title: 5%_Input_594_24h

status: Public on Aug 27 2019

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Sequencing reads were aligned to mouse genome build mm10 using BWA version 0.5.7 (bwa aln sampe); Bam files were sorted using Sambamba version 0.5.5.
Bedtools bamtobed version 2.26.0 was used to convert the BAM files to the required BED format for SICER. Peak enrichment was computed using SICER v1.1 with the following parameters: redundancy threshold = 1, effective genome fraction = 0.74,  FDR = 0.001,  window size = 200bp, gap size = 600bp.
Genome_build: mm10
Supplementary_files_format_and_content: Bed files with fifth column: int(-10*log10(FDR))

source_name: Whole frontal cortex

growth_protocol: C57BL/6 mice were maintained under standard animal house conditions (12 hour dark-light cycles on ad libitum food and water intake). Mice were euthanized 6 and 18 hours after first light stimulus (corresponding to times 12:00 and 24:00 respectively)

extract_protocol:
Frontal cortices were removed and crosslinked, nuclei extracted and chromatin sonicated and clarified. MeCP2-Chromatin complexes were isolated with the indicated antibodies.
End Repair and 5’ Phosphorylation reactions were incubated for 30 minutes at room temperature. DNA samples were then purified, DNA was eluted with Qiagen EB buffer. A single dA overhang was added to the 3’ ends of DNA fragments (New England Biolabs). Illumina adaptors were ligated and products were then purified. Adaptor ligated libraries were PCR amplified and barcoded by custom indexing primers. PCR amplified libraries were size selected and quantified using Qubit HS DNA assay and average sizes determined by using Agilent HS DNA assay chips (Thermo Fisher). Library pool was sequenced paired-end 75 on HiSeq 2500 (Illumina).

tag: Sex

value: male

tag: tissue type

value: brain frontal cortex

value: 24 hours

tag: antibody


title: IP_E2_615_24h

type: SRA

description: IP_E2_615_24h vs 5%_Input_615_24h enriched regions were compared to IP_E2_638_12h vs 5%_Input_638_12h enriched regions

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

value: female

tag: time

value: MeCP2 E2 isoform (In-house antibody)


title: IP_E2_594_24h

description: IP_E2_594_24h vs 5%_Input_594_24h enriched regions were compared to IP_E2_637_12h vs 5%_Input_637_12h enriched regions


title: IP_E1_594_24h

description: IP_E1_594_24h vs 5%_Input_594_24h enriched regions were compared to IP_E1_637_12h vs 5%_Input_637_12h enriched regions

value: MeCP2 E1 isoform (In-house antibody)


title: 5%_Input_638_12h

value: 12 hours


title: 5%_Input_615_24h


title: IP_E1_638_12h

description: IP_E1_638_12h vs 5%_Input_638_12h enriched regions were compared to IP_E1_615_24h vs 5%_Input_615_24h enriched regions


title: IP_E2_637_12h

description: IP_E2_637_12h vs 5%_Input_637_12h enriched regions were compared to IP_E2_594_24h vs 5%_Input_594_24h enriched regions


title: IP_E2_638_12h

description: IP_E2_638_12h vs 5%_Input_638_12h enriched regions were compared to IP_E2_615_24h vs 5%_Input_615_24h enriched regions


title: MPE CD4+ T cells from IL-10-/- mice, biological rep3

city: Beijing

first: Yuan

last: Yang

address: 8 Gongti Nanlu, Chaoyang District

country: China

institute: Beijing Chaoyang Hospital, Capital Medical University

library_source: transcriptomic

data_processing:
Illumina HiSeq2500 sequencer and software used for sequencing and basecalling.
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Genome_build: GRCm38.92
Supplementary_files_format_and_content: tab-delimited text files include p-value or q-value for each Sample.

molecule: total RNA

source_name: MPE CD4+ T cells from IL-10-/- mice

growth_protocol: Ten days after injection of MC38 cells, mice were euthanized by CO2 asphyxiation, and MPE samples were collected and then centrifuged at 400 × g for 6 minutes.

extract_protocol:
Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell pellets of MPE were resuspended in PBS, and mononuclear cells were isolated by Ficoll-Hypaque gradient centrifugation (Pharmacia, Uppsala, Sweden) within 1 hour. Viable cells excluding tumor cells were sorted by means of BD Aria II flow cytometry (BD Bioscience). CD4+ T cells were gated on FSC/SSC/CD3+/CD4+;


title: MPE CD4+ T cells from WT mice, biological rep3

source_name: MPE CD4+ T cells from WT mice


title: MPE CD4+ T cells from IL-10-/- mice, biological rep2


title: MPE CD4+ T cells from IL-10-/- mice, biological rep1


title: MPE CD4+ T cells from WT mice, biological rep2


title: PGLYRP4KO AM, Streptococcus pneumoniae, rep3

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

description: Gene expression data from infected PGLYRP4KO AMs

hyb_protocol: Standard Affymentrix Hybridization, Wash and Staining reagents were used, along with the specific Mouse Gene 2.0 ST Array ‘Genechip’ arrays required for the project. GeneChips were washed and stained in the Affymetrix GeneChip™ Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G’

data_processing: The analysis of this gene expression profiling experiment involved the analysis of the raw data against quality standards, prior to normalisation and statistical evaluation, in order to provide an overview of the differentially regulated genes and their respective fold-changes and annotations. A custom laboratory pipeline was used to automatically perform this analysis.

label: biotin

source_name: primary alveolar macrophages cells from male BALB/c mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The lungs were lavaged multiple times with 2 mM EDTA PBS (final volume 5 ml). The lavages were centrifuged (300 × g, 10 min, 4◦C) and the cell pellets were resuspended in 1 ml of RPMI1640 (10% FCS , 1% glutamine, 1% penicillin/streptomycin). The AMs were seeded into cell culture plates and incubated at 37◦C for 2 h. Then the medium was changed and cells were incubated overnight. Two hours before stimulation, medium was changed again to RPMI1640 with 2% FCS and 1% Glu.

extract_protocol: RNA was isolated unsing TRIzol reagent (Life Technologies GmbH)

treatment_protocol: Cells were treated with S.pneumoniae (NCTC 7466, MOI 1) for 6h or left untreated as control.

value: BALB/c

tag: tissue

value: primary alveolar macrophages cells

tag: genotype

value: knockout for PGLYRP4


title: PGLYRP4KO AM, uninfected, rep3

description: Gene expression data from uninfected PGLYRP4KO AMs


title: wt AM uninfected, rep2

description: Gene expression data from uninfected wt AMs

value: wild type for PGLYRP4


title: PGLYRP4KO AM, Streptococcus pneumoniae, rep2


title: wt AM Streptococcus pneumoniae, rep3

description: Gene expression data from infected wt AMs


title: wt AM Streptococcus pneumoniae, rep2


title: PGLYRP4KO AM, Streptococcus pneumoniae, rep1


title: PGLYRP4KO AM, uninfected, rep2


title: wt AM uninfected, rep3


title: wt AM uninfected, rep1


title: IP_E1_637_12h

description: IP_E1_637_12h vs 5%_Input_637_12h enriched regions were compared to IP_E1_594_24h vs 5%_Input_594_24h enriched regions


title: PGLYRP4KO AM, uninfected, rep1


title: 5%_Input_637_12h


title: 2_WAGR

city: NEW YORK CITY

first: Sergio

last: Espeso-Gil

state: New York

address: 1470 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: RNAseq

data_processing:
Pair-end (50bp) RNA sequenced libraries were mapped to human (GRCh38.p10_v26) with STAR (v2.5.3a) using a two-method step protocol following tool specifications. Reads were counted in exon regions using featureCounts tool (subread v1.5.2) producing a table that was normalized to rpkms
Supplementary_files_format_and_content: RPKM

organism: Homo sapiens

source_name: lymphoblast

growth_protocol: Fasting  venous blood samples were obtained from patients. Peripheral blood mononuclear cells were isolated using a Ficoll-Paque gradient (GE Heathcare Life Sciences, Pittsburgh, PA), then infected with Epstein Barr virus, and after sufficient cell line expansion, stored in freezing media at -80°C

extract_protocol:
Total RNA was isolated from four lymphoblastoid cell lines including one derived from healthy control subject, one WAGR patient with C11orf46 gene intact and two WAGR patients with C11orf46 gene deletions using a total RNA extraction kit (Qiagen) according to manufacturer instructions
RNA integrity determined in Bioanalyzer (Agilent’s Technologies) and a total RNA-seq was performed at Eurofins genomics. DNA libraries were prepared from total RNA samples, the adaptor-ligated libraries (125bp) were enriched by PCR amplification and gel purified (average library size of ~270bp). Libraries were sequenced with the Genome Analyzer II (Illumina) using pair-end 50-bp raw fastq reads

tag: nih id


title: 3_WAGR

description: RNAseq


title: 1_Control

description: RNAseq


title: B2B30GROseq-D2

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

data_processing:
Library strategy: GRO-seq
Reads were first converted to their reverse complement using FASTX Toolkit fastx reverse complement (v. 0.0.13) with the argument ‘-Q33’.
Reads were trimmed for adapters, minimum length, and minimum quality using the BBMap Suite (v. 38.05) bbduk.sh tool with arguments ‘ref = truseq.fa.gz literal = CCCGTGTTGAGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTT ktrim = r qtrim = 10 k = 23 mink = 11 hdist = 1 maq = 10 minlen = 2’.
Trimmed reads were mapped to the human genome (hg38; downloaded from Illumina iGenomes with corresponding Bowtie2 index files) using Bowtie2 (v. 2.1.0) in ‘--end-to-end’ alignment mode with ‘--very-sensitive’ preset options.
Resulting SAM files were converted to BAM format using samtools view (v. 1.8) with arguments ‘-S -b’ and then sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.25.0) for both positive and negative strands with arguments ‘-bg -ibam -g hg38 -strand [+/-]’. The fourth column (read coverage) of the negative strand file was negated and then concatenated with the positive strand file to generate a strand-differentiated bedGraph file.
FStitch (v. 1.0) was first used to filter regions of inactive transcription in all samples to lessen downstream compute processing requirements. FStitch train was used with arguments ‘-r (sample.positiveStand.bedGraph) -t (trainingFile.bed) -o (outputTrainingParameters.hmminfo)’ using the IGV (v. 2.3.75) Region Navigator tool to produce a BED format training file generated from one of the 10 min dex-treated samples that was determined to be most representative of the data in terms of read coverage, complexity, and total reads mapped.
FStitch segment was then run on all single-strand non-normalized bedGraph files with arguments ‘-r (sample.pos.bedgraph) -w (outputTrainingParameters.hmminfo) -o (sample.bed)’. Positive and negative strand files were then concatenated and sorted using sortBed in the BEDTools suite (v. 2.25.0).
Tfit (v. 1.0) was used to generate the predictions of bidirectionals/eRNAs. BED file annotations of preliminary bidirectional calls were generated using the Tfit bidir old module with arguments ‘-ij (sample.concatenated.bedGraph) -N (bidir old) -k (sample.concatenatedFStitch.bed) -mle 1 -o (output directory) -log out (output directory) -tss (hg38 RefSeq gene transcription start site file).
Using the bidirectional predictions file, the Tfit model module was run to get higher confidence calls with arguments ‘-ij (sample.concatenated.bedGraph) -k (preliminaryBidirectionals.bed) -N (tfit mod) -log out (output directory) -o (output directory) -config (config file)’ to produce a final BED annotation file of predicted bidirectionals.
Using the RefSeq : NCBI Reference Sequences for hg38, including both NM and NR accession types (downloaded from the UCSC track browser on May 18, 2018), counts were calculated for each sorted BAM file using multibBamCov in the BEDTools suite (v. 2.25.0). Genes (NM accession type) and lncRNAs (NR accession type) were then filtered such that only the isoform with the highest number of reads per annotated length was kept in order to minimize duplicate samples being included in differential transcription analysis.
DESeq2 (v. 1.20.0, Bioconductor release v. 3.7) was then used to determine which genes were differentially transcribed between the different treatments for each time point separately. For bidirectional/enhancer comparisons, all bidirectional prediction Tfit calls were first merged using mergeBed (argument -d 60) from the BEDTools suite (v. 2.25.0) to generate an annotation file. Counts were then calculated for each sample using multicov from the BEDTools suite (v. 2.25.0) and DESeq2 was used to calculate differentially transcribed bidirectionals/eRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files are strand-differentiated coverage files, as described above.

source_name: Beas-2B airway epithelial cells

growth_protocol: Beas-2B cells obtained from ATCC were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing L-glutamine and 4.5 g/L glucose and supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Plates were washed in PBS and cells were scraped in Lysis Buffer prior to isolation of nuclei. Nuclear run-on reactions were performed in the presence of Br-UTP, then total RNA was isolated using TRIzol Reagent. RNA was hydrolyzed with NaOH to yield fragments ~200 bp long and then treated with DNase prior to two sequential nascent RNA enrichment steps performed by anti-Br-UTP immunoprecipitation.
A random-priming library preparation kit (NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)) was used according to the Protocol for use with NEBNext rRNA Depletion Kit provided by the manufacturer to generate uniquely barcoded libraries for sequencing. Libraries were size-selected for a target size of ~300 bp and sent to an Illumina HiSeq instrument for 50 bp single-end sequencing.

treatment_protocol: Cells were plated on 15 cm tissue culture dishes at 3.75E6 cells/dish (2 plates per treatment per time-point) and grown to confluence (~3 days). Cells were treated with vehicle (ethanol), TNF (20 ng/ml), dexamethasone (dex; 100 nM), or TNF+dex for exactly 10 or 30 minutes.

tag: treatment

value: dex

tag: treatment time (min)


title: B2B30GROseq-TD

value: TNF+dex


title: B2B30GROseq-TE2

value: TNF


title: B2B10GROseq-TD


title: B2B30GROseq-TE


title: B2B30GROseq-E2

value: vehicle


title: B2B10GROseq-TD2


title: B2B30GROseq-E


title: B2B30GROseq-D


title: NC

city: Wuhan

first: Xiaowei

last: Zhang

state: Hubei province

address: Xiao Hong Shan No.44

institute: Wuhan Institute of Virology, Chinese Academy of Sciences

data_processing:
The gene expression level was calculated and normalized by using the TPM (the number of transcripts per million clean tags) method.
False Discovery Rate (FDR) ≤ 0.001 and the absolute value of log2Ratio ≥ 1 were used as the threshold to judge the significance of the differential gene expression.
Differentially expressed genes were mapped to Gene Ontology (GO) terms in GO database (http://www.geneontology.org/) by hypergeometric test and the Bonferroni-corrected P-value ≤ 0.05 was used as the threshold.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: The Excel files include the number of unambiguous clean tags and normalized TPM (number of transcripts per million clean tags) for each gene.

source_name: CCF-STTG1 glioma cells

growth_protocol: CCF-STTG1 (CCF; a human malignant glioma cell line; ATCC CRL-1718) cells were grown in RPMI1640 supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin (Life Technologies).

extract_protocol:
Total RNA samples from CCF glioma cells after EV71 or mock infection were used for RNA-seq analysis by using Illumina HiSeqTM 2000 System.
Extract 6 µg total RNA, use Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize the first and second-strand cDNA. The 5' ends of tags can be generated by two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 105bp fragments are purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules are fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 49bp.

treatment_protocol: Cell monolayers were infected with EV71 BrCr strain at a multiplicities of infection (MOIs) of 1 for 60 min at room temperature. Inoculated cell cultures were washed three times with phosphate-buffered saline (PBS) and then replenished with complete medium. Cytopathic effects were judged using phase-contrast microscopy. Cell monolayers were harvested at the indicated times for further analysis.

tag: cell type

value: glioblastomas (malignancy grade IV)

tag: infection status

value: mock-infected


title: MPE CD4+ T cells from WT mice, biological rep1


title: B2B10GROseq-D2


title: B2B30GROseq-TD2


title: E71


title: B2B10GROseq-E2


title: 167468

city: South Birmingham

first: Hind

last: Lal

state: AL

address: 1720 2nd Ave South Birmingham, AL 35294-1913

department: Division of Cardiovascular Disease

institute: The University of Alabama at Birmingham

description: Gene expression, left ventricular, sham 6wks

hyb_protocol: RNA samples were amplified, labeled, hybridized, and scanned according to Affymetrix standard protocol

data_processing: Raw data files (CEL files) were analyzed using standard data quality checks and samples failing these checks were removed from subsequent analyses.  Raw data was then pre-processed using the RMA (Robust Multi-chip Average) pipeline  in combination with the most current re-annotated probeset definitions.

source_name: left ventricle

extract_protocol: Samples were collected and flash frozen in liquid nitrogen then stored at -80oC. For RNA isolation, ~100mg samples were used in 1ml Trizol and isolation was done according to the manufacturers

treatment_protocol: C57BL/6 male mice were subjected to transaortic constriction (TAC) to induce heart failure (n=4) or sham surgery (n=5).  At 6 weeks post-TAC or post-sham, RNA samples from the left ventricle were collected and subjected to microarray analysis

tag: organ

value: heart

value: male

value: Sham

tag: time point

value: 6 weeks

tag: group

value: control


title: B2B10GROseq-TE


title: 167466

scan_protocol: RNA samples were amplified, labeled, hybridized, and scanned according to Affymetrix standard protocol


title: B2B10GROseq-E


title: 167481

description: Gene expression, left ventricular, TAC 6wks

label_protocol: RNA samples were amplified, labeled, hybridized, and scanned according to Affymetrix standard protocol

value: TAC

value: experiment


title: 167475


title: 167478


title: 167464


title: 167467


title: Mitochondrial RNA isolated from untreated HepG2 control cells

city: Palo Alto

first: Jifan

last: Hu

state: CA

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

description: mitochondria localized RNA in hepatocelluar carcinoma cells and normal liver cells identified by RNA-Seq

data_processing:
Raw data were filtered with Seqtk
Clean reads were mapped by human GRCh38 with Hisat2（version:2.0.4）

source_name: mitochondrial RNA

growth_protocol: Cell was cultured in DMEM with high glucose medium (HyClone) containing 10% fetal bovine serum (HyClone; GE Healthcare Life Sciences, Logan, UT, USA), 100 U/mL Penicillin-Streptomycin (ThermoFisher), at 37˚C with 5% CO2.

extract_protocol:
Mitochondria was isolated following the Qproteome Mitochondria Isolation Kit (Cat No./ID: 37612), and RNA was extracted by miRNeasy Mini Kit (Cat# 217004, Qiagen)
Library construction protocol was processed following purification and mRNA fragmentation ，first Strand cDNA Synthesization, Second Strand cDNA Synthesization, 3′Ends Adenylattion,  Adapters Ligation, DNA fragments enrichment ,and libraries checking.

treatment_protocol: EMT was induced by TGF‑β1 (PeproTech, NJ). Briefly, cells were seeded into 6‑well plates in duplicate. Following 24 h, EMT‑inducing medium (containing 10 ng/ml TGF‑β1) was used to replace the common medium and the cells were incubated for additional 24‑72 h.

tag: cell line

value: hepatocellular carcinoma


title: 167465


title: Mitochondrial RNA isolated from HepG2-EMT cells induced by TGF-b1 treatment

value: epithelial-mesenchymal transition (EMT) cells induced by TGF-b1 treatment


title: Mitochondrial RNA isolated from normal HL7702 liver cells

value: normal human liver cells


title: CATACGCA_TGTTCAGG

city: Cambridge

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

institute: Broad institute

description:
mouse LSK
index sorted hematopoietic stem and progenitor cells

data_processing:
gene counting matrix generated using scPipe 1.3.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a cell

molecule: polyA RNA

source_name: hematopoietic stem and progenitor cells

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions at WEHI, according to institutional guidelines. C57BL/6 (CD45.2), C57BL/6 Pep3b (CD45.1), Cas9-Tg or Dach1-GFP mice aged between 8-16 weeks were used.

extract_protocol:
marrow cells from C57BL/6 mice  were harvested, made into a single cell suspension, incubated with red cell removal buffer (NH4Cl), followed by incubation with anti-CD117-APC, then incubation with anti-APC magnetic beads, followed by purification on a LS column (Miltenyit biotech).
we used 96 indexed polydT primers with a 6N unique molecular identifier (UMI) sequence followed by an 8 bp index sequence (inhouse design) and the Illumina TruSeq adapter sequences: CGATTGAGGCCGGTAATACGACTCACTATAGGGCAGACGTGTGCTCTTCCGATCTNNNNNNACTTGGCATTTTTTTTTTTTTTTTTTTTV). Single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. We pooled the samples after the first strand synthesis and the second strand synthesis was performed using NEBNext Second Strand Synthesis module. NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps.

treatment_protocol: marrow cells from C57BL/6 mice  were harvested, made into a single cell suspension, incubated with red cell removal buffer (NH4Cl), followed by incubation with anti-CD117-APC, then incubation with anti-APC magnetic beads, followed by purification on a LS column (Miltenyit biotech). This enriched fraction was then stained with a cocktail of antibodies including anti-Sca1, anti-Il7Ra-biotin, anti-CD16/32, anti-CD135-PE, anti-CD150, anti-CD48. Cells were sorted either in bulk or using the single cell mode of a BD Fusion cell sorter.

value: hematopoietic stem and progenitor cells

tag: ckit


title: CATACGCA_TGTGATCG


title: CATACGCA_TGTTAGGC


title: CATACGCA_TGGTAGTC


title: CATACGCA_TGGTAGCT


title: CATACGCA_TGGACTCA


title: CATACGCA_TGCAGTAC


title: B2B10GROseq-TE2


title: CATACGCA_TGCCTAAG


title: CATACGCA_TCGTAGCA


title: CATACGCA_TGACGCAT


title: CATACGCA_TGGTGTCA


title: CATACGCA_TCCTAGAG


title: CATACGCA_TCGAGTCA


title: CATACGCA_TCCATAGG


title: CATACGCA_TCGACATG


title: CATACGCA_TACACACG


title: CATACGCA_TACGCAGT


title: CATACGCA_TCACGTAG


title: CATACGCA_GTTGTTGG


title: CATACGCA_GTTGCACA


title: CATACGCA_GTCGATAC


title: CATACGCA_GTTATCGG


title: CATACGCA_TCACGGAT


title: CATACGCA_TAAGGCTC


title: CATACGCA_GGCCATAT


title: B2B10GROseq-D

value: dex


title: CATACGCA_GGTACGTT


title: CATACGCA_GGACTACT


title: CATACGCA_GTTATGGC


title: CATACGCA_GGACCTTA


title: CATACGCA_GCTATGTG


title: CATACGCA_GCTAGTCA


title: CATACGCA_TCGCTAGA


title: CATACGCA_GCGGTTAT


title: CATACGCA_GCCATGTA


title: CATACGCA_GCGAACTT


title: CATACGCA_GCCATAGT


title: CATACGCA_GCACTAAC


title: IP_E1_615_24h

description: IP_E1_615_24h vs 5%_Input_615_24h enriched regions were compared to IP_E1_638_12h vs 5%_Input_638_12h enriched regions

tag: Sex

value: female

value: brain frontal cortex

value: 24 hours

value: MeCP2 E1 isoform (In-house antibody)


title: CATACGCA_GCACACAT


title: CATACGCA_GATAGCTC


title: CATACGCA_GTATACCG


title: CATACGCA_GATTACCG


title: CATACGCA_GAGTCTGT


title: CATACGCA_GAGTTCAC


title: CATACGCA_GACTTGCA


title: CATACGCA_GAGTCCAT


title: CATACGCA_CTGACATG


title: CATACGCA_CGCATAAC


title: CATACGCA_CGCAACTA


title: CATACGCA_CGTGGTAT


title: CATACGCA_GACCGATT


title: CATACGCA_CTGTTAGG


title: CATACGCA_CTTGATGG


title: CATACGCA_CTAATGGC


title: CATACGCA_CGACAATC


title: CATACGCA_CTGCAGTA


title: CATACGCA_CGAACTTG


title: CATACGCA_CGCAATGT


title: CATACGCA_CCGAACTA


title: CATACGCA_CCGTAAGT


title: CATACGCA_CCAGAACT


title: CATACGCA_CCATTGAG


title: CATACGCA_CATTGCAG


title: CATACGCA_CCAACCAA


title: CATACGCA_CATGCCAA


title: CATACGCA_CATTCGGA


title: CATACGCA_CAGCCAAT


title: CATACGCA_CATCAACG


title: CATACGCA_CAGTGCAT


title: CATACGCA_CACTGACA


title: CATACGCA_CAATGTGC


title: CATACGCA_CAATGCCA


title: CATACGCA_CAGACTCA


title: CATACGCA_CAACCGTA


title: CATACGCA_ATGCATCG


title: CATACGCA_ATGCCAAC


title: CATACGCA_CACGCTAA


title: CATACGCA_AGTGGTCT


title: 167483


title: CATACGCA_CGACTATG


title: CATACGCA_AGCGTACT


title: CATACGCA_ACTTGGCA


title: CATACGCA_ACTAGTGC


title: CATACGCA_ACTACGAC


title: CATACGCA_AGTGGTTC


title: CATACGCA_ACGTGATC


title: CATACGCA_ACGACTAC


title: CATACGCA_ACCATCAG


title: CATACGCA_CAGCTAGT


title: 4_WAGR

description: RNAseq


title: CATACGCA_ACATGTCG


title: CATACGCA_AAGCTCTG


title: CATACGCA_AAGCCGTT


title: CATACGCA_ACACTGCA


title: CATACGCA_AACAGCTC


title: AGCGTCAT_TGTTCAGG


title: CATACGCA_ATTCCGAG


title: CATACGCA_ATCCATGG


title: CATACGCA_ATCAGTGC


title: AGCGTCAT_TGTTAGGC


title: AGCGTCAT_TGTGATCG


title: AGCGTCAT_TGGTGTCA


title: AGCGTCAT_TGGTAGTC


title: AGCGTCAT_TGCCTAAG


title: AGCGTCAT_TGGACTCA


title: AGCGTCAT_TGGTAGCT


title: S2 cells, 60min digestion, exp.1, seq.3

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: S2 cells, 60min digestion, sequencing 3

data_processing:
DNA sequences were aligned to the D. melanogaster reference genome dm6 and S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, 2012) with parameters -X 1000 --very-sensitive.
Nucleosome counts (defined as the number of Drosophila DNA fragments with the length between 100-200 bp) and spike-in counts (number of S. cerevisiae DNA fragments with the length between 100-200 bp) were obtained using MATLAB (Bioinformatics toolbox).
Genome-wide profiles (tdf files) containing the spike-in normalized nucleosome counts were generated using MATLAB and igvtools.
Genome_build: dm6
Supplementary_files_format_and_content: tdf files containing the spike-in normalized genome-wide nucleosome counts (for IGV browser)

organism: Drosophila melanogaster

source_name: Drosophila S2 cells chromatin

growth_protocol: Drosophila melanogaster S2 cells were obtained from Invitrogen (10831-014) and grown in HyClone SFX-Insect media supplemented with 18 mM L-glutamine.

extract_protocol:
Drosophila S2 cell nuclei were isolated and subjected to MNase digestion for 1, 2, 5, 15, 40, 60 minutes. S. cerevisiae spike-in DNA was used for normalization.
Paired-end sequencing (PE25x25) was performed on barcoded libraries using an Illumina HiSeq 2500

treatment_protocol: MNase-seq was performed on unfixed cells as described (Ramachandran et al., 2017) with the following modifications: For each time point, ~2 million cells were suspended in 10 mM HEPES pH 7.4, 0.5 mM PMSF, 0.5% NP40 on ice in a 166 µL volume. MNase was added at a concentration of 2.5 U per million cells. The mixture was warmed to 37C before addition of 3.5 µL 100 mM CaCl2 (to 2 mM) to activate the MNase. Reactions were stopped by addition of 170 µL of 2XSTOP (4.345 ml TM2, 340 µL 5M NaCl, 200 µL 0.5M EDTA, 100 µL 0.2M EGTA, 25 µL RNase A and 2 pg/ml yeast mononucleosomal spike-in DNA). After phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation, the DNA pellet was dissolved in 50 µL 1 mM Tris-HCl pH 8, 0.1 mM EDTA and used directly for 1.5% agarose gel analysis and for making sequencing libraries as described (Ramachandran et al., 2017).

value: S2 cells

value: triplo-X tetraploid cell line from Invitrogen (10831-014)


title: AGCGTCAT_TGACGCAT


title: AGCGTCAT_TCGCTAGA


title: AGCGTCAT_TCGTAGCA


title: S2 cells, 15min digestion, exp.1, seq.3

description: S2 cells, 15min digestion, sequencing 3


title: S2 cells, 5min digestion, exp.1, seq.3

description: S2 cells, 5min digestion, sequencing 3


title: AGCGTCAT_TCGACATG


title: AGCGTCAT_TCGAGTCA


title: S2 cells, 2min digestion, exp.1, seq.3

description: S2 cells, 2min digestion, sequencing 3


title: CATACGCA_AACTCCAG


title: S2 cells, 40min digestion, exp.1, seq.3

description: S2 cells, 40min digestion, sequencing 3


title: S2 cells, 1min digestion, exp.1, seq.3

description: S2 cells, 1min digestion, sequencing 3


title: AGCGTCAT_TCCTAGAG


title: S2 cells, 40min digestion, exp.1, seq.2

description: S2 cells, 40min digestion, sequencing 2


title: S2 cells, 60min digestion, exp.1, seq.2

description: S2 cells, 60min digestion, sequencing 2


title: S2 cells, 15min digestion, exp.1, seq.2

description: S2 cells, 15min digestion, sequencing 2


title: AGCGTCAT_TCCATAGG


title: AGCGTCAT_TCACGTAG


title: AGCGTCAT_TACGCAGT


title: S2 cells, 5min digestion, exp.1, seq.2

description: S2 cells, 5min digestion, sequencing 2


title: AGCGTCAT_TCACGGAT


title: S2 cells, 2min digestion, exp.1, seq.2

description: S2 cells, 2min digestion, sequencing 2


title: AGCGTCAT_TACACACG


title: AGCGTCAT_TGCAGTAC


title: AGCGTCAT_TAAGGCTC


title: AGCGTCAT_GTTGCACA


title: AGCGTCAT_GTTATGGC


title: S2 cells, 40min digestion, exp.1, seq.1

description: S2 cells, 40min digestion, sequencing 1


title: S2 cells, 15min digestion, exp.1, seq.1

description: S2 cells, 15min digestion, sequencing 1


title: S2 cells, 1min digestion, exp.1, seq.2

description: S2 cells, 1min digestion, sequencing 2


title: AGCGTCAT_GTTATCGG


title: S2 cells, 5min digestion, exp.1, seq.1

description: S2 cells, 5min digestion, sequencing 1


title: S2 cells, 1min digestion, exp.1, seq.1

description: S2 cells, 1min digestion, sequencing 1


title: S2 cells, 2min digestion, exp.1, seq.1

description: S2 cells, 2min digestion, sequencing 1


title: AGCGTCAT_GTCGATAC


title: AGCGTCAT_GTATACCG


title: Neuronal_rescue_rep3

city: Boston

first: Meeta

last: Mistry

address: 655 Huntington Ave

institute: Harvard School of Public Health

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were assessed for low-quality sequence, then mapped against the WBcel235 transcriptome where reads were quantified at the transcript level using Salmon
Transcript-level abundance estimates  from Salmon were collapsed to gene-leve estimates and  converted to raw count values using the R Bioconductor package tximport
Differentially expressed genes were identified using the R Bioconductor package DESeq2
Genome_build: Ensembl94 (WBcel235)
Supplementary_files_format_and_content: tab-delimited text file is a raw count matrix where columns correspond to samples and rows correspond to genes; a DESeq2 normalized count matrix (median of ratios method)  is also included. The first column is gene ID and the last column is gene symbol

organism: Caenorhabditis elegans

source_name: mid-L4 stage worm

growth_protocol: Worms were bleached to HT115 bacteria carrying L4440 vector. Synchronized L4 populations were obtained via timed egg lay

extract_protocol:
Aproximately 1000 mid-L4 stage animals were washed, resuspended in QIAzol lysis reagent (Qiagen, Venlo, Netherlands, #79306), snap frozen in liquid nitrogen, and stored in -80°C freezer until RNA extraction. To break the worm cuticle and improve RNA yield, all samples underwent 5 freeze-thaw cycles. In each cycle, samples were thawed at 37˚C and then snap-frozen in liquid nitrogen. RNA extraction was performed immediately using QIAGEN RNeasy Mini Kit (QIAGEN, #74104) following manufacturer’s instructions. RNA quality was confirmed using Agilent Bioanalyzer 2100 (Agilent Technologies). All samples passed the quality control standard of RIN>8.0.
mRNA libraries were prepared using TruSeq® Stranded mRNA LT - Set A kit (Illumina, CA, USA RS-122-2101) following manufacturer’s instructions and linked to different adaptors to enable pooling. Library quality was checked using 2200 High Sensitivity D1000 Tape Station (Agilent Technologies)
RNA-Seq with Illumina HiSeq 2500 using 50-cycle, pair-end settings

tag: worm collection date


title: Neuronal_rescue_rep4


title: Neuronal_rescue_rep2


title: AGCGTCAT_GGACTACT


title: AGCGTCAT_GGCCATAT


title: AGCGTCAT_GGTACGTT


title: S2 cells, 60min digestion, exp.1, seq.1

description: S2 cells, 60min digestion, sequencing 1


title: RagA_mutant_rep2


title: AGCGTCAT_GCTATGTG


title: RagA_mutant_rep4


title: RagA_mutant_rep3


title: Neuronal_rescue_rep1


title: AGCGTCAT_GCGGTTAT


title: AGCGTCAT_GGACCTTA


title: AGCGTCAT_GCTAGTCA


title: AGCGTCAT_GCCATGTA


title: AGCGTCAT_GTTGTTGG


title: Wildtype_rep3

value: Wildtype


title: AGCGTCAT_GCGAACTT


title: Wildtype_rep4


title: RagA_mutant_rep1


title: Wildtype_rep1


title: Wildtype_rep2


title: AGCGTCAT_GATTACCG


title: AGCGTCAT_GCACACAT


title: AGCGTCAT_GCCATAGT


title: AGCGTCAT_GAGTTCAC


title: AGCGTCAT_GATAGCTC


title: AGCGTCAT_GAGTCCAT


title: AGCGTCAT_CTTGATGG


title: AGCGTCAT_GACCGATT


title: AGCGTCAT_GACTTGCA


title: AGCGTCAT_CTGTTAGG


title: AGCGTCAT_GCACTAAC


title: AGCGTCAT_CTAATGGC


title: AGCGTCAT_CTGACATG


title: NCI-H716 cells, H716 Low Glucose

city: Charlottesville

first: Joe

last: Mychaleckyj

state: VA

institute: University of Virginia

data_processing:
Illumina HiSeq 2500 using Rapid Flow Cell v2, 76 cycle paired end reads
trim last base and any adapter sequences from all reads (trim_galore 0.5.0) -q 0 (no quality trimming to avoid biases)
Alignment to Human Genome build38 and gene models from GENCODE v28 primary assembly using STAR 2.6.0
Gene read quantification was performed using RSEM v1.3.1
Genes with very low total expression (total expected counts < 1, low+high conditions) were removed
Remaining genes normalized using the trimmed mean of M-values method as implemented in the edgeR
log2 counts per million (CPM) was estimated with default prior of 0.25 CPM per gene (edgeR).
cpmSample = 2^(log2Sample)
Genome_build: Build 38
Supplementary_files_format_and_content: Tab delimited file of genes x columns: log2LOWGLUC, log2HIGHGLUC, log2Mean, log2Delta, cpmLOWGLUC, cpmHIGHGLUC, cpmMean, foldc

growth_protocol: NCI-H716 cells were grown in suspension culture in RPMI 1640 media supplemented with 10% fetal bovine serum (FBS) and 100 units/ml of penicillin/streptomycin at 5% CO2. For the RNA extraction, NCI-H716 cells were plated on Matrigel in 6-well plates containing ~800,000 cells/well, allowing cells to attach to the culture plates. After 24 hours, the medium was changed and cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 units/ml of penicillin/streptomycin in low glucose (5.5 mM) or high glucose (25 mM) for 48 hours.

extract_protocol:
Total RNA was extracted using RNeasyPlus Mini Kit (Qiagen), according to the manufacturer's instructions.
Illumina TruSeq RNA Library Prep Kit v2 with polyA selection

value: cecum

value: Cecum colorectal adenocarcinoma cell line NCI-H716

tag: disease state

value: colorectal adenocarcinoma

value: Low glucose growth medium (5.5mM)


title: NCI-H716 cells, H716 High Glucose

source_name: Cecum colorectal adenocarcinoma cell line

value: High glucose growth medium (25mM)


title: AGCGTCAT_CGTGGTAT

tag: strain


title: AGCGTCAT_GAGTCTGT


title: 69W

city: Ar Ramtha

first: Laith

last: Al-Eitan

state: Irbid

address: Petra Street

country: Jordan

institute: Jordan University of Science and Technology

data_processing:
The primary sequence data was generated using the illumina bcl2fastq 2.20.0.422 pipeline, the bcl2fastq conversion software v2.20.0.422 demultiplexes sequencing data and converts base call (BCL) files into FASTQ files.
The sequence reads from all 24 samples were analysed according to AGRF quality control measures. The per base sequence quality for the 24 samples looked excellent with >94% bases above Q30 across all samples. The reads were also screened for the presence of any illumina adapter/overrepresented sequences and cross-species contamination.
Reads were trimmed using trim_galore (0.4.4). The cleaned sequence reads were then aligned against the Homo sapiens genome (Build version HG38). The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences.
The raw gene counts or the DGE (digital gene expression) values was used with "edgeR" for computing differential gene expression. Counts are summarised at gene level using the featureCounts v1.5.3 utility of the subread package.
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text file (.txt) consists of a first column of NCBI gene IDs, followed by a column of read counts for each of the samples. The first row shows the sample name for each of the columns. The read counts are the number of reads for the sample denoted by the column that mapped to the gene denoted by the row.

source_name: Skin

extract_protocol:
Shave biopsies of warts and adjacent normal skin were obtained and immediately placed in microcentrifuge tubes containing RNA-SafeGuard reagent (GMbiolab Co., Ltd, Taiwan) and refrigerated at -20°C until homogenization. RNA was extracted from the homogenates using an RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Using the RNase-Free DNase Set (Qiagen, Germany), the optional on-column DNase digestion step was employed in compliance with the needs of downstream processing. Purified total RNA was then used to construct sequencing libraries on the Illumina HiSeq 2500 (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: patient diagnosis

value: HPV-positive

value: Skin

value: wart

value: male

tag: age

tag: site of shave biopsy

value: foot


title: AGCGTCAT_CGCAATGT

value: hematopoietic stem and progenitor cells


title: 67W

tag: tissue

value: hand


title: 69C

value: healthy skin


title: 66W


title: 67C


title: 64W

value: forehead


title: AGCGTCAT_CGCATAAC


title: 66C


title: Hepa1-6, Elaidic acid treatment

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

source_name: Hepa1-6 cells

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Hepa1-6 cells (# CRL-1830) were obtained from American Type Culture Collection (ATCC; Manassas, VA) and cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 1000 µg/mL streptomycin (Lonza, Verviers, Belgium) in a humidified chamber at 37oC with 5% CO2.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol. RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) using 6000 Nano Chips according to manufacturer’s instructions. RNA was considered suitable for array hybridization only if RNA integrity number exceeded 8.0.  RNA from 6 samples per group was pooled for microarray analysis

treatment_protocol: Hepa1-6 cells were seeded and incubated overnight, followed by treatment with 500 µM concentration of fatty acids for 24 hrs. All fatty acid stocks were initially reconstituted in absolute ethanol. Sub-stocks of fatty acids at 25 mM were prepared in filter-sterilised KOH at 70 mM. Complete DMEM supplemented with fatty acid-free bovine serum albumin (BSA; Sigma-Aldrich, St. Louis, MO) were filter sterilised, and incubated for 30 min with fatty acids to complex BSA to fatty acids. Ratio of BSA to fatty acids were approximately 1:2. Vehicle control treatments only contained equivalent mixture of ethanol and KOH.

tag: treatment

value: Elaidic acid (500 µM)


title: AGCGTCAT_CGCAACTA

tag: cell type


title: Hepa1-6, Oleic acid treatment

value: Oleic acid (500 µM)


title: Hepa1-6, Palmitic acid treatment

value: Palmitic acid (500 µM)


title: 3T3-L1, Palmitic acid treatment

source_name: 3T3-L1 pre-adipocytes

growth_protocol: 3T3-L1 pre-adipocytes (# CL-173) were obtained from American Type Culture Collection (ATCC; Manassas, VA) and cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 1000 µg/mL streptomycin (Lonza, Verviers, Belgium) in a humidified chamber at 37oC with 5% CO2. Cells were seeded in 6-well plates. Two-days post-confluence, the cell culture media was changed to induction medium (0.5 mM IBMX, 5 µg/mL insulin, 1 µM dexamethasone) for 2 days. Induction medium was then replaced with insulin medium (5 µg/mL insulin) for 3 days, after which the fully differentiated cells were treated with fatty acids.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol. RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) using 6000 Nano Chips according to manufacturer’s instructions. RNA was considered suitable for array hybridization only if RNA integrity number exceeded 8.0.  RNA from 3 samples per group was pooled for microarray analysis.

treatment_protocol: Differentiated 3T3-L1 cells were incubated with 1 mM final concentrations of fatty acids. All fatty acid stocks were initially reconstituted in absolute ethanol. Sub-stocks of fatty acids at 25 mM were prepared in filter-sterilised KOH at 70 mM. Complete DMEM supplemented with fatty acid-free BSA (Sigma-Aldrich, St. Louis, MO) were filter sterilised, and incubated for 30 min with fatty acids to complex BSA to fatty acids. Ratio of BSA to fatty acids were approximately 1:2. Vehicle control treatments only contained equivalent mixture of ethanol and KOH.

value: Palmitic acid (1 mM)


title: 3T3-L1, Elaidic acid treatment

value: Elaidic acid (1 mM)


title: 3T3-L1, Oleic acid treatment

value: Oleic acid (1 mM)


title: 64C


title: AGCGTCAT_CGACAATC


title: 62W


title: 62C


title: Hepa1-6, Control treatment

value: Control


title: 3T3-L1, Control treatment


title: AGCGTCAT_CGACTATG


title: AGCGTCAT_CCGTAAGT


title: AGCGTCAT_CGAACTTG


title: 60W


title: 60C


title: 43W


title: H1_PSM_690m_rep2

city: Madison

first: Li-Fang

last: Chu

address: 330 N. Orchard St.

institute: Morgridge Institute for Research

description: H1 embryonic stem cells or derivatives

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include expected count (EC) values for each sample

growth_protocol: H1 human ES cells were routinely maintained as undifferentiated in E8 medium.

extract_protocol:
Cell grown in 6-well or 12-well plate were directly lysaed with RLT Plus lysis buffer (Qiagen), stored in -80C for later processing. Total RNA was purified from the RLT Plus lysates using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard the LM-seq protocol.

treatment_protocol: Mesendoderm and PSM differentiation, individualized H1 cells were first seeded in E8 supplemented with Activin A (R&D Systems,100ng/mL) and Chir99021 (3 μM) for the first 24 hours, then switched to PSM medium: E6 base medium (E8 medium minus FGF2, minus TGFβ1) supplemented with A83-01 (2 μM), CHIR99021 (3 μM) and FGF2 (100 ng/mL) and NOGGIN (R&D Systems, 100ng/mL) for another 24 hours. Somite medium: E6 base medium supplemented with PD0325901 (1 μM), IWR1 (2.5 μM), A83-01 (2 μM) and NOGGIN (100ng/mL).

value: presomitic mesoderm time course

tag: passage

tag: genotype

value: wild type


title: H1_PSM_690m_rep1

description: H1 embryonic stem cells or derivatives

tag: time point


title: 43C

value: HPV-positive

value: Skin


title: AGCGTCAT_CCAGAACT


title: H1_PSM_660m_rep1

description: H1 embryonic stem cells or derivatives


title: H1_PSM_660m_rep2

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_CCATTGAG


title: AGCGTCAT_CATTGCAG


title: AGCGTCAT_CCAACCAA


title: Liver, saturated fat, replicate 5

source_name: liver

growth_protocol: Animal studies were performed using 4 to 6-month-old pure-bred male mice on a C57Bl/6 background.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol. RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) using 6000 Nano Chips according to manufacturer’s instructions. RNA was considered suitable for array hybridization only if RNA integrity number exceeded 8.0.

treatment_protocol: Mice were randomly assigned to three groups (n = 8 mice per group). For 7 weeks, each group was fed a high-fat diet rich in trans-unsaturated (Trans), cis-unsaturated (Cis) or saturated (Saturated) fatty acids (modified TestDiet 58V8; TestDiet LTD, London). Fat sources were from partially hydrogenated soy oil for the Trans diet, canola and palm olein oil for the Cis diet, and cocoa butter for the Saturated diet. Total fat content in all three diets was 45% energy percent.

tag: background

tag: diet

value: enriched in saturated fatty acids


title: Liver, saturated fat, replicate 8


title: Liver, saturated fat, replicate 6


title: 5W

value: wart

value: male


title: Liver, cis-unsaturated fat, replicate 3

value: enriched in cis-unsaturated fatty acids


title: AGCGTCAT_CATGCCAA

value: hematopoietic stem and progenitor cells

tag: ckit


title: Liver, cis-unsaturated fat, replicate 4


title: Liver, saturated fat, replicate 1


title: Liver, cis-unsaturated fat, replicate 7


title: Liver, saturated fat, replicate 7


title: Liver, cis-unsaturated fat, replicate 5


title: Liver, cis-unsaturated fat, replicate 8


title: Liver, cis-unsaturated fat, replicate 6


title: Liver, saturated fat, replicate 4


title: Liver, saturated fat, replicate 3


title: Liver, cis-unsaturated fat, replicate 2


title: 42W

tag: Sex

value: hand


title: AGCGTCAT_CATTCGGA


title: H1_PSM_600m_rep1

description: H1 embryonic stem cells or derivatives

tag: cell line


title: Liver, cis-unsaturated fat, replicate 1


title: 4W

tag: disease state


title: H1_PSM_630m_rep2

description: H1 embryonic stem cells or derivatives


title: H1_PSM_600m_rep2

description: H1 embryonic stem cells or derivatives


title: H1_PSM_630m_rep1

description: H1 embryonic stem cells or derivatives


title: 5C

value: healthy skin


title: 4C


title: AGCGTCAT_CATCAACG

tag: strain


title: AGCGTCAT_CAGTGCAT


title: AGCGTCAT_CAGCTAGT


title: 3C

tag: subject id


title: H1_PSM_570m_rep2

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_CAGACTCA


title: 3W

tag: patient diagnosis


title: AGCGTCAT_CAGCCAAT


title: AGCGTCAT_CCGAACTA


title: H1_PSM_570m_rep1

description: H1 embryonic stem cells or derivatives


title: H1_PSM_540m_rep2

description: H1 embryonic stem cells or derivatives


title: Liver, trans-unsaturated fat, replicate 6

value: enriched in trans-unsaturated fatty acids


title: Liver, trans-unsaturated fat, replicate 8


title: H1_PSM_480m_rep2

description: H1 embryonic stem cells or derivatives


title: H1_PSM_540m_rep1

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_CTGCAGTA


title: H1_PSM_510m_rep1

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_CAATGTGC


title: Liver, trans-unsaturated fat, replicate 3


title: AGCGTCAT_CACTGACA


title: Liver, trans-unsaturated fat, replicate 7


title: 2W

tag: age


title: 2C

tag: site of shave biopsy


title: H1_PSM_510m_rep2

description: H1 embryonic stem cells or derivatives


title: Liver, trans-unsaturated fat, replicate 4


title: 42C

tag: tissue


title: Liver, trans-unsaturated fat, replicate 5


title: H1_PSM_450m_rep2

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_CACGCTAA


title: AGCGTCAT_CAACCGTA


title: X08-FGFJI-5

city: Dresden

first: Andreas

last: Androutsellis-Theotokis

address: Fetscherstr. 74

department: Department of Internal Medicine III

institute: University Hospital Carl Gustav Carus at the Technische Universität Dresden

data_processing:
basecalling: bcl2fastq 1.8.4
alignment: alignment of single-end data against hg38 with gsnap version 2014-12-17; splice sites were supported by using Ensembl version 78 (gsnap -d hg38 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-78.ss.hg38.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.4.6 (-a EnsemblGene-78.hg38.TR.gtf -s 2 -Q 1) and the Ensembl version 78 gtf file
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.hg38.e78.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosome, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 27 sequenced samples

source_name: X08 GBM cells grown in FGF + JAK inhibitor containing medium for 5 days

extract_protocol:
Total RNA was isolated using Roche High Pure RNA extraction kit as described by the manufacturer
Samples were subjected the standard workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB).

value: Glioblastoma


title: X08-Serum-3

source_name: X08 GBM cells grown in serum containing medium for 5 days


title: X08-Serum-2


title: H1_PSM_480m_rep1

description: H1 embryonic stem cells or derivatives


title: X08-FGFJI-4


title: AGCGTCAT_ATGCCAAC


title: AGCGTCAT_CAATGCCA


title: Liver, trans-unsaturated fat, replicate 2


title: H1_PSM_450m_rep1

description: H1 embryonic stem cells or derivatives


title: Liver, trans-unsaturated fat, replicate 1


title: hBJV600E_Dox24_Clob2_rep8

city: Gif sur Yvette

first: Jean-Yves

last: Thuret

address: CEA Saclay Bat 142

country: France

institute: CEA

description: replicate 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized using quantile normalization with the beadarray package in R

source_name: hBJV600E, doxycycline 24h then clobetasol 2h

label_protocol: Biotinylated cRNA was synthesized, amplified and purified using TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip

extract_protocol: Total RNA was extracted using NucleoSpin RNA kits (Macherey Nagel)

tag: inducer

value: doxycycline 1000 ng.mL-1

tag: timewithinducer

value: 26 hours

tag: treatment

value: clobetasol 2nM

tag: timewithtreatment

value: 2 hours


title: H1_PSM_420m_rep2

description: H1 embryonic stem cells or derivatives

tag: time point

tag: cell type

value: presomitic mesoderm time course

tag: passage

tag: genotype


title: H1_PSM_390m_rep2

description: H1 embryonic stem cells or derivatives

value: wild type


title: X08-FGFJI-2


title: H1_PSM_420m_rep1

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_ATTCCGAG

tag: ckit


title: AGCGTCAT_ATGCATCG


title: AGCGTCAT_ATCAGTGC


title: H1_PSM_360m_rep2

description: H1 embryonic stem cells or derivatives

tag: cell line


title: AGCGTCAT_AGTGGTTC


title: X08-EGF-3

source_name: X08 GBM cells grown in EGF containing medium for 5 days


title: X04-Serum-3

source_name: X04 GBM cells grown in serum containing medium for 5 days


title: X08-Serum-1


title: AGCGTCAT_AGTGGTCT


title: X08-EGF-2


title: H1_PSM_390m_rep1

description: H1 embryonic stem cells or derivatives


title: hBJV600E_Dox24_Clob2_rep6

description: replicate 6


title: hBJV600E_Dox24_DMSO2_rep4

description: replicate 4

source_name: hBJV600E, doxycycline 24h then DMSO 2h

value: DMSO


title: X08-EGF-1


title: H1_PSM_360m_rep1

description: H1 embryonic stem cells or derivatives


title: hBJV600E_Dox24_Clob2_rep5

description: replicate 5


title: hBJV600E_Dox24_DMSO2_rep3

description: replicate 3


title: hBJV600E_Dox24_Clob2_rep3

description: replicate 3


title: X04-FGFJI-3

source_name: X04 GBM cells grown in FGF + JAK inhibitor containing medium for 5 days


title: AGCGTCAT_ACTAGTGC


title: AGCGTCAT_ACTACGAC


title: X04-FGFJI-4


title: hBJV600E_Dox24_Clob2_rep4

description: replicate 4


title: X04-Serum-2


title: X04-FGFJI-1


title: H1_PSM_330m_rep2

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_ATCCATGG


title: Liver, saturated fat, replicate 2

tag: background

tag: diet


title: AGCGTCAT_AGCGTACT

tag: strain


title: X04-Serum-1


title: AGCGTCAT_ACTTGGCA


title: H1_PSM_330m_rep1

description: H1 embryonic stem cells or derivatives


title: H1_PSM_270m_rep1

description: H1 embryonic stem cells or derivatives


title: hBJV600E_Dox24_Clob2_rep1

description: replicate 1


title: hBJV600E_Dox24_Clob2_rep2

description: replicate 2


title: H1_PSM_300m_rep2

description: H1 embryonic stem cells or derivatives


title: H1_PSM_300m_rep1

description: H1 embryonic stem cells or derivatives


title: hBJV600E_Dox24_DMSO2_rep2

description: replicate 2


title: hBJV600E_Dox72_Clob2_rep4

description: replicate 4

source_name: hBJV600E, doxycycline 72h then clobetasol 2h

value: 74 hours


title: AGCGTCAT_ACGTGATC


title: AGCGTCAT_ACACTGCA


title: AGCGTCAT_ACATGTCG


title: H1_PSM_270m_rep2

description: H1 embryonic stem cells or derivatives


title: X04-EGF-2

source_name: X04 GBM cells grown in EGF containing medium for 5 days


title: H1_PSM_240m_rep2

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_ACCATCAG

source_name: hematopoietic stem and progenitor cells


title: AGCGTCAT_ACGACTAC


title: hBJV600E_Dox122_Clob122_rep3

description: replicate 3

source_name: hBJV600E, doxycycline and clobetasol 122h

value: 122 hours


title: X01-FGFJI-3

source_name: X01 GBM cells grown in FGF + JAK inhibitor containing medium for 5 days


title: H1_PSM_240m_rep1

description: H1 embryonic stem cells or derivatives


title: X04-EGF-1


title: hBJV600E_Dox120_DMSO2_rep4

description: replicate 4

source_name: hBJV600E, doxycycline 120h then DMSO 2h


title: H1_PSM_180m_rep2

description: H1 embryonic stem cells or derivatives


title: H1_PSM_210m_rep2

description: H1 embryonic stem cells or derivatives


title: X01-FGFJI-2


title: hBJV600E_Dox120_Clob2_rep4

description: replicate 4

source_name: hBJV600E, doxycycline 120h then clobetasol 2h


title: H1_PSM_150m_rep2

description: H1 embryonic stem cells or derivatives


title: hBJV600E_EtOH24_DMSO2_rep4

description: replicate 4

source_name: hBJV600E, ethanol 24h then DMSO 2h

value: ethanol


title: hBJV600E_Dox48_DMSO2_rep4

description: replicate 4

source_name: hBJV600E, doxycycline 48h then DMSO 2h

value: 50 hours


title: AGCGTCAT_AACAGCTC


title: X01-Serum-2

source_name: X01 GBM cells grown in serum containing medium for 5 days


title: H1_PSM_210m_rep1

description: H1 embryonic stem cells or derivatives


title: Lypd1-EGFP-L10a-OI82, CA-IP Rep3

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description: 1294_Lypd1_EGFP_L10a_OI82_CxA_IP_Rep3_S8

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Cortex-amygdala transition zone (CxA)

growth_protocol: Not applicable

extract_protocol:
The cortex-amygdala transition zone was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Control mice only. No treatment

value: Cortex-amygdala transition zone (CxA)

tag: animal line

value: Lypd1-TRAP OI82

tag: fraction

value: Immunopurified (IP)

tag: antibody

value: anti-EGFP


title: AGCGTCAT_AAGCCGTT

value: hematopoietic stem and progenitor cells


title: AGCGTCAT_AAGCTCTG


title: X04-EGF-3

value: Glioblastoma


title: X01-Serum-3


title: X01-EGF-2

source_name: X01 GBM cells grown in EGF containing medium for 5 days


title: X01-Serum-1


title: H1_PSM_180m_rep1

description: H1 embryonic stem cells or derivatives


title: AGCGTCAT_AACTCCAG


title: X01-EGF-1


title: H1_PSM_090m_rep2

description: H1 embryonic stem cells or derivatives


title: H1_PSM_150m_rep1

description: H1 embryonic stem cells or derivatives


title: X01-FGFJI-1


title: hBJV600E_Dox48_DMSO2_rep3

description: replicate 3

value: doxycycline 1000 ng.mL-1


title: X01-EGF-3


title: Neo_BM_immB_HET_rep4

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

data_processing:
Paired-end sequenced RNA-seq data was processed as following: RNA-sequenced reads were trimmed TrimeGalore for removal of adapter –and low quality sequences. Resulting reads were then mapped onto the mouse genome build mm10 with STAR (Dobin et al., 2013)  and post-processed with RSEM (http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build mm10 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf. For analysis of statistical significance among differentially expressed genes the expected gene counts were derived for each RSEM gene result file and catenated to one table which was imported into R using tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) and analyzed for differential expression using the DESeq2 package ( https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html) (Love et al., 2014).
Paired-end reads' average insert size and standard deviation determined using bamPEFragmentSize 3.1.3 from the Picard suite on genome coordinate derived bam-file from RSEM v1.2.28.
Genome_build: mm10
Supplementary_files_format_and_content: Expected count matrix generated with rsem

source_name: Bone marrow immature B cells

extract_protocol: BM cells from tet-Lin28b or WT mice fed DOX food for 2 weeks; or 3d old neonatal Lin28b wild-type, heterozygous or knockout mice were extracted by crushing the bones from hind limbs, hips, and spine with mortar and pestle. Adult BM cells were subjected to red blood cell lysis, neonatal BM was not subjected to RBC lysis. Total adult BM cells were then pre-enriched by MACS (Miltenyi Biotec) depletion of Lineage+ cells (Ter119+Gr1+CD11b+CD3e+) according to manufacturer’s instructions prior to FACS sorting. Neonatal BM was not pre-enriched before sorting. Antibody staining was performed in FACS buffer (HBSS,supplemented with 0.5% BSA and 2 mM EDTA) at a density of maximum 1x107 cells/100uL volume for 30 min on ice. Immature B cells (CD19+B220loCD93+IgM+CD24hi) were sorted into cold FACS buffer, spun down and resuspended in RNAzol reagent (Sigma-Aldrich). Total RNA was extracted according to the manufacturers instructions. Libraries were generated using the Smartseq V4 Ultra Low input RNA Library Prep Kit (Clontech) and the Nextera XT DNA indexing kit (Illumina) according to the manufacturer’s instructions. Libraries were indexed using the Nextera XT v2 indexing kit (Illumina) according to the manufacturers instructions. Libraries were sequenced on an Illumina Nextseq system using a Nextseq V500/550 150cycle high output kit. Reads were aligned using STAR aligner v2.7.1 (80) and counted using RSEM v.1.28.

tag: age

value: 3 day old neonate

value: Lin28b heterozygous (HET)

tag: Sex

value: Not determined

value: Bone marrow immature B cells


title: Neo_BM_immB_WT_rep4

value: Lin28b wildtype (WT)


title: Neo_BM_immB_KO_rep4

value: Lin28b knockout (KO)


title: hBJV600E_EtOH122_Clob122_rep3

description: replicate 3

source_name: hBJV600E, ethanol and clobetasol 122h

tag: inducer

tag: timewithinducer

value: clobetasol 2nM


title: hBJV600E_EtOH24_Clob2_rep4

description: replicate 4

source_name: hBJV600E, ethanol 24h then clobetasol 2h

value: 26 hours

tag: treatment

tag: timewithtreatment

value: 2 hours


title: hBJV600E_Dox120_DMSO2_rep3

description: replicate 3

value: 122 hours

value: DMSO


title: hBJV600E_EtOH24_CpdA2_rep4

description: replicate 4

source_name: hBJV600E, ethanol 24h then CpdA 2h

value: ethanol

value: Compound A 2µM


title: H1_PSM_120m_rep2

description: H1 embryonic stem cells or derivatives

tag: time point

tag: cell type

value: presomitic mesoderm time course

value: wild type


title: hBJV600E_Dox48_Clob2_rep4

description: replicate 4

source_name: hBJV600E, doxycycline 48h then clobetasol 2h

value: 50 hours


title: hBJV600E_Dox120_Clob2_rep3

description: replicate 3

value: doxycycline 1000 ng.mL-1


title: H1_PSM_060m_rep2

description: H1 embryonic stem cells or derivatives

tag: passage

tag: genotype


title: Lypd1-EGFP-L10a-OI82, CA-IP Rep2

description: 1293_Lypd1_EGFP_L10a_OI82_CxA_IP_Rep2_S7

tag: tissue

value: Cortex-amygdala transition zone (CxA)

value: Lypd1-TRAP OI82

value: Immunopurified (IP)

value: anti-EGFP


title: H1_PSM_120m_rep1

description: H1 embryonic stem cells or derivatives

tag: cell line


title: Lypd1-EGFP-L10a-OI82, CA-IP Rep1

description: 1292_Lypd1_EGFP_L10a_OI82_CxA_IP_Rep1_S6


title: H1_PSM_090m_rep1

description: H1 embryonic stem cells or derivatives


title: H1_PSM_030m_rep1

description: H1 embryonic stem cells or derivatives


title: Experiment B, 3AT-treated cells - 100 units AluI

data_processing:
Library strategy: Quantitative DNA accessibility assay - "qDA-seq"
Sequences were aligned to the S.cerevisiae genome (sacCer3) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab.
Genome-wide profiles (bw files) containing the fraction of cut DNA at each site were generated using Matlab and igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: bw files containing the fraction of cut DNA at each AluI site along the yeast genome

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in synthetic complete (SC) medium (control) or, for treatment with 3-aminotriazole (3AT), in SC medium lacking histidine, to mid-log phase at 30degC with shaking at 250 rpm. Cells grown in SC medium without histidine were treated with 3AT at a final concentration of 10 mM for 20 minutes (30degC with shaking). Cells were harvested by filtration and stored at -80.

extract_protocol:
AluI digestion was stopped and the DNA was sonicated.
Purified sonicated DNA was prepared for Illumina paired-end sequencing using New England Biolabs kit E7370. 50-nt paired reads were obtained using an Illumina NextSeq-500 machine.

treatment_protocol: Control cells were spheroplasted in SM medium (SC medium containing 1M sorbitol and 50 mM TrisHCl pH 8.0); 3AT-treated cells were spheroplasted in SM medium lacking histidine. Nuclei were prepared and digested with increasing amounts of the restriction enzyme AluI.

value: 3AT-treated cells - 100 units AluI


title: H1_PSM_060m_rep1

description: H1 embryonic stem cells or derivatives


title: Experiment B, 3AT-treated cells - 800 units AluI

value: 3AT-treated cells - 800 units AluI


title: Neo_BM_immB_KO_rep3

value: 3 day old neonate

value: Lin28b knockout (KO)

value: Not determined

value: Bone marrow immature B cells


title: Experiment B, 3AT-treated cells - 400 units AluI

value: 3AT-treated cells - 400 units AluI


title: hBJV600E_Dox122_Clob122_rep2

description: replicate 2

value: 122 hours

value: clobetasol 2nM


title: hBJV600E_Dox72_DMSO2_rep4

description: replicate 4

source_name: hBJV600E, doxycycline 72h then DMSO 2h

value: 74 hours

value: DMSO

value: 2 hours


title: Experiment B, 3AT-treated cells - 20 units AluI

value: 3AT-treated cells - 20 units AluI


title: Sample 77P_1_gDNA - 20 units AluI

description: Genomic DNA digested with AluI

data_processing:
Sequences were aligned to the S.cerevisiae genome (sacCer3) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab.
Genome-wide profiles (bw files) containing the fraction of cut DNA at each site were generated using Matlab and wigToBigWig.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files containing the fraction of cut DNA at each AluI site along the yeast genome (for IGV genome browser)

source_name: Sample 77P_1_gDNA - 20 units AluI

growth_protocol: Yeast cells were grown in synthetic complete medium .

extract_protocol:
AluI digestion was stopped and the DNA was sonicated.
Purified sonicated DNA was prepared for Illumina paired-end sequencing using New England Biolabs kit E7370. 50-nt paired reads were obtained using an Illumina NextSeq-500 machine.
New method: Quantitative DNA accessibility assay - "qDA-seq"

treatment_protocol: Genomic DNA was purified from cells using standard protocols and digested to completion with AluI.

value: MATa can1-100 his3-11,15  leu2-3,112 lys2delta trp1-1 ura3-1

value: 20U AluI, overnight digestion


title: hBJV600E_EtOH24_Clob2_rep3

description: replicate 3

value: ethanol

value: 26 hours


title: hBJV600E_EtOH24_DMSO2_rep3

description: replicate 3


title: H1_PSM_030m_rep2

description: H1 embryonic stem cells or derivatives

value: presomitic mesoderm time course

value: wild type


title: Neo_BM_immB_WT_rep3

value: 3 day old neonate

value: Lin28b wildtype (WT)


title: Experiment B, 3AT-treated cells - 200 units AluI

value: 3AT-treated cells - 200 units AluI


title: H1_Day3_replicate1

description: H1 embryonic stem cells or derivatives

value: somite


title: Neo_BM_immB_WT_rep2

value: Not determined

value: Bone marrow immature B cells


title: Experiment B, 3AT-treated cells - 40 units AluI

value: 3AT-treated cells - 40 units AluI


title: H1_Day3_replicate3

description: H1 embryonic stem cells or derivatives


title: Neo_BM_immB_HET_rep3

value: Lin28b heterozygous (HET)


title: hBJV600E_Dox48_DMSO2_rep2

description: replicate 2

value: doxycycline 1000 ng.mL-1

value: 50 hours

value: DMSO


title: Neo_BM_immB_WT_rep1


title: hBJV600E_Dox72_DMSO2_rep3

description: replicate 3

value: 74 hours

value: 2 hours


title: H1_Day2_replicate2

description: H1 embryonic stem cells or derivatives

value: presomitic mesoderm


title: Experiment B, 3AT-treated cells - 2.5 units AluI

value: 3AT-treated cells - 2.5 units AluI


title: H1_Day3_replicate2

description: H1 embryonic stem cells or derivatives


title: Neo_BM_immB_HET_rep2


title: Experiment B, 3AT-treated cells - 10 units AluI

value: 3AT-treated cells - 10 units AluI


title: Neo_BM_immB_KO_rep1

value: Lin28b knockout (KO)


title: H1_Day1_replicate2

description: H1 embryonic stem cells or derivatives

value: mesendoderm

value: wild type


title: hBJV600E_EtOH24_CpdA2_rep3

description: replicate 3

value: ethanol

value: 26 hours

value: Compound A 2µM


title: ImmB_adult_WT3

value: Col1a1tm2tetO-LIN28B x  R26m2rtTA

value: Adult

value: Male

value: Bone marrow immature B cells


title: Experiment B, 3AT-treated cells - 5 units AluI

value: 3AT-treated cells - 5 units AluI


title: Neo_BM_immB_KO_rep2

value: 3 day old neonate

value: Not determined


title: Neo_BM_immB_HET_rep1

value: Lin28b heterozygous (HET)


title: hBJV600E_Dox48_Clob2_rep3

description: replicate 3

value: doxycycline 1000 ng.mL-1

value: 50 hours

value: clobetasol 2nM

value: 2 hours


title: Experiment B, 3AT-treated cells - 1 unit AluI

value: 3AT-treated cells - 1 unit AluI


title: H1_Day2_replicate1

description: H1 embryonic stem cells or derivatives

value: presomitic mesoderm

value: wild type


title: H1_Day1_replicate1

description: H1 embryonic stem cells or derivatives

value: mesendoderm


title: hBJV600E_Dox72_Clob2_rep3

description: replicate 3

source_name: hBJV600E, doxycycline 72h then clobetasol 2h

value: 74 hours


title: ImmB_adult_tet_Lin28b_3

value: Col1a1tm2tetO-LIN28B x  R26m2rtTA

value: tet-Lin28b transgene


title: Experiment B, 3AT-treated cells - 0 units AluI

value: 3AT-treated cells - 0 units AluI


title: H1_Day1_replicate3

description: H1 embryonic stem cells or derivatives


title: hBJV600E_EtOH122_Clob122_rep2

description: replicate 2

value: ethanol

value: 122 hours


title: ImmB_adult_WT1

value: Adult

value: Male

value: Bone marrow immature B cells


title: Experiment B, Uninduced cells - 800 units AluI

value: Uninduced cells - 800 units AluI


title: H1_Day2_replicate3

description: H1 embryonic stem cells or derivatives


title: Experiment B, Uninduced cells - 40 units AluI

value: Uninduced cells - 40 units AluI


title: ImmB_adult_tet_Lin28b_2


title: Experiment B, Uninduced cells - 200 units AluI

value: Uninduced cells - 200 units AluI


title: ImmB_adult_WT2


title: Experiment B, Uninduced cells - 400 units AluI

value: Uninduced cells - 400 units AluI


title: H1_Day0_replicate3

description: H1 embryonic stem cells or derivatives

value: embryonic stem cells


title: Ctr_HSC3

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

data_processing:
All the fastq.gz files are mapped to NCBIM37 mice genome by hisat2 program, and genes expression rawcounts are calculated by featureCounts.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The "Genes_expression"  file contains the rawcounts of all the RNAseq samples.

growth_protocol: One thousand HSCs are sorted from eight weeks old NrasG12D or NA or wild type (Ctr) mice.

extract_protocol:
The full length cDNA of sorted 1,000-cell aliquots are generated and amplified using published protocol (PMID:20203668).
The quality of the amplified cDNA is assessed by qPCR analysis of housekeeping genes (B2m, Actb, Gapdh and Ecf1a1). Samples that passed quality control are  used for sequencing library preparation using  illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096).

value: wild type (control)

value: Bone marrow HSCs


title: hBJV600E_EtOH122_Clob122_rep1

description: replicate 1

value: clobetasol 2nM


title: hBJV600E_Dox72_Clob2_rep2

description: replicate 2

value: doxycycline 1000 ng.mL-1

value: 74 hours

value: 2 hours


title: hBJV600E_Dox24_Clob2_rep7

description: replicate 7

source_name: hBJV600E, doxycycline 24h then clobetasol 2h

value: 26 hours


title: hBJV600E_EtOH24_CpdA2_rep2

description: replicate 2

value: ethanol

value: Compound A 2µM


title: hBJV600E_Dox48_Clob2_rep2

description: replicate 2

value: 50 hours


title: hBJV600E_Dox72_DMSO2_rep1

description: replicate 1

value: DMSO


title: H1_Day0_replicate2

description: H1 embryonic stem cells or derivatives

value: wild type


title: Experiment B, Uninduced cells - 20 units AluI

value: Uninduced cells - 20 units AluI


title: H1_Day0_replicate1

description: H1 embryonic stem cells or derivatives


title: hBJV600E_EtOH24_Clob2_rep2

description: replicate 2


title: hBJV600E_Dox120_Clob2_rep2

description: replicate 2

value: 122 hours


title: ImmB_adult_tet_Lin28b_1

value: Col1a1tm2tetO-LIN28B x  R26m2rtTA

value: Adult

value: tet-Lin28b transgene

value: Male

value: Bone marrow immature B cells


title: hBJV600E_Dox24_CpdA2_rep2

description: replicate 2

source_name: hBJV600E, doxycycline 24h then CpdA 2h


title: hBJV600E_Dox24_CpdA2_rep3

description: replicate 3


title: Experiment B, Uninduced cells - 1 unit AluI

value: Uninduced cells - 1 unit AluI


title: Muscle2

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

description:
36-month-old wild-type macaque raised by The Yunnan Key Laboratory of Primate Biomedical Research.
small RNA

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides.
Keep the sequences whose lengths are greater than or equal to 18 bp (the 3' adapter sequences of reads had been removed by the sequencing facility).
Sort and remove repetitive sequences.
Calculate the counts of unique sequences.
The unique sequences were aligned to a self-assembled transcriptome with SOAP2.
Genome_build: None provided
Supplementary_files_format_and_content: *txt: Tab-delimited text files include sequences and count values.

organism: Macaca mulatta

source_name: muscle

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacturer's protocol.
Small RNA libraries were prepared by following the Illumina's protocol.

treatment_protocol: No treatment.

tag: genotype/variation

value: Wild-type

value: 36 months

value: Muscle


title: SpinalCord

source_name: spinal cord

growth_protocol: 36-month-old wild-type macaque raised by The Yunnan Key Laboratory of Primate Biomedical Research.

value: Spinal cord


title: Experiment B, Uninduced cells - 100 units AluI

value: Uninduced cells - 100 units AluI

tag: strain


title: hBJV600E_Dox120_DMSO2_rep2

description: replicate 2

source_name: hBJV600E, doxycycline 120h then DMSO 2h

value: doxycycline 1000 ng.mL-1

value: 2 hours


title: SmallInt2

source_name: small intestine

value: Small intestine


title: Experiment B, Uninduced cells - 10 units AluI

value: Uninduced cells - 10 units AluI


title: Nras_HSC3

value: NrasG12D transgenic

value: Bone marrow HSCs


title: Experiment B, Uninduced cells - 5 units AluI

value: Uninduced cells - 5 units AluI


title: hBJV600E_EtOH24_DMSO2_rep2

description: replicate 2

source_name: hBJV600E, ethanol 24h then DMSO 2h

value: ethanol

value: 26 hours

value: DMSO


title: hBJV600E_Dox72_DMSO2_rep2

description: replicate 2

value: 74 hours


title: SmallInt1


title: hBJV600E_Dox48_DMSO2_rep1

description: replicate 1

source_name: hBJV600E, doxycycline 48h then DMSO 2h

value: 50 hours


title: Ctr_HSC2

value: wild type (control)


title: Nras_HSC1


title: Experiment B, Uninduced cells - 2.5 units AluI

value: Uninduced cells - 2.5 units AluI


title: OccLobe

source_name: occipital lobe

value: Wild-type

value: 36 months

value: Occipital lobe


title: Ctr_HSC1


title: LargeInt2

source_name: large intestine

value: Large intestine


title: hBJV600E_Dox120_DMSO2_rep1

description: replicate 1

value: doxycycline 1000 ng.mL-1

value: 122 hours

value: 2 hours


title: NA_HSC3

value: NA transgenic


title: Experiment A, 3AT-treated cells - 100 units AluI

value: 3AT-treated cells - 100 units AluI


title: hBJV600E_Dox122_Clob122_rep1

description: replicate 1

source_name: hBJV600E, doxycycline and clobetasol 122h

value: clobetasol 2nM


title: Experiment B, Uninduced cells - 0 units AluI

value: Uninduced cells - 0 units AluI


title: Muscle1

value: Muscle


title: Nras_HSC2

value: NrasG12D transgenic

value: Bone marrow HSCs


title: NA_HSC2


title: Experiment A, 3AT-treated cells - 20 units AluI

value: 3AT-treated cells - 20 units AluI


title: Experiment A, 3AT-treated cells - 800 units AluI

value: 3AT-treated cells - 800 units AluI


title: Kidney1

source_name: kidney

value: Kidney


title: Experiment A, 3AT-treated cells - 200 units AluI

value: 3AT-treated cells - 200 units AluI


title: Lung

source_name: lung

value: Wild-type

value: 36 months

value: Lung


title: Experiment A, 3AT-treated cells - 10 units AluI

value: 3AT-treated cells - 10 units AluI


title: Liver

source_name: liver

value: Liver


title: Experiment A, 3AT-treated cells - 400 units AluI

value: 3AT-treated cells - 400 units AluI


title: NA_HSC4

value: NA transgenic


title: hBJV600E_Dox48_Clob2_rep1

description: replicate 1

source_name: hBJV600E, doxycycline 48h then clobetasol 2h

value: doxycycline 1000 ng.mL-1

value: 50 hours

value: 2 hours


title: Experiment A, 3AT-treated cells - 40 units AluI

value: 3AT-treated cells - 40 units AluI


title: Experiment A, 3AT-treated cells - 5 units AluI

value: 3AT-treated cells - 5 units AluI


title: GAS-delmtsR-100um-manganese-OD1-0-rep-2

city: Houston

first: Muthiah

last: Kumaraswami

state: TX

address: 6670 Bertner Ave

department: Infectious Diseases

institute: Houston Methodist Research Institute

data_processing:
multiplexed SE libraries were sequenced on an Illumina HiSeq 2500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-Seq reads from strain MGAS10870 were mapped to reference strain MGAS315 (GenBank accession number AE014074.1) using Edge-pro v1.3.1(Estimated Degree of Gene Expression for Prokaryotes).
mapping reads from each strain to respective refrence using Edge-pro v1.3.1 yields raw and normalized (RPKM) expression values for each gene.
varible gene content and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
differential expression analysis was perfomed using DESeq2 v1.6.3 runing in R version 3.1.3. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approcah was used to generate fold change values for each gene. Multiple testing correction was performed using Benjamini-Hochberg method.

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Epicentre)
resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Epicentre)

treatment_protocol: at the desired growth stage, late-exponential OD 600nm 1.0, the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: serotype

tag: tag

value: invasive infection isolate

tag: growth phase

value: Late-exponential (LE, OD600nm=1.0)


title: Experiment A, 3AT-treated cells - 2.5 units AluI

value: 3AT-treated cells - 2.5 units AluI


title: LargeInt1

tag: age

value: Large intestine


title: hBJV600E_EtOH24_DMSO2_rep1

description: replicate 1

value: ethanol

value: 26 hours

value: DMSO


title: hBJV600E_Dox24_CpdA2_rep1

description: replicate 1

value: Compound A 2µM


title: GAS-WT-100um-manganese-OD1-0-rep-3


title: Experiment B - 20 units AluI

data_processing:
Sequences were aligned to the Mus musculus genome (mm10) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab.
Genome-wide profiles (bw files) containing the fraction of cut DNA at each site were generated using Matlab and wigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing the fraction of cut DNA at each AluI site along the mouse genome (for IGV genome browser)

source_name: Experiment B - 20 units AluI

growth_protocol: Livers were dissected from female NIH/S mice (E13.5) and stored at -80C.

treatment_protocol: Nuclei were prepared from homogenised liver and digested with increasing amounts of the restriction enzyme AluI.

value: NIH/S

tag: gender

value: Female

value: liver

value: 20 units AluI


title: Experiment A, 3AT-treated cells - 0 units AluI

value: 3AT-treated cells - 0 units AluI


title: Kidney2

value: Wild-type

value: 36 months

value: Kidney


title: NA_HSC1

value: NA transgenic

value: Bone marrow HSCs


title: hBJV600E_EtOH24_Clob2_rep1

description: replicate 1

source_name: hBJV600E, ethanol 24h then clobetasol 2h

tag: inducer

value: clobetasol 2nM

value: 2 hours


title: hBJV600E_Dox24_DMSO2_rep1

description: replicate 1

source_name: hBJV600E, doxycycline 24h then DMSO 2h

value: doxycycline 1000 ng.mL-1

tag: timewithinducer


title: GAS-WT-100um-manganese-OD1-0-rep-1

value: invasive infection isolate

value: Late-exponential (LE, OD600nm=1.0)


title: Experiment B - 320 units AluI

source_name: Experiment B - 320 units AluI

tag: treatment

value: 320 units AluI


title: Experiment A, Uninduced cells - 800 units AluI

value: Uninduced cells - 800 units AluI


title: GAS-WT-no-manganese-OD1-0-rep-3


title: GAS-delmtsR-100um-manganese-OD1-0-rep-3


title: Experiment B - 160 units AluI

source_name: Experiment B - 160 units AluI

value: NIH/S

value: 160 units AluI


title: Experiment B - 2.5 units AluI

source_name: Experiment B - 2.5 units AluI

value: Female

value: liver

value: 2.5 units AluI


title: GAS-delmtsR-100um-manganese-OD1-0-rep-1


title: Experiment A, 3AT-treated cells - 1 unit AluI

value: 3AT-treated cells - 1 unit AluI


title: HA_WT_29ºC_rep2

city: Philadelphia

first: Yann

last: Aubert

state: Pennsylvania

address: Biomedical Research Building 421 Curie Blvd

department: Penn Dermatology Research

institute: University of Pennsylvania

data_processing:
read were aligned to mouse mm9 reference genome with bowtie2-2.1.0 using -k 1 and -n 1 options.
tag directories were generated for individual replicates with Homer v4-10 using a fragment length of 150bp (-fragLength 150), allowing a maximum of one tag per base pairs (-tbp 1)
tag directories from individual replicates were pooled together to generate pooled tag directories using Homer v4-10, using a fragment length of 150bp (-fragLength 150) without the -tbp 1 option.
visualization tracks were generated usinh Homer-v4.10 with following parameters -fsize 5e7 -tbp 1 -res 1 -norm 3e7 input -subtract using the correponding pooled WT directory as input
peaks were called using Homer v4-10 default parameters using the correponding pooled WT tag directories as input
peaks were gene annotated using Homer v.4-10 and tags were counted and FPKM normalized using pooled samples tag directories and the corresponding pooled input tag directories, using a fragment length of 150 base pairs. FPKM values from inputs were subtracted from samples FPKM values and peaks with a FPKM >=3 were kept for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files inculded gene annotated peaks and their FPKM values

source_name: Brown Adipose Tissue

extract_protocol: Libraries were prepared according to Illumina's ChIP Sequencing Sample Preparation Guide.

treatment_protocol: Mice were housed at 4C or at thermoneutrality for one week.

value: thermoneutrality (29C)

value: Brown Adipose Tissue

tag: chip antibody

value: HA magnetic beads (Pierce, 88837)

value: WT


title: Ctr_HSC4

value: wild type (control)

value: Bone marrow HSCs


title: Experiment B - 5 units AluI

source_name: Experiment B - 5 units AluI

value: 5 units AluI


title: HA_WT_4ºC_rep1

value: exposed to chronic cold (4C)


title: Experiment B- 40 units AluI

source_name: Experiment B- 40 units AluI

value: 40 units AluI


title: GAS-WT-100um-manganese-OD1-0-rep-2

value: invasive infection isolate

value: Late-exponential (LE, OD600nm=1.0)


title: hBJV600E_EtOH24_CpdA2_rep1

description: replicate 1

source_name: hBJV600E, ethanol 24h then CpdA 2h

value: ethanol

value: 26 hours

value: Compound A 2µM

tag: timewithtreatment

value: 2 hours


title: HA_RevA_BAT_29ºC_3019

value: HA-RevErba


title: hBJV600E_Dox120_Clob2_rep1

description: replicate 1

source_name: hBJV600E, doxycycline 120h then clobetasol 2h

value: doxycycline 1000 ng.mL-1

value: 122 hours

value: clobetasol 2nM


title: hBJV600E_Dox72_Clob2_rep1

description: replicate 1

source_name: hBJV600E, doxycycline 72h then clobetasol 2h

value: 74 hours


title: HA_WT_4ºC_rep2

value: Brown Adipose Tissue

value: HA magnetic beads (Pierce, 88837)

value: WT


title: HA_WT_29ºC_rep1

value: thermoneutrality (29C)


title: Experiment A, Uninduced cells - 100 units AluI

value: Uninduced cells - 100 units AluI


title: Experiment B - 80 units AluI

source_name: Experiment B - 80 units AluI

value: NIH/S

value: Female

value: liver

value: 80 units AluI


title: Experiment A, Uninduced cells - 200 units AluI

value: Uninduced cells - 200 units AluI


title: HA_RevA_BAT_29ºC_3037


title: Experiment A, Uninduced cells - 400 units AluI

value: Uninduced cells - 400 units AluI


title: Experiment B - 1.3 units AluI

source_name: Experiment B - 1.3 units AluI

value: 1.3 units AluI


title: HA_RevA_BAT_29ºC_3028

value: HA-RevErba


title: GAS-WT-no-manganese-OD1-0-rep-2

value: invasive infection isolate

value: Late-exponential (LE, OD600nm=1.0)


title: Experiment A - 320 units AluI

source_name: Experiment A - 320 units AluI

value: 320 units AluI


title: HA_RevA_BAT_4ºC_3040

value: exposed to chronic cold (4C)


title: Experiment B - 0.6 units AluI

source_name: Experiment B - 0.6 units AluI

value: 0.6 units AluI


title: Experiment B - 0.3 units AluI

source_name: Experiment B - 0.3 units AluI

value: 0.3 units AluI


title: HA_RevA_BAT_29ºC_3017

value: Brown Adipose Tissue

value: HA magnetic beads (Pierce, 88837)


title: Kc167 cells, 15min digestion, exp.1, seq.1

data_processing:
DNA sequences were aligned to the D. melanogaster reference genome dm6 and S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, 2012) with parameters -X 1000 --very-sensitive.
Nucleosome counts (defined as the number of Drosophila DNA fragments with the length between 100-200 bp) and spike-in counts (number of S. cerevisiae DNA fragments with the length between 100-200 bp) were obtained using MATLAB (Bioinformatics toolbox).
Genome-wide profiles (tdf files) containing the spike-in normalized nucleosome counts were generated using MATLAB and igvtools.
Genome_build: dm6
Supplementary_files_format_and_content: tdf files containing the spike-in normalized genome-wide nucleosome counts (for IGV browser)

source_name: Drosophila Kc167 cells chromatin

growth_protocol: D. mel Kc167 cells were obtained from DGRC (Stock Number: 1) and grown in HyClone SFX-Insect media supplemented with 18 mM L-glutamine and 10% Fetal bovine serum.

extract_protocol:
Drosophila S2 and Kc167 cell nuclei were isolated and subjected to MNase digestion for 1, 2, 5, 15, 40, 60 minutes. S. cerevisiae spike-in DNA was used for normalization.
Paired-end sequencing (PE25x25) was performed on barcoded libraries using an Illumina Hi-seq 2500
Quantitative MNase-Seq

tag: strain name

value: Kc167 cells

value: approximately tetraploid cell line from Drosophila Genomics Resource Center (Stock Number:1)


title: Kc167 cells, 60min digestion, exp.1, seq.1


title: Experiment A, Uninduced cells - 20 units AluI

value: Uninduced cells - 20 units AluI


title: HA_RevA_BAT_4ºC_3030


title: Experiment B - 0 units AluI

source_name: Experiment B - 0 units AluI

value: NIH/S

value: Female

value: liver

value: 0 units AluI


title: Experiment A, Uninduced cells - 10 units AluI

value: Uninduced cells - 10 units AluI


title: GAS-WT-no-manganese-OD1-0-rep-1

source_name: cell pellet


title: Experiment A, Uninduced cells - 40 units AluI

value: Uninduced cells - 40 units AluI


title: HA_RevA_BAT_4ºC_3038

value: HA-RevErba


title: Kc167 cells, 5min digestion, exp.1, seq.1


title: Experiment A, Uninduced cells - 5 units AluI

value: Uninduced cells - 5 units AluI


title: HA_RevA_BAT_4ºC_3031


title: Kc167 cells, 40min digestion, exp.1, seq.1


title: Kc167 cells, 2min digestion, exp.1, seq.1


title: TCE rep 4

first: Jason

last: Papin

address: 415 Lane Rd

department: Biomedical Engineering

data_processing:
Illumina 1.9 was used for basecalling
Sequenced reads were pseudo-aligned to the rno reference transcriptome using Kallisto v. 0.43. with parameters -b 100
Supplementary_files_format_and_content: tab-separated value files include estimated counts and transcripts per million for each Sample

organism: Rattus norvegicus

source_name: Hepatocyte

extract_protocol:
After supernatants were collected, cells from each time point were treated with TRIzol® and then scraped and collected into tubes. Chloroform was added to each tube and after shaking, cells were poured into pre-spun phase-lock gel tubes (5PRIME). Tubes were then spun in a cold room, the upper phase was collected, and IPA and glycogen were added to each tube followed by gentle inversion. Supernatants were again spun in a cold room and the resulting pellet was washed twice with 75% ethanol. The pellet was semi-dried and then dissolved in nuclease-free H2O. RNA samples were treated with DNA-free DNA removal kit (Ambion/Invitrogen), according to manufacturer’s instructions, to remove any remaining DNA. RNA was quantified using the Qubit RNA broad range kit and sample integrity assessed using Agilent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hepatocytes were exposed to a hepatotoxicant, and general toxins at sub-toxic levels. Sub-toxic levels were defined as concentrations that resulted in minimal cell death but observed phenotypic changes (i.e., decreases in albumin production and increases in cytochrome p450 activity). The compounds were acetaminophen (APAP) at 3mM, trichloroethylene (TCE) at 1mM, and 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) at 1nM. Acetaminophen is a known hepatotoxicant, while TCDD and TCE are not considered primary heptatotoxicants, but do indeed induce hepatotoxicity. Solutions were made in WEM containing 0.1% DMSO with 0.1% DMSO as a control. Cells were exposed to the compounds for six hours.

value: TCE


title: Experiment A, Uninduced cells - 2.5 units AluI

value: Uninduced cells - 2.5 units AluI


title: TCE rep 3


title: Experiment A, Uninduced cells - 0 units AluI

value: Uninduced cells - 0 units AluI


title: Experiment A - 80 units AluI

source_name: Experiment A - 80 units AluI

value: 80 units AluI


title: Experiment B - 10 units AluI

source_name: Experiment B - 10 units AluI

value: 10 units AluI


title: TCE rep 2


title: Experiment A - 40 units AluI

source_name: Experiment A - 40 units AluI

value: 40 units AluI


title: Experiment A - 20 units AluI

source_name: Experiment A - 20 units AluI

value: 20 units AluI


title: Replicate 2 - 1.6 units MNase

data_processing:
Library strategy: Quantitative DNA accessibility assay - "qDA-seq"
Sequences were aligned to the S.cerevisiae genome (sacCer3) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab. Genome-wide profiles (bigwig files) containing the fraction of cut DNA at each site and nucleosome occupancy were generated using Matlab and wigToBigWig tool.
MNase-seq reads were size selected, and we kept all mono-nucleosomal fragments with the lengths between 120 and 180 bp. Genome-wide coverage profiles were computed in Matlab, and they were normalized such that the average coverage for every chromosome is 1. Bigwig files were generated using wigToBigWig tool.
Genome_build: sacCer3
Supplementary_files_format_and_content: BigWig files containing the fraction of cut DNA at each AluI site, and nucleosome occupancy.

source_name: Yeast genomic plasmid library

growth_protocol: Not applicable (in vitro experiment).

treatment_protocol: Nucleosomes were assembled on a yeast genomic plasmid library at a ratio of 1 recombinant yeast histone octamer per 206 bp (80% w/w) by salt dialysis. The reconstituted chromatin was digested with AluI for 0, 20 or 40 minutes, or with 1.6 units micrococcal nuclease (MNase) for 3 minutes at 25degC.

value: 1.6 units MNase

tag: source

value: Yeast genomic plasmid library (Thermo Scientific cat. # YSC4613).


title: S2 cells, 60min digestion, exp.2, seq.1

source_name: Drosophila S2 cells chromatin

growth_protocol: D. mel S2 cells were obtained from Invitrogen (10831-014) and grown in HyClone SFX-Insect media supplemented with 18 mM L-glutamine.

value: S2 cells

tag: genotype

value: triplo-X tetraploid cell line from Invitrogen (10831-014)


title: Experiment A, Uninduced cells - 1 unit AluI

value: Uninduced cells - 1 unit AluI


title: Experiment A - 160 units AluI

source_name: Experiment A - 160 units AluI

value: NIH/S

value: Female

tag: tissue

value: liver

value: 160 units AluI


title: S2 cells, 40min digestion, exp.2, seq.1


title: Replicate 2 - 40 minutes AluI

value: 40 minutes AluI


title: S2 cells, 5min digestion, exp.2, seq.1


title: TCE rep 1

value: TCE