title: Df(1)ED6957_F_Df(1)/w1118_rep_1 [Sample_100101]


title: Donor 2 P33 (Late Passage)

status: Public on Mar 26 2015

type: SRA

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: DNA methylation levels of a fibroblast cell at late passage (P33) for a 43 old donor.

library_source: genomic

data_processing:
Methylcap-Seq was subjected to quality control check and preprocessing steps using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Flexbar (Dodt et al., 2012).
The alignment to the human genome 19 was done with Burrows-Wheeler Transform (BWA) (Li and Durbin, 2009). More than 20 million reads per sample were mapped to genome. We calculated differentially methylated regions for each donor individually by comparing early passage versus corresponding late passage. DMR detection was performed with Model-based analysis of ChIP-Seq(MACS) (default parameters)(Zhang et al., 2008).
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: dermis

growth_protocol: Human dermal fibroblasts were isolated from patients undergoing surgical interventions after written consent, using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (Permit Number EK163/07). Cells were culture expanded in DMEM culture medium (PAA; 1g/L glucose) supplemented with glutamine (PAA), penicillin/streptomycin (PAA), and 10% fetal calf serum (FCS; Biochrom, Berlin, Germany) in a humidified atmosphere at 5% CO2.

extract_protocol:
DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, USA) and gel electrophoresis. DNA was sheared with an S220 focused-ultrasonicator (Covaris Inc., Woburn, USA) to a size range of 200-400 bp and then incubated with 2 µg of recombinant MBD2-glutathion-S-transferase fusion protein with a histidine tag (H6). Methylated DNA fragments were then captured on NTA-agarose magnetic beads (Sigma, H9914) and following washing, eluted by 0.4 M NaCl.
Library preparation of methylated DNA fragments and deep sequencing with Illumina technology (IlluminaInc., San Diego, USA) with a read length of 36 bases was performed at EMBL gene core facility (Heidelberg, Germany).

treatment_protocol: Cells were culture expanded until replicative senescence as determined by ultimate growth arrest. Late passages (as indicated in the text) were within the last three to five passages before entering senescence.

tag: cell type

value: Fibroblast

tag: passage

value: Passage 33


title: Donor 1 P30 (Late Passage)

description: DNA methylation levels of a fibroblast cell at late passage (P30) for a 43 old donor.

value: Passage 30


title: VC_KO_1

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

country: USA

institute: Harvard Medical School

description: Total RNA was depleted of rRNA by hybridization (using RiboZero) and heat fragmented. Strand-specific RNA-Seq libraries were prepared using the dUTP method, and sequenced on an Illlumina Hiseq instrument

library_source: transcriptomic

data_processing:
Base calling was performed using standard approaches.
Illumina raw reads in .fastq files were aligned using bwa 0.6.2.  Target sequences included (1) mm9  autosomal and sex chromosomes plus (2) a read-length-dependent splice library (~3M sequences, each 50-98bp).  The latter comprised all possible minimal intragenic sequences of two or more exons (based on the RefSeq annotation) for which one or more exon-exon junctions could be crossed by reads of the required length.  After bwa-indexing the targets with the bwtsw algorithm, reads were aligned with zero trimming, zero gaps, and allowing up to 5 mismatches. The sam/bam files output by bwa were indexed and sorted and served as input for further processing.
Aligned reads were minimally filtered for QC, removing any reads with uncalled bases or with unmapped or nonuniquely mapped sequences.
Employing "MAPtoFeatures" perl scripts, the loci of uniquely mapped reads were compared to the loci of all genic features (exons, introns, UTRs, CDSs, etc., and all junctions between them) of (1) all genes based on the RefSeq annotation and (2) all rRNA genes based on RepeatMasker, for the alignment target genome. Average exon Density (read coverage per bp) was calculated, equal to rdbp per feature length.  Each sample's Densities were renormalized from total reads not in noncoding genes and not in rRNA to a standard total of 10M reads, and to a standard read length of 35bp.  With these conventions, units of Density always equal RPKM times 0.35.  Quantile normalized exon densities were treated as expression levels comparable among all samples.
Genome_build: For all samples mm9 (NCBI37, Jul7. 2007).
Supplementary_files_format_and_content: Entrez gene ID, refseq gene name, gene length, and exon densities are listed for each of the 14168 genes analyzed across expression platforms in this study.

molecule: total RNA

organism: Mus musculus

source_name: Visual Cortex, 8 weeks of age

extract_protocol:
Visual Cortex was dissected from 8-10 week old MeCP2 knockout mice (Mecp2tm1.1Bird) or wild-type littermate controls. RNA was trizol and extracted using Qiagen Rneasy purification with on column DNase steps. ERCC control RNAs were spiked into the samples with equal mass added per visual cortex (note: they were not used in subsequent analysis).
Illumina library construction and sequencing was carried out as follows: total RNA was depleted of ribosomal RNA using the Ribozero rRNA removal kit (Epicentre), heat-fragmented to 200-700 bp in length and cloned using Uricil-N-Glycosylase-based strand-specific cloning. cDNA fragments were sequenced using an Illumina HiSeq 2000
Strand-specific, rRNA depleted total RNA, Single-end 49 bp sequencing

treatment_protocol: Mice were housed under standard conditions in the animal facility and dissected at the same time point in the light-dark cycle for each dissection.

tag: genotype

value: MeCP2 KO

tag: tissue

value: visual cortex


title: Donor 2 P5 (Early Passage)

description: DNA methylation levels of a fibroblast cell at early passage (P5) for a 43 old donor.

value: Passage 5


title: Donor 1 P3 (Early Passage)

description: DNA methylation levels of a fibroblast cell at early passage (P3) for a 43 old donor.

value: Passage 3


title: 0C_RNAseq

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: polyadenylated RNA

data_processing:
For RNA-seq, data processing was performed as described by Trapnell et al. 2012 Nature Protocols.
Briefly, RNA-seq reads were aligned to the mouse mm9 reference genome with a mouse transcriptome guide (NCBI37) using Tophat v2.0.11 with coverage search turned off, followed by cufflinks, cuffmerge, and cuffdiff.
Cuffdiff differential expression analysis was performed for 1) untreated_unstimulated vs. untreated_LPS to designate LPS-induced genes and 2) untreated_LPS vs. crotonate_LPS to indentify genes further induced by crotonate pre-treatment.
Genome_build: mm9
Supplementary_files_format_and_content: TDF files contain tag density data for all ChIPseq and RNA-seq samples. Cuffdiff output files contain normalized FPKM values and calculated fold difference as log2 values.

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1x Glutamax

extract_protocol:
For RNA-seq, RNA was harvested from cells with the RNeasy kit (Qiagen) with on-column DnaseI treatment.
For RNA-seq, purified RNA was prepared for sequencing with the TruSeq RNA Sample Prep Kits (Illumina) as per manufacturer's instructions. Libraries were sequenced on HiSeq2000 (Illumina) with 50bp reads.

treatment_protocol: For LPS stimulation, 100ng/mL of LPS from Salmonella typhosa (Sigma L2387) was added to full media for 2hrs. For Crotonate pre-treatment, 10mM sodium crotonate (pH 7.4) was added to full media for 6 hours prior to LPS stimulation.

tag: cell line

tag: s. typhosa lps (minutes)

tag: sodium crotonate pre-treatment

value: 10mM crotonate


title: 120U_RNAseq

description: polyadenylated RNA


title: 120C_RNAseq

description: polyadenylated RNA


title: 0U_RNAseq

description: polyadenylated RNA


title: input_120_ChIPseq

description: crosslinked chromatin

data_processing:
For ChIP-seq, data was aligned using bowtie (version 1.0.1) to the mouse mm9 genome reporting only unique reads in the best stratum, with up to 2 mismatches (bowtie -p 8 -S -q -v 2 -m 1 -k 1 --best –strata).
Samtools (version 0.1.19) was used to convert files to bam, sort, and remove PCR duplicates.
TDF files were generated by IGVtools (2.3.7) count function with processed bam files as input
Genome_build: mm9
Supplementary_files_format_and_content: TDF files contain tag density data for all ChIPseq and RNA-seq samples. Cuffdiff output files contain normalized FPKM values and calculated fold difference as log2 values.

extract_protocol:
For ChIP-seq, cells were fixed on plate with 1% formaldehyde, nuclei were isolated and then sonicated by a Bioruptor bath sonicator (Diagenode). Lysates were clarified and DNA-histone complexes were isolated by either H3K18Ac (ab1191) or H3K18Cr (PTM-517) immobilized by protein A  dynabeads (Life).
For ChIP-seq, purified DNA was prepared for sequencing with the TruSeq ChIP sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on HiSeq2000 (Illumina) with 50bp reads.


title: H3K18Cr_120_ChIPseq

description: crosslinked chromatin


title: input_0_ChIPseq

description: crosslinked chromatin


title: Df(1)ED6957_F_Df(1)/w1118_rep_3 [Sample_100103]

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
Processed data files:
cufflinks_fpkm_gene_ERCC_249.txt
DESeq2_normalized_read_counts_gene_249.txt
HTSeq_raw_read_counts_gene_ERCC_249.txt
cufflinks_fpkm_gene_235.txt
DESeq2_normalized_read_counts_gene_235.txt
HTSeq_raw_read_counts_gene_ERCC_235.txt

data_processing:
Basecalls were performed using CASAVA-1.8.2/RTA 1.17.21.3/HiSeq Control Software 2.0.10.0 on an Illumina HiSeq 2000 (Illumina Inc., San Diego, CA).
We mapped RNA reads to D. melanogaster genome (release 5, from the FlyBase, excluding “U” or “Uextra”), along with the 96 ERCC spike-in sequences (Zook et al. Plos ONE 2012, 7(7): e41356), with Tophat (v2.0.10) (Kim et al. Genome Biology 2013, 14:R36). We used parameter -g 1 to retain only uniquely mapped reads and provided a GTF format annotation with the -G option. The GTF format annotation includes the annotation for genes on existing chromosomes (derived from FlyBase annotation release 5.57 in GFF format, excluding genes on “U” or “Uextra”), as well as the annotation for 96 exogenous controls.
We measured gene expression levels using cufflinks v2.1.1 (Trapnell et al. Nature Protocols 2012, 7(3):562-78) in Fragments Per Kilobase of transcript per Million mapped reads (FPKM). We also measured the gene expression level in normalized read counts using HT-Seq v0.5.4p1 (Anders et al. Bioinformatics 2015, 31(2):166-9) and R package DESeq2 v1.6.3 (Love et al. Genome Biology 2014, 15(12):550).
There are two sets of processed data. One includes all 249 samples. The other was filtered in two steps (see "flag” for each sample) to make sure every DrosDel deficiency (Df) had at least two reliable replicates in each karyotype/sex combination. First, we checked to see if genes within the reported DrosDel deficiencies (Dfs) had reduced expression, and removed samples without expression reduction at the Dfs; 2) We removed samples without replicates in any one of the three karyotype/sex combinations (XX female, XX female transformed to male and XY male). The remaining 235 samples include 113 samples with 19 Dfs on the X chromosome, 99 samples with 11 Dfs on the autosome 3L, and 23 controls without Dfs.
Genome_build: Drosophila melanogaster Release 5
Supplementary_files_format_and_content: DESeq2_normalized_read_counts_gene_235.txt contains a matrix with read counts of all the genes normalized by DESeq2 for the 235 samples that have replicates and validated deletions. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: DESeq2_normalized_read_counts_gene_249.txt contains a matrix with read counts of all the genes normalized by DESeq2 for all the 249 samples. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: HTSeq_raw_read_counts_gene_ERCC_235.txt contains matrix with raw read counts of all the genes and spike-ins for the 235 samples that have replicates and validated deletions. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID and ERCC ID.
Supplementary_files_format_and_content: HTSeq_raw_read_counts_gene_ERCC_249.txt contains matrix with raw read counts of all the genes and spike-ins for all the 249 samples. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID and ERCC ID.
Supplementary_files_format_and_content: cufflinks_fpkm_gene_235.txt contains matrix with FPKM values of all the genes in the 235 samples that have replicates and validated deletions. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: cufflinks_fpkm_gene_ERCC_249.txt contains matrix with FPKM values of all the genes and spike-ins in all the 249 samples. Column names in the file correspond to sample names, row names correspond to FlyBase gene_ID and ERCC ID.

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Flies were grown at 25°C on cornmeal media Fly Food A (LabExpress, Ann Arbor, MI). Adults were aged 5 days before dissection.

extract_protocol:
We used RNeasy 96 Kit (Qiagen, Valencia, CA) to extract total RNA from a pool of 10 dissected heads for each sample. Frozen heads were added to 2ml Axygen 96-well plates (Corning, Life Sciences, Union City, CA) pre-loaded with 200 µL 1mm glass beads (Biospec Products, Inc., Bartlesville, OK) and 200 µL RLT Buffer (Qiagen, Valencia, CA). After covering the plates with Axygen sealing mats, we homogenized the samples with Mini-BeadBeater-96 (Biospec Products Inc., Bartlesville, OK). Manual purification was carried out using QIAvac 96 vacuum manifold (Qiagen, Valencia, CA).
We followed TruSeq RNA Sample Preparation V2 high-throughput protocol (Illumina Inc., San Diego, CA) to construct RNA-seq libraries from polyA+ RNA. For each sample, 100ng of total RNA was used as input in the initial step and 10pg ERCC spike-in RNA (Zook et al. Plos ONE 2012, 7(7): e41356., pool 78A) was added to the Elute, Prime, Fragment Mix in the "Purify and fragment mRNA” step.

tag: drosdel deficiency

tag: developmental stage

value: Adult

tag: Sex

value: F

tag: x chromosome dose

tag: replicate

tag: flag

value: pass

tag: crosses


title: H3K18Cr_0_ChIPseq

description: crosslinked chromatin


title: H3K18Ac_0_ChIPseq

description: crosslinked chromatin


title: H3K18Ac_120_ChIPseq

description: crosslinked chromatin


title: D.mel x D.sec 3

status: Public on Mar 25 2015

city: Stanford

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Dr, Alway M341

department: Genetics

institute: Stanford University

description: mmPCR-seq

data_processing:
Library strategy: microfluidic multiplex PCR (mmPCR-seq)
Primer sequences were trimmed off paired or single-end sequencing reads before mapping to both the dm3 and droSec1 genomes plus 120bp of exonic sequence surrounding known splice junctions using BWA allowing 10 mismatches per read.
Custom python scripts were used to determine the species origin of each read based on matches to the genome outside of editing sites and the A and G counts at known editing sites.
RNA editing levels were calculated as the percentage of G reads at each site.
Genome_build: dm3/droSec1
Supplementary_files_format_and_content: Processed data files include editing levels of D. melanogaster alleles and D. sechellia alleles in each sample. The tab delimited columns are formatted, D. melanogaster chromosome, position, D. mel A reads, D. mel G reads, D. mel editing level, D. sec A reads, D. sec G reads, D. sec editing level.

source_name: Drosophila melanogaster x Drosophila sechellia_F1_head

growth_protocol: Heads were dissected from adult female flies ages 0-2 days old.

extract_protocol:
Total RNA was extracted from fly heads.
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.

value: 0-2 day old adult

tag: gender

value: female

value: head


title: D.mel + D.sec 1

description: mmPCR-seq

organism:
Drosophila melanogaster
Drosophila sechellia

source_name: Drosophila melanogaster + Drosophila sechellia_head


title: D.mel x D.sec 2

description: mmPCR-seq

organism: Drosophila melanogaster x Drosophila sechellia


title: VC_KO_2


title: D.sec 2

description: mmPCR-seq

organism: Drosophila sechellia

source_name: Drosophila sechellia_head


title: D.sec 1

description: mmPCR-seq


title: D.mel x D.sec 1

description: mmPCR-seq


title: Foetal Primordial Germ Cells (PGCs)

city: Madrid

first: Jesus

last: Garcia Lopez

address: C/Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Cib (CSIC)

data_processing:
Bowtie (release 0.12.7) were used for alignments
Sequences were aligned to the miRBase release 20 (http://www.mirbase.org/) against the sequences previously annotated as miRNAs.
Sequences that were not aligned with miRBase were aligned against the sequences previously annotated as piRNAs contained in RNAdb (http://jsm-research.imb.uq.edu.au/rnadb/).
Sequences that were not aligned with RNAdb were aligned against the sequences contained in deepBase (http://deepbase.sysu.edu.cn/)
Sequences that were not aligned to deepBase were aligned against the sequences contained in Rfam release 11.0 (http://rfam.sanger.ac.uk/).
Sequences that were not aligned to Rfam were aligned against the whole mouse genome.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited *.txt files include the expression analysis performed using DeSeq (Bioconductor version: 2.11) normalized by TMM: trimmed mean of M values method. Size factors obtained for each sample were: 1.067 (OCY sample)/ 0.742 (SPZ sample)/ 0.732 (ZYG sample)/ 1.488 (SPG sample)/ 1.022 (PGC sample).
Supplementary_files_format_and_content: csv files include the read values for all miRNAs, rasRNAs and snoRNA-derived small RNAs classified in the present work. The differential gene expression analysis were performed using DeSeq (Bioconductor version: 2.11) by TMM: trimmed mean of M values method. Size factor obtained for each sample were: 1.067 (OCY sample)/ 0.742 (SPZ sample)/ 0.732 (ZYG sample)/ 1.488 (SPG sample)/ 1.022 (PGC sample).

source_name: Mouse PGCs

growth_protocol: Fully-grown oocytes and zygotes were collected from the oviducts of mice. Briefly, superovulation was induced in 4-5 week old C57BL6 mouse female mice by intraperitoneal injection of 5 IU pregnant mare serum (PMSG), followed 48 hours later by 5 IU human chorionic gonadotropin (HCG). Female mice were mated with DBA/6J males after HCG administration. Fully-grown oocytes and zygotes were treated with hyaluronidase (300 µg/ml, Sigma H3884) to remove the cumulus cells and they were washed by passing through several drops of M2 medium (Sigma M7167). To purify fetal PGCs and postnatal SPGs, a cell suspension was prepared from 13.5 dpc male gonads and 8.5 dpn testes, respectively. The PGCs were purified from the cell suspension by immunopurification using anti-CD15 (anti-SSEA-1 in mouse) magnetic beads and the purity of the cells was validated by alkaline phosphatase staining. The SPGs were purified from the cell suspension by performing a short cell culture discrimination procedure (3-4 hours) that promotes the sedimentation and adhesion of somatic cells. Accordingly, the SPGs suspended in the supernatant can be readily recovered. The purity of the SPGs was validated by the presence of Stra8 (germline-specific gene) and the absence of Fn1 (soma-specific gene). Cauda epididymis and vasa deferentia from mature CD-1 males were collected in 500 µl of M2 medium after which adipose tissue and blood vessels were removed. Cleaned structures were placed in a new 200 µl drop of M2 medium covered with mineral oil. Epididymal fluid was squeezed out and sperm was suspended in M2 medium. Concentrations were determined with a Neubauer hemocytometer. The sperm suspension was layered in a 15 ml conical tube on a discontinuous 90%/45% Percoll gradient in a 1:1:1 ratio (cell sample: 45% Percoll: 90% Percoll) and centrifuged at 700 g during 20 min. The bottom pellet was washed in PBS and centrifuged at 350 g during 5 min. In order to entirely remove contaminant cells, a hiposmotic shock was induced by resuspension of spermatozoa in H2O-DEPC.

extract_protocol:
Total RNA from Oocytes, Zygotes, Spermatozoa, Spermatogonia and Primordial Germ Cells (PGCs) was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's instructions.To purify fetal PGCs and postnatal SPGs, a cell suspension was prepared from 13.5 dpc male gonads and 8.5 dpn testes, respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina sequencing reported sequences 18-32 nucleotides long.

treatment_protocol: For high-throughput sequencing 15210 fully-grown oocytes and 15416 zygotes were collected. In all cases, the zona pellucida was removed by incubation in 30 ml of prewarmed acidic Tyrode solution under mineral oil for approximately 15 seconds, followed by careful washing in three drops of M2 medium under a stereomicroscope.

tag: strain

tag: developmental stage/cell type

value: PGCs were isolated from 13.5 fetal male gonads


title: Spermatogonia (SPG)

source_name: Mouse spermatogonia

value: Spermatogonia isolated from 8.5 d.p.n testes


title: Zygote (ZYG)

source_name: Mouse zygotes

value: C57BL/6 females mated with DBA/6J males

value: 15-18h post-fertillization Zygotes


title: Spermatozoa (SPZ)

source_name: Mouse spermatozoa

value: Cauda epididymis Spermatozoa


title: Oocyte (OCY)

source_name: Mouse oocytes

value: Metaphase II Oocytes


title: Df(3L)ED4457_F_Df(3L)/+_rep_3 [Sample_301103]


title: Sample_HYT_23-2

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads mapped to rn5 whole genome using STAR version 2.3.0e {Dobin 2012}; parameters were set using the annotation as a splice junction reference, un-annotated non-canonical splice junction mappings and non-unique mappings were removed from downstream analysis.
Transcript assembly, abundance estimates, and differential expression analysis was performed using Cufflinks v2.1.1 and Cuffdiff 2{Trapnell 2013}.
Genome_build: rn5
Supplementary_files_format_and_content: Tab delimited text with rows of transcript ID's and columns of sample ID's

organism: Rattus norvegicus

source_name: Hypothalamus

extract_protocol:
Trizol RNA Extraction reagent (Life Technologies) and QiaShredder (Qiagen) were used to lyse and homogenize whole hypothalamus. An RNEasy kit from Qiagen was then used to extract RNA. An Agilent 2100 Bioanalyzer was used to assess RNA purity and quality.
One microgram of total RNA was then used to build mRNA sequencing libraries using standard Illumina protocols

treatment_protocol: Two days post-weaning (Adolescent Cohort; PND 25) rats were pair-housed and assigned to either the Lab Rodent Diet 5001 (standard chow; n=7) or a high-fructose diet (fructose; n=6). The fructose diet used (Research diets D05111802) is 55% fructose while the standard chow normally used is 0.30% fructose. Both diets were supplemented with comparable levels of vitamins and minerals deemed necessary for rodent health, and were reviewed by veterinary staff and approved by IACUC.  In preparation for a glucose challenge at PND79, rats were fasted overnight.  On PND80, after baseline weight and fasting blood glucose readings were taken, rats were either given an intraperitoneal glucose bolus (2 g/kg dissolved in saline; n=31) or an equivalent volume of saline (n=29). After one hour, all rats were rapidly decapitated, trunk blood was collected, and brains were removed and immediately frozen.

tag: diet

value: High Fructose Chow


title: Sample_HYT_21-7


title: Sample_HYT_26-2


title: Sample_HYT_20-5


title: Sample_HYT_19-3


title: Sample_HYT_7-1

value: Standard Chow


title: Sample_HYT_18-4


title: Sample_HYT_5-5


title: Sample_HYT_4-5


title: Sample_HYT_3-6


title: Sample_HYT_2-5


title: Sample_HYT_1-7


title: D.mel + D.sec 2

description: mmPCR-seq


title: Sample_HYT_1-1


title: D.mel 2

description: mmPCR-seq

source_name: Drosophila melanogaster_head


title: D.mel 1

description: mmPCR-seq


title: Paf1mut8_spb2013_1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

data_processing:
All samples were sequenced (together with other libraries) on one lane of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the TruSeq barcode. Illumina software Casava v 1.8 was used.  The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Alignments to the S. pombe genome (May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/) were performed for the minus strand by the software bowtie (version 0.9.9.1) ( Langmead et al., 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Alignments were normalized for the size of the each library, transformed into log2 scale and corrected with a pseudocount of 3. Annotations were used as described in Woolcock et al., Genes Devc 2012, PMID: 22431512
Genomic read coverage plots were made created separately for the plus (wiggle files with _p_) and minus (wiggle files with _m_) strand, transformed into log2 scale and normalized for the size of each library based on weights of the alignments
Genome_build: May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/
Supplementary_files_format_and_content: wiggle files containing log2 scaled and normalized coverage values

organism: Schizosaccharomyces pombe

growth_protocol: Strains grown at 30 degress in YES medium to OD600=0.5

extract_protocol:
Total RNA was isolated from exponentially growing cells using the hot phenol method (Leeds, 1991). The RNA was fractionated using RNeasy Midi columns (Qiagen) following the „RNA cleanup protocol“ provided by the manufacturer. The flow-through fraction was precipitated („small RNA“ fraction). 25 μg of the "small RNA" fraction were separated on a 17.5% PAGE and the 18 – 28 nt population was purified.
The isolated small RNA populations were prepared for sequencing using the Illumina® TruSeq small RNA preparation protocol (Cat.# RS-930-1012).

tag: genotype/variation

value: Paf-1Q264Stop, ade6-hp+


title: Leo1mut_spb2012_1

value: Leo1-W157Stop, ade6-hp+


title: RNAseq_TTX_shTet3_rep2

city: Baltimore

first: Jaehoon

last: Shin

state: Maryland

address: 733 N Broadway

institute: Johns Hopkins University

data_processing:
The raw reads were mapped to the mouse genome build mm9 using tophat56. The differential expression was called by cuffdiff57 with a default FDR of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: fpmk

source_name: hippocampal primary culture

growth_protocol: Hippocampi were dissected from E16.5-17.5 mouse embryos and dissociated neurons were plated on poly-lysine coated coverslips in Neurobasal-A medium supplemented with B27 (Invitrogen).

extract_protocol:
Total RNA was poly-A tail selected and then heat fragmented. The fragmented RNA was reverse transcribed and the second strand was synthesized to make double stranded DNA. After end repair and 3’ adenylation, adapters for multiplexing were ligated to the end of double stranded DNA fragments. The ligation products were amplified and purified to generate illumina compatible libraries.
Illumina Truseq RNA sample prep

treatment_protocol: AAV gene delivery vectors were constructed by cloning the EF1a-Gene-WPRE cassette into an AAV backbone by SalI and ECoRV. The shRNA sequences used were listed in Supplementary Table 1b of the published manuscript. Cultures were treated with 1 μM TTX or 20 μM bicuculline for 48 hours and then subjected to electrophysiological analyses of mEPSCs.

value: Hippocampus

tag: drug treatment

value: Tetradotoxin

tag: shRNA

tag: age


title: RNAseq_control_shTet3_rep3

tag: tissue

value: control


title: Rot1mut_spb2011_1

value: Rot1-Q472Stop, ade6-hp+


title: Cdc73mut_spb2010_1

value: Cdc73-G313R, ade6-hp+


title: RNAseq_TTX_shTet3_rep1


title: RNAseq_control_shTet3_rep1


title: Paf1mut3_spb2009_1

value: Paf1-G104R, ade6-hp+


title: RNAseq_control_shTet3_rep2


title: RNAseq_Bicuculin_shTet3_rep3

value: Bicuculin


title: Leo1D_spb1955_1

value: Leo1Δ, ade6-hp+


title: Paf1D_spb1953_1

value: Paf1Δ, ade6-hp+


title: wt_spb464_1


title: RNAseq_TTX_scramble_rep3

value: scramble


title: RNAseq_TTX_scramble_rep2


title: RNAseq_control_scramble_rep3


title: RNAseq_TTX_scramble_rep1


title: RNAseq_Bicuculin_shTet3_rep1


title: RNAseq_control_scramble_rep2


title: RNAseq_Bicuculin_scramble_rep3


title: RNAseq_TTX_shTet3_rep3


title: RNAseq_Bicuculin_scramble_rep1


title: RNAseq_Bicuculin_scramble_rep2


title: hindbrain Ttr::RFP+ choroid plexus epithelial cells, replicate 2

city: Boston

first: Matthew

middle: Bonser

last: Johnson

address: 300 Longwood Ave.

department: Genetics and Genomics

institute: Boston Children's Hospital

data_processing:
base-calling with Illumina CASAVA 1.8.2
fastq files aligned to the mouse mm9 genome and UCSC Known Genes transcriptome references using tophat 2.0.4/bowtie 2.0.5
aligned reads were summarized with the htseq-count script, part of the HTSeq package, using the same UCSC Known Genes reference transcriptome, producing the read counts per gene per replicate provided here as the processed data file
library normalization and differential expression analyses were performed using the R/Bioconductor package DESeq (version 1)
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet containing raw read counts, with genes in rows and samples in columns

source_name: choroid plexus

extract_protocol:
Total RNA was isolated from whole ChP or FACS-purified ChP epithelial cells by using the RNeasy Micro Kit (Qiagen) and converted to cDNA and pre-amplified using the Ovation RNA-seq System V2 (NuGEN) following the manufacturer’s protocol.
cDNA was converted to Illumina paired-end sequencing libraries following the standard protocol (TruSeq v2).

value: ICR (CD1)

tag: cell type

value: FACS-purified Ttr::RFP+ choroid plexus epithelial cells (CPEC)


title: hindbrain Ttr::RFP+ choroid plexus epithelial cells, replicate 1


title: telencephalic Ttr::RFP+ choroid plexus epithelial cells, replicate 2


title: hindbrain choroid plexus, replicate 2

value: whole choroid plexus


title: hindbrain choroid plexus, replicate 1


title: Adar- D.mel x D.sec 3

description: mmPCR-seq

source_name: Drosophila melanogaster (Adar mutant) x Drosophila sechellia_F1_head

value: 0-2 day old adult

value: female

value: head


title: Adar- D.mel x D.sec 2

description: mmPCR-seq


title: telencephalic choroid plexus, replicate 2


title: normal BM-5hmC

city: Cho-ku

first: yoko

last: ogawara

state: Tokyo

address: 5-1-1, Tsukiji

country: Japan

institute: National Cancer Center Research Institute

data_processing:
5-hmC reads were mapped to the reference genome mm10 using Avadis NGS version 1.5.
Alignment algorithm was a COBWeb.
Peak detection comparing control and NIDF-AML samples was performed using PICS algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: BED format files generated with PICS. These regions shows the locus with lower 5hmC in NIDF-AMLcells compared to normal BM cells.

source_name: normal BM cells

extract_protocol:
5-hmC enrichment reactions were performed in a 100-μl solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 150-300 ng μl−1 sonicated genomic DNA (100–500 bp), 250 μM UDP-6-N3-Glu, and 2.25 μM wild-type β-glucosyltransferase. Reactions were incubated for 1 hour at 37 °C. DNA substrates were purified via Qiagen DNA purification kit or by phenol- chloroform precipitation and reconstituted in H2O. Click chemistry was performed with the addition of 150 μM dibenzocyclooctyne modified biotin into the DNA solution, and incubated for 2 h at 37 °C. Samples were then purified by Pierce Monomeric Avidin Kit (Thermo) following the manufacturer's recommendations. After elution, biotin-5-N3-gmC–containing DNA was concentrated by 10 K Amicon Ultra 0.5-ml Centrifugal Filters (Millipore) and purified using a Qiagen DNA purification kit.
Illumina sequencing libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A). 25-40 ng of input genomic DNA or 5-hmC–captured DNAs were used. DNA fragments of ~150–300 bp were gel-purified after the adaptor ligation step. PCR-amplified DNA libraries were quantified on an Agilent 2100 Bioanalyzer and diluted to 6–8 pM for cluster generation and sequencing. 100-cycle paired- end sequencing was performed using Illumina HiSeq2000.

treatment_protocol: Genome were purified from BM cells by using Nucleospin Tissue (Takara).

value: bone marrow cells


title: input DNA

city: Beijing

first: Wenzhe

last: Si

state: Beijing

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

country: China

institute: Peking University Health Science Center

data_processing:
Basecalls performed using CASAVA version 1.4
The high quality reads were mapped to the Human genome of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed.
The expression peaks were detected by MACS(Model-based Analysis for ChIP-Seq) using the parameter:-f BOWTIE -g hs -n C_Ip -w.
Genome_build: GRCh37
Supplementary_files_format_and_content: wig files were generated using MACS.

source_name: MCF-7 cells

growth_protocol: MCF-7 cancer cells were grown to 70-80% confluence in DMEM (Hyclone) supplemented with 10% FBS (Hyclone) in 150 mm dishes.

extract_protocol:
All DNA samples were processed as per the Illumina  ChIP-seq sample processing methods. 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturerâs instructions.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For a ChIP experiment, we routinely used approximately 1 x 10^8 cells from 5-6, 150 mm diameter cell culture plates.

tag: chip antibody

tag: cell line


title: NIDF-AML-5hmC rep2

source_name: IDH2/R140Q, NPMc, DNMT3A/R882H and FLT3-ITD-induced AML cells


title: G9A

value: G9A (sigma)


title: Adar- D.mel x D.sec 1

description: mmPCR-seq

tag: developmental stage


title: RNAseq_Bicuculin_shTet3_rep2

value: Hippocampus


title: RNAseq_control_scramble_rep1

value: control


title: H cDNA sequencing library

city: Haikou

first: xia

last: zhiqiang

address: 4 Xueyuan Road

institute: The Institute of Tropical Bioscience and Biotechnology

description: Planted in 2000 and regularly tapped with a tapping system (S/2 d/4, i.e. half spiral cut tapped at the fourth daily frequency) plus application of 1.5% ethephon two days before tapping (once every three tappings)

data_processing:
Raw reads produced from sequencing machines were filtered by the Illumina pipeline and the dirty raw reads with adaptors and unknown nucleotides larger than 5%, and low quality reads (the rate of reads which quality value ≤ 10 is more than 20%) were removed. Transcriptome de novo assembly was then carried out with short reads assembling program – Trinity (release 20130225 ) ( http://trinityrnaseq.sourceforge.net/) [76,77]. First, Unigenes, the result sequences of trinity, from each sample's assembly were taken into further process of sequence splicing and redundancy removing to acquire non-redundant Unigenes as long as possible. Second, the Unigenes were divided into two classes via gene family clustering: clusters (CL, there were several Unigenes which similarity between them was more than 70%) and singletons (Unigene). In the final step, Blast X alignment (an E-value < 0.00001) between the Unigenes and protein databases like NT (non-redundant NCBI nucleotide database), NCBI's non-redundant protein databases (NR), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and COG (Cluster of Orthologous Groups) was performed and the best aligning results were used to decide sequence direction of the Unigenes and assign functional annotations to the Unigenes. With the NR annotation, the Blast2GO program [78] was used to generate the Gene Ontology (GO) annotation for the Unigenes and thereafter the WEGO software [79]) to do the GO functional classification for the Unigenes for understanding the distribution of gene functions of the species from the macro level. With the help of KEGG database [80], unigene metabolic pathway analysis was carried out to further study genes’ biological complex behaviors and get pathway annotation for the Unigenes.
FPKM  method (Fragments Per kb per Million reads) was applied to calculate the expression of the Unigenes . Therefore the calculated gene expression could be directly used for comparing the difference of gene expression between the two samples. Based on the method by Audic and Claverie (1997), a rigorous algorithm to identify differential transcript accumulation between the two samples was developed for screening the differentially expressed genes (DEGs). The FDR (false discovery rate) was used to determine the threshold of the P-value in multiple tests and analyse for calculating the expression between two samples.
Genome_build: de novo transcriptome; fasta file is available on the series record.
Supplementary_files_format_and_content: FPKM

organism: Hevea brasiliensis

source_name: Healthy rubber trees with normal latex flow

extract_protocol:
Poly(A) mRNA was first isolated from 20 μg of total RNA using magnetic beads containing poly-T molecules.
Bark RNA was extracted and two cDNA libraries, H (healthy rubber trees) and T (TPD-affected trees), were prepared using the mRNA-Seq 8 sample prep Kit (Illumina).  Poly(A) mRNA was first isolated from 20 μg of total RNA using magnetic beads containing poly-T molecules. Then, the purified samples were fragmented into small pieces using divalent cations at 94°C for 5 minutes and reverse transcribed into cDNAs with the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA). Then, end repair and adenylation of 3' ends were conducted and purified using the QIAquick PCR Purification Kit (QIAGEN). After that, Illumina paired end adapters were ligated to the resulting cDNA fragments. Finally, each cDNA library with an insert size of 200 bp was generated. After quality checking by an Agilent Technologies 2100 Bioanalyzer, the libraries were deep sequenced using Illumina HiSeqTM 2000 (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Healthy (H) rubber trees were regularly tapped with a tapping system (S/2 d/4, i.e. half spiral cut tapped at the fourth daily frequency) plus application of 1.5% ethephon two days before tapping (once every three tappings). Tapping was stopped for the TPD-affected (T) rubber trees which tapping panel become completely dry

tag: cultivar

value: clone PR107

value: bark

tag: disease status

value: healthy


title: T cDNA sequencing library

description: Planted in 2000 and tapping stopped due to TPD

source_name: TPD-affected rubber trees which tapping panel become completely dry

value: Tapping panel dryness (TPD)


title: ΔNCU03699_NC_DC_PE

city: Tianjin

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NC12 whole genome using bowtie v2.2.3.0, TopHat v: 2.0.12
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Detailed parameters for single-end libraries: tophat2 -p 14 -g 1 -a 10 --min-segment-intron 20 --max-segment-intron 4000 --min-coverage-intron 20 --max-coverage-intron 4000 -i 20 -I 4000 --segment-length 24  --microexon-search --coverage-search --b2-very-sensitive -G NC12.gtf  NC12_index xx.fq
Detailed parameters for paired-end libraries: tophat2 -p 14 -g 1 -a 10 --min-segment-intron 20 --max-segment-intron 4000 --min-coverage-intron 20 --max-coverage-intron 4000 -i 20 -I 4000  --microexon-search --coverage-search  --no-discordant --no-mixed --b2-very-sensitive -G NC12.gtf  NC12_index ./xx_1.fq ./xx_2.fq
Genome_build: NC12; GCA_000182925.2
Supplementary_files_format_and_content: abundance measurements

organism: Neurospora crassa

source_name: hyphal cells

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain ΔNCU03699 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour.

tag: strain/genotype

tag: er stress agent

value: hyphal cells


title: NCU02413_DTTAES_DC_PE

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain ΔNCU02413 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 5 mM DTT (final concentration)  for 1 hour to induce ER stress.

value: DTT (5mM)


title: ΔNCU03699_DTTAES_DC_PE

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain ΔNCU03699  were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 5 mM DTT (final concentration)  for 1 hour to induce ER stress.


title: WT_NC_DC_PE

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain FGSC2489 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour.


title: WT_DTTAES_DC_PE

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain FGSC2489 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 5 mM DTT (final concentration)  for 1 hour to induce ER stress.


title: ΔNCU02724_DTTAES_DC_PE

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain ΔNCU02724 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 5 mM DTT (final concentration)  for 1 hour to induce ER stress.


title: NCU02413_NC_DC_PE

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain ΔNCU02413 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour.


title: ΔNCU02724_NC_DC_PE

treatment_protocol: Paired-end (PE) library constructed based on direct culture (DC): The conidia of WT strain ΔNCU02724 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour.


title: ΔHac1_NC_TC_SE

treatment_protocol: Single-end (SE) library constructed based on transfer culture (TC): The conidia of Δhac-1 grown in minimal medium  for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour. All medium plus histidine.


title: FGSC9720_DTTAES_TC_SE

treatment_protocol: Single-end (SE) library constructed based on  transfer culture(TC): The conidia of FGSC9720 grown in minimal medium  for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture  treated with 5 mM DTT (final concentration) for 1 hour to induce ER stress. All medium plus histidine.


title: FGSC9720_NC_TC_SE

treatment_protocol: Single-end (SE) library constructed based on transfer culture (TC): The conidia of FGSC9720 grown in minimal medium  for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour. All medium plus histidine.


title: telencephalic Ttr::RFP+ choroid plexus epithelial cells, replicate 1


title: ΔIre1_DTTAES_TC_SE

treatment_protocol: Single-end (SE) library constructed based on transfer culture (TC): The conidia of Δire-1 grown in minimal medium for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture treated with 5 mM DTT (final concentration) for 1 hour to induce ER stress.


title: telencephalic choroid plexus, replicate 1


title: WT_DTTAES_DC_SE

treatment_protocol: Single-end (SE) library constructed based on direct culture (DC): The conidia of WT strain FGSC2489 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 5 mM DTT (final concentration)  for 1 hour to induce ER stress.


title: MTA3

value: MTA3 (upstate）


title: ΔHac1_DTTAES_TC_SE

treatment_protocol: Single-end (SE) library constructed based on transfer culture (TC): The conidia of Δhac-1 grown in minimal medium  for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture  treated with 5 mM DTT (final concentration) for 1 hour to induce ER stress. All medium plus histidine.


title: WT_TMMES_DC_SE

treatment_protocol: Single-end (SE) library constructed based on direct culture (DC): The conidia of WT strain FGSC2489 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 5 μg/ml TM (final concentration) for 1 hour to induce ER stress.

value: TM (5ug/ml)


title: WT_TMAES_DC_SE

treatment_protocol: Single-end (SE) library constructed based on direct culture (DC): The conidia of WT strain FGSC2489 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 40 μg/ml  (final concentration) for 1 hour to induce ER stress.

value: TM (40ug/ml)


title: WT_NC_DC_SE

treatment_protocol: Single-end (SE) library constructed based on direct culture (DC): The conidia of WT strain FGSC2489 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with corresponding amount of H20  (no chemical, NC) for ER stress inducing agents for 1 hour.


title: WT_DTTMES_DC_SE

treatment_protocol: Single-end (SE) library constructed based on direct culture (DC): The conidia of WT strain FGSC2489 were inoculated in Avicel medium and grown for 36 hours, then the culture treated with 0.1 mM DTT  (final concentration) for 1 hour to induce ER stress.

value: DTT (0.1mM)


title: ΔIre1_NC_TC_SE

treatment_protocol: Single-end (SE) library constructed based on transfer culture (TC): The conidia of Δire-1 grown in minimal medium for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour .


title: WT_NC_TC_SE

treatment_protocol: Single-end (SE) library constructed based on transfer culture (TC): The conidia of WT strain  FGSC2489 grown in minimal medium for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture treated with corresponding amount of H20 (no chemical, NC) for ER stress inducing agents for 1 hour .


title: Hela_digest_LMNB1

status: Public on Mar 24 2015

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Processed file created with EDD using Hela_digest_Input.fastq.gz as input in addition to the raw file "Hela_digest_LMNB1.fastq.gz" as IP

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth by downsampling the deeper sequenced experiment using picard DownsampleSam
Peak calling was done using EDD version 1.1 ; Hela_digest_Input.fastq.gz was used as input file for the "Hela_digest_LMNB1" sample.
Genome_build: HG19
Supplementary_files_format_and_content: bed

source_name: Hela

growth_protocol: Cells were cultured in MEM containing Glutamax (Gibco), 1% non-essential amino acids, 10% fetal calf serum and 1% penicillin/streptomycin.

extract_protocol:
Sonication: Cells (10e7 per ChIP) were cross-linked in suspension for 10 min in PBS containing 1% formaldehyde before quenching with 1.25 mM glycine. Cells were lysed for 30 min at 4oC on a rotator in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 1 mM PMSF, 1x protease inhibitor cocktail) adjusted to 1% SDS, and sonicated for 3 times 15 min in a Bioruptor (Diagenode) with 30 sec ON/OFF at high power to generate chromatin fragments of ~200-400 base pairs (bp). After sedimentation, chromatin (supernatant from 107 cell-equivalents) was diluted 10 times in RIPA buffer without SDS, and incubated on a rotator overnight at 4oC with 50 µg anti-lamin A/C antibody (Santa Cruz sc-7292) pre-coupled to magnetic Dynabeads Protein G (Invitrogen). An irrelevant mouse IgG was used as control. ChIP material was collected and washed 3 times in 1 ml of ice-cold RIPA buffer without protease inhibitors. The crosslink was reversed and DNA eluted for 6 h on a shaker at 37oC in elution buffer (50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 1% SDS) containing 0.5 µg/ml RNase A and 2 µg/ml Proteinase K). DNA was purified as described, processed for library preparation.
Chromatin preparation by micrococcal nuclease (MNase) digestion: For chromatin preparation by MNase, cells were fixed with 1% formaldehyde for 10 min, washed and formaldehyde quenched with 125 mM glycine for 5 min. After a wash in PBS, cells were scrapped in cold PBS containing 0.5 mM PMSF, sedimented and suspended in hypotonic buffer (10 mM Tris pH 7.5, 5 mM NaCl, 1.5 mM MgCl2, 0.5 mM DTT, 0.5 mM PMSF, protease inhibitors) for 30 min on ice before Dounce homogenization (50 strokes). MgCl2 was adjusted to 5 mM and NP-40 added to 0.1%. The lysate was kept on ice for 10 min before centrifugation at 2400 g for 10 min. The pellet was resuspended in MNase buffer (20 mM Tris pH 7.5, 15 mM NaCl, 1 mM CaCl2) at 25x106 cells/ml and pre-incubated at 37oC for 5 min before adding 0.37 U MNase (Sigma; N5386) per 106 cells. Incubation was at 37°C for 5 min and digestion stopped with 10 mM EDTA on ice for 10 min. Samples were diluted to 8x10E6 cells/ml with lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS, 0.5 mM PMSF and 1x protease inhibitors). Release of digested chromatin and lamins was facilitated by pulse-sonication with a 3 mm probe for 6 times 10 sec (1 sec on/off) at 20% amplitude with cooling on ice between each round (see Results). Samples were centrifuged at 10,000 g for 10 min at 4°C and the supernatants (chromatin fraction) collected.  Chromatin was then diluted 5x in NP-40 buffer (20 mM Tris pH 8.0, 5 mM EDTA, 150 mM NaCl, 1% NP-40, 1x protease inhibitors) without SDS to decrease SDS concentration to 0.1%. Chromatin was pre-cleared for 1 h at 4oC with Protein A/G agarose beads (Santa Cruz sc-2003) and incubated overnight at 4oC with the same anti-lamin A/C antibody as above (6 µg for 6x106 cells) or with anti-lamin B1 antibodies (Abcam ab16048; 3 µg for 6x10E6 cells). Immune complexes were collected using Protein A/G agarose beads for 2 h on a rotator at 4°C, washed 6x 5 min on a rotator at 4°C as follows: once in 20 mM Tris pH 8.0, 5 mM EDTA, 150 mM NaCl, 1% NP-40, 0.1% SDS, protease inhibitors; twice in 20 mM Tris pH 8.0, 5 mM EDTA, 500 mM NaCl, 1% NP-40, 0.1% SDS, protease inhibitors; twice in 10 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% deoxycholate, protease inhibitors; and once in TE buffer. Note that the NaCl- and LiCl-based washes used here are recommended in ChIP protocols using agarose beads. Crosslink was reversed and DNA was eluted and purified as above. Library preparation and sequencing were done as above.
The sequencing library was prepared according to the Illumina protocol for the HSeq2500 at the Norwegian Sequencing Center.

treatment_protocol: Cells were cultured as described under growth protocol, to confluency.

tag: passages

tag: chip-antibody

value: Abcam ab16048


title: Hela_digest_Input

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth by downsampling the deeper sequenced experiment using picard DownsampleSam
Peak calling was done using EDD version 1.1
Genome_build: HG19
Supplementary_files_format_and_content: bed


title: GATA3

treatment_protocol: For a ChIP experiment, we routinely used approximately 1 x 10^8 cells from 5-6, 150 mm diameter cell culture plates.

value: GATA3 (sigma)


title: Hela_digest_LMNA

description: Processed file created with EDD using Hela_digest_Input.fastq.gz as input in addition to the raw file in this line as IP

value: Santa Cruz sc-7292


title: Sample_3141: C57BL/6J Control

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

institute: University of Geneva

description: Sperm from C57BL/6J Control mice

data_processing:
Sequences were aligned with Bowtie v0.12.7 on UCSC mm10 reference genome (parameters -a -S -X600 -n1 -m1 -p8)
Resulting BAM files were processed with the method summarizeOverlaps() from Bioconductor package GenomicAlignment in order to count the number of read in the promoters of each gene. We make use of the parameters ignore.strand=TRUE,inter.feature=FALSE,singleEnd=FALSE,fragments=FALSE,param=ScanBamParam(flag=scanBamFlag(isProperPair=TRUE)); and implement a custom mode that remove duplicated read-pairs and filter fragments that do not overlap a CpG site before calling the standard Union() mode. The genes annotations are taken from Bioconductor package Mus.musculus v1.1.2, and promoters are defined as the region spanning 2kb upstream and 200bp downstream of the start of the gene.
Consider the counts returned by summarizeOverlaps(), and filter-out promoters if less than 2 samples have a count >=3
Normalize the counts with the RLE method implemented in Bioconductor package EdgeR, and previously fill the object library size with the number of mapped read.
Compute p-values, FDR, with GLM method of the EdgeR package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including the average estimate of promoters methylation accross the quintuplicates for each gene, and the result of the statistical tests checking for differentially methylated promoters

source_name: Sperm

growth_protocol: Two-month-old female mice are naturally mated with male. Females with a copulation plug the next morning are separated in two groups.

extract_protocol:
The mouse vas deferens and epididymis is dissected out, put onto a Petri dish with a droplet of Phosphate-Buffered Saline (PBS), and scored with a razor blade into small pieces to allow sperm to diffuse into the medium. The latter is then transferred into an Eppendorf tube and the fragments were allowed to sediment during 30 min at 37°C. The supernatant is carefully transferred to another tube and this procedure is repeated 3 times. The final supernatant is carefully removed and centrifuged at 6’000 x g for 3 minutes to pellet the sperm. DNA extraction from sperm cells is performed with the QIAamp DNA Micro kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
DNA was fragmented into ~200bp with Covaris S2, subjected to MethylCap kit (Diagenode, Seraing, Belgium) before libraries amplification for multiplex sequencing following an adapted version of ChIP-seq protocol by NXT-DX.

treatment_protocol: Bis(2-ethylhexyl)phthalate (Sigma-Aldrich, St. Louis, USA) diluted in corn oil (Sigma-Aldrich, St. Louis, USA) is administered orally in doses of 300 mg/kg/day for the first group from day 9 to 19 of pregnancy. The second group consists in control mice that receive the vehicle (corn oil) only from days 9 to 19 of pregnancy.  The male offspring of the treated females are sacrificed at 8 weeks of age by cervical dislocation.

value: sperm

tag: strain

value: 8 weeks

tag: treatment

value: Control


title: Sample_3140: C57BL/6J Control

description: Sperm from C57BL/6J Control mice


title: Sample_3135: FVB/N Control

description: Sperm from FVB/N Control mice

value: FVB/N


title: Sample_3136: FVB/N Control

description: Sperm from FVB/N Control mice


title: WT_DTTAES_TC_SE

treatment_protocol: Single-end (SE) library constructed based on transfer culture (TC): The conidia of WT strain  FGSC2489 grown in minimal medium for 16 hours then shift to Avicel medium for another 4 hours for cellulase induction, finally the culture treated with 5 mM DTT (final concentration) for 1 hour to induce ER stress.


title: Sample_3139: C57BL/6J Control

description: Sperm from C57BL/6J Control mice


title: Sample_3137: C57BL/6J Control

description: Sperm from C57BL/6J Control mice


title: Hela_sonic_LMNA

description: Processed file created with EDD using Hela_sonic_Input.fastq.gz as input in addition to the raw file in this line as IP


title: Sample_2180: C57BL/6J DEHP300mg/kg/day

description: Sperm from C57BL/6J mice whose mother is treated with 300mg/kg/day of DEHP from gestation day 9 to 19

value: DEHP 300mg/kg/day


title: Sample_3134: FVB/N Control

description: Sperm from FVB/N Control mice


title: Sample_3133: FVB/N Control

description: Sperm from FVB/N Control mice


title: Sample_2178: FVB/N DEHP300mg/kg/day

description: Sperm from FVB/N mice whose mother is treated with 300mg/kg/day of DEHP from gestation day 9 to 19


title: Sample_2177: FVB/N DEHP300mg/kg/day


title: Sample_2172: C57BL/6J DEHP300mg/kg/day


title: Sample_2173: C57BL/6J DEHP300mg/kg/day


title: Sample_3132: FVB/N Control

description: Sperm from FVB/N Control mice


title: Sample_2179: C57BL/6J DEHP300mg/kg/day


title: Sample_2176: FVB/N DEHP300mg/kg/day


title: Sample_2170: FVB/N DEHP300mg/kg/day


title: Sample_2171: C57BL/6J DEHP300mg/kg/day


title: E14.5_liver_Rlf_mutant_RNA-Seq_rep2

city: Bundoora

first: Harald

last: Oey

state: Vic

address: Kingsbury Drive

country: Australia

institute: La Trobe University

data_processing:
reads were mapped to the mouse genome with Tophat using the parametres  -I 100000 --no-coverage-search --read-mismatches 2 --library-type fr-unstranded
Transcript read counts (obtained from Ensembl, version 67) were extracted with the script htseq-count using the options -s no -m intersection-strict
Differentially expressed genes were identified using DeSeq
Genome_build: mm9
Supplementary_files_format_and_content: Transcript read counts

source_name: E14.5 liver

extract_protocol:
Tissues were homogenized in Buffer RLT Plus (Qiagen) and RNA extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
Libraries were prepared and sequenced by the Australian Genome Research Facility (AGRF) using the Illumina TruSeq protocol from polyA-selected RNA

value: FVB

value: liver

tag: genotype/variation

value: Rlf mutant

tag: gender

value: Male


title: E14.5_liver_Rlf_mutant_RNA-Seq_rep1


title: E14.5_liver_Rlf_mutant_RNA-Seq_rep3

value: Female


title: Hela_sonic_Input


title: E14.5_liver_wildtype_RNA-Seq_rep3

value: wildtype


title: E14.5_liver_wildtype_RNA-Seq_rep2


title: E14.5_liver_wildtype_RNA-Seq_rep1


title: Sample_3138: C57BL/6J Control

description: Sperm from C57BL/6J Control mice


title: MommeD28/MommeD28 mutant E18.5 liver rep1

data_processing:
3' ends were trimmed for low quality bases using trim_seq with the settings (www.biopieces.org)
Reads were mapped to the mouse genome (build mm9)  using Bismark and Bowtie2 with the options -N 1 -D 30
PCR duplicates were removed from mapped reads using deduplicate_bismark_alignment_output.pl
Methylation values extracted using bismark_methylation_extractor  with the setttings --ignore_r2 2
CpG methylation values were finally merged into a single value per CpG
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph showing %mCG. Additionally, columns with counts for unconverted Cs and converted Cs are included.

source_name: E18.5 liver rep1

extract_protocol:
Qiagen AllPrep
Illumina

value: MommeD28/MommeD28 mutant


title: MommeD28/MommeD28 mutant E18.5 liver rep2

source_name: E18.5 liver rep2


title: Wildtype E18.5 liver rep2

value: Wildtype


title: MommeD28/MommeD28 mutant E14.5 liver rep2

source_name: E14.5 liver rep2


title: Wildtype E18.5 liver rep1


title: Wildtype E14.5 liver rep2


title: MommeD28/MommeD28 mutant E14.5 liver rep1

source_name: E14.5 liver rep1


title: MommeD28/MommeD28 mutant E10.5 embryo rep1

source_name: E10.5 embryo rep1


title: Wildtype E14.5 liver rep1


title: Wildtype E10.5 embryo rep1


title: Wildtype E10.5 embryo rep2

source_name: E10.5 embryo rep2


title: MommeD28/MommeD28 mutant E10.5 embryo rep2


title: H3K4me1 ChIPseq - homo2

data_processing:
Libraries were subsampled to equal read counts and mapped with BWA using default paramaters.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle plot showing density of mapped ChIP-seq reads in 32 bp windows

source_name: E14.5 Liver

extract_protocol: Single end

value: Liver

value: Rlf homozygous mutant


title: Splenic dendritic cell +IL10 +LPS replicate 1

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: splenic dendritic cells, purified using BDIMag Mouse Dendritic Cell Enrichment Set –DM

data_processing:
rsem v1.2.1/bowtie v0.12.9 was used to align to the ensembl transcriptome (mm9, v67) using the settings '--seed-length 28 --bowtie-m 50 --phred64-quals'
transcripts with more than 20 sequence tags in more than 4 conditions were kept for further analysis
mapping tag counts were GC normalized using EDASeq v1.8.0
Genome_build: mm9
Supplementary_files_format_and_content: tab delimeted text file containing ensembl transcript accession, gene name and normalized abundance estimates for each transcript

source_name: spleen-purified dendritic cells

extract_protocol:
TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were treated with 100ng/ml IL-10 for 4 hours and 100ng/ml LPS for a further 4 hours.

value: IL10, LPS


title: Splenic dendritic cell -IL10 -LPS replicate 2


title: Splenic dendritic cell +IL10 -LPS replicate 2


title: Splenic dendritic cell +IL10 +LPS replicate 2


title: Splenic dendritic cell +IL10 -LPS replicate 1


title: naïve CD4+ T cells anti-CD3/28 treated 24 hours

description: naïve CD4+ T cells, purified using MACS naïve CD4+ enrichment kit

source_name: CD4+ naïve T cells

value: anti-CD3, anti-CD28


title: H3K4me1 ChIPseq - homo1


title: H3K4me1 ChIPseq - wild1


title: Splenic dendritic cell -IL10 -LPS replicate 1


title: Splenic dendritic cell -IL10 +LPS replicate 1

value: LPS


title: Neutrophil +IL10 +LPS replicate 1

description: Bone marrow neutrophils, derived according to Boxio et al., 2004; Journal of leukocyte biology

source_name: Bone marrow neutrophil


title: Neutrophil +IL10 +LPS replicate 2


title: Sample_2169: FVB/N DEHP300mg/kg/day

value: sperm

value: 8 weeks


title: Neutrophil +IL10 -LPS replicate 2


title: H3K4me1 ChIPseq - wild2


title: Neutrophil +IL10 -LPS replicate 1


title: Neutrophil -IL10 +LPS replicate 1


title: Neutrophil -IL10 +LPS replicate 2


title: Neutrophil -IL10 -LPS replicate 2


title: P7Un

first: David

middle: P.

last: Corey

state: MA

address: 220 longwood avenue

department: Neurobiology Department

institute: Harvard Medical School

description: RNA-seq of 3' enriched polyA mRNA

data_processing:
Illumina Casava1.7.0 software used for base calling.
The sequence quality was assessed using the open-source FastQC program.
Quality-filtered reads were mapped against NCBI build 37/mm9 mouse genome assembly at DNAnexus (dnanexus.com). Multiple sequencing runs of the same sample library were combined.
Assignment of non-unique alignments were weighed by the posterior probability of their mapping .The read counts of 20207 RefSeq mouse genes were calculated using the 3SEQ transcriptome based quantification analysis pipeline.
Custom scripts were developed to generate raw read-counts tables.
The data were summarized, normalized, and statistically tested for differential gene expression for each gene under various comparison schemes using the DESeq package in R/BioConductor
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene name, genomic coordinates, and normalized 3'-tag abundance measurements for each gene in each sample

molecule: polyA RNA

source_name: Utricle sensory epithelia

extract_protocol:
Utricles were dissected from the temporal bone and (at postnatal stages) incubated for 2 minutes in protease XXIV (0.1 mg/ml) to remove the otoconia. Cochleas were dissected and freed from the spiral ganglion and Reisner’s membrane to expose the sensory epithelium. The organs were collected in DMEM (LifeTechnologies, )+5% fetal bovine serum (FBS) on ice. The cells were dissociated by incubating the organs in 1 mg/ml dispase (Gibco) and 1 mg/ml collagenase I (Worthington) in 100 µl for about 10-12 utricles or 200 µl for 10 to 12 cochleas for 30 to 45 minutes (depending on the developmental stage) at 37°C and triturating with a pipette. The dissociation was controlled visually with an inverted microscope. Dissociation buffer (Gibco 13151-014)-5% FBS was added to complete the dissociation and the samples then placed on ice. The dissociated tissues were filtered through a 40 µm cell strainer to eliminate clumps prior to sorting. Cells were sorted on a BD FACS Aria II cell sorter using a 100 µm nozzle and low pressure. Hair cells were collected using the brightest GFP signal and other cell types were collected using the lowest fluorescence signal. Cells were collected directly into a lysis buffer from the RNeasy Plus Micro kit (Qiagen). Total RNA extraction was performed using the manufacturer's recommendation and the quality was assessed with Agilent 2100 Bioanalyzer picochips.
mRNA was amplified using the Ovation® 3'-DGE System (Nugen). 3’-enriched transcriptome tags were converted into non-directional Illumina sequencing libraries.

treatment_protocol: A transgenic mouse strain expressing eGFP under the control of the hair-cell specific Pou4f3 promoter was used.  Sensory epithelia were dissected, enzymatically dissociated and FACS-purified

tag: tissue type

value: Utricle sensory epithelia

value: surrounding cells

value: postnatal day 7


title: P7Up

description: RNA-seq of 3' enriched polyA mRNA

value: hair cells

tag: age


title: Splenic dendritic cell -IL10 +LPS replicate 2


title: P7Cp

description: RNA-seq of 3' enriched polyA mRNA

source_name: Cochlea sensory epithelia

value: Cochlea sensory epithelia


title: P7Cn

description: RNA-seq of 3' enriched polyA mRNA


title: Mast cell +IL10 +LPS replicate 2

description: Bone marrow-derived mast cells, derived according to Jensen et al., 2006; Curr Protoc Immunol

source_name: Bone marrow-derived mast cell


title: P4Up

description: RNA-seq of 3' enriched polyA mRNA

value: postnatal day 4


title: Mast cell +IL10 +LPS replicate 1


title: P4Un

description: RNA-seq of 3' enriched polyA mRNA


title: Mast cell +IL10 -LPS replicate 2


title: Mast cell -IL10 +LPS replicate 2


title: Mast cell -IL10 -LPS replicate 2


title: P4Cp

description: RNA-seq of 3' enriched polyA mRNA


title: P4Cn

description: RNA-seq of 3' enriched polyA mRNA


title: P0Up-1

description:
RNA-seq of 3' enriched polyA mRNA
paired-end experiment

value: postnatal day 0


title: P0Un

description: RNA-seq of 3' enriched polyA mRNA


title: P0Up-2

description:
RNA-seq of 3' enriched polyA mRNA
single-end experiment


title: Mast cell -IL10 -LPS replicate 1


title: PEC macrophage +IL10 -LPS replicate 2

description: Peritoneal macrophages, isolated by peritoneal lavage and cells allowed to adhere to plastic culture ware dishes overnight

source_name: Peritoneal exudate cells (adherent cells)


title: PEC macrophage +IL10 +LPS replicate 2


title: P0Cp-1


title: P0Cn

description: RNA-seq of 3' enriched polyA mRNA


title: E16Up

description: RNA-seq of 3' enriched polyA mRNA

value: embryonic day 16


title: PEC macrophage -IL10 +LPS replicate 2


title: E16Un

description: RNA-seq of 3' enriched polyA mRNA


title: E16Cp

description: RNA-seq of 3' enriched polyA mRNA


title: PEC macrophage -IL10 +LPS replicate 1


title: P0Cp-2


title: NIDF-AML-5hmC rep1

source_name: IDH2/R140Q, NPMc, DNMT3A/R882H and FLT3-ITD-induced AML cells

treatment_protocol: Genome were purified from BM cells by using Nucleospin Tissue (Takara).

tag: tissue

value: bone marrow cells


title: PEC macrophage +IL10 +LPS replicate 1


title: Mast cell +IL10 -LPS replicate 1


title: PEC macrophage -IL10 -LPS replicate 2


title: PEC macrophage +IL10 -LPS replicate 1

description:
Peritoneal macrophages, isolated by peritoneal lavage and cells allowed to adhere to plastic culture ware dishes overnight
Re-analysis of GSM782668


title: Eosinophils -IL-10 +LPS replicate 2

description: Bone-marrow derived eosinophils, derived according to Dyer et al., 2008; J Immunol

source_name: Bone marrow-derived Eosinophils


title: RNAseq DE Sample 5: ERCC no1

city: Paris

first: Giovanni

last: Bussotti

address: 25-28 Rue du Dr Roux

country: France

institute: Institute Pasteur

description: PBMC RNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Before mapping FastQC was utilized to confirm sequence quality. Reads were trimmed with the Trim Galore Cutadapt11 wrapper using the –paired option.
For K562 and PBMC ERCC capture, sequenced reads (.fastq files) were aligned to the human genome using Tophat2 12 with the firststrand library type option selected. A human Bowtie213 index containing the ERCC controls was utilized for Tophat2 mapping, along with a transcriptome index.
For lncRNA capture from tissues and cell lines, sequenced reads (.fastq files) were aligned to the human genome using STAR 14. A reference annotation from GENCODE V19 was supplied during alignment. A splice junction library file was then derived from alignments and used for a second-round alignment solely using TopHat2 12.
To reduce memory requirements and improve runtimes the lncRNA cell line capture samples were preprocessed with trinity’s read normalization 17 release 2013-02-25 with parameter --max_cov 30. Reads from separated sequencing runs and lanes were mapped to the human genome (GRCh37, ENSEMBL 74) considering GENCODE version 19 reference annotations using STAR 14 version 2.3.1z with parameters --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout. The resulting sam files were processed to remove the soft-clipping. Transcriptome assemblies were generated using cufflinks version 2.1.1 masking rRNA genes and providing the parameters -u --library-type fr-firststrand -b. The comprehensive transcriptome assembly (merged_transcript_assembly.gtf) was generated merging the individual assemblies with cuffmerge version 2.1.1, and selecting with bedtools intersect v2.19.1 the transcript overlapping the capture probes. The gene expression was estimated by merging for each tissue the individual mapping files with samtool version 0.1.19-44428cd. Then the gene counts for each tissue (norm.counts.tsv) were estimated by HTSeq (version 0.6.1) and normalized by DESeq2 (version 1.2.10)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with spike-in ERCC counts

source_name: PBMC

growth_protocol: Human K562, MCF-7 and SK-N-SH cells were purchased from Cellbank. All cell lines were cultured at 37°C, 5% C02 with ten percent fetal bovine serum and penicillin/streptomycin. K562 and HeLa cells were cultured in RPMI and DMEM respectively, MCF-7 and SK-N-SH cells were cultured in MEM. Briefly, RNA was extracted by TRIzol, DNase treated with Turbo™ DNase (Life Technologies), confirmed DNA-free4 and its integrity confirm by Agilent 2100 Bioanalyzer (Agilent Technologies). 5 μg quantities of RNA were ribodepleted with Ribo-Zero™ (Epicentre). The Ambion® FirstChoice® Human Total RNA Survey Panel (Life technologies) was utilized to examine 20 human tissues. 5 μg quantities of RNA were ribodepleted with Ribo-Zero™ (Epicentre) and successful rRNA removal validated with Agilent 2100 Bioanalyzer (Agilent Technologies). Collection and RNA extraction from peripheral blood mononuclear cells (PBMCs) Whole blood was collected from individuals (Princess Alexandra Hospital REC approval 2005/221). PMBCs were purified by a ficoll gradient and RNA extracted by TRIzol. Purified RNA was prepared for Capture as per cell line RNA.

extract_protocol: Capture sequencing was performed by combining and modifying the NimbleGen SeqCap EZ Library SR User’s Guide V3.0 and the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery v3.2. RNA sequencing libraries of ribodepleted total RNA from three K562 biological replicates were created using the TruSeq® Stranded mRNA Sample Preparation Kit (Illumina). Different index adaptors (4,6,12) were added to each K562 biological replicate. Library input consisted of ribodepleted RNA from 5 μg original total RNA after quality checking. ERCC RNA Spike-In Control mix 1 (Invitrogen) was added to ribodepleted RNA to give a final ERCC concentration of 1% (replicate 1 and 2) and 1.08% (replicate 3). Library preparation was begun at the fragmentation step by the addition of 9 μl EPH buffer and the standard protocol followed until “Enrich DNA Fragments”. The 20 μl obtained at the end of the “Ligate Adaptors” step was increased to 21 μl with resuspension buffer and mixed well. One microliter of this solution was added to 19 μl resuspension buffer in a new 0.3ml PCR plate and mixed. This new plate was utilised for the “Enrich DNA Fragments” step to create amplified test libraries to guide PreCapture LMPCR with the remaining 20 μl. Precapture LMPCR and QIAquick PCR Purification Kit (Qiagen) were performed as described by the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. To test LMPCR yields K562 biological replicate 3 libraries were amplified for 8, 9 or 10 cycles, quantified on the bioanalyzer and then pooled. K562 biological replicate 1 and 2 libraries were thus amplified for 9 cycles and the yield quantified by bioanalyzer. Capture hybridization was modified from the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery V3.2. The NimbleGen Hybridization System was set to 42°C and allowed 3 h to equilibrate. Equal nanograms of library from each K562 biological replicate were pooled, some of pooled library was allocated for pre-capture sequencing and 1ug of the pooled library utilized for capture. The library for capture was mixed with 300 µg human Cot-1 DNA (Invitrogen) and 3.34 µl 100 μm TS-INV-HE (hybridisation enhancing) Index Oligos (IDT) to each index adaptor plus 1 µl 1000 μm TS-HE Universal Oligo 1 (IDT) in a 1.5 ml tube. Lid of tube was pierced with an 18 gauge needle and the sample dried at 60 °C in a vacuum concentrator. Once dry the tube was given a new lid to prevent contamination through the needle hole. Library/Cot/Oligo mix was resuspended in 11.2 µl of nuclease and nucleic acid free water, vortexed for 10 s and centrifuged at max speed for 10 s. Sample was solubilised at 70 °C for 10 m before repeating vortexing and centrifugation. Nimblegen 2 x SC Hybridization Buffer (18.5 µl) and SC Hybridization Component A (7.3 µl) were added and vortexing and centrifugation repeated. Sample was denatured at 95°C for 10 m. During this time the “Prepare Mixers” procedure from the NimbleGen Arrays User’s Guide was performed with the omission of the compressed gas step. After denaturation samples was vortexed for 10 s, centrifuged at max speed for 10 s and incubated at 42°C until ready to load onto the NimbleGen Hybridization system. The ‘Load and Hybridize Samples’ procedure from the NimbleGen Arrays User’s Guide was performed to begin array hybridization. Hybridization was conducted for ~3 days. The NimbleGen Arrays User’s Guide protocol was followed to prepare the elution chamber, disassemble, wash and elute the captured DNA from the microarray, with the following modifications. Gasket and elution chamber was setup in a DNA-free laminar flowhood. All washes were conducted with 50 ml buffer in 50 ml falcon tubes. Minelute purification (Qiagen) was conducted using a microfuge. Captured DNA was recovered with two 30 µl elutions from a Minelute column and the final volume adjusted to 60 µl. Post-capture LMPCR and cleanup was performed similar to the NimbleGen SeqCap EZ Library SR User’s Guide V3.0, with the following modifications. LMPCR was run using 5x Phusion buffer for 17 cycles. Each PCR contained 70 µl of master mix and 30 µl of captured DNA. Quantity and quality of amplified captured DNA was determined by bioanalyzer. Enrichment of captured transcripts was measured by qPCR using SYBR Green PCR Master Mix and real time cyclers (Applied Biosystems). Enrichment was determined by the ratio of transcript abundance between the pre and post capture samples using equal nanograms of each. Enrichment was determined for three Nimblegen capture controls and 3 sequences captured specifically by the branchpoint array. Two transcripts not targeted by the capture array were also tested to examine the specificity of capture. Concentrations and volumes were as per the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. Precapture and post capture samples (3 K562 biological replicates) were each sequenced on a single lane of an Illumina® HiSeq.

tag: cell type

value: PBMC


title: RNAseq DE Sample 1: ERCC no1

description: PBMC RNAseq


title: RNAseq DE Sample 4: ERCC no1

description: PBMC RNAseq


title: RNAseq DE Sample 2: ERCC no1

description: PBMC RNAseq


title: RNAseq DE Sample 3: ERCC no1

description: PBMC RNAseq


title: RNAseq DE Sample 4: ERCC no2

description: PBMC RNAseq


title: Eosinophils -IL-10 +LPS replicate 1


title: Mast cell -IL10 +LPS replicate 1


title: RNAseq DE Sample 1: ERCC no2

description: PBMC RNAseq


title: Technical Replicate Capture B rep3

description: K562 CaptureSeq

data_processing:
Library strategy: CaptureSeq
Illumina Casava1.7 software used for basecalling.
Before mapping FastQC was utilized to confirm sequence quality. Reads were trimmed with the Trim Galore Cutadapt11 wrapper using the –paired option.
For K562 and PBMC ERCC capture, sequenced reads (.fastq files) were aligned to the human genome using Tophat2 12 with the firststrand library type option selected. A human Bowtie213 index containing the ERCC controls was utilized for Tophat2 mapping, along with a transcriptome index.
For lncRNA capture from tissues and cell lines, sequenced reads (.fastq files) were aligned to the human genome using STAR 14. A reference annotation from GENCODE V19 was supplied during alignment. A splice junction library file was then derived from alignments and used for a second-round alignment solely using TopHat2 12.
To reduce memory requirements and improve runtimes the lncRNA cell line capture samples were preprocessed with trinity’s read normalization 17 release 2013-02-25 with parameter --max_cov 30. Reads from separated sequencing runs and lanes were mapped to the human genome (GRCh37, ENSEMBL 74) considering GENCODE version 19 reference annotations using STAR 14 version 2.3.1z with parameters --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout. The resulting sam files were processed to remove the soft-clipping. Transcriptome assemblies were generated using cufflinks version 2.1.1 masking rRNA genes and providing the parameters -u --library-type fr-firststrand -b. The comprehensive transcriptome assembly (merged_transcript_assembly.gtf) was generated merging the individual assemblies with cuffmerge version 2.1.1, and selecting with bedtools intersect v2.19.1 the transcript overlapping the capture probes. The gene expression was estimated by merging for each tissue the individual mapping files with samtool version 0.1.19-44428cd. Then the gene counts for each tissue (norm.counts.tsv) were estimated by HTSeq (version 0.6.1) and normalized by DESeq2 (version 1.2.10)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with spike-in ERCC counts

value: K562 cell line


title: Voyager Rep 1

city: East Lansing,

first: Carolina

last: Astudillo

state: MI

address: A494 PSSB 1066 Bogue St.

institute: Michigan State University

description: Genotype grown at sufficient Zn supply

data_processing:
The RNA sequence was received in FASTQ formatted files containing 75-bp paired-end reads. The file contained sequences and quality information about each sequence. The data were filtered using scripts from FASTX-Toolkit (FASTQ Quality Trimmer and FASTQ Quality Filter http://hannonlab.cshl.edu/fastx_toolkit/ ). FASTQ Quality Trimmer clipped the low quality ends with a quality threshold of 20 and removed the reads shorter than 64 bp. Subsequently, FASTQ Quality Filter script was used to remove low quality sequences with quality scores of 20 or less.
The P. vulgaris reference genome sequence v. 1.0 (DOE-JGI and USDA-NIFA and corresponding gene model annotation files were obtained directly from  http://www.phytozome.net).  A P. vulgaris genome index was built using Bowtie v. 0.12.7 [22].  Paired-end clean reads for each individual were aligned to the reference genome by TopHat v 1.4.1 [23] with the provided guidance of annotated gene models (GTF file)
The transcript profile and abundance estimation was carried out using Cufflinks v1.3.0 with default parameters [26].  The resulting alignment of RNA-seq reads to the common bean reference genome from TopHat was used into Cufflinks to assemble into transcripts [27].  Normalization, estimated abundance, and tests for differential expression between tissue samples were performed using the program Cuffdiff with default parameters.  The value of the test statistic used to compute significance of the observed change of the transcript abundance was measured in fragments per kilobase of transcript per million mapped reads (FPKM)
Genome_build: common bean reference genome
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample.

organism: Phaseolus vulgaris

source_name: Developing pods

extract_protocol:
Two pods per replication were ground to a fine powder with a mortar and pestle while completely frozen.  Liquid nitrogen was continuously added to ensure tissue remained frozen throughout the grinding process.  Total RNA was extracted from the samples using an RNA easy Plant kit (Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Voyager

tag: zn condition

value: Normal zinc concentration

value: 20 days after anthesis


title: Voyager Rep 2

description: Genotype grown at sufficient Zn supply


title: PEC macrophage -IL10 -LPS replicate 1

description:
Peritoneal macrophages, isolated by peritoneal lavage and cells allowed to adhere to plastic culture ware dishes overnight
Re-analysis of GSM782669


title: Albion Rep 1

description: Genotype grown at sufficient Zn supply

value: Albion

value: Low zinc concentration


title: NIW_0.5-1.5_MPI_3

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

data_processing:
Illumina Casava 1.9 software used for basecalling
Raw fastq files were generated for all 12 libraries for both lanes. Fastq files for each sample from both lanes (L001 and L002) were combined in one fastq file. This leads to a total of 12 fastq files for downstream analysis.
Quality control of fastq raw data was performed using Fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). As sequences showed overall high quality no filtering step was applied on the reads.
Sequences were aligned to the 12x grape genome (IGGP_12x, European Nucleotide Archive (ENA) accession number: GCA_000003745.2) using Tophat including Bowtie aligner with default parameters. Raw read counts for all annotated features were obtained with HTSeq (v0.5.4p5) and the script htseq-count using the default option 'union'. This mode calls reads as ambigous if they map to more than one gene and subsequently exclude them from counting for any feature/gene. If reads do not map to any feature/gene, the read was counted as no_feature.
Normalization of read counts was performed within the DESeq package (v1.10) by normalizing for effective library sizes using the function estimateSizeFactors and by estimating variance using the function estimateDispersions (with default option 'pooled'). This gives the normalized read count text file which was used as input to test for differential expression
For inference, a multifactoral design was chosen and two models were specified within DESeq: The full model regresses gene expression based on two factors, time (levels: 0 MPI and 0.5-1.5 MPI) and treatment (levels: Non-infected wounded (NIW) and infected wounded (IW). The reduced model regresses gene expression only on the factor time. For each gene, a generalized linear models (GLMs) was fitted according to the two models, and then compared in order to infer whether the additional specification of the factor treatment has significant effect on gene expression.
Genome_build: IGGP_12x
Supplementary_files_format_and_content: tab-delimited text files, which include raw and normalized read counts for each sample and gene as produced by HTSeq and DESeq, respectively.

organism: Vitis vinifera

growth_protocol: The experiment was conducted in the greenhouse on plants, which were propagated in 10 x 10 cm pots from green cuttings 12 months before inoculation. After inoculation, plants were arranged in a completely randomized design on the central bench of a greenhouse with lighting for 14 hours per day.

extract_protocol:
For each RNA extraction, frozen leaves from three plants were mixed and grinded to a fine powder using mortar and pistil under liquid nitrogen. Total RNA was isolated using a rapid cetyltrimethylammonium bromide (CTAB)-based extraction method with minor modifications (Gambino et al., 2008).  DNA was removed by RNase-Free DNase (Qiagen) digestion in solution and then purified using RNAeasy Mini Kit (Qiagen).  Primers for leucoanthocyanidin reductase 1 gene were used to check all RNA preparations for genomic DNA contamination (Bogs et al., 2005).  RNA quality was analyzed using Experion RNA StdSens Chips (BioRad) to verify intact ribosomal bands [rRNA ratio (25s/18s) = 1.8-2.0] and RNA Quality Indicator (RQI) values > 8. For 0 MPI samples, 2 ug of the extracted total RNA was used to make the library. For the mixed second time point (0.5-1.5 MPI) 0.66 ug of extracted RNA from 0.5 MPI, 1 MPI and 1.5 MPI were mixed to give a total of 2ug RNA which was used to make the library. RNA extraction and library preparation was performed on biological triplicates for each of the four treatment time combination (IW 0 MPI, IW 0.5-1.5 MPI, NIW 0 MPI, NIW 0.5-1.5 MPI) to give a total of 12 libraries for RNA-Seq.
RNA libraries for sequencing were prepared from 2ug of total RNA using a modified version of the Illumina TruSeq RNA Library Prep Protocol which is accessible at the website of the DNA Technologie Core, UC Davis (http://dnatech.genomecenter.ucdavis.edu/wp-content/uploads/2013/11/TruSeq_RNA_Sample_Prep_Sept2012.pdf). TruSeq Adapter used were AGTCAA (TruSeq Adapter, Index 13) for IW_0_MPI_1, AGTTCC (TruSeq Adapter, Index 14) for IW_0_MPI_2, ATGTCA (TruSeq Adapter, Index 15) for IW_0_MPI_3, CCGTCC  (TruSeq Adapter, Index 16) for IW_0.5-1.5_MPI_1, GTCCGC  (TruSeq Adapter, Index 18) for IW_0.5-1.5_MPI_2, GTGAAA  (TruSeq Adapter, Index 19) for IW_0.5-1.5_MPI_3, GTGGCC  (TruSeq Adapter, Index 20) for NIW_0_MPI_1, GTTTCG  (TruSeq Adapter, Index 21) for NIW_0_MPI_2, CGTACG  (TruSeq Adapter, Index 22) for NIW_0_MPI_3, GAGTGG  (TruSeq Adapter, Index 23) for NIW_0.5-1.5_MPI_1, ACTGAT  (TruSeq Adapter, Index 25) for NIW_0.5-1.5_MPI_2, ATTCCT (TruSeq Adapter, Index 27) for NIW_0.5-1.5_MPI_3. The 12 libraries were pooled, sequenced on two lanes of the same flow cell of a HiSeq2500 and de-multiplexed to produce 24 raw fastq files. TruSeq Adapter Index sequences are incorporated in the names of the raw fastq files.

treatment_protocol: For IW plants, 20 μl of a homogenized, 3-day liquid culture of N. parvum was pipetted into the wound in the woody part of the plant that was sealed with Vaseline and Parafilm (Travadon et al., 2013).  NIW plants were ‘mock-inoculated’ with 20 µl of sterile water. The third leaf of each plant, counted from the shoot tip, was collected with flame-sterilized forceps at 10 min. post inoculation, which served as the first sampling point (0 MPI) and also at subsequent time points (0.5 MPI, 1 MPI and 1.5 MPI). Leaf samples were immediately frozen in liquid Nitrogen, and then stored at -80°C for RNA extraction.

value: asymptomatic young leaf

tag: pathogen

value: Neofusicoccum parvum

tag: time post inoculation

value: mix of late time points:0.5 - 1.5 months post inoculation

value: Cabernet Sauvignan


title: Technical Replicate Capture A rep3

description: K562 CaptureSeq


title: E16Cn

description: RNA-seq of 3' enriched polyA mRNA

value: surrounding cells


title: Albion Rep 2

description: Genotype grown at sufficient Zn supply


title: Technical Replicate Capture A rep2

description: K562 CaptureSeq


title: Eosinophils -IL-10 -LPS replicate 1


title: Technical Replicate Capture A rep1

description: K562 CaptureSeq


title: Albion Rep 3

description: Genotype grown at sufficient Zn supply


title: NIW_0_MPI_3

value: early time point:10 minutes post inoculation


title: Technical Replicate Capture B rep1

description: K562 CaptureSeq


title: Eosinophils -IL-10 -LPS replicate 2


title: Matched RNAseq rep3

description: K562 RNAseq


title: NIW_0_MPI_2


title: Matched RNAseq rep2

description: K562 RNAseq


title: IW_0.5-1.5_MPI_3


title: Neutrophil -IL10 -LPS replicate 1


title: IW_0.5-1.5_MPI_2


title: NIW_0_MPI_1


title: Voyager Rep 3

description: Genotype grown at sufficient Zn supply


title: CaptureSeq DE Sample 5: ERCC no1

description: PBMC CaptureSeq


title: Technical Replicate Capture B rep2

description: K562 CaptureSeq


title: NIW_0.5-1.5_MPI_2


title: CaptureSeq DE Sample 4: ERCC no1

description: PBMC CaptureSeq


title: IW_0_MPI_3


title: IW_0_MPI_2


title: CaptureSeq DE Sample 3: ERCC no1

description: PBMC CaptureSeq


title: CaptureSeq DE Sample 2: ERCC no1

description: PBMC CaptureSeq


title: CaptureSeq DE Sample 1: ERCC no1

description: PBMC CaptureSeq


title: NIW_0.5-1.5_MPI_1


title: CaptureSeq DE Sample 3: ERCC no2

description: PBMC CaptureSeq


title: CaptureSeq DE Sample 4: ERCC no2

description: PBMC CaptureSeq


title: CaptureSeq DE Sample 2: ERCC no2

description: PBMC CaptureSeq


title: IW_0_MPI_1


title: CaptureSeq DE Sample 1: ERCC no2

description: PBMC CaptureSeq


title: CASP1 input control

city: Memphis

first: Steven

middle: William

last: Paugh

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences Department

institute: St. Jude Children's Research Hospital

data_processing:
Glucocorticoid receptor binding sites were identified using the MACS peak caller.
Genome_build: hg18
Supplementary_files_format_and_content: bed

source_name: Nalm6 CASP1 cells

extract_protocol:
Cells were cross-linked with formaldehyde (1% final concentration) for 10 minutes at room temperature and then incubated with glycine (0.125 M final concentration) for 5 minutes to stop the cross-linking reaction.  Cells were pelleted and washed with 1X PBS containing protease inhibitors (Roche Protease Inhibitor Cocktail Tablets, 11836153001) and stored at –80C prior to further experimentation.  Crosslinked cell pellets were resuspended in cold lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40 solution) containing protease inhibitors (Roche Protease Inhibitor Cocktail Tablets, 11836153001), and pelleted to isolate nuclei.  The pellet was resuspended in cold RIPA lysis buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS solution).  Sonication was performed using a Bioruptor sonication system (Diagenode).  Sonicated chromatin was added to Dynabeads (Invitrogen) coated with anti-glucocorticoid receptor antibodies (sc-1003) and incubated overnight at 4C.  The solution was washed with a LiCl wash solution (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40 and 1% sodium deoxycholate) at 4oC, and a final wash using 1X TE buffer.  Dynabeads were resuspended in an elution buffer (1% SDS and 0.1 M NaHCO3) and placed at 65C to reverse crosslinks.
DNA purified and a standard library preparation was performed prior to sequencing on an Illumina HiSeq 2000 sequencer.

tag: cell line

tag: chip antibody

value: input

value: CASP overexpressing


title: Matched RNAseq rep1

description: K562 RNAseq


title: CASP1 Replicate 2

value: anti-glucocorticoid receptor antibodies (sc-1003)


title: CASP1 Replicate 1


title: Wild type Replicate 2

source_name: Nalm6 vector control

value: wild type


title: Wild type input control


title: Wild type Replicate 1