title: 0-2 hr embryo

city: Singapore

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: rRNA-depleted total RNA

data_processing:
Sequenced and aligned reads were passed through a Perl filtering algorithm to determine if they were internal to an intron or overlapped with the 5' or 3' junction of each intron in the Drosophila melanogaster (dm3) genome. Each intron was indexed and reads that aligned to the index were parsed and counted to determine molecule size. Sequence information was then extracted for each putative molecule, and pairwise aligned using Blast (43). Positive Blast hits were then aligned with Clustalw2 to determine actual sequence alignment for further downstream analysis (44).
Genome_build: dm3
Supplementary_files_format_and_content: intron coordinates and read counts

organism: Drosophila melanogaster

source_name: 0-2 hr embryo

extract_protocol:
RNA was extraction in accordance to Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 0-2 hr embryo

value: y w


title: C_merged_HTT

status: Public on Oct 10 2015

type: SRA

city: Boston

first: Adam

last: Labadorf

state: MA

address: 72 East Concord Street E301

department: Neurology

country: USA

institute: Boston University Medical School

description: Control sample reads aligning to HTT

library_source: transcriptomic

data_processing:
Bases were called with the Illumina CASAVA 1.7 pipeline
mRNA-Seq reads were trimmed to remove low-quality sequenced bases using the sickle program (https://github.com/najoshi/sickle)
mRNA-Seq reads were aligned to hg38 with the STAR aligner with parameters --readFilesCommand /bin/zcat --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterMultimapNmax 200 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
aligned reads for samples within each condition were merged together using samtools
reads were analyzed for splicing patterns and visualized using custom python scripts
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files containing intron/exon counts
Supplementary_files_format_and_content: all_merged_HTT.bed contains all splicing events detected in the      concatenated read dataset. The columns are chromosome, beginning of splice      junction hg38 coordinate, end of splice junction hg38 coordinate, internal      name of feature, and the number of reads supporting the splice junction.

molecule: polyA RNA

organism: Homo sapiens

source_name: post-mortem prefrontal cortex (Brodman Area 9)

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

tag: disease state

value: Control

tag: tissue

value: prefrontal cortex (Brodman Area 9)


title: AC3_786OlcAr_02_06_15

first: William

middle: G

last: Kaelin

state: Massachusetts

address: 450 Brookline Ave, M457

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using Tophat v2.0 and bowtie 0.12.7 with parameters -p 6 --transcriptome-only --no-novel-juncs
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks 1.3
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: 786-O ccRCC cells

extract_protocol:
Total RNA was extracted using Trizol from cultured cells expresing either Control (VEC) or expressing sh/sgRNA targeting ARNT1
Libraries for sequencing were constructed using standard illumina library preparation protocols

tag: cell type

value: Clear Cell Renal Carcinoma cells

tag: genotype/variation

value: loss of ARNT protein using a lenti-crispr mediated sgRNA

tag: group

value: low HIF state


title: Lab3113leaf-JJ

city: Yangling

first: zai

last: biechu

state: Shaanxi, P.R.China

address: 3 Taicheng Road

department: College of Horticulture

country: China

institute: Northwest A & F University

description:
on the base of 18 6-year-old M. hupehensis (Pamp.) Rehd. trees
Plant sample from Malus hupehensis' leaves on the base of trees for degradome sequencing

data_processing:
Library strategy: degradome-Seq
degradome Pooled libraries were sequenced on an Illumina HiSeq 2000
Mapped reads were matched to potential miRNA target sites in apple cDNAs, identied using the TargetFinder v1.6 script
In order to allow for inaccurate target cleavage or variations in miRNA 5’ ends, the pipeline was modified to recognize targets cleaved at the 9th  or  11th  position  of  the  miRNA,  as  well  as  at  the  10th  position.
In CleaveLand 3, per single miRNA the likelihood for one or more random matches, at a given position,to the degradome data is calculated, using the binomial distribution.
Genome_build: Reference genome is Malus × domestica Borkh
Supplementary_files_format_and_content: PairFinder-JJ text files include pairfinder between miRNA and their targets for J Sample

organism: Malus hupehensis

source_name: Leaf

extract_protocol:
Total RNA extractions from A and J leaves were performed using the RNeasyPlant Mini Kit (Qiagen, Hilden, Germany) and collected into A and J RNA pools. The small RNAs with the adapters were transcribed into cDNA using Super-Script II Reverse Transcriptase (Invitrogen, Shanghai), and then the cDNA products were amplified by polymerase chain reaction (PCR).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves

tag: leaf phase

value: Juvenile phase (J)


title: AC2_786OshAr_02_06_15

value: loss of ARNT protein by virtue of RNAi-mediated knockdown using a shRNA targeting ARNT


title: AC1_786OCon_02_06_15

value: parental Vhl-null cells

value: high HIF state


title: Lab3113leaf-A

description:
the tops of 18 6-year-old M. hupehensis (Pamp.) Rehd. trees
Plant sample from Malus hupehensis' leaves of top of trees

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads produced using an Illumina 1G Genome Analyzer at BGI were processed into clean full-length reads by removing the low-quality reads (e.g., those larger than 30 nt or smaller than 18 nt, those with between 30 and 50 adapter contaminants, those with polyA sequences and those without insert tags) by a data-cleaning pipeline. All high-quality sequences were queried using NCBI GenBank (http://www.ncbi.nlm.nih.gov/genbank) databases and Rfam databases (http://www.sanger.ac.uk/resources/databases/rfam.html), and used for further analyses.
To map every unique small RNA to only one annotation, we followed the following priority rule: rRNAetc (GenBank > Rfam) > known miRNA > repeat > exon > intron3 (Shenzhen, China).
Reads Per of library size  were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Reference genome is Malus × domestica Borkh
Supplementary_files_format_and_content: A and J text files include reads values for each Sample

value: Adult phase (A)


title: Lab3113leaf-J

description:
on the base of 18 6-year-old M. hupehensis (Pamp.) Rehd. trees
Plant sample from Malus hupehensis' leaves on base of trees


title: EScell_Input_exp1B

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

library_source: genomic

data_processing:
Illumina Casava software used for basecalling and making Fastq files.
Short-read sequences were aligned to the mouse genome sequences (mm9 from University of California, Santa Cruz Genome Browser; http://genome.ucsc.edu/) using the Eland program. Sequences with two or more mismatches per sequence were excluded from the analysis.
Each aligned read sequence was extended to 120 bp in order to efficiently detect duplicate reads aligned to identical locations. These 120 bp tags were used for further analysis (Bed files)
Genome_build: mm9
Supplementary_files_format_and_content: Bed files

molecule: genomic DNA

organism: Mus musculus

source_name: B6N-22 ES cells

growth_protocol: B6N-22 ES cells were cultivated on mitomycin C (MMC) -treated mouse embryonic fibroblast (MEF) in DMEM containing 0.1 mM 2-mercaptoethanol, 1000 units/ml leukemia inhibitory factor (LIF), nonessential amino acids (NEAA), sodium pyruvate and 20% fetal bovine serum (FBS)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
IP and input sample libraries were prepared using ChIP-Seq Sample Prep kit (Illumina). Adaptor-ligated DNA fragments were size fractionated by 12% acrylamide gel, and the 170- to 250-bp fraction was recovered. DNA thus obtained was amplified by 18 cycles of PCR. One nanogram of DNA was used for the sequencing reaction of the Illumina GAIIx or Illumina Hiseq 2500, according to the manufacturer’s instructions. A total of 250,000–370,000 clusters was generated per tile, and 36 cycles of the sequencing reactions were performed.

tag: strain

value: B6N-22 ES cell

tag: chip antibody


title: EScell_Bmi1_exp1B

value: Bmi1 (Santa Cruz, catalog# sc-10745, lot#  K1008)


title: EScell_Ezh2_exp1B

value: Ezh2 (Diagenode, catalog# pAb-039-050, lot# 001)


title: EScell_ControlAb_exp1B

value: Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877)


title: EScell_RNAPII_exp1B

value: RNA polymerase II (Abcam, catalog# ab5408, lot# 646081)


title: Bcell_ControlAb_exp1B

source_name: Primary B220_B cells isolated from 6-8 week old mice (C57BL/6)

growth_protocol: Spnelic B220_B cells were purified using magnetic beads and an AutoMACS sorter (Miltenyi Biotec) that yielded purity of >98%.

value: B220 B cell


title: CD4Tcell_Input_exp1B

source_name: Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6)

growth_protocol: Splenic CD4_T cells were purified using magnetic beads and an AutoMACS sorter (Miltenyi Biotec) that yielded purity of >98%.

value: CD4 T cell


title: EScell_Menin_exp1B

value: Menin (Bethyl, catalog# A300-105A, lot#  A300-105A-1)


title: CD4Tcell_ControlAb_exp1B


title: CD4Tcell_Ezh2_exp1B


title: Bcell_Input_exp1B


title: Bcell_Ezh2_exp1B


title: Bcell_RNAPII_exp1B


title: CD4Tcell_RNAPII_exp1B


title: Th2-2nd_Menin_exp1A

source_name: Two-week cultured Th2 cells generated from primary splenic CD4_T cells

growth_protocol: Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro. The Th2 cells were further cultured in vitro for another 2 days in the absence of any exogenous cytokines. The cultured CD4 T cells were then restimulated with immobilized anti-TCR mAbs with IL-2 and anti-IL-4 mAbs for 5 days.

value: Th2 cell


title: Th2-2nd_input_exp1A


title: Th2-2nd_controlAb_exp1A


title: Th2cell_Bmi1_exp1A

source_name: Five-day cultured Th2 cells generated from primary splenic CD4_T cells

growth_protocol: Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro.


title: Th2cell_Menin_exp1A


title: Th2cell_controlAb_exp1A


title: Th2cell_input_exp1A


title: Th1cell_Bmi1_exp1A

source_name: Five-day cultured Th1 cells generated from primary splenic CD4_T cells

growth_protocol: Splenic CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 1 ng/ml IL-12) for 5 days in vitro.

value: Th1 cell


title: Th1cell_Menin_exp1A


title: Th1cell_controlAb_exp1A


title: CD4Tcell_controlAb_exp1A


title: CD4Tcell_Menin_exp1A


title: CD4Tcell_Bmi1_exp1A


title: Th1cell_input_exp1A


title: Bcell_controlAb_exp1A


title: Bcell_Menin_exp1A


title: Bcell_input_exp1A


title: Bcell_Bmi1_exp1A


title: Th2-2nd_Bmi1_exp1A


title: yeast RNA-seq fast BioRep3

city: Manchester

first: Craig

last: Lawless

address: Dover Street

department: Faculty of Life Sciences

country: United Kingdom

institute: University of Manchester

data_processing:
Sequence reads were mapped to the prebuilt Saccharomyces cerevisiae reference genome obtained from the Bowties website and aligned using Bowtie v1.0.0 with the -m 1 option
Cufflinks version 2.0.0 was run against a the reference GTF file obtained from Saccharomyces Genome Database (SGD), to produce FPKM values per transcript.
Genome_build: Saccharomyces genome obtained from bowtie website.
Supplementary_files_format_and_content: tab delimited text files generated from Cufflinks (version 2), providing FPKM values for each transcript for each sample.

organism: Saccharomyces cerevisiae

source_name: yeast sample

growth_protocol: Saccharomyces cerevisiae (EUROSCARF accession number Y11335 BY4742; Mat ALPHA; his3delta1; leu2delta0; lys2delta0; ura3delta0; YJL088w::kanMX4) was grown in defined minimal C-limiting (F1) medium (71) using 10 g.l-1 of glucose as the sole carbon source. The F1 medium was additionally supplemented with 0.5 mM arginine and 1 mM lysine to meet the added auxotrophic requirements of the strain. For biological replication, four cultures were grown in chemostat mode at a dilution rate of 0.1 h-1 and aliquots (15 ml) of the culture were centrifuged (4000 rpm; 4 °C; 10 minutes). The supernatant was discarded, the pellet flash frozen in liquid nitrogen and stored at -80 °C.

extract_protocol:
All solutions used were prepared with DEPC (diethylpyrocarbonate 0.1% v/v) treated water. Frozen sample aliquots were ground to a fine powder under liquid nitrogen(73).  Pestle and mortar were soaked in 10% bleach to destroy residual RNase activity and washed with diethylpyrocarbonate (DEPC) treated water. RNA was extracted using TriZol® reagent according to the methods of Hayes et al.(71) and the final concentration was measured prior to RNA sequencing using a NanoDrop system.
Sequencing libraries were generated using the whole Transcriptome Library Preparation protocol provided with the SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA).  Briefly, rRNA depleted samples were fragmented using RNase III, and subsequently cleaned up using the RiboMinus™ Concentration Modules (Life technologies, Carlsbad, CA).  Fragmentation was assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using the RNA picochip.  Fragmented RNAs were reverse transcribed and size selected on a denaturing polyacrylamide gel selecting for 150-250nt cDNA.  cDNA was then amplified and barcoded with SOLiD™ RNA barcoding Kit.  Samples were then purified using PureLink™ PCR Micro Kit (Life Technologies, Carlsbad, CA) and assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using the High Sensitivity DNA chip.

tag: growth rate

value: fast

tag: condition

value: chemostat


title: yeast RNA-seq fast BioRep4


title: yeast RNA-seq fast BioRep1


title: N98_MB_24H

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: Sample 75

data_processing:
Computational analyses were performed on a 32-node Compute Server with Linux Ubuntu (version 12.04.2). An initial quality check was performed on each of the raw reads data files using the FastQC software (version 0.10.1) to determine the most appropriate read cleaning strategy. Subsequently, a custom Perl script was used to: (1) deconvolute the pooled libraries into individual libraries based on the unique index barcode; (2) filter out paired-end reads containing adapter sequence contamination; and (3) remove paired-end reads of poor quality. The quality of the individual libraries files was then reassessed post-filtering using the FastQC software. Paired-end reads, from each filtered individual library, were aligned to the B. taurus reference genome (B. taurus UMD3.1.71 genome release) using the STAR aligner software (version 2.3.0), and were further aligned to the complete genome of M. bovis AF2122/97 (reference sequence NC_002945.3) to determine the level of M. bovis sequence read contamination (see pipeline accessible online).
For each library, raw counts for each gene based on sense strand data were obtained using the featureCounts software from the Subread package (version 1.3.5-p4). The featureCounts parameters were set to unambiguously assign uniquely aligned paired-end reads in a stranded manner to the exons of genes within the B. taurus reference genome annotation from Ensembl (B. taurus UMD3.1.71 genome annotation) [34]. The gene count outputs were used to perform differential gene expression analysis using the edgeR Bioconductor package (version 3.2.4) within the R statistical programming environment. The differential gene expression pipeline within the edgeR package was customised to: (1) filter out all bovine rRNA genes; (2) filter out genes displaying expression levels below the minimally-set threshold of one count per million [CPM] in at least ten individual libraries; (3) calculate normalisation factors for each library using the trimmed mean of M-values method; (4) generate the density of counts per gene and multidimensional scaling (MDS) plots based on data from each individual library; (5) estimate the dispersion parameter for each library using the Cox-Reid method; (6) identify differentially expressed genes between M. bovis-infected versus non-infected control samples from the same animal (i.e., paired-sample statistical model) within each time point using a negative binomial generalised linear model; and (7) correct for multiple testing using the Benjamini-Hochberg method with a FDR threshold of 0.05 (see pipeline accessible online).
For antisense gene analyses, the B. taurus reference genome annotation (B. taurus UMD3.1.71 genome annotation) was modified such that antisense genes were located on the opposite strand of their associated sense genes and to include a promoter and terminator region. Furthermore, to limit false positive antisense detection, proximal genes closer than 5.0 kb were ignored for the custom B. taurus antisense genome annotation. For each library, a custom Perl script was used to select uniquely aligned paired-end reads not previously assigned to any sense gene. The featureCounts parameters were set to unambiguously assign selected reads in a stranded manner to the full gene length (including promoter, exon, intron and terminator regions) of genes within the custom B. taurus antisense genome annotation.  To remove antisense gene artefacts, which may arise due to bias in the RNA-seq library preparation protocol, we performed an antisense gene counts ratio filtering procedure modified from a method described by Perocchi and colleagues. For this step, the featureCounts software was used to generate the following for each library: (1) raw counts per antisense gene over exons only; and (2) raw counts per sense gene over the full gene length. Subsequently, for each library, the edgeR package was used to combine: (1) the sense gene raw counts over exons only; (2) the antisense gene raw counts over exons only; (3) the sense gene raw counts over the full gene length; and (4) the antisense gene raw counts over the full gene length. Genes displaying expression levels below the minimally-set threshold of 20 CPM in at least ten individual libraries were filtered out. A percentage ratio of antisense counts over total counts was calculated for over exons only and over the full gene length data sets for each gene and individual library:  [Exon ratio]^(g,l)=([AS exon]^(g,l)  ×100)/([AS exon]^(g,l)+[S exon]^(g,l) )  [Full gene ratio]^(g,l)=([AS full gene]^(g,l)  ×100)/([AS full gene]^(g,l)+[S full gene]^(g,l) )  AS = antisense count; S = sense count; g = gene; l = library.  A greater-sided pairwise Wilcoxon signed-rank tests was then used to assess significant differences between the full gene ratio and the exon ratio for each gene. Antisense genes found to be significant with this ratio method were then used for differential gene expression analysis (between M. bovis-infected versus non-infected control samples for each time point) using the edgeR package and the raw counts (over full gene lengths) for each antisense gene according to the sense gene differential expression method described above (see pipeline accessible online).
For novel genes analyses, aligned reads were processed via the Cufflinks software package (version 2.1.1) using the reference annotation based transcript assembly method and the B. taurus reference genome annotation (B. taurus UMD3.1.71 genome annotation) to generate a de novo transcripts assembly. The de novo transcripts assembly files, obtained for each RNA-seq library, were combined into a single merged transcript assembly using the Cuffmerge script within the Cufflinks software package.  The reciprocal best hit (RBH) method was used to annotate putative novel genes. Nucleotide sequences for these putative novel genes were obtained using the gffread utility within the Cufflinks software package. Putative novel gene sequences were blasted against all Homo sapiens reference protein sequences (H. sapiens GRCh37.73 protein sequence) using standalone BLAST® (version 2.2.28+). A custom Perl script was then used to select the best H. sapiens protein hit for each B. taurus novel gene. Subsequently, the best H. sapiens protein sequence hits were reciprocally blasted against all B. taurus gene sequences (including reference genes and novel genes). Finally, a custom Perl script was used to determine the RBH among the bovine novel genes identifed; RBH genes with a BLAST Expectation value (E-value) ≥ 1 × 10−4 were filtered out.  For each library, a custom Perl script was used to select uniquely aligned paired-end reads not previously assigned to any sense or antisense gene. Following this, the featureCounts software was used to unambiguously assign selected reads in a stranded manner to exons for each gene ID from the de novo B. taurus genome annotation. For each library, the raw counts per novel gene were used for differential expression analysis (between M. bovis-infected versus non-infected control samples for each time point) using the edgeR package according to the previously described sense gene differential expression method; however, in this case the low expression filtering threshold was set to a minimum of 30 CPM in at least ten libraries (see pipeline accessible online).
Genome_build: Bos taurus reference genome version UMD3.1.71
Supplementary_files_format_and_content: Tab-delimited text files include raw count values per genes (*sense.txt: sense gene raw count; *antisense.txt;antisense gene raw count; *novel.txt; Novel gene raw count)

organism: Bos taurus

source_name: M. bovis-infected_24hr post-infection

growth_protocol: Ethical approval for this study was obtained from the University College Dublin (UCD) Animal Ethics Committee (protocol number AREC-13-14-Gordon). Fourteen unrelated, age-matched Holstein-Friesian male calves (7-12 weeks old) were selected from a tuberculosis-free herd and maintained under uniform housing conditions and nutritional regimens at the UCD Lyons Research Farm (Newcastle, County Kildare, Ireland). Total lung cells were harvested by pulmonary lavage of lungs obtained post-mortem. All lungs were inspected by a veterinary surgeon for signs of inflammation and pathology before proceeding with lung washes in a laminar flow hood. Sterile calcium- and magnesium-free Hank's Balanced Salt Solution (HBSS; Invitrogen™, Life Technologies Corp., Paisley, UK) was infused into the lungs (500 ml per infusion; repeated approximately six times) via the trachea. Lungs were gently massaged and the HBSS-cell suspension was collected into sterile beakers. An aliquot of HBSS-cell suspension was screened for microbial contamination; all animals tested negative for microbial contamination in the lungs.  The remaining HBSS-cell suspension was transferred to 50 ml sterile tubes and centrifuged (200 × g for 10 min at room temperature [RT]). The resulting cell pellets were pooled and resuspended in 50 ml cold R10− media (RPMI 1640 medium [Invitrogen™, Life Technologies Corp.] supplemented with 10% foetal bovine serum (FBS), 2.5 µg/ml amphotericin B, and 2 mM L-glutamine [all sourced from Sigma-Aldrich Ltd., Dublin, Ireland]). The cell suspension was centrifuged (200 × g for 10 min at RT) and resuspended in 10 ml R10+ media (R10− media supplemented with 100 μg/ml ampicillin and 25 μg/ml gentamycin [all sourced from Sigma-Aldrich Ltd.]). Cells were counted using a haemocytometer, centrifuged (200 × g for 10 min at RT) and resuspended in 90% FBS with 10% dimethyl sulfoxide (Sigma-Aldrich Ltd.) at a density of 2.5 × 107 cells/ml. Cells were aliquoted in 2 ml sterile cryovials (Sarstedt Ltd., Wexford, Ireland), which were placed into Mr. Frosty® Cryo 1 °C Freezing Containers (Nalgene®, Thermo Fisher Scientific, Waltham, MA, USA) containing 100% isopropyl alcohol. Cryovials were stored at −80 °C for a period of 20 h after which they were transferred to −140 °C freezer storage until required.  Approximately 1.5 × 108 total lung cells from each animal were removed from −140 °C storage and thawed in a 37 °C water bath for 1 min. Cells from the same animal were transferred into 20 ml pre-warmed R10+ media (note: all pre-warmed media and solutions were heated to 37 °C prior to use) and centrifuged (200 × g for 5 min at RT). The cell pellet was resuspended in 15 ml of R10+ media, placed in a 75 cm2 vented culture flask (CELLSTAR®, Greiner Bio-One Ltd., Stonehouse, UK) and incubated for 24 h at 37 °C, 5% CO2. After incubation, media was removed and adherent cells were washed with 15 ml pre-warmed HBSS. Adherent cells were dissociated by adding 10 ml pre-warmed cell dissociation solution non-enzymatic 1× (Sigma-Aldrich Ltd.) per culture flask and incubating at RT for 10 min. Cells were transferred to 30 ml of pre-warmed R10+ media, centrifuged (200 × g for 5 min at RT), resuspended in 10 ml pre-warmed R10+ media and the number of viable cells was counted using a Beckman Coulter® Vi-CELL™ XR Cell Viability Analyzer and reagent kit (Beckman Coulter Inc., Hugh Wycombe, UK). Cell concentrations for each animal were adjusted to 5 × 105 viable cells/ml using pre-warmed R10+ media, seeded at 1 ml/well in 24-flat well tissue culture plates (Sarstedt Ltd.) and incubated for 24 h at 37 °C, 5% CO2, until required for infection.  The identity and purity of the seeded macrophages were confirmed by flow cytometry (Conway Institute, UCD, Ireland) with anti-CD14 antibody; flow cytometry data were analysed within the R statistical programming environment (version 3.0.1) using the flowCore (version 1.26.2) and flowViz (version 1.24.0) Bioconductor packages (see pipeline accessible online) .

extract_protocol:
All RNA extractions were performed using an RNeasy® Plus Mini kit (Qiagen Ltd.) according to the manufacturer’s instructions. RNA quantity and quality was assessed using a NanoDrop™ 1000 spectrophotometer (Thermo Fisher Scientific Inc.) and an Agilent 2100 Bioanalyzer with a RNA 6000 Nano kit (Agilent Technologies Ltd., Cork, Ireland). All samples displayed a concentration ranging from 10 up to 135 ng/μl (median 50 ng/μl), a 260/280 ratio greater than 2.0 and RNA integrity numbers greater than 8.5. RNA samples were stored at −80 °C until required.
For the current study, 78 strand-specific RNA-seq libraries were prepared. These comprised M. bovis- and non-infected samples from each post-infection time points (2, 6, 24 and 48 h) across 10 animals (with the exception of one animal that did not yield sufficient alveolar macrophages for in vitro infection at the 48 h post-infection time point).
For RNA-seq library preparation, 200 ng of total RNA from each sample was used to prepare individually barcoded strand-specific RNA-seq libraries. Two rounds of poly(A)+ RNA purification were performed for all RNA samples using the Dynabeads® mRNA DIRECT™ Micro Kit (Invitrogen™, Life Technologies Corp.) according to the manufacturer’s instructions. The purified poly(A)+ RNA was then used to generate strand-specific RNA-seq libraries using the ScriptSeq™ v2 RNA-Seq Library Preparation Kit, the ScriptSeq™ Index PCR Primers (Sets 1 to 4) and the FailSafe™ PCR enzyme system (all sourced from Epicentre®, Illumina® Inc., Madison, WI, USA) according to the manufacturer’s instructions. RNA-seq libraries were purified using the Agencourt® AMPure® XP system (Beckman Coulter Genomics, Danvers, MA, USA) according to the manufacturer’s instructions for double size selection (0.75× followed by 1.0× ratio). RNA-seq libraries were quantified using a Qubit® fluorometer and Qubit® dsDNA HS Assay Kit (Invitrogen™, Life Technologies Corp.), while library quality checks were performed using an Agilent 2100 Bioanalyzer and High Sensitivity DNA Kit (Agilent Technologies Ltd.). Individually barcoded RNA-seq libraries were pooled in equimolar quantities and the quantity and quality of the final pooled libraries (three pools in total) were assessed as described above.
Cluster generation and sequencing of the pooled RNA-seq libraries were performed by BGI (BGI–Hong Kong, Hong Kong, China) using an Illumina® HiSeq™ 2000 sequencer. Each of the pooled libraries was sequenced as paired-end 2 × 90 nucleotide reads on eight Illumina® flow cell lanes.

treatment_protocol: Culturing of M. bovis AF2122/97 was performed in a Biosafety Containment Level 3 laboratory and conformed to Irish national guidelines on the use of Hazard Group 3 infectious organisms. M. bovis AF2122/97 strain was obtained from the Animal Health and Veterinary Laboratory Agencies (AHVLA, Addlestone, Surrey, UK) and was cultured to late logarithmic phase in 200 ml Middlebrook 7H9 media (Difco™, Becton, Dickinson Ltd., Oxford, UK) enriched with 1× Middlebrook albumin-dextrose-catalase (ADC; Difco™) and a final concentration of 10 mM sodium pyruvate (Sigma-Aldrich Ltd.). The M. bovis culture stocks were aliquoted (1 ml per aliquot) into sterile 2 ml cryovial tubes (Thermo Fisher Scientific Inc., Waltham, MA, USA) and stored at −80 °C until required.  Approximately 14 days prior to alveolar macrophage infection, 1 ml M. bovis culture stock was thawed, added to 4 ml Middlebrook 7H9-ADC medium containing 10 mM sodium pyruvate and cultured at 37 °C, 5% CO2 until mid-logarithmic phase (5-7 days). The 5 ml starter cultures were then transferred to 25 ml fresh Middlebrook 7H9-ADC medium containing 10 mM sodium pyruvate and cultured statically in vented 500 ml Corning™ Erlenmeyer flasks (Thermo Fisher Scientific Inc.) at 37 °C, 5% CO2 until late-logarithmic phase (approximately 10 days).  On the day of alveolar macrophage infection, the 25 ml M. bovis culture was centrifuged (200 × g for 10 min); subsequently the cell pellet was disrupted by vortexing at top speed for 1 min in the presence of ten 3 mm sterile glass beads (Sigma-Aldrich Ltd.). Cells were resuspended in 5-10 ml pre-warmed R10− media and sonicated at full power for 1 min in a Bransonic 2510 ultrasonic cleaner (Branson Ultrasonics Corp., Danbury, CT, USA). The OD600nm of the culture was then measured and the number of cells was calculated based on an OD600nm of 0.1 being equivalent to 1 × 107 bacterial cells. The cell number was adjusted to 5 × 106 bacterial cells/ml using R10− media.  For infections, the R10+ media from all tissue culture plate wells containing alveolar macrophage (5 × 105 cells/well) was removed and replaced with 1 ml R10− media containing M. bovis (5 × 106 cells/ml), yielding a multiplicity of infection (MOI) of 10 bacilli per macrophage. Parallel non-infected control alveolar macrophage samples received 1 ml R10− media only. Alveolar macrophages were then incubated at 37 °C, 5% CO2 for 2, 6, 24 and 48 h. After 2 h post-infection, the media from all 6, 24 and 48 h infection experiments was replaced with 1 ml/well of R10− media and tissue culture plates were reincubated at 37 °C, 5% CO2 until the cells were required for harvesting. This resulted in an average uptake of 2 bacteria per macrophage. Infected and non-infected control alveolar macrophages were lysed by adding 250 μl/well RLT buffer supplemented with 1% β-mercaptoethanol (Qiagen Ltd., Crawley, UK). Alveolar macrophage lysates from duplicate wells were pooled and stored at −80 °C until required for RNA extraction.

tag: breed

value: Holstein-Friesian

tag: Sex

value: male

tag: age

value: 7-12 weeks

tag: animal id

value: Alveolar macrophages

tag: infection status

value: M. bovis-infected

tag: time point

value: 24hr post-infection


title: N98_MB_6H

description: Sample 78

source_name: M. bovis-infected_6hr post-infection

value: 6hr post-infection


title: N98_MB_2H

description: Sample 76

source_name: M. bovis-infected_2hr post-infection

value: 2hr post-infection


title: N98_CN_24H

description: Sample 71

source_name: Control_24hr post-infection

value: Control


title: N98_CN_48H

description: Sample 73

source_name: Control_48hr post-infection

value: 48hr post-infection


title: lySEP3-biorep2

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the Araly1 genome assembly using SOAPv2 with up toof two mismatches and no gaps were allowed, and reads were iteratively trimmed from the 5` end until mapped or their length fell below 31 nt.
Only uniquely mapped reads were retained. Sequence reads mapping to the plastid and mitochondrial genomes were eliminated. For A lyrata, only reads mapping to the 9 longest scaffolds were retained (length > 1MB)
peaks were called using CSAR with default parameters except backg which was set to 14
Genome_build: Araly1
Supplementary_files_format_and_content: peak files shows the coordinates and score value obtained by CSAR

organism: Arabidopsis lyrata

source_name: Inflorescences

growth_protocol: A. lyrata plants were germinated and vernalized for 7-10 weeks at 8 oC day/ 4 oC night, 12 h light/12 h dark. Bolting was initiated at 18-22 oC under long-day conditions.

extract_protocol:
Chromatin was essentially extracted according to Kaufmann et al, Nature Protocols 2010
Libraries were essentially constructed according to Kaufmann et al., Nature Protocols 2010

tag: develomental stage

value: inflorescence with floral buds of stage 1-10/11

value: Inflorescences


title: N1870_MB_48H

description: Sample 69

source_name: M. bovis-infected_48hr post-infection


title: N1870_MB_6H

description: Sample 70


title: N98_CN_2H

description: Sample 72

source_name: Control_2hr post-infection


title: N98_CN_6H

description: Sample 74

source_name: Control_6hr post-infection


title: N1870_MB_2H

description: Sample 68


title: N1870_MB_24H

description: Sample 67


title: CD4Tcell_input_exp1A

value: CD4 T cell


title: N1870_CN_6H

description: Sample 66


title: N1870_CN_48H

description: Sample 65


title: yeast RNA-seq fast BioRep2


title: N98_MB_48H

description: Sample 77


title: N1870_CN_2H

description: Sample 64


title: thInflo rep2

data_processing: For each library independently reads were mapped to the transcriptome sequence of corresponding organism. We download the sequences of the primary transcript from Phytozome version 8.0, file:”Athaliana_167_TAIR10.transcript_primaryTranscriptOnly.fa” for A . thaliana and “Alyrata_107_transcript_primaryOnly.fa” for A. lyrata. Read mapping was done with SOAPv2 with default parameter values. Reads mapping to more than one transcript or to the mitochondrial or chloroplast transcriptome were discarded. Only reads mapping to the forward strand of the transcript were used for further analysis.

organism: Arabidopsis thaliana

growth_protocol: A. lyrata: long day at 18 degrees, A. thaliana: standard greenhouse conditions, long day

extract_protocol:
invitrap spin plant RNA mini kit, including the additional DNA digestion
Fasteris directional RNA-seq

value: plants after bolting

tag: genotype

value: wild type


title: N1870_CN_24H

description: Sample 63


title: thInflo rep1

tag: tissue


title: N1864_MB_48H

description: Sample 61

tag: cell type


title: N1864_CN_6H

description: Sample 58


title: N1864_MB_2H

description: Sample 60


title: N1864_MB_24H

description: Sample 59


title: N1864_CN_48H

description: Sample 57


title: N1864_MB_6H

description: Sample 62


title: N1864_CN_24H

description: Sample 55


title: N1861_MB_2H

description: Sample 53


title: N1864_CN_2H

description: Sample 56


title: N1861_CN_2H

description: Sample 50


title: N1861_MB_6H

description: Sample 54


title: N1861_MB_24H

description: Sample 52


title: N1861_CN_6H

description: Sample 51


title: N1859_MB_24H

description: Sample 45


title: N1861_CN_24H

description: Sample 49


title: thInflo rep3


title: N1859_MB_48H

description: Sample 47


title: N1859_MB_2H

description: Sample 46


title: N1859_CN_6H

description: Sample 44


title: N1859_MB_6H

description: Sample 48


title: N1859_CN_24H

description: Sample 41


title: N1855_MB_48H

description: Sample 39


title: N1855_MB_2H

description: Sample 38


title: N1855_MB_6H

description: Sample 40


title: N1855_MB_24H

description: Sample 37


title: N1855_CN_24H

description: Sample 33


title: N1855_CN_48H

description: Sample 35


title: N1855_CN_6H

description: Sample 36


title: N158R_MB_2H

description: Sample 30


title: N158R_MB_6H

description: Sample 32


title: N1859_CN_48H

description: Sample 43


title: N158R_MB_24H

description: Sample 29


title: N1859_CN_2H

description: Sample 42


title: N158R_CN_6H

description: Sample 28


title: N158R_CN_2H

description: Sample 26


title: N138_MB_48H

description: Sample 23


title: N138_MB_6H

description: Sample 24


title: N138_CN_6H

description: Sample 20


title: N138_MB_24H

description: Sample 21


title: N138_CN_48H

description: Sample 19


title: N158R_MB_48H

description: Sample 31


title: N121_CN_2H

description: Sample 10


title: N121_CN_48H

description: Sample 11


title: N158R_CN_48H

description: Sample 27


title: N121_MB_2H

description: Sample 14


title: N121_CN_24H

description: Sample 9


title: N121_MB_24H

description: Sample 13


title: N121_CN_6H

description: Sample 12


title: N1178_MB_6H

description: Sample 8


title: N1178_MB_48H

description: Sample 7


title: N121_MB_48H

description: Sample 15


title: N1178_MB_2H

description: Sample 6


title: N1178_CN_6H

description: Sample 4


title: N138_MB_2H

description: Sample 22


title: N1178_CN_2H

description: Sample 2


title: N158R_CN_24H

description: Sample 25


title: N1178_MB_24H

description: Sample 5


title: N1178_CN_24H

description: Sample 1


title: N121_MB_6H

description: Sample 16


title: N1178_CN_48H

description: Sample 3


title: N138_CN_24H

description: Sample 17


title: input DNA

city: Mainz

first: Vijay

middle: K

last: Tiwari

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
FAIRE-seq and H3K27ac reads were aligned to the mm9 genome assembly using Bowtie version 0.12.9  with -p set to 10, -m to 1, RNA-seq reads were  aligned using TopHat with parameter -p set to 24 aligned using
For FAIRE-seq and ChIP-seq data: peaks were called on a merged bam file of all the conditions were called using MACS2.
For FAIRE-seq and ChIP-seq data: Enrichment in FAIRE mark for the two conditions (untreated and UV 6h)  were computed at promoter regions or at peak locations using the formula proposed in Tiwari et al. 2011 (PMID:22179133), see Material and Methods.
For RNA-seq data: Counts were normalized using estimateSizeFactors function from DESeq2 package.
For RNA-seq data: Differentially expressed genes were determined using DESeq2 package with cut-off of 0.1 for p-value adjusted for multiple testing.
Genome_build: mm9
Supplementary_files_format_and_content: For FAIRE and ChIP-seq data: We provide a unique files containing the merged peaks (AllMergedPeaksWithModel_FAIRE_peaks.bed and AllMergedPeaksWithModel_H3K27ac_peaks.bed) found in all conditions (using a merged files of all aligned samples). We also provide a file (NormalizedEnrichment_Peaks_FAIRE_merged.txt and NormalizedEnrichment_Peaks_H3K27ac_merged.txt) with the enrichment values at peaks for the different conditions with merged replicates (i.e. one enrichment value for untreated, and one for 6h UV). Finally, we provide enrichments at promoters (NormalizedEnrichment_Promoter_FAIRE_merged.txt and NormalizedEnrichment_Promoter_H3K27ac_merged.txt). For RNA-seq data: normalized counts processed by  are provided as well as differentially expressed genes detected by DESeq2 using cut-off of 0.1 for p-value adjusted for multiple testing.

source_name: NIH3T3 cells

growth_protocol: NIH3T3 cells purchased from ATCC (NIH/3T3 (ATCC® CRL-1658™)) were cultured at 37°C, 7% CO2 and 88% relative air humidity. Culture medium contained DMEM supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, and 1x non-essential amino acids.

extract_protocol:
For FAIRE: Nuclei of formaldehyde crosslinked cells were isolated, lysed and sonicated. Accessible DNA was isolated from the clarified lysates by phenol-chloroform extraction. For ChIP-seq: Nuclei of formaldehyde crosslinked cells were isolated, lysed and sonicated. H3K27ac-DNA complexes were isolated from the clarified lysates with antibody against H3K27ac. For RNA-seq: RNA from harvested cells were column purified with Purelink RNA Mini kit (12183025, life technologies).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Two days before the experiment, cells were seeded at a density of 3000 cells/cm2. Then culture medium was removed and the cells washed twice with DPBS. Any residual solution was carefully removed and the uncovered cells were irradiated with 80 J/m2 UV-C (254 nm) in a CL-1000 Ultraviolet Crosslinker (UVP). Fresh culture medium containing 1:2000 DMSO was added to the cells and cultured again for six hours.

tag: cell line

tag: treatment

tag: antibody

tag: replicate

value: input


title: Th2cell-TSA_RNA_exp2

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Five-day cultured Th2 cells generated from primary splenic CD4_T cells were treated with trichostatin A (TSA)

growth_protocol: Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro. For TSA treatment, splenic CD4 cells were cultured under Th2 conditions and 10 nM TSA (Sigma, St Louis, MO) was added in the culture on day 2 and after another 3-days of culture, Th2 cells were collected for analysis.

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq RNA Sample Prep Kit v2  (Illumina) was used according to the manufacturer's protocol.

tag: strain

value: Th2 cell

value: TSA


title: RNA-seq_UV_6h_R2

value: 80 J/m2 UV-C (254 nm) for 6hrs


title: RNA-seq_UV_6h_R1


title: Th2cell-TSA_Menin_exp2

tag: chip antibody

value: Menin (Bethyl, catalog# A300-105A, lot#  A300-105A-1)


title: RNA-seq_untreated_R2


title: RNA-seq_untreated_R3


title: RNA-seq_untreated_R1


title: Th2cell-TSA_RNA_exp1


title: Th2cell-TSA_Input_exp2


title: D8A rep2

city: Woolloongabba

first: Inge

last: Seim

state: Queensland

address: 37 Kent St

country: Australia

institute: Queensland University of Technology

data_processing:
FASTQ files were aligned to the yeast genome, ensembl build R64-1-1 downloaded from the Illumina iGenome resource at http://goo.gl/LspLBZ, using Bowtie2 v2.1.0 [PMID 22388286] and the spliced-read mapper TopHat (v2.0.9) [PMID 23618408] and reference gene annotations to guide the alignment (-G argument in TopHat).
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Cufflinks v2.1.1 [PMID 22383036], with default parameters.
Genome_build: ensembl R64-1-1 (GCA_000146045.2)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample (abundance measurements).

source_name: thiol peroxidase null yeast strain

growth_protocol: yeast extract-peptone-dextrose (YPD) medium

extract_protocol:
Frozen aliquots were thawed and lysed in 400 μL of lysis buffer (mRNA DIRECT kit; Invitrogen). A 250-μL aliquot of magnetic beads and two rounds of purification were implemented according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: MATa, his3 leu2 met15 ura3 delta-tsa1:KAN, delta-tsa2:LEU2,delta-dot5:MET15, delta-ahp1:HIS3, delta-prx1:URA3, delta-gpx2:HYG, delta-gpx1:URA3, delta-gpx3:KAN,delta-srx1:NAT


title: N138_CN_2H

description: Sample 18

tag: breed

value: Holstein-Friesian

value: male

value: 7-12 weeks

value: Alveolar macrophages


title: D8B rep2


title: H3K27ac_untreated_R1


title: H3K27ac_UV_6h_R1


title: Th2cell-TSA_Ezh2_exp2

value: Ezh2 (Diagenode, catalog# pAb-039-050, lot# 001)


title: D8B rep1


title: RNA-seq_UV_6h_R3


title: FAIRE_untreated_R1


title: H3K27ac_untreated_R2


title: Th2cell_Input_exp2


title: Th2cell_RNA_exp2


title: CD4Tcell_Menin_exp2

source_name: Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6)


title: FAIRE_UV_6h_R2


title: Wt-M11 rep1

source_name: Wtmonosome-XI

value: MAT a, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, [phi+], intergenic region (430900-431000) betweenYKL006C-A and YKL006W::HIS3, intergenic region (430900-431000) between YKL006C-A and YKL006W::KanMX6


title: CD4Tcell_Input_exp2


title: FAIRE_UV_6h_R1


title: Wt-M11 rep2


title: D8A rep1


title: H3K27ac_UV_6h_R2


title: Th2cell_Menin_exp2

source_name: Five-day cultured Th2 cells generated from primary splenic CD4_T cells


title: Th2cell_Ezh2_exp2


title: CD4Tcell_Ezh2_exp2


title: EScell_Menin_exp2

source_name: B6N-22 ES cells

value: B6N-22 ES cell


title: InputDNA-biorep1

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the Araly1 genome assembly using SOAPv2 with up to two mismatches and no gaps were allowed, and reads were iteratively trimmed from the 5` end until mapped or their length fell below 31 nt.
Only uniquely mapped reads were retained. Sequence reads mapping to the plastid and mitochondrial genomes were eliminated. For A lyrata, only reads mapping to the 9 longest scaffolds were retained (length > 1MB)
peaks were called using CSAR with default parameters except backg which was set to 14
Genome_build: Araly1
Supplementary_files_format_and_content: peak files shows the coordinates and score value obtained by CSAR

growth_protocol: A. lyrata plants were germinated and vernalized for 7-10 weeks at 8 oC, 16 h light/8 h dark. Bolting was initiated at 18-22 oC under long-day conditions.

extract_protocol:
Chromatin was extracted according to Kaufmann et al, Nature Protocols 2010
Libraries were essentially constructed according to Kaufmann et al., Nature Protocols 2010

value: none (input)

tag: developmental stage

value: inflorescence with floral buds of stage 1-10/11

value: Inflorescences


title: EScell_Input_exp2


title: lyInflo rep3

value: lyrata

tag: age

value: plants after bolting

value: wild type


title: lySEP3-biorep1


title: EScell_Ezh2_exp2


title: CD4Tcell_RNA_exp2

value: CD4 T cell


title: lyInflo rep1


title: Bcell_RNA_exp1

source_name: Primary B220_B cells isolated from 6-8 week old mice (C57BL/6)

growth_protocol: Splenic B220_B cells were purified using magnetic beads and an AutoMACS sorter (Miltenyi Biotec) that yielded purity of >98%.

value: B220 B cell


title: CD4Tcell_RNA_exp1A


title: EScell_RNA_exp2


title: EScell_RNA_exp1


title: lyleaves rep3

source_name: leaves

value: leaves


title: Short photoperiod sample 4

status: Public on Oct 09 2015

first: Shona

middle: Hiedi

last: Wood

address: Oxford road

description: Sample name: SP_4

data_processing:
Mapping to the genome using bowtie to generate alignment files
Raw counts per genomic feature using HTSeq and the sheep GTF file provided by ensembl
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Raw count files generated by Htseq listing the number of reads mapping to ensembl genes (used  Ovis_aries.Oar_v3.1.78.gtf to give annotation)

organism: Ovis aries

source_name: pars tuberalis

extract_protocol:
Qiagen RNAeasy kit
standard illumina cDNA fragment library prep

tag: Sex

tag: condition

value: neutered

value: scottish blackface

tag: time

value: Short photoperiod

value: pars tuberalis


title: Short photoperiod sample 3

description: Sample name: SP_3

value: male


title: Short photoperiod sample 5

description: Sample name: SP_5


title: Short photoperiod sample 2

description: Sample name: SP_2


title: lyleaves rep1


title: Short photoperiod sample 1

description: Sample name: SP_1


title: Long photoperiod day 28 sample 6

description: Sample name: LPD28_6

value: Long photoperiod day 28


title: Long photoperiod day 28 sample 5

description: Sample name: LPD28_5


title: lyleaves rep2


title: Long photoperiod day 28 sample 4

description: Sample name: LPD28_4


title: Long photoperiod day 28 sample 1

description: Sample name: LPD28_1


title: Long photoperiod day 28 sample 2

description: Sample name: LPD28_2


title: Th2cell_RNA_exp1

value: Th2 cell


title: Long photoperiod day 28 sample 3

description: Sample name: LPD28_3


title: FAIRE_untreated_R2


title: Long photoperiod day 7 sample 6

description: Sample name: LPD7_6

value: Long photoperiod day 7


title: N1855_CN_2H

description: Sample 34

value: Holstein-Friesian

value: 7-12 weeks

tag: animal id

value: Alveolar macrophages

tag: infection status

value: Control

tag: time point

value: 2hr post-infection


title: Th17_rmSAA1_2

city: New York

first: Wendy

last: Huang

address: 540 First Ave Skirball 2-14

institute: NYU School of Medicine

description: compound: R&D (catalog number 2948-SA)

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 mm9 whole genome using Tophat2
Transcripts FPKM were calculated by Cufflink using Reference Annotation: mm10.gtf from UCSC
Differential gene expression were called by CuffDiff using Reference Annotation: mm10.gtf from UCSC
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: In vitro Th17

growth_protocol: 48hrs in vitro Th17 culture

extract_protocol:
Total RNAs from cultured Th17 cells were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with or without 2ng/ml murine SAA1 (R&D, catalog number 2948-SA)

tag: cell type

value: T cell

value: 2ng/ml recombinant murine SAA1


title: Th17_rmSAA1_1

description: compound: R&D (catalog number 2948-SA)


title: Th17_veh_1


title: lyInflo rep2

value: lyrata

tag: tissue

value: Inflorescences

value: plants after bolting

tag: genotype

value: wild type


title: Hypobiotic-A

city: St. Louis

first: Makedonka

last: Mitreva

state: Missouri

address: 4444 Forest Park Ave

institute: McDonnell Genome Institute at Washington University

data_processing:
BASE CALLING
Reads were trimmed for cDNA synthesis adaptors using Flexbar.
Reads were trimmed for Illumina adapters, quality trimmed and length filtered using Trimmomatic.
Reads were complexity filtered using Seq_crumbs filter_by_complexity scripts.
Susupected human, bacterial, rRNA and cow contaminants were removed by mapping reads to contaminant sequence databases using Bowtie2 and/or Tophat2 and removing reads that matched.
Reads were mapped to the Dictyocaulus viviparus genome assembly (WormBase ParaSite BioProject PRJNA72587) using Tophat2, and read counts per feature were generated using htseq-count.
Fragments per kilobase per million reads mapped (FPKM) were calculated.
Genome_build: WormBase ParaSite BioProject PRJNA72587
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts and FPKM counts per feature.

organism: Dictyocaulus viviparus

source_name: whole worms from cow

growth_protocol: Parasites were obtained from experimentally infected Holstein-Friesian calves (Bos taurus).

extract_protocol:
Individual lungworm stages were homogenized in 600mL RLT-buffer (RNeasy® Mini Kit, Qiagen, Hilden, Germany) and 6mL 2-mercaptoethanol (Roth, Karlsruhe, Germany) using the Precellys® 24 tissue homogenizer (Peqlab Biotechnologie), and total RNA was isolated from the homogenate using RNeasy® Mini Kit (Qiagen) according the manufacturer’s suggested protocol, including the optional on-column DNase digest.
RNA libraries were prepared for sequencing using standard Illumina protocols using a NuGen Ovation2 cDNA synthesis kit.

value: 35 days post infection with L3

tag: source

value: cow lung

tag: isolation protocol

value: lung perfusion

tag: treatment

value: L3 chilled prior to infection to induce hypobiosis


title: Long photoperiod day 7 sample 5

description: Sample name: LPD7_5

value: male

value: neutered

value: scottish blackface

value: pars tuberalis


title: Hypobiotic-B

tag: strain


title: Long photoperiod day 7 sample 1

description: Sample name: LPD7_1

value: Long photoperiod day 7


title: Long photoperiod day 1 sample 6

description: Sample name: LPD1_6

value: Long photoperiod day 1


title: Long photoperiod day 7 sample 4

description: Sample name: LPD7_4


title: Bcell_RNA_exp2

value: B220 B cell


title: Long photoperiod day 7 sample 3

description: Sample name: LPD7_3


title: Long photoperiod day 1 sample 3

description: Sample name: LPD1_3


title: AdultFemale-B


title: Long photoperiod day 7 sample 2

description: Sample name: LPD7_2


title: Long photoperiod day 1 sample 4

description: Sample name: LPD1_4


title: Long photoperiod day 1 sample 1

description: Sample name: LPD1_1


title: shExosc3_YY1_r1_batch4

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
Genome_build: mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic stem cells

growth_protocol: Cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with streptavidin beads.
The chromatin extracts containing DNA fragments with an average size of 500 bp were affinity purified using streptavidin beads. Purified DNA was prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: BirA

tag: purification target

tag: bead manufacturer

value: Life Technologies


title: AdultMale-A


title: AdultMale-B


title: Long photoperiod day 1 sample 2

description: Sample name: LPD1_2

tag: breed


title: AdultFemale-A

tag: age


title: shExosc3_Input_r2_batch4


title: shExosc3_YY1_r2_batch4

value: Invitrogen


title: Th17_veh_2

value: T cell


title: shExosc3_Input_r1_batch4


title: L5female-A

value: 15 days post infection with L3


title: shLuc_Input_r2_batch4

treatment_protocol: shLuciferase


title: L5male-A


title: L5mix-B


title: shLuc_YY1_r2_batch4


title: Input DNA

city: Beijing

first: Xiao

last: Li

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.7
Data were processed to remove adapter sequences, N and low quality reads to get clean reads
ChIP-seq clean reads were aligned to S. coelicolor M145 genome assembly using bowtie version 2 2.1.0 with the following configurations…
peaks were called using MACS 1.4.2 with the following setting:  Enrichment Fold1.5
Genome_build: NC_003888.3
Supplementary_files_format_and_content: tab-delimited text files include read start, read end, fold enrichment and  FDR, and peak location relative to ajacent CDS.

organism: Streptomyces coelicolor

source_name: Streptomyces coelicolor M145 mycelium

growth_protocol: Spores of S. coelicolor were incubated in SMM liquid medium for 30h and 42h, at 28°C 250rpm

extract_protocol:
Lysates were clarified from sonicated nuclei and ScbR or ScbR2-DNA complexes were isolated with antibodies.
Libraries were prepared according to Illumina's TruSeqTM DNA Sample Prep Kit – Set A

treatment_protocol: Cells were treated with 1% formaldehyde for 30 min at room temperature before glycine was added to a final concentration of 0.125 M to halt cross-linking

tag: culture time

tag: chip antibody


title: L4-B

value: 7 days post infection with L3


title: L5mix-A


title: shLuc_Input_r1_batch4


title: ScbR-30h ChIP-seq

value: Mouse monoclonal antibody of ScbR


title: L3-A

value: 6 days after expulsion from host

value: in vitro culture


title: Rel_30_YY1_batch3

treatment_protocol: 100 uM DRB under ES culture conditions for 30min


title: L5female-B

value: cow lung

value: lung perfusion


title: L4-A


title: shLuc_YY1_r1_batch4


title: ScbR2-42h ChIP-seq

value: Mouse monoclonal antibody of ScbR2


title: L2-A

value: 1 day after expulsion from host


title: Long photoperiod day 1 sample 5

description: Sample name: LPD1_5

tag: Sex

value: male

tag: condition

value: neutered

value: scottish blackface

tag: time

value: pars tuberalis


title: L1-B

value: 0 days after expulsion from host

value: cow feces

value: baermann method


title: L1-A


title: Egg-A

value: intra uterine, pre hatch

value: mother worm from lung


title: Egg-B


title: L5male-B

value: 15 days post infection with L3


title: Short photoperiod 16 weeks sample 4

tag: photoperiod

value: Short photoperiod 16 weeks


title: Short photoperiod 16 weeks sample 3


title: Short photoperiod 16 weeks sample 2


title: control_P1_cortex_input

city: Goettingen

first: Cemil

last: Kerimoglu

address: Grisebachstr. 5

institute: UMG Göttingen

data_processing:
Illumina pipeline scripts used for basecalling.
ChIP-Seq reads were aligned to mm10 genome assembly using STAR aligner v2.3.0.
Replicates from the same group were merged into a single BAM file using samtools.
Profile plots were created with NGSPlot using merged BAM files as input.
WIG files were created from BAM files using the script of MEDIPS package from Bioconductor.
H3K27me3 enrichment on and around different candidate loci was visualized by Integrated Genome Browser using WIG files as input.
Genome_build: m10
Supplementary_files_format_and_content: WIG files contain genomic coverage for visualization in Integrated Genome Browser.
The "avgprof.txt" data files contain read count per million mapped reads for each base pair along the gene bodies (+/- 5000 bp) that were used by the NGSPlot program to create the plots (presented in the GSE73855-associated publication). There are data columns for control, transgenic strain and input samples. The Whole_Genome" files contain the analysis over the whole genome (i.e. overall the gene bodies detectable in mouse genome (mm10)). The Candidate_Genes* file contains the analysis for only certain candidate genes based on a microarray experiment (described in the GSE73855-associated publication).

extract_protocol:
Murine embryonic cortices were homogenized in sucrose solution and fixed with 37% formaldehyde. In subsequent steps histone-DNA comlexes were isolated with antibody.
Library preparation was performed according to standard protocols of Illumina (TruSeq, Illumina).

tag: strain background

tag: developmental stage

tag: cre expression

value: Nex-Cre

tag: genotype/variation

tag: sample group

value: Control

value: cortex


title: dcKO_E13.5_cortex_input

value: BAF155fl/fl, BAF170fl/fl

value: conditional double knock-out (dcKO) of BAF155/BAF170 complex (dcKO)

tag: tissue


title: control_E13.5_cortex_input


title: control_E13.5_cortex_H3K27me3 ChIP-Seq [R685]

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: dcKO_P1_cortex_input


title: L3-B

tag: strain

value: 6 days after expulsion from host

tag: source

value: in vitro culture


title: Long photoperiod 22 weeks sample 4

value: male

value: neutered

tag: breed

value: scottish blackface

value: Long photoperiod 22 weeks


title: L2-B

tag: age

value: 1 day after expulsion from host


title: Long photoperiod 22 weeks sample 3

tag: Sex

value: pars tuberalis


title: dcKO_E13.5_cortex_H3K27me3 ChIP-Seq [R651]

tag: chip antibody


title: control_E13.5_cortex_H3K27me3 ChIP-Seq [R650]


title: dcKO_E13.5_cortex_H3K27me3 ChIP-Seq [R649]


title: Long photoperiod 4 weeks sample 4

tag: condition

value: Long photoperiod 4 weeks


title: Long photoperiod 4 weeks sample 1

tag: photoperiod


title: Short photoperiod 4 weeks sample 4

value: Short photoperiod 4 weeks


title: Long photoperiod 4 weeks sample 2


title: Short photoperiod 4 weeks repeat sample 1


title: Long photoperiod 22 weeks sample 1


title: dcKO_E13.5_cortex_H3K27me3 ChIP-Seq [R648]

tag: strain background


title: Short photoperiod 4 weeks sample 3


title: Short photoperiod 4 weeks sample 2


title: dcKO_P1_cortex_H3K27me3 ChIP-Seq [R542]

tag: developmental stage


title: Short photoperiod 4 weeks sample 1


title: dcKO_P1_cortex_H3K27me3 ChIP-Seq [R540]

tag: cre expression


title: Short photoperiod 16 weeks sample 1

value: Short photoperiod 16 weeks


title: Input_DNA_ChIP-Seq

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

description: Input Chromatin

data_processing:
ChIP-Seq reads were aligned to the reference genome hg19 using bowtie v1.1. The flag "-m 1" was used
Peaks were called using macs2 using the default fdr threshold of p-value < 0.05
BedGraph tracks were generated using macs2 and then converted to BigWig using bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: Tab-delimited peak files generated by macs2
Supplementary_files_format_and_content: BigWig track files containing aligned read densities

source_name: Hct 116 Cells

growth_protocol: Hct 116 cells were cultured in Dulbecco's modified Eagles's Medium (DMEM) supplemnted with 10% fetal bovine serum (FBS) at 37C with 5% CO2 (HyClone).

extract_protocol:
Chromatin was cross-linked with 1% formaldehyde for 10 min at room temperature in culture media, and the reaction was stopped by the addition of glycine (125 mM final).  Cells were washed twice with PBS and re-suspended in 1 ml of nuclei extraction buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, protease inhibitor (Roche)) at 2x107 cells/ml and incubated for 10 min at 4°C.  Cell nuclei were collected by centrifugation at 3000 rpm for 5 min at 4°C, and re-suspended in Szak's RIPA buffer (50 mM Tris-HCl pH 8.0, 1% NP-40, 150 mM NaCl, 0.5% deoxycholate, 0.1% SDS, 5 mM EDTA, 0.5 mM PMSF, protease inhibitor) at 5x107 nuclei/ml.  Nuclear pellets were sonicated using the Bioruptor water bath sonicator (Diagenode) using the high setting with 30 sec on 30 sec off for 50 minutes to generate 100-300 bp DNA fragments.  Approximately 25-50x106 nuclei were used for each ChIP.  For the ChIP step, 2-4 ug of antibody was conjugated with 40 uL of protein G dynabeads (Invitrogen) and blocked with 0.16% bovine serum albumin for 1 hour at 4°C.  Antibody-conjugated dynabeads were incubated with sheared chromatin suspension for 2 hr at 4°C.  Then the beads were sequentially washed sequentially two times with the following buffers: Szak's RIPA buffer (see above), low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), LiCl wash buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 20 mM Tris, pH 8.0), and 1 mM Tris-EDTA pH 8.0.  Chromatin immunocomplexes were eluted by incubation for 10 min at 65°C with 1% SDS and 100 mM NaHCO3, and cross-linking was reversed by incubation in the solution adjusted to 200 mM NaCl and proteinase K (20 μg) for 1 hr at 65°C.  DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit (Zymo Research). Final ChIP DNA was quantified on a Qubit 2.0 Fluorometer (Invitrogen) and approximately 20 ng of DNA were submitted for library preparation.
ChIP DNA was submitted to McDermott Center Sequencing Core at UT Southwestern Medical Center for library preparation and high-throughput sequencing. Samples were end repaired, 3’-end adenylated and barcoded with multiplex adapters (Applied Biosystems) and samples were PCR amplified (~14 cycles) and size selected with Ampure Beads. Sequencing was done using the Illumina NextSeq 500 using 50 bp read length.

tag: cell line

tag: cell type

value: Colonic Endothelial Cells

value: none (input)


title: control_P1_cortex_H3K27me3 ChIP-Seq [R539]

value: Nex-Cre

tag: genotype/variation

tag: sample group

value: Control

tag: tissue

value: cortex


title: H3K4me3_ChIP-Seq

description: ChIP-Seq data set for Trimethylated Lysine 4 of Histone H3

value: H3K4me3 (Abcam; ab8580)


title: control_E13.5_cortex_H3K27me3 ChIP-Seq [R653]

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: control_P1_cortex_H3K27me3 ChIP-Seq [R535]


title: Cdk9_ChIP-Seq

description: ChIP-Seq data set for the Cdk9 Kinase Subunit of P-TEFb


title: Long photoperiod 4 weeks repeat sample 2

tag: breed


title: Hexim1_ChIP-Seq

description: ChIP-Seq data set for the 7SK snRNP Component Hexim1

value: Hexim1 (Abcam; ab25388)


title: H3K4me1_Chip-Seq

description: ChIP-Seq data set for Monomethylated Lysine 4 of Histone H3

value: H3K4me1 (Abcam; ab8895)


title: control_E13.5_cortex_H3K27me3 ChIP-Seq [R654]


title: Larp7_ChIP-Seq

description: ChIP-Seq data set for the 7SK snRNP Component Larp7

value: Larp7 (Sigma; av40847)


title: Long photoperiod 4 weeks sample 3

value: male

value: neutered

value: scottish blackface


title: control_P1_cortex_H3K27me3 ChIP-Seq [R534]


title: Long photoperiod 22 weeks sample 2

value: Long photoperiod 22 weeks

value: pars tuberalis


title: dcKO_P1_cortex_H3K27me3 ChIP-Seq [R530]

value: BAF155fl/fl, BAF170fl/fl

value: conditional double knock-out (dcKO) of BAF155/BAF170 complex (dcKO)


title: control_P1_cortex_H3K27me3 ChIP-Seq [R533]


title: Ser-5P_Pol_II_ChIP-Seq

description: ChIP-Seq data set for Phospho-Serine 5 of the C-terminal heptad repeat of Pol II

value: Colonic Endothelial Cells

value: Pol II CTD 4H8 (Abcam; ab5408)


title: KAP1_ChIP-Seq

description: ChIP-Seq data set for KAP1

value: KAP1 (Abcam; ab22553)


title: G127_SFB35Ct_VillCreTRAPseq

description: total RNA post GFPL10 IP

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 mm9 whole genome using Tophat2
Transcripts FPKM were calculated by Cufflink using Reference Annotation: mm9.gtf from UCSC
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SFB negative

extract_protocol:
Total RNAs and IP enriched RNAs from epithelial EDTA fraction were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Small intestine

tag: age

tag: genotype

tag: rip antibody

value: rabbit anti-GFP

tag: rip antibody vendor

value: Life Technology

tag: rip antibody cat. #

tag: rip antibody lot#


title: d18_pellet2_rnaseq

city: Parkville

first: Melissa

middle: H

last: Little

state: Victoria

address: Flemington Road

department: Cell Biology

institute: Murdoch Childrens Research Institute

data_processing:
Basecalling: Illumina Real-Time Analysis (RTA) v2.1.3
bcl to fastq conversion, including trimmming of adapters: Illumina bcl2fastq2 v2.1.4
Mapping: STAR v2.3.0e
Read counts per gene: htseq-count (HTSeq-0.6.1), with Illumina iGenomes UCSC hg19 annotation
Normalised counts: DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values of raw counts and normalised counts (all replicates)

source_name: C32 iPSC_d18_pellet_rnaseq

growth_protocol: Human iPSCs were plated on a Matrigel-coated (Millipore) culture dish and cultured in MEF-conditioned hES medium. Then, cells were again plated on a Matrigel-coated at 5,000 cells/cm2.

extract_protocol:
Total RNA was extracted from cells using Purelink RNA mini kit (Life Technologies)
TruSeq stranded total RNA Ribo Zero Gold library prep (Illumina); RNA-seq; 1x76bp

treatment_protocol: When cells reached to 40-50 % of confluent, cells were treated with 8 mM of CHIR99021 in APEL basal medium (STEMCELL Technologies) supplemented with Antibiotic-Antimycotic (Life Technologies) for 4 days, followed by FGF9 (200 ng mL-1) and Heparin (1 mg mL-1) for another 3 days, with changing medium every second day. Then, cells were collected and dissociated into single cells using Trypsin or TrypLE select (Life Technologies). Cells (0.5-1 × 10^6) were spun down at ×400g for 2 min to form a pellet and then placed onto a Transwell 0.4 mm pore polyester membrane (#CLS3450 Corning). A pellet was treated with 5 mM of CHIR99021 in APEL for 1 h, and then cultured with FGF9 (200 ng mL-1) and Heparin (1 mg mL-1) for 5 days, followed by another 6-13 days in APEL basal medium, with changing medium every second day.

value: C32 iPSC

tag: days cultured

value: mini-kidney derived from human induced pluripotent stem cells (C32 iPSC)


title: d11_pellet2_rnaseq

source_name: C32 iPSC_d11_pellet_rnaseq

tag: cell line


title: d11_pellet5_rnaseq

tag: cell type


title: d18_pellet1_rnaseq


title: d18_pellet5_rnaseq


title: H3K27ac_Chip-Seq

description: ChIP-Seq data set for Acetylated Lysine 27 of Histone H3

tag: chip antibody

value: H3K27Ac (Abcam; ab4729)


title: d3_pellet3_rnaseq

source_name: C32 iPSC_d3_pellet_rnaseq


title: d11_pellet1_rnaseq


title: d3_pellet2_rnaseq


title: G111_SFB20Ct_VillCreTRAPseq

description: total RNA post GFPL10 IP

source_name: SFB positive


title: d3_pellet1_rnaseq


title: d0_pellet5_rnaseq

source_name: C32 iPSC_d0_pellet_rnaseq


title: ILC3

description: Sorted for GFP+ ILC3 cells

data_processing:
Reads were mapped to mm8 using Tophat version 2.0.6 and the following paramters: --no-novel-juncs, --read-mismatches 2
Reads mapped per gene were counted using the function HTSeq.scripts.count from the Python HTSeq package version 0.5.4p3 with the following parameters: --stranded=no, --mode=union, -q, -a 30
The R package DESeq version 1.12.0 was used for gene normalization and differentail expression (fold-changes and significance estimation).
Genome_build: mm8

extract_protocol:
Total RNAs from sorted cells were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: IL23R_GFP Knockin mice


title: d0_pellet4_rnaseq


title: d0_pellet3_rnaseq


title: Input, Replicate 1

status: Public on Oct 08 2015

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Demultiplexing of NextSeq data was performed using bcl2fastq v2.16.0.10 with default parameters.
Data were aligned to the GRCh37 (hg19) assembly of the human genome using bowtie2 with command-line parameters -k1 -N1 --local (allowing and reporting a single alignment per read with one or zero mismatches permitted in the seed region).
ChIP-seq visualization tracks were created in the following way. Aligned sequence tags were subjected to bedtools' genomeCoverageBed tool, making bedGraphs that were multiplied by the RPM coefficient.  A similarly normalized input bedGraph was then subtracted from Lamin B1 and LC3, and bedGraphs were made into bigWigs using UCSC Genome Browser's bedGraphToBigWig utility.
Enriched domains for Lamin B1 and LC3 were called using EDD with default bin size estimation and gap penalty estimation and unalignable regions (the hg19 assembly gap track from Genome Reference Consortium) were masked.  The FDR was controlled at the default value of 5%.
Genome_build: hg19
Supplementary_files_format_and_content: Tracks (bigWig files) were created by running genomeCoverageBed from the bedtools software package to create bedGraphs and adjusting tag counts by the RPM coefficient for each replicate of lamin B1, LC3, and input. Input bedGraphs were then subtracted from lamin B1 and LC3 bedGraphs and these were converted to bigWigs using bedGraphToBigWig from the UCSC Genome Browser utilities. BED files describing large domains of lamin B1 or LC3 enrichment were obtained by running EDD using default bin size estimation and gap penalty estimation. Unalignable regions (gaps) were masked and the FDR was controlled at 5%.

source_name: IMR90 fibroblasts in culture

growth_protocol: IMR90 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 μg/ml streptomycin (Invitrogen) under physiological oxygen (3%).

extract_protocol:
Cells were crosslinked with 1% formaldehyde diluted in PBS, without the addition of other co-crosslinkers, for 5 min at room temperature.  After glycin quenching, the cell pellets were lysed in buffer containing  50 mM Tris, pH 7.5, 150 mM NaCl, 1% Triton, 0.1% Na-Deoxycholate, 0.1% SDS, supplemented with complete protease inhibitor cocktail (Thermo Scientific), and sonicated with Covaris sonicator, resulting in chromatin fragments of 250 bp average size.  The supernatant was diluted 10 times with the above buffer without SDS, and subjected to immunoprecipitations with 2 ug of antibody or control IgG conjugated with Dynabeads Protein A or G (Invitrogen) at 4 °C for overnight.  The beads were then washed 5 times with buffer containing 50 mM Tris, pH 7.5, 150 mM NaCl, 1% Triton, and 1 time with final wash buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 50 mM NaCl), followed by elution with incubation of elution buffer (final wash buffer plus 1% SDS) at 65 °C for 30 min with agitation in a thermomixer.
The ChIP and input were purified and used for qPCR analysis or for constructing sequencing libraries with the NEBNext Ultra kit (New England Biolabs).

treatment_protocol: No treatment was performed on these cells.

tag: antibody


title: Input, Replicate 2


title: LC3, Replicate 2

value: Cell Signaling Technology #3868


title: Th17

description: Sorted for GFP+ T cells

tag: tissue

value: IL17A_IRES_GFP Knockin mice


title: Lamin B1, Replicate 2

value: Abcam #ab16048


title: Total_Pol_II_ChIP-Seq

description: ChIP-Seq data set for Total Pol II

value: Pol II (N-20) (SCBT; sc-899X)


title: Lamin B1, Replicate 1


title: LC3, Replicate 1


title: 1000_BM11

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

institute: St. Vincent's University Hospital

description: liver by percutaneuos punch (PMID: 12545545)

data_processing:
Basecalls using CASAVA 1.8
Alignment; BWA
Variant Calling: GATK best practices for DNA, using HaplotypeCaller
Genome_build: UMD3.1.70 (close to Bos_taurus_UMD_3.1 with the ENsembl build version 70)
Supplementary_files_format_and_content: The processed data files are in genomic variant call format (GVCF), described at https://www.broadinstitute.org/gatk/guide/tagged?tag=gvcf#docs4017
Supplementary_files_format_and_content: The BM*.gvcf files contain calls for variants in each sample individually and 'BM1-16.gvcf' contains calls at every sample BM1..16, using the GenotypeGVCF GATK algorithm.

extract_protocol:
Zymo Quick-gDNA MiniPrep kit; Zymo Genomic DNA Clean and Concentrator
Roche Nimblegen Developer Library Kit Hybridisation; Illumina TruSeq v2 kit
Our strategy for hybridisation and sequencing was to make one single equimolar pool of all 16 gDNA libraries, each having different adapter barcodes to allow us to de-multiplex sequence data into the correct sample for analysis. We then split the pool in four parts and performed hybridisation captures on each part using 2x capture reagents, resulting in 1x capture for every 2 samples. All captures were then re-pooled and then split into three parts for sequencing on three HiSeq lanes. We used pooling strategies to attempt to reduce variation in hybridisation, and because we were ultimately pooling the captured libraries to sequence over three lanes.

treatment_protocol: Percutaneuos punch, PMID: 12545545

value: Holstein

tag: fertility group

value: Fert-

value: liver


title: 996_BM10


title: 3445_BM15

value: Fert+


title: 3434_BM14


title: 3397_BM13


title: 3847_BM16


title: 419_BM3


title: 782_BM7


title: 829_BM8


title: 756_BM6


title: 3847_M_48

description: semitendinosus muscle (PMID: 22720928)

data_processing:
Basecalls using CASAVA 1.8
Trimming; Trimmomtatic sliding window from end 30 or below removed; Alignment; STAR, Dobin et al doi:10.1093/bioinformatics/bts635, version 2.2.0; default run except ‘--outFilterMismatchNoverLmax’ set to 0.02 (i.e. 2 mismatches per 100bp)
Count generation; featureCounts, flags -p, -P, -C, and with a maximum insert size of 590 kb flag –D
Filtering by FPKM following TMM normalisation of the library using edgeR, retained 18,000 genes
Genome_build: UMD3.1.70 (close to Bos_taurus_UMD_3.1 with the ENsembl build version 70)
Supplementary_files_format_and_content: Format: tab separated; content: column1=bovine gene ID, column2=number of sequence reads overlapping bovine gene ID as defined by GTF
Supplementary_files_format_and_content: The *1-48.count.txt files contain all 48 counts files from each tissue group.

source_name: Muscle_Mid Lactation_Fert+

extract_protocol:
Standard trizol extraction [PMID:2440339]
Illumina TruSeq v2 kit

treatment_protocol: Percutaneuos punch [PMID: 22365213]

value: Muscle

tag: timepoint

value: Mid Lactation


title: 430_BM5


title: 3847_M_47

description: semitendinosus muscle (PMID: 22720928)

source_name: Muscle_Early Lactation_Fert+

value: Early Lactation


title: 426_BM4


title: 33_BM1


title: 3847_M_46

description: semitendinosus muscle (PMID: 22720928)

source_name: Muscle_Late Pregnancy_Fert+

value: Late Pregnancy


title: 982_BM9


title: 3434_M_42

description: semitendinosus muscle (PMID: 22720928)


title: 3445_M_43

description: semitendinosus muscle (PMID: 22720928)


title: 3445_M_45

description: semitendinosus muscle (PMID: 22720928)


title: 3434_M_40

description: semitendinosus muscle (PMID: 22720928)


title: 3434_M_41

description: semitendinosus muscle (PMID: 22720928)


title: 3397_M_39

description: semitendinosus muscle (PMID: 22720928)


title: 3397_M_38

description: semitendinosus muscle (PMID: 22720928)


title: 3397_M_37

description: semitendinosus muscle (PMID: 22720928)


title: 3445_M_44

description: semitendinosus muscle (PMID: 22720928)


title: 1179_BM12


title: 1179_M_36

description: semitendinosus muscle (PMID: 22720928)

source_name: Muscle_Mid Lactation_Fert-


title: 1179_M_35

description: semitendinosus muscle (PMID: 22720928)

source_name: Muscle_Early Lactation_Fert-


title: 1000_M_33

description: semitendinosus muscle (PMID: 22720928)


title: 1000_M_32

description: semitendinosus muscle (PMID: 22720928)


title: 1000_M_31

description: semitendinosus muscle (PMID: 22720928)

source_name: Muscle_Late Pregnancy_Fert-


title: 996_M_30

description: semitendinosus muscle (PMID: 22720928)


title: 164_BM2


title: 996_M_29

description: semitendinosus muscle (PMID: 22720928)


title: 982_M_26

description: semitendinosus muscle (PMID: 22720928)


title: 996_M_28

description: semitendinosus muscle (PMID: 22720928)


title: 829_M_23

description: semitendinosus muscle (PMID: 22720928)


title: 982_M_25

description: semitendinosus muscle (PMID: 22720928)


title: 782_M_20

description: semitendinosus muscle (PMID: 22720928)


title: 782_M_21

description: semitendinosus muscle (PMID: 22720928)


title: 782_M_19

description: semitendinosus muscle (PMID: 22720928)


title: 829_M_24

description: semitendinosus muscle (PMID: 22720928)


title: 756_M_18

description: semitendinosus muscle (PMID: 22720928)


title: 426_M_12

description: semitendinosus muscle (PMID: 22720928)


title: 430_M_15

description: semitendinosus muscle (PMID: 22720928)


title: 756_M_17

description: semitendinosus muscle (PMID: 22720928)


title: 756_M_16

description: semitendinosus muscle (PMID: 22720928)


title: 426_M_11

description: semitendinosus muscle (PMID: 22720928)


title: 430_M_14

description: semitendinosus muscle (PMID: 22720928)


title: 1179_M_34

description: semitendinosus muscle (PMID: 22720928)


title: 430_M_13

description: semitendinosus muscle (PMID: 22720928)


title: 419_M_9

description: semitendinosus muscle (PMID: 22720928)


title: 426_M_10

description: semitendinosus muscle (PMID: 22720928)


title: 164_M_4

description: semitendinosus muscle (PMID: 22720928)


title: 33_M_3

description: semitendinosus muscle (PMID: 22720928)


title: 164_M_5

description: semitendinosus muscle (PMID: 22720928)


title: 419_M_7

description: semitendinosus muscle (PMID: 22720928)


title: 419_M_8

description: semitendinosus muscle (PMID: 22720928)


title: 164_M_6

description: semitendinosus muscle (PMID: 22720928)


title: 829_M_22

description: semitendinosus muscle (PMID: 22720928)


title: 33_M_2

description: semitendinosus muscle (PMID: 22720928)


title: 982_M_27

description: semitendinosus muscle (PMID: 22720928)


title: 33_M_1

description: semitendinosus muscle (PMID: 22720928)


title: 3847_L_48

source_name: Liver_Mid Lactation_Fert+

value: Liver


title: 3847_L_46

source_name: Liver_Late Pregnancy_Fert+


title: 3445_L_43


title: 3434_L_42


title: 3434_L_40


title: 3434_L_41

source_name: Liver_Early Lactation_Fert+


title: 3397_L_39


title: 3445_L_44


title: 2PN Dicer rep1

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

data_processing:
Ion Torrent suite software was used for basecalling.
Sequenced reads were matched to known murine small noncoding RNA using Sequery software
Unmatched sequenced reads were mapped to mm10 whole genome using Bowtie (n = 2)
Aligned reads were matched to genomic coordinates of known murine small noncoding RNA using in-house Python scripts
Reads Per Million aligned reads (RPM) were calculated
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain the unnormalized or normalized (RPM) endo-siRNA and miRNA read counts .txt tab-delimited format

source_name: 2PN embryo

growth_protocol: All mice were housed and maintained under specific pathogen-free conditions with a temperature- and humidity-controlled animal facility in the University of Nevada, Reno. All flox and Cre lines used in this study were purchased from the Jackson Laboratory. All mouse lines were backcrossed for five generations to get onto the C57B6/6J background. The Cre-loxp strategy was used to generate the germ line conditional knockout mice.

extract_protocol:
The total RNA was isolated using the mirVana miRNA Isolation Kit (Life Technologies) following the manufacturer’s instructions with modifications at the lysis stage. In brief, after addition of lysis buffer, the frozen sperm pellets were homogenized at low settings for 90 seconds, followed by a five minute incubation at 65 °C.  Complete lysis of sperm heads was verified by microscopic examination.  Once a total lysis of sperm heads was achieved, the samples were then placed on ice, and the default protocol was resumed.  Samples were then placed on ice, and the default protocol was resumed.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sperm were collected in HTF medium at 37 degree from adult WT and Dicer cKO / Drosha cKO mouse cadua epididymis. Sperm suspension was then centrifuged by 700g to pellet the sperm. Oocytes were collected from WT oivducts after superovulation. 2PN stage embryos were collected after ICSI using WT spermatozoa, Dicer cKO/Drosha cKO spermatozoa.

value: 2PN embryo

value: Adult

value: Dicer cKO


title: 3397_L_38


title: 2PN wt rep1

value: wild type


title: 3445_L_45


title: 1179_L_35

source_name: Liver_Early Lactation_Fert-


title: oocyte wt rep1

source_name: Oocyte

value: Oocyte


title: 3397_L_37


title: sperm Drosha rep2

source_name: Sperm

value: Sperm

value: Drosha cKO


title: sperm Drosha rep3


title: sperm Drosha rep1


title: 1179_L_34

source_name: Liver_Late Pregnancy_Fert-


title: 1000_L_33

source_name: Liver_Mid Lactation_Fert-


title: 2PN Drosha rep1


title: 1000_L_32


title: sperm Dicer rep2


title: sperm Dicer rep1


title: sperm wt rep1


title: 1000_L_31


title: sperm wt rep2


title: 3847_L_47


title: 996_L_30


title: ATR_PR-Set7_RNAi_rep2

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

institute: Duke University

data_processing:
Single-end sequencing reads were aligned with Bowtie 0.12.7 with the following parameters: -n 2 -l 30 -m 1 --best --strata -y.
RPKM (reads per thousand kb, per million mappable reads) was determined with RSamtools and GenomicRanges packages in R. For early origin and H4K20me1 experiments, genome is divided into 10 kb bins stepping every 1 kb. For γ-H2Av experiment, genome is divided into nonoverlapping 5 kb bins.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: csv files with columns chr, start,end,RPKM.

growth_protocol: Drosophila Kc167 cells were cultured at 25℃ in Schneider’s Insect Cell Medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (Gemini) and 1% penicillin/streptomycin/glutamine (Invitrogen).

extract_protocol:
In early origin experiments, chromatin was isolated and BrdU was immunoprecipted as described in (Ryba et al., Nat Protoc, 2011). H4K20me1 and γ-H2Av ChIP were performed as described in (MacAlpine et al., Genome Research, 2010).
Sequencing libraries were prepared using Illumina's TruSeq protocols

tag: experiment

value: early origin

value: Mouse anti-BrdU (BD Biosciences #555627)

tag: RNAi treatment

value: ATR & PR-Set7

tag: replicate


title: ATR_RNAi_rep2

value: ATR


title: 1179_L_36

tag: breed

value: Holstein

value: Fert-


title: control_RNAi_rep2

value: control


title: PR-Set7_RNAi_rep2


title: MiSeq_Liver_Pol2

city: Emeryville

first: Philipp

last: Tropberger

address: 4560 Horton Street

institute: Novartis Institutes for BioMedical Research

data_processing:
Basecalls performed using CASAVA version 1.8
paired reads were aligned to the hbv genome (ayw, GenBank V01460.1, or de novo assembled from sequencing data with samtools mpileup) using Bowtie2  ( parameters: --no-unal --no-discordant --no-mixed -I 120 -X 200 (or  -I 30 -X 300 for Polymerase2)
Midpoint of each aligned paired-end reads was determined with a self-written python script
SAM files with midpostion of each aligned paired-end read were converted with SAMtools into .BAM format and sorted
sorted BAM files with midpostion of each aligned paired-end read were converted with bedtools into .bedgraph file format.
Genome_build: HBV
Supplementary_files_format_and_content: genome coverage in bedgraph formal

source_name: liver

extract_protocol:
Cells for chromatin immunoprecipitation (ChIP) were harvested with Accutase (Millipore) and crosslinked in PBS with 1% freshly cracked formaldehyde (Pierce) for 5 min. Fixation was quenched by adding 125mM glycine final concentration for 2 min. Next cells were washed with 10ml ice cold PBS with 0.1% Triton-X 100, 0.1% NP-40, 1mM DTT 10mM sodium butyrate, 1x protease inhibitor (Roche), resuspended in 1ml of the same buffer and incubated on ice for 10min with occasional mixing. Crude nuclei were pelleted and resuspended in Mnase digestion buffer (50mM Tris pH 7.5, 4mM MgCl2, 1mM CaCl2, 10% glycerol, 10mM sodium butyrate, 1x protease inhibitor) with 600U/ml Mnase (Fermentas). Chromatin was digested for 10 min at 37°C to mainly mononucleosomes before digestion was quenched with 10mM EGTA on ice for 30min. The digested nuclei were spun at 10,000 rpm for 5min and the supernatant (S1) saved into a fresh tube. The pellet was resuspended in Mnase buffer with 10mM EGTA and 300mM NaCl and mildly sonicated on ice 4x for 10 pulses in Heat Systems W-375 sonicator at 50% duty cycle and power setting 3. The sample was spun at 10,000 rpm for 5min and the supernatant (S2) combined with the S1 fraction. S1 and S2 fraction were mixed with an equal volume of 0% sucrose buffer (50mM Tris pH 7.5, 50mM NaCl, 5mM EDTA pH 8.0, 0.01% NP-40, 10mM sodium butyrate, 1x protease inhibitor) and concentrated in a Vivaspin 4 spin column (Sartorius) with 100K cutoff membrane to ~250ul. The concentrated sample was applied to a 5-30% sucrose gradient and centrifuged in a SW41TI at 40,000rpm at 4°C for 4h. Mononucleosome-containing fractions were pooled, concentrated to ~500ul and 100ng/ul BSA added. For ChIP antibodies were prebound to 20-30ul Protein G Dynabeads (Life Technologies) on a rotator at 4°C for 2h. The following antibodies were used: 0.5ug H3K4me3 (Abcam ab8580), 2ug H3K9me3 (Abcam ab8898), 1ug H3K27me3 (Millipore 07-449), 2ug H3K36me3 (Millipore ABE435), 0.6ug H3K27ac (Abcam ab4729), 1.2ug H3K122ac (Abcam ab33309), 2ug RNA Polymerase 2 (Abcam ab817). 1ug purified mononucleosomes (for histone modifications) or 20ug of Mnase-digested chromatin (for Polymerase 2 ChIP) were diluted in 400ul ChIP dilution buffer (20mM Tris pH 8.0, 150mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 10mM sodium butyrate, 1x protease inhibitor), added to the bead-antibody complex and incubated on a rotator at 4°C overnight. Samples were washed in LiCl was buffer (500mM LiCl, 50mM Tris pH 8.0, 1mM EDTA pH 8.0, 1% NP-40, 0.7% sodium deoxycholate) five times and eluted in elution buffer (1% SDS, 100mM NaHCO3). The samples were decrosslinked at 65°C for 5-6h in the presence of Proteinase K (Ambion) and purified with Qiagen PCR purification columns. ChIP DNA yield was quantified using QuBit Fluorometric Quantitation (Life Technologies).
1-2ng of DNA was used to prepare sequencing libraries with the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer's instructions. For indexing, 2ul of adaptors from a TruSeq ChIP Sample Preparation Kit (Illumina) were used. Libraries were amplified with 13 PCR cycles and sequenced on a HiSeq2500 instrument (Illumina) in rapid run mode with 2x33bp paired end reads. Custom designed xGen Lockdown probes (Integrated DNA Technology) of 60bp each tiling the entire HBV genome with two-fold coverage were designed and equal amounts of libraries were pooled (500-1000ng DNA total amount) and enriched for HBV DNA according to the manufacturer's xGen rapid capture protocol v2 with slight modifications: Hybridization was performed at 50°C, and 50ul Dynabeads MyOne Streptavidin C1 (Life Technologies) were used per capture reaction. Target enriched libraries were amplified with 8 PCR cycles (KAPA HIFI HotStart ReadyMix) and sequenced on a MiSeq (Illumina) with 2x33bp paired end reads.

value: liver tissue

tag: infection

value: HBV (endogenous)

value: RNA Polymerase 2 (Abcam ab817)


title: 996_L_28

value: Liver

value: Late Pregnancy


title: MiSeq_Liver_H3K122ac

value: H3K122ac (Abcam ab33309)


title: MiSeq_Liver_H3K36me3

value: H3K36me3 (Millipore ABE435)


title: MiSeq_Liver_H3K27ac

value: H3K27ac (Abcam ab4729)


title: 982_L_27

value: Mid Lactation


title: MiSeq_Liver_H3K4me3

value: H3K4me3 (Abcam ab8580)


title: TumorsCohortC_DNAseq

first: Yejing

last: Ge

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
Sample 17
PCR amplified library from genomic DNA

data_processing:
Sample 1-12: Sequenced reads were trimmed for adaptor sequence, and then mapped to miRBASE mature.fa using BWA:
bwa aln -n5 -t4 mature_mmu.fa $i > alignments/aligned_$i.sai 2>alignments/aligned_$i.stderr;
bwa samse mature_mmu.fa alignments/aligned_$i.sai $i > alignments/sams/aligned_$i.sam;
samtools view -bt mature_mmu.fa.fai -o alignments/sams/aligned_$i.bam alignments/sams/aligned_$i.sam;
samtools sort alignments/sams/aligned_$i.bam alignments/sams/aligned_$i.sort;
samtools view -f4 -o alignments/unmapped/unmapped_$i.sam alignments/sams/aligned_$i.sort.bam;
samtools index alignments/sams/aligned_$i.sort.bam;
samtools idxstats alignments/sams/aligned_$i.sort.bam > alignments/counts/counts_$i.txt;
Sample 13-17: Sequenced reads were trimmed for adaptor sequence, and then mapped to SA-miRNA reference library using BWA:
bwa aln -n3 -t4 miR_lib.fa $i > alignments/aligned_$i.sai 2>alignments/aligned_$i.stderr;
bwa samse miR_lib.fa alignments/aligned_$i.sai $i > alignments/sams/aligned_$i.sam;
samtools view -bt miR_lib.fa.fai -o alignments/sams/aligned_$i.bam alignments/sams/aligned_$i.sam;
samtools sort alignments/sams/aligned_$i.bam alignments/sams/aligned_$i.sort;
samtools view -f4 -o alignments/unmapped/unmapped_$i.sam alignments/sams/aligned_$i.sort.bam;
samtools index alignments/sams/aligned_$i.sort.bam;
samtools idxstats alignments/sams/aligned_$i.sort.bam > alignments/counts/counts_$i.txt;
Genome_build: mm9; miRBase 21 (ftp://mirbase.org/pub/mirbase/CURRENT/)
Supplementary_files_format_and_content: tab-delimited text files include miR per million mapped reads values for samples 1-12; count values for samples 13-17 (miR name, map length, uniquely mapped reads, non-uniquely mapped reads)

source_name: Skin

growth_protocol: Samples 13-17: in utero lentiviral transduced animals collected at embryo E12.5 or at adult P50, or treated with DMBA/TPA at P50 and collect tumors formed and adjacent backskin

extract_protocol:
Sample 1-12 Total RNA extracted via Trizol/Zymo RNA extraction kit; Sample 13-17: genomic DNA extracted via Qiagen Tissue/blood gDNA extraction kit
Sample 1-12 Illumina TruSeq RNA Sample Preparation; Sample 13-17: PCR amplify targeted SA-miR region and Ampure purification
Single Read Clustering and 51 Cycles Sequencing (per lane)

treatment_protocol: Samples 13-17: in utero lentiviral transduction; at P50 topical DMBA once and TPA twice per week

tag: Sex

value: female and male

tag: strain

value: tumor-initiating stem cells from oncogenic HRas-induced tumors

tag: sort markers

value: Integrin A6+, B1+


title: 982_L_26

value: Early Lactation


title: MiSeq_PHH_H3K27me3

value: primary hepatocytes

value: HBV (ayw)

value: H3K27me3 (Millipore 07-449)


title: MiSeq_PHH_H3K36me3


title: MiSeq_Liver_Nuc

description: Nucleosome input for Sample 21-26

value: liver tissue


title: MiSeq_PHH_H3K122ac


title: MiSeq_PHH_Pol2


title: 829_L_24

value: Holstein

value: Fert-


title: 982_L_25

value: Liver


title: TumorsCohortB_DNAseq

description:
Sample 16
PCR amplified library from genomic DNA


title: 829_L_23


title: MiSeq_PHH_H3K27ac


title: P50-AdjSkin_DNAseq

description:
Sample 14
PCR amplified library from genomic DNA

value: adult skin epithelia


title: MiSeq_Liver_H3K27me3

value: HBV (endogenous)


title: MiSeq_PHH_H3K4me3


title: Embryos_DNAseq

description:
Sample 13
PCR amplified library from genomic DNA

value: embryonic skin epithelia


title: P0epi_miRNAseq

description:
Sample 11
small RNA library made from total RNA

value: female


title: 996_L_29


title: TumorsCohortA_DNAseq

description:
Sample 15
PCR amplified library from genomic DNA


title: 829_L_22

value: Late Pregnancy


title: P0HF_miRNAseq

description:
Sample 12
small RNA library made from total RNA


title: MiSeq_HepG2_Pol2

value: hepatoblastoma cells

value: RNA Polymerase 2 (Abcam ab817)


title: E17HF_miRNAseq

description:
Sample 10
small RNA library made from total RNA


title: MiSeq_HepG2_H3K122ac

value: H3K122ac (Abcam ab33309)


title: 782_L_19

value: Fert+


title: MiSeq_HepG2_H3K4me3

value: H3K4me3 (Abcam ab8580)


title: MiSeq_HepG2_Nuc

description: Nucleosome input for Sample 6-12


title: 756_L_18

value: Mid Lactation


title: MiSeq_PHH_Nuc

description: Nucleosome input for Sample 14-19

value: primary hepatocytes

value: HBV (ayw)


title: E12All_miRNAseq

description:
Sample 8
small RNA library made from total RNA

value: Integrin A6+, B1+


title: SCC63AHi_miRNAseq

description:
Sample 7
small RNA library made from total RNA

value: tumor-initiating stem cells from oncogenic HRas-induced benign papillomas

value: Integrin A6Hi, B1Hi


title: SCC63ALow_miRNAseq

description:
Sample 6
small RNA library made from total RNA

value: Integrin A6Low, B1Low


title: 756_L_17

value: Holstein

value: Liver

value: Early Lactation


title: 756_L_16


title: SCC47Hi_miRNAseq

description:
Sample 5
small RNA library made from total RNA

value: female

value: tumor-initiating stem cells from oncogenic HRas-induced SCCs


title: epi_miRNAseq

description:
Sample 3
small RNA library made from total RNA

value: adult skin epithelia


title: 430_L_13

value: Late Pregnancy


title: ORS_miRNAseq

description:
Sample 2
small RNA library made from total RNA


title: MiSeq_HepG2_H3K27me3

value: hepatoblastoma cells

value: H3K27me3 (Millipore 07-449)


title: MiSeq_HepG2_H3K9me3

value: H3K9me3 (Abcam ab8898)


title: 430_L_15

value: Mid Lactation

value: Fert+


title: 426_L_12

value: Fert-


title: 782_L_21


title: SCC47Low_miRNAseq

description:
Sample 4
small RNA library made from total RNA


title: 782_L_20


title: PR-Set7_RNAi_γ-H2Av_rep2

value: Mouse anti-γ-H2Av (DSHB UNC93-5.2.1-s)


title: Bulge_miRNAseq

description:
Sample 1
small RNA library made from total RNA


title: control_RNAi_γ-H2Av_rep2

value: control


title: MiSeq_HepG2_H3K36me3

value: HBV (ayw)

value: H3K36me3 (Millipore ABE435)


title: 426_L_11

description: liver by percutaneuos punch (PMID: 12545545)

value: Holstein