title: Thymus rep 1 (Illumina HiSeq 2000)

description: barcode: GT


title: H3A_shBRG1_rep3

status: Public on Apr 02 2015

type: SRA

city: Illkirch

first: Patrick

last: Laurette

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

library_source: transcriptomic

data_processing:
Illumina Casava v1.8 software was used for basecalling.
Sequence reads were mapped onto the hg19 assembly of the human human using Tophat v1.4.1 and the bowtie v0.12.7 aligner.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file corresponding to abundance measurements (raw read counts for each ensembl gene id) for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Hermes 3A

extract_protocol:
Total RNA isolation from 501M or Hermes3A cells was performed according to standard procedure (Qiagen kit). 1,5 μg of RNA was reverse transcribed using a mix 1/1 of SuperScript II RNase H-reverse transcriptase (Invitrogen) and AMV retrotranscriptase (Roche) with 500 ng of oligodT22 primer, hexanucleotides or specific primers according to the manufacter’s instructions
Total RNA-seq libraries were prepared following the Illumina protocol with some modifications. Briefly, 2 µg of total RNA was hybridized with rRNA sequence-specific 5’biotin labeled oligonucleotide probes to selectively deplete ribosomal RNA. The rRNA/5’biotin labeled probe was removed from the sample with streptavidin-coated magnetic beads. (Ribominus Eukaryote kit for RNA-seq, #A10837-08, Invitrogen Corporation). The rRNA depleted RNAs were then fragmented using divalent cations at 95°C for 5 minutes and used to generate a reverse transcribed cDNA library. 100 ng of each DNA library was then denatured at 98°C for 2 minutes, incubated at 68°C for 5 hours and then incubated in the presence Duplex-Specific thermostable Nuclease enzyme (DSN, #EA001, Evrogen) for DSN normalization following the Illumina protocol. DSN treated libraries were purified using Agencourt AMPure XP beads, enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 6 cycles; 5 min at 72°C) and purified again using Agencourt AMPure XP beads.

tag: cell line

value: Hermes 3A

tag: cell type

value: melanocyte

tag: knockdown


title: siCtrl4

status: Public on Apr 01 2015

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

country: USA

institute: PTC Therapeutics

data_processing:
The details of the method was described previously (Hoque, et al., 2014). Briefly, the 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT). Reads were mapped to the mouse genome (mm9) using Bowtie2 (local mode). 5' four random nucleotides were removed before mapping using "-5 4" parameter in bowtie2. Reads with a mapping quality score (MAPQ) ≥10 were selected for further analysis. Reads with ≥2 non-genomic As after alignment were called polyA site supporting (PASS) reads.
All PASS reads mapped to the 3’-most exons of a gene were used to calculate the expression level of the gene, shown as the reads per million total PASS reads (RPM) value.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file containing information of gene symbol, pA coordinates, read number of pAs in different samples

organism: Mus musculus

source_name: siRNA control, batch 4

growth_protocol: C2C12 cells were maintained in Dulbecco's Modified Eagles Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Differentiation of C2C12 cells was induced by switching cell media to DMEM+ 2% horse serum (Sigma) when cells were ~100% confluent. All media were also supplemented with 100 units/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
For nuclear RNA extraction, cells collected by a scrapper were suspended in cell lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 0.5% NP40, 1 mM DTT), followed by vortexing for 10 sec and incubation on ice for 10 min. After centrifugation of the lysate at 500 x g for 5 min at 4oC, the pellet was re-suspended in the cell lysis buffer for nuclear RNA extraction. Both total and nuclear RNAs were extracted using Trizol (Invitrogen) according to manufacturer's protocol. RNA quality was analyzed in an Agilent Bioanalyzer using the RNA pico600 kit before processing for deep sequencing.
The 3’READS method used in this study was previously described (Hoque et al., 2014). Briefly, 25 μg of total RNA was used for each sample, and poly(A)+ RNA was selected using oligo d(T)25 magnetic beads (NEB), followed by on-bead fragmentation using RNase III (NEB). Poly(A)+ RNA fragments were then selected using the chimeric U5 and T45 (CU5T45) oligo conjugated on streptavidin beads, followed by RNase H digestion (NEB). Eluted RNA fragments were ligated with 5’ and 3’ adapters, followed by RT and PCR (15x) to obtain cDNA libraries for sequencing on the Illumina platform.

treatment_protocol: Differentiated C2C12 cell samples in this study are those harvested four days after differentiation. Transfection with siRNAs was carried out by Lipofectamine™ 2000 (Invitrogen) according to manufacturer’s recommendations. Transfection was carried out for 48 hr or 32 hr. The U1D oligo (5'-gCcAgGuAaGuau) and mutant U1D (mU1D) oligo (5'-gCcAgGcAcGuau), where locked nucleic acid (LNA) residues are in uppercase and 2’-OMe RNA bases are in lowercase, were previously described in Goraczniak et al. (Goraczniak et al., 2009). These oligos were transfected into C2C12 cells at 35 μM using Lipofectamine 2000 when the confluency of cells was about 50%. Cells were harvested 8 hr or 24 hr after transfection.

tag: treatment time

value: 48 hr

tag: kd batch id


title: siCtrl3

source_name: siRNA control, batch 3


title: siRBBP6.4

source_name: knock down RBBP6 in proliferating C2C12 cells


title: siPP1β.3

source_name: knock down PP1β in proliferating C2C12 cells


title: MITF_CHIP-seq

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Sequenced reads were mapped to the reference genome Human, hg19 using Bowtie 1.0.0 that was run using the following arguments -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200bp)

molecule: genomic DNA

extract_protocol:
BRG1 ChIP experiments were performed on native Mnase-digested chromatin isolated from 501Mel cells (Kasinathan et al., 2014). SOX10 and 3HA-MITF ChIP experiments were performed on 0,4% PFA-fixed chromatin isolated from 501Mel and Cl8 cells respectively according to standard protocols as previously described (Strub et al., 2011). Up to 60 ug of chromatin was subjected to immunoprecipation with a specific antibody.
The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina’s instructions

value: melanoma

tag: chip antibody

value: HA :IGBMC (12CA5)


title: siPABPC1.3

source_name: knock down PABPC1 in proliferating C2C12 cells


title: siPP1α.3

source_name: knock down PP1α in proliferating C2C12 cells


title: siPcf11.4

source_name: knock down Pcf11 in proliferating C2C12 cells


title: SRSF10-KO heart

city: Shanghai

first: Ning

last: Wei

address: 320 Yueyang RD.

country: China

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Embryonic heart at E13.5 were collected and frozened in Liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: BALB/c

tag: genotype/variation

tag: age

value: Embryonic day 13.5

tag: tissue

value: heart


title: siClp1.4

source_name: knock down Clp1 in proliferating C2C12 cells


title: siPABPN1.3

source_name: knock down PABPN1 in proliferating C2C12 cells


title: siCstF-50.4

source_name: knock down CstF-50 in proliferating C2C12 cells


title: siτCstF-64.4

source_name: knock down τCstF-64 in proliferating C2C12 cells


title: input

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description: input

data_processing: Reads were mapped to the mouse genome Mm10 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to rat chow and water.

extract_protocol:
Freshly dissected mouse sciatic nerve was minced in 1% formaldehyde for 10min and then quenched for 10min with glycine to a final concentration of 0.125M. Samples were sequentially lysed in buffers LB1, LB2, and LB3 + 0.03% SDS (Schmidt et. al., 2009, PMCID:  PMC4052679).   DNA was fragmented to an average size of 0.5-2kb using 4x10min Bioruptor (Diagenode) cycles on the medium setting.  Each aliquot of sonicated chromatin (300ug) was incubated overnight at 4°C with 5ug of H3K27me3 antibody (Millipore 07-449, Lot#2064519).  A 10% aliquot was saved for input analysis.  An 80ul aliquot of Protein G Dynabead (Invitrogen) slurry was added to each ChIP sample for 4hrs at 4°C.  IPs were washed 5x in RIPA buffer than eluted at 65°C with reverse crosslinking buffer (50mM Tris, 10mM EDTA, 1% SDS).    ChIP DNA was purified by phenol chloroform extraction and resuspended in 10mM Tris pH 8.0.
Libraries were prepared from  H3K27me3 ChIP sample, and corresponding input, using the Illumina TruSeq ChIP Sample Preparation Kit.

tag: strain

tag: gender

value: male

value: 8 weeks

tag: antibody


title: siCPSF-30.3

source_name: knock down CPSF-30 in proliferating C2C12 cells


title: H3K27me3 ChIP-seq

description: ChIP DNA

tag: antibody vendor/catalog/lot


title: siWDR33.4

source_name: knock down WDR33 in proliferating C2C12 cells


title: STR_R6_polII_rep2

city: ILLKIRCH

first: Karine

last: Merienne

address: 1 rue Laurent Fries

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

extract_protocol: ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads.

treatment_protocol: Striata from 4 transgenic mice were pooled (sex-matched between R6/1 and WT animals), cut into small fragments, fixed in 1% formaldehyde and incubated for 15 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then homogenized in sonication buffer, and lysates were sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (Millipore) for 1 h at 4°C. Subsequently, samples were incubated overnight at 4°C with antibodies to AcH3K27 (Abcam, ab4729) or 7C2 RNAPII antibody. Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3 h at 4°C. Agarose beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.

value: CBA x C57BL/6 (50% CBA and 50% C57BL6)

value: R6/1; transgenic for exon 1 of the HD gene carrying CAG expansion (115)

value: striatum

value: PolII:7C2 RNA Pol II

tag: chip antibody vendor


title: STR_R6_polII_rep1


title: STR_R6_H3k27ac_rep2

value: Abcam

tag: chip antibody cat. #


title: STR_R6_H3k27ac_rep1


title: R6_1_387_St

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Alignment : Reads were mapped to mm9 assembly of mouse genome using Tophat v1.4.1
Quantification : Gene expression was quantified using HTSeq v0.5.4p3 and annotations from Ensembl release 67
Normalization : Data normalization was performed with DESeq2 v1.0.19 Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts. BedGraph files were computed on unique reads (tophat v1.4.1) and normalized using the size factors calculated with DESeq2 v1.0.19 Bioconductor package

extract_protocol: RNA-seq libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” (# RS-122-2301, Illumina). Briefly, starting with 1 µg of total RNA, the first step involved the removal of cytoplasmic and mitochondrial ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

treatment_protocol: Total RNA was extracted using TRI Reagent (Molecular research center) and the Precellys lysing system (Precellys).


title: WT_321_St

value: WT


title: STR_R6_Input


title: WT_320_St


title: WT_319_St


title: R6_1_323_St


title: STR_WT_H3k27ac_rep2


title: STR_WT_H3k27ac_rep1


title: siSymplekin.4

source_name: knock down Symplekin in proliferating C2C12 cells


title: STR_WT_polII_rep2


title: siCPSF-100.3

source_name: knock down CPSF-100 in proliferating C2C12 cells


title: STR_WT_Input


title: p53KORasV12 MEF Input

city: Montpellier

first: Claude

last: Sardet

address: 208 rue des Apothicaires

department: Inserm U1194 - Université de Montpellier - Institut Régional du Cancer de Montpellier (ICM)

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

data_processing:
Basecalls performed using Illumina software RTA (Bustard).
Alignment performed using CASAVA 1.8 for Illumina HiSeq 2000 runs (elandv2e).
10 millions of mm9 uniquely mapped tags were randomly sampled from each sequencing run. Redundant reads occurrence's is adjusted to one, chromosome Y and M are removed. Input tags distribution is analyzed with hts_windowsummaryv2.exe hts_peakdetectorv2.exe cisgenomeV2 to identify artifactual reads aggregates. False positive tag enriched regions are then removed from IP and input files prior peak calling.
E4F1 peak calling is done with CisgenomeV2 (Seqpeak) and Qeseq V0.2.2 with the following parameters. Seqpeak -b 50 -w 1 -e 150 -ts 1 -c 3 -maxgap 50 -minlen 100 -br 1 -bar 1 -dat 1 - bw 5 -lpois 1 -lpwin 10000 -lpcut 1e-5 and QESEQ -s 150 -v 1 -p 0.01 -c 20. Genomic regions identified by both algorithms (intersection) were retained as E4F1-bound genomic regions. All pre and post data processing were done with R and Galaxy.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Cisgenome ChIP-seq peak calling results and statistics are summarized in .cod files.
Supplementary_files_format_and_content: Qeseq ChIP-seq peak calling results and statistics are summarized in .txt files.
Supplementary_files_format_and_content: bed files contain the intersection of detected peaks by cisgenomeV2 new two sample analysis module and Qeseq V0.2.2.
Supplementary_files_format_and_content: bar files contain the tag density profiles.

source_name: p53KORasV12 MEF, input

growth_protocol: Primary mouse embryonic fibroblasts (MEFs) and p53-/- MEFs were derived from 13.5-day mouse embryos and were grown at 37°C in Dulbecco's modified medium supplemented with 10% Fetal Bovine Serum, glutamax, pyruvate and 4.5g/l D-glucose under 5% CO2, 100% saturated H2O incubator. Transformed p53-/- MEFs were generated by infection with a recombinant retrovirus encoding for an Ha-RasV12 expression.

extract_protocol: Input and immunoprecipitated DNA were purified and prepared for Illumina/Solexa sequencing following their standard protocol.

treatment_protocol: Cells were trypsinized, counted and crosslinked with 1% formaldehyde for 8 minutes. Nuclei were then isolated and lysed. Chromatin was sheared by sonication to fragments below 500 nucleotides. Sonicated chromatins of primary mouse embryonic fibroblasts (MEFs) and p53-/-, Ha-RasV12-transformed MEFs were immunoprecipitated with an in-house rabbit polyclonal antibody raised against full-length E4F1 protein.

tag: strain/background

value: mixed (C57BL/6; 129Sv/J)

value: 13.5-day embryo

value: p53-/-, Ha-RasV12 mouse embryonic fibroblasts


title: ChIP E4F1 in p53KORasV12 MEF

source_name: p53KORasV12 MEF, E4F1 ChIP

value: rabbit polyclonal anti-E4F1


title: ChIP E4F1 in primary MEF

source_name: MEF, E4F1 ChIP

value: primary mouse embryonic fibroblasts


title: Primary MEF Input

source_name: MEF, input


title: SmallRNASeq_8.5.3

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

data_processing:
Base-calling and alignment was performed with NARWAL [ref]
Bowtie, TopHat,Cufflings,  sequence adapter trimming
Reads, from Bam files containing reads 36 nucleotide of length aligned, were extracted from mm9 RefSeq annotated exonic and non-exonic region, exonic reads were summed per transcript
Reads, smaller then 36 nucleotide of length due to adapter trimming from readcount files, were aligend to miRbase v19, tRNA and 5/5.8s rRNA sequences using the R bioconductor package Biostrings.
Abundancy was calculated by extracting primary aligned reads (ScanBamParam(IsNotPrimaryRead=FALSE)) or unique small reads
Regions or reads were called expressed when present above a threshold in all biological replicates in at least one of the two experimental groups.
Statistical analysis of expressed regions or reads was performed with the R bioconductor package EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing expression of regions/transcripts or abundance (unique presence or alignment) of regions/transcripts.

source_name: Embryonic Stem cell

growth_protocol: Cells were grown for 2 passages on feeder coated plates and 1 pasage on gelatin coated plates before taken into experiment

extract_protocol:
miRNeasy kit (qiagen) used to extract Total RNA
smallRNASeq library preparation was performed using TruSeq smallRNA kit v1.5 from Illumina.
Indexes used for mRNASeq and RNAomeSeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  GCCAAT: 8.4.16, CAGATC: 8.5.16, CTTGTA:  8.6.16) and smallRNASeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  CGATGT: 8.4.16,  TGACCA: 8.5.16, ACAGTG:  8.6.16)

treatment_protocol: 2.5uM of Cisplatin or DMSO (volume equal of 100%) was added to the medium

value: HPRT deficient ES cells

tag: treatment

value: Cisplatin

tag: passage


title: SmallRNASeq_8.5.16

tag: cell type

value: Control


title: SmallRNASeq_8.4.3


title: RNAomeSeq_8.4.16

description:
RNAome sequencing is a method to sequence small and large RNA species from ribosomal RNA-depleted total RNA in a single run.
rRNA depleted total RNA
RNAomeSeq_longRNA_expression.txt
RNAomeSeq_longRNA_abundance.txt
RNAomeSeq_smallRNA_expression_abundance.txt

extract_protocol:
miRNeasy kit (qiagen) used to extract Total RNA
RNAomeSeq library preparation was performed using our own protocol. Total RNA was depleted of ribosomal RNA (RiboMinus, Life science) and subsequently fragmented (Covaris S200). Adapters were ligated to the fragmented rRNA depleted RNA pool (adapters from the TruSeq smallRNA kit v1.5) and cDNA was made by reverse transcriptase. After amplification of the cDNA (11 cycli) the RNA was fractionated to sizes of 15-500nt by gel.
Indexes used for mRNASeq and RNAomeSeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  GCCAAT: 8.4.16, CAGATC: 8.5.16, CTTGTA:  8.6.16) and smallRNASeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  CGATGT: 8.4.16,  TGACCA: 8.5.16, ACAGTG:  8.6.16)


title: SmallRNASeq_8.4.16


title: RNAomeSeq_8.6.16


title: RNAomeSeq_8.5.3


title: STR_WT_polII_rep1


title: SmallRNASeq_8.3.3


title: RNAomeSeq_8.4.3


title: SmallRNASeq_8.6.16


title: Fetal

city: Shenzhen

first: Gaille

last: Joo

address: Beishan Industrial Zone, Yantian District

institute: BGI

data_processing:
Raw sequencing data was processed by the Illumina base-calling pipeline. Effective reads were generated by removing the low-quality sequences, as well as 3' adaptor sequence.
The clean reads were aligned to the UCSC mouse reference genome (mm9) in an unbiased way for bisulfite sequencing data: (i) all the observed cytosines were replaced by thymines and the guanines were replaced by adenosines in silico, forming two “alignment form” references; (ii) observed cytosines on the forward read of each read pair were replaced by thymines, and observed guanines on the reverse read of each read pair were replaced by adenosines, in silico; (iii) we then mapped the “alignment form” reads to the“alignment form” reference using SOAP aligner (http://soap.genomics.org.cn/).
The uniquely aligned reads that contained MspI enzyme digestion site at the ends were used for further analysis and methylation levels of cytosines were analyzed as previously described (5). Differentially methylated regions genome-wide were further analyzed as previously reported (6).
Briefly, the number of methylated and unmethylated CpG reads was counted for each region, and the methylation fold change (adult versus fetal) for each region was calculated as the log2Ratio using the CpG number values. Chi-square test was then applied to determine the differentially methylated status. The regions with a calculated p-value ≤ 0.01 and a | log2Ratio | ≥ 1 were defined as differentially methylated regions.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include methylation level for each Sample

source_name: Fetal

extract_protocol:
Genomic DNA was extracted from mouse liver samples via proteinase K digestion, followed by phenol/chloroform extraction and ethanol precipitation
Briefly, 5 ug of genomic DNA was digested with 300U of MspI enzymes (NEB) in 100μl reactions at 37°C for 16–19h. After purification, the digested products were blunt-ended, and then dA was added, followed by ethylated-adapter ligation. To obtain DNA fractions of 40-120bp and 120-220bp ranges of MspI-digested products, two ranges of 160-240bp and 240-340bp adapter-ligated fractions were excised from a 2% agarose gel, respectively. Bisulfite conversion was conducted using the ZYMO EZ DNA Methylation-Gold Kit ™ (ZYMO) according to the manufacturer’s instructions. The final libraries were generated by PCR amplification using JumpStart ™ Taq DNA Polymerase (Sigma).

value: liver


title: mRNA_8.5.16

description:
mRNASeq_longRNA_abundance.txt
mRNASeq_longRNA_expression.txt

extract_protocol:
miRNeasy kit (qiagen) used to extract Total RNA
mRNASeq library preparation was performed using TruSeq mRNA sample preparation kit from Illumina.
Indexes used for mRNASeq and RNAomeSeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  GCCAAT: 8.4.16, CAGATC: 8.5.16, CTTGTA:  8.6.16) and smallRNASeq (CGATGT: 8.3.3, TGACCA:  8.4.3, ACAGTG:  8.5.3,  CGATGT: 8.4.16,  TGACCA: 8.5.16, ACAGTG:  8.6.16)


title: RNAomeSeq_8.3.3


title: mRNA_8.4.16


title: mRNA_8.3.3


title: mRNA_8.4.3


title: Adult

source_name: Adult


title: met1(n4337); glp1_D2_rep2_mRNASeq

city: Ithaca

first: Mintie

last: Pu

state: New York

address: Biotechnology Building 341

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequencing reads were aligned to the C.elegans reference genome sequence (ce6) using the Burrows-Wheeler Aligner (BWA) for ChIP-seq, or tophat and tophat2 for mRNA-seq
Data were filtered base on unique mapping
for mRNA-seq, Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cuffdiff.
Genome_build: ce6
Supplementary_files_format_and_content: for ChIP-seq, wig files were generated to present H3K36me3 enrichment normalized to H3 by calculatiing read count ratio; for mRNA-seq, tab-delimited text files include FPKM values is used to present expression level.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strain glp-1(e2141) and met-1(n4337); glp-1(e2141) stocks were kept at 16°C and grown under standard growth condition (Brenner 1974).  met-1(n4337) was outcrossed with our lab N2 three times and  further crossed with glp-1(e2141) to generate met-1(n4337); glp-1(e2141).  For ChIP-seq and mRNA-seq experiments, embryos prepared from 16°C glp-1(e2141) or met-1(n4337); glp-1(e2141) stocks by bleaching were hatched and cultured at 25°C with about 3,000 embryos per 15 cm Nematode Growth Media (NGM) plate seeded with concentrated E. coli OP50 (1.5 mL 30 x overnight culture) with carbenicillin (50 μg/mL) and tetracycline (15 μg/mL).  For day 12 samples, worms were re-fed once on day 4.

extract_protocol:
Adult worms at day 2, day 4 and day 12 stages were washed with ice cold M9 three times.  Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction. For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 min.  Worm fragments were collected by spinning at 3,000 g for 5 min and resuspended in FA buffer followed by sonication with Bioruptor. For mRNA-seq, total RNA was extracted from worms harvested at the same stages as ChIP-seq sample preparation for glp-1(e2141), met-1(n4337); glp-1(e2141), or RNAi treated glp-1(e2141) worms.  mRNA was purified through poly A enrichment and mRNA-seq before library preparation.
For ChIP-seq,chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Chromatin extract was incubated with H3 antibody (Rabbit, ab1791, Abcam), H3K36me3 antibody (Rabbit, ab9050, Abcam), and control rabbit IgG overnight at 4°C.  Antibodies used were prescreened for specificity using dot blots.  The optimal amounts of antibodies used were determined by titration in preliminary experiment with ChIP-qPCR.  10-15 ng precipitated DNA from each sample was used for illumina sequencing library preparation.  DNA from ChIP was first end-repaired to generate blunt end, followed by adding single adenine base for adaptor ligation.  Ligation product with adaptor was size selected and amplified by PCR with primers targeting adaptor.  For mRNA-seq, mRNA was purified through poly A enrichment and mRNA-seq library was prepared with Illumina Truseq RNA and DNA sample prep kit.


title: met1(n4337); glp1_D12_rep1_mRNASeq


title: met1(n4337); glp1_D12_rep2_mRNASeq


title: RNAomeSeq_8.5.16


title: glp1_control_of_met1_D12_rep1_mRNASeq

description: glp1_gene_expression_as_control_of_met1.txt


title: glp1_control_of_met1_D12_rep2_mRNASeq


title: glp1_control_of_met1_D2_rep1_mRNASeq


title: glp1_control_of_met1_D2_rep2_mRNASeq


title: glp1_met1RNAI_D12_rep2_mRNASeq


title: glp1_met1RNAi_D2_rep2_mRNASeq


title: met1(n4337); glp1_D2_rep1_mRNASeq


title: glp1_L4440_D12_rep1_mRNASeq


title: glp1_L4440_D2_rep2_mRNASeq


title: glp1_L4440_D12_rep2_mRNASeq


title: glp1_met1RNAi_D2_rep1_mRNASeq

description:
met-1 stands for the mutant histone METhyltransferase- like
L4440_met1RNAi_gene_expression.txt


title: glp1_D12_rep2_parallel_ChIPseqrep4_mRNASeq

description: D2vsD12_glp1_isoform_expression_parallel_ChIPseq.txt


title: glp1_D2_rep2_parallel_ChIPseqrep4_mRNASeq


title: glp1_D12_rep1_parallel_ChIPseqrep3_mRNASeq


title: glp1_D2_rep1_parallel_ChIPseqrep3_mRNASeq


title: H3_D12_rep3_ChIPSeq

description: D12A_H3K36me3_H3_Biorep3_enrichment_w50s20.wig

tag: chip-antibody

tag: antibody source

value: H3 (ab1791, Abcam)


title: glp1_L4440_D2_rep1_mRNASeq


title: mRNA_8.5.3


title: H3_D12_rep4_ChIPSeq

description: D12A_H3K36me3_H3_Biorep4_enrichment_w50s20.wig


title: H3_D2_rep3_ChIPSeq

description: D2A_H3K36me3_H3_Biorep3_enrichment_w50s20.wig


title: H3_D12_rep2_ChIPSeq

description: D12A_H3K36me3_H3_Biorep2_enrichment_w50s20.wig


title: H3_D2_rep2_ChIPSeq

description: D2A_H3K36me3_H3_Biorep2_enrichment_w50s20.wig


title: H3K36me3_D12_rep4_ChIPSeq

value: H3K36me3 (ab9050, Abcam)


title: H3K36me3_D12_rep3_ChIPSeq


title: H3K36me3_D12_rep2_ChIPSeq


title: glp1_met1RNAi_D12_rep1_mRNASeq


title: H3K36me3_D2_rep4_ChIPSeq

description: D2A_H3K36me3_H3_Biorep4_enrichment_w50s20.wig

extract_protocol:
Worms at day 2 adult, day 4 adult and day 12 adult stages were washed with ice cold M9 three times.  Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction.
Extraction:
For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 minutes.  Worm fragments were collected by spinning at 3,000 g for 5 minutes and resuspended in FA buffer followed by sonication with Bioruptor.
For mRNA-seq, total RNA was extracted from D2 adult and D12 adult worms by TRIzol.  mRNA was purified through poly A enrichment before library preparation.
Library preparation:
For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Chromatin extract was incubated with H3 antibody (Rabbit, ab1791, Abcam), H3K36me3 antibody (Rabbit, ab9050, Abcam), and control rabbit IgG overnight at 4°C.  Antibodies were prescreened for specificity using dot blots.  The optimal amounts of antibodies for ChIP were determined by titration in preliminary experiments with ChIP-qPCR.  10-15 ng precipitated DNA from each sample was used for illumina sequencing library preparation.  DNA from ChIP was first end-repaired to generate blunt end, followed by adding single adenine base for adaptor ligation.  Ligation product with adaptor was size selected and amplified by PCR with primers targeting adaptor.
For mRNA-seq, mRNA was purified through poly A enrichment and mRNA-seq library was prepared with Illumina Truseq RNA and DNA sample prep kit.


title: H3K36me3_D2_rep2_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
D2A_H3K36me3_H3_Biorep2_enrichment_w50s20.wig

extract_protocol:
Worms at day 2 adult and day 12 adult stages were washed with ice cold M9 three times.  Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction.
Extraction:
For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 minutes.  Worm fragments were collected by spinning at 3,000 g for 5 minutes and resuspended in FA buffer and sonicated by Bioruptor.
For mRNA-seq, total RNA was extracted from D2 adult and D12 adult worms by TRIzol.  mRNA was purified through poly A enrichment before library preparation.
Library preparation:
For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Chromatin extracts were incubated with H3 antibody (Rabbit, ab1791, Abcam), H3K36me3 antibody (Rabbit, ab9050, Abcam), or control rabbit IgG overnight at 4°C.  Antibodies were prescreened for specificity using dot blots.  The optimal amounts of antibodies for ChIP were determined by titration in preliminary experiments with ChIP-qPCR.  10-15 ng precipitated DNA from each sample was used for illumina sequencing library preparation.  DNA from ChIP was first end-repaired to generate blunt end, followed by adding single adenine base for adaptor ligation.  Ligation product with adaptor was size selected and amplified by PCR with primers targeting adaptor.
For mRNA-seq, mRNA was purified through poly A enrichment and mRNA-seq library was prepared with Illumina Truseq RNA and DNA sample prep kit.


title: Sciatic nerve H3K27ac ChIP-seq

description: ChIP DNA

data_processing:
Illumina Pipeline
Casava 1.8.2
Reads were mapped to the Rattus norvegicus genome Rn5 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.
Peak finding performed using Homer with default parameters to detect histone mark enrichment.
Genome_build: Rn5
Supplementary_files_format_and_content: Bed and bedgraph files were generated using Homer: Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432.
Supplementary_files_format_and_content: bed file of H3K27ac peaks
Supplementary_files_format_and_content: Bedgraph file of H3K27ac

organism: Rattus norvegicus

extract_protocol:
P15 rats were sacrificed and freshly dissected rat sciatic nerves were pooled and minced in 1% formaldehyde for 10min and then quenched for 10min with glycine to a final concentration of 0.125M. Samples were initially lysed with a cell membrane buffer (5mM PIPES pH 8.0, 85mM KCl, 1% Ipegal) for 10min at 4°C. Then, nuclei were resuspended and lysed with a dounce homogenizer in a nuclear lysis buffer (50mM Tris pH8.1, 10mM EDTA, 1% SDS, protease inhibitor cocktail, PMSF) for 10min on ice. DNA was fragmented to an average size of 0.5-2kb using 4x10min Bioruptor (Diagenode) cycles on the medium setting.  Each aliquot of sonicated chromatin (300ug) was incubated overnight at 4°C with 5ug of antibody. An 80ul aliquot of Protein G Dynabead (Invitrogen) slurry was added to each ChIP sample for 4hrs at 4°C.  IPs were washed 5x in RIPA buffer than eluted at 65°C with reverse crosslinking buffer (50mM Tris, 10mM EDTA, 1% SDS).    ChIP DNA was purified by phenol chloroform extraction and resuspended in 10mM Tris pH 8.0. Antibody used in the study: H3K27ac (Active Motif 39133)
Libraries were prepared from P15 sciatic nerve for H3K27ac ChIP, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

value: Sprague Dawley

value: sciatic nerve


title: Sciatic nerve input

description: input

extract_protocol:
P15 rats were sacrificed and freshly dissected rat sciatic nerves were pooled and minced in 1% formaldehyde for 10min and then quenched for 10min with glycine to a final concentration of 0.125M. Samples were initially lysed with a cell membrane buffer (5mM PIPES pH 8.0, 85mM KCl, 1% Ipegal) for 10min at 4°C. Then, nuclei were resuspended and lysed with a dounce homogenizer in a nuclear lysis buffer (50mM Tris pH8.1, 10mM EDTA, 1% SDS, protease inhibitor cocktail, PMSF) for 10min on ice. DNA was fragmented to an average size of 0.5-2kb using 4x10min Bioruptor (Diagenode) cycles on the medium setting.  Each aliquot of sonicated chromatin (300ug) was incubated overnight at 4°C with 5ug of antibody. An 80ul aliquot of Protein G Dynabead (Invitrogen) slurry was added to each ChIP sample for 4hrs at 4°C.  IPs were washed 5x in RIPA buffer than eluted at 65°C with reverse crosslinking buffer (50mM Tris, 10mM EDTA, 1% SDS).    ChIP DNA was purified by phenol chloroform extraction and resuspended in 10mM Tris pH 8.0. Antibody used in the study: H3K27ac (Active Motif 37133)
Libraries were prepared from P15 sciatic nerve for H3K27ac ChIP, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.


title: Spinal cord 2 input

description: input

data_processing:
Illumina Pipeline
Casava 1.8.2
Reads were mapped to the Rattus norvegicus genome Rn5 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.
Peak finding performed using the R package MOSAiCS (MOdel-based one and two Sample Analysis and inference for ChIP-seq Data) controlled for a false discovery rate (FDR) at 0.05. Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, Keles S. 2011. A Statistical Framework for the Analysis of ChIP-Seq Data. Journal of the American Statistical Association. p 891-903.
Statistically different peaks were determined using DBChIP: Liang K, Keles S. 2012. Detecting differential binding of transcription factors with ChIP-seq. Bioinformatics 28:121-2.
Genome_build: Rn5
Supplementary_files_format_and_content: Bed files of called and differential peaks were generated by Mosaics and DBChIP. Bedgraph files were generated using Homer.
Supplementary_files_format_and_content: Sox10_CNS_DB_peaks.bed: bed file of CNS DB peaks
Supplementary_files_format_and_content: Sox10_PNS_DB_peaks.bed: bed file of PNS DB peaks
Supplementary_files_format_and_content: Sox10_peaks_CNS.bed: bed file of Sox10_peaks_in CNS condition
Supplementary_files_format_and_content: Sox10_peaks_PNS.bed: bed file of Sox10_peaks_in PNS condition
Supplementary_files_format_and_content: Sox10_SN_run204.ucsc.bedGraph.gz: Bedgraph file of Sox10 reads PNS condition
Supplementary_files_format_and_content: Sox10_SC_run128.ucsc.bedGraph.gz: Bedgraph file of Sox10 reads CNS condition

source_name: spinal cord

growth_protocol: P15 Sprague Dawley rats (Harlan Laboratory) were used for ChIP-Seq of sciatic nerve

extract_protocol:
ChIP assays were performed as described in Srinivasan, R., Sun, G., Keles, S., Jones, E.A., Jang, S.W., Krueger, C., and Svaren, J. (2012) Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve, Nucleic Acids Research, 40(14):6449-60 PMC3413122
Libraries were prepared from P15 spinal cord or sciatic nerve for Sox10 ChIP samples, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

value: spinal cord


title: Sciatic nerve 1 input

description: input


title: Control reads (random shear) from HCT116

city: Bethesda

first: Mirit

middle: I

last: Aladjem

state: MD

address: 37 Convent Dr. Building 37, Room 5068D

department: DNA Replication Group

institute: National Cancer Institute

description:
HCT116 Control
HCT116 control - random shear.
Illumina single read 35bp sequencing.

data_processing:
Illumina software pipeline (basecalls was done by using Illumina RTA 1.6 and RTA1.8. Alignment was done by using Illumina GAPipeline-1.4.0, CASAVA_v1.6.0, CASAVA-1.7.0 pipelines).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Bed file format of replication initiation peaks.

source_name: Cultured cancer cell line

growth_protocol: Cancer cells were grown in RPMI medium.

extract_protocol: Illumina Genomic DNA protocol. The average insert size of single reads was as follows: 222bp for HCT116_NS and 222bp for HCT116_MUS81_NS.

treatment_protocol: DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.

tag: cell line

value: Colon carcinoma

tag: read type

value: Single end


title: Nascent strands reads from HCT116

description:
HCT116 NS
HCT116 nascent strand reads.
Illumina single read 35bp sequencing.


title: Sciatic nerve 2 Sox10 ChIP-seq

description: ChIP DNA

value: Sox-10; Santa Cruz Biotechnology, sc-17342x


title: mut-16 trans-silenced

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using the fastX toolkit fastx_collapser module
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed to give only unique sequence, along with read count for each, the using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: Fasta header: id_number of reads

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions and followed by an overnight precipitation at -20C using isopropanol and glycogen as a carrier.  For RIP, custom Anti HRDE-1 polyclonal antibody was generated by Genomic Antibody Technology(GAT) by SDIX (Newark USA) against amino acids 12-161 of HRDE-1.
Before library preparation, 1-5ug of total RNA was treated with 1ul of RNA polyphosphatase (Epicentre) for 30 minutes at 37C.  RNA was then extracted using Phenol/chloroform and precipitated overnight at -20C using Ethanol and Sodium Acetate.  Following this we followed the Illumina Truseq small RNA protocol according to the manufacturer's instructions

tag: genotype/variation

value: WT

tag: developmental stage

value: adult

tag: transgenes

value: operon

value: whole animal


title: 5' to 3' spreading, operon trans-silenced

description: 5' polyphosphatase treated

value: operon+piRNA sensor

tag: tissue


title: mcherry H2A unsilenced

description: 5' polyphosphatase treated

value: wormcherry H2A


title: Nascent strands reads from Mus81-deficient HCT116

description:
HCT116 MUS81 NS
HCT116 MUS81 nascent strand reads.
Mus81 gene has been knocked out.
Illumina single read 35bp sequencing.

value: HCT116 MUS81


title: 5' to 3' spreading, operon silenced via wormcherry

description: 5' polyphosphatase treated

value: operon+wormcherry piRNA sensor


title: 5' to 3' spreading, operon paramutated

description: 5' polyphosphatase treated


title: hrde-1 HRDE-1RIP

description: 5' polyphosphatase treated

source_name: RNA immunoprecipitation

value: GFP piRNA sensor

tag: rip antibody

value: Anti-HRDE-1 polyclonal antibody against amino acids 12-161 of HRDE-1


title: operon silenced by RNAi, F2

description: 5' polyphosphatase treated

value: "operon"


title: H3_D2_rep4_ChIPSeq

tag: strain

value: H3 (ab1791, Abcam)


title: 5' to 3' spreading, operon wild type

description: 5' polyphosphatase treated


title: LB-01_Pso-NL_all

city: New York

first: Miguel

last: Brown

address: 1230 York Ave Box 186

institute: The Rockefeller University

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TGTGTTCGTATGCCGTCTTCTGCTTG

data_processing:
Samples are demultiplexed by assigning by 5 nt barcodes and adapters and barcodes are removed from fastq files converted to fasta using perl scripts.
Fasta file is collapsed into a non-redundant fasta file in which the read count is contained within the read header and mapped against an in-house ncRNA reference derived from GenBank and an internally curated set of miRNAs.  BWA v0.5.9 used, with parameters aln -n 2 -t 16 -i 0 -d 0 to align reads to the reference.
Multi-mapping reads are first assigned to hits with the lowest number of errors, then the count is split equally between the number of locations mapped.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated file summarizing reads attributed to an internal reference of ncRNAs.  First column is the read, second is the count, last column a comma-separated list of mapped annotation

source_name: human whole skin (epidermis + dermis)

extract_protocol:
miRNEasy Micro Kit (Qiagen)
A barcoded cDNA library for small RNA sequencing was prepared according to Hafner M. et al., Methods 44; 3-12, 2008 and Hafner M et al., Methods 58; 164-170, 2012.

value: Whole tissue extract

tag: indication

value: Non-Lesional Psoriatic Skin


title: operon silenced by RNAi, P0

description: 5' polyphosphatase treated


title: H3K36me3_D2_rep3_ChIPSeq

extract_protocol:
Adult worms at day 2, day 4 and day 12 stages were washed with ice cold M9 three times.  Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction. For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 min.  Worm fragments were collected by spinning at 3,000 g for 5 min and resuspended in FA buffer followed by sonication with Bioruptor. For mRNA-seq, total RNA was extracted from worms harvested at the same stages as ChIP-seq sample preparation for glp-1(e2141), met-1(n4337); glp-1(e2141), or RNAi treated glp-1(e2141) worms.  mRNA was purified through poly A enrichment before library preparation.
For ChIP-seq,chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Chromatin extract was incubated with H3 antibody (Rabbit, ab1791, Abcam), H3K36me3 antibody (Rabbit, ab9050, Abcam), and control rabbit IgG overnight at 4°C.  Antibodies used were prescreened for specificity using dot blots.  The optimal amounts of antibodies used were determined by titration in preliminary experiment with ChIP-qPCR.  10-15 ng precipitated DNA from each sample was used for illumina sequencing library preparation.  DNA from ChIP was first end-repaired to generate blunt end, followed by adding single adenine base for adaptor ligation.  Ligation product with adaptor was size selected and amplified by PCR with primers targeting adaptor.  For mRNA-seq, mRNA was purified through poly A enrichment and mRNA-seq library was prepared with Illumina Truseq RNA and DNA sample prep kit.

value: H3K36me3 (ab9050, Abcam)


title: TR-15_Pso-NL_all

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TATCATCGTATGCCGTCTTCTGCTTG


title: LB-01_Pso-L_all

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TGATGTCGTATGCCGTCTTCTGCTTG

value: Lesional Psoriatic Skin


title: 0089_Pso-NL_all

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TAGAGTCGTATGCCGTCTTCTGCTTG


title: TR-15_Pso-L_all

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TAGGATCGTATGCCGTCTTCTGCTTG


title: rrf-1

description: 5' polyphosphatase treated


title: 0089_Pso-L_all

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TAATATCGTATGCCGTCTTCTGCTTG


title: FQ_Pso-NL_all

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TGTGTTCGTATGCCGTCTTCTGCTTG


title: FQ_Pso-L_all

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TGATGTCGTATGCCGTCTTCTGCTTG


title: MI-45_Pso-L_all

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TAGGATCGTATGCCGTCTTCTGCTTG


title: MI-45_Pso-NL_all

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TATCATCGTATGCCGTCTTCTGCTTG


title: mRNA_8.6.16

description:
mRNASeq_longRNA_abundance.txt
mRNASeq_longRNA_expression.txt

value: HPRT deficient ES cells

value: Control


title: SD_Pso-NL_all

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TAGAGTCGTATGCCGTCTTCTGCTTG


title: TR-15_Pso-NL_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCTGATCGTATGCCGTCTTCTGCTTG

source_name: human reticular dermis (RD)

value: Dermis


title: SD_Pso-L_all

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TAATATCGTATGCCGTCTTCTGCTTG


title: LB-01_Pso-L_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TTAAGTCGTATGCCGTCTTCTGCTTG

source_name: human reticular dermis/inflammatory aggregate (RD/ICs)


title: WT HRDE-1RIP

description: 5' polyphosphatase treated

value: WT

value: adult


title: 0089_Pso-NL_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCTAGTCGTATGCCGTCTTCTGCTTG


title: MI-45_Pso-NL_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCCGTTCGTATGCCGTCTTCTGCTTG


title: TR-15_Pso-L_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCTCCTCGTATGCCGTCTTCTGCTTG


title: MI-45_Pso-L_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCCACTCGTATGCCGTCTTCTGCTTG


title: SD_Pso-NL_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCATCTCGTATGCCGTCTTCTGCTTG


title: FQ_Pso-L_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCCTATCGTATGCCGTCTTCTGCTTG


title: LB-01_Pso-NL_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TAACGTCGTATGCCGTCTTCTGCTTG


title: KR2-42

first: Federico

last: Rey

address: 1550 Linden Dr.

institute: University of Wisconsin-Madison

data_processing:
Library strategy: COPRO-Seq
Demultiplexing: sequences were demultiplexed by 4 nt barcode, requiring an exact match (sequences without a barcode match were excluded from the analysis)
Trimming: after demultiplexing, all sequences were trimmed to 25 bases to eliminate low-quality bases at the ends of each read
Mapping: sequences were aligned to the reference genomes of the 13 bacteria included in the study using Illumina's ELAND aligner (as provided in GAPipeline-1.4.0). Only perfect, non-redundant matches were carried forward in the analysis.
Normalization: raw counts were normalized based on the informative genome size (IGS) of each organism included in the analysis, as described by McNulty et al. in a previous publication (PMID: 22030749).
Summarization: the proportional representation of each organism in the analysis was determined by dividing its normalized counts within a sample by the total normalized counts for all organisms within that sample.
Genome_build: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482, Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131
Supplementary_files_format_and_content: Excel file. The column header (B1-BE1) specifies the sample from which data were derived. Subsequent rows specify the organism/reference genome, raw counts, and normalized relative proportion for each taxon included in the alignment. Small intestine samples with less then 1000 reads (total raw counts) were not used in final analysis. Cecum and large intestine samples with less than 10,000 reads (total raw counts) were not used for final analysis. These samples are marked in red.
Supplementary_files_format_and_content: KR_Norm_Decimal_Percent_w_Raw_Counts.xlsx [Samples KR1 to KR56]
Supplementary_files_format_and_content: KR2_Norm_Decimal_Percent_w_Raw_Counts.xlsx [Samples KR2-1 to KR2-60]

organism: mouse metagenome

source_name: Distal Large Intestine

growth_protocol: Bacteria from frozen culture stocks were introduced as an artificial community (AC) into 6-24 week old male and female gnotobiotic C57BL/6J and NMRI mice.  Cells were therefore maintained over the course of the experiment within mice until sampling occurred.

extract_protocol:
DNA was extracted from intestinal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Macherey-Nagel PCR Purification column. DNA was blunted and poly-A tailed. The A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence.  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were give to the University of Wisconsin-Madison Biotechnology Center for quality assurance and library sequencing following the manufacturer's protocols (Illumina MiSeq 1x50bp).

treatment_protocol: Immediately after collection, samples were subjected to flash-freezing in ethanol chilled with dry ice and stored at -80 C until total community DNA extractions could be performed.

value: NMRI

tag: gender

value: Male

tag: community composition

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131

tag: diet

value: Choline +

tag: mouse number


title: LB-01_Pso-L_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TTAAGTCGTATGCCGTCTTCTGCTTG

source_name: human epidermis (Epi)

value: Epidermis


title: LB-01_Pso-NL_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TAACGTCGTATGCCGTCTTCTGCTTG


title: 0089_Pso-NL_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCTAGTCGTATGCCGTCTTCTGCTTG


title: TR-15_Pso-NL_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCTGATCGTATGCCGTCTTCTGCTTG


title: 0089_Pso-L_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCGCGTCGTATGCCGTCTTCTGCTTG


title: siCtrl8T

source_name: siRNA control, batch 8N

extract_protocol:
For nuclear RNA extraction, cells collected by a scrapper were suspended in cell lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 0.5% NP40, 1 mM DTT), followed by vortexing for 10 sec and incubation on ice for 10 min. After centrifugation of the lysate at 500 x g for 5 min at 4oC, the pellet was re-suspended in the cell lysis buffer for nuclear RNA extraction. Both total and nuclear RNAs were extracted using Trizol (Invitrogen) according to manufacturer's protocol. RNA quality was analyzed in an Agilent Bioanalyzer using the RNA pico600 kit before processing for deep sequencing.
The 3’READS method used in this study was previously described (Hoque et al., 2014). Briefly, 25 μg of total RNA was used for each sample, and poly(A)+ RNA was selected using oligo d(T)25 magnetic beads (NEB), followed by on-bead fragmentation using RNase III (NEB). Poly(A)+ RNA fragments were then selected using the chimeric U5 and T45 (CU5T45) oligo conjugated on streptavidin beads, followed by RNase H digestion (NEB). Eluted RNA fragments were ligated with 5’ and 3’ adapters, followed by RT and PCR (15x) to obtain cDNA libraries for sequencing on the Illumina platform.

tag: treatment time

value: 32 hr

tag: kd batch id


title: 0089_Pso-L_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCGCGTCGTATGCCGTCTTCTGCTTG


title: FQ_Pso-L_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCCTATCGTATGCCGTCTTCTGCTTG


title: siPcf11.8T

source_name: knock down Pcf11 in proliferating C2C12 cells


title: TR-15_Pso-L_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCTCCTCGTATGCCGTCTTCTGCTTG


title: FQ_Pso-NL_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCGATTCGTATGCCGTCTTCTGCTTG


title: MI-45_Pso-NL_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCCGTTCGTATGCCGTCTTCTGCTTG


title: siPABPN1.8T

source_name: knock down PABPN1 in proliferating C2C12 cells


title: siFip1.8T

source_name: knock down Fip1 in proliferating C2C12 cells


title: siPABPC1.8T

source_name: knock down PABPC1 in proliferating C2C12 cells


title: FQ_Pso-NL_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCGATTCGTATGCCGTCTTCTGCTTG


title: siCFI-68.8T

source_name: knock down CFI-68 in proliferating C2C12 cells


title: C2C12.Diff.4d.2

source_name: 4 day differentiated C2C12 cells, replicate 2


title: MI-45_Pso-L_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCCACTCGTATGCCGTCTTCTGCTTG


title: mU1D24h

source_name: mutant U1D 24 hr in proliferating C2C12 cells

value: 24 hr


title: mU1D8h

source_name: mutant U1D 8 hr in proliferating C2C12 cells

value: 8 hr


title: SD_Pso-L_D

description:
lane: Marianne_C_NoIndex_L002_R1_001.fastq.gz
barcode + 3' adaptor: TCACTTCGTATGCCGTCTTCTGCTTG


title: siCtrl5

source_name: siRNA control, batch 5

value: 48 hr


title: siPcf11.8N


title: siPABPC1.8N


title: C2C12.Pro.2

source_name: Proliferating C2C12 cells, replicate 2


title: siCtrl8N


title: siCtrl6

source_name: siRNA control, batch 6


title: siPABPN1.8N


title: U1D_8h

source_name: U1D 8 hr in proliferating C2C12 cells


title: siFip1.8N


title: siCFI-68.8N


title: siPAPα.6

source_name: knock down PAPα in proliferating C2C12 cells


title: siRRP44_siRRP6.6

source_name: knockdown RRP44 and RRP6 in proliferating C2C12 cells


title: siPAPγ.6

source_name: knock down PAPγ in proliferating C2C12 cells


title: SD_Pso-L_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCACTTCGTATGCCGTCTTCTGCTTG

source_name: human epidermis (Epi)


title: siCstF-77.5

source_name: knock down CstF-77 in proliferating C2C12 cells


title: Dif3.5

data_processing:
Reads were mapped to the mouse genome (mm9) using Bowtie2 (local mode), and those with a mapping quality score (MAPQ) ≥10 were selected for further analysis. Reads with ≥2 non-genomic As after alignment were called polyA site supporting (PASS) reads and all PASS reads mapped to the 3’UTR of a genes were used to calculate the expression level of the gene.
Gene expression level was represented as reads per million (RPM) total PASS reads. The log2-based ratio of RPM of 3.5-day differentiated vs. undifferentiated P19 cells was used to reflect the expression change during P19 cell differentiation.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file containing information of gene symbol, read number and RPM values

source_name: 3.5-day differentiated P19 cells

growth_protocol: P19 cells (ATCC) were routinely propagated in P19 growth medium (P19GM) containing α-MEM (Hyclone), 10% Fetal Bovine Serum (FBS; Hyclone, characterized grade), 100 IU/ml penicillin and 100 µg/ml streptomycin (Invitrogen).

extract_protocol:
We extracted RNA extraction by the Trizol method.
We made cDNA libraries using the 3′READS technique as previously described (Hoque et al., 2013). Libraries were  sequenced on an Illumina HiSeq 2500 machine.

treatment_protocol: P19 cells were differentiated in principle as described (Makeyev et al, 2007). To initiate EB formation, P19 cells were plated at 1×105/ml into bacterial-grade dishes in P19 induction medium (P19IM) containing α-MEM (Hyclone), 5% FBS (Hyclone, characterized grade) and 1 mM of all-trans retinoic acid (RA, Sigma). Two days post plating, P19IM was replaced and the EBs were cultured for another 2 days. The EBs harvested from a single 10 cm were washed with 1xPBS and dissociated in 2 ml of 0.25% trypsin–EDTA (Invitrogen) supplemented with 100 mg/ml DNase I (Roche) for 10 min at 37°C. The cell suspensions were passed through 100 mm strainers (BD Biosciences) and plated into poly-D-lysine (Sigma) treated dishes in P19IM lacking RA. Twelve hours after plating, the medium was changed to Neurobasal (Invitrogen) additionally containing 1xN-2 supplement (Invitrogen) and 2 mM GlutaMAX (Invitrogen) and the cells were allowed to undergo neural differentiation for up to 6 more days.

tag: cell type

value: 3.5-day differentiated


title: SD_Pso-NL_E

description:
lane: Marianne_A_NoIndex_L001_R1_001.fastq.gz
barcode + 3' adaptor: TCATCTCGTATGCCGTCTTCTGCTTG

value: Non-Lesional Psoriatic Skin


title: U1D_24h

data_processing:
The details of the method was described previously (Hoque, et al., 2014). Briefly, the 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT). Reads were mapped to the mouse genome (mm9) using Bowtie2 (local mode). 5' four random nucleotides were removed before mapping using "-5 4" parameter in bowtie2. Reads with a mapping quality score (MAPQ) ≥10 were selected for further analysis. Reads with ≥2 non-genomic As after alignment were called polyA site supporting (PASS) reads.
All PASS reads mapped to the 3’-most exons of a gene were used to calculate the expression level of the gene, shown as the reads per million total PASS reads (RPM) value.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file containing information of gene symbol, pA coordinates, read number of pAs in different samples

source_name: U1D 24 hr in proliferating C2C12 cells


title: Plasmacytoma cell line (MPC11)

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

description: Sample 29

data_processing:
Reads were aligned to the GRCm37/mm9 build of the Mus musculus genome with the Subread aligner. Ten 'subreads' were extracted from each read, and at least three consensus 'subreads' were required for a hit to be reported. Hamming distance or mapping-quality score was used to break the tie when more than one best location was found for a read. Only uniquely mapped reads were retained.
Gene-wise counts were obtained with featureCounts. Reads overlapping exons in annotation build 37.2 of the NCBI RefSeq database were included. Genes were filtered from downstream analysis if they did not have a CPM (counts per million mapped fragments) value of at least 1 in at least one library. Immunoglobulin genes were excluded from expression analysis when we compared B cell populations with ASC populations, because of the large difference in the fraction of immunoglobulin reads between them. Expression analysis for immunoglobulin genes was done separately.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Empirical Bayes moderated-t P values were computed relative to a fold-change cutoff of 1.5-fold using treat. P values were adjusted to control the global false discovery rate (FDR) across all comparisons with the global option of the limma package. Genes were considered differentially expressed if they had an FDR of 0.05 or less and also had at least 8 FPKMs (fragments per kilobase of exon length per million mapped fragments) in one or both of the two cell types being compared.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include normalized log2-FPKM values for each sample.

source_name: Cell line

extract_protocol:
RNA was isolated from cells using Qiagen RNeasy Micro or Mini Kits (based on cell number), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Plasmacytoma cell line

tag: stimulus

tag: time

tag: markers

tag: culture

value: In vitro


title: UnDiff

source_name: undifferentiated P19 cells

tag: developmental stage

value: undifferentiated


title: Day 4 CD40L+IL4+IL5 stimulated cells, Small, B220+, Syndecan1-, CTV+ cells, sorted by division 1 (Div 1) rep1

description: Sample 23

source_name: Spleen

value: Spleen

value: 96 hours


title: Germinal center-like B lymphoma cell line (A20)

description: Sample 28

tag: cell line


title: Day 4 CD40L+IL4 stimulated cells, Syndecan1+ (40/4 PB) rep1

description: Sample 27

tag: tissue

value: CD40L/IL4 plasmablasts


title: Day 4 CD40L+IL4+IL5 stimulated cells, Small, B220+, Syndecan1-, CTV+ cells, sorted by division 7 (Div 7) rep1

description: Sample 26


title: Day 4 CD40L+IL4+IL5 stimulated cells, Small, B220+, Syndecan1-, CTV+ cells, sorted by division 3 (Div 3) rep1

description: Sample 24


title: Day 2 CD40L+IL4 stimulated B cells, CD19+, B220hi, Syndecan1- (40/4 blasts) rep1

description: Sample 19

value: 48 hours

value: CD40L/IL4 B cell blasts

value: CD19+, B220hi, Syndecan1-


title: Day 4 CD40L+IL4+IL5 stimulated cells, Small, B220+, Syndecan1-, CTV+ cells, sorted by division 5 (Div 5) rep1

description: Sample 25


title: B cells stimulated for 24h with CD40L+IL4, Small, B220+, Syndecan1- (Div 0) rep1

description: Sample 22

value: 24 hours

value: Small, B220+, Syndecan1-


title: Day 3 LPS stimulated B cells, B220+, Syndecan1+,  Blimp1-GFP+ (LPS PB) rep2

description: Sample 18

value: Lipopolysaccharide

value: 72 hours

value: LPS plasmablasts

value: B220+, Syndecan1+,  Blimp1-GFP+


title: Day 2 CD40L+IL4 stimulated B cells, CD19+, B220hi, Syndecan1- (40/4 blasts) rep2

description: Sample 20


title: Small resting B cells from Blimp1-GFP mice (Unstim) rep1

description: Sample 21

value: Small, B220+


title: Day 3 LPS stimulated B cells, B220+, Syndecan1-,  Blimp1-GFP+ (LPS Syn-PB) rep1

description: Sample 15

value: LPS Syn- plasmablasts

value: B220+, Syndecan1-,  Blimp1-GFP+


title: Bone marrow plasma cells (BMPC) rep1

description: Sample 13

source_name: Bone marrow

value: Bone marrow

value: Bone marrow plasma cells

value: CD138/Syndecan1+, Blimp1-GFP-hi

value: Ex vivo


title: Day 3 LPS stimulated B cells, B220+, Syndecan1-, Blimp1-GFP- (LPS blasts) rep1

description: Sample 14

value: Spleen

value: LPS B cell blasts

value: B220+, Syndecan1-, Blimp1-GFP-

value: In vitro


title: Splenic plasma cells (SplPC) rep3

description: Sample 12

value: Splenic plasma cells


title: Splenic plasma cells (SplPC) rep1

description: Sample 10


title: Splenic plasma cells (SplPC) rep2

description: Sample 11


title: Marginal zone B cells (MZB) rep2

description: Sample 6

value: Marginal zone B cells


title: Germinal center B cells (GCB) rep2

description: Sample 8

value: Germinal center B cells

value: CD19+, Fas+, PNA+


title: Splenic plasmablasts (SplPB) rep1

description: Sample 9

value: Splenic plasmablasts

value: CD138/Syndecan1+, Blimp1-GFP-lo


title: Peritoneal B1 cells (B1) rep2

description: Sample 4

source_name: Peritoneal lavage

value: Peritoneal lavage

value: Peritoneal B1 cells


title: Peritoneal B1 cells (B1) rep1

description: Sample 3


title: Germinal center B cells (GCB) rep1

description: Sample 7


title: Marginal zone B cells (MZB) rep1

description: Sample 5


title: Follicular B cells (FoB) rep2

description: Sample 2

value: Follicular B cells


title: Follicular B cells (FoB) rep1

description: Sample 1


title: Day 3 LPS stimulated B cells, B220+, Syndecan1+,  Blimp1-GFP+ (LPS PB) rep1

description: Sample 17

value: Lipopolysaccharide

value: 72 hours

value: LPS plasmablasts

value: B220+, Syndecan1+,  Blimp1-GFP+


title: LOAD2

city: Miami

first: Marco

last: Magistri

state: FL

address: 1501 NW 10th Ave

department: Psychiatry

institute: University of Miami

data_processing:
We performed directional RNA sequencing using Illumina Hiseq 2000. Directional RNAseq was performed running one sample per lane and we generated ~177.000.000 reads per sample
Sequenced reads were trimmed for adaptor sequence. TopHat wass used to align reads to the human genome, while transcriptome reconstruction of each individual sample was performed using Cufflinks. Reconstructed transcriptomes for each individual samples were compared to each other using Cuffcompare that also merges overlapping constructs and annotates them according to the reference transcriptome provided (Ensembl GRCh37)
In order to discriminate real transcripts from sequencing artifacts we adopted a filtering strategy based of two main criteria: 1) the presence of at least one splice junction in the transcripts and 2) the recurrent expression of single exon transcripts across multiple samples.
Genome_build: grch 37
Supplementary_files_format_and_content: Gene Transfer File (.gtf). The gtf file was generated by first performing ab initio reconstruction of transcripts for individual samples with Cufflinks, combining the individual gtf files with Cuffcompare and filtering spurious transcripts. It contain annotation of both coding and non-coding transcripts.

extract_protocol:
RNA was extracted using phenol chloroform method, subjected to Dnase treatment and Riosomal RNA removal using RiboZero
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age (yrs)

tag: subject group

value: LOAD (late onset of Alzheimer’s disease)

value: female

tag: apoe genotype

tag: braak stage

value: V

value: Hippocampus


title: CTRL3

source_name: age-matched control_hippocampi

value: age-matched control

tag: gender

value: male

value: II


title: CTRL1

value: I


title: LOAD4

value: VI


title: Sample_2

city: Chicago

first: Gye Young

last: Park

state: IL

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

data_processing:
Illumina HiSeq 2000 sequencing system was used.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome.
Calculation of Fragments Per Kilobase of exon per Megabase (FPKM) values and the expression analysis were done by using Cuffdiff and TopHat softwares.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample. genes.count_tracking: gene count measurement; genes.fpkm_tracking: FPKM measurement; gene_exp1: expression comparison (comparison of FPKM values between pre- and post-allergen challenged samples).

source_name: Alveolar macrophages, post-allergen challenge

extract_protocol:
RNA was harvested using PureLink RNA micro Scale kit (Life Technologies). 1 ug of total RNA was used for the construction of sequencing libraries. The samples were treated with DNase, and rRNA removal was done by RiboZero kit (Illumina).
Directional RNA libraries were prepared for sequencing using PrepX RNA-Seq library kit (Wafergen).

treatment_protocol: Alveolar macrophages were purified by using Percall gradient method and adhesion purification.

tag: disease state

value: asthma

value: alveolar macrophages from BAL fluid

tag: sampling time

value: post-allergen challenge 48 hr


title: Day 3 LPS stimulated B cells, B220+, Syndecan1-,  Blimp1-GFP+ (LPS Syn-PB) rep2

description: Sample 16

tag: strain

value: Spleen

value: LPS Syn- plasmablasts

value: B220+, Syndecan1-,  Blimp1-GFP+

value: In vitro


title: Sample_1

source_name: Alveolar macrophages, pre-allergen challenge

value: pre-allergen challenge


title: CTRL2

value: Not available


title: CTRL4

value: female


title: MOMA#22

city: Aarhus

first: Jian

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

description:
06/003395T1-2
RRBS-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
The adaptor sequences were filtered out from the subsequent analysis and the resulting reads were aligned using Bismark software. Only uniquely mapped reads, which had restriction enzyme cutting site at the 5’ end were used to subsequent methylation analysis.
The sequencing depth and the percentage of methylated cytosines/total investigated cytosines for each C location were calculated. The genomic annotation information was based on the hg19 human genome (http://genome.ucsc.edu). Differentially methylated cytosines were identified by QDMR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes the significantly differented cytosines and the correpsonding methylation level (percentage) values for each sample in the colon cancer cell line models and the clinical samples.

source_name: Clinical colorectal samples

growth_protocol: The cell lines HCT116 and HT29 were obtained from the NCI/Development Therapeutics Program, while LoVo was obtained from the American Tissue Culture Collection. Cells were maintained at 37 ˚C, 5% CO2 in RPMI 1640+Glutamax growth medium (Invitrogen, Naerum, Denmark) supplemented with 10% foetal calf serum (Invitrogen).

extract_protocol:
Genomic DNA was isolated from the cell lines and clinical samples using DNeasy® Blood & Tissue Kit (QIAGEN) following manufacturer's protocol. The extracted genomic DNA was verified by agarose gel electrophoresis, and the concentration was estimated by NanoDrop (Thermo Scientific). Furthermore, BioAnalyzer 2100 DNA Chip was used to ensure the quality, quantity and integrity for the genomic DNA.
Five µg genome DNA from the cell line models and the clinical samples was digested by restriction enzyme, MspI (New England BioLabs) over night at 37 °C and QIAGEN Mini Purification kit was used to purify the digested products. End repair, adding A and adaptors, where the cytosines in the paired end adaptor sequence were methylated, was performed. The ligated product was subjected to size selection in 2% agarose gel (Bio-RAD) at 100 V for 2 hours. Agarose gel bands with the inserted genomic DNA size 40 ~ 110 bp and the inserted genomic DNA size 110 ~ 220 bp were excised, so that two libraries were generated from the MOMA3, MOMA4, MOMA5, MOMA7, MOMA8 and MOMA9 (one consisting of 40 ~ 110 bp target sequences and the other of 110 ~ 220 bp target sequences). The rest clinical samples and all cell line samples were generated with a single library with inserted DNA fragments with 40-300 bp. The DNA from the excised gel pieces was recovered by QIAGEN Gel Extraction Purification Kit, followed by bisulfite treatment using ZYMO EZ DNA Methylation-Gold kit. The resulting converted DNA was amplified by PCR and purified. The RRBS libraries were performed paired-end 50 nt sequencing with HiSeq 2000 (Illumina).

treatment_protocol: Oxaliplatin or SN-38 resistant cell lines were generated in our laboratory over a period of 8-10 months by continuous exposure to gradually increasing concentrations of drug. The cell lines were passaged three times at each drug concentration and cell vials were frozen at each increase in drug concentration. Prior to subsequent experiments, the cells were maintained in drug-free growth medium for at least 1 week.

value: Clinical colorectal metastatic sample from surgery prior to any chemotherapy


title: MOMA#16

description:
07/013300T1-2
RRBS-seq


title: MOMA#19

description:
C08T00889T
RRBS-seq


title: MOMA#17

description:
03/020609T1-1
RRBS-seq


title: MOMA#12

description:
06/030495T1
RRBS-seq


title: MOMA#10

description:
C07T01083T
RRBS-seq


title: MOMA#14

description:
05/033618T1-2
RRBS-seq


title: MOMA#8

description:
04/015782T1-1
RRBS-seq


title: MOMA#9

description:
03/021141T1-1
RRBS-seq


title: MOMA#3

description:
C05T01402A
RRBS-seq


title: MOMA#4

description:
06/000171T1-1
RRBS-seq


title: MOMA#5

description:
05-5324A1
RRBS-seq


title: LoVo OxPt resistant (H)

description:
H
RRBS-seq

source_name: Colon cancer cell line

value: Derived from the LoVo cell line and showing OxPt resistance


title: LoVo SN38 resistant (I)

description:
I
RRBS-seq

value: Derived from the LoVo cell line and showing SN38 resistance


title: LOAD3

value: LOAD (late onset of Alzheimer’s disease)

value: male

value: Hippocampus


title: HT-29 SN38 resistant (F)

description:
F
RRBS-seq

value: Derived from the HT-29 cell line and showing SN38 resistance


title: HT-29 OxPt resistant (E)

description:
E
RRBS-seq

value: Derived from the HT-29 cell line and showing OxPt resistance


title: HT-29 parental (D)

description:
D
RRBS-seq

value: HT-29 parental cell line is sensitive for both OxPt and SN38


title: HCT-116 SN38 resistant (C)

description:
C
RRBS-seq

value: Derived from the HCT-116 cell line and showing SN38 resistance


title: MOMA#20

description:
05/06073T1-1
RRBS-seq


title: HCT-116 OxPt resistant (B)

description:
B
RRBS-seq

value: Derived from the HCT-116 cell line and showing OxPt resistance


title: athb1-1 Rep1

city: Santa Fe

first: Raquel

middle: Lia

last: Chan

state: Santa Fe

address: Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nac. Nº 168 km. 0, Paraje El Pozo

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral (CONICET/UNL)

description: RNA-Seq of athb1-1 replicate 1

data_processing: Total reads were then aligned to the latest Arabidopsis Col-0 genome assembly (TAIR10; released in June 2009) with TopHat version 2.0.8 using Bowtie2 version 2.1.0.

organism: Arabidopsis thaliana

source_name: whole 4-day-old seedling (root, hypocotyl, cotyledon)

growth_protocol: Wild-type and athb1-1 mutant seeds were plated in Petri dishes containing 0.5 % Murashige and Skoog basal medium supplemented with vitamins (PhytoTechnology LaboratoriesTM) and 0.9 % agar. Seeds were then stratified for 3 days at 4ºC in darkness, and then transferred to a growth chamber (120 umol/m2/s) during 4 days under short day conditions. Seedlings were harvested 1 h before the end of the night.

extract_protocol:
Total RNAs were isolated using the RNeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4d 8h light/16h darkness (72 hours post-stratification) at 22-24ºC (120 umol/m2/s)

tag: genotype/variation

tag: growth conditions

value: Short day

tag: ecotype

value: Columbia


title: athb1-1 Rep3

description: RNA-Seq of athb1-1 replicate 3


title: athb1-1 Rep2

description: RNA-Seq of athb1-1 replicate 2


title: HCT-116 parental (A)

description:
A
RRBS-seq

value: HCT-116 parental cell line is sensitive for both OxPt and SN38


title: WT Rep3

description: RNA-Seq of wild-type replicate 3

value: wild-type


title: unsilenced operon

description: 5' polyphosphatase treated

source_name: Total RNA whole animal

value: WT

value: adult

tag: transgenes

value: "operon"

value: whole animal


title: WT-0 rep1 and rep2

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Tair10 whole genome using tophat with parameters -p -r -G -o genome C1_R1_1.fq C1_R1_2.fq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: plant

extract_protocol:
Total RNA was isolated from 11-d-old seedlings treated with MS liquid medium or MS liquid medium containing 200 mM NaCl for 4 h with Trizol reagent (Invitrogen) as recommended by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plant

tag: age

tag: genotype

value: wild type

tag: treatment

value: MS liquid medium


title: skip-S rep1 and rep2

value: skip

value: MS liquid medium containing 200 mM NaCl for 4 h


title: WT cherrysensor

description: 5' polyphosphatase treated

tag: developmental stage

value: wormcherry piRNA sensor


title: MOMA#7

last: Li

description:
05/02285TH1
RRBS-seq

tag: tissue

value: Clinical colorectal metastatic sample from surgery prior to any chemotherapy


title: rrf-2

description: 5' polyphosphatase treated

value: GFP piRNA sensor


title: ego-1

description: 5' polyphosphatase treated


title: ego-1 rrf-1

description: 5' polyphosphatase treated


title: 1:100 dilution, day 10, repeat 2 (9B)

city: Oxford

first: Ji-Long

last: Liu

address: South Parks Road

department: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics

institute: University of Oxford

description: PCR product from gDNA

data_processing:
Custom Perl script to extract different barcoded libraries and trim to unique 19 nt sgRNA sequence
Custom Perl script to count sgRNA sequences from each library
Genome_build: dm3
Supplementary_files_format_and_content: sgRNA_counts.out - Tab delimited text file describing counts for every sgRNA in the library for each of the 18 samples
Supplementary_files_format_and_content: metadata.txt - Information about barcoding strategy and sample details

organism: Drosophila melanogaster

source_name: S2R+ cell line

growth_protocol: 28C, Schneider's medium (Sigma) + 10% FBS (Invitrogen)

extract_protocol:
gDNA was extracted with a Zymo Quick gDNA extraction kit. sgRNA sequences were amplified using primers ScreenF2 (TAGGTATGTTTTCCTCAATACTTCG) and ScreenR (CGGACTAGCCTTATTTTAACTTGC)
Adaptors were added with a second round of PCR including 5' and 3' barcodes, as described in metadata.txt. 9 different 5' variable length barcode, and 2 different 6 nt barcodes at the 3' end

tag: cell line

tag: library dilution

value: 100x dilution

tag: timepoint

value: Day 10

tag: biological repeat


title: zebrafish-sperm

city: Guangzhou

first: kun

middle: tong

last: jia

state: Guangdong

address: 135 Xingang Road West Guangzhou, Guangdong,china

institute: SUN YAT-SEN UNIVERSITY

description: Small non coding RNAs

data_processing:
The sequencing data were analyzed as described previously by Xu et al (2014).
The low-quality reads were filtered to remove reads without the 3’ adaptor, 5’ adaptor-contaminant reads, reads without the insert fragment, reads containing poly(A) stretches, and reads of less than 18 nt. Next, the remaining sequences (clean reads) were mapped to the zebrafish genome using SOAP with a tolerance of one mismatch to analyze their distribution
The sequences were aligned against known miRNA precursors and mature miRNAs deposited in the miRBase 20.0 to identify conserved miRNAs. The clean reads were compared against the sRNAs (rRNAs, tRNAs, snRNAs, snoRNA, miRNA) deposited in the GenBank and Rfam (http://www.sanger.ac.uk/resources/databases/rfam.html) databases to annotate the sRNA sequences. Because some sRNA tags might map to more than one category we used priority rules to ensure that every unique sRNA was mapped to only one annotation as follows: rRNA etc. (GenBank >Rfam) >known miRNA >repeat >exon >intron).
Genome_build: miRBase 20.0
Supplementary_files_format_and_content: zebrafish miRNA_count.txt include RPKM values of each known miRNA in this sample

organism: Danio rerio

source_name: Zebrafish Spermatozoa

extract_protocol:
Total RNA was isolated from sample using Trizol reagent (Invitrogen, USA) in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies).
RNA samples that passed the quality check were sent to BGI (Shenzhen, China) for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.

tag: cell type

value: Spermatozoa

value: AB wild-type


title: 1:100 dilution, day 1, repeat 2 (7B)

description: PCR product from gDNA

value: Day 1


title: WT-S rep1 and rep2


title: 1:100 dilution, day 10, repeat 1 (9A)

description: PCR product from gDNA


title: 1:100 dilution, day 4, repeat 2 (8B)

description: PCR product from gDNA

value: Day 4


title: 1:100 dilution, day 4, repeat 1 (8A)

description: PCR product from gDNA


title: 1:100 dilution, day 1, repeat 1 (7A)

description: PCR product from gDNA


title: WT

description: 5' polyphosphatase treated

value: WT

value: adult


title: rrf-3

description: 5' polyphosphatase treated

value: whole animal


title: 1:10 dilution, day 10, repeat 2 (6B)

description: PCR product from gDNA

value: 10x dilution


title: 1:10 dilution, day 10, repeat 1 (6A)

description: PCR product from gDNA


title: WT Rep2

description: RNA-Seq of wild-type replicate 2

value: wild-type

value: Short day

value: Columbia


title: WT Rep1

description: RNA-Seq of wild-type replicate 1


title: Thymus rep 3 (Illumina GAII)

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

institute: Hubrecht Institute

description: barcode: GC

data_processing:
Library strategy: 4C-Seq
sat4C reads were aligned to sequences flanking restriction sites in the mm9 genome assembly using a custom mapping pipeline written in Perl
Data from individual experiments were normalized for sequencing depth to the average number of mapped reads in all experiments
Genome-wide sat4C coverage profiles were calculated by averaging over running windows of 101 sat4C fragment and resulting sat4C profiles were quantile normalized
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using custom R script; Scores represent normalized sat4C coverage

source_name: Adult thymus tissue

growth_protocol: Thymus tissue was isolated from adult male mice (C57/Bl6) and disaggregated through a nylon cell strainer. Mouse embryonic stem cells (IB10) and neural precursor cells derived from these ESC were a gift from Bas van Steensel and maintained as previously described (Peric-Hupkes et al. 2010, Mol. Cell). Astrocytes were derived from these NPC in our own lab according to established protocols (Peric-Hupkes et al. 2010, Mol. Cell).

extract_protocol:
In general, satellite 4C follows the regular 4C protocol as detailed by Splinter et al. (2012, Methods) with several modifications. Chromatin is fragmented with ApoI and MfeI (both NEB), and subsequently ligated under diluted conditions. After reversal of the cross-links, the DNA is purified and treated with the NlaIII. After a second re-ligation step, the sample is purified and a 4C PCR is applied. 4C PCR samples were purified using Ampure beads (Beckman Coulter) and sent for next generation sequencing (illumina).
Library is generated by 4C PCR with primers carrying illumina adapter sequences

treatment_protocol: Approximately 10 million cells were crosslinked using 1% formaldehyde for 10minutes at room temperature


title: Raw library (pre-transfection) (0A)

description:
PCR product
PCR product from cloned sgRNA library

organism: synthetic construct

source_name: Synthesised sample


title: 1:0 dilution, day 10, repeat 2 (3B)

description: PCR product from gDNA

value: No dilution


title: 1:0 dilution, day 10, repeat 1 (3A)

description: PCR product from gDNA


title: 1:0 dilution, day 4, repeat 1 (2A)

description: PCR product from gDNA


title: Thymus rep 1 (Illumina GAII)

description: barcode: GT


title: 1:10 dilution, day 4, repeat 1 (5A)

description: PCR product from gDNA


title: 1:0 dilution, day 1, repeat 1 (1A)

description: PCR product from gDNA


title: Thymus rep 2 (Illumina GAII)

description: barcode: GC


title: 1:10 dilution, day 4, repeat 2 (5B)

description: PCR product from gDNA


title: 1:0 dilution, day 4, repeat 2 (2B)

description: PCR product from gDNA


title: 1:10 dilution, day 1, repeat 2 (4B)

description: PCR product from gDNA


title: 1:0 dilution, day 1, repeat 2 (1B)

description: PCR product from gDNA


title: C2C12.Pro.1

city: Bridgewater

first: Wencheng

institute: PTC Therapeutics

source_name: Proliferating C2C12 cells, replicate 1

tag: treatment time

tag: kd batch id


title: Input_DNA (ChIP-Seq control)

city: Berlin

first: Hans-Jörg

last: Warnatz

address: Ihnestrasse 63-73

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Base calling was done with Illumina's standard base caller Bustard (version 1.6.1).
Single-end 36bp reads were mapped with BWA software (Li and Durbin, 2009) against the mm9 version of the mouse genome.
Peak-calling was performed using the MACS peak-calling algorithm (Zhang et al., 2008).
Genome_build: mm9
Supplementary_files_format_and_content: Peak bed file contains peaks called by the MACS peak calling algorithm; Scores represent fold enrichment of ChIP-seq reads versus input DNA reads in peak regions.

source_name: ES cells

extract_protocol:
Mouse R1 embryonic stem cells (Nagy et al., 1993) (10^8 cells) were cross-linked in complete medium (10% FBS) containing 1% formaldehyde for 10 min, the reaction was terminated by addition of 125 mM glycine. Fixed cells were washed three times (5 min each) in cold PBS and lysed in LB1 buffer (LB2 buffer containing 0.5% NP-40 and 0.25% triton X-100). Nuclei were then washed in LB2 buffer (10mM Tris-HCl pH=8 and 200mM NaCl) to remove detergents and resuspended in LB3 buffer (LB2 buffer containing 0.1% Na-deoxycholate and 0.5% N-lauroylsarcosine). Chromatin was sonicated 5 times for 30 sec cycles at 30% of the maximum power of a Branson 450 sonicator to generate 100-400 bp chromatin fragments. After clearing by centrifugation, sonicated chromatin was incubated with antibody-bound protein A-conjugated magnetic beads (Invitrogen, Carlsbad, USA). For each IP we used 10 ug antibody. IP with rabbit IgG was performed as negative control. After overnight IP at 4°C, the bound complexes were washed twice in WB1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X100, 0.1% Na-doexycholate), twice in WB2 (50 mM Hepes-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton-X100, 0.1% Na-doexycholate) and twice in LiCl WB (10 mM Tris-Cl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA). Immunoprecipitated complexes were eluted from the beads by incubation for 30 min in EB (2% SDS in TE) at 37°C. The eluted material was reverse cross-linked at 65°C overnight and incubated for 1 h at 55°C with proteinase K. The obtained material was extracted with phenol-chloroform and ethanol precipitated. After RNAse treatment, the DNA was purified with a PCR purification kit (Qiagen, Netherlands). About 10 ng of immunoprecipitated DNA were processed for sequencing.
The input and ChIP DNA were used for preparation of sequencing libraries according to the manufacturer’s instructions for the Genome Analyzer GAII instrument (Illumina). After DNA purification with a DNA Clean & Concentrator-5 kit (Zymo Research), the DNA libraries were separated on 2% agarose TAE gels. The 150- to 250-bp fragments were excised from the gel on a Dark Reader (Claire Chemical Research) and purified with a MinElute Gel Extraction Kit (Qiagen). Sequencing was performed on a Genome Analyzer GAII instrument (Illumina) with 36 cycles.

tag: strain

value: wild type

value: embryonic stem cells

tag: chip antibody


title: C2C12.Diff.4d.1

source_name: 4 day differentiated C2C12 cells, replicate 1


title: Mouse.ES.wild_type (RNA-Seq)

data_processing:
Base calling was done with Illumina's standard base caller Bustard (version 1.6.1).
Reads were mapped and transcript expression estimated using RSEM (Li and Dewey, 2011) using mouse Ensembl 63 gene models.
Quantification results from RSEM were analyzed with the Bioconductor package DESeq (Anders and Huber, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl 63 mouse gene models, numbers of aligned RNA-seq reads and RPKM values.

molecule: polyA RNA

extract_protocol:
RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of polyA+ RNA sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation


title: siCtrl7

source_name: siRNA control, batch 7

value: 48 hr


title: siCtrl2

source_name: siRNA control, batch 2


title: 1:10 dilution, day 1, repeat 1 (4A)

description: PCR product from gDNA


title: siCtrl1

source_name: siRNA control, batch 1


title: Mouse.ES.Prep1_KO (RNA-Seq)


title: Prep1 (ChIP-Seq)

value: PREP-1 N-15 (Santa Cruz Biotechnology, sc-6245)


title: siU1-70K.7

source_name: knock down U1-70K in proliferating C2C12 cells


title: ESC rep 1 (Illumina HiSeq 2000)

description: barcode: GG

source_name: Embryonic stem cell line


title: siSF3b155.7

source_name: knock down SF3b155 in proliferating C2C12 cells


title: siCFI-59.1

source_name: knock down CFI-59 in proliferating C2C12 cells


title: siU2AF65.7

source_name: knock down U2AF65 in proliferating C2C12 cells


title: siCFI-68.1

source_name: knock down CFI-68 in proliferating C2C12 cells


title: siCstF-64.1

source_name: knock down CstF-64 in proliferating C2C12 cells


title: siCFI-25.1

source_name: knock down CFI-25 in proliferating C2C12 cells


title: Sciatic nerve 1 Sox10 ChIP-seq

city: Madison

first: John

last: Svaren

address: 1500 Highland Ave.

institute: University of Wisconsin

description: ChIP DNA

data_processing:
Illumina Pipeline
Casava 1.8.2
Reads were mapped to the Rattus norvegicus genome Rn5 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.
Peak finding performed using the R package MOSAiCS (MOdel-based one and two Sample Analysis and inference for ChIP-seq Data) controlled for a false discovery rate (FDR) at 0.05. Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, Keles S. 2011. A Statistical Framework for the Analysis of ChIP-Seq Data. Journal of the American Statistical Association. p 891-903.
Statistically different peaks were determined using DBChIP: Liang K, Keles S. 2012. Detecting differential binding of transcription factors with ChIP-seq. Bioinformatics 28:121-2.
Genome_build: Rn5
Supplementary_files_format_and_content: Bed files of called and differential peaks were generated by Mosaics and DBChIP. Bedgraph files were generated using Homer.
Supplementary_files_format_and_content: Sox10_CNS_DB_peaks.bed: bed file of CNS DB peaks
Supplementary_files_format_and_content: Sox10_PNS_DB_peaks.bed: bed file of PNS DB peaks
Supplementary_files_format_and_content: Sox10_peaks_CNS.bed: bed file of Sox10_peaks_in CNS condition
Supplementary_files_format_and_content: Sox10_peaks_PNS.bed: bed file of Sox10_peaks_in PNS condition
Supplementary_files_format_and_content: Sox10_SN_run204.ucsc.bedGraph.gz: Bedgraph file of Sox10 reads PNS condition
Supplementary_files_format_and_content: Sox10_SC_run128.ucsc.bedGraph.gz: Bedgraph file of Sox10 reads CNS condition

source_name: sciatic nerve

extract_protocol:
ChIP assays were performed as described in Srinivasan, R., Sun, G., Keles, S., Jones, E.A., Jang, S.W., Krueger, C., and Svaren, J. (2012) Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve, Nucleic Acids Research, 40(14):6449-60 PMC3413122
Libraries were prepared from P15 spinal cord or sciatic nerve for Sox10 ChIP samples, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

value: sciatic nerve

value: Sprague Dawley

tag: antibody

value: Sox-10; Santa Cruz Biotechnology, sc-17342x


title: LOAD1

tag: age (yrs)

tag: subject group

value: LOAD (late onset of Alzheimer’s disease)

tag: gender

value: female

tag: apoe genotype

tag: braak stage

value: VI

value: Hippocampus


title: siFip1.2

source_name: knock down Fip1 in proliferating C2C12 cells


title: Sciatic nerve 2 input

description: input

tag: tissue

tag: age


title: siCPSF-160.1

source_name: knock down CPSF-160 in proliferating C2C12 cells

tag: cell line


title: siCPSF-73.1

source_name: knock down CPSF-73 in proliferating C2C12 cells


title: Spinal cord 1 input

description: input

source_name: spinal cord

value: spinal cord


title: Spinal cord 2 Sox10 ChIP-seq

description: ChIP DNA


title: Spinal cord 1 Sox10 ChIP-seq

description: ChIP DNA


title: LoVo parental (G)

description:
G
RRBS-seq

source_name: Colon cancer cell line

value: LoVo parental cell line is sensitive for both OxPt and SN38