title: pNorm2

city: Copenhagen

first: Kristian

last: Almstrup

address: Blegdamsvej 9, Section GR-5064

department: Dept. of Growth and Reproduction

country: Denmark

institute: Rigshospitalet, Copenhagen University Hospital

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

source_name: pre-pubertal Normal 2

extract_protocol:
Total RNA was extracted using RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Life Technologies, Naerum, Denmark)
The Ovation Human FFPE RNA-Seq Multiplex Systems 1-8 and 9-16 (NuGEN, Leek, Netherlands) were used for library preparation from 150-200 ng of total RNA according to the manufacturer’s recommendations with the following modifications: following cDNA synthesis, samples were fragmented to yield fragment sizes of approximately 150 bp using the Covaris E210 sonicator (Covaris Ltd., Brighton, UK). Depending on the initial RNA sizes, the samples were either not fragmented or fragmented for 90, 180 or 360 s. For the final library amplification, a primer amount of 6 μL for each sample and 20 cycles of amplification were used. Following library quality assessment using the Agilent High Sensitivity DNA Kit (Agilent technologies), an extra DNA purification was performed with a 1.4 times overload of Agencourt AMPure XP beads (Beckman Coulter, Copenhagen, Denmark) to get rid of adaptors and primers. Following this, the final library was qualified using the Agilent High Sensitivity DNA kit and quantified using the Qubit dsDNA HS Assay Kit (Life Technologies). DNA was pooled in groups of 5 samples with equal amount of each.

value: Testis

tag: age of patient

tag: karytype

value: Unknown

tag: fixative

value: Stieve


title: pNorm3

status: Public on May 30 2018

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: pre-pubertal Normal 3

tag: tissue

value: Cleland


title: Mutant.High.Whole.Rep2.F2

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

description:
F2.High2-FoxAdel-1nuc_S12.R1.fastq.gz
processed data file: Mutant.High.Whole.Rep2.bw

library_source: genomic

data_processing:
Demultiplexing: demultiplexing of raw sequencing data was done using bcl2fastq v2.16.0.10.
Alignment: tracks were aligned to mouse genome assembly NCBI36 using bowtie v0.12.5 with command-line parameters -m 1 --best. Paired-end data were joined into matching fragments.
Track Generation: aligned fragment records were pooled across technical repeats, then MNase-seq tracks for whole-nucleosome particle sequencing runs were generated by taking the central 140 bp region of each aligned fragment, then binning centered fragments in non-overlapping, contiguous 10 bp bins.  Tag counts per bin were normalized to the number of millions of reads sequenced, to correct for lane or sample biases, and to the average fragment size, to correct for fragment size variability between the high and low MNase-seq. A similar procedure was undertaken for sub-nucleosome sequencing runs, except that the entire fragment and not the central 140 bp was used.
Genome_build: mm8
Supplementary_files_format_and_content: BigWigs: for each sample, aligned fragments from two technical replicates (flowcells) were pooled and the composite pool was made into a track. We additionally pooled tags from two biological replicates for the sub-nucleosomal data (low MNase digestion, mutant and WT) to make Low1.2-FoxAdel-0-5nuc.Fragments.merge.shorter80.bw and Low1.2-WT-0-5nuc.Fragments.merge.shorter80.bw.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: No special protocols for rearing mice; animal use was approved by an IACUC committee.

extract_protocol:
Two weeks after AAV-Cre injection, which was previously shown to yield efficient deletion (Lee et al., 2014), livers were perfused with 45 ml of 37°C Liver Perfusion Medium (Life technologies, 17701-038), followed by 45 ml of 37°C Liver Digestion Medium (Life technologies, 17703-034) at a speed of 5 ml /min.  The perfused liver was excised, washed with SST (150 mM NaCl, 15 mM Na citrate, 10 mM Tris [pH 7.4]), and minced using cell scrapers to release the hepatocytes.  The hepatocytes were filtered through a 100 mm cell strainer into a 50 ml conical tube, which was then filled up to 50 ml with SST.  Hepatocytes were centrifuged at 50 g for 3 min at 4°C to pellet only hepatocyte cells.  The supernatant was aspirated and the pellet was resuspended in 50 ml SST.  Hepatocytes were centrifuged at 50 g for 3 min at 4°C.  The SST wash was repeated.  Hepatocytes were resuspended in 5 ml RSB (10 mM Tris [pH7.4], 10 mM NaCl, 3 mM MgCl2, 10 mM sodium butyrate, 0.5 mg/ml aprotinin, 0.5 mg/ml leupeptin, 1 mg/ml pepstatin) plus 0.5% NP40 and were swollen on ice for 5 min.  Liver and spleen from C3H mice were minced with scalpels in SST (150 mM NaCl, 15 mM Na Citrate, 10 mM Tris [pH 7.4]) on ice and washed with SST in 30 ml Corex tubes three times.  The tissue was resuspended in RSB (10 mM Tris [pH7.4], 10 mM NaCl, 3 mM MgCl2 with 10 mM sodium butyrate, 0.5 mg/ml aprotinin, 0.5 mg/ml leupeptin, 1 mg/ml pepstatin) and 0.5% NP40, and was swollen on ice for 5 min (liver) or 10 min (spleen).  The tissue was homogenized with a glass Teflon pestle in a glass homogenizer and a portion was observed under the microscope to confirm nuclear isolation. The nuclear suspension was filtered through a 100 mm cell strainer and pelleted by centrifugation at 1.4 K rpm for 7 min at 4°C in 15 ml Corex tubes with a swinging bucket rotor.  The pellet was washed in RSB plus 0.5% NP40 and pelleted by centrifugation at 900 rpm for 10 min at 4°C in 15 ml Corex tubes with a swinging bucket rotor; this wash step was repeated once.  The nuclear pellet was re-suspended in RSB and adjusted to O.D. A260 of 1 for liver and 0.68 for spleen.  CaCl2 (3 mM final) was added, the nuclear suspension was pre-warmed for 1.5 min at 37°C, and was treated with MNase (Worthington Biochemicals) at 0 U/ml for control, 0.5 or 1 U/ml for low digestion and 20 U/ml for high digestion for 2 min at 37°C.  Quench control (“Q” sample) to assess endogenous nucleases was without MNase and CaCl2 and was not warmed.  The reactions were stopped by adding an equal volume of 2x TNESK (20 mM Tris [pH7.4], 200 mM NaCl, 2 mM EDTA, 2% SDS, 0.2 mg/ml Proteinase K), and incubated overnight at 37 °C.  DNA was purified using phenol-chloroform extraction followed by ethanol precipitation.  The nucleic acid was digested with 10 ng/ml of RNase for 20 min at 37°C and DNA was purified using phenol-chloroform extraction followed by ethanol precipitation.  50 ug samples of low MNase and 10 ug samples of high MNase were run on 6% polyacrylamide gels (TBE).  The mono-nucleosomal DNA was excised from the 140 bp~200 bp size range and sub-nucleosomal DNA was excised from 25-140 bp size range.  The gel was sliced into small pieces, put in 2 vol of diffusion buffer (500 mM ammonium acetate, 10 mM magnesium acetate, 1 mM EDTA, 0.1% SDS), and rotated overnight. The supernatant was filtered through Whatman GF/C and ethanol precipitated.  DNA was purified using QIA EX II (QIAGEN) for sub-nucleosomal DNA and AMPure XP (Beckman) beads for mono-nucleosomal DNA. Mono-nucleosomal DNA from low MNase digestion averaged 1.5~2.5% of bulk DNA. Mono-nucleosomal DNA from high MNase digestion averaged 25~30% of bulk DNA.  The percent of mononucleosomal DNA of bulk DNA was estimated based on the amount of mononucleosomal DNA recovered from a preparative PAGE gel, multiplied by 1.25 (PAGE gel extraction recovers about 80% of sample in our hands) compared to the amount of bulk DNA loaded onto to the PAGE gel.
We prepared multiplexed libraries from two biological replicates of low and high MNase digested mono-nucleosomal DNA from WT liver, low and high MNase digested mono/sub-nucleosomal DNA from FoxA1/FoxA2 flox;AAV-Cre and WT;AAV-Cre.  The standard Illumina multiplexing library preparation protocol was employed with the following changes: 1) All QIAGEN purification steps were substituted with AMPure XP bead (Beckman) purifications. 2) For MNase digested mono-nucleosomal DNA, gel purification following adapter ligation was substituted with AMPure XP bead purification in order to remove excess adapters. 3) 10 ng of adapter ligated DNA was used as a template for PCR, wth 10 PCR cycles for MNase DNA, and 12 PCR cycles for ChIP DNA. 4) Gel purification after PCR was substituted with AMPure XP beads purification in order to remove excess primers.  The DNA libraries were assessed using an Agilent Technologies 2100 Bioanalyzer.  MNase-seq libraries from FoxA1/FoxA2 flox;AAV-Cre and WT;AAV-Cre were were sequenced as 37-bp paired-end by Illumina NextSeq500.

treatment_protocol: The FoxA2loxP and FoxA1loxP alleles have been reported previously (Gao et al., 2008; Sund et al., 2000). Two FoxA1loxP/loxP;FoxA2loxP/loxP mice (Li et al., 2011) and two wild type mice were anaesthetized with isofluorane and injected with AAV expressing Cre recombinase (AAV-Cre) under the control of the Tbg (also known as Serpina7) promoter (Lee et al., 2014) for liver-specific deletion of FoxA1loxP/loxP;FoxA2loxP/loxP alleles.

tag: strain background

tag: genotype/variation

value: FoxA1,FoxA2 Deletion

tag: age

value: adult

value: liver

tag: mnase digestion

value: High

tag: particle size

value: Whole Nucleosome

tag: biological replicate

tag: technical replicate


title: pKS3

source_name: pre-pubertal Klinefelter syndrome 3

value: Known patient with Klinefelter syndrome


title: pKS2

source_name: pre-pubertal Klinefelter syndrome 2


title: pKS4

source_name: pre-pubertal Klinefelter syndrome 4


title: pNorm1

source_name: pre-pubertal Normal 1


title: pKS1

source_name: pre-pubertal Klinefelter syndrome 1


title: pNorm4

source_name: pre-pubertal Normal 4


title: aNorm2

source_name: adult Normal 2

value: GR-fix


title: aNorm3

source_name: adult Normal 3


title: aNorm4

source_name: adult Normal 4


title: aNorm1

source_name: adult Normal 1


title: aSCO3

source_name: adult Sertoli Cell-Only 3


title: aSCO1

source_name: adult Sertoli Cell-Only 1


title: aKSL3

source_name: adult Klinefelter-like 3


title: Mutant.Low.Whole.Rep2.F1

description:
F1.Low2-FoxAdel-1nuc_S10.R1.fastq.gz
processed data file: Mutant.Low.Whole.Rep2.bw

value: Low


title: DH14_48h

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: PolyA-enriched RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Blumeria graminis f. sp. hordei DH14 (BluGen genome assembly, version 3.0) using tophat v2.0.10 with parameters --read-mismatches 10 --read-gap-length 10 --read-edit-dist 20 --read-realign-edit-dist 0 --mate-inner-dist 260 --mate-std-dev 260 --min-anchor 5 --splice-mismatches 2 --min-intron-length 30 --max-intron-length 10000 --max-insertion-length 20 --max-deletion-length 20 --num-threads 10 --max-multihits 10 --coverage-search --library-type fr-firststrand --segment-mismatches 3 --min-segment-intron 30 --max-segment-intron 10000 --min-coverage-intron 30 --max-coverage-intron 10000 --b2-very-sensitive
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: Blumeria graminis fsp. hordeii (Bgh) DH14, BluGen (http://www.blugen.org/) genome assembly version 3.0
Supplementary_files_format_and_content: tab-delimited text file including raw read counts per gene per sample

molecule: polyA RNA

organism: Blumeria hordei

source_name: Bgh-infected barley leaves

extract_protocol:
RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen) according to the manufacurer's instruction, with susequent DNA removal using the DNase Turbo Kit (Thermo Fisher Scientific) and RNA clean-up Kit (Zymo Research).
RNA-seq libraries were prepared from mRNA-enriched materials by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).

tag: host organism

value: leaves of Barley cultivar 'Pallas'

tag: isolate

tag: time post inoculation


title: DH14_16h

description: PolyA-enriched RNA


title: aKS3

source_name: adult Klinefelter syndrome 3


title: aKSL1

source_name: adult Klinefelter-like 1


title: aKS2

source_name: adult Klinefelter syndrome 2

value: Bouin


title: aKS1

source_name: adult Klinefelter syndrome 1


title: shIMP3-75 rep1

status: Public on May 29 2018

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-sequencing reads were trimmed by cut first 10 nucleotide off before aligning against human reference genome hg19 using TopHat( v.2.0.9, bowtie2/2.1.0)[1] with the following parameters: “ -G [ucsc_hg19_knownGene] --b2-very-sensitive”
ucsc_hg19_knownGene annotation file was downloaded from UCSC table browser.
The differential expressed genes were determined by Cufflinks (v2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of cuffdiff output with the FPKM values for each sample

source_name: SUM-1315 cells

growth_protocol: F12 Media with 5% FBS supplemented with  Insulin, EGF and 1% Penicillin/Streptomycin. One million cells were seeded in 100 mm cell culture dishes.

extract_protocol:
Total RNA was isolated using Trizol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with lentivirus containing shGFP, shIMP3-75 and shIMP3-77 for 3 days. Following infection, the virus was removed and cells were selected in 2 µg/mL puromycin for 2 to 4 days

tag: cell type

value: triple negative breast cancer cells

tag: passage

value: Passage 12-15

tag: shRNA


title: shIMP3-77 rep2


title: shIMP3-77 rep1


title: aSCO4

source_name: adult Sertoli Cell-Only 4

tag: age of patient


title: shGFP rep2

value: control shRNA


title: aSCO2

source_name: adult Sertoli Cell-Only 2

value: Testis

tag: karytype


title: TMR_336

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
Bowtie2 (v 2-2.1.0) and Tophat2 (v 2.0.14) were used for alignment
Cufflinks(v2.2.1) was used to determine fpkms and cuffmerge and cuffdiff were used to identify differentially expressed genes
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: tab-delimited txt file includes FPKM values for all samples

source_name: WAB 336

growth_protocol: Mammary epithelial cells were isolated from 3-5 10-12 week-old virgin females and plated on collagen I coated plates and maintained in DMEM/F12 media containing 1% pen/strep, 5% fetal calf serum, 100ug/ml EGF, and insulin. When cells reached 90% confluence, RNA was isolated. Tumors were dispersed with collagenase and plated on collagen I coated plates. After 2 passages, cells were plated in regular tissue culture dishes. Once cell lines were established, RNA was isolated.

extract_protocol:
Cells were disrupted with RLT buffer and scraped from dishes. RNA was extracted using the RNEasy kit from Qiagen (#74106).
Illumina TruSeq kit

tag: strain

value: Breast tumor Cell line

tag: genotype

value: Mapk8KO Mapk9KO Cre+


title: aKSL2

source_name: adult Klinefelter-like 2

tag: tissue

value: Two copies of SHOX

tag: fixative


title: TMR_233

source_name: WAB 233


title: WT_2

source_name: Cre+ Control 2

value: Mammary epithelial cells

value: WAPCre+


title: WT_1

source_name: Cre+ Control 1


title: WT_3

source_name: Cre+ Control 3


title: TMR_199

source_name: WAB 199


title: MAX8

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
Quality controlled FASTQ files were alignment to Mus musculus UCSC mm10 reference genome sequence (or Rattus norvegicus UCSC rn6 sequence) using the STAR (version 2.5.1) aligner software. To measure differential gene expression, DESeq2 was used.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Mus musculus UCSC mm10; Rattus norvegicus UCSC rn6
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

organism: Rattus norvegicus

source_name: blastocyst

growth_protocol:
Mouse pXEN and rat XENP cells were cultured essentially as previously described (Lo Nigro et al., 2012).
Mouse XEN cells were cultured on mouse embryo fibroblasts in 20% FBS as previously described (Kunath et al., 2005).
Mouse ES cells were cultured in 15% FBS and supplied with LIF and '2i' as previously described (Czechanski et al., 2014).

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2500 (101 cycles PE lane).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: XENP

value: WKY

tag: passages

tag: gender

value: Female


title: JNK_WT_TUMOR_1

source_name: Mammary Tumor Cell Line

growth_protocol: Tumors were dispersed with collagenase and plated on collagen I coated plates. After 2 passages, cells were plated in regular tissue culture dishes. Once cell lines were established, RNA was isolated.

tag: cell line

value: mammary tumor cell line


title: MAX2


title: JNK_WT_TUMOR_2


title: CX1

value: Male


title: MAX3


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (5) small RNA

city: Geneva

first: Claudia

last: Kathe

address: Chemin des MInes 9

department: Center for Neuroprosthetics

country: Switzerland

institute: EPFL

description: Sample 17

data_processing:
Basecalling was performed with Illumina's bcl2fastq v1.8.4
Read quality and potential sequencing biases were assessed using custom scripts for quality control of the raw sequencing data
50bp single reads were adaptor trimmed using 'skewer' prior to mapping with the short-read aligner Bowtie2.
Reads mapping to miRBase annotated miRNAs were counted using htseq-count to create a raw count table
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: text file: raw count matrix table for all sample combined

source_name: C6-8 dorsal root ganglion

extract_protocol: Total RNA for RNA sequencing was extracted from C6-C8 DRGs from the rats from the pyramidotomy study. Tissue was homogenized in QIAZOL (Qiagen, 79306) and nucleic acids were separated in Phase Locked Gel columns (5Prime, 230 2830). 1.5 volume of 100% ethanol was added to the aqueous phase and transferred to filtered spin columns from the RNA extraction kit (miRNeasy kit, Qiagen, 217004) and we proceeded according to manufacturer's instructions. Samples were also DNase I treated with double volume of the recommended amount (Qiagen, 79254). We estimated the total RNA quality and quantity by spectrophotometry (NanoDrop, ND-1000) and measured the RIN scores (Agilent RNA 6000 Nano Reagents Part I and Agilent 2100 Bioanalyzer). The integrity number for each sample was greater than 7.6, with an average of 8.

value: dorsal root ganglion

tag: timepoint post-injury

value: 10 weeks

tag: treatment

value: AAV1 prepro-neurotrophin-3

value: lister hooded rats


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (4) small RNA

description: Sample 16


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (6) small RNA

description: Sample 18


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (1) small RNA

description: Sample 13


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (2) small RNA

description: Sample 14


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (3) small RNA

description: Sample 15


title: shIMP3-75 rep2

value: triple negative breast cancer cells

value: Passage 12-15


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (6) small RNA

description: Sample 12

value: AAV1 GFP


title: shGFP rep1

value: control shRNA


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (5) small RNA

description: Sample 11


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (2) small RNA

description: Sample 8


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (1) small RNA

description: Sample 7


title: JNK_KO_TUMOR_3


title: naïve (6) small RNA

description: Sample 6


title: JNK_KO_TUMOR_1


title: naïve (4) small RNA

description: Sample 4


title: naïve (5) small RNA

description: Sample 5


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (6) mRNA

description: Sample 18

data_processing:
Basecalling was performed with Illumina's bcl2fastq v1.8.4
Read quality and potential sequencing biases were assessed using custom scripts for quality control of the raw sequencing data
The 50bp paired-end reads were aligned to the reference genome (Rattus Norvegicus rn6) using TopHat2 with default parameters (except for setting mate-inner-dist=100 and mate-std-dev=50
Duplicate reads were identified using picard tools MarkDuplicates and the highest quality read at each position was retained
Reads mapping to each gene feature were counted using htseq-count to create a raw gene count table (RefSeq annotations)
Genome_build: Rnor_6.0 for mRNA
Supplementary_files_format_and_content: text file: raw count matrix table for all sample combined

extract_protocol:
Total RNA for RNA sequencing was extracted from C6-C8 DRGs from the rats from the pyramidotomy study. Tissue was homogenized in QIAZOL (Qiagen, 79306) and nucleic acids were separated in Phase Locked Gel columns (5Prime, 230 2830). 1.5 volume of 100% ethanol was added to the aqueous phase and transferred to filtered spin columns from the RNA extraction kit (miRNeasy kit, Qiagen, 217004) and we proceeded according to manufacturer's instructions. Samples were also DNase I treated with double volume of the recommended amount (Qiagen, 79254). We estimated the total RNA quality and quantity by spectrophotometry (NanoDrop, ND-1000) and measured the RIN scores (Agilent RNA 6000 Nano Reagents Part I and Agilent 2100 Bioanalyzer). The integrity number for each sample was greater than 7.6, with an average of 8.
The samples were subjected to poly-A enrichment with oligo-dT beads (Illumina) and the library was prepared using the TruSeq Stranded prep kit (Illumina)


title: naïve (1) small RNA

description: Sample 1


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (5) mRNA

description: Sample 17


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (4) mRNA

description: Sample 16


title: naïve (3) small RNA

description: Sample 3


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (1) mRNA

description: Sample 13


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (2) mRNA

description: Sample 14


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (4) mRNA

description: Sample 10


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (6) mRNA

description: Sample 12


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (3) mRNA

description: Sample 9


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (3) small RNA

description: Sample 9


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (5) mRNA

description: Sample 11


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (2) mRNA

description: Sample 8


title: naïve (4) mRNA

description: Sample 4


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (1) mRNA

description: Sample 7


title: naïve (3) mRNA

description: Sample 3


title: naïve (5) mRNA

description: Sample 5


title: naïve (6) mRNA

description: Sample 6


title: naïve (2) mRNA

description: Sample 2


title: naïve (1) mRNA

description: Sample 1


title: E6.5A

city: Shanghai

first: Naihe

last: Jing

address: Yue Yang Road 320

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology

description: embryo.gene.fpkm.txt

data_processing:
Raw reads were mapped to mm10 using the TopHat version 2.0.13 program
We assigned FPKM (fragment per kilo base per million) as an expression value for each gene using Cufflinks version 1.3.0 software
Cuffdiff software was used to identify differentially expressed genes between treatment and control samples
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each gene in each Sample

source_name: Anterior embryonic tissue dissected from E6.5 embryo

extract_protocol:
For cell lines, total RNAs were extracted by using Trizol (Invitrogen) according to the manufacturer’s instructions. For embryonic sample, small tissue sample were dissolved in lysis solution, and reverse transcription was then performed. After the 1st-strand synthesis, cDNA was directly preamplified with KAPA HiFi Hotstart ReadyMix (KAPA Biosystems) by IS-PCR primer for 18 cycles
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: Anterior embryonic tissue

tag: Stage

value: Embryonic day 6.5


title: E7.0AP

description: embryo.gene.fpkm.txt

source_name: Anterior proximal embryonic tissue dissected from E7.0 embryo

value: Anterior proximal embryonic tissue

value: Embryonic day 7.0


title: E7.0AD

description: embryo.gene.fpkm.txt

source_name: Anterior distal embryonic tissue dissected from E7.0 embryo

value: Anterior distal embryonic tissue


title: E7.5AP

description: embryo.gene.fpkm.txt

source_name: Anterior proximal embryonic tissue dissected from E7.5 embryo

value: Embryonic day 7.5


title: E7.5AD

description: embryo.gene.fpkm.txt

source_name: Anterior distal embryonic tissue dissected from E7.5 embryo


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (4) small RNA

description: Sample 10


title: naïve (2) small RNA

description: Sample 2


title: 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (3) mRNA

description: Sample 15


title: E7.5P

description: embryo.gene.fpkm.txt

source_name: Posterior embryonic tissue dissected from E7.5 embryo

value: Posterior embryonic tissue


title: E6.5P

description: embryo.gene.fpkm.txt

source_name: Posterior embryonic tissue dissected from E6.5 embryo


title: E6.0Epi

description: embryo.gene.fpkm.txt

source_name: Embryonic tissue dissected from E6.0 embryo

value: Embryonic tissue

value: Embryonic day 6.0


title: EpiSCS/F-1

description: cell line genes.fpkm.original.txt

source_name: Epiblast stem cells cultured in Nodal inhibited medium


title: ESD-EpiSC

description: cell line genes.fpkm.original.txt

source_name: ES cells derived epiblast stem cells

value: ES cells derived epiblast stem cells


title: EpiSC

description: cell line genes.fpkm.original.txt

source_name: Epiblast stem cells

value: Epiblast stem cells


title: EpiSCS/F-input DNA

data_processing:
Raw reads were mapped to mm10 using Bowtie2 version 2.2.2 program
MACS2 version 2.1.1.20160309 was used to call ChIP-seq peaks using broad peak calling mode (with --broad option), as well as to identify differential ChIP-seq signals in different conditions
ChIPseeker was used to annotate ChIP-seq peaks by using the mouse gene annotation GENCODE version M9
deepTools was used to smooth and calculate the ChIP-seq signal as the ratio between ChIP-seq data and corresponding input control data, as well as to visualize ChIP-seq signals.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: EpiSCS/F

growth_protocol: EpiSCs were maintained on serum-coated plates in chemical defined medium (CDM) supplemented with Activin (20ng/ml) and bFGF (10ng/ml). To derive EpiSCsS/F, EpiSCs were dissociated as small clumps with collagenase IV and replated on serum-coated plates in CDM supplemented with 2μM SB431542 and bFGF (10ng/ml). EpiSCsS/F were passaged using collagenase IV every 2 days. EpiSCsS/F can be cryopreserved using KSR plus 10% DMSO (dimethylsulfoxide) and thawed with similar viability compared with EpiSC.

extract_protocol:
Cells were collected and fixed in 1% formaldehyde solution and quenched by 0.125M glycine. Fixed cells were fragmented to a size range of 200-500bp by using Bioruptor Pico. Solubilized fragmented chromatin was immunoprecipitated with antibodies.Fragmented DNA was extracted with phenol-chloroform and precipitated with ethanol
DNA fragments acquired from immunoprecipitation would be subjected to end-repaired, adaptor ligation and PCR amplification under the instruction of the manufacturers (New England Biolabs E7370 ).

value: Epiblast stem cells cultured in Nodal inhibited medium

tag: chip antibody


title: EpiSCS/F-H3K27ac-ChIP seq

value: H3K27ac (Active motif,39133)


title: EpiSCS/F-H3K4me3-ChIP seq

value: H3K4me3 (Abcam,ab8580)


title: R3_Ribo_+iFGFR1

city: HOUSTON

first: Jeffrey

middle: M

last: Rosen

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: ribosome protected RNA fragment

data_processing:
Library strategy: Ribo-Seq
Base-calling was performed using Real Time Analysis (RTA) v.1.18.64. File conversion and demultiplexing were conducted using bcl2fastq-1.8.3.
The adapter sequences were removed from the Ribo-Seq and RNA-Seq reads using Cutadapt. To remove rRNA contamination, both Ribo-Seq and RNA-Seq reads were first mapped to the mouse rRNA library. rRNA contaminating reads were then filtered out, and rRNA-free reads were extracted for further analysis.
For RNA-Seq, the rRNA-free reads were mapped to the mouse genome mm10 using STAR. For Ribo-Seq, rRNA-free reads were first mapped to the mouse genome mm10 using Bowtie2. The unmapped reads were extracted and then mapped to mm10 using STAR. The Bowtie2 and STAR mapped reads were then merged. HTSeq was used to count the reads mapped to the known genes for both RNA-Seq and Ribo-Seq.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes read counts for each sample

source_name: Mammary epithelial cells

extract_protocol:
The 3rd, 4th and 5th mammary glands were isolated from mice with and without iFGFR1 activation and immediately transferred to DMEM/F-12 (Thermo Scientific, 11330032) media with 100 μg/ml CHX (Sigma-Alrich, C4859) at room temperature. The glands were then chopped into small pieces and subsequently digested in 1 mg/ml Collagenase A (Sigma-Alrich, 11088793001) in DMEM/F-12 with 100 μg/ml CHX for 2 hrs at 37 °C and 125 rpm rotation. Pieces of glands were resuspended up and down every 30 min to break up aggregates, and 0.5 μg/ml DNase I (StemCell Technologies, 07900) was added 30 min prior to MEC harvest. Cell suspensions were pelleted at 1500 rpm for 5 min. MECs were then purified with serial centrifugation by washing twice in PBS containing 5% FBS (Thermo Scientific, 10437010) and 100 μg/ml CHX with at 1500 rpm for 7 s. The cell pellet was subsequently processed for purification of ribosome protected fragments (RPFs) and RNA. RNA was harvested using TRIzol Reagent in accordance with manufacturer’s protocol (Thermo Scientific, 15596018). RPFs were isolated using a published protocol (Ingolia et al., 2012; PMID:22836135) with a few modifications. Instead of sucrose gradient centifugation, recovery of RPFs following nuclease treatment was performed using Illustra MicroSpin S-400 HR columns (GE Healthcare, 27514001) and the RNA Clean & ConcentratorTM-25 kit (Zymo Research, R1017) as described in the protocol of TrueSeq® Ribo Profile kit (Illumina, RPHMR12126).
RNA-Seq libraries were prepared for sequencing using TruSeq® Stranded mRNA Library Prep Kit Set A (Illumina, RS1222101). Ribo-Seq libraries were prepared as described in "extract protocol" section.

treatment_protocol: 4-week old MMTV-Wnt1 / MMTV-iFgfr1 female mice were treated i.p. with vehicle (-iFGFR1) or AP20187 (Clontech, 635069) for 6 hours to activate iFGFR1 signaling (+iFGFR1).

value: FVB/N

value: Mammary gland

tag: age

value: 4-week old

value: MMTV-Wnt1 / MMTV-iFgfr1


title: EpiSC-H3K27ac-ChIP seq

tag: cell type


title: Scyliorhinus_3_RNASeq

city: San Francisco

first: Duncan

last: Leitch

state: California

department: Physiology

institute: University of California - San Francisco

description: non-electroreceptor covered skin

data_processing:
All reads were trimmer for low complexity or low quality ends (Sickle version 1.3).
Forward and reverse reads were pooled. A transcriptome was assembled using Trinity (version 2.1.0)
Estimates of relative abundance for differential expression were performed using RSEM (version 1.1.17)
Genome_build: de novo assembled transcriptome Scyliorhinus_assembly.txt
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each

organism: Scyliorhinus retifer

source_name: Body skin

extract_protocol:
Tissues were removed, preserved in RNAlater solution at -20C, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Library Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Adult

tag: tissue/cell type

value: Body skin


title: Scyliorhinus_1_RNASeq

description: electroreceptor cells

source_name: Ampullary receptor cells

value: Ampullary receptor cells


title: Scyliorhinus_4_RNASeq

description: skeletal muscle

source_name: Muscle

value: Muscle


title: EpiSCS/F-H3K27me3-ChIP seq

value: H3K27me3 (Millipore,07-449)


title: Scyliorhinus_2_RNASeq

description: forebrain sample

source_name: Brain

value: Brain


title: R2_Ribo_+iFGFR1

description: ribosome protected RNA fragment


title: E7.0P

description: embryo.gene.fpkm.txt

source_name: Posterior embryonic tissue dissected from E7.0 embryo

value: ICR

value: Posterior embryonic tissue

value: Embryonic day 7.0


title: R1_Ribo_+iFGFR1

description: ribosome protected RNA fragment


title: R3_RNA_+iFGFR1

data_processing:
Base-calling was performed using Real Time Analysis (RTA) v.1.18.64. File conversion and demultiplexing were conducted using bcl2fastq-1.8.3.
The adapter sequences were removed from the Ribo-Seq and RNA-Seq reads using Cutadapt. To remove rRNA contamination, both Ribo-Seq and RNA-Seq reads were first mapped to the mouse rRNA library. rRNA contaminating reads were then filtered out, and rRNA-free reads were extracted for further analysis.
For RNA-Seq, the rRNA-free reads were mapped to the mouse genome mm10 using STAR. For Ribo-Seq, rRNA-free reads were first mapped to the mouse genome mm10 using Bowtie2. The unmapped reads were extracted and then mapped to mm10 using STAR. The Bowtie2 and STAR mapped reads were then merged. HTSeq was used to count the reads mapped to the known genes for both RNA-Seq and Ribo-Seq.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes read counts for each sample


title: R1_Ribo_-iFGFR1

description: ribosome protected RNA fragment


title: R2_Ribo_-iFGFR1

description: ribosome protected RNA fragment


title: E5.5Epi

description: embryo.gene.fpkm.txt

source_name: Embryonic tissue dissected from E5.5 embryo

value: Embryonic tissue

value: Embryonic day 5.5


title: EpiSC-H3K27me3-ChIP seq

value: Epiblast stem cells


title: EpiSC-H3K4me3-ChIP seq

value: H3K4me3 (Abcam,ab8580)


title: R1_RNA_+iFGFR1

value: FVB/N


title: EpiSCS/F-2

description: cell line genes.fpkm.original.txt

value: Epiblast stem cells cultured in Nodal inhibited medium


title: R2_RNA_+iFGFR1

value: Mammary gland

value: 4-week old


title: R3_Ribo_-iFGFR1

description: ribosome protected RNA fragment

value: MMTV-Wnt1 / MMTV-iFgfr1


title: R3_RNA_-iFGFR1


title: R2_RNA_-iFGFR1


title: EpiSC-input DNA

source_name: EpiSC


title: ES2

source_name: blastocyst

value: ES

value: Male


title: XEN5

value: XEN


title: 21dpa mRNA, rep3

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

data_processing:
Read quality control diagnostic analyses using FastQC version 0.11.2.
Small RNA-Seq reads were adapter clipped and mapped to annotated zebrafish miRNAs from miRGeneDB version 1.117 using miRExpress version 2.018.
mRNA-Seq read data were also subjected to quality control diagnostic analyses using FastQC.
Reads were trimmed using Trimmomatic version 0.3220.
Trimmed paired-end reads were aligned to the Ensembl annotated transcriptome (version 79)21 using RSEM version 1.2.2522 and Bowtie 1.1.223.
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files with mapped read counts for microRNAs or TPM for mRNA-seq

organism: Danio rerio

source_name: heart

growth_protocol: Adult Ekkwill (EK) zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.

extract_protocol:
Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.
Illumina TruSeq small RNA and strand-specific PolyA+ mRNA libraries.

treatment_protocol: Adult wildtype Ekkwill (EK) zebrafish of 6-9 months of age were anesthetized by immersion in 1:1000 dilution of 2-phenoxyethanol and subjected to ventricular resection. Approximately 20% of the apex was removed, as previously described (Poss, KD et al. Science. 2002). Whole ventricles were collected at 0, 1, 3, 7, 14, 21 and 30 dpa for RNA extraction.

value: Ekkwill

value: 6-9 months

value: heart

tag: days post amputation

tag: library type

value: mRNA


title: 14dpa mRNA, rep3

tag: strain


title: 21dpa mRNA, rep1


title: pXEN6

value: pXEN

value: ICR

value: Female


title: XEN1


title: 30dpa mRNA, rep1


title: 21dpa mRNA, rep2


title: XEN2


title: 14dpa mRNA, rep1


title: pXEN4


title: pXEN2


title: 3dpa mRNA, rep3


title: 7dpa mRNA, rep1


title: 7dpa mRNA, rep3


title: 7dpa mRNA, rep2


title: Input DNA, short-term hematopoietic stem cell

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Base-calling and bcl to fastq generation was done with CASAVA 1.8.2 from illumina.
Data was aligned to the mouse genome from UCSC (mm10) using bowtie2 (2.2.0) with -k 1.
bigWig tracks were generated in R 3.2.2 by dividing by the total number of alignments and multiplying by 1e6 (rpm).
Peaks were called using macs (2.1.0.20140616)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks with rpm-normalized coverages.

source_name: Hematopoeitic stem cells

extract_protocol:
10,000 HSPCs were sorted into PBS buffer and cross-linked with 1% formaldehyde at RT for 10 min, and 0.125 M glycine was added to stop the reaction at RT for 5 min, followed by washing once with ice-cold Hank's buffered salt solution (HBSS) containing protease inhibitor cock¬tail (PIC).
Libraries were constructed with the KAPA library preparation kit for Illumina (Kapa Biosystems).

value: 8-12 weeks old

value: short-term hematopoietic stem cell


title: Input DNA, intermediate-term hematopoietic stem cell


title: H3K27 acetylation ChIP, multi-potent progenitor

value: multi-potent progenitor

value: H3K27ac (Abcam, ab4729)


title: 3dpa mRNA, rep2


title: Input DNA, long-term hematopoietic stem cell

value: long-term hematopoietic stem cell


title: 30dpa mRNA, rep3


title: Input DNA, multi-potent progenitor


title: 3dpa mRNA, rep1


title: ES3


title: 30dpa mRNA, rep2


title: 14dpa mRNA, rep2


title: 1dpa mRNA, rep2


title: H3K27 acetylation ChIP, intermediate-term hematopoietic stem cell


title: H3K27 acetylation ChIP, short-term hematopoetic stem cell

value: short-term hematopoetic stem cell


title: 1dpa mRNA, rep1


title: 0dpa mRNA, rep2


title: H3K27 acetylation ChIP, long-term hematopoietic stem cell


title: 0dpa mRNA, rep1


title: multi-potent progenitor rep 1

data_processing:
Base-calling and bcl to fastq generation was done with CASAVA 1.8.2 from illumina.
Reads were trimmed with trim_galore (0.4.0) with default options. Adapter sequence AGATCGGAAGAGC was trimmed.
Ran bismark (0.14.3) with option --non_directional. Ran bismark methylation extractor with --report --ignore 10 --ignore_3prime 1 --bedGraph --counts --buffer_size 10G --cytosine_report.
Used R (3.2.2) with bsseq package (1.6.0) to smooth methylation data and find differentially methylated regions.
bigWig tracks were generated in R 3.2.2 by dividing by the total number of alignments and multiplying by 1e6 (rpm).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks with rpm-normalized coverages.

source_name: Hematopoietic stem cells

extract_protocol:
Genomic DNA was isolated from sorted HSPCs using the QIAamp DNA blood mini kit (QIAGEN).
Libraries were constructed using the Pico Methyl-Seq™ library prep kit (Zymo Research), and each library was subjected to 50 bp single-end sequencing on a single lane of a HiSeq 2500 device (Illumina).


title: 0dpa mRNA, rep3


title: short-term hematopoeitic stem cell rep 1

value: short-term hematopoeitic stem cell


title: intermediate-term hematopoietic stem cell rep 2


title: 30dpa small RNA, rep2

value: small RNA


title: multi-potent progenitor rep 2


title: intermediate-term hematopoietic stem cell rep 1


title: 1dpa mRNA, rep3


title: 21dpa small RNA, rep2


title: 21dpa small RNA, rep3


title: 21dpa small RNA, rep1


title: 14dpa small RNA, rep2


title: DERARE KO Reserve rep3

description: wild type reserve ko

data_processing:
Base-calling and bcl to fastq generation was done wit CASAVA 1.8.2 from illumina.
RNA-seq was aligned to genome mm10 from UCSC using tophat 2.0.10.
Cufflinks was used to generate FPKM table
Genome_build: mm10
Supplementary_files_format_and_content: FPKM table

source_name: Bone marrow

extract_protocol:
LT-HSCs were sorted into 96-well plates with 7 ul lysis buffer containing RNase inhibitor (2 U/μl) from BM. First-strand cDNA synthesis and cDNA libraries were constructed using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech).
RNA-seq libraries were prepared using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech Nextera)

tag: genotype

value: wild type reserve ko


title: long-term hematopoietic stem cell rep 1


title: long-term hematopoietic stem cell rep 2


title: DERARE KO Reserve rep1

description: wild type reserve ko


title: 30dpa small RNA, rep1

tag: tissue


title: 14dpa small RNA, rep1


title: DERARE WT Reserve rep2

description: wide type reserve

value: wild type reserve


title: DERARE WT Reserve rep3

description: wide type reserve


title: 7dpa small RNA, rep3

value: Ekkwill


title: DERARE WT Reserve rep1

description: wide type reserve


title: 7dpa small RNA, rep2

value: 6-9 months


title: 30dpa small RNA, rep3

value: heart


title: 7dpa small RNA, rep1


title: DERARE KO Wnt5a rep3

description: Wnt5a knockout rescue

value: Wnt5a knockout rescue


title: 3dpa small RNA, rep3


title: DERARE KO Wnt5a rep2

description: Wnt5a knockout rescue


title: DERARE KO Ctrl rep3

description: knockout wt control

value: knockout wt control


title: 3dpa small RNA, rep2


title: DERARE KO Reserve rep2

description: wild type reserve ko


title: 14dpa small RNA, rep3


title: DERARE KO Ctrl rep2

description: knockout wt control


title: DERARE KO Wnt5a rep1

description: Wnt5a knockout rescue


title: 1dpa small RNA, rep1


title: 1dpa small RNA, rep3


title: 0dpa small RNA, rep3


title: DERARE Wnt5a rep1


title: DERARE KO Ctrl rep1

description: knockout wt control


title: DERARE Wnt5a rep2


title: 1dpa small RNA, rep2


title: 0dpa small RNA, rep1


title: DERARE Wnt5a rep3


title: DERARE WT rep2

description: wide type

value: wild type


title: 0dpa small RNA, rep2


title: DERARE WT rep1

description: wide type


title: Cam-tTA:Fl-H1.0_MeCP2_IP_3

status: Public on May 28 2018

city: Houston,

first: Hari Krishna

last: Yalamanchili

address: 1250 Moursund St #1125,

description: Chip-IP

data_processing:
Multiplexed ChIP-seq reads were pooled
Pooled ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.1.0 with preset parameter --very-sensitive
Sam files were converted and coordinate sorted using samtools version 0.1.19-96b5f2294a
ChIP samples (bam files) were normalized to their respective inputs and converted to bigwig format using the bamCompare (with parameters: --ratio, --normalizeTo1x) module from deepTools  version 2.2.4
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bigwig files genarated using deeptools

source_name: Frontal cortex

extract_protocol:
Nuclear lysates were sonicated and MeCP2-DNA complexes were isolated with Anti-MeCP2 antibody.
Library was prepared by Genomic and RNA Profiling Core at Baylor College of Medicine using ThruPLEX DNA-seq kit (Rubicon).

tag: genotype/variation

value: MeCP2 (Millipore, #17-10491)

value: Frontal cortex


title: Cam-tTA:Fl-H1.0_MeCP2_IP_2

description: Chip-IP


title: DERARE WT rep3

description: wide type


title: CHOROID_PLEXUS_LT8_SE_2_5_09

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Adaptators were removed using cutadapt, then reads which did not have the proper UMI construction (N4H4 followed by GGG) or with less than  50 bases were discarded.
Mapping was performed with STAR_2.4.0a versus mm10
UMI counts were obtained using the Dropseq Core Computational Protocol version 1.0.1 (dropseq.jar) from McCarrol (Macosko et al., 2015) using GTF gene model from Ensembl release GRCm38.83. DigitalExpression function of dropseq.jar was called with default parameters (edit distance=1) to produce matrix of molecule counts which was used in subsequent statistical analysis.
Low UMI count genes were filtered out.
Normalisation was performed using R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of normalized UMI counts for genes in row, and samples in columns.

extract_protocol:
Sorted cells were directly collected into 0.2ml tube stripes in a lysis reaction with a final volume of 13.5 µl according to Arguel et al (Arguel, NAR 2017).
Template switching oligonucleotide (TSO) was design as in Picelli et al., with a LNA in 3 prime extremity 5’-GCA ATG AAG TCG CAG GGT TGN NNN HHH HrGrG lnG-3’.
Barcoded cDNA were pooled and 20 ng used as template for Ion Proton sequencer tagmentation protocol as described in Arguel et al (Arguel et al., 2017).

treatment_protocol: Mice were exposed to an enriched environment (EE) starting 4 weeks after birth (i.e. at weaning) for a 4 weeks period. 12-15 age-matched mice were housed in large-sized cages (9120 cm2; L x l x h: 120 x 76 x 21 cm) with nesting material, houses, running wheels, hammocks, scales, plastic toys and tunnels. Objects were changed twice a week. Mice in standard conditions (SE) were housed in medium sized cages (666 cm2; L x l x h: 36 x 18.5 x 14 cm) with 5-6 mice/cage without objects. All mice had access to tap water and standard lab chow (diet SAFE A04, 2900 kcal/kg) ad libitum and were housed on a 12 hr light/12 hr dark cycle at 22-23°C with 40-60% humidity. The animals analyzed for each experiment raised either in SE or EE came from the same cage.

value: choroid plexus

tag: environment (se

value: standard environment; ee:enriched environment):SE

tag: animal id

tag: number of collected cells

tag: Sex

value: female


title: Cam-tTA:Fl-H1.0_MeCP2_IP_1

description: Chip-IP


title: 3dpa small RNA, rep1


title: Cam-tTA:Fl-H1.0_MeCP2_input_3

description: Chip-Input


title: Cam-tTA:Fl-H1.0_MeCP2_input_2

description: Chip-Input


title: CHOROID_PLEXUS_LT8_SE_1_6_10


title: Cam-tTA:Fl-H1.0_MeCP2_input_1

description: Chip-Input


title: CHOROID_PLEXUS_LT8_SE_1_2_20


title: CHOROID_PLEXUS_LT8_SE_1_3_09


title: CHOROID_PLEXUS_LT8_SE_2_5_15


title: WT_MeCP2_IP_2

description: Chip-IP

value: WT


title: WT_MeCP2_IP_3

description: Chip-IP


title: CHOROID_PLEXUS_LT8_SE_1_4_14


title: CHOROID_PLEXUS_LT8_SE_1_1_09


title: WT_MeCP2_IP_1

description: Chip-IP


title: WT_MeCP2_input_2

description: Chip-Input


title: WT_MeCP2_input_3

description: Chip-Input


title: CHOROID_PLEXUS_LT4_SE_1_6_15


title: WT_MeCP2_input_1

description: Chip-Input


title: CHOROID_PLEXUS_LT4_SE_2_6_06


title: CHOROID_PLEXUS_LT4_SE_1_5_10


title: CHOROID_PLEXUS_LT4_SE_2_5_15


title: CHOROID_PLEXUS_LT4_SE_1_3_10


title: CHOROID_PLEXUS_LT4_SE_2_2_13


title: fh-Mecp2-/y IP_3

description: Chip-IP

data_processing:
ChIP-seq reads from all three runs were pooled
Cutadapt version 1.7.1 was used to remove/trim adapter sequences.
Pooled ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.1.0 with preset parameter --very-sensitive
Sam files were converted and coordinate sorted using samtools version 0.1.19-96b5f2294a
ChIP samples (bam files) were normalized to their respective inputs and converted to bigwig format using the bamCompare (with parameters: --ratio, --normalizeTo1x) module from deepTools  version 2.2.4
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bigwig files genarated using deeptools

extract_protocol:
Nuclear lysates were sonicated and Flag-H1.0-DNA complexes were isolated with Anti-Flag antibody.
Library was prepared by Genomic and RNA Profiling Core at Baylor College of Medicine using ThruPLEX DNA-seq kit (Rubicon).

value: Camk2a+ excitatory cells

value: Flag


title: fh-Mecp2-/y IP_2

description: Chip-IP


title: CHOROID_PLEXUS_LT4_SE_1_2_12


title: fh-Mecp2-/y Input_3

description: Chip-Input


title: fh-Mecp2-/y IP_1

description: Chip-IP


title: CHOROID_PLEXUS_LT4_SE_1_1_13


title: fh-Mecp2-/y Input_1

description: Chip-Input


title: CHOROID_PLEXUS_LT8_EE_1_6_15

value: standard environment; ee:enriched environment):EE


title: fh-Mecp2+/y IP_3

description: Chip-IP


title: fh-Mecp2-/y Input_2

description: Chip-Input


title: CHOROID_PLEXUS_LT8_EE_2_6_13


title: fh-Mecp2+/y IP_1

description: Chip-IP


title: fh-Mecp2+/y IP_2

description: Chip-IP


title: CHOROID_PLEXUS_LT8_EE_1_4_09


title: fh-Mecp2+/y Input_1

description: Chip-Input


title: CHOROID_PLEXUS_LT8_EE_1_5_17


title: CHOROID_PLEXUS_LT8_EE_2_3_15


title: CHOROID_PLEXUS_LT8_EE_2_2_14


title: fh-Mecp2+/y Input_3

description: Chip-Input


title: CHOROID_PLEXUS_LT8_EE_2_4_14


title: R1_RNA_-iFGFR1

value: FVB/N

value: Mammary gland

value: 4-week old

value: MMTV-Wnt1 / MMTV-iFgfr1


title: fh-Mecp2+/y Input_2

description: Chip-Input


title: LR-NT-2_miRNA-seq

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
After TruSeq small RNA adapters were eliminated among the sequenced reads by Trimommatic software (v.0.33), the remained sequence data were mapped to the human genome (hg19) using bowtie2 (v.2.2.2).
The quantification of each miRNA was estimated using HTSeq software package.
Then, the fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of miRNA

source_name: H3122 lung cancer cell line

extract_protocol:
Total RNA was isolated using the mirVana miRNA isolation kit (Ambion).
Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified.

tag: cell line

tag: treatment

value: Certinib


title: LR-LBH-1_miRNA-seq

value: Certinib + Panobinostat


title: CHOROID_PLEXUS_LT4_EE_2_5_13


title: CHOROID_PLEXUS_LT4_EE_1_6_13


title: CHOROID_PLEXUS_LT4_EE_1_4_10


title: LR-LBH-2_miRNA-seq


title: PR-NT-1_miRNA-seq


title: CHOROID_PLEXUS_LT4_EE_1_2_15


title: PR-NT-2_miRNA-seq


title: LR-NT-1_miRNA-seq


title: CHOROID_PLEXUS_LT4_EE_2_4_15


title: CHOROID_PLEXUS_LT4_EE_2_3_13


title: H3122_LR_Pano_2_RNA-seq

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of transcripts

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.


title: H3122_LR_2_RNA-seq


title: H3122_2_RNA-seq


title: SPLEEN_LT8_SE_6_58

value: standard; ee=enriched):SE

value: spleen

tag: number of cells


title: SPLEEN_LT4_SE_6_17


title: H3122_1_RNA-seq


title: SPLEEN_LT4_SE_5_15


title: H3122_LR_1_RNA-seq


title: H3122_LR-2_MBD-seq

data_processing:
Base calling performed using CASAVA version 1.7
Single-end reads (75 bp) were aligned against the human reference genome 19 with the BWA aligner (v.0.7.8).
The MEDIPS R package (v. 1.18.0) was used for data process and estimating methylation levels of MBD-seq data.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MEDIPS package. Scores represent log2 transformed RPKM values.

extract_protocol:
Standard DNA extraction protocol using Qiagen prep kit.
Libraries were prepared according to Illumina's instructions.


title: H3122-2_MBD-seq


title: H3122_LR_Pano-2_MBD-seq


title: H3122_LR_Pano-1_MBD-seq


title: SPLEEN_LT4_SE_4_13


title: CHOROID_PLEXUS_LT4_EE_1_5_14


title: SPLEEN_LT8_SE_2_10


title: H3122_LR-1_MBD-seq


title: H3122_LR_Pano_H3K27ac_ChIP-seq

data_processing:
Base calling performed using CASAVA version 1.7
The sequencing reads were aligned to the reference sequence (hg 19) using the Bowtie2 (v.2.2.2) software.
Finding, estimation and annotation of ChIP-seq peaks were carried out by the Homer (v.4.8.2) platform.
ChIP-fragment density at each position in the genome was estimated by starting with each tag and extending it by the estimated fragment length determined by autocorrelation.
The ChIP-fragment density is then defined as the total number of overlapping fragments at each position in the genome.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated by makeUCSCfile module in the Hommer software. Scores represent ChIP-seq density value as described in data processing step.


title: H3122_LR_H3K4me1_ChIP-seq


title: SPLEEN_LT8_EE_6_30

value: standard; ee=enriched):EE


title: CHOROID_PLEXUS_LT4_EE_1_1_09


title: H3122_LR_Pano_1_RNA-seq


title: CHOROID_PLEXUS_LT4_EE_1_3_10


title: SPLEEN_LT8_SE_1_08


title: SPLEEN_LT4_SE_3_11


title: H3122-1_MBD-seq


title: H3122_LR_Pano_input_ChIP-seq


title: H3122_H3K4me1_ChIP-seq


title: SPLEEN_LT8_EE_5_28


title: H3122_H3K27Ac_ChIP-seq


title: SPLEEN_LT4_EE_5_27


title: SPLEEN_LT4_EE_6_29


title: SPLEEN_LT8_EE_3_24


title: SPLEEN_LT8_EE_4_26


title: SPLEEN_LT8_SE_3_12


title: SPLEEN_LT8_EE_1_20


title: SPLEEN_LT4_EE_4_25


title: H3122_LR_H3K27Ac_ChIP-seq


title: H3122_LR_input_ChIP-seq


title: SPLEEN_LT4_EE_3_23


title: SPLEEN_LT4_EE_2_21


title: SPLEEN_LT8_EE_2_22


title: H3122_input_ChIP-seq


title: SPLEEN_LT4_SE_1_07


title: DO4

status: Public on May 27 2018

city: Elk Grove

first: joseph

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

data_processing:
Sequencing reads were pre-processed with FASTX-Toolkit (hannonlab.cshl.edu) to trim the adaptor sequences, and discard low quality reads. The filtered reads were mapped to the mouse genome (GRCm38/mm10) with Bowtie version 0.12.8
The Bowtie alignment files were analyzed with BEDTools to generate expression data by counting the reads that align to tRNA genes in the Genomic tRNA Database.
miRDeep2 was used to detection miRNAs and generate their expression values.
Differential expression was examined using the EdgeR package.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: a tab-delimited text file that includes the novel and known miRNAs detected by the miRDeep2.pl program package in the deep sequencing data.

source_name: Dwarf Old

extract_protocol:
Total RNA was extracted from serum samples using miRNeasy kit (Qiagen).
RNA libraries were prepared using the iIllumina TruSeq Small RNA Sample Prep Kit (#RS-200-0012, Illumina, San Diego, CA).

tag: age

value: old

tag: sample type

value: serum

value: Ames dwarf (heterogeneous genetic background)

value: 21-22 months

tag: gender


title: DO5

value: female


title: DO1


title: DO3


title: DY3

source_name: Ames Dwarf Young

value: young

value: 5-6 months


title: DO2


title: DY5


title: DY1


title: short-term hematopoeitic stem cell rep 2

value: 8-12 weeks old

tag: cell type

value: short-term hematopoeitic stem cell


title: DY4


title: DY2


title: NY4

source_name: Normal Young


title: NO5

source_name: Normal Old


title: NO3


title: NO1


title: NO4


title: NY2


title: 7459_ASD

status: Public on May 26 2018

city: Atlanta

first: Ying

last: Cheng

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description:
Captured 5hmC-enriched DNA
Old.DhMRs.txt

data_processing:
Library strategy: 5hmC.capture-seq
FASTQ sequence files from biological replicates were concatenated and aligned to the M. musculus reference genome (NCBI37v1/mm9) using Bowtie 1.1.0, keeping only unique non-duplicate genomic matches with no more than 2 mismatches within the first 25 bp. Unique, non-duplicate reads from input genomic DNA and each 5-hmC–enriched sequence set were counted in 100-, 1,000- and 10,000-bp bins genome wide and normalized to the total number of non-duplicate reads in millions. Input normalized values were subtracted from 5-hmC–enriched values per bin to generate normalized 5-hmC signals. Bins from each sample were clustered using uncentered correlation with pairwise complete linkage (Cluster3.0) to broadly asses patterns of 5-hmC–regulated loci. Overall, clustering of different sized bins generated similar clustering profiles. All data presented are those binned at 10,000 bp.
To identify Dynamically Hydroxymethylated Loci (DhML) between samples in mouse brain, we employed a Poisson-based peak identification algorithm (MACS) using unique non-duplicate reads. DhML form each replicate were merged by BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file; including position, log2 folder change value, p-value, fdr

source_name: Human cerebellum

growth_protocol: Brain samples from 17 ASD and 19 control individuals were acquired from the Harvard Brain Tissue Resource Center. Sample acquisition protocols were followed for brain bank.

extract_protocol:
Genomic DNA was isolated from brain samples with standard protocols. Tissues were homogenized on ice and then treated with proteinase K (0.667 µg/µl) in 600 μl digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl) at 55°C for overnight. The second day, 600 μl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (P-3803, Sigma) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppendorf tube and precipitated with 600 μl isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion).
5hmC enrichment was performed using a previously described procedure with an improved selective chemical labeling method. DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25–50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. All sequencing libraries were run on Illumina Hi-seq 2000 machines.

value: cerebellum

tag: diagnosis

value: ASD

tag: age group

value: Old


title: 7436_ASD

description:
Captured 5hmC-enriched DNA
Middle.DhMRs.txt

value: Middle


title: 7376_ASD


title: NY5

tag: strain


title: 7119_CTRL

value: Control


title: RDsh_1

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

data_processing:
Paired-end reads were first trimmed to 30bp to remove adapter sequences. Then, aligned to the reference genome (hg19) using bowtie software (version 1.1.2).
Duplicated reads and those mapping to the mitochondrial chromosome were removed. Only those paired-end reads that represent a 100bp fragment or smaller were retained.
Accessibility peaks were obtained using MACS2 8version 2.1.1.20160309)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format. Accessibility peaks upon multiH1 KD compared to a random shRNA

source_name: Breast cancer cell line

growth_protocol: Breast cancer T47D-MTVL cells (carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) or derivative cells, were grown at 37ºC with 5% CO2 in RPMI 1640 medium

extract_protocol:
75.000 cells were harvested and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen).
All samples were then amplified by PCR using NEBNextHigh-Fidelity 2x PCR Master Mix (New Englands Labs.) and primers containing a barcode to generate the libraries. DNA was again purified using MinElute PCR Purification Kit and samples were sequenced using Illumina HiSeq 2500 system.

tag: phenotype

tag: replicate

value: Replicate 1

tag: shRNA

value: shRNA random


title: RDsh_2

value: Replicate 2


title: 7109_ASD

tag: tissue


title: NO2

value: old


title: SPLEEN_LT4_EE_1_19

tag: environment (se

value: standard; ee=enriched):EE

value: spleen

tag: animal id


title: 7085_ASD


title: 6259_CTRL


title: multiH1sh_1

value: Knock-down

value: shRNA multiH1 variants


title: 616_CTRL

description:
Captured 5hmC-enriched DNA
Young.DhMRs.txt

value: Young


title: 5297_ASD


title: 5873_CTRL


title: 7014_ASD


title: 6206_CTRL


title: 5251_CTRL


title: 5308_ASD


title: 5115_ASD


title: NY3

value: young

value: serum

value: Ames dwarf (heterogeneous genetic background)

value: 5-6 months

value: female


title: multiH1sh_2


title: 5079_CTRL

value: cerebellum


title: 4781_CTRL

value: Old


title: 7333_CTRL

value: Control


title: 4327_CTRL


title: 451_CTRL


title: 4671_ASD

value: ASD


title: 4099_ASD

value: Middle


title: 4271_CTRL


title: 4166_ASD


title: 3924_ASD


title: 3253_CTRL


title: 6994_ASD


title: 1455_CTRL


title: 4899_ASD


title: 2149_CTRL


title: 1981_CTRL


title: LysMcre/+;Dicer+/+;ApoE-/- vehicle rep3

status: Public on May 25 2018

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

data_processing:
The reads were mapped to the mouse genome mm10 (GRCm38.p5) and reads per gene counted using STAR version 2.5 with the following settings: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 -- alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 100000 --quantMode GeneCounts.
Counts were filtered for their expression strength by selecting only genes with counts above the 10th percentile of the sample with the lowest library complexity as expressed in murine BMDMs. Gene count normalization and differential expression analysis was performed with DESeq2.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt version 2.32.1 and information from Ensembl (GRCm38.p5).
Genome_build: mm10 (GRCm38.p5)

source_name: control macrophages treated with vehicle replicate 3

growth_protocol: Macrophages were differentiated from the bone marrow of either LysMcre/+;Dicerfl/fl;ApoE-/- or LysMcre/+;Dicer+/+;ApoE-/- male mice. Shortly femur and tibia were dissected from mice and the bone marrow flushed into Falcon tubes with RPMI (ThermoFisher Scientific). AKC lysis was performed to remove erythrocytes and cells seperated from tissue residues by Ficoll gradient (Ficoll-Paque Premium; GE Healthcare #17-5442-02 ). The isolated bone marrow-derived cells were differentiated in DMEM (4.5 g/l glucose, Sigma) containing 30% of supernatant from L929 cells (producing M-CSF and GM-CSF), 20% heat-inactivated FBS and 1% Pen/Strep for 7 days on non-tissue culture treated plates. The medium was changed after 3 days. After 7 days the differentiated macrophages were dissociated using Versene (ThermoFischer Scientific #15040066) at RT and seeded at 2 mio cells/6-well in serum-free conditions (macrophage-SFM medium (ThermoFisher Scientific #12065074)) for treatment and RNA isolation.

extract_protocol:
RNA was extracted using the Quiagen Rneasy Mini Kit according to manufacture's manual.
The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies). Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: Differentiated macrophages were treated o/n with 1:1000 EtOH and 6h with either D-PBS (vehicle) or 100 ng/ul LPS (LPS).

tag: genotype

value: wildtype

value: EtOH/PBS

value: macrophage

value: Bone marrow


title: LysMcre/+;Dicer+/+;ApoE-/- LPS rep2

source_name: control macrophages treated with 100ng/ul LPS for 6hrs replicate 2

value: EtOH/6h 100 ng/ul LPS


title: 1324_CTRL


title: 1409_CTRL


title: 1977_ASD


title: LysMcre/+;Dicerfl/fl;ApoE-/- vehicle rep3

source_name: DicerKO macrophages treated with vehicle replicate 3

value: DicerKO


title: LysMcre/+;Dicerfl/fl;ApoE-/- vehicle rep2

source_name: DicerKO macrophages treated with vehicle replicate 2


title: LysMcre/+;Dicerfl/fl;ApoE-/- LPS rep3

source_name: DicerKO macrophages treated with 100ng/ul LPS for 6hrs replicate 3


title: NY1


title: 1442_CTRL


title: LysMcre/+;Dicer+/+;ApoE-/- vehicle rep1

source_name: control macrophages treated with vehicle replicate 1


title: LysMcre/+;Dicer+/+;ApoE-/- LPS rep3

source_name: control macrophages treated with 100ng/ul LPS for 6hrs replicate 3


title: LysMcre/+;Dicer+/+;ApoE-/- LPS rep1

source_name: control macrophages treated with 100ng/ul LPS for 6hrs replicate 1


title: LysMcre/+;Dicer+/+;ApoE-/- vehicle rep2

source_name: control macrophages treated with vehicle replicate 2


title: Perth_24h_rep3

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

data_processing:
Basecalls performed using CASAVA version 1.7
Mapping reads to reference. Raw reads were mapped to the reference human genome (hg19, inlcluding chrUn_gl000220 for rRNA reads) by Tophat (v2.0.8b) (http://tophat.cbcb.umd.edu/index.shtml) with settings --bowtie-n --no-discordant --no-mixed -r 120 --mate-std-dev 75 and using refFlat file for -G option.  Reads mapping to chrUn_gl000220  were removed as rRNA.
Differential Expression Analysis.   We measured differential gene expression using DefinedRegionDifferentialSeq (USeq 8.7.6) (Nix et al., 2010; http://useq.sourceforge.net/), using a flattened refFlat table for annotation (merged transcripts using MergeUCSCGeneTable [USeq]). This application calculates a Negative Binomial P-value using DESeq (Anders and Huber, 2010), followed by a Benjamin and Hochberg false discovery rate (FDR). Differentially expressed genes were those with an FDR ≤10%, absolute log2 ratio above 1.
Differential Splicing Analysis.  Alternative splicing analysis was performed using MISO (version 0.5.2) (Katz et al., Nature Methods, 2010; http://genes.mit.edu/burgelab/miso/) with settings --paired-end 125 50 --read-len 50 and --num-inc 2 --num-exc 20 --num-sum-inc-exc 30 --delta-psi 0.30 --bayes-factor 20 for filtering events.
Coverage Tracks.  Single-basepair resolution, normalized, stranded read coverage tracks were made using bamToBed (BEDTools; v2.16.2; Quinlan and Hall, Bioinformatics, 2010; https://github.com/arq5x/bedtools2), custom scripts for read count normalization, genomeCoverageBed (BEDTools) and bedGraphToBigWig (genome.ucsc.edu).  Tracks were normalized based on total read counts (human+virus) for each sample.
De novo Assembly.  Reads not mapped to hg19 were mapped to a combination of influenza genomes (A/Udorn/72(H3N2): CY009636-43; A/Brisbane/10/2007(H3N2): CY039087-94; A/California/04/2009(H1N1): FJ966079-80, FJ966082-84, FJ969513-14, JF915188).  Reads mapped to influenza genomes were converted to fastq using bam2fastx (TopHat2 package).  Overlapping reads were merged with PEAR (v0.9.0) (http://sco.h-its.org/exelixis/web/software/pear/) using settings -v 10 -q 10 -y 15G -j 8 -p 0.0001.  Unmerged reverse reads were reset to the original orientation using fastx_reverse_complement from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Merged and unmerged reads were assembled de novo with SOAPdenovo2 (v2.04) (Luo et al., GigaScience, 2012; http://soap.genomics.org.cn/soapdenovo.html).  Viral genomes were assembled for each replicate separately using 1 hpi reads initially (with -K 41) and using reads from 6 hpi and 24 hpi (assembled with values ranging from 13-49 for -K) to supplement difficult regions.  A consensus sequence was determined for each virus using SeqMan (Lasergene) and manual inspection of contig assembly.  Additional Ns were added at the 5' end to make coordinates match between the viruses. Genomes for A/Perth/16/2009(H3N2) and A/Brisbane/10/2007(H3N2) were annotated and submitted to Genbank as KJ609203-218 using the Influenza Research Database (http://www.fludb.org) submission tool.
Genome_build: hg19;  Reads not mapped to hg19 were mapped to a combination of influenza genomes (A/Udorn/72(H3N2): CY009636-43; A/Brisbane/10/2007(H3N2): CY039087-94; A/California/04/2009(H1N1): FJ966079-80, FJ966082-84, FJ969513-14, JF915188)
Supplementary_files_format_and_content: bigWig files contain normalized read coverage at single base resolution.  Fasta files contain sequences for de novo assembled viral segments.  geneStats_USeq_MISO.xlsx Excel file contains raw gene counts and normalized expression values.

organism: Influenza A virus (A/Perth/16/2009(H3N2))

growth_protocol: Stock viruses were prepared by one passage in 9-day-old embryonated chicken eggs for 48 h at 37°C or at 33 °C for IBV, and aliquots were stored at -80°C until used (current protocol 2006, KS). Viruses were titrated in Madin-Darby canine kidney (MDCK) cells and titers calculated by the method developed by Reed and Muench (Reed and Muench, 1938). Virus titer was determined as log10 50% tissue culture infective dose (TCID50)/ml as reported in (Current protocol, 2006KS).  The human bronchial epithelial cell line BEAS-2B from American Type Culture Collection (Manassas, VA) (ATCC® CRL-9609™) was cultured in base media supplemented with all addictive factors (BEGM, Bullet Kit Catalog No. CC-3170 and without gentamycin-amphotericin B mixture (Lonza biologics, Walkersville, MD). Cells were frozen in freezing media (BEGM supplemented with 1% PVP) and 7.5% DMSO to create stocks that were used for the entire screen at a controlled cell passage (not higher than passage 5). BEAS-2B cell culturing required a coating step for 2-3 h at 37°C. Coating solution was prepared in the culture media with the addition of 0.01 mg/mL fibronectin 0.03 mg/mL bovine collagen type I and 0.01 mg/mL bovine serum albumin (BSA) (all from Sigma Chemicals, St. Louis, MO). MDCK cells (ATCC® CCL-34™) were grown in complete Dulbecco’s modified Eagle’s medium (DMEM Invitrogen, San Diego, CA) supplemented with 7.5% fetal bovine serum (Invitrogen.), 100U/ml penicillin G, 100 mg/ml streptomycin and 2 mM glutamine (Invitrogen). Cells were plated (0.5´106/12-well plate) and incubated at 37°C under 5%CO2 until they reached confluency. Infection of BEAS-2B and MDCK cells was performed at multiplicity of infection (MOI) of 1 in serum-free media. After 1 h of incubation virus-cell monolayers with gentle rocking at room temperature, virus was removed and fresh media containing Trypsin, TPCK-Treated, Irradiated (Worthington Biochemical Corporation, Lakewood, NJ) (1mg/ml) was added, because the two cell lines do not support the growth of influenza virus without. The TPCK concentration for BEAS-2B was determined experimentally.

extract_protocol:
Total RNA was extracted from uninfected and influenza-infected or from IFN stimulated cells using RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Starting from 1 μg of DNA-free total RNA, ribosomal RNA (rRNA) was first removed by two rounds of selection using Ribo-Zero rRNA removal kit  (Epicentre). The resulting RNA was then used to construct RNA-seq library using Illumina Truseq strand-specific library preparation kit according to the manufacturer’s protocol. To obtain final sequencing library, 14 cycles of PCR were performed using Phusion Hot Start High-Fidelity DNA Polymerase (Finnzymes). For each sample replicate we obtained ~30 million paired 50mer reads (with 3 biological replicates per sample) using Illumina Hiseq2000 platform.

treatment_protocol: Cultures were infected with one of three viruses (MOI 1) or mock-infected and cultured for 1h, 6h, or 24h before harvesting.

tag: host

value: Homo sapiens

tag: viral passage

value: E6, BEAS-2B 1

tag: moi

tag: hours post infection

tag: host cell type

value: lung epithelial

tag: host cell line


title: Perth_1h_rep1

source_name: Influenza A virus (A/Perth/16/2009(H3N2))


title: Brisbane_24h_rep2

organism: Influenza A virus (A/Brisbane/10/2007(H3N2))

value: E3, BEAS-2B 1


title: Perth_1h_rep3


title: Perth_24h_rep2


title: Perth_24h_rep1


title: Brisbane_24h_rep1

source_name: Influenza A virus (A/Brisbane/10/2007(H3N2))


title: 3845_ASD

tag: age


title: Brisbane_24h_rep3


title: Perth_6h_rep1


title: LysMcre/+;Dicerfl/fl;ApoE-/- LPS rep1

source_name: DicerKO macrophages treated with 100ng/ul LPS for 6hrs replicate 1

tag: treatment

tag: cell type


title: Perth_6h_rep3


title: Perth_6h_rep2


title: Perth_1h_rep2


title: LysMcre/+;Dicerfl/fl;ApoE-/- LPS rep2

source_name: DicerKO macrophages treated with 100ng/ul LPS for 6hrs replicate 2

tag: strain


title: LysMcre/+;Dicerfl/fl;ApoE-/- vehicle rep1

source_name: DicerKO macrophages treated with vehicle replicate 1


title: Brisbane_6h_rep3


title: Brisbane_1h_rep1


title: d15_2_merged_*.fastq

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The RNA-seq reads were aligned to the mm9 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks in Bigwig filesby using the BEDTools software package  (Quinlan et al, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

source_name: cervix

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen) according to the manufacturer’s instructions from 8 individual mouse cervices per timepoint (day 15 gestation, day 15 sham, day 15 LPS, and day 18 gestation) for 2 biological replicate libraries (4 cervices each) at each timepoint.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).  The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011).  The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina HiSeq 2000

tag: mouse strain

value: no treatment


title: d15_LPS_TX_1_merged_*.fastq

value: intrauterine LPS 5mg/mL, 6h treatment


title: No_virus_24h_rep2

description: Mock-infected cells

source_name: lung epithelial

tag: cell line


title: No_virus_24h_rep3

description: Mock-infected cells


title: d18_1_merged_*.fastq


title: d15_LPS_Sham_2_merged_*.fastq

value: intrauterine water, 6hr treatment


title: d15_LPS_TX_2_merged_*.fastq


title: d18_2_merged_*.fastq


title: d15_1_merged_*.fastq


title: No_virus_1h_rep2

description: Mock-infected cells


title: No_virus_6h_rep1

description: Mock-infected cells


title: d15_LPS_Sham_1_merged_*.fastq


title: Brisbane_6h_rep2


title: Brisbane_6h_rep1


title: Brisbane_1h_rep3


title: Brisbane_1h_rep2


title: No_virus_6h_rep2

description: Mock-infected cells


title: No_virus_1h_rep1

description: Mock-infected cells


title: No_virus_24h_rep1

description: Mock-infected cells


title: No_virus_6h_rep3

description: Mock-infected cells


title: Pos-2-4_dNK

city: Jerusalem

first: Ofer

last: Mandelbaum

state: Select a State or Province

address: Hebrew University Medical School

department: The Lautenberg Center for General and Tumor Immunology

country: Israel

institute: The Hebrew University Faculty of Medicine, Jerusalem, Israel

description:
annotated peak file: GSE100636_ATAC_peak_file_per_gene.txt
sample name in annotated peak file: NKG2C high (Pos)

data_processing:
Trimming was performed using trim_galore with the specifications trim_galore --fastqc --paired -a CTGTCTCTTATA -a2 CTGTCTCTTATA --trim1
Alignment was performed using bowtie2 with the specifications bowtie2 -p 8 -t --phred33-quals
De-duplication was performed using picard 2.4.1 with the specifications  MarkDuplicates REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT
Reads were counted using htseq-count
Peaks were called using Homer using specifications findPeaks -style factor
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files were generated using Homer findPeaks; bedGraph.gz files were generated using bedtools  genomeCoverageBed -ibam -bg

source_name: decidual Natural killer cells

growth_protocol: Non relevant

extract_protocol: Directly afterwards, the sample was purified using a Qiagen MinElute kit. Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification the libraries were purified using a QiagenMinElute Kit and sequenced. ATAC-Seq libraries were mapped using bowtie2 (PMID 22388286) to the GRCh37/hg19 human genome. PCR-duplicate reads were removed with Picard (http://broadinstitute.github.io/picard/). Peaks of open chromatin were called from all of the mapped reads using Homer software (PMID 20513432). Reads within peaks were counted using HTseq-count (PMID 25260700).

treatment_protocol: dNK cells (pooled and purified from 3 different multigravidae decidua samples) were sorted to NKG2Chigh and NKG2Cneg populations (confirmed by staining with anti CD56 and anti NKG2C antibodies). 5*105cells from each population were used for the ATAC-seq assay. The cells were centrifuged at 500g for 3 min, followed by a washing step. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Next, the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C and immediately put on ice.

value: dNK cells positive for NKG2C

tag: pregnancy status

value: multigravidae


title: No_virus_1h_rep3

description: Mock-infected cells


title: Neg-2-3_dNK

description:
annotated peak file: GSE100636_ATAC_peak_file_per_gene.txt
sample name in annotated peak file: NKG2C neg (Neg)

value: dNK cells negative for NKG2C


title: Udorn_6h_rep2

organism: Influenza A virus (A/Udorn/307/1972(H3N2))

value: Clone 3A1, E2, BEAS-2B 1


title: Udorn_6h_rep3

source_name: Influenza A virus (A/Udorn/307/1972(H3N2))


title: GEK9

city: Porto Alegre

first: Guilherme

last: Cordenonsi da Fonseca

state: RS

address: Av. Bento Gonçalves, 9500

department: Centro de Biotecnologia

country: Brazil

institute: UFRGS

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Glycine max

source_name: carpels

growth_protocol: The samples were collected from the soybean cultivar ‘Urano’ grown at the experimental field of University of Passo Fundo (UPF) (Passo Fundo, Brazil) during the R2-R3 soybean developmental stage.

extract_protocol: Collected samples were immediately powdered in Trizol (Invitrogen, CA, USA) and stored until the RNA extraction. Total RNA was isolated using Trizol (Invitrogen, CA, USA), and following the manufacturer’s instructions. The RNA quality was evaluated by electrophoresis in 1.0% agarose gel and the amount of the RNA was checked using a Quibit fluorometer and Quant-iT RNA assay kit according to the manufacturer’s instructions (Invitrogen, CA, USA). Approximately 10 µg of total RNA was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing and sequencing using Solexa technology on the Illumina Genome Analyzer GAII. Briefly, the processing by Illumina consisted of the following successive steps: acrylamide gel purification of RNA bands corresponding to the size range 20–30 nucleotides (nt), ligation of 3′ and 5′ adapters to the RNA in two separate subsequent steps each followed by acrylamide gel purification, cDNA synthesis and a final step of PCR amplification to generate DNA colonies template library for Illumina sequencing.

tag: sample

value: pool

tag: tissue

value: carpels


title: GEK11

source_name: petals

value: petals


title: GEK12

source_name: whole flowers

value: whole flowers


title: GEK10

source_name: stamens

value: stamens


title: Udorn_6h_rep1


title: P. pringlei root apex; Terminal 2

city: Cuernavaca

first: Gustavo

last: Rodriguez-Alonso

state: Morelos

address: Av.Universidad 2001, Col. Chamilpa

department: Biología Molecular de Plantas

country: Mexico

institute: Instituto de Biotecnología

data_processing:
All processing steps were performed on the CLC-Genomics workbench (v7.5). The terminal 13 nt from the 5' end were trimmed.
Overlapped paired end reads were merged.
Quality and adaptor trimming step was run on merged and unmerged reads.
Processed reads shorter than 40 nt were discarded. Minimal contigs length was set at 400 nt; contigs longer than 3 kb were extended with the Genome Finishing Module of the CLC-GW.
Best assembly was obtained with WordSize=58 and BubbleSize=400
Genome_build: de-novo assembled transcriptome
Supplementary_files_format_and_content: comma delimited table; includes annotation, raw counts, and RPKM normalization values.
Supplementary_files_format_and_content: Fasta file of the de novo assembled contigs. Used as reference for abundance measurements / mapping.

organism: Pachycereus pringlei

source_name: Apex of the primary root

growth_protocol: Steriziled seeds were grown on vertically oriented petri dishes with 0.2x Linsmaier and Skoog medium, no sucrose added. Plants were grown at 28 C with a 12/12 photoperiod with 80 umol m-2 s-1 light intensity.

extract_protocol:
1mm Root tip samples were collected and frozen in liquid nitrogen. Collected tissue was stored at -70 C until use. Total RNA was extracted with TRIzol reagent.
Library preparation and high-troughput mRNA sequencing were performed at BGI-Tech, Hong Kong, following standard Illumina protocols.

tag: developmental stage

value: Terminal

tag: organ

value: Primary root


title: Udorn_24h_rep3

tag: host

value: Homo sapiens


title: P. pringlei root apex; Initial 1

value: Initial


title: P. pringlei root apex; Intermediate 1

value: Intermediate


title: Udorn_24h_rep2

tag: viral passage

value: lung epithelial


title: Udorn_1h_rep1

tag: moi


title: P. pringlei root apex; Initial 2


title: P. pringlei root apex; Intermediate 2


title: 5F UNGKO control 2

status: Public on May 24 2018

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

data_processing:
150bp pairend Raw reads were firstly sent for adaptor and quality trimming using trim_galore, and reads shorter than 25 nt after trimming were excluded. For spike-in DNA  sequences calculation, bowtie2 was used to reads mapping to corresponding  sequences. For genome-wide dU sites identification, processed reads mapped to spike-  in sequence were discarded, and then mapped to human reference genome (hg38) using  bowtie2. By default, bowtie2 searches for multiple alignments bowtie2 search and only  reports a random one in the best matches; for repeat sequences, bowtie reports the best  matched locus or random one from the best-matched loci. After alignment, peaks were  called using model-based analysis of ChIP-Seq (MACS2) using nonredundant  reads. Peaks overlap with that in the control sample were removed. Genomic annotations  were performed using Homer software. Gene annotations(RefSeq) were download from  UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: bed

growth_protocol: cells was maintained in DMEM with 10% FBS and penicillin/streptomycin.

extract_protocol:
DNA was extracted by Universal Genomic DNA Kit (CWbiotech, CW2298).
Genomic DNA was digested to 100-500 bp and purified with Agencourt AMPure XP beads (BECKMAN COULTER) following Spin-6 column (Bio-rad) purification. 2 μg DNA fragments and 15 pg spike_in sequences were used for end repair with NEBNext® End Repair Module (NEB, E6050) and 1 μl E.coli ligase was added to repair nicks in DNA. DNA was then purified with 1.8×AMPure XP beads. dA was added to the 3’ end of double-stranded DNA by NEBNext® dA-Tailing Module (NEB, E6053) and purified with 1.8×AMPure XP beads.
Damages that may interfere the following labeling step were repaired. DNA was purified and subjected to in vitro BER labeling. For samples named "biotin-dCTP", biotin-dCTP was utilized in the in vitro BER labeling;other samples utilized biotin-dUTP. After purification, fragments labeled with biotin were enriched by streptavidin C1 beads (Invitrogen) following the manufacturer’s guidelines.
Y adaptor  was ligated to double-stranded DNA on streptavidin C1 beads so that free adaptor can be removed by beads washing. DNA was then eluted from beads by 95 °C 3 min using deionized water. Eluted DNA was subjected to PCR amplification and sequencing.

treatment_protocol:
"5F" samples mean cells was treated with 5 μM  5-fluorodeoxyuridine for 48h.
None

tag: atcc number

tag: enrichment

value: dU enrichment

tag: genotype

value: UNG-/-


title: 5F UNGKO input 2


title: Udorn_24h_rep1

tag: hours post infection

tag: host cell type

tag: host cell line


title: 5F UNGKO control 1


title: 5F UNGKO PD 2


title: 5F UNGKO PD 1


title: 5F UNGKO input 1


title: 5F HEK293T control 2

value: wild-type


title: 5F HEK293T PD 2


title: 5F HEK293T control 1


title: 5F HEK293T PD 1


title: biotin-dCTP HEK293T PD 2

treatment_protocol:
None
None

value: biotin-dCTP labeling and enrichment


title: 5F HEK293T input 1


title: Udorn_1h_rep2


title: P. pringlei root apex; Terminal 1


title: Udorn_1h_rep3


title: biotin-dCTP HEK293T PD 1


title: biotin-dCTP HEK293T control 2


title: biotin-dCTP HEK293T input 1


title: biotin-dCTP K562 PD 1


title: biotin-dCTP HEK293T input 2


title: biotin-dCTP HEK293T control 1


title: biotin-dCTP K562 control 1


title: biotin-dCTP K562 input 1


title: biotin-dCTP K562 input 2


title: biotin-dCTP K562 control 2


title: biotin-dCTP K562 PD 2


title: UNGKO PD 1

source_name: HEK293T UNG KO

value: HEK293T UNG KO


title: 5F HEK293T input 2


title: UNGKO PD 2


title: UNGKO PD 3


title: UNGKO PD 4


title: UNGKO control 4


title: UNGKO control 3


title: UNGKO control 2


title: UNGKO input 4


title: UNGKO control 1


title: UNGKO input 3


title: UNGKO input 2


title: HEK293T PD 1


title: HEK293T control 1


title: HEK293T input 2


title: NZM9 [RRBS]

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
DNA from 12 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment was done using Bismark program.
UNIX scripts and our in house developed tool DMAP (Chatterjee et al 2012, Nucleic Acids Research) was used for post processing of the data
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .txt files describing methylation status of each significant MspI freagmnets (that were filtered based on high coverage)

source_name: Constitutive PD-L1 melanoma cell line

extract_protocol:
Cells were grown under standard conditions (5% CO2, 37°C, humidified atmosphere). : DNA from the cell pellets were extracted using Pure link Genomic DNA mini kit (Invitrogen, Hilden, Germany) following the manufacturer’s protocol, with the modification of proteinase K treatment being performed overnight at 55°C.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 100bp run.

tag: cell type

value: Constitutive PD-L1 melanoma cell line


title: NZM40 [RRBS]


title: HEK293T input 1


title: CM143-post [RRBS]


title: WPMY-1 PD 2

description: WpPD.uniq.peaks.bed


title: CM143-pre [RRBS]


title: CM142-post [RRBS]


title: WPMY-1 PD 1

description: WpPD.uniq.peaks.bed


title: WPMY-1 control 2

description: WpPD.uniq.peaks.bed


title: HEK293T PD 2


title: HEK293T control 2


title: UNGKO input 1


title: WPMY-1 input 2

description: WpPD.uniq.peaks.bed


title: WPMY-1 input 1

description: WpPD.uniq.peaks.bed


title: WPMY-1 control 1

description: WpPD.uniq.peaks.bed


title: NZM22 [RRBS]

source_name: Inducible PD-L1 melanoma cell line

value: Inducible PD-L1 melanoma cell line


title: CM150-post [RRBS]


title: CM138 [RRBS]


title: CM145-pre [RRBS]


title: MEL-RMU [RRBS]


title: K562 PD 2


title: K562 PD 1


title: NZM40 [RNA-Seq]

data_processing:
RNA-seq library from 12 cell lines were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment of the sequenced reads were perfromed using Tophat package
Differential expression analysis was perfomed using cufflink and cuffdiff packages
Exon usage analysis was perfromed using DEXSeq R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file contains FPKM values of 2 groups with P-value and fold changes for significant genes  (excel)

extract_protocol:
RNA was extracted from the cell lines using RNeasy Plus mini prep kit (QIAGEN, Limburg, Nether- lands), quantified using a Nanodrop (Thermo Scientific, Wilmington, DE)
Total RNA was isolated with RNeasy Mini Kit (Qiagen) following manufacturer’s protocol. Two rounds of RNase-free DNase I digestion (Qiagen) was performed to eliminate genomic DNA during the extraction process. RNA concentrations were determined using NanoDrop 2000 (Thermo Scientific). The quality and integrity of the RNA was determined using the RNA 6000 Pico chip on 2100 Bioanalyzer (Agilent Technologies). The median RNA integrity number (RIN) for the 12 samples was 8.0. RNA libraries were constructed using 1 µg of total RNA with TruSeq stranded mRNA Sample Preparation kit (Illumina, USA) following the manufacturer’s protocol.


title: K562 control 1


title: K562 control 2


title: K562 input 2


title: K562 input 1


title: MEL-RMU [RNA-Seq]

source_name: MEL-RMU

value: MEL-RMU


title: NZM9 [RNA-Seq]


title: CM142-post [RNA-Seq]


title: NZM42 [RRBS]


title: NZM42 [RNA-Seq]


title: NZM22 [RNA-Seq]


title: CM145-post [RRBS]


title: CM150-post [RNA-Seq]


title: CM145-post [RNA-Seq]


title: CM143-pre [RNA-Seq]


title: CM143-post [RNA-Seq]


title: CM145-pre [RNA-Seq]