title: Cotyledon (300-400 mg) Control mRNA-Seq biorep 2

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: mRNA-Seq

data_processing:
Standard Illumina pipeline including CASSAVA
The raw data were preprocessed to remove low quality reads, clip adapter sequences, and remove rDNA sequences
Sequenced reads were aligned to Glyma cDNA models from the current assembly Sequenced reads were aligned to Glyma cDNA models from the current assembly Wm82.a2 from Phytozome (Joint Genome Institute) of the Williams 82 genome determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009).
Bowtie parameters allowed no mismatches and up to 25 alignments per read. The total hit counts to each of the 88,515 Glyma models are shown as well as annotation columns. determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie v1 (Langmead et al. 2009). Bowtie parameters allowed no mismatches and up to 25 alignments per read. The total hit counts to each of the 88,515 Glyma models are shown as well as annotation columns.
Genome_build: Wm82.a2 from Phytozome (Joint Genome Institute; http://www.phytozome.net/soybean.php) of the Williams 82 genome
Supplementary_files_format_and_content: tab-delimited text files include hit values to 88,585 Glyma gene models for each sample

organism: Glycine max

source_name: Cotyledon

growth_protocol: Soybean (Glycine max cv. Williams) plants were grown in a greenhouse.  Seeds were collected at different developmental stages such as early maturation green 25-50 mg, mid maturation yellow-green 100-200 mg and late maturation yellow 300-400 mg fresh weight seed. Immediately, cotyledons and seed coats were separated by dissecting whole seeds and then stored at -80˚C.

extract_protocol:
Ribosome protected fragments were purified by the Sephacryl S400 spin column (GE Healthcare Life Sciences) chromatography according to the ribosome profiling kit (Epicentre) manuals and total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation using a modified procedure from McCarty DR (1986). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq 2000.
Ribosome profiling and RNA sequencing libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Optimal green house growth conditions

tag: cultivar

value: Williams

tag: developmental stage

value: Beans fresh weight 300-400 mg

tag: preservation

value: Frozen

value: Cotyledon

tag: purification

value: Total RNA


title: Cotyledon (300-400 mg) Ribosome Profiling biorep 2

status: Public on Mar 23 2018

type: SRA

country: USA

description: Ribo-Seq

library_source: transcriptomic

molecule: total RNA

tag: tissue

value: Ribosome bound mRNA


title: Seed Coat (100-200 mg) Control mRNA-Seq biorep 2

description: mRNA-Seq

source_name: Seed Coat

value: Beans fresh weight 100-200 mg

value: Seed Coat


title: Cotyledon (300-400 mg) control mRNA-Seq biorep 1

description: mRNA-Seq


title: Cotyledon (300-400 mg) Ribosome Profiling biorep 1

description: Ribo-Seq


title: Seed Coat (100-200 mg) Ribosome Profiling biorep 1

description: Ribo-Seq


title: Cotyledon (100-200 mg) Control mRNA-Seq biorep 2

description: mRNA-Seq


title: Cotyledon (100-200 mg) Ribosome Profiling biorep 2

description: Ribo-Seq


title: Cotyledon (100-200 mg) Ribosome Profiling biorep 1

description: Ribo-Seq


title: Cotyledon (100-200 mg) control mRNA-Seq biorep 1

description: mRNA-Seq


title: Seed Coat (25-50 mg) Ribosome Profiling biorep 2

description: Ribo-Seq

value: Beans fresh weight 25-50 mg


title: Seed Coat (25-50 mg) Control mRNA-Seq biorep 2

description: mRNA-Seq


title: Seed Coat (25-50 mg) Ribosome Profiling biorep 1

description: Ribo-Seq


title: Seed Coat (25-50 mg) control mRNA-Seq biorep 1

description: mRNA-Seq


title: Seed Coat (100-200 mg) Ribosome Profiling biorep 2

description: Ribo-Seq


title: Cotyledon (25-50 mg) Ribosome Profiling biorep 2

description: Ribo-Seq


title: Cotyledon (25-50 mg) Ribosome Profiling biorep 1

description: Ribo-Seq


title: wtCSCs1 (A1_rep2)

city: Catanzaro

first: Daniele

last: Torella

address: Viale Europa

department: Medical and Surgical Sciences

country: Italy

institute: Magna Graecia University

data_processing:
All libraries were sequenced on the Illumina HiSeq 1000 generating 100 bp paired end reads.
RNA-seq has been performed by using StrandNGS with its default parameters
Raw data sequences have been pre-processed and then related to mus musculus genome. Alignment parameters have been set as it follows: minimum percentage identity = 90 %; maximum percentage gaps = 5 %; maximum number of novel splices = 1; minimum match length = 25.
Reads with less than 5 valid matches have been filtered out, finally obtaining expression values for reads (quantification phase). To detect novel genes and exons we set the parameters, in term of percentile, as it follows: minimum exon length equals to 10.0; minimum intron length equals to 10.0; maximum intron length equals to 90.0; minimum gene length equals to 10.0; minimum exon RPKM equals to 50.0.
Differential expressions were performed using DESeq algorithm. We performed fold change (FC) analysis on filtered expression values using normalized signal values in log-scale. We considered a fold change cut off equals to 2.5 to identify up and down regulated genes.
Gene Ontology, DAVID and Ingenuity Pathways Analysis (IPA) have been used to functional enrich the data.
Genome_build: mm10
Supplementary_files_format_and_content: The .xls file includes read counts and normalized values for the wtCSCs (indicated as A1, A2, A3) and WcreCSCs (indicated as B1, B2, B3).

organism: Mus musculus

source_name: Cardiac Stem Cells

growth_protocol: CSCs were plated in gelatin-coated dishes in CSC growth medium supplemented with 10% ESQ-FBS. Cells were maintained at 37 °C in ambient O2 (21%) and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol Reagent. The extracted RNA integrity was measured with an Agilent 2100 Bioanalyzer, and a sample with an RNA Integrity Number greater than or equal to 8 was considered acceptable.
The libraries were generated using depleted RNA obtained from 1μg total RNA by TruSeq Sample Preparation RNA Kit according to the manufacturer’s without further modifications. The first step involves the removal of ribosomal RNA rRNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads that depletes samples of both cytoplasmic and mitochondrial rRNA. Following purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter  (Multiple indexing adapters were ligate to the ends of the ds cDNA). The products are purified and enriched with PCR to create the final cDNA library.
All libraries were sequenced on the Illumina HiSeq 1000 generating 100 bp paired end reads.

tag: strain

value: Cardiac Stem Cells


title: wtCSCs3 (A3_rep1)


title: Cotyledon (25-50 mg) Control mRNA-Seq biorep 2

description: mRNA-Seq


title: CD4creERafl/fl_1

city: Turku

first: Imran

middle: Ahammad

last: Mohammad

state: Finland

address: Tykistokatu 6

department: Lymphocytes and Inflammation

country: Finland

institute: Turku center for Biotechnology

description: colitis was induced in Rag-/- mice by injecting FACS sorted CD4 T cells from control (ERαfl/fl) and ERα deficient (CD4CreERαfl/fl). After 8 weeks of injection, the CD4+ T cells were FACS sorted from Rag-/- spleens.

data_processing:
After filtering and cleaning, the sequencing reads (50bp single-end) were mapped to a reference genome using the HISAT/Bowtie2 tool. Gene expression level was calculated by RSEM. Differentially expressed genes were screened using Poisson distribution. Corrected P-values were obtained using Bonferroni correction.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD4 T cells

extract_protocol:
RNA was isolated from the sorted CD4 T cells using  RNeasy isolation kit (Qiagen).
Libraries were prepared according to the protocols of Illumina

treatment_protocol: Colitis was induced in Rag-/- mice by injecting FACS sorted naïve CD4 T cells from  ERafl/fl and CD4creERafl/fl mice. After 8 weeks post injection, CD4 T cells were isolated from spleens. The CD4  T cells were subjected to RNA isolation.

tag: cell type

value: CD4 T cells

tag: genotype/variation


title: ERafl_fl_2

value: ERafl/fl


title: ERafl_fl_1


title: Control shRNA in 786-O, replicate #2

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Paired-end fastq files were interleaved.
Reads were mapped to GRCh37 assembly of human genome using STAR.
Number of reads mapping to each gene was calculated using HTSeq based on gene annotations from GENCODE v19.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.htseq_count.gencodev19.txt: Tab-delimited text files containing the number of reads that map to each gene.
Supplementary_files_format_and_content: DESeq.average_10_reads_per_sample.log2fc.shRNA_vs_ctrl.matrix.txt

organism: Homo sapiens

source_name: 786-O, control shRNA

extract_protocol:
Total RNA was extracted from cells infected with MBNL2, ESRP2, or control shRNAs, using miRNeasy kit (Qiagen) according to the supplier protocols.
The RNA was used to generate rRNA-depleted first-strand cDNA libraries using TruSeq Stranded Total RNA-LT (Ribo-Zero Gold, Illumina).

tag: cell line

value: clear cell renal cell carcinoma (ccRCC) cell line

tag: shRNA target

value: Control


title: Control shRNA in 786-O, replicate #1


title: Seed Coat (100-200 mg) control mRNA-Seq biorep 1

description: mRNA-Seq


title: MBNL2-shRNA in 786-O, shRNA #2

source_name: 786-O, MBNL2-shRNA


title: MBNL2-shRNA in 786-O, shRNA #1


title: Control shRNA in A-498, replicate #1

source_name: A-498, control shRNA


title: MBNL2-shRNA in A-498, shRNA #1

source_name: A-498, MBNL2-shRNA


title: Control shRNA in PRPTEC, replicate #2

source_name: PRPTEC, control shRNA

value: PRPTEC

value: normal primary renal proximal tubule epithelial cell line


title: Control shRNA in A-498, replicate #2


title: MBNL2-shRNA in A-498, shRNA #2


title: Cotyledon (25-50 mg) control mRNA-Seq biorep 1

description: mRNA-Seq


title: ESRP2-shRNA in PRPTEC, shRNA #1

source_name: PRPTEC, ESRP2 shRNA


title: CD4creERafl/fl_2


title: Control shRNA in PRPTEC, replicate #1


title: ESRP2-shRNA in PRPTEC, shRNA #2


title: IP: Myc (no SM) Experiment 1 [AGH84-01]

city: Bethesda

first: Yashpal

last: Rawal

state: Maryland

address: 6 Center Dr., Bldg 6, Room 233

department: 1Laboratory of Gene Regulation and Development

institute: NICHD-NIH

library_source: genomic

data_processing:
Sequencing data were mapped to the S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, Nature Methods, 2012) with the default settings. Duplicate reads were removed using the samtools rmdup command, and unique reads with the length between 50-300 bp were size-selected in R.
IGV tracks (UCSC bigWig format) with the genome-wide occupancy profiles were generated in R using the rtracklayer package. The occupancy profiles were normalized such that the average occupancy for every chromosome is 1.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig files containing the normalized occupancy profiles

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP: Myc (no SM) experiment

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).

extract_protocol:
Formaldehyde-fixed and sonicated
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: strain info.

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 SPT15-myc13::HIS3MX6

tag: chip antibody

value: anti-Myc antibody

tag: chip antibody vendor

value: Roche

tag: chip antibody cat.#


title: IP: Myc (+SM) Experiment 2 [AGH84-06]

source_name: IP: Myc (+SM) experiment


title: IP: Myc (+SM) Experiment 1 [AGH84-05]


title: IP: Rpb3 (+SM) Experiment 2 [AGH94-08]

source_name: IP: Rpb3 (+SM) experiment

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 bio4-GBS::BamHI

value: anti-Rpb3 antibody

value: NeoClone


title: IP: Myc (no SM) Experiment 2 [AGH84-02]


title: IP: Rpb3 (+SM) Experiment 1 [AGH94-05]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 tyr1-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 2 [AGH94-06]


title: IP: Rpb3 (+SM) Experiment 1 [AGH86-07]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 wtm1-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 1 [AGH94-07]


title: IP: Rpb3 (+SM) Experiment 2 [AGH86-08]


title: IP: Rpb3 (+SM) Experiment 2 [AGH86-10]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pos5-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 2 [AGH86-04]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 hos4-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 2 [AGH86-02]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 yfr045w-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 1 [AGH86-03]


title: IP: Rpb3 (+SM) Experiment 1 [AGH86-01]


title: IP: Rpb3 (+SM) Experiment 2 [AGH85-12]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 his2-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 1 [AGH85-11]


title: IP: Rpb3 (+SM) Experiment 1 [AGH86-09]


title: IP: Rpb3 (+SM) Experiment 2 [AGH85-10]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 phm8-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 1 [AGH85-09]


title: IP: Rpb3 (+SM) Experiment 1 [AGH85-07]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 aro10-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 2 [AGH85-08]


title: IP: Rpb3 (+SM) Experiment 2 [AGH85-06]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 vps41-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 2 [AGH85-02]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rot2-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 1 [AGH85-05]


title: naïve_WT_3

city: New York

first: Robert

last: Darnell

state: New York

address: 1230 York Ave

institute: Rockefeller University

data_processing:
alignment with STAR
feature counts with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: read counts in tabular format (txt) with ensembl gene IDs, gene information, and read counts per sample

source_name: CD4+ T-cells

growth_protocol: CD4+ T-cells were sorted from pooled spleen and lymph nodes of WT or  TTP KO mice and activated with anti-CD3 antibody in the presence of formalin-fixed WT bone-marrow-derived dendritic cells, under Th1 polarizing conditions (10U/ml hIL-2 and 5 ng/ml mIL-12).  Cells were harvested at 4 hours or 3 days after activation.  Cells harvested on day 3 were first re-stimulated for 2 hours with PMA (20ng/ml) and ionomycin (1mM).

extract_protocol:
Trizol extraction followed by HiPure RNA column (Roche) with DNAse treatment.
Illumina High-throughput TruSeq RNA Sample preparation after riboZero depletion of rRNA (Illumina)

tag: genotype

value: WT

tag: condition

value: naïve

tag: time point

value: 0 hours

tag: biol. rep.


title: IP: Rpb3 (+SM) Experiment 2 [AGH85-04]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 hbt1-GBS::BamHI


title: IP: Rpb3 (+SM) Experiment 1 [AGH85-03]


title: IP: Rpb3 (+SM) Experiment 1 [AGH85-01]


title: IP: Rpb3 (+SM) Experiment 3 [AGH23-11]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 gcn4Δ::kanMX4


title: IP: Gcn4 (+SM) Experiment 2 [AGH24_02]

source_name: IP: Gcn4 (+SM) experiment

value: Affinity purified Gcn4 antibody

value: Covance

value: anti-Gcn4 polyclonal antiserum (HL2871)


title: IP: Gcn4 (+SM) Experiment 3 [AGH24_03]


title: IP: Rpb3 (+SM) Experiment 2 [AGH12-02]

value: anti-Rpb3 antibody

value: NeoClone


title: IP: Gcn4 (no SM) Experiment 2 [AGH32_HQ46]

source_name: IP: Gcn4 (no SM) experiment

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: IP: Gcn4 (no SM) Experiment 3 [AGH32_HQ47]


title: IP: Gcn4 (+SM) Experiment 1 [AGH24_01]


title: IP: Gcn4 (no SM) Experiment 1 [AGH32_HQ45]


title: IP: Rpb3 (+SM) Experiment 1 [AGH12-01]


title: IP: Gcn4 (+SM) Experiment 3 [AGH24_06]


title: IP: Gcn4 (+SM) Experiment 4 [AGH32_86]


title: IP: Gcn4 (+SM) Experiment 2 [AGH24_05]


title: IP: Gcn4 (+SM) Experiment 5 [AGH32_87]


title: IP: Gcn4 (+SM) Experiment 1 [AGH24_04]


title: naïve_WT_1


title: WT-LN-Treg-Biological-Replicate3

status: Public on Mar 26 2018

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
CD45+CD3+CD4+YFP+ Tregs isolated from skin draining LNs
WT-LN-Treg-Replicate3

data_processing:
Alignment: RNA-seq: Tophat, version 2.0.6
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Read_Counts_All_Cell_Types.txt, Differential_Expression_WT_LN_Treg_vs_WT_Skin_Treg.txt

source_name: Foxp3 cre-eyfp LN Treg RNA-seq

extract_protocol:
Superficial and deep axillary LNs were isolated and homogenized in complete DMEM followed by FACS staining for sorting of Tregs
Total RNA was extracted with Pico pure kit (Life technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: No treatment

value: LN

value: Adult FOXP3+ Tregulatory cells (immune)

value: Foxp3 cre-eyfp


title: human 4c 1h rep 1

status: Public on Mar 22 2018

city: Guangzhou

first: Yizhao

last: Luan

state: Guangdong

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

country: China

institute: Sun Yat-sen university

data_processing:
bcl2fastq was used for base calling.
Trimmed reads were aligned to Ictidomys tridecemlineatus genome reference (Ensembl spetri2)  with Tophat v2.0.11. The parameter options applied in alignment were -g 20, -p 8, --no-coverage-search, --library-type fr-firststrand and -G corresponding GTF file.
only the reads aligned to exons uniquely were counted using the Rsubread package
Genome_build: spetri2, hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count values of genes for each Sample ...

source_name: iPSC induced neurons

growth_protocol: Human iPSC lines and iPSC-derived neural precursor cells were established and deposited at the Stem Cell Unit of the National Institutes of Health (B. Mallon; barbara.mallon@nih.gov). Human neurons were cultured as described at https://stemcells.nih.gov/research/nihresearch/scunit/protocols.htm. GS iPSC-derived neuron cultures mainly followed the human protocol except that additional 5% knock-out serum replacement was included in the neural precursor medium, and 5% knock-out serum replacement and 20 ng/ml ACTIVIN A were included in the first 2 days of neuronal differentiation medium. The human and GS NPCs were first expanded in NPC medium described above for 3 days, and then switched to neural differentiation medium (Neural basal A/B-27 or N21-Max/L-Glutamine /antibiotics/BDNF/GDNF) for at least 7 days.

extract_protocol:
Cells were collected and lysed in TRIzol (Thermo Fisher)
total RNA were purified with RNeasy kit (Qiagen), and further processed for RNA-sequencing

treatment_protocol: On the day of experiment, neural differentiation medium was removed from the cultures, fresh hibernate-medium was added, and the cultures were placed

value: neuron

tag: treatment

value: cold


title: human 37c 1h rep 1

value: control


title: 2 d4 M2 sRNA

city: Pasadena

first: Diane

middle: E

last: Trout

state: CA

address: 1200 E California Blvd M/C 156-29

department: Biology

institute: California Institute of Technology

data_processing:
Sequencing adapters were removed from reads by finding the 3'-most complete match to the adapter sequence and trimming the read after that position.
Reads were first mapped to the collection of ribosomal repeats (annotated using the repeatMasker file downloaded from the UCSC genome browser), snoRNAs and snRNAs in the mouse genome (version mm9) using Bowtie (version 0.12.7) in order to remove common contaminants.
The unmapped reads from this filtering step were then mapped against the mm9 genome.
Genome_build: mm9

source_name: differentiating ES cells

extract_protocol: The NEBNext Small RNA Sample Prep Set 1 (Illumina Compatible) library construction protocol was followed (NEB #E6120S/L).

value: differentiating ES cells

value: 129 x castaneus

tag: developmental stage

value: day 4


title: human 37c 4h rep 0


title: human 4c 4h rep 0


title: human 37c 4h rep 1


title: human 4c 4h rep 1


title: human 4c 1h rep 0


title: naïve_WT_2

value: WT

value: naïve

value: 0 hours


title: d4 M2 kd

data_processing:
Genome_build: mm9Reads were mapped using TopHat-2.0.8 against the mm9 version of the mouse genomes while supplying a gtf file containing the ENSEMBL annotation. Read-coverage tracks were generated using custom-written python scripts
Genome_build: mm9

extract_protocol: The NEBNext Small RNA Sample Prep Set 1 (Illumina Compatible) library construction protocol was followed (NEB #E6120S/L), along with the SMART kit and Nextera kit for Illumina sequencing for RNA-seq libraries.


title: human 37c 1h rep 0


title: d8 M2 kd

value: day 8


title: d8 ox sRNA


title: d4 M2 sRNA-2


title: 3 d0 ML sRNA

source_name: undifferentiated ES cells

value: undifferentiated ES cells

value: day 0


title: HIV_48h_D225

city: Seattle

first: Jarrod

last: Johnson

state: Washington

address: 307 Westlake Ave, Suite 500

institute: Center for Infectious Disease Research

description: ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

data_processing:
Basecalls were performed using CASAVA
Reads were aligned to a combined genome including human chromosomes (hg19), HIV (laboratory construct highly similar to NY5/BRU recombinant clone pNL4-3, GenBank ID = M19921.2) and SIV (isolate Mm251, GenBank ID = M19499.1) sequences using gsnap [Wu, Bioinformatics, 2010] (2015-09-10) and stripping off adapter sequences in a pairwise manner.
Only pairs that aligned uniquely and concordantly to non-mitochondrial human chromosomes were retained. Duplicate pairs of reads were removed based on their start and end chromosomal locations. .  Start and end positions of the sequences were adjusted to extend 4 and 5 base pairs respectively to account for transposase adapter insertion (see [Buenrostro, Nature, 2013]).
Peak calling was performed with MACS2 (2.1.0) [Zhang, Genome Biol., 2008] using the start and end locations of the pairs to define fragment lengths. ‘Blacklisted’ regions of known artificially high signal as defined by the Human ENCODE project (www.encodeproject.org/annotations/ENCSR636HFF) were filtered out of peak regions.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for each biological group were generated by running MACS2 peak calling and outputting a normalized bedgraph file followed by file conversion to bigWig using the bedGraphToBigWig program from genome.ucsc.edu.

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 48, drug: none, donor: D225

growth_protocol: To generate monocyte-derived dendritic cells, CD14+ monocytes from PBMC buffy coats were isolated with anti-human CD14 magnetic beads (Miltenyi) and cultured in RPMI containing 10% heat-inactivated fetal bovine serum (FBS), 50 U/ml penicillin, 50 ug/ml streptomycin (P/S), 10 mM HEPES, beta mercaptoethanol, and 2 mM glutamine, in the presence of recombinant human GM-CSF at 10 ng/ml and IL-4 at 50 ng/ml (Peprotech). To overcome restriction to HIV-1 reverse transcription, virus-like particles packaging Vpx were added to isolated cells on day 0.  Fresh media and cytokines were added to cells (40% by volume) on day 1. On day 4, cells were collected, resuspended in fresh media with cytokines used for infection.

extract_protocol:
50,000 sorted DCs from each condition were immediately prepped for ATAC-seq (Buenrostro et al., 2013).  Cells were pelleted by spinning at 500g for 5min at 4C.  Cells were washed in cold PBS and centrifuged again at 500g for 5min at 4C.  Cell pellets were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and immediately spun at 500g for 10 min at 4C.  The nuclear pellet was used directly for the transposition reaction by resuspending in a reaction mix (20 μL 2× TD buffer, 2 μL Tn5 transposase (Illumina) and 18 μL nuclease-free water).  Transposition was performed for 30 min at 37C and sample DNA was purified using a MinElute kit (Qiagen).
Library fragments were amplified by PCR using NEBnext PCR master mix (Illumina) and custom Nextera primers using the following conditions: 72 °C for 5 min; 98 °C for 30 s; and then cycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To stop amplification before saturation in order to reduce bias, we monitored the PCR reaction using SybrGreen-based qPCR.  Samples were cycled an average of 15 times.

treatment_protocol: DCs from three unique donors were infected in the presence of Vpx for 16, 32, or 48 h with or without Raltegravir (25 uM). The time course was performed in reverse order such that all samples were harvested at the same time on day 6 after DC differentiation.  Cells were stained for Live/Dead Violet (ThermoFisher) and CD86 (eBioscience) to assess activation status and then all live cells were sorted on a FACSAria II (BD Biosciences).

value: monocyte derived dendritic cells


title: HIV_RAL_32h_D225

description: ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 32, drug: Raltegravir, donor: D225


title: HIV_32h_D225

description: ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 32, drug: none, donor: D225


title: RAL_D225

description: ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 0, drug: Raltegravir, donor: D225


title: HIV_RAL_16h_D225

description: ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 16, drug: Raltegravir, donor: D225


title: HIV_16h_D225

description: ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 16, drug: none, donor: D225


title: HIV_RAL_32h_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 32, drug: Raltegravir, donor: D224


title: HIV_RAL_48h_D225

description: ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 48, drug: Raltegravir, donor: D225


title: d8 ctrl


title: HIV_RAL_48h_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 48, drug: Raltegravir, donor: D224


title: HIV_RAL_16h_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 16, drug: Raltegravir, donor: D224


title: HIV_32h_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 32, drug: none, donor: D224


title: HIV_48h_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 48, drug: none, donor: D224


title: mock_D225

description: ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 0, drug: none, donor: D225


title: RAL_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 0, drug: Raltegravir, donor: D223


title: HIV_RAL_16h_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 16, drug: Raltegravir, donor: D223


title: mock_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 0, drug: none, donor: D224


title: d4 ctrl

source_name: differentiating ES cells


title: HIV_RAL_48h_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 48, drug: Raltegravir, donor: D223


title: HIV_48h_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 48, drug: none, donor: D223


title: RAL_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 0, drug: Raltegravir, donor: D224


title: 4 d0 M2 sRNA

source_name: undifferentiated ES cells


title: mock_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 0, drug: none, donor: D223


title: HIV_16h_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 16, drug: none, donor: D223


title: HIV_32h_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 32, drug: none, donor: D223


title: MSN LV-DKIN-K543M n4 (K4)

city: Corbeil-Essonnes

first: MARGOT

last: JARRIGE

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem/INSERM U861

data_processing:
Torrent Suite Software was used for basecalling, trimming of adaptator sequence, quality check and to generated FASTQ file
FastQ files were exported to PartekFlow software (v4,0) for alignement and quantification step. Briefly sequence were mapped to hg19 reference genome (2015-11-06)  using TOPHAT2 and bowtie 2 following the WT Pipeline for Ion Torrent. Mapped reads were quantified with Partek E/M algorithm , normalized on total count and differential gene were identified using Partek Gene Specific Algorithm (GSA)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPM (read per million)

source_name: MSN LV-DKIN-K543M

growth_protocol: Striatal neuron progenitors were derived from hESCs as described Arber and al,,2015 Nicoleau and al,, 2013

extract_protocol:
Medium was remove and 350µl RLTplus was add, Sample were extracted on QUIACUBE following the Rneasy Plus Micro kit protocole (Qiagen)
The Ion Ampliseq Transcriptome Human Gene expression kit was used with 50ng of mRNA for the construction of sequencing libraries following the manufacturer protcol.
Ampliseq Transcriptome Human gene expression kit (Termofisher Scientific)

treatment_protocol: post-mitotic neuronal cultures were transduced with lentiviral vectors encoding GFP, DCLK3-KIN WT or DCLK3 -K543M

value: striatal neuron progenitors

value: human embryonic stem cell derived neuronal

value: wild type

tag: lentivirus

value: MSN LV-DKIN-K543M


title: MSN LV-DKIN-K543M n3 (K3)


title: squirrel 4c 4h rep 0

organism: Ictidomys tridecemlineatus

source_name: iPSC induced neurons

value: neuron


title: squirrel 37c 4h rep 0


title: squirrel 4c 4h rep 1

value: cold


title: squirrel 37c 1h rep 2

value: control


title: MSN LV-DKIN-K543M n1 (K1)


title: squirrel 4c 1h rep 2


title: MSN LV-DKIN-K543M n2 (K2)


title: MSN LV-DKIN-WT n3 (D3)

source_name: MSN LV-DKIN-WT

value: LV-DKIN-WT


title: HIV_16h_D224

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 16, drug: none, donor: D224


title: squirrel 37c 4h rep 1


title: BHKOp rep3

city: Wuhan

first: han

middle: ling

last: ling

state: Hubei

address: Bayi road

department: College of life science

institute: Wuhan University

data_processing:
the library preparations were sequenced on an  Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter,  reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30  and GC content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
TopHat v2.0.12 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the GOseq R package, in which gene length bias wascorrected. GO terms  with corrected Pvalue less than 0.05 were considered significantly enriched by differential  expressed genes.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample: BHK21-1.txt

organism: Mesocricetus auratus

source_name: BHKOp

growth_protocol: All cells were grown in Minimum Essential Medium  supplemented with 10% heat-inactivated fetal bovine serum at 37°C with 5% CO2

extract_protocol:
The cells were collected and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA LibraryPrep Kit (NEB, USA) was used with 3ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown in Minimum Essential Medium  supplemented with 10% heat-inactivated fetal bovine serum at 37°C with 5% CO2, and when cells grew to 80-90% confluence, cell were  collected and used for RNA extraction

value: Kidney cells

tag: passages

tag: genotype/phenotype

value: FMDV persistent infection cells (BHKOp)


title: MSN LV-GFP n4 (G4)

source_name: MSN LV-GFP

tag: cell type


title: squirrel 37c 1h rep 1


title: BHKOp rep2


title: BHKOp rep1


title: squirrel 4c 1h rep 1


title: HIV_RAL_32h_D223

source_name: monocyte derived dendritic cells infected with HIV in the presence of Vpx, time (hours): 32, drug: Raltegravir, donor: D223


title: MSN LV-GFP n2 (G2)


title: squirrel 37c 1h rep 0


title: MSN LV-DKIN-WT n1 (D1)


title: MSN LV-DKIN-WT n4 (D4)


title: VEC rep1

source_name: VEC

value: FMDV-free cells of persistent infection (VEC)


title: squirrel 4c 1h rep 0


title: VEC rep2


title: VEC rep3


title: MSN LV-GFP n3 (G3)


title: MSN LV-GFP n1 (G1)


title: BHK21 rep1

value: wild-type


title: MSN LV-DKIN-WT n2 (D2)


title: Photinus_pyralis_MethylC-seq_library_1_of_4

city: Athens

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Reads generated from MethylC-seq were aligned to Ppyr1.3 assembly using the latest version of methylpy (Schultz et al. 2015; doi:10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home).
MethylC-seq analysis was performed as described in Schmtiz et al. (2013; doi:10.1101/gr.152538.112).
Genome_build: Ppyr1.3
Supplementary_files_format_and_content: Tab delimited; please see metadata file for column headers.

organism: Photinus pyralis

source_name: Whole body

extract_protocol:
High molecular weight DNA was purified from four Photinus pyralis Mercer Meadows New Jersey (MMNJ) males using 100/G Genomic Tips with the Genomic Buffers kit (Qiagen, USA).
MethylC-seq libraries were prepared using the protocol described in Urich et al. (2015; doi:10.1038/nprot.2014.114). Lambda phage DNA was used as a control for the sodium bisulfite non-conversion rate.

tag: tissue

value: Whole body

value: Adult

tag: Sex

value: male

value: Wild type


title: Photinus_pyralis_MethylC-seq_library_2_of_4


title: Photinus_pyralis_MethylC-seq_library_3_of_4


title: Photinus_pyralis_MethylC-seq_library_4_of_4


title: PE_TSA_shJIP1_1

status: Public on Mar 21 2018

city: Aurora

first: Philip

middle: David

last: Tatman

state: Colorado

department: Department of Pharmacology

institute: University of Colorado

data_processing:
Aligned with tophat2.0
Quantified with cufflinks
Genome_build: rn6
Supplementary_files_format_and_content: normalized expression

organism: Rattus norvegicus

source_name: NRVM, Phenylephrine treated, TSA treated, JIP1 Knockout

extract_protocol:
Quigen rna kit
Illumina trueseq

treatment_protocol: NRVMS were treated with either PE and sh Control, PE and TSA and sh Control, or PE TSA and SHjip1 for three days

value: neonatal rat ventricular myocytes (NRVM)

tag: tag

value: Phenylephrine treated

value: TSA treated

value: JIP1 Knockout


title: STRT Replicate 2

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

data_processing:
Library strategy: STRT
Fastq files were hard clipped and de-multiplexed for each method requiring it (see manuscript for details).
Fastq files for Five-Prime methods were mapped to hg19 with STAR (version 2.4.2a) using two-pass mode, and the softclip option to trim reads and otherwise default parameters.
For standard RNA-Seq data, we aligned untrimmed reads with Tophat (version v1.4.1) using default parameters except mate-inner-dist set to 300 and mate-std-diff set to 500, followed by Cufflinks (v2.2.1) using the default settings.
Aligned reads were downsampled (to 20 million unique reads for the non-replicate samples (except for NanoCAGEXL), to 7 million for CAGE replicates, and to 5 million for the remaining replicates)
Peaks were called with Paraclu
Peaks were filtered for CAGE/RAMPAGE/NanoCAGE-XL/STRT with Capfilter
Genome_build: hg19
Supplementary_files_format_and_content: Bed files, containing called peaks (putative TSSs) and normalized scores for each peak.

source_name: Chronic Myeloid Leukemia cell line K-562 grown in tissue culture (Ambion)

extract_protocol:
STRT
From Ambion (Thermo Fisher Scientific). Prepared from cells homogenized in ToTALLY RNA™ Lysis/Denaturation  Solution (Part no. AM8540G), flash-frozen in liquid nitrogen, and stored at –80°C until use. RNA isolated using  Ambion® RNA isolation reagents. Purified RNA underwent a stringent DNase treatment.

tag: cell line

tag: total rna input

value: 10 ng


title: PE_TSA_shcontrol_2

source_name: NRVM, Phenylephrine treated, TSA treated


title: PE_shcontrol_1

source_name: NRVM, Phenylephrine treated


title: RAMPAGE replicate 1

description: The downsampled (20M) file is based only on Rampage replicate 1.

data_processing:
Library strategy: RAMPAGE
Fastq files were hard clipped and de-multiplexed for each method requiring it (see manuscript for details).
Fastq files for Five-Prime methods were mapped to hg19 with STAR (version 2.4.2a) using two-pass mode, and the softclip option to trim reads and otherwise default parameters.
For standard RNA-Seq data, we aligned untrimmed reads with Tophat (version v1.4.1) using default parameters except mate-inner-dist set to 300 and mate-std-diff set to 500, followed by Cufflinks (v2.2.1) using the default settings.
Aligned reads were downsampled (to 20 million unique reads for the non-replicate samples (except for NanoCAGEXL), to 7 million for CAGE replicates, and to 5 million for the remaining replicates)
Peaks were called with Paraclu
Peaks were filtered for CAGE/RAMPAGE/NanoCAGE-XL/STRT with Capfilter
Genome_build: hg19
Supplementary_files_format_and_content: Bed files, containing called peaks (putative TSSs) and normalized scores for each peak.

extract_protocol:
RAMPAGE
From Ambion (Thermo Fisher Scientific). Prepared from cells homogenized in ToTALLY RNA™ Lysis/Denaturation  Solution (Part no. AM8540G), flash-frozen in liquid nitrogen, and stored at –80°C until use. RNA isolated using  Ambion® RNA isolation reagents. Purified RNA underwent a stringent DNase treatment.


title: PE_TSA_shcontrol_1


title: STRT Replicate 1

description: The downsampled (20M) file is based only on STRT replicate 1.


title: RAMPAGE replicate 2


title: Het_rep1

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

data_processing:
Raw sequencing reads were aligned to full human genome and transcriptome using STAR v2.5.1b splice-aware alignment software (22). Primary part of GRCh38.p3 human genome assembly and Gencode v23 annotation were used to generate the genomic and transcriptomic reference index (23)
The resulting transcriptome-aligned sequences were used for expression quantification with RSEM v1.2.26 (24).
After this, gene expression was analyzed in R (v3.3.1) using DESeq2 v1.12.4 (25).
Gene set enrichment analysis was done using fgsea v0.99.6 (27). GO analysis was done using GOrilla online tool (28), and MsigDB analysis was done using MsigDB website (29) with only CP canonical pathways selected.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: expression table with additional gene ID annotation (Ensembl, symbol, type of a gene)

source_name: ectopic endometrial lesion

extract_protocol:
Tissue samples from fifteen women with pelvic endometriosis were used in the study. Four patients were recruited for Ion Torrent AmpliSeq RNA-sequencing analysis. Independently, an additional eleven patients were involved in the study to perform real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) analysis for the validation of sequencing data. Clinical characteristics of the patients are shown in Supplemental Table 1. All women were Caucasian. The patients ranged in age from 24 to 39 years (average age 31.5±1.1 years). Seven and six patients were seen with primary and secondary infertility, respectively. Two patients did not have reproductive history. The same patient provided both eutopic and ectopic endometrium samples. Endometriotic lesions from the pelvic region were removed at laparoscopy. Biopsy tissues of eutopic endometrium from the patients were collected by hysteroscopy. Laparoscopy and hysteroscopy procedures were performed during the same surgical intervention in the mid secretory phase of the menstrual cycle. No patients were taking medications and receiving hormone therapy at the time of the surgery or in the previous six months. After surgical resection, the samples were immediately placed in an RNAlater (Ambion, UK), incubated at 4˚C a day and then stored at -70˚C until used. Among the fifteen patients, two women had stage I, nine – stage II, two – stage III, and two - stage IV endometriosis. The severity of endometriosis was classified into stage according to the revised American Society for Reproductive Medicine classiﬁcation of endometriosis.   Total RNA was extracted from tissues with the PureLink RNA Mini Kit (Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer’s protocol and quantiﬁed by Qubit 2.0 Fluorimeter with Qubit® RNA HS Assay Kit (Invitrogen, Carlsbad, CA, USA). Integrity of the RNA was assessed on 2200 TapeStation Instrument with High Sensitivity RNA ScreenTape and High Sensitivity RNA ScreenTape Reagents (all purchased from Agilent Technologies, Santa Clara, CA, USA). Purified RNA samples were stored at ‑70˚C until used.
The sequencing libraries were prepared with the Ion AmpliSeq RNA Library Kit (Thermo Fisher Scientiic, Inc.) using a custom Ion Torrent AmpliSeq Panel according the manufacturer's protocol. The construction of the library involved the following steps: reverse transcription reaction, multiplex polymerase chain reaction (PCR), digestion primers, ligation of the adapters and the libraries amplification. Briefly, for each sample, 10 ng of total RNA was used as the starting template to synthesize single strand cDNA. For this RNA samples were mixed with 5X VILO RT Reaction Mix and 10X SuperScript III Enzyme Mix (all taken from Ion AmpliSeq™ RNA RT Module), incubated at 42˚C for 30 min and 85˚C for 5 min, and then cooled on ice. The cDNA was amplified using custom primers, described as above, and Ion AmpliSeq™ HiFi master mix (Ion AmpliSeq™ Library Kit 2.0). Then multiplex PCR was performed under the following cycling conditions: denaturation at 99 °C for 2 min; 16 cycles of amplification for 15 sec at 99 °C and for 4 min at 60 °C; then 4˚C for hold. Following target amplification the samples were treated with 2 μL FuPa reagent (Ion AmpliSeq™ Library Kit 2.0) to partially digest primer sequences and phosphorylate the amplicons at 50°C for 10 min, followed by 55°C for 10 min, then 60°C for 20 min. The amplicons were then ligated to adapters (Ion AmpliSeq™ Library Kit 2.0) with the diluted barcodes of the Ion Xpress™ Barcode Adapters kit (Thermo Fisher Scientific, Inc.) for 30 min at 22°C then 72°C for 20 min. To remove high molecular-weight DNA and primers, the amplicons with adapters were purified using Ion AmpliSeq™ RNA Dynabeads® Cleanup Module. The subsequent PCR were performed using purified amplicons with Library Amplification Primer Mix and Platinum PCR SuperMix High Fidelity (Ion AmpliSeq™ Library Kit 2.0). Cycling conditions were as follows: 98˚C for 2 min, 5 cycles of 98˚C for 15 sec and 60˚C for 1 min, then 10˚C for hold. Amplified libraries were purified using Ion AmpliSeq™ RNA Dynabeads® Cleanup Module. For assessment of the yield, size distribution and molar concentration of libraries after cleanup, the samples were run on 2200 TapeStation Instrument with High Sensitivity D1K ScreenTape and High Sensitivity D1K Reagents (all purchased from Agilent Technologies, Santa Clara, CA, USA). All libraries were diluted to 100 pM according to the manufacturer's protocol (Ion AmpliSeq™ RNA Library Kit, Thermo Fisher Scientific, Inc.).

value: ectopic lesion


title: Het_rep2


title: Het_rep3


title: Ctrl_rep4

source_name: endometrial biopsy

value: eutopic endometrium


title: Ctrl_rep2


title: Ctrl_rep1


title: Het_rep4


title: BHK21 rep3


title: Ctrl_rep3


title: PE_TSA_shJIP1_2


title: NanoCAGE-XL

data_processing:
Fastq files were hard clipped and de-multiplexed for each method requiring it (see manuscript for details).
Fastq files for Five-Prime methods were mapped to hg19 with STAR (version 2.4.2a) using two-pass mode, and the softclip option to trim reads and otherwise default parameters.
For standard RNA-Seq data, we aligned untrimmed reads with Tophat (version v1.4.1) using default parameters except mate-inner-dist set to 300 and mate-std-diff set to 500, followed by Cufflinks (v2.2.1) using the default settings.
Aligned reads were downsampled (to 20 million unique reads for the non-replicate samples (except for NanoCAGEXL), to 7 million for CAGE replicates, and to 5 million for the remaining replicates)
Peaks were called with Paraclu
Peaks were filtered for CAGE/RAMPAGE/NanoCAGE-XL/STRT with Capfilter
Genome_build: hg19
Supplementary_files_format_and_content: Bed files, containing called peaks (putative TSSs) and normalized scores for each peak.

extract_protocol:
NanoCAGE-XL
From Ambion (Thermo Fisher Scientific). Prepared from cells homogenized in ToTALLY RNA™ Lysis/Denaturation  Solution (Part no. AM8540G), flash-frozen in liquid nitrogen, and stored at –80°C until use. RNA isolated using  Ambion® RNA isolation reagents. Purified RNA underwent a stringent DNase treatment.


title: BHK21 rep2


title: PE_shcontrol_2

value: control


title: CSH1_C1

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the Rattus norvegicus (Rnor 5.0) by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
After getting the Expression level of all genes in all samples, differentially expressed genes were analyzed by using edgeR(Robinson et al., 2010), one of R packages.
Genome_build: Rnor 5.0
Supplementary_files_format_and_content: tabular data of  txt , the RPKM of expressed genes

molecule: polyA RNA

source_name: CS thalamus

extract_protocol:
Total RNA was extracted from 30 mg of ground tissue by using hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1DNase (Promega) to remove DNA. The quality and quantity of the purified RNA we redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad).
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen) before used for directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer.

tag: strain

value: Wistar

tag: mouse model

value: combined-stress (CS) model

value: hypothalamus


title: UCH1_E1

source_name: UC thalamus

value: ulcerative-colitis (UC) rat model


title: CSH2_C2


title: CSC1_D1

source_name: CS colon

value: colon


title: NCC2_B2

source_name: NC colon

value: control (NC)


title: CSC2_D2


title: UCC1_F1

source_name: UC colon


title: UCH2_E2


title: UCC2_F2


title: NCC1_B1


title: NCH1_A1

source_name: NC thalamus


title: NCH2_A2


title: WT (36)

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Fastq file were imported to Galaxy and groomer was performed.
Sequence tags were mapped onto the NCBI37 mm9 genome with TopHat.
Transcript assembly and FPKM estimation was performed using Cufflinks.
Differences between FPKM was determined by log2 fold change between KO samples and WT with an offset value of 1
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files include the FKPM for each sample

source_name: CD4–CD8+ G9a WT

extract_protocol:
Total RNA was extracted with a Nucleospin RNA XS extraction kit.
5ng of less of total RNA was reversed transcribed and amplified using the SmartSeq v.4 ultra low input RNA kit (Clontech). Library was constructed with a Nextera DNA Library Prep Kit (Illumina).

value: spleen and lymph nodes

value: CD4-CD8+ T cells


title: WT (740)


title: KO DP (738)

source_name: CD4+CD8+ G9a KO

value: CD4+CD8+ T cells


title: KO DP (739)


title: WT (741)


title: KO DP (35)


title: KO sp (738)

source_name: CD4–CD8+ G9a KO


title: KO sp (739)


title: W5_ACAAAC_L007_R1_001

city: Sn diego

first: sumetha

last: kannan

state: California

address: 5500 Campanile Dr

institute: San DIego State University

data_processing:
Filtered reads were mapped against the human TAIR10 and Boechera Stricta reference using Tophat v1.4.1 (--library-type fr-firststrand)
Alternative splicing events were identified used rMATS.3.0.9
Differentially expressed genes were identified using DeSeq2
Genome_build: TAIR10, Bstricta.v1.2 (https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Bstricta)
Supplementary_files_format_and_content: count matrix

organism: Arabidopsis thaliana

source_name: root

extract_protocol:
Total RNA 88 was isolated using AMBION RNAeasy isolation kits.The quality of RNA was examined using a BioAnalyzer.
A 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Inc., Brea, CA) were used to purify resulting cDNA, and 1 ng cDNA was subsequently used to prepare a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection.
RNAseq libraries were sequenced using Illumina HiSeq 2500 according to the standard protocol.

treatment_protocol: Plants were grown at 22°C[normal], 38°C [Basal] and 43°C [Acquired]

value: root


title: WT (37)


title: KO DP (34)


title: W3_GTGTTA_L007_R1_001


title: W2_CACACA_L007_R1_001


title: W4_TGTGAA_L007_R1_001


title: High dose_15

city: Freising

first: Veronika

middle: L

last: Flöter

address: Weihenstephaner Berg 3

department: Life Science Center Weihenstephan

country: Germany

institute: Technische Universität München

description: 1000 µg/kg bw/d

data_processing:
Fastq files were analyzed with a locally installed version of Galaxy (Giardine B et al., Genome Res. 2005, 15:1451-1455)
Reads were trimmed from the 5´and 3´end with “Fastq quality trimmer”(Blankenberg et al., Bioinformatics 2010, 26:1783-1785) (window size: 3, step size: 1, quality score ≥ 30.0, aggregate action for window: mean of scores), the adapter sequence was clipped (min. sequence length: 17, discard sequences with unknown (N) bases: yes), and reads were filtered with “filter by quality” (quality cut-off value: 25, percentage of bases in the sequence that must have a quality of at least the cut-off value: 100).
Retrained reads were used for the quality report with FastQC (Babraham Bioinformatics, UK, Version 0.10.1).
Subsequently, the abundance of each unique sequence was determined, the table of the read counts from all samples was then filtered to remove very low abundant sequences and to keep potential transcripts that are turned on or off by the E2 treatment (condition: at least 10 reads of each miRNA must be present in 3-4 samples of at least one group).
Databases of mature miRNAs (pig, human, mouse, cow; miRBase release 20.0) were used to generate a BLAST database using “make blast database” (http://www.ncbi.nlm.nih.gov/books/NBK1763/) (molecule type of input: nucleotide, hash-index: true). Reads were mapped against these databases with “blastn” (Zhang Z et al., J. Comput. Biol. 2000, 7:203-214) (blastn-short, expectation value: 1.0, word size: 5), followed by filtering of the blast output (condition: length of query sequence = length of target sequence = alignment length and number of identical bases within the alignment) in order to selected only miRNAs which aligned 100 % with the database sequence.
Genome_build: Sscrofa10.2
Genome_build: GRCh37.p5
Genome_build: UMD3.1
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with the abundance of each sequence (read counts)

organism: Sus scrofa

source_name: Endometrium

extract_protocol:
The uterus was flushed with 10 ml and another 50 ml of phosphate-buffered saline (autoclaved, ph 7.4). Then, endometrial samples were collected, shock frozen in liquid nitrogen and stored at – 80 °C. RNA was harvested by means of TRIzol reagent.
For preparation of the small RNA-Seq libraries, the NEBNext© Small RNA Sample Prep Set 1 (New England Biolabs, Frankfurt-Höchst, Germany) was utilized according to the manufacturer´s instructions.

value: Endometrium

tag: Stage

value: adult, day 10 of pregnancy

value: oral E2 treatment 1000 microg/kg bw/d


title: W1_ACACGA_L007_R1_001


title: High dose_14

description: 1000 µg/kg bw/d


title: High dose_13

description: 1000 µg/kg bw/d


title: NOEL_11

description: 10 µg/kg bw/d

value: oral E2 treatment 10 microg/kg bw/d


title: NOEL_9

description: 10 µg/kg bw/d


title: Cut-and-Run_human_K27me3_800_(20170516_SH_HsSc_K27_4_0506)

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&RUN K27me3 using 800 cells

data_processing:
Library strategy:  Cleavage under targets and Release using nuclease
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We used picard 1.131 MarkDuplicates command to mark PCR duplicates in the sam file.  3. We extracted properly paired reads from the marked alignments. 4. We took a random sample of 7.5 million paired reads (Supplementary file .bed.gz). 5. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000 to create a track file (Supplementary file .bedgraph.gz).

source_name: Chromatin immunocleavage and release

extract_protocol:
CUT-and-RUN_NatProt.rtf
PMID 25827087

value: K562 cells

tag: antibody

value: anti-K27me3 Cell Signalling #9733


title: High dose_12

description: 1000 µg/kg bw/d


title: NOEL_10

description: 10 µg/kg bw/d


title: Cut-and-Run_human_K27me3_6000_(20170516_SH_HsSc_K27_1_0506)

description: CUT&RUN K27me3 using 6000 cells


title: Cut-and-Run_human_K27me3_400_(20170516_SH_HsSc_K27_5_0506)

description: CUT&RUN K27me3 using 400 cells


title: Cut-and-Run_human_K27me3_200_(20170516_SH_HsSc_K27_6_0506)

description: CUT&RUN K27me3 using 200 cells


title: NOEL_8

description: 10 µg/kg bw/d


title: ADI_7b

description: 0.05 µg/kg bw/d

value: oral E2 treatment 0.05 microg/kg bw/d


title: W6_CACCTC_L007_R1_001


title: Cut-and-Run_human_K27me3_100_(20170516_SH_HsSc_K27_7_0506)

description: CUT&RUN K27me3 using 100 cells


title: ADI_7a

description: 0.05 µg/kg bw/d


title: Cut-and-Run_human_K27me3_1500_(20170516_SH_HsSc_K27_3_0506)

description: CUT&RUN K27me3 using 1500 cells


title: ADI_5

description: 0.05 µg/kg bw/d


title: DrugM-3_S9

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Illumina BaseSpace FASTQ Generation. Version: 1.0.0
quality check on raw sequencing reads was performed using FastQC 0.11.2
We used trimmomatic 0.32 to filter reads  for quality score and read length. Reads with average quality below 20 (within 4-base wide sliding window) and/or shorter than 36 bases were removed
star 2.4.1c was used to align the reads to the reference genome
Genome_build: Homo_sapiens.GRCh38.83
Supplementary_files_format_and_content: tab-delimited text file providing values for each sample.

growth_protocol: 150,000 cells per well were seeded in a 6 well plates, and were incubated for 24h before treatment at 37°C, 5% CO2. ARN8 cells were grown and incuabted in DMEM supplemented with 10% fetal bovine serum and 1% penycilin/streptomycin mix.

extract_protocol:
The cells were harvested by trypsinization as suggested by the mirVana™ miRNA Isolation Kit for isolation of total RNA (Life Technologies, AM1560)
Libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: The cells were treated with 5 μM of compound A and 20 μM of compound M for 5h. DMSO was used as vehicle, with final concentration of 0.05%.

tag: replicate

value: DrugM


title: DrugM-1_S3


title: Control_4

description: 0 µg/kg bw/d

value: oral E2 treatment 0 microg/kg bw/d


title: Control_3

description: 0 µg/kg bw/d


title: Cut-and-Run_human_CTCF_50000_(20170502_SH_HsSc_CTCF_2_0426)

description: CUT&RUN CTCF using 50000 cells

data_processing:
Library strategy:  Cleavage under targets and Release using nuclease
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We used picard 1.131 MarkDuplicates command to mark PCR duplicates in the sam file.  3. We extracted properly paired reads from the marked alignments. 4. We took a random sample of 4 million paired reads (Supplementary file .bed.gz). 5. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000 to create a track file (Supplementary file .bedgraph.gz).

value: anti-CTCF Millipore #07-729


title: Control_2

description: 0 µg/kg bw/d


title: Cut-and-Run_human_CTCF_8000_(20170502_SH_HsSc_CTCF_5_0426)

description: CUT&RUN CTCF using 8000 cells


title: Cut-and-Run_human_CTCF_4000_(20170502_SH_HsSc_CTCF_6_0426)

description: CUT&RUN CTCF using 4000 cells


title: DrugA-2_S5

value: DrugA


title: Cut-and-Run_human_K27me3_3000_(20170516_SH_HsSc_K27_2_0506)

description: CUT&RUN K27me3 using 3000 cells


title: DMS0-3_S7

value: DMSO


title: Control_1

description: 0 µg/kg bw/d


title: DMS0-2_S4


title: Cut-and-Run_human_CTCF_1000_(20170502_SH_HsSc_CTCF_8_0426)

description: CUT&RUN CTCF using 1000 cells


title: DMS0-1_S1


title: Cut-and-Run_human_CTCF_12500_(20170502_SH_HsSc_CTCF_4_0426)

description: CUT&RUN CTCF using 12500 cells


title: Cut-and-Run_human_CTCF_100000_(20170502_SH_HsSc_CTCF_1_0426)

description: CUT&RUN CTCF using 100000 cells


title: Oligo Capping

data_processing:
Library strategy: oligo capping
Fastq files were hard clipped and de-multiplexed for each method requiring it (see manuscript for details).
Fastq files for Five-Prime methods were mapped to hg19 with STAR (version 2.4.2a) using two-pass mode, and the softclip option to trim reads and otherwise default parameters.
For standard RNA-Seq data, we aligned untrimmed reads with Tophat (version v1.4.1) using default parameters except mate-inner-dist set to 300 and mate-std-diff set to 500, followed by Cufflinks (v2.2.1) using the default settings.
Aligned reads were downsampled (to 20 million unique reads for the non-replicate samples (except for NanoCAGEXL), to 7 million for CAGE replicates, and to 5 million for the remaining replicates)
Peaks were called with Paraclu
Peaks were filtered for CAGE/RAMPAGE/NanoCAGE-XL/STRT with Capfilter
Genome_build: hg19
Supplementary_files_format_and_content: Bed files, containing called peaks (putative TSSs) and normalized scores for each peak.

source_name: Chronic Myeloid Leukemia cell line K-562 grown in tissue culture (Ambion)

extract_protocol:
Oligo capping
From Ambion (Thermo Fisher Scientific). Prepared from cells homogenized in ToTALLY RNA™ Lysis/Denaturation  Solution (Part no. AM8540G), flash-frozen in liquid nitrogen, and stored at –80°C until use. RNA isolated using  Ambion® RNA isolation reagents. Purified RNA underwent a stringent DNase treatment.


title: DrugA-3_S8


title: Cut-and-Run_human_IgG_1million_(20170420_SH_HsSc_IgG_30m_0410)

description: CUT&RUN IgG using 1million cells

data_processing:
Library strategy:  Cleavage under targets and Release using nuclease
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We used picard 1.131 MarkDuplicates command to mark PCR duplicates in the sam file.  3. We extracted properly paired reads from the marked alignments. 4. We took random samples of 7.5 and 4 million paired reads (Supplementary files .bed.gz). 5. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000 to create a track file (Supplementary files .bedgraph.gz).

value: guinea pig anti-rabbit Antibodies Online ABIN101961


title: ADI_6

description: 0.05 µg/kg bw/d


title: DrugM-2_S6


title: H3K9ac AOX/NDI1 - day 9 rep 1

city: RTP

first: Janine

last: Santos

state: NC

address: 111 TW Alexander drive

department: GISBL

institute: NIEHS

data_processing:
The raw ChIP-Seq reads were initially processed by filtering with average quality scores greater than 20.
The reads passing the initial processing were aligned to the human reference genome (hg19; Genome Reference Consortium GRCh37 from February 2009) with with Bowtie2 –sensitive-local settings and 1,000-bp maximum fragment length (−D 15 −R 2 −N 0 −L 20 −i S,1,0.75 −X 1000) .
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bedgraph files using bedGraphToBigWig; Scores represent mapped read coverage

source_name: mtDNA depleted + ectopic NADH oxidation

growth_protocol: Cells were grown in DMEM high glucose medium supplemented with uridine and pyruvate.

extract_protocol: Genomic DNA was isolated from sonicated formaldehyde-fixed pellets by chromatin immunoprecipitation

treatment_protocol: HEK293 were exposed to 10 ng/µL doxycycline to induce the DN-POLG transgene

tag: chip antibody

value: H3K9ac (Active Motif, Cat. No. 39137)


title: CAGE Replicate 6

description: The downsampled CAGE_20M.bed file represents Replicates 1, 4 and 6.  This file is available on GSM2772305.

extract_protocol:
CAGE
From Ambion (Thermo Fisher Scientific). Prepared from cells homogenized in ToTALLY RNA™ Lysis/Denaturation  Solution (Part no. AM8540G), flash-frozen in liquid nitrogen, and stored at –80°C until use. RNA isolated using  Ambion® RNA isolation reagents. Purified RNA underwent a stringent DNase treatment.


title: H3K9ac AOX/NDI1 - day 9 rep 2


title: H3K9ac AOX/NDI1 - day 6 rep 2


title: Input DNA AOX/NDI1 - day 9 rep 2

source_name: mtDNA depleted + ectopic NADH oxidation, input DNA


title: Input DNA AOX/NDI1 - day 9 rep 1


title: CAGE Replicate 1

description: The downsampled CAGE_20M.bed file represents Replicates 1, 4 and 6.


title: CAGE Replicate 4


title: H3K9ac AOX/NDI1 - day 6 rep 1


title: Standard RNA-Seq

extract_protocol:
RNase H rRNA depletion with TruSeq strand-specific RNA-Seq
From Ambion (Thermo Fisher Scientific). Prepared from cells homogenized in ToTALLY RNA™ Lysis/Denaturation  Solution (Part no. AM8540G), flash-frozen in liquid nitrogen, and stored at –80°C until use. RNA isolated using  Ambion® RNA isolation reagents. Purified RNA underwent a stringent DNase treatment.


title: Input DNA AOX/NDI1 - day 6 rep 2


title: Input DNA AOX/NDI1 - day 6 rep 1


title: Cut-and-Run_human_CTCF_25000_(20170502_SH_HsSc_CTCF_3_0426)

description: CUT&RUN CTCF using 25000 cells


title: H3K9ac AOX/NDI1 - day 3 rep 1


title: DrugA-1_S2

tag: treatment


title: RNA-seq in siGPS2 2

first: Valentina

last: Perissi

address: 72 E. Concord St

institute: Boston University

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using tophat aligner.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8

growth_protocol: 3T3-L1 cells were grown in 10% BCS/DMEM supplemented with 0.1 mM MEM non-essential aminoacids, 2mM L-glutamine, 1mM sodium pyruvate

extract_protocol:
The experiments were performed as previously described (Cardamone et al, Cell Reports 2014)
The library construction protocol followed  the manufacturer’s instructions.

treatment_protocol: siRNAs specific for GPS2 were purchased from Invitrogen (Silencer Select siRNAs).

tag: genotype/variation

value: knock-down of GPS2


title: Input DNA AOX/NDI1 - day 0 rep 2

source_name: control + ectopic NADH oxidation


title: CAGE Replicate


title: Input DNA AOX/NDI1 - day 0 rep 1


title: Input DNA AOX/NDI1 - day 3 rep 1


title: RNA-seq in siGPS2

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using tophat aligner.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8
Supplementary_files_format_and_content: bedgraph files displaying the continuous-valued data, as computed by HOMER (homer.salk.edu).


title: H3K9ac AOX/NDI1 - day 0 rep 1


title: Input DNA DN-POLG - day 9 rep 2

source_name: mtDNA depleted, input DNA


title: H3K9ac DN-POLG - day 9 rep 1

source_name: mtDNA depleted


title: Input DNA DN-POLG - day 9 rep 1


title: RNA-seq in siCTL

value: control


title: H3K9ac DN-POLG - day 6 rep 2


title: H3K9ac DN-POLG - day 9 rep 2


title: wt1aGFP_4_pos

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25.
Genome_build: Ensembl genebuild 10, release 82 (Danio rerio assembly Zv9).
Supplementary_files_format_and_content: matrix_counts.xlsx file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

organism: Danio rerio

source_name: Heart

growth_protocol: All experiments were conducted with adult zebrafish between 3 and 9 months of age, raised at a density of 3 fish/l.

extract_protocol:
Whole zebrafish heart ventricles were dissotiated using pronase, elastase, DNase and liberase TH. mCherry-positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure (Thermofisher) following manufacturer instructions.0.2-0.6 ng of total RNA was used to generate barcoded RNA-seq libraries using the Ovation Single Cell RNA-Seq System (NuGEN) with two rounds of library amplification.  The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina). 3-5 pooled hearts were used per sample.
Index-tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA).

treatment_protocol: No treatment was applied.

tag: pool


title: H3K9ac DN-POLG - day 3 rep 2


title: Input DNA DN-POLG - day 6 rep 1


title: Input DNA DN-POLG - day 6 rep 2


title: wt1aGFP_3_neg


title: wt1aGFP_2_pos


title: wt1aGFP_4_neg


title: wt1aGFP_3_pos


title: wt1aGFP_2_neg


title: Input DNA AOX/NDI1 - day 3 rep 2


title: Input DNA DN-POLG - day 3 rep 2


title: wt1aGFP_1_pos


title: RNA-seq in siCTL 2


title: H3K9ac AOX/NDI1 - day 0 rep 2


title: Input DNA DN-POLG - day 3 rep 1


title: wt1aGFP_1_neg


title: H3K9ac DN-POLG - day 0 rep 2

source_name: control


title: H3K9ac DN-POLG - day 0 rep 1


title: neg_7dpi_08

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25.
Genome_build: Ensembl genebuild 10, release 82 (Danio rerio assembly Zv9).
Supplementary_files_format_and_content: Matrix_table.xlsx file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

extract_protocol:
3-5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry-positive and citrine-positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure (Thermofisher) following manufacturer instructions.0.2-0.6 ng of total RNA was used to generate barcoded RNA-seq libraries using the Ovation Single Cell RNA-Seq System (NuGEN) with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).
Index-tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA).

treatment_protocol: Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.

value: 7 days post injury


title: neg_7dpi_09


title: PGD1:OsNAC14 rep2

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

data_processing:
Single-end seq were generated and raw seq reads were trimmed to removed adaptor seq, and those with a quality lower than Q20 were removed using the clc quality trim software (CLCBIO).
Duplicate paired short reads were removed using FastUniq.
All reads were assembled with the clc_ref_assmble 6 (version 4.06) program, using annotated genes from the rapdb (http://rapdb.dna.affrc.go.jp).
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: abundance measurements

organism: Oryza sativa

source_name: PGD1:OsNAC14 (whole body promoter transgenic plants)

growth_protocol: Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.

extract_protocol:
Total RNA was extracted from the leaves of 2-week-old OsNAC14 overexpressors and NT rice seedlings grown under normal growth conditions using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
A modified TruSeq method was used to construct a strand-specific RNA-seq library with different index primers and libraries were sequenced in the Illumina HiSeq 2500 system in the MACROGEN. Cutoff criteria to eliminate genes that showed no significant difference were more than 2 fold up- and down-regulation in PGD1:OsNAC14 compared to NT (Nakdong).

value: Leaves

tag: age

value: 20 days

tag: cultivar

value: Nipponbre


title: H3K9ac DN-POLG - day 6 rep 1


title: PGD1:OsNAC14 rep1


title: Input DNA DN-POLG - day 0 rep 2

source_name: control, input DNA


title: DN-POLG - day 9 rep 3_RNA-seq

data_processing:
The raw RNA-Seq reads were initially processed by filtering with average quality scores greater than 20.
The reads passing the initial processing were aligned to the human reference genome (hg19; Genome Reference Consortium GRCh37 from February 2009) with TopHat version 2.0.4 with TopHat-Fusion function.\n!Sample_data_processing = Composite per kilobase per million reads (RPKM) counts within genomic coordinates of HGNC-annotated genes were used to calculate gene expression differences based on log2-transformed fold-change (log2FC) relative to average gene RPKM at Day 0 (adj. Benjamini-Hochberg p<0.05).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from normalized bedgraph files using bedGraphToBigWig; Scores represent normalized mapped read coverage

extract_protocol:
RNA was isolated using the QIAGEN mini kits and the QIAshredder
Each template was ligated and amplified into sequencing libraries using different indexed adapters (TruSeq RNA v2).


title: Input DNA DN-POLG - day 0 rep 1


title: nontransgenic control rep2

source_name: NT (nontransgenic rice plant)


title: neg_7dpi_07

tag: cell type


title: neg_7dpi_06


title: H3K9ac DN-POLG - day 3 rep 1


title: nontransgenic control rep1

tag: tissue


title: neg_7dpi_05


title: DN-POLG - day 9 rep 1_RNA-seq


title: DN-POLG - day 9 rep 2_RNA-seq


title: postnb_citrine_7dpi_10


title: postnb_citrine_7dpi_07


title: postnb_citrine_7dpi_09


title: White Leaf and Panicle 2

city: Hangzhou

first: lv

middle: yu

last: song

address: CNRRI

institute: CNRRI

description: mRNA sequencing

data_processing:
Prior to assembly, we removed the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) in the raw data. And then we aligned reads of sample yl-1 and sample wild-type to the JGI (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Osativa) rice reference genome using Tophat package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. Tophat allows multiple  alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.Tophat build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.  Transcript abundance estimation and differentially expressed testing  The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the tianscripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The feference GTF annotation file used in Cufflinks was downloaded from the JGI database. Cufflink was used to de novo assemble the transcripiome at first; The second ,Cuffmerge was used to comerge all transcripts of sample A and B to generate unique transcripts. The downloaded JGI GTF file was passed to Cuffdiff along with the original alinment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the GTF file using aligments from the SAM file and concurrently test for different expression. Only the comparisons with “q_value”less than 0.05 and status marked as “OK” in the Cuffdiff output were regarded as showing differential expression.
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: excel,expression profiles

source_name: plants leaves

growth_protocol: The seedlings were cultivated in 1/2 MS medium

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

treatment_protocol: The seedlings were in a growth chamber (12/12h light/dark; light intensity 300 μmol m−2 s−1) at a constant temperature of  32ºC

tag: genotype

value: mutant

tag: cultivar/variety

value: EMS-induced mutant library of  Zhonghua11

value: leaf


title: DN-POLG - day 6 rep 3_RNA-seq

tag: cell line


title: wild-type

description: mRNA sequencing

value: wild type

value: japonica rice variety Zhonghua11


title: kdrl_mCherry_7dpi_07


title: DN-POLG - day 6 rep 2_RNA-seq


title: DN-POLG - day 6 rep 1_RNA-seq


title: neg_7dpi_10


title: DN-POLG - day 0 rep 3_RNA-seq


title: kdrl_mCherry_7dpi_09


title: DN-POLG - day 3 rep 2_RNA-seq


title: kdrl_mCherry_uninjured_03

value: Uninjured


title: kdrl_mCherry_7dpi_06


title: kdrl_mCherry_uninjured_02


title: kdrl_mCherry_7dpi_05


title: DN-POLG - day 3 rep 1_RNA-seq


title: kdrl_mCherry_uninjured_04


title: DN-POLG - day 0 rep 1_RNA-seq


title: postnbCreERT2_60dpi_2

extract_protocol:
Ventricular apex were dissotiated using pronase, elastase, DNase and liberase TH. mCherry-positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure (Thermofisher) following manufacturer instructions.0.2-0.6 ng of total RNA was used to generate barcoded RNA-seq libraries using the Ovation Single Cell RNA-Seq System (NuGEN) with two rounds of library amplification.  The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina). 3-5 pooled hearts were used per sample.
Index-tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA).

treatment_protocol: postnb:CreERT2;ubb:loxP-GFP-loxP-mCherry fish were treated over night with 4-OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.

value: 60 dpi


title: postnbCreERT2_7dpi_1

value: 7 dpi


title: ChiP1_Input.fastq

city: Melbourne

first: Katrina

middle: M

last: Bell

state: Victoria

address: RCH, Flemington Rd, Parkville

country: Australia

institute: MCRI

data_processing:
Data was trimmed for adapters using program trimmomatic
Bowtie2 (v2.10) using default parameters was used to map the 100bp single end reads to the human reference genome (hg19)
The Macs14 (version 1.4.2 ) program was used  to call ChIP peaks from the three NKX2-5  antibody samples (two Abcam antibodies, (Ab1, Ab3) and 1 Santa Cruz antibody (Sc_1))  using one of two input samples (IgG antibody) as a control
Genome_build: hg19
Supplementary_files_format_and_content: Bed files outputed from MACS peak calling program for each of the ChIP seq replicates. Consensus file lists the peaks (or part of peak) identified in all three replicates

source_name: embryonic stem cells (hESCs)

growth_protocol: Differentiated cells were fixed on day 10

extract_protocol:
DNA was purified using a PCR purification kit (QIAGEN)
illumina ChIP Seq protocol

value: IgG

tag: antibody vendor/catalog#

value: Signma


title: DN-POLG - day 3 rep 3_RNA-seq


title: ChiP2_Input.fastq


title: postnbCreERT2_7dpi_4


title: ChiP3_Ab.fastq

value: Abcam ab3584


title: postnbCreERT2_60dpi_1


title: DN-POLG - day 0 rep 2_RNA-seq


title: postnbCreERT2_7dpi_2


title: EW14_CACCTC_L007_R1_001

organism: Boechera depauperata

value: root


title: PID2

city: Beijing

first: Wenkai

last: Hui

state: Beijing

address: Qinghua East Street

institute: Beingjing Forestry 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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NCBI Jatropha curcas Annotation Release 101
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Jatropha curcas

source_name: female flower

extract_protocol:
Total RNA from all samples was extracted separately using TIANDZ Plant RNA Kit (TIANDZ column type RNAout 2.0, Beijing). The quantity and purity of total RNA were examined using agarose gel electrophoresis and Nanodrop 2100 (Agilent, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: floral bud

tag: source

value: Nujiang city, Yunnan province, China

value: three years


title: ChiP2_Sc.fastq

value: Santa Cruz sc-14033


title: EW13_ACAAAC_L007_R1_001

data_processing:
Filtered reads were mapped against the human TAIR10 and Boechera Stricta reference using Tophat v1.4.1 (--library-type fr-firststrand)
Alternative splicing events were identified used rMATS.3.0.9
Differentially expressed genes were identified using DeSeq2
Genome_build: TAIR10, Bstricta.v1.2 (https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Bstricta)
Supplementary_files_format_and_content: count matrix

source_name: root

extract_protocol:
Total RNA 88 was isolated using AMBION RNAeasy isolation kits.The quality of RNA was examined using a BioAnalyzer.
A 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Inc., Brea, CA) were used to purify resulting cDNA, and 1 ng cDNA was subsequently used to prepare a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection.
RNAseq libraries were sequenced using Illumina HiSeq 2500 according to the standard protocol.


title: STD1

source_name: male flower


title: EW12_TGTGAA_L007_R1_001


title: ChiP1_Ab.fastq


title: DA_N2

data_processing:
Tophat2 aligner was used to map the 100bp single end reads to hg19
Uniquely mapped reads were summarized across genes with featureCounts (Rsubread v1.20.6), using UCSC refseq hg19 gene annotation.
RKPMs were generated
Genome_build: hg19

extract_protocol:
RNA was extracted using a High Pure RNA Isolation kit (Roche) and 1 µg was analysed for RNA integrity
Standard Illumina Protocol

treatment_protocol: GFP positive cells were FACS sorted on day 10 of differentiation and snap frozen. Cells were subsequently thawed and collected in PBS to generate 4 pools of >1.0 x 106 cells for both NKX2-5GFP/+ and NKX2-5-/- cell lines

value: Null NKX2-6


title: IND

source_name: Inflorescence  of 0.5 cm diameter

value: inflorescence bud


title: DA_N3

value: Null NKX2-7


title: postnbCreERT2_7dpi_3


title: EW10_CACACA_L007_R1_001


title: DA_N1

value: Null NKX2-5


title: EW9_ACACGA_L007_R1_001


title: STD2


title: DA_H4

value: Het NKX2-7


title: EW11_GTGTTA_L007_R1_001


title: DA_H2

value: Het NKX2-6


title: PID1


title: postnbCreERT2_60dpi_4


title: DA_H1

value: Het NKX2-5


title: ΔNp63-/- input ChIP-Seq

status: Public on Mar 20 2018

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

data_processing:
Reads were mapped to the mouse genome build UCSC mm10/NCBI 38 using Bowtie2. Peaks were called using the macs2 software package for each individual replicate. Final peak calls were obtained by union of the peak calls for individual replicates.
Genome_build: UCSC mm10/NCBI 38
Supplementary_files_format_and_content: BED files with peaks

source_name: E18.5 derived primary murine keratinocytes

growth_protocol: Wild type, TAp63-/-, and ΔNp63-/- keratinocytes were isolated from E18.5 day embryos by treating the skin with Dispase II (Roche). The separated epidermis was minced and incubated in 0.25% trypsin/EDTA (GIBCO) for 20 min. Cells were plated on mitomycin c (Roche)-treated J2-3T3 feeder cells in F media (Sigma) supplemented with 0.4 mg/ml hydrocortisone, 24 ng/ml adenine, 8.4 ng/ml cholera toxin, 5 mg/ml insulin, 13 ng/ml 3,3,5-triiodo-L-thyronine, and 10 ng/ml EGF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Chromatin immunoprecipitated DNA was prepared for sequencing following a modified version of Illumina's Genomic DNA protocol. Sheared DNA fragments undergo end repair by T4 DNA polymerase to fill in 5′ overhangs, Klenow polymerase to remove 3′ overhangs, and T4PNK to phosphorylate the 5′-OH. For Illumina adapter ligation, a single adenine nucleotide overhang must be added to the polished DNA. A 1:30 dilution of the Adaptor Oligo Mix (20) was used in the ligation step. The resulting adapted constructs are amplified by 18 cycles of PCR enriching the DNA fragments with adapters flanking each end. The amplified product was quantified using a spectrophotometer at 260 nm (Nanodrop) then a portion of final sample is size separated on a 6% TBE (Invitrogen) to verify correct target range amplification. The validated DNA library is submitted at a 10 nmol/L concentration for sequencing. All protocols for Illumina library sequence preparation, sequencing, and quality control are provided by Illumina (20).

tag: strain

value: primary murine keratinocytes

tag: passage number


title: TAp63-/- rep2 ChIP-Seq


title: ΔNp63-/- rep2 ChIP-Seq


title: TAp63-/- input ChIP-Seq


title: WT rep1 ChIP-Seq


title: TAp63-/- rep1 ChIP-Seq


title: ΔNp63-/- rep1 ChIP-Seq


title: WT rep2 ChIP-Seq


title: ΔNp63-/- rep1 RNA-Seq

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: UCSC mm10/NCBI 38

extract_protocol:
RNA from the primary murine keratinocytes extracted using the TRIZOL method.
5 μg of polyA+ RNA was used to construct RNA-Seq libraries using the standard Illumina protocol.


title: WT input DNA ChIP-Seq


title: ΔNp63-/- rep2 RNA-Seq


title: TAp63-/- rep3 RNA-Seq


title: TAp63-/- rep2 RNA-Seq


title: TAp63-/- rep1 RNA-Seq


title: WT rep3 RNA-Seq


title: WT rep2 RNA-Seq


title: H3K9ac AOX/NDI1 - day 3 rep 2

source_name: mtDNA depleted + ectopic NADH oxidation

value: H3K9ac (Active Motif, Cat. No. 39137)


title: WT rep1 RNA-Seq


title: GRO-Seq analysis in CUTLL1 cells, 640 minutes post γSI wash, replicate 3

city: New York

first: Nikos

last: Kourtis

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
Library strategy: GRO-Seq
Basecalls performed using CASAVA
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
raw counts per gene were calculated and normalized using DESeq2 package for R and were quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text, raw counts per gene were calculated and normalized using DESeq2 package for R and were quantile normalized.

source_name: CUTLL1 with γSI (640min after wash)

growth_protocol: CUTLL1 cells were grown RPMI 1640 medium supplemented with 20% FBS, penicillin and streptomycin

extract_protocol:
Trizol reagent extraction (Invitrogen)
BrUTP labeled nascent RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.

treatment_protocol: γ-secretase inhibitor was added fom 3 days (500nm) and then it was washed off (0min to 640min after wash)

value: T-cell lymphoma cell line (CUTLL1)


title: GRO-Seq analysis in CUTLL1 cells, 320 minutes post γSI wash, replicate 1

source_name: CUTLL1 with γSI (320min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 640 minutes post γSI wash, replicate 2


title: GRO-Seq analysis in CUTLL1 cells, 640 minutes post γSI wash, replicate 1


title: GRO-Seq analysis in CUTLL1 cells, 320 minutes post γSI wash, replicate 3


title: GRO-Seq analysis in CUTLL1 cells, 320 minutes post γSI wash, replicate 2


title: GRO-Seq analysis in CUTLL1 cells, 160 minutes post γSI wash, replicate 2

source_name: CUTLL1 with γSI (160min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 160 minutes post γSI wash, replicate 1


title: GRO-Seq analysis in CUTLL1 cells, 160 minutes post γSI wash, replicate 3


title: GRO-Seq analysis in CUTLL1 cells, 80 minutes post γSI wash, replicate 3

source_name: CUTLL1 with γSI (80min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 80 minutes post γSI wash, replicate 2


title: GRO-Seq analysis in CUTLL1 cells, 80 minutes post γSI wash, replicate 1


title: GRO-Seq analysis in CUTLL1 cells, 40 minutes post γSI wash, replicate 1

source_name: CUTLL1 with γSI (40min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 40 minutes post γSI wash, replicate 3


title: GRO-Seq analysis in CUTLL1 cells, 20 minutes post γSI wash, replicate 3

source_name: CUTLL1 with γSI (20min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 10 minutes post γSI wash, replicate 3

source_name: CUTLL1 with γSI (10min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 10 minutes post γSI wash, replicate 2


title: GRO-Seq analysis in CUTLL1 cells, 40 minutes post γSI wash, replicate 2


title: GRO-Seq analysis in CUTLL1 cells, 10 minutes post γSI wash, replicate 1


title: GRO-Seq analysis in CUTLL1 cells, 5 minutes post γSI wash, replicate 3

source_name: CUTLL1 with γSI (5min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 20 minutes post γSI wash, replicate 1


title: GRO-Seq analysis in CUTLL1 cells, 0 minutes post γSI wash, replicate 3

source_name: CUTLL1 with γSI (0min after wash)


title: GRO-Seq analysis in CUTLL1 cells, 20 minutes post γSI wash, replicate 2


title: GRO-Seq analysis in CUTLL1 cells, 5 minutes post γSI wash, replicate 2


title: GRO-Seq analysis in CUTLL1 cells, 5 minutes post γSI wash, replicate 1


title: GRO-Seq analysis in CUTLL1 cells, steady state (DMSO), replicate 3

source_name: CUTLL1 with DMSO


title: GRO-Seq analysis in CUTLL1 cells, 0 minutes post γSI wash, replicate 1


title: GRO-Seq analysis in CUTLL1 cells, steady state (DMSO), replicate 2


title: GRO-Seq analysis in CUTLL1 cells, steady state (DMSO), replicate 1


title: ChIP-Seq analysis of HSF1 in P12 cells (rep2)

data_processing:
Alignment was performed with Bowtie2
Peak calling was performed using HOMER
GenomicTools v2.7.2 was used for performing interval operations
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format containing relative enrichments

growth_protocol: cells in suspension, growing in RPMI

extract_protocol:
Twenty million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1. Twenty million cells were used for the ChIP and precipitated using 5 micrograms of antibody (santa cruz biotechnology, N-262) against human MYC
Libraries were generated as described before (Ntziachristos et al., Nat Med, 2012), including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

value: human T cell leukemia cells

tag: antibody

value: HSF1 (Cell Signaling 4356)


title: ChIP-Seq analysis of HSF1 in P12 cells (rep1)


title: ChIP-Seq analysis of MYC in CUTLL1 cells (rep2)

value: MYC (Santa Cruz Biotech, N262)


title: Sequencing analysis of Input (for HSF1 ChIP) in CUTLL1 cells

value: none (input)


title: RNA-Seq analysis in CUTLL1 cells treated with gSI and shHSF1 (rep1)

data_processing:
Basecalling by using CASAVA
Alignment was performed using STAR aligner
DESeq2 for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited-text - DESeq2 normalized FPKM values

extract_protocol:
RNeasy kit (Qiagen)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.

treatment_protocol: cells were treated with gSI for 24H. HSF1 was downregulated for 48H.


title: Sequencing analysis of Input (for MYC ChIP) in CUTLL1 cells


title: Sequencing analysis of Input in P12 cells


title: ChIP-Seq analysis of MYC in CUTLL1 cells (rep1)


title: ChIP-Seq analysis of HSF1 in CUTLL1 cells (rep1)


title: ChIP-Seq analysis of HSF1 in CUTLL1 cells (rep2)


title: RNA-Seq analysis in CUTLL1 cells treated with GSI (rep2)


title: RNA-Seq analysis in CUTLL1 cells treated with GSI (rep1)


title: RNA-Seq analysis in CUTLL1 cells treated with gSI and shHSF1 (rep2)


title: RNA-Seq analysis in CUTLL1 cells treated with shHSF1 (rep1)


title: RNA-Seq analysis in CUTLL1 cells treated with DMSO (rep2)


title: RNA-Seq analysis in CUTLL1 cells treated with DMSO (rep1)


title: GRO-Seq analysis in CUTLL1 cells, 0 minutes post γSI wash, replicate 2


title: K562:GCGTCATTATG

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

institute: EMBL

description: control

data_processing:
demultiplexing of reads using well barcode in read1 (read1 contains well barcode 11bp directly followed by 10bp molecule barcode (UMI) followed by 9bp of fragment; read2 contains transcript sequence part of fragment). Demultiplexed files (one per barcode) contain read2 and the UMI extracted from read1 has been added to the read name.
trimming of read2 with cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -a GGGGGGGGGGGGGGGGGGGGG -a AAAAAAAAAAAAAAAAAAAAA -a GCGTCGTGTAGGGAA -g TTCCCTACACGACGC  -n 2 -m 15 --trim-n  -q 25 -f fastq
mapping with STAR  --runMode alignReads --outFilterMismatchNoverLmax 0.1 --outSAMtype BAM SortedByCoordinate
read counting with featureCounts -R -d 15 -s 1 -g gene_id -t exon -a Mus_musculus.GRCm38.79.gtf
UMI counting (UMI barcode correction and filtering)
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: The file countMatrix.txt contains a matrix of UMI counts (rows: gene identifiers as in Mus_musculus.GRCm38.79.gtf and columns: well barcodes as sample names).

extract_protocol:
Wafergen iCELL8 standard protocol
Nextera XT DNA (Illumina), sc-RNA Seq (single cell RNA Seq)

tag: wellbarcode

value: GCGTCATTATG

tag: sampletype

tag: chiprowid

tag: chipcolumnid


title: K562:GCGGTTGCCTT

description: control

value: GCGGTTGCCTT


title: K562:GGTCCAGAGCC

description: control

value: GGTCCAGAGCC


title: K562:GAACCTTCGTA

description: control

value: GAACCTTCGTA


title: K562:AACGCTCAATA

description: control

value: AACGCTCAATA


title: K562:AAGACCGCATA

description: control

value: AAGACCGCATA


title: K562:AACGCTTCGTT

description: control

value: AACGCTTCGTT


title: K562:AAGACGACGTA

description: control

value: AAGACGACGTA


title: K562:CTTCTACTGCA

description: control

value: CTTCTACTGCA


title: K562:GCGAGTTCTTG

description: control

value: GCGAGTTCTTG


title: K562:AACGATAATCC

description: control

value: AACGATAATCC