was performed on approximately 1.5e7 cells in a final volume of 6 mL lysis buffer with BSA in 15 mL tubes. Chromatin was incubated with antibodies as indicated in the list above for 3 hours at 4°C with upside-down rotation. Protein A sepharose beads were added and samples were incubated overnight at 4°C with upside-down rotation. Beads were washed in 12 mL by the following wash steps: 2x wash buffer 1 (0.1% SDS, 0.1% NaDOC, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM HEPES), 1x wash buffer 2 (0.1% SDS, 0.1% NaDOC, 1% Triton X-100, 0.5 M NaCl, 1 mM EDTA, 20 mM HEPES), 1x wash buffer 3 (0.25 M LiCl, 0.5% NaDOC, 0.5% NP-40, 1 mM EDTA, 20 mM HEPES), and 2x wash buffer 4 (1 mM EDTA, 20 mM HEPES). Samples were treated with 10 µg RNase A in 100 µL for 20 min at 37°C. Elution was carried out in 2x200 µL elution buffer (0.1M NaHCO3, 1% SDS) for 2x15 min at room temperature with upside-down rotation. Samples were then treated with 60 µg Proteinase K for 1 hour at 55°C and subjected to decrosslinking in 300 mM NaCl by overnight incubation at 65°C. DNA was purified by standard PCI/chloroform extraction and ethanol precipitation and resuspended in 60 µL molecular biology-grade water. For input samples, 0.7% sonicated material was processed in parallel to the ChIP-seq samples from the RNase-treatment step.
Sequencing libraries were prepared according to the Illumina protocol, and sequenced on an Illumina Hiseq4000 (RBPJ, Notch1) or Illumina Nextseq500 (RelA, H3K27ac) machine at the Genomics Core Facility at Oslo University Hospital, Norway.

treatment_protocol: Untreated cells were cultured as described in the growth protocol section until crosslinking and harvest. For knockdown experiments, cells were transfected with 27 nM siRNA targeting Notch1 or negative control siRNA (Scr) using Lipofectamine RNAiMAX and 60 hours later stimulated with or without 5 ng/ml of IL-1β for 1 hour.

tag: passages

value: Passage 4

tag: state/ treatment

value: Superconfluent, untreated

value: anti-Notch1, Cell Signaling #3608

tag: chip antibody lot # and amount used pr. chip-seq


title: HUVEC_UT_RBPJ

value: Human umbilical vein endothelial cells (HUVECs)

value: anti-RBPJ, Cell Signaling #5313


title: H&H 31_Mesenchyme_II

city: Arlington

first: Ang

last: Li

state: TX

address: 655 W Mitchell St, SEIR 244

department: Kinesiology

institute: University of Texas at Arlington

data_processing:
Prealignment QA/QC, adaptor sequence trimming, alignment of reads (TOPHAT 2, UCSC galGal4), and postalignment QA/AC were done in Partek Flow
Reads Per Kilobase of exon per Megabase of library size (RPKM) were caculated in Partek Genomic Suite
Genome_build: galGal4
Supplementary_files_format_and_content: Excel files include RPKM value for each sample

organism: Gallus gallus

source_name: dorsal skin mesenchyme

extract_protocol:
Dorsal skin epithelium and mesenchyme were separated in 2xCMF, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Version2 was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: dorsal skin mesenchyme

tag: batch

value: II


title: SU26xZI418N_2


title: ZI418NxZI418N_2

value: Z418 (Zambia)


title: HUVEC_Notch1_RBPJ_Input


title: PBK inhibition in C4-2 cell DMSO control rep 2

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description: RNA seq from C4-2 cells treated with DMSO control

data_processing:
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.05.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: prostate cancer epithelium

growth_protocol: Cells were grown in RPMI media with 10% FBS at 37C

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: 1 micro molar of PBKi was used to treat C4-2 cells grown in 10%RPMI media.

tag: sample group

value: prostate cancer epithelium


title: SU58xSU58_2

value: S58 (Sweden)


title: SU26xSU58_1

value: S26 x S58 hybrid


title: SU58xSU58_1


title: ZI418NxZI418N_1


title: MCF7_E2_2

city: Brisbane

first: Eva

last: Baxter

state: QLD

address: 300 Herston Road

department: Cell and Molecular Biology

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Oestradiol

data_processing:
Sequences were aligned to the human genome hg38 using STAR (v2.4.1c) on default settings except the following parameters: --outFilterMultimapNmax 10 --outSAMunmapped within --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 34359738368.
BAM files from the same sample were merged, sorted, and indexed using samtools (version 0.1.19-96b5f2294a).
A BED file containing genomic coordinates for RefSeq genes was downloaded from the UCSC genome browser (28th March 2016) and tags falling in those exonic regions were counted and tallied using bedtools (version 2.17.0; parameters -split -S -D).
Read counts in the processed data file Cell lines_E2_3hrs_TMM.txt were normalised using edgeR in R (version 3.1.1) using default settings (TMM normalisation).
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file containing normalised abundance measurements for each sample.

source_name: Breast cancer

growth_protocol: Cells were grown in phenol-red free DMEM for 72 hours prior to treatment.

extract_protocol:
RNA was harvested using Trizol reagent according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 10nM oestradiol or vehicle (ethanol) for three hours.

value: Breast

tag: treatment

value: Oestradiol


title: MCF7_Veh_2

description: Vehicle

value: Vehicle


title: SU26xSU26_2

value: female

value: 6 days (adult)

value: S26 (Sweden)


title: MCF7_E2_1

description: Oestradiol


title: MCF7_Veh_1

description: Vehicle


title: JHUEM14_E2_2

description: Oestradiol

source_name: Endometrial cancer

value: Endometrium


title: 02R

value: Sprague Dawley

tag: stress

value: control

value: 0 days (control)

value: supraspinatus muscle


title: Ah NOD Rep1

city: Kolkata

first: Maitrayee

last: DasGupta

state: WestBengal

address: 35 Ballygunge Circular Road

department: Biochemistry

country: India

institute: University of Calcutta

data_processing:
Image analysis are performed with the Illumina HiSeq Control Software (HCS). Image analysis identify clusters position, intensity and associated background noise.
The base calling is done by the RTA sofware provided by Illumina
Samples quality control are done by FastQC software.
Contaminants screening done by software FastQ Screen and PhiX genome  and Illumina adapters (TruSeq and Nextera) are also tested for this screening
Reads have been aligned to the Arachis duranensis and Arachis ipaensis references using TopHat2. It aligns RNA-Seq reads using the ultra high-throughput short read aligner Bowtie2, and then analyzes the mapping results to identify splice junctions between exons.
Genome_build: Arachis duranensis & Arachis ipaensis
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

organism: Arachis hypogaea

source_name: ROOT

growth_protocol: Arachis hypogaea seeds were surface sterilized and alloowed to germinate in soil

extract_protocol:
Infected roots were harvested at different mentioned time point, flash frozen in Liq Nitrogen, total RNA was isolated using Trizol reagent(Ambion). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The different time point Infection was done to Arachis hypogaea  by SEMIA 6144

tag: symbiont

value: Bradyrhizobium sp. (SEMIA 6144)

value: ROOT

value: 28 days after infection


title: Ah 1DPI Rep2

tag: age

value: 1 day after infection


title: JHUEM14_E2_1

description: Oestradiol


title: 605L

value: bilateral full-thickness supraspinatus tear and suprascapular neurectomy

tag: time

value: 60 days


title: JHUEM14_Veh_2

description: Vehicle

tag: cell line


title: JHUEM14_Veh_1

description: Vehicle


title: Ishikawa_E2_2

description: Oestradiol

value: Ishikawa


title: SU26xSU58_2

value: S26 x S58 hybrid


title: Ishikawa_E2_1

description: Oestradiol

value: Oestradiol


title: Ishikawa_Veh_2

description: Vehicle

value: Vehicle


title: HUVEC_Notch1kd_IL1beta_FA_Input

value: Human umbilical vein endothelial cells (HUVECs)

value: Passage 4

value: Confluent, treated with Notch1 siRNA and stimulated with IL-1β

tag: chip antibody


title: HUVEC_Scr_IL1beta_DSG_Input

value: Confluent, treated with Scr siRNA and stimulated with IL-1β


title: SU26xSU26_1

value: female

value: 6 days (adult)

tag: strain

value: S26 (Sweden)


title: HUVEC_Scr_IL1beta_FA_Input

tag: tissue


title: HUVEC_Scr_DSG_Input

value: Confluent, treated with Scr siRNA


title: HUVEC_Notch1kd_IL1beta_DSG_Input


title: HUVEC_Notch1kd_IL1beta_RelA

value: anti-NF-κB/RelA, Santa Cruz Biotechnology sc-372


title: HUVEC_Notch1kd_IL1beta_H3K27ac

value: anti-H3K27ac, Diagenode C15410174


title: 611054

status: Public on Aug 28 2018

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

description: Different brain regions were isolated from F1 hybrids of TPR50 tau Transgenic mice crossed with DBA, FVB and C57BL6 strains and run for mRNA sequencing

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NCBIM37 whole genome using Tophat2 v2.07 with parameters -g 10 -p 8 -r 99 --no-novel-juncs -G GRCh37.73.gtf
Counts were estimated using union exon model using HTSeq-Counts v0.6.1
Genes were kept if they were expressed in 80% of the samples with >10 reads. The resulting read counts were normalized for library size using cpm function of egdeR package in R Robinson et al 2010 to get fragments per kilobase million mapped reads (FPKM) values. Log2 transformed FPKM values were quantile normalized using betweenLaneNormalization function of EDAseq package in R
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include Normalized log2 RPKM values for each Sample ...

source_name: stem

extract_protocol:
Total RNA was isolated using miRNeasy kit, Qiagen following manufacture's protocol
RNA libraries were prepared for sequencing using Unstranded poly-A library preparation kit, Illumina
50-bp paired end Unstranded RNA-Seq using HiSeq2000

value: stem

value: 6 month

tag: mousestrain

tag: transgenic

value: Tg

tag: rin


title: 611044


title: 611034


title: 611064


title: 609064

value: Wt


title: 609034


title: 611014


title: HUVEC_Scr_RelA

tag: passages

tag: state/ treatment


title: 609024


title: Ishikawa_Veh_1

description: Vehicle

value: Endometrium

value: Ishikawa


title: 609014


title: 607064

value: FVB


title: 607034


title: 607044


title: 607024


title: HUVEC_Scr_H3K27ac

value: Human umbilical vein endothelial cells (HUVECs)

tag: chip antibody lot # and amount used pr. chip-seq


title: HUVEC_Scr_FA_Input

value: Passage 4


title: 607014


title: 605064


title: 605054


title: HUVEC_Scr_IL1beta_H3K27ac


title: HUVEC_Scr_IL1beta_RelA


title: 605014


title: 605034


title: 605024


title: 609044


title: 603054

value: DBA


title: 603034


title: 603024


title: 603044


title: 601064


title: 601054


title: 607054


title: 601044


title: 601034


title: 603014


title: 311064

value: 3 month


title: 601024


title: 601014


title: 311014


title: 311024


title: 311054


title: 309064


title: 311034


title: 311044


title: 309044


title: 309034


title: 307064


title: 307054


title: 307034


title: 307024


title: 307044


title: 307014


title: 305034


title: 305044


title: 303064


title: 303054


title: 303034


title: 305024


title: 305014


title: 303024


title: 303014


title: 305054


title: 605044


title: 301034


title: 301054


title: 611062

source_name: hippocampus

value: hippocampus


title: 301044


title: 301014


title: 611012


title: 611042


title: 611022


title: 609052


title: 305064


title: 609062


title: 609042


title: 611032


title: 609012


title: 607052


title: 301064


title: 607042


title: 609022


title: 605062


title: 607012


title: 605042


title: 301024


title: 605052


title: 611052


title: 609032


title: 607032


title: 309024


title: 603042


title: 605032


title: 603052


title: 603062


title: 605012


title: 603032


title: 605022


title: 601052


title: 607022


title: 601062


title: 601032


title: 603022


title: 601022


title: 311042


title: 311052


title: 311022


title: 311032


title: 311012


title: 309052


title: 309022


title: 309032


title: 309012


title: 311062


title: 309014


title: 309062


title: 307062


title: 307052


title: 307022


title: 309042


title: 307032


title: 305062


title: 601042


title: 305052


title: 305042


title: 307042


title: 603012


title: 305022


title: 303062


title: 601012


title: 303022


title: 303032


title: 303012


title: 301062


title: 303042


title: 301052


title: 307012


title: 301022


title: 301012


title: 611041

source_name: cortex

value: cortex


title: 301042


title: 301032


title: 611051


title: 611061


title: 305032


title: 611021


title: 305012


title: 609041


title: 609051


title: 609031


title: 609011


title: 303052


title: 607061


title: 609021


title: 607051


title: 607021


title: 607031


title: 605041


title: 605021


title: 605051


title: 605011


title: 611031


title: 603041


title: 603051


title: 603031


title: 601061


title: 605031


title: 611011


title: 603011


title: 603061


title: 607041


title: 601031


title: 601041


title: 311061


title: 311051


title: 601021


title: 605061


title: 311031


title: 607011


title: 311011


title: 309061


title: 309041


title: 311041


title: 309051


title: 601011


title: 307041


title: 309031


title: 309021


title: 307051


title: 307021


title: 307031


title: 307061


title: 303041


title: 303011


title: 305021


title: 305031


title: 303061


title: 301061


title: 305041


title: 305011


title: 303051


title: 303021


title: 303031


title: 305051


title: 309011


title: 301051


title: 301021


title: 301031


title: 301041


title: 307011


title: 301011


title: 611063

source_name: cerebellum

value: cerebellum


title: 305061


title: 601051


title: 611053


title: 611043


title: 611033


title: 611023


title: 611013


title: 609063


title: 609053


title: 609043


title: 605053


title: 605063


title: 609023


title: 607033


title: 609033


title: 605033


title: 607043


title: 603053


title: 607063


title: 603033


title: 605043


title: 603063


title: 603043


title: 601063


title: 605013


title: 601053


title: 607053


title: 601043


title: 601033


title: 601013


title: 311043


title: 603013


title: 311033


title: 311053


title: 609013


title: 607013


title: 311063


title: 311023


title: 309053


title: 309063


title: 311013


title: 605023


title: 309043


title: 309033


title: 309013


title: 307043


title: 309023


title: 307063


title: 307033


title: 307053


title: 307013


title: 305063


title: 305043


title: 307023


title: 305053


title: 305023


title: 303043


title: 303063


title: 303023


title: 311021


title: 305033


title: 303033


title: 303013


title: 303053


title: 301053


title: 301043


title: 301013


title: 301033


title: 603061 [miRNA]

description: Different brain regions were isolated from F1 hybrids of TPR50 tau Transgenic mice crossed with DBA, FVB and C57BL6 strains and run for miRNA sequencing

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, mapped and  annotated using mirDeep2 package
Counts were estimated using mirDeep2 package
Normalized counts were estimated using miRDeep2 package. Only those miRNAs were used which had at least 10 counts in 80% of samples
Genome_build: miRbase 20, NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include Normalized log2 counts values for each Sample ...

extract_protocol:
Total RNA was isolated using miRNeasy kit, Qiagen following manufacture's protocol
RNA libraries were prepared for sequencing using Standard miRNA sequencing kit, Illumina

value: TPR50 Tau transgenic


title: 603024 [miRNA]


title: 607061 [miRNA]


title: 603031 [miRNA]


title: 601042 [miRNA]


title: 605022 [miRNA]


title: 609041 [miRNA]


title: 605034 [miRNA]


title: 305013


title: 609043 [miRNA]


title: 301063


title: 603042 [miRNA]


title: 605042 [miRNA]


title: 605041 [miRNA]


title: 603064 [miRNA]


title: 611014 [miRNA]


title: 603054 [miRNA]


title: 605023 [miRNA]


title: 607021 [miRNA]


title: 611041 [miRNA]


title: 601043 [miRNA]


title: 603013 [miRNA]


title: 611064 [miRNA]


title: 611054 [miRNA]


title: 607063 [miRNA]


title: 601053 [miRNA]


title: 603014 [miRNA]


title: 605032 [miRNA]


title: 603062 [miRNA]


title: 605012 [miRNA]


title: 603053 [miRNA]


title: 609051 [miRNA]


title: 611061 [miRNA]


title: 609013 [miRNA]


title: 607011 [miRNA]


title: 601052 [miRNA]


title: 611021 [miRNA]


title: 611032 [miRNA]


title: 607052 [miRNA]


title: 603043 [miRNA]


title: 601064 [miRNA]


title: 609034 [miRNA]


title: 611031 [miRNA]


title: 607041 [miRNA]


title: 603023 [miRNA]


title: 605013 [miRNA]


title: 607042 [miRNA]


title: 609062 [miRNA]


title: 611033 [miRNA]


title: 601061 [miRNA]


title: 603044 [miRNA]


title: 605062 [miRNA]


title: 607013 [miRNA]


title: 605021 [miRNA]


title: 611011 [miRNA]


title: 609021 [miRNA]


title: 607012 [miRNA]


title: 603041 [miRNA]


title: 601054 [miRNA]


title: 607014 [miRNA]


title: 607024 [miRNA]


title: 605044 [miRNA]


title: 601011 [miRNA]


title: 601013 [miRNA]


title: 609031 [miRNA]


title: 609053 [miRNA]


title: 605052 [miRNA]


title: 607022 [miRNA]


title: 611034 [miRNA]


title: 611044 [miRNA]


title: 603032 [miRNA]


title: 601063 [miRNA]


title: B042

description: Lentiviral overexpression of full-length SOX5  protein for 14 days. Total RNA isolated using miRNeasy kit, Qiagen

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NCBIM37 whole genome using rna-STAR with default parameters
Counts were estimated using union exon model using HTSeq-Counts v0.6.1
FPKM values were estimated using CQN package (Hansen et al 2012) in R using default options, but setting cqn=FALSE which turns of quantile normalization
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include log2 FPKM values for each Sample

source_name: FACS Sorted Neurons

extract_protocol:
FACS sorted neurons were isolated using Nucleospin RNA XS kit, Clontech in 10ul total volume
RNA libraries were prepared for sequencing using SMARter V4 Total RNA sample prep kit, Clontech

value: FACS sorted cortical neurons

tag: construct

value: GFP

tag: time point (weeks)


title: B039


title: 607064 [miRNA]

value: stem


title: B034

description: Lentiviral overexpression of GFP for 14 days. Total RNA isolated using miRNeasy kit, Qiagen


title: 609064 [miRNA]

value: 6 month


title: 603012 [miRNA]


title: B029


title: 607054 [miRNA]


title: B031


title: 601034 [miRNA]


title: B033


title: 611062 [miRNA]


title: B032


title: 603051 [miRNA]


title: 611063 [miRNA]


title: 609014 [miRNA]


title: 609044 [miRNA]


title: 607032 [miRNA]


title: 611051 [miRNA]


title: 603033 [miRNA]


title: B025

description: AAV2/9 overexpression of miRNA203 or scrambled miRNA for 3 or 6-weeks. GFP+ve Neurons were FACS sorted and total RNA isolated using Clontech kit.


title: 605061 [miRNA]


title: 605054 [miRNA]


title: 601021 [miRNA]


title: B023


title: 605051 [miRNA]


title: B015


title: 301023


title: 601022 [miRNA]


title: 605053 [miRNA]


title: B027


title: 605011 [miRNA]


title: 611043 [miRNA]


title: 605024 [miRNA]


title: B014


title: B028


title: B012


title: 609063 [miRNA]


title: 601031 [miRNA]


title: 611013 [miRNA]


title: 611052 [miRNA]


title: B013


title: 607062 [miRNA]


title: 607033 [miRNA]


title: B006


title: B011


title: 609033 [miRNA]


title: 601051 [miRNA]


title: B005


title: 609052 [miRNA]


title: 601024 [miRNA]


title: 609023 [miRNA]


title: B004


title: 601012 [miRNA]


title: 601062 [miRNA]


title: B003


title: 609024 [miRNA]


title: 607044 [miRNA]


title: B002


title: 601041 [miRNA]


title: 607023 [miRNA]


title: 601032 [miRNA]


title: B001


title: 609011 [miRNA]


title: 605064 [miRNA]


title: 607034 [miRNA]


title: 601023 [miRNA]


title: 611022 [miRNA]


title: 605043 [miRNA]


title: 603063 [miRNA]


title: 603011 [miRNA]


title: 605031 [miRNA]


title: 601033 [miRNA]


title: 601044 [miRNA]


title: 607051 [miRNA]


title: 605014 [miRNA]


title: 605063 [miRNA]


title: 601014 [miRNA]


title: 603034 [miRNA]


title: 603052 [miRNA]


title: 603022 [miRNA]


title: 607031 [miRNA]


title: 607043 [miRNA]


title: 609022 [miRNA]


title: 611053 [miRNA]


title: 609012 [miRNA]


title: 611042 [miRNA]


title: 607053 [miRNA]


title: 605033 [miRNA]


title: 609032 [miRNA]


title: 311054 [miRNA]


title: 311064 [miRNA]


title: 311044 [miRNA]


title: 311034 [miRNA]


title: 311024 [miRNA]


title: 309044 [miRNA]


title: 309034 [miRNA]


title: 309054 [miRNA]


title: 309064 [miRNA]


title: 309014 [miRNA]


title: 309024 [miRNA]


title: 307064 [miRNA]


title: 307044 [miRNA]


title: 307014 [miRNA]


title: 307024 [miRNA]


title: 611012 [miRNA]


title: 611023 [miRNA]


title: 305064 [miRNA]


title: 305054 [miRNA]


title: 305024 [miRNA]


title: 305034 [miRNA]


title: 305044 [miRNA]


title: 303054 [miRNA]


title: 303064 [miRNA]


title: 303014 [miRNA]


title: 305014 [miRNA]


title: 303034 [miRNA]


title: 311014 [miRNA]


title: 301054 [miRNA]


title: 301044 [miRNA]


title: 307034 [miRNA]


title: 301064 [miRNA]


title: 307054 [miRNA]


title: 301014 [miRNA]


title: 311063 [miRNA]


title: 311053 [miRNA]


title: 311023 [miRNA]


title: 311043 [miRNA]


title: 309063 [miRNA]


title: 309043 [miRNA]


title: 309053 [miRNA]


title: 311013 [miRNA]


title: 311033 [miRNA]


title: 307063 [miRNA]


title: 303044 [miRNA]


title: 309033 [miRNA]


title: 303024 [miRNA]


title: 307043 [miRNA]


title: 307053 [miRNA]


title: 309023 [miRNA]


title: 307023 [miRNA]


title: 307033 [miRNA]


title: 307013 [miRNA]


title: 305053 [miRNA]


title: 305043 [miRNA]


title: 305033 [miRNA]


title: 301024 [miRNA]


title: 301034 [miRNA]


title: 305023 [miRNA]


title: 305013 [miRNA]


title: 303063 [miRNA]


title: 303043 [miRNA]


title: 303013 [miRNA]


title: 303023 [miRNA]


title: 303033 [miRNA]


title: 301063 [miRNA]


title: 301053 [miRNA]


title: 301033 [miRNA]


title: 301043 [miRNA]


title: 309013 [miRNA]


title: 301013 [miRNA]


title: 311062 [miRNA]


title: 311052 [miRNA]


title: 311042 [miRNA]


title: 305063 [miRNA]


title: 311032 [miRNA]


title: 311022 [miRNA]


title: 309052 [miRNA]


title: 311012 [miRNA]


title: 309042 [miRNA]


title: 309032 [miRNA]


title: 309012 [miRNA]


title: 303053 [miRNA]


title: 307062 [miRNA]


title: 309022 [miRNA]


title: 307022 [miRNA]


title: 307032 [miRNA]


title: 307042 [miRNA]


title: 305052 [miRNA]


title: 301023 [miRNA]


title: 305022 [miRNA]


title: 305012 [miRNA]


title: 303062 [miRNA]


title: 305062 [miRNA]


title: 303032 [miRNA]


title: 303012 [miRNA]


title: 305032 [miRNA]


title: 303022 [miRNA]


title: 301022 [miRNA]


title: 301032 [miRNA]


title: 301012 [miRNA]


title: 301062 [miRNA]


title: 311061 [miRNA]


title: 303042 [miRNA]


title: 311021 [miRNA]


title: 311031 [miRNA]


title: 311041 [miRNA]


title: 307012 [miRNA]


title: 311051 [miRNA]


title: 309021 [miRNA]


title: 311011 [miRNA]


title: 309061 [miRNA]


title: 309051 [miRNA]


title: 309041 [miRNA]


title: 307061 [miRNA]


title: 307021 [miRNA]


title: 307031 [miRNA]


title: 309031 [miRNA]


title: 309011 [miRNA]


title: 307051 [miRNA]


title: 301042 [miRNA]


title: 307011 [miRNA]


title: 305061 [miRNA]


title: 305041 [miRNA]


title: 303061 [miRNA]


title: 305011 [miRNA]


title: 305031 [miRNA]


title: 303041 [miRNA]


title: 303051 [miRNA]


title: 301061 [miRNA]


title: 303021 [miRNA]


title: 301031 [miRNA]


title: 303031 [miRNA]


title: 301041 [miRNA]


title: 303052 [miRNA]


title: 301021 [miRNA]


title: 301011 [miRNA]


title: H3K4me1_Pretreated-0h-Macrophage

city: Sapporo

first: Rui

last: Kamada

address: N10 W8, Kita-ku

department: Department of Chemistry, Faculty of Science

country: Japan

institute: Hokkaido University

data_processing:
Resulting reads were aligned to the mouse reference genome (mm10) using BWA(Li H. and Durbin R. (2009)) with default parameters.
Uniquely mapped reads were retained for downstream analysis.
Peak calling was performed using SICER (Bioinformatics 25:1952-1958). SICER was used with window size setting of 200 bp, a gap setting of 600 bp, and FDR setting of 0.001.
Data from immunoprecipitated samples were compared to those with input DNA.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using in-house python code for visualization in the genome browser/IGV.

growth_protocol: MEFs derived from H3.3-HA knockin mice in which the H3f3b locus was replaced by a H3.3-HA cDNA, were cultured on uncoated plastic in DMEM supplemented with 10% of FBS. Bone-marrow derived macrophages derived from H3.3-HA knockin mice  in which the H3f3b locus was replaced by a H3.3-HA cDNA were routinly generated by 10% of L-cell conditioned media in DMEM supplemented with 10% FBS

extract_protocol:
Lisates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using a Mondrian SP (NuGEN Technologies Inc.) and the Ovation SP Ultralow Library system (NuGEN). Fragments ranging from 250 to 450 bp were selected for single-read sequencing on a HiSeq2000 (Illumina).

treatment_protocol: MEF cells were treated with 100 U/ml of Interferon beta. Bone-marrow macrophages were treated with 100 U/ml of Interferon gamma.

tag: cells

value: Bone-marrow derived Macrophages

tag: genotype

value: H3.3-HA knock-in

value: H3K4me1 (ab8895, abcam)


title: HA_Naïve-0h-Macrophage

value: anti-HA (ab9110, abcam)


title: HA_Pretreated-0h-Macrophage


title: H3K36me3_Pretreated-0h-Macrophage

value: H3K36me3 (ab9050, abcam)


title: H3K4me1_Naïve-0h-Macrophage


title: PolII_Pretreated-0h-Macrophage

value: Pol II (8WG16, Covance)


title: PolII_Pretreated-1h-Macrophage


title: Input-Pretreated-1h-Macrophage

value: input


title: PolII_Naïve-1h-Macrophage


title: Input-Pretreated-0h-Macrophage


title: 305021 [miRNA]

value: FVB

value: Wt


title: Input-Naïve-1h-Macrophage


title: 303011 [miRNA]

value: 3 month

value: DBA


title: PolII_Naïve-0h-Macrophage


title: Input-Naïve-0h-Macrophage


title: H3K4me1_Naïve-0h-MEF

value: MEFs


title: H3K4me3_Pretreated-0h-MEF

value: H3K4me3 (ab8580, abcam)


title: H3K4me1_Pretreated-0h-MEF


title: H2AZ_Pretreated-0h-MEF

value: H2AZ (ab4174, abcam)


title: H3K4me3_Naïve-0h-MEF


title: H2AZ_Naïve-0h-MEF


title: H3K36me3_Pretreated-0h-MEF


title: HA_Pretreated-0h-MEF


title: H3K36me3_Naïve-0h-Macrophage


title: H4ac_Naïve-0h-MEF

value: H4ac (06-866, Millipore)


title: H3K36me3_Naïve-0h-MEF


title: PolII_Pretreated-0h-MEF


title: HA_Naïve-0h-MEF


title: PolII_Pretreated-0.5h-MEF


title: Input-Pretreated-0h-MEF


title: PolII_Naïve-0h-MEF


title: Pretreated-4h

data_processing:
Paired-end reads were aligned to the Mus musculus reference genome mm10 using Bowtie/Tophat allowing up to two mismatches.  Transcript abundance was quantified using Cufflinks 1.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include tag count and RPKM values for each Sample.

growth_protocol: MEFs derived from H3.3-HA knockin mice in which the H3f3b locus was replaced by a H3.3-HA cDNA, were cultured on uncoated plastic in DMEM supplemented with 10% of FBS.

extract_protocol:
RNA was harvested from MEFs using Trizol (Invitrogen) and purified by the Rneasy mini kit (Qiagen).
RNA library were prepared for sequencing using standard illumina protocols

treatment_protocol: Cells were treated with 100 U/ml of Interferon-beta

tag: cell type

value: MEF

value: H3.3b-HA knock-in


title: Pretreated-6h


title: Input-Naïve-0.5h-MEF


title: PolII_Naïve-0.5h-MEF


title: Input-Pretreated-0.5h-MEF


title: Pretreated-0h


title: Naïve-6h


title: Input-Naïve-0h-MEF


title: Pretreated-1h


title: Naïve-2h


title: Pretreated-2h


title: Naïve-1h


title: Naïve-4h


title: Naïve-0h


title: Non-immune IgGs

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
The data analysis was carried out as described before (Kim et al, 2017). In brief, raw sequences were aligned to the human reference genome (Ensembl release, version GRCh38) with the software BWA (version 0.7.12; Li and Durbin, 2009).
Overall sequencing quality and absence of contaminants were assessed with the tool FASTqc (version 0.11.2, FASTQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). To compare peaks in regions of interest across different samples, we generated signal tracks by computing the number of fragments found at each genomic position. These values are normalized in millions of reads, to account for the library size, and stored in the bedGraph format. The bedGraph files were subsequently converted to the bigWig format using the UCSC tool begGraphToBigWig (Kent et al., 2010).
To compare peaks in regions of interest across different samples, we generated signal tracks by computing the number of fragments found at each genomic position. These values are normalized in millions of reads, to account for the library size, and stored in the bedGraph format. The bedGraph files were subsequently converted to the bigWig format using the UCSC tool begGraphToBigWig (Kent et al., 2010).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files

source_name: human dermal fibroblasts (HDFs)

extract_protocol:
Chromatin  immune-precipitation  was carried from 15 × 10^6 HDFs as for the ChIP assay with anti-AR  antibody  versus  nonimmune  IgGs.
The  bead-bound chromatin was tagged with Tn5 transposase (Nextera DNA Sample Prep kit, Illumina). The “tagmented” chromatin was de-cross-linked, purified, and amplified (20 cycles) using tag-specific  primers.  The amplified products were subjected to size selection (200-400 bp) and sequenced using Illumina Hi-seq.

value: Non-immune IgGs

value: dermal fibroblast


title: sh_AR_3

data_processing:
Fastq files were  subjected to quality control by means of FastQC.
Trimming was performed with Cutadapt (https://cutadapt.readthedocs.org/en/stable/) to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads.
Alignment was done using STAR (https://github.com/alexdobin/STAR/releases) and reads were counted by means of featureCounts (http://bioinf.wehi.edu.au/featureCounts/), asking for a gene-level report.
During annotation, ENSEMBL gene id and gene symbols were associated to gene-level data. Finally DeSeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) were used to normalize count data, estimate biological variance and determine differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts

source_name: Dermal fibroblasts

extract_protocol:
Total RNA was extracted 7 d after shRNA infection for AR knockdown samples using the  directZol  RNA  miniprep  kit  (Zymo Research) with on-column DNase treatment.
RNA quality  was  verified  on  the bioanalyzer  (Agilent  Technologies) with  an  RNA  integrity  number  greater  than  8.  1μg of total RNA was depleted of Ribosomal RNA using Ribo-zero RNA removal kit (Illumina) and was used for library preparation using the Truseq kit (Illumina)

tag: knockdown

value: shAR

tag: hdf strain


title: sh_AR_2


title: Anti-AR antibody

value: endogenous AR antibody (Santa Cruz Biotechnology)


title: shCTRL_1

value: shRNA control


title: sh_AR_1


title: fetal Klinefelter syndrome 3

city: Copenhagen

first: Kristian

last: Almstrup

address: Blegdamsvej 9, Section GR-5064

department: Dept. of Growth and Reproduction

country: Denmark

institute: Rigshospitalet, Copenhagen University Hospital

data_processing:
Reads were demultiplexed using a custom perl script and adapter sequences trimmed using AdaptorRemoval v1.5 (https://doi.org/10.1186/1756-0500-5-337) with the following command: AdapterRemoval --file1 <(zcat {R1}) --file2 <(zcat {R2}) --basename {basename_out} --trimns --trimqualities --collapse --minquality 2 --stats --mm 3 --minlength 25 --qualitybase 64 --pcr1 AATGATACGGCGACCACCGA --pcr2 CAAGCAGAAGACGGCATACGA --output1 >(gzip > {truncated_1}) --output2 >(gzip > {truncated_2}) --outputstats {stats} --discarded >(gzip > {discarded}) --outputcollapsedtruncated >(gzip > {collapsed_truncated}) --outputcollapsed >(gzip > {collapsed}) --singleton >(gzip > {singleton_truncated})
Reads were mapped to the human reference genome (GRCh38) in which the pseudoautosomal regions on the Y chromosome (PARY; chrY:10001-2781479,chrY:56887903-57217415) were masked using STAR v. 2.5.2b (https://doi.org/10.1093/bioinformatics/bts635) with the following parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate.
Read counts were summarised using HTseq v. 0.6.0 (https://doi.org/10.1093/bioinformatics/btu638) with the following parameters: --stranded=no --minaqual=10
Genome_build: GRCh38 with masked pseudoautosomal regions on the Y chromosome (PARY); chrY:10001-2781479,chrY:56887903-57217415
Supplementary_files_format_and_content: Table of normalized read counts

source_name: Fetal gonad

extract_protocol:
Total RNA was extracted using RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Life Technologies, Naerum, Denmark)
The Ovation Human FFPE RNA-Seq Multiplex Systems 1-8 and 9-16 (NuGEN, Leek, Netherlands) were used for library preparation from 150-200 ng of total RNA according to the manufacturer’s recommendations with the following modifications: following cDNA synthesis, samples were fragmented to yield fragment sizes of approximately 150 bp using the Covaris E210 sonicator (Covaris Ltd., Brighton, UK). Depending on the initial RNA sizes, the samples were either not fragmented or fragmented for 90, 180 or 360 s. For the final library amplification, a primer amount of 6 μL for each sample and 20 cycles of amplification were used. Following library quality assessment using the Agilent High Sensitivity DNA Kit (Agilent technologies), an extra DNA purification was performed with a 1.4 times overload of Agencourt AMPure XP beads (Beckman Coulter, Copenhagen, Denmark) to get rid of adaptors and primers. Following this, the final library was qualified using the Agilent High Sensitivity DNA kit and quantified using the Qubit dsDNA HS Assay Kit (Life Technologies). DNA was pooled in groups of 9 samples with equal amount of each.

tag: weeks of gestation

tag: karytype

tag: fixative

value: Formalin


title: fetal Klinefelter syndrome 2


title: fetal Klinefelter syndrome 1


title: H4ac_Pretreated-0h-MEF

tag: strain

value: H3.3-HA knock-in

tag: chip antibody


title: fetal Normal 6

value: Unknown


title: fetal Normal 5


title: fetal Normal 4


title: fetal Normal 1


title: Individual 29

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

data_processing:
Reads have been aligned to contigs with bwa (version 0.7.12) with standard parameters. Resulting sam files were sorted and indexed with samtools (version 1.1) with standard parameters. Expression counts were generated from the bam files with samtools.
Filtered reads were assembled using DRAP version 1.7 and the Trinity assembler (www.sigenae.org/drap)
Genome_build: Cflum.fas
Supplementary_files_format_and_content: raw counts : comma-separated csv file including count values for each sample / assembly : fasta file

organism: Corbicula fluminea

source_name: Reference site_digestive gland

extract_protocol:
SV Total RNA isolation system kit (Promega) according to manufacturer’s instructions
TruSeq RNA Library Prep Kit v2

tag: location

value: Reference site

tag: tissue

value: digestive gland


title: Individual 31


title: Individual 30


title: Individual 21


title: Individual 20


title: Individual 47

source_name: WWTP_digestive gland

value: WWTP


title: Individual 48


title: shCTRL_2


title: sh_AR_4


title: Individual 46


title: Individual 41


title: Individual 42


title: Individual 25


title: Individual 38


title: Individual 60

source_name: urban runoff_digestive gland

value: urban runoff


title: Individual 63


title: Individual 62


title: Individual 33


title: Individual 55


title: fetal Normal 3


title: Individual 49


title: Individual 50


title: Individual 53


title: Individual 56


title: Individual 23


title: RNA_OIL_66-2

status: Public on Aug 27 2018

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
RNA_OIL_5
RNA isolated for cDNA synthesis

data_processing:
SOLiD 5500 deep sequencer run (single, 50 nt) was performed with single index to generate color-space data in XSQ format.
XSQ files were subjected to analyses using LifeScope software package (Life Technologies), which provided RNA-seq and MBD-seq (as MethylMiner-seq) modules. LifeScope aligned color space read data to ther NCBI37/mm9 mouse genome reference sequence to generate BAM files.
LifeScope processed RNA-seq BAM files to generate normalized amounts of mRNA expression based no the mm9 annotation.
MBD-seq BAM files generated by LifeScope were subjected to analysis using the MEDIPS package of R/bioconductor to generate annotated peaks of DNA methylation. MEDIPS performs normalization using the edgeR package of R/bioconductor.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Microsoft Excel xlsx spreadsheets including normalized relative intensity of mRNA expression and DNA methylation.

source_name: epididymal fat

growth_protocol: CD-1 mice were subjected to timed mating.

extract_protocol:
Epididymal fat was collected from 19-weeks-old males by dissection and subjected to isolation of genomic DNA and total RNA using AllPrep Mini kit (QIAGEN).
Genomic DNA was fragmented to 200-300 bp in length by sonication and subjected to enrichment of methylated DNA fragments using biotinylated, recombinant human methylCpG binding domain 2 (MBD2) protein provided in Invitrogen MethylMiner kit.
Total RNA was subjected to ribosomal RNA removal using RiboMinus Eukaryote System v2 kit (Life Technologies).
DNA fragments enriched for CpG methylation was subjected to deep sequencing library construction using the SOLiD fragment library core kit (Thermo Fisher) and the EZ Bead emulsion PCR system (Life Technologies).
Ribosomal RNA-depleted total RNA was subjected to deep sequencing library construction using the SOLiD Total RNA-seq kit (Thermo Fisher) and the EZ Bead emulsion PCR system (Life Technologies).

treatment_protocol: Pregnant CD-1 mice were exposed to BPA (500 ug/kg/day) or vehicle (corn oil) orally during gestational day 9-18. Pups were fed ad libitum with a standard chow (Purina 5001, 4% fat) and grown until 19 weeks after birth.

tag: Sex

value: male

tag: exposure

value: vehicle

value: epididymal fat


title: RNA_OIL_75-13

description:
RNA_OIL_6
RNA isolated for cDNA synthesis


title: fetal Klinefelter syndrome 7


title: RNA_OIL_38-6

description:
RNA_OIL_3
RNA isolated for cDNA synthesis


title: RNA_OIL_181-11

description:
RNA_OIL_2
RNA isolated for cDNA synthesis


title: RNA_OIL_124-9

description:
RNA_OIL_1
RNA isolated for cDNA synthesis


title: RNA_BPA_46-5

description:
RNA_BPA_5
RNA isolated for cDNA synthesis

value: 500 ug/kg/day prenatal BPA


title: RNA_OIL_39-8

description:
RNA_OIL_4
RNA isolated for cDNA synthesis


title: RNA_BPA_87-12

description:
RNA_BPA_6
RNA isolated for cDNA synthesis


title: RNA_BPA_220-3

description:
RNA_BPA_4
RNA isolated for cDNA synthesis


title: Individual 37


title: RNA_BPA_101-9

description:
RNA_BPA_1
RNA isolated for cDNA synthesis


title: Individual 22


title: MBD_OIL_75-13

description:
MBD_OIL_6
DNA for CpG methylome analysis


title: MBD_OIL_66-2

description:
MBD_OIL_5
DNA for CpG methylome analysis


title: RNA_BPA_102-6

description:
RNA_BPA_2
RNA isolated for cDNA synthesis


title: RNA_BPA_195-7

description:
RNA_BPA_3
RNA isolated for cDNA synthesis


title: MBD_OIL_39-8

description:
MBD_OIL_4
DNA for CpG methylome analysis


title: MBD_OIL_181-11

description:
MBD_OIL_2
DNA for CpG methylome analysis


title: MBD_OIL_38-6

description:
MBD_OIL_3
DNA for CpG methylome analysis


title: MBD_OIL_124-9

description:
MBD_OIL_1
DNA for CpG methylome analysis


title: MBD_BPA_46-5

description:
MBD_BPA_5
DNA for CpG methylome analysis


title: MBD_BPA_102-6

description:
MBD_BPA_2
DNA for CpG methylome analysis


title: MBD_BPA_101-9

description:
MBD_BPA_1
DNA for CpG methylome analysis


title: MBD_BPA_195-7

description:
MBD_BPA_3
DNA for CpG methylome analysis


title: G.HB.I.20

status: Public on Aug 26 2018

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

country: China

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

data_processing:
Reads quality was examined by “fastQC”
Filtered reads were aligned to rhesus monkey genome database (AV et al. 2014) by tophat v2.1.0
Only uniquely mapped reads were used to calculate the counts of each gene by HTSeq (Anders et al. 2015).
Reads counts were normalized to library size by DESeq2 , and normalized reads were then used for calculate the FPKM (Fragments Per Kilobase of transcript per Million fragments mapped).
Genome_build: MacaM
Supplementary_files_format_and_content: Contains the expression level of each gene in all samples, measured by FPKM

organism: Macaca mulatta

source_name: hatcded blastocyst, inner cell

growth_protocol: Cycling female monkeys were ovarian stimulated by injection of rhFSH (recombinant human follitropin alfa, GONAL-F, Merck Serono) 18 IU twice-daily for 8 days from the onset of menstrual cycle. On day 9, 1000 IU of rhCG (recombinant human chorionic gonadotropin alfa, OVIDREL, Merck Serono) was injected. After 32–35 hr of rhCG administration, mature oocytes were collected by laparoscopic follicular aspiration 63. Oocytes were removed of cumulus cells and those with extrusion of the first polar body (metaphase II stage) were collected for downstream experiments. Successful fertilization was assessed by the presence of two pronuclei. Embryos were then cultured at 37℃, 5% CO2 in 50 μl drops of equilibrated HECM-9 containing 10% FBS (HyClone Laboratories Inc.). Culture medium was changed every other day. Morphologically normal embryos with few fragments were used in the study. 16-cell embryos with good morphology were collected at about E3. Early morulae with compacted blastomeres were collected at about E4. Late morulae with more blastomeres were collected at about E4.5. Early blastocysts having a small cavity were collected at about E5. Middle blastocysts with a cavity occupying around half size of embryos were collected at about E5.5. Late blastocysts with fully expanded cavity were collected at about E6. Hatched blastocysts from the zona pellucida were collected at about E7.

extract_protocol:
To collect single blastomeres, embryos with good quality were transferred into 0.5% Pronase in TL-HEPES to remove zona pellucida, followed by three washes in PVP-BSA. To distinguish the outer and inner cells, embryos were incubated with PKH2 dye (Sigma) which labels the live outer cells with red fluorescence. After labeling, embryos were rinsed with Ca2+/Mg2+ free PVP-PBS and treated with 0.125% trypsin-EDTA for at least 5 min at 37℃ until the cell surface looks rough. Disaggregating was done by a mouth pipette aided by several finely pulled glass capillaries of different internal diameter. After most cells were separated apart, single cells were individually transferred into small droplets of PVP-PBS and the inner/outer cell identity was identified by the fluorescent microscopy. Cells showing no fluorescence were inner cells, whereas those with red fluorescence were outer cells.
Briefly, single cells were washed three times in PVP-PBS and those with a clear round shape were added into cell lysis buffer, followed by cDNA synthesis, primer removal, poly(A) tailing, second-strand cDNA synthesis, and PCR amplification. PCR products were purified by Ampure XP beads and used for libraries construction.
Libraries were deep sequenced on Illumina HiSeq 2500 platform, using 100-bp single-end strategy.

tag: Stage

value: HB

tag: position

value: Inner


title: G.HB.I.16


title: G.HB.I.10


title: G.HB.I.05


title: G.HB.I.15


title: G.HB.I.11


title: Prdm16 ChIP-Seq

city: Boston

first: Yi

last: Chen

state: Massachusetts

address: 450 Brookline Ave CLS 11116

institute: Dana-Farber Cancer Institute

data_processing:
Raw reads were mapped with the mapping tool in the CLC Genomics Workbench software.
Peaks were called with the model-based analysis for ChIP-seq (MACS) method, and the P-value threshold was set at 0.05.
Subsequent analyses, including genomic distribution, peak set overlap, and transcription factor motif enrichment, were performed with tools on the DFCI Galaxy Cistrome Web site
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: interscapular brown adipose tissue

extract_protocol:
BAT from 10–15 mice (male, 8–10 wk old) were dissected and homogenized with a douncer. Paraformaldehyde was added to the homogenate to 1% final concentration. Homogenization was performed prior to cross-linking because it is difficult to collect mature brown adipocytes by centrifugation. The homogenate was then quenched with 125 mM glycine, and the nuclei were collected  by centrifugation. The nuclei were lysed with lysis buffer (1% SDS, 50 mM Tris-HCl, 10 mM EDTA at pH 8.0) and sonicated to yield an average size of DNA fragment of 150–200 base pairs (bp). The lysate was diluted 10-fold with a dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl at pH 8.0) and incubated with the desired antibody overnight. The protein–DNA complex was isolated with protein G Dynabeads, washed, and eluted off the beads. The eluent was treated with RNase A and proteinase K before reversing crosslinking.DNA was then harvested by ethanol precipitation.
The library was prepared with the NEBNext ChIP-seq library preparation master mix set for Illumina (New England Biolabs, E6240S).

value: Prdm16 antibody R&D Systems (AF6295)

tag: developmental stage

value: 8-12 week


title: G.LB.I.22

value: LB


title: G.LB.I.27


title: G.HB.I.02


title: MBD_BPA_87-12

description:
MBD_BPA_6
DNA for CpG methylome analysis


title: G.LB.I.16


title: MBD_BPA_220-3

description:
MBD_BPA_4
DNA for CpG methylome analysis


title: G.LB.I.04


title: H.LB.I.15


title: H.LB.I.14


title: H.HB.I.15


title: H.HB.I.11


title: H.HB.I.14


title: G.LB.I.03


title: H.HB.I.07


title: H.HB.I.05


title: H.HB.I.09


title: H.HB.I.10


title: H.HB.I.01


title: H.HB.I.03


title: G.LB.I.06

source_name: later blastocyst, inner cell


title: G.HB.I.14


title: G.LB.I.02


title: H.LB.I.09


title: G.LB.I.20


title: G.LB.I.09


title: G.LB.I.12


title: G.LB.I.14


title: G.LB.I.18


title: G.LB.I.23


title: H.LB.I.03


title: H.MB.I.10

source_name: middle blastocyst, inner cell

value: MB


title: G.MB.I.10


title: H.MB.I.05


title: H.MB.I.03


title: H.MB.I.09


title: G.MB.I.03


title: G.LB.I.11


title: G.EB.I.11

source_name: early blastocyst, inner cell

value: EB


title: G.MB.I.04


title: G.MB.I.02


title: H.EB.I.05


title: G.EB.I.13


title: H.EB.I.03


title: B.MB.I.06


title: B.MB.I.03


title: B.MB.I.02


title: B.MB.O.06

source_name: middle blastocyst, outer cell

value: Outer


title: B.MB.O.03


title: B.MB.O.07


title: G.EB.I.18


title: B.MB.O.01


title: A.EB.I.07


title: A.EB.I.10


title: B.MB.I.05


title: A.EB.I.03


title: B.MB.O.02


title: A.EB.I.05


title: A.EB.I.08


title: A.EB.O.10

source_name: early blastocyst, outer cell


title: A.EB.O.08


title: A.EB.O.09


title: CRE-seq pCrx DNA replicate 3

city: St. Louis

first: Joseph

last: Corbo

address: 660 S. Euclid

institute: Washington University School of Medicine

description:
oligos.txt
counts.txt
sf.txt
expression.txt
lfc.txt

data_processing:
Library strategy: amplicon seq
Reads were demultiplexed with ea-utils (v1.02.772).
Barcodes were identified by exact matches to designed barcodes (see oligos.txt), including exact matches to 22 bp of upstream sequence (CCTGAGGAGTGCGGCCGC) and 4 bp of downstream sequence (GGTA). Barcode counts for each sample are provided (counts.txt).
RNA and DNA barcode counts were pseudocounted (+1) and scaled separately using the median ratio method (Anders and Huber, Genome Biol 2010) (see size_factors.txt for size factors). Barcodes with <5 scaled DNA counts for any sample were removed, and targeted elements with <5 barcodes were removed. For each targeted element, activity was estimated as the log2 of cDNA counts (summed over barcodes) over DNA counts (summed over barcodes). Finally, activity values were quantile normalized across replicates of each condition (pRho or pCrx).
A Welch's t-test was used to test for differential activity between wild-type and variant constructs.
Genome_build: mm9
Supplementary_files_format_and_content: oligo table: tab-delimited file. bc: 13-bp barcode. id.oligo: target element name (including mm9 coordinates of 200 bp parent ChIP-seq peak). seq.alt: target element sequence (central 100 bp of region indicated in id.oligo). seq.wt: sequence of corresponding wild-type element. pos.alt: comma-separated list of variant positions. ref: wild-type nucleotides at indicated position(s) ("." denotes insertion). alt: variant nucleotides at indicated position(s) ("." denotes deletion).
Supplementary_files_format_and_content: barcode count table: tab-delimited file. bc: 13-bp barcode. id.oligo: target element name (including mm9 coordinates of 200 bp parent ChIP-seq peak). Additional columns: cDNA or DNA counts for each sample.
Supplementary_files_format_and_content: size factors: tab-delimited file. sample: sample ID. size_factor: size factor used to scale raw counts.
Supplementary_files_format_and_content: normalized expression: tab-delimited file. id.cre: target element name (including mm9 coordinates of 200 bp parent ChIP-seq peak). Additional columns: normalized expression values for each sample.
Supplementary_files_format_and_content: differential expression: tab-delimited file. id.cre: target element name (including mm9 coordinates of 200 bp parent ChIP-seq peak). Condition: promoter used for assay (pRho or pCrx). median.wt: median expression for wild-type constructs. median.alt: median expression for variant constructs. lfc: log2 fold change (median.alt-median.wt). p.value: p-value for Welch's t-test comparing wild-type and variant expression values. p.adj: adjusted p-value (Benjamini-Hochberg). Additional columns: normalized expression values for each sample.

source_name: Explant retina

growth_protocol: Intact retinas were harvested from newborn (P0) CD1 pups and electroporated with 30 micrograms of CRE-seq plasmid library (either pRho or pCrx) and 30 micrograms of CAG-GFP as described previously (Kwasnieski et al. PNAS 2012). Retinas were grown in culture for eight days and then harvested and stored in TRIzol at -80 C. Five retinas were pooled for each biological replicate, and three replicates were performed for each condition (i.e., each promoter).

extract_protocol:
RNA and DNA were isolated from TRIzol according to manufacturer instructions. RNA was treated with TURBO DNase and cDNA synthesis was performed with SuperScript IV using an oligo(dT) primer.
197 bp amplicons (including barcodes) were amplified from cDNA and DNA samples by PCR (Phusion Hot Start Flex 2X Master Mix, 21 cycles) using the following primers: ACACTCTTTCCCTACACGACGCTCTTCCGATCTGATAGGCAGCCTGCACCTGAGGAGT (F), and AGACGTGTGCTCTTCCGATCTGTCCATCTACATGGCCAAGAAGCCC (R). PCR products were purified with a minElute PCR Purification Kit, and indexed Illumina adapters were added with an additional 6 cycles of PCR using the following primers: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (F), and CAAGCAGAAGACGGCATACGAGATNNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA (R). PCR products were purified with a PureLink PCR Purification kit and sequenced on an Illumina HiSeq 3000 (1x50 reads).

tag: age

value: postnatal day 0

value: WT


title: CRE-seq pCrx DNA replicate 2

tag: genotype


title: CRE-seq pCrx cDNA replicate 2


title: CRE-seq pCrx DNA replicate 1


title: A.EB.O.05


title: A.EB.O.02


title: CRE-seq pRho cDNA replicate 3


title: CRE-seq pCrx cDNA replicate 3


title: CRE-seq pRho DNA replicate 3


title: D.LM.I.10

source_name: later morula, inner cell

value: LM


title: CRE-seq pCrx cDNA replicate 1


title: CRE-seq pRho cDNA replicate 1


title: CRE-seq pRho cDNA replicate 2


title: CRE-seq pRho DNA replicate 1


title: D.LM.I.07


title: D.LM.I.04


title: D.LM.O.06

source_name: later morula, outer cell


title: D.LM.O.01


title: CRE-seq pRho DNA replicate 2


title: D.LM.O.10


title: D.LM.O.05


title: H.EM.I.08

source_name: early morula, inner cell

value: EM


title: H.EM.I.04


title: H.EM.I.05


title: D.LM.O.03


title: A.EB.O.06


title: H.EM.I.03


title: H.EM.O.06

source_name: early morula, outer cell


title: H.EM.O.05


title: H.EM.O.04


title: D.LM.I.08


title: H.EM.I.02


title: H.EM.O.03


title: H.EM.O.02


title: B.16C.O.01

source_name: 16-cell stage, outer cell


title: D.LM.I.01


title: B.16C.O.09


title: P4_10: Day 30 Lesion 3

status: Public on Aug 25 2018

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

description: library of 96 cells day 30, lesioned mouse 3

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The 50bp right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The 50bp left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for quantification.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Text files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: ventral pons, ipsilateral neurodegeneration, right

growth_protocol: SPF mouse facility

extract_protocol:
Isolated microglial cells were stained with antibodies against CD45, CD11b and MHC Class II and single cells were FACS-sorted using BD Influx in 384-well plates.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: unilateral facial nerve axotomy at the right stylomastoid foramen

tag: transgenic line

value: brain

value: 12 weeks


title: P4_9: Day 30 Control 3

description: library of 96 cells day 30, control mouse 3

source_name: ventral pons, contralateral, left


title: B.16C.O.02


title: P4_5: Day 7 Control 3

description: library of 96 cells day 7, control mouse 3


title: P3_3: Day 7 Lesion 2

description: library of 96 cells day 7, lesioned mouse 2


title: P3_4: Day 0 Control 3

description: library of 96 cells day 0, control mouse 3


title: P2_10: Day 30 Lesion 2

description: library of 96 cells day 30, lesioned mouse 2


title: P2_8: Day 30 Lesion 1

description: library of 96 cells day 30, lesioned mouse 1


title: P2_9: Day 30 Control 2

description: library of 96 cells day 30, control mouse 2


title: P2_7: Day 0 Control 2

description: library of 96 cells day 0, control mouse 2


title: P1_3: Day 7 Lesion 1

description: library of 96 cells day 7, lesioned mouse 1


title: P3_2: Day 7 Control 2

description: library of 96 cells day 7, control mouse 2


title: P1_1: Day 0 Control 1

description: library of 96 cells day 0, control mouse 1


title: B.16C.I.01

source_name: 16-cell stage, inner cell


title: B.16C.I.02


title: GT added high-fat diet_mRNA_liver_2

city: Gwangju

first: Ji-Young

last: Choi

address: 30, Chosundae 3-gil, Dong-gu

department: Food and Nutrition

country: South Korea

institute: Chosun University

description: Sample name: L_GT_2

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
Mapped to M. musculus whole genome using STAR v2.4.0
Transcripts were assembled and quantitated using Cufflinks v2.1.1
Genome_build: M. musculus Ensembl 72
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "ND","HFD" and "GT" samples.

source_name: Mouse liver

growth_protocol: Thirty male C57BL/6J mice (four-week-old, male) were obtained from the Jackson Laboratories (Bar Harbor, ME, USA). All mice were individually housed under a constant temperature (24°C) and 12-h light/dark cycle and, fed a normal chow diet for acclimation for 1 week after arrival.

extract_protocol:
Total RNA was extracted from the adipose tissue using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
Libraries were constructed from mRNA using the Illumina TruSeq RNA Sample Prep Kit following  manufacturer's protocols.

treatment_protocol: At 5 weeks of age, they were randomly divided into 3 groups of 10 mice per each group and fed a normal diet (ND), high-fat diet (HFD), HFD + 0.25% (w/w) green tea ethanol extract (GT) for 12 weeks

tag: gender

value: male

value: 17 weeks

value: liver


title: P4_8: Day 7 Lesion 3

description: library of 96 cells day 7, lesioned mouse 3


title: GT added high-fat diet_mRNA_liver_3

description: Sample name: L_GT_3


title: GT added high-fat diet_mRNA_liver_1

description: Sample name: L_GT_1


title: HCC70_shRNA_FOXA1_1

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

data_processing:
Read data demultiplxing & mapping was done using the CELseq pipeline script https://github.com/yanailab/CEL-Seq-pipeline
UMI correction was done using the formula transcript # = -(4^umi_length)*ln(1-(umi_count/umi_length) to convert UMI into transcript
Transcript data was grouped from two sequencing runs to form a single matrix
Data was normalized into transcripts per million (tpm) by dividing the number of each transcripts for each gene with the total number of transcripts for the sample and multiply by 500K
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: HCC70  breast cancer cell line

growth_protocol: Cell lines were obtained from ATCC. HCC70 cells were grown in 96 well plates with RPMI medium containing 10% FBSand supplemented with penicillin and streptomycin.

extract_protocol:
RNA was extracted using the Single Cell RNA Purification Kit (Norgen) and 3’ cDNA was synthesized and barcoded in batches of 12 samples, followed by RNA synthesis and amplification by in vitro transcription based on the CELseq protocol DOI: 10.1186/s13059-016-0938-8. Some samples were ran a second time due to low representation in the first run.
Libraries were prepared and libraries were prepared and sequenced using Illumina’s RNA sequencing protocol.

treatment_protocol: Cells were infected with the indicated shRNA or treated as indicated

tag: cell line

tag: shRNA id/treatment


title: High-fat diet_mRNA_liver_1

description: Sample name: L_HFD_1


title: High-fat diet_mRNA_liver_2

description: Sample name: L_HFD_2


title: Normal diet_mRNA_liver_3

description: Sample name: L_ND_3


title: Normal diet_mRNA_liver_2

description: Sample name: L_ND_2


title: HCC70_shRNA_shLUC_1


title: HCC70_shRNA_shLUC_2


title: P3_1: Day 0 Control 3


title: P1_6: Day 30 Control 1

description: library of 96 cells day 30, control mouse 1


title: Normal diet_mRNA_liver_1

description: Sample name: L_ND_1


title: P1_2: Day 7 Control 1

description: library of 96 cells day 7, control mouse 1


title: GT added high-fat diet_mRNA_adipose_2

description: Sample name: e_GT_2

source_name: Mouse Epididymal adipose tissue

value: epididymal adipose tissue


title: HCC70_shRNA_shLACZ_1


title: HCC70_shRNA_shRFP_2


title: GT added high-fat diet_mRNA_adipose_1

description: Sample name: e_GT_1


title: HCC70_shRNA_shRFP_1


title: High-fat diet_mRNA_adipose_3

description: Sample name: e_HFD_3


title: High-fat diet_mRNA_liver_3

description: Sample name: L_HFD_3


title: HCC70_shRNA_FOXA1_2


title: High-fat diet_mRNA_adipose_2

description: Sample name: e_HFD_2


title: HCC70_shRNA_RBPJ_2


title: HCC70_shRNA_NFIB_1


title: High-fat diet_mRNA_adipose_1

description: Sample name: e_HFD_1


title: HCC70_shRNA_RBPJ_1


title: Normal diet_mRNA_adipose_3

description: Sample name: e_ND_3


title: HCC70_shRNA_KLF5_1


title: Normal diet_mRNA_adipose_2

description: Sample name: e_ND_2


title: HCC70_shRNA_KLF5_2


title: HCC70_shRNA_shLACZ_2


title: Normal diet_mRNA_adipose_1

description: Sample name: e_ND_1


title: GT added high-fat diet_mRNA_adipose_3

description: Sample name: e_GT_3


title: HCC70_shRNA_plko_2


title: HCC70_shRNA_plko_1


title: MDA-MB-468_K14

description:
MDA-MB-468 cells positive for Keratin18+Keratin14
468-K14_TAGCTT

data_processing:
Reads were trimmed using FastX
Reads were mapped to Human genome  using TopHat2
Quantification of reads was done using cuffquant
Flooring set to 0.1 FPKM
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: [.txt] Tab-delimited text file includes FPKM values for each sample

growth_protocol: Cell lines were obtained from ATCC. HCC70 cells were grown in RPMI medium containing 10% FBS, and MDA-MB-468 cells in Leibovitz L15 medium containing 10% FBS and supplemented with penicillin and streptomycin.

extract_protocol:
To extract RNA from fixed and stained cell subpopulations isolated by FACS from cell lines and mRNA was extracted using the Recover All Total Nucleic Acid Isolation Kit (Ambion).
Libraries were prepared and libraries were prepared and sequenced using Illumina’s RNA sequencing protocol

treatment_protocol: For staining of cells for differentiation markers by FACS, the cells were detached by trypsin-EDTA, fixed and permeabilized for 10 min in 100% methanol on ice, and stained with antibodies against K18 (sc-31700, Santa Cruz), K14, and vimentin (NCL-L-VIM- V9, Novocastra), followed by conjugated secondary antibodies.

value: MDA-MB-468 breast cancer cell line

tag: cell population

value: Keratin 18+ Keratin14+


title: MDA-MB-468_K18

description:
MDA-MB-468 cells positive for Keratin18
468-K18_GATCAG

value: Keratin 18+


title: HCC70_K18_VIM

description:
HCC70 cells positive for Keratin18+Vimentin
HCC70-Vim_GTGAAA

value: HCC70 breast cancer cell line

value: Keratin 18+ Vimentin+


title: HCC70_K18_14

description:
HCC70 cells positive for Keratin18+Keratin14
HCC70-K14_GTCCGC


title: G.HB.I.06

source_name: hatcded blastocyst, inner cell

value: HB

value: Inner


title: HCC70_K18

description:
HCC70 cells positive for Keratin18
HCC70-K18_GTGAAA


title: Gilzflox/flox UBC-CreER (TAM-KO) spermatogonia rep 4

status: Public on Aug 24 2018

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

institute: Hudson Institute of Medical Research

data_processing:
Used RNAsik pipeline to bam, counts and gather different metrics on RNAseq data https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe
Used Degust  to analysis table of counts, output form RNAsik. Degust is a webapp that uses either edgeR or limma-voom for differential gene analysis http://degust.erc.monash.edu
Genome_build: Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
Supplementary_files_format_and_content: raw counts file was generated by featureCounts, which than was uploaded to Degust

source_name: TAM-KO

growth_protocol: Adult transgenic mice (6-8 weeks old) containing both Gilzflox/flox (Control) and Gilzflox/flox UBC-CreER (TAM-KO) were injected for two consecutive days with 2mg Tamoxifen (Sigma) in sesame oil intraperitoneally and harvested after 7 days.

extract_protocol:
Sorted cells were lysed in TRIzol LS reagent (Thermo Fisher Scientific) then RNA was purified and DNase treated using a Direct-zol RNA Microprep kit (Zymo Research).
SPIA libraries: - Nugen Ovation RNA-Seq system V2 (for SPIA amplifications  and cDNA generation) using Nugen protocol M01206v5, 2013; followed by  Ovation Ultralow System V2 (for rest of library preparation) using Nugen protocol  M01379v1, 2014.

treatment_protocol: Testis cell suspensions were prepared by a standard two step digestion protocol with collagenase and trypsin. Cells were sorted on a BD Influx Cell Sorter (BD Biosciences). The undifferentiated population was gated according to expression of E-cadherin and surface markers c-Kit and CD49f. E-cadherin is a well-established marker of undifferentiated spermatogonia plus cells at early differentiation stages. c-Kit marks differentiating spermatogonia and CD49f is enriched on functional stem cells. Undifferentiated cells were initially sorted for E-cadherin positive then isolated by CD49f positive and c-Kit negative.

value: mixed C57BL/6 x CBA

value: Testis

tag: genotype/variation

value: TAM-KO


title: 02A10-9 rep1

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Magnaporthe oryzae 70-15 (MG8) whole genome using tophat 2.0.8b with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: MG8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Pyricularia oryzae

source_name: Mycelium

growth_protocol: The strains were cultured in liquid CM medium at 25˚C with shaking at 180 rpm for 2 d

extract_protocol:
Total RNA was extracted from ground mycelia in liquid nitrogen with RNeasy Plant mini kit (QIAGEN)
RNA libraries were prepared for sequencing using NEBNext RNA sample preparation kit (NEB) with standard Illumina protocols

treatment_protocol: The mycelia were collected and incubated in H2O at 25˚C for 4 h

tag: strain

value: Mycelia under starvation


title: 02A10-9 rep3


title: Gilzflox/flox UBC-CreER (TAM-KO) spermatogonia rep 3


title: Gilzflox/flox (Control) spermatogonia rep 2

source_name: Control

value: Control


title: Gilzflox/flox UBC-CreER (TAM-KO) spermatogonia rep 2


title: Gilzflox/flox (Control) spermatogonia rep 4


title: WT rep3 (3)

value: wild type


title: WT rep1 (3)


title: 02A10-9 rep2


title: Gilzflox/flox (Control) spermatogonia rep 1


title: Gilzflox/flox (Control) spermatogonia rep 3


title: Gilzflox/flox UBC-CreER (TAM-KO) spermatogonia rep 1


title: DEX-1

first: Renyi

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Arabidopsis thaliana genome sequence (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/MASKED/ler_0.v7.PR_in_lowercase.fas) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (readss per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 6 Samples .

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Arabidopsis is grown in growth room at 23C under Longday condition (16 h light/8 h dark)

extract_protocol:
The inflorescences were dissected under a stereomicroscope to remove flowers of stage 7 or older, and RNA was isolated with Transzol reagent (TransGen Biotech).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 uM DEX dissolved in DMSO, along with 0.015% Silwet L-77,is used to treat the inflorescences of 3-week-old indicated plants.

value: three-week old plant

value: floral meristems

value: ARF3:ARF3-GR arf3-29


title: MDA-MB-468_VIM

description:
MDA-MB-468 cells positive for Keratin18+Vimentin
468-Vim_GGCTAC


title: DEX-3


title: DMSO-2


title: DMSO-3


title: Vehicle_1d_NN_IP_Rep2

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

data_processing:
library strategy: TempO-Seq (Templated Oligo assay with Sequencing readout)
Sequencing was performed using a 50 cycle single-end read flow cell on a NextSeq 550 Sequencing System (Illumina, San Diego, CA, united States). Processing of sequencing data was conducted using Illumina’s BCL2FASTQ software employing default parameter settings.  Sequencing data were demultiplexed to generate fastq files.
We require that >=75% of the reads have an average quality score >=QC30.  The sequences were then filtered for Illumina p5 and p7 adaptors.
Bowtie2-2.1.0
Aligned to a pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos). Indels not allowed.  Up to 2 base pair mismatches  allowed. Multimapping sequences not allowed.
The counts were summarized using QuasR version 1.8.4.
Genome_build: pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos)
Supplementary_files_format_and_content: tab-delimited text file with read count per gene

extract_protocol:
Livers were harvested 24 hours after the last dose as 100 mg punches using six millimeter disposable biopsy punches. An appropriately staggered schedule was employed so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.  Automated RNA isolation was performed according to the manufacture’s protocol using the RNeasy Kit from Qiagen (Germantown, MD).
The sequencing library for the rat liver RNA samples was prepared by BioSpyder (BioSpyder Technologies, Inc., Carlsbad, CA, United States) according to their protocol  guidelines. One μl of each RNA sample (500-660 ng/uL) was hybridized with the S1500+ beta detector oligo pool mix (2 μl per sample) using the following thermocycler settings: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, and ending with 45°C for 1 min. Hybridization was followed by nuclease digestion (24 μl nuclease mix addition followed by 90 min at 37°C), ligation (24 μl ligation mix addition followed by 60 min at 37°C, then heat denaturation at 80°C for 30 min).. Ten microliters of each ligation product were then transferred to a 96-well PCR amplification microplate that also contained 10 μl of PCR mix per well. Through amplification well-specific, “barcoded” primer pairs were introduced to templates. Five microliters of the PCR amplification products from each well were then pooled into a single sequencing library. The TempO-Seq library was then processed with a PCR clean-up kit (Machery-Nagel, Mountain View, CA, United States) prior to sequencing.

treatment_protocol: Male Sprague-Dawley rats (aged 6–8 weeks and weighing 200–260 g) were dosed once daily in triplicate for 3, 5, or 7 days, depending on the test chemical.

value: Sprague-Dawley

tag: animal id

value: Male

value: 6-8 weeks

value: Liver

tag: compound

value: VEHICLE CONTROL

tag: compound abbreviation

tag: moa

tag: dose (mg/kg)

tag: duration (days)

tag: vehicle

value: SALINE %

tag: nutritive status

value: Non nutritive

tag: route

value: ORAL GAVAGE

tag: sample id


title: Vehicle_1d_NN_IP_Rep4

tag: Sex

tag: age

tag: tissue

tag: exposure


title: DMSO-1

tag: genotype


title: Vehicle_3d_NN_IP_Rep5


title: Vehicle_7d_NU_OG_Rep6

value: CORN OIL %

value: Nutritive


title: Vehicle_1d_NU_OG_Rep1


title: Vehicle_1d_NN_IP_Rep1


title: WT rep2 (3)

tag: developmental stage


title: Vehicle_1d_NN_IP_Rep3

tag: strain


title: DEX-2


title: 48h_10C

city: Pozuelo de Alarcón

first: Manuel

last: Pineiro

address: Autopista M-40, Km 38

institute: Centro de Biotecnologia y Genomica de Plantas (CBGP)

data_processing:
The original image data produced by the sequencer (Illumina HiSeq2000) is transferred into sequences, which are defined as “raw reads” (or “raw data”) and saved as “.fastq” files.
Raw data was cleaned removing adaptor sequences, reads with a percentage of unknown Ns greater than 10% and low quality reads (reads with >50% bases with quality index <5). Clean reads were saved as ".fastaq" files
Reads were mapped to reference tomato genome ITAG2.3 release using SOAP2 software (Li et al, 2009). No more than two mismatches per read were allowed
The gene expression level was calculated using the RPKM method (Mortazavi et al, 2008) using uniquely mapped reads.
Genome_build: ITAG2.3
Supplementary_files_format_and_content: Text files includes the number of uniquely mapped clean reads  and the corresponding estimation of expression level (RPKM) for each gene model .

organism: Solanum lycopersicum

source_name: 1st pair of true leaves

growth_protocol: Tomato seeds were germinated in the dark at 25°C for 5 days before planting in universal substrate (COMPO, GmbH). Seedlings were grown for 16 days in a growth chamber set at 25°C with a 12h photoperiod (day/night) and a photosynthetically active radiation of 100 µmol m-2 s-1.

extract_protocol:
Leaf tissue was sampled, inmediately frozen on liquid nitrogen and stored at -80C. For total RNA extraction, frozen tissue was homogenized to a fine powder and total RNA was extracted using TRIzol® Reagent (Life Technologies), treated with DNaseI (Roche) and further purified with RNeasy Plant Mini Kit (Quiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three-weeks-old tomato seedlings were incubated at 10°C with a 12h photoperiod (day/night) and a photosynthetically active radiation of 40 µmol m-2 s-1 for the indicated periods of time.

tag: cultivar

value: Moneymaker

value: Three-weeks-old plants

tag: exposed to

value: suboptimal growth temperature (10C) for 48h

value: 1st pair of true leaves


title: RNA ΔH4.V R1

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description: ERCC spike-in added

data_processing:
Cutadapt
Read mapping with BWA mem (BWA version 0.7.12)
Counting of read per feature with bedtools intersect (bedtools version 2.25.0)
Genome_build: Tb427v8 (the genome was assembled as part of this study)

organism: Trypanosoma brucei brucei

source_name: whole liquid cell culture

growth_protocol: All replicates were grown in HMI-11 (37 °C, 5% CO2) to a maximum of 1x10^6 cells/ml. Drug selection after transfection was applied if necessary.

extract_protocol:
Total RNA from 45 million cells was extracted in triplicates (NucleoSpin RNA, Macherey & Nagel) and spiked with a synthetic RNA control (ERCC, invitrogen). rRNA was depleted from the sample using custom-made anti-rRNA oligos that were hybridized to the targed RNA and subsequently digested with RNAseH. Residual DNA was digested away with a DNAse and the sample was purified using RNeasy Minelute columns (Qiagen).
Libraries were prepared as follows: cDNA was produced from 100 ng of rRNA depleted RNA using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® until second strand cDNA synthesis. The double-stranded cDNA was purified using Agencourt AMPure XP Beads and eluted in 0.1X TE Buffer. cDNA was end-repaired using T4 DNA polymerase (NEB),
Klenow large Fragment (NEB) and  T4 DNA Polynucleotide Kinase (NEB). Protruding A-bases were added to the 3` end using  Klenow fragment (3´ to 5´ exo minus) and dATP. TruSeq adapters were ligated to the cDNA fragments using Quick Ligase (NEB) and was purified using AMPure XP magnetic beads. Y-shaped adapters were converted to dsDNA with Illumina primers for 5 cycles, purified with magnetic beads  and library fragments of 200-500 bp were size selected from an agarose gel. The gel-purified library was further amplified for 10-17 cycles using Illumina primers and purified using magnetic beads. Libaries were quantified using Qubit and qPCR and were sequenced on an Illumina flow cell  in an Illumina NextSeq aparatus following the manufacturer's instructions

value: Lister 427 MITat 1.2 single marker

tag: life cycle stage

value: Bloodstream form


title: RNA ΔH4.V R3

description: ERCC spike-in added


title: RNA wild-type R3

description: ERCC spike-in added

value: Lister 427 MITat 1.2

value: wild-type


title: RNA wild-type R2

description: ERCC spike-in added


title: RNA ΔH4.V R2

description: ERCC spike-in added


title: RNA ΔH3.V/ΔH4.V R2

description: ERCC spike-in added


title: RNA ΔH3.V R2

description: ERCC spike-in added


title: RNA ΔH3.V R3

description: ERCC spike-in added


title: 3h_10C

value: suboptimal growth temperature (10C) for 3h


title: 24h_10C

value: suboptimal growth temperature (10C) for 24h


title: 0h_10C

value: suboptimal growth temperature (10C) for 0h


title: RNA ΔH3.V/ΔH4.V R1

description: ERCC spike-in added


title: RNA ΔH3.V/ΔH4.V R3

description: ERCC spike-in added