title: DGRP900 M_E1_8_L1

description:
EP2A121
Drosophila Genetic Reference Panel 900, Male, Environment 1, Fly 8, Library 1

data_processing:
We performed single-end 76 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer.  De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. Reads were mapped to FlyBase release 5 version 57 (FlyBase file: dmel-all-chromosome-r5.57.fasta) and release 6 version 01 (FlyBase file: dmel-all-chromosome-r6.01.fasta) of the Drosophila melanogaster genome and appended sequence corrected ERCC sequences (ERCC_reference.fa, See Jiang et al., Genome Research, 2011, PMID 21816910) and annotations using TopHat2 (v2.0.10) with parameters  "-g 1 --library-type fr-firststrand" (Kim et al., Genome Biol, 2013, PMID 23618408).  We aligned to Drosophila melanogaster chromosome scaffolds only (release 5 chrU and chrUextra were excluded).  We used a Perl script to convert the dmel-all-r5.57.gff to a GTF file (dme5_57_ERCC.gtf) compatible with TopHat2 and HTSeq (v0.5.4p1) (Anders et al., Bioinformatics, 2015, PMID 25260700).  We extracted features, including pre-miRNAs, pseudogenes, mRNAs, ncRNAs, rRNAs, snoRNAs, snRNAs, tRNAs, genes, CDSs and exons, and changed the 304 features for “miRNA” to “exon”.   We changed the following features: 9 mRNA transcripts without strand assignment were assigned to the parent gene strand; 11 Exons and 9 CDSs without strand assignment were assigned to the parent transcript strand; and 10 CDSs, with ends longer than the parent, were truncated to fit the parent ends.  TopHat2 called Bowtie 2 (v2.1.0) to make indexes. We used SAMtools (v0.1.19) (Li et al., Bioinformatics, 2009, PMID 19505943) to index chromosomes, to sort and merge alignments, and for read statistics.  Mapped reads at the gene-level were counted by HTSeq with parameter "--stranded=reverse -i gene_id -t exon".
Supplementary_files_format_and_content: There are five supplemental files.  The tab-delimited 5_57_HTSeq_raw_read_counts.txt and 6_01_HTSeq_raw_read_counts.txt files contain the gene-level output, for each library, for genome releases 5.57 and 6.01 respectively. Column 1 and 2 are FlyBase FBgn#s and gene symbols, or ERCC  identifiers as applicable.  The remaining columns are library names (as GEO GSM#s).  The GEO_run_summary.xls file contains detailed information on each sequencing run and a readme sheet with field definitions.  The dme5_57_ERCC.gtf file contains the annotation for the alignment to release 5.57 plus the ERCC spike-ins.  ERCC_reference.fa is a FASTA file of the sequence corrected ERCCs.

source_name: Whole body

extract_protocol:
Single flies frozen on dry ice were placed into each well of Axygen 96 Deep Well Plates (Corning, Corning, NY) pre-loaded with 200µL of 1 mm glass beads (Biospec Products, Bartlesville, OK).  Fly placement in the wells of each plate was randomized within a replicated environment. We isolated total RNA using the RNeasy 96 Plate Kit according to the manufacturer using either vacuum or centrifugation technology (Qiagen, Valencia, CA), with the following modifications. We added 200µl RLT buffer to each well, sealed the plates with Axygen Sealing Mats (Corning, Corning, NY), and homogenized flies at room temperature for 30sec using a fixed-speed Mini Bead Beater (Biospec Products, Bartlesville, OK).  We added 200µl of 70% ethanol to the crude homogenate, mixed by pipetting several times, and transferred the supernatant to RNeasy plates.  We measured total RNA yield using the Quant-iTTM RiboGreen(R) RNA Assay Kit (Invitrogen, Carlsbad, CA) in black FLUORTRAC 600 384-well PS plates (Greiner Bio-One, Inc., Longwood, FL) using a Gemini EM Fluorescence Microplate Reader (Molecular Devices, Sunnyvale, CA).  We used Dynabeads Oligo (dT) 25 (Life Technologies, Carlsbad, CA) to purify polyA RNA according to manufacturer instructions, except that we used 50-200ng of total RNA depending on yield, adjusted the volume to 50µl with distilled H2O, added 10µl of the washed Dynabeads in a 50µl binding buffer slurry, heated the samples at 65°C for 5min, and immediately chilled the samples on ice.  To prepare RNA-Seq stranded libraries we modified an existing protocol (Wang et al., PLoS One, 2011, PMID 22039485).  All steps were done in 96-well plate format. We incubated all reactions in a Tetrad PTC-225 Thermal Cycler (MJ Research, Waltham, MA). To clean up enzymatic reactions and size select at any of several steps below, we used 0.1% w/v carboxyl-modified Sera-Mag Magnetic Speed-beads (MagNA beads, Thermo Fisher Scientific, Waltham, MA) in XP buffer [20% PEG 8000, 2.5 M NaCl, (Sigma Aldrich, St. Louis, MO)] following the protocol in (Rohland et al., Genome Res, 2012, PMID 22267522), except that we incubated samples with beads for 10 min and used 80% ethanol for washing.  The volume of MagNA beads in XP buffer and corresponding concentration of PEG in the solution was 1.6× XP buffer for no size-selection (except where noted) and 1× XP buffer for selecting fragments > 200bp. Unless noted, we left the beads in the sample after each step.  We used 96-well PCR plates (USA Scientific, Ocala, Fl) paired with Alpaqua 96R Ring Magnet Plates (Alpaqua, Beverly, MA) for magnetic bead separation. We measured RNA quantity with Quant-iTTM RiboGreen(R) and DNA with Quant-iTTM PicoGreen(R) (Invitrogen, Carlsbad, CA) in 384-well plates, PS, FLUOROTRAC 600, black (Greiner Bio-One Inc, Longwood, Fl) using a Gemini EM Fluorescence Microplate Reader (Molecular Devices, Sunnyvale, CA) according to manufacturer instructions.  We used Agilent Bioanalyzer RNA chips and High Sensitivity DNA chips on the 2100 Bioanalyzer system (Agilent, Santa Clara, CA) according to manufacturer instructions and visually inspected electrophoregrams for RNA degradation, library size (DNA), and adapter dimer contamination (DNA).
We fragmented polyA RNA bound to Dynabeads at 94°C for 8min in 16µl of 1.25× first strand MMuLV RT buffer (New England Biolabs, Beverly, MA), with 100ng random primers (Invitrogen, Carlsbad, CA), and 10pg ERCC spike-in controls (Jiang et al., Genome Res, 2011, PMID 21816910) from pools 78A and 78B (Zook et al., PLoS ONE, 2012, PMID 22859977) obtained from Marc Salit (National Institute of Standards and Technology, Gaithersburg MD).  We chilled the samples immediately on ice for 2min and eluted from the beads.  We transferred 15µl of the eluate to a fresh 96-well PCR plate. We added 5µl of the first strand synthesis mixture [0.3mM dNTPs, 5mM DTT, and 10U M-MuLV RT (New England Biolabs, Beverly, MA), and 0.5U SuperRase-In (Life Technologies, Carlsbad, CA)] to the fragmented RNA in the fragmentation buffer and performed a reverse transcription reaction. We bound RNA/cDNA hybrid with 32µl MagNA bead XP buffer slurry, washed, and eluted samples in 16µl of distilled H2O.  We then performed a second strand synthesis with dUTP by adding 5µl of 1× NEB buffer2 (New England Biolabs, Beverly, MA), with 1mM each of dATP, dCTP, dGTP and 2mM dUTP (Thermo Fisher Scientific, Waltham, MA), 10U DNA PolI, 2.5U RNAseH, and 2.5mM DTT (New England Biolabs, Beverly, MA) and incubated at 16°C for 5 hours.  We rebound, washed, and eluted as above. We repaired ends by adding 4µl of NEBNext End Repair Module (New England Biolabs, Beverly, MA) to the eluate following manufacturer instructions.  We then rebound samples to MagNA beads, washed, and eluted as above. Next we performed dA-tailing by adding 4µl of 1× Blue Buffer, with 1U Klenow 3’-5’ exo- (Enzymatics, Beverly, MA) and 1mM dATP, to the eluate and incubated at 37°C for 30min.  We then rebound samples to MagNA beads and washed as above, eluted with 21µl distilled H2O, and transferred 10µl of cDNA to each of two fresh plates. One plate was used in the following steps and one plate was frozen as a back-up.  We ligated RNA Adapter Indexes (Illumina, San Diego, CA) to dsDNA by adding 1µl of an adapter to each 10µl sample and 13µl of 1× Rapid Ligation Buffer with 30U T4 DNA Ligase (Enzymatics, Beverly, MA), and incubated at 25°C for 10min. We stopped reactions with a final concentration of 0.01M EDTA. We added 25µl of MagNA beads in XP buffer (final PEG = 13.6%), bound cDNA to the beads, washed and eluted in 30µl of distilled H2O as above.  We size-selected libraries by adding 1× XP buffer (30µl), washed, eluted samples with 24µl distilled H2O, and transferred 23µl of cDNA to a fresh plate. 11.5µl of the eluate was transferred to another plate and used in the next step; the remaining samples were frozen as a back-up.  We mixed dsDNA product with 2.5U (0.5µl) of Uracil DNA Glycosylase (New England Biolabs, Beverly, MA) and 3µl of PCR Primer Cocktail (Illumina, San Diego, CA) and incubated at 37°C for 30min to digest the second strand DNA.  We added 15µl 2× KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Woburn, MA) directly to the UDG digested DNA mixture and performed a PCR amplification with the following programmed cycle: 95°C for 2min, followed by 12 cycles of 98°C for 20sec, 65°C for 30sec, and 72°C for 30sec; then 72°C for 5min. We purified the product by adding 30µl MagNA beads in 1× XP buffer, eluted in 30µl distilled H2O and transferred 29µl of cDNA library to a fresh plate as described above. To assay plate-level failure, we took 11 samples from each 96-well plate and examined electropherograms for a strong signal in the 300-350 bp library target size and weak signal in the 100-150bp range (primer dimer products).  Each 96-well plate was composed of 4 sets of samples with 24 unique indexes. We pooled equal amounts (5-15 ng) of each library into pools for multiplex sequencing.  All multiplexed libraries were again quantified and checked for quality as above.  Excess library pools were frozen for re-sequencing if required.

tag: developmental stage

value: Adult

tag: Sex

value: Male

tag: tissue

value: Whole body


title: Zscan10_f/f-Tx_rep2

status: Public on Dec 20 2015

type: SRA

city: Kobe

first: Hitoshi

last: Niwa

state: Hyogo

address: 2-2-3 Minatojima-minamimachi,Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
Gene expression without Zscan10 deletion
rRNA depleted RNA

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to the mouse genome (mm10) using TopHat after trimming of adaptor sequences with trim_galore and quality check with FastQC.
Gene expression level measured as FPKM was determined with Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cells, Zscan10 floxed, replicate2

extract_protocol:
Total RNAs were prepared by QuickGene RNA cultured cell HC kit (KURABO) following the manufacturer's instruction and treated with Ribo-Zero Gold Sample Prep Kit (Illumina) for deplete ribosomal RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: ESC

tag: genotype/variation

value: control


title: ANME-1 Mcr-producing M. acetivorans grown on methanol, Replicate 1

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

description:
total RNA (with rRNA partially removed)
TMML1

data_processing:
Reads were mapped to the reference genome of M. acetivorans (Genbank accession NC_003552.1) using STAR.
The mapped reads were assembled using Cufflink v2.2.1 to identify potential novel transcripts. Assembled, unannotated novel transcripts for all the strains were combined with the list of known genes.
Differential expression of genes and potential novel transcripts were determined using Cuffdiff at a significance cutoff at q < 0.07 with a false discovery rate of 0.05.
Expression changes are determined by the ratio of FPKM of culture replicates grown on methane to FPKM of culture replicates grown on methanol.
Genome_build: NC_003552.1
Supplementary_files_format_and_content: Read count of each replicate and the average FPKM value (adjusted to sequencing depth) for each mapped locus.

organism: Methanosarcina acetivorans

growth_protocol: All starter cultures of M. acetivorans with pES1-MATmcr3 (200 mL) were grown on methanol for 5 days, and harvested by centrifugation. Cell pellets were washed three times with HS medium, and resuspended using 5 mL HS medium, 2 µg/mL puromycin, and 0.1 mM FeCl3. For growth on methane, methane was filled into the headspace of the cultures. For growth on methanol, 150 mM methanol was added. All cultures were incubated at 37C for 5 days.

extract_protocol:
Rapid centrifugation in the presence of 50 µL RNAlater solution (Ambion, Austin, TX) per mL of culture, followed by flash-freezing of cell pellets. Total RNA was isolated using RNeasy Mini kit (Qiagen, Valencia, CA), and were further digested with terminator 5’-phosphate-dependent exonuclease (Epicentre, Madison, WI) to partially remove ribosomal RNA. Digested RNA were cleaned up using AgenCourt RNAClean XP beads (AgenCourt Bioscience, Beverly, MA).
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Library kit).

value: containing pES1-MATmcr3; ANME-1 Mcr-producing

tag: components of growth medium

value: HS medium, 2 µg/mL puromycin, and methanol

tag: gas in headspace


title: WT_HC

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Libray preparison:mRNA is enriched by using the oligo(dT) magnetic beads, following to be fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.
Sequencing: The library products are ready for sequencing via Illumina HiSeqTM 2000.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to mouse reference sequences (Li R., Yu C., Li Y., et al . 2009, Bioinformatics).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: hippocampus

extract_protocol:
Total RNA was isolated from mouse hippocampus using RNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were measured using a RNA Pico chip on an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: wild type

value: brain

tag: age

value: 6 month


title: ANME-1 Mcr-producing M. acetivorans grown on methane, Replicate 3

description:
total RNA (with rRNA partially removed)
TMME3

value: HS medium, 2 µg/mL puromycin, and 0.1 mM FeCl3

value: methane


title: Zscan10_f/f-Tx_rep1

source_name: Embryonic stem cells, Zscan10 floxed, replicate1


title: ANME-1 Mcr-producing M. acetivorans grown on methane, Replicate 1

description:
total RNA (with rRNA partially removed)
TMME1


title: ANME-1 Mcr-producing M. acetivorans grown on methane, Replicate 2

description:
total RNA (with rRNA partially removed)
TMME2


title: WTTRE-R2

status: Public on Dec 19 2015

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

country: China

institute: Zhejiang University

description:
Replicate experiment 2 of library WTTRE
processed data file: WTTRE-BbSNF1TRE.xls

data_processing:
Illumina HiSeq™ 2000 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
NOISeq approach is used to determine the threshold of P-value in paired comparison with replicates (Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A and Conesa A. Differential expression in RNA-seq: A matter of depth. Genome Research, 2011, 21: 2213-2223). The mean value of RPKMs from two replicates was calculated as the representative gene expression in each library.
The differential expression statistics in NOISeq approach are the log-ratio (M) and the absolute value of difference (D) between two conditions, and these two statistics were used to calculate the probability (P) of a gene being differentially expressed. Differentially expressed genes  were screened in WTGLU/BbSNF1GLU set and WTTRE/BbSNF1TTRE set, respectively, at the threshold of P value>0.8 and log2 ratio (fold change) > 1 or < -1.
Genome_build: Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files, including Gene ID, gene length, RPKM values, log2(fold change) and P-value  for each paired sample.

organism: Beauveria bassiana

source_name: BbWT

growth_protocol: The nitrogen source (NaNO3) of Czapek-Dox medium was replaced by 0.5% peptone, and either glucose or trehalose (3%) was included to prepare the PEPGLU and PEPTRE media, respectively. For each of PEPGLU and PEPTRE media, conidia suspension (5 ml,107 conidia ml-1) of WT and ΔBbSNF1 of Beauveria bassiana were inoculated into 50 ml media, respectively, and incubated at 25 °C for 3 day with shaking.

extract_protocol:
Resultant mycelia of each treatment were harvested and ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested and washed in sterile water twice. Each library was replicated twice in independent experiment.

tag: strain background

tag: culture media

value: PEPTRE (trehalose)

tag: culture time

value: 3 days

value: mycelia


title: DBbSNF1TRE-R2

description:
Replicate experiment 2 of library DBbSNF1TRE
processed data file: WTTRE-BbSNF1TRE.xls

value: BbSNF1 disruption mutant


title: DBbSNF1TRE-R1

description:
Replicate experiment 1 of library  DBbSNF1TRE
processed data file: WTTRE-BbSNF1TRE.xls


title: WTGLU-R2

description:
Replicate experiment 2 of library BbWT
processed data file: WTGLU-BbSNF1GLU.xls

value: PEPGLU (glucose)


title: Zscan10_KO_rep3

description:
Gene expression in subcloned Zscan10-null ES cells
rRNA depleted RNA

source_name: Embryonic stem cells, Zscan10 KO, replicate3


title: DBbSNF1GLU-R2

description:
Replicate experiment 2 of library DBbSNF1GLU
processed data file: WTGLU-BbSNF1GLU.xls


title: DBbSNF1GLU-R1

description:
Replicate experiment 1 of library DBbSNF1GLU
processed data file: WTGLU-BbSNF1GLU.xls


title: WTGLU-R1

description:
Replicate experiment 1 of library BbWT
processed data file: WTGLU-BbSNF1GLU.xls


title: Rb ChIP-Seq in LNCaP cells treated with 10nM DHT for 4 hours

city: Boston

first: Dong

last: Han

state: MA

address: 100 Morrissey Blvd

department: Biology-CPCT

institute: Umass Boston

library_source: genomic

data_processing:
Basecalling was done by Illumina MiSeq automatically
ChIP-seq reads were aligned to the Human UCSC hg19 reference genome using MACS2 based ChIPSeq v1.0.0 provided by Illumina Basespace Labs with the following configurations, Q-value: 0.05; Fold Enrinchment: 10,30;
Peaks were called using the same software with Q-value: 0.05; Fold Enrinchment: 10,30;
HOMER is also built into the same software to discover motifs with Motif Lengths: 8,10,12; Number of Motifs per length: 20; Search Window: 50
Genome_build: UCSC hg19
Supplementary_files_format_and_content: BED files and TXT files were generated by MACS2 based ChIPSeq in Illumina Basespace Labs, and TXT files containing peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate Cancer Cells

growth_protocol: VCaP cells are cultured routinely in 10% FBS containing DMEM and passed every 5-6 days. LNCaP cells are cultured in 10% FBS containing RPMI 1640 and passed every 3-4 days.

extract_protocol:
Cells were crosslinked with formaldehyde and then sonicated. DNA were immunoprecipitatted with Rb antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
ChIP DNA Library were prepared with NEBNext ChIP-Seq Library Prep Reagent set for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1)

treatment_protocol:
VCaP cells grown in 5% Charcoal/Dextran treated FBS for 3 days, then treat cells with 10 nM DHT for 4 hours
LNCaP cells grown in 5% Charcoal/Dextran treated FBS for 3 days, then treat cells with 10 nM DHT for 4 hours

tag: cell line

value: LNCaP

value: Prostate cancer

tag: passage

tag: antibody

value: Rb antibody (Cell Signaling Technology (Mouse mAb 4H1, #9309S, Lot:9))


title: Rb ChIP-Seq in VCaP cells treated with 10nM DHT for 4 hours

value: VCaP


title: cardiac fibroblast-derived exosomes sample 2

city: Hannover

first: Claudia

last: Bang

address: Carl-Neuberg-Straße 1

country: Germany

institute: Medical School Hannover

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed using cutadapt version 1.2.1
mature miRNA sequences for rattus norvegicus were downloaded from miRBase version 20
trimmed reads were mapped using NCBI blast version 2.2.28+ against the miRNA reference database created from mature miRNA
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized read counts and differential expression analysis from DESeq. In the file Differential_expression_DESeq.txt, baseMeanA represents Cardiac fibroblast and baseMeanB represents Cardiac fibroblast exosome.

organism: Rattus norvegicus

source_name: cardiac fibroblast-derived exosomes

growth_protocol: Neonatal rat cardiac fibroblasts were isolated from newborn rats by enzymatic digestion and were cultured in DMEM (PAA) supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in 5% CO2.

extract_protocol:
Cells were harvested and exosomes were collected from fibroblast conditioned medium and  RNA was isolated using Trizol reagent.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For exosome purification, neonatal rat cardiac fibroblasts were cultured in DMEM + 1% exosome-depleted FBS for 48h. Conditioned medium was collected and exosomes were purified by several centrifugation and filtration steps, following ultracentrifugation. Afterwards total RNA from cardiac fibroblasts and exosomes was isolated for miRNA sequencing.

value: wistar

value: heart

tag: rna source

value: cardiac fibroblast-derived exosomes


title: cardiac fibroblasts sample 2

source_name: cardiac fibroblasts

value: cardiac fibroblasts

tag: developmental stage


title: cardiac fibroblast-derived exosomes sample 1


title: cardiac fibroblast-derived exosomes sample 3


title: chr11_LacR_Suv39h1_UT_subTAD_400Kb_vp_4C-Seq_R1

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

country: Netherlands

institute: Hubrecht Institute

data_processing:
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank HindIII sites (4C fragment ends), using custom Perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome mm9.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle tracks contain uniquely mapped reads at 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located.  Scores represent the number of reads mapping to a HindIII restriction fragment end.

source_name: LacO transgenic embryonic stem cells

growth_protocol: Mouse embryonic stem cells C57Bl/6-129/Sv were cultured on gelatin-coated plates in BRL (buffalo–rat liver cells)-conditioned DMEM (Hooper et al., 1987)(high glucose, Gibco) with 15% FBS, 1x non-essential amino acids (NEAA; Gibco), 1x penicillin–streptomycin (Gibco), 1:1000 b-mercaptoethanol (Invitrogen), 1x L-glutamine (Gibco) and 1000 U ml-1 leukaemia inhibitory factor (LIF; Gibco).

extract_protocol:
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Cells are cross-linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with HindIII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (DpnII or NlaIII). After a second re-ligation step, the sample is purified and a 4C PCR is performed.
4C PCR

treatment_protocol: cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

value: LacO transgenic embryonic stem cells

tag: tissue/cell line

value: cell line

value: F1s from 129/Sv x C57BL/6


title: Zscan10_f/f-Tx_rep3

source_name: Embryonic stem cells, Zscan10 floxed, replicate3

value: ESC

value: control


title: chr11_LacR_Suv39h1_UT_subTAD_209Kb_vp_4C-Seq_R1


title: chr11_LacR_Suv39h1_TA_subTAD_400Kb_vp_4C-Seq_R1


title: chr11_LacR_Suv39h1_TA_subTAD_335Kb_vp_4C-Seq_R1


title: chr11_LacR_Suv39h1_TA_subTAD_80Kb_vp_4C-Seq_R1


title: WTTRE-R1

description:
Replicate experiment 1 of library WTTRE
processed data file: WTTRE-BbSNF1TRE.xls

value: wild type

value: PEPTRE (trehalose)

value: 3 days

tag: tissue


title: chr11_LacR_Ezh2_UT_subTAD_400Kb_vp_4C-Seq_R1

tag: cell type


title: 894rA

city: University Park

first: David

middle: Asher

last: Galbraith

state: Pennsylvania

address: 19a Chemical Ecology Lab

institute: Penn State University

description: processed data file: PSGE_gene_expression.txt, PSGE_reproductive.txt

data_processing:
We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10.
The transcriptome sequencing reads were aligned to the most recent honey bee genome assembly (Amel_4.5) using Tophat.
The data was normalized using a trimmed mean of M-values (TMM) method.
The EdgeR package in R statistical program was used to identify significantly differentially expressed genes.
The transcriptome sequencing reads were also aligned to pseudo-parent genomes (reference genome with parental SNPs included, one for paternal and one for maternal) allowing 0 mismatches with Tophat to look at parent specific gene expression.  This data can be found in PSGE_sterile.txt and PSGE_reproductive.txt
Genome_build: Amel4.5
Supplementary_files_format_and_content: PSGE_gene_expression.txt contains the gene expression data for each individual. PSGE_sterile.txt contains read counts for each sterile individual at each parental snp. PSGE_reproductive.txt contains read counts for each reproductive  individual at each parental snp.

molecule: polyA RNA

organism: Apis mellifera

source_name: Fat body and ovary of one individual with active ovaries

growth_protocol: Individuals from reciprocal crosses of Africanized and European honey bees were raised in queenless colonies for ~18 days, allowing time for the workers to activate the ovaries and become reproductively active.

extract_protocol:
Eviscerated abdomens with attached fat bodies and ovaries from individual bees were dissected in ice-cold RNAlater® (Qiagen, Valencia, CA) and excess RNAlater® was removed from the samples.  RNA was isolated using TRIzol® Reagent (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each individual had their ovaries dissected to determine if they were reproductive or sterile based on the level of ovary activation.

value: Eviscerated abdomen with attached fat bodies and active ovaries

value: Adult workers >18 days post emergence


title: 894qA


title: 894bA


title: chr11_LacR_Ezh2_UT_subTAD_335Kb_vp_4C-Seq_R1


title: chr11_LacR_Ezh2_UT_subTAD_80Kb_vp_4C-Seq_R1


title: cardiac fibroblasts sample 1


title: chr11_LacR_Ezh2_TA_subTAD_400Kb_vp_4C-Seq_R1


title: chr11_LacR_Suv39h1_TA_subTAD_209Kb_vp_4C-Seq_R1


title: 888jA


title: 888hA


title: chr11_LacR_Ezh2_TA_subTAD_335Kb_vp_4C-Seq_R1


title: chr11_LacR_Suv39h1_UT_subTAD_335Kb_vp_4C-Seq_R1


title: chr11_LacR_Ezh2_TA_subTAD_209Kb_vp_4C-Seq_R1


title: 882cA


title: chr11_LacR_Ezh2_TA_subTAD_80Kb_vp_4C-Seq_R1


title: 875gA


title: cardiac fibroblasts sample 4


title: 875cA


title: 8820A


title: chr11_LacR_4C-Seq_R4


title: chr11_LacR_Suv39h1_UT_subTAD_80Kb_vp_4C-Seq_R1


title: chr11_LacR_4C-Seq_R3


title: chr11_LacR_Suv39h1_dChromo_4C-Seq_R2


title: 894cI

description: processed data file: PSGE_gene_expression.txt, PSGE_sterile.txt

source_name: Fat body and ovary of one individual with inactive ovaries

value: Eviscerated abdomen with attached fat bodies and inactive ovaries


title: 894fI


title: 894iI


title: chr11_LacR_Suv39h1_dChromo_4C-Seq_R1


title: 888aA


title: chr11_LacR_Ezh2_UT_subTAD_209Kb_vp_4C-Seq_R1


title: chr8_LacR_Suv39h1_4C-Seq_R2


title: 882pA


title: 888eI


title: chr8_LacR_Ezh2_4C-Seq_R1


title: chr8_LacR_Ezh2_4C-Seq_R2


title: 882mI


title: chr8_LacR_Nanog_4C-Seq_R2


title: 888qI


title: 8827I


title: 882gI


title: chr8_LacR_4C-Seq_R2


title: chr8_LacR_Nanog_4C-Seq_R1


title: 882kI


title: 875aI


title: chr8_LacR_4C-Seq_R1


title: 8756I


title: Thymus PCMV-infected

city: Ya’an

first: Xiao

last: Liu

state: Sichuan Province

address: 46# Xinkang Road

department: College of Veterinary Medicine

institute: Sichuan Agricultural University

description:
microRNA profiling
miRNA_Expression_Analysis.xls
Differentially_Expressed_miRNAs.xls
All_Comparisons_of_Expressed_miRNAs.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
After sequencing, the total raw sequencing reads were filtered using Solexa CHASTITY quality control filter. The clean reads which passed quality filtering were then filtered by searching for reads, whose 3’-ends aligned to at least 6 nt of the 3’-adapter.
The adapter sequences were trimmed and the adapter-trimmed-reads (>= 15nt) were aligned to the known Sus scrofa pre-miRNA sequences in the miRBase 19 (miRNA) using Novoalign program (v2.07.11) with at most one mismatch. The unmapped reads were discarded as unusable reads.Any sequence that matched the mature miRNA region ±4nt within a known pre-miRNA hairpin were grouped and the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin were also indicated.
To correct for the difference in tag counts between samples, the tag counts were scaled to tpm (the copy number of transcripts per million) based on the total number of tag aligned to known Sus scrofa pre-miRNAs in miRBase 19. When comparing the differentially expressed miRNA profiles between two samples, fold change was calculated.
Genome_build: mm8, miRBase 19
Supplementary_files_format_and_content: Tag counts

organism: Sus scrofa

source_name: Porcine Thymus-PCMV infected

growth_protocol: PCMV Sichuan strain and porcine macrophages (Provided by the Animal Biotechnology Center of Sichuan Agricultural University) were used in this study. Cell cultures were performed in Corning 25 cm2 culture bottles (Corning, Shanghai, China) containing modified RPMI-1640 nutrient solution (Thermo Fisher Scientific, Waltham, UK) supplemented with 10% fetal bovine serum and 50 mg/ml penicillin/streptomycin antibiotic solution (GIBCO, Beijing, China), and were maintained under standard conditions of 5% CO2 and 37°C. Porcine macrophages were infected with PCMV at 10 PFU per cell, and then PCMV infected and normal porcine macrophages were collected at 72 hours post-infection (hpi). Our experiment consisted of pooled samples, samples were performed in triplicates. All infected and control samples were stored until use in a single RNA isolation assay.     The PCMV Sichuan (SC) strain and three-week-old male Yorkshire piglets were provided by the Animal Biotechnology Center of Sichuan Agricultural University (Ya’an, China). The 10 piglets were divided into two groups of five pigs each and maintained under controlled temperature and humidity. Serum samples collected from all 10 piglets were confirmed as PCMV antibody-negative before the start of the experiment. Each pig in the first group was inoculated with 5 ml of 109 PFU/ml PCMV SC strain by intramuscular and intranasal  injection at the same time, and each pig in the control group was injected with 5 ml of RPMI-1640 nutrient solution (Thermo Fisher Scientific, Waltham, UK) in the same way. The anti-PCMV antibody levels in the serum samples collected from the infected and control pigs at 13 dpi were determined as described previously.

extract_protocol:
RNA was harvested using Trizol reagent. The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Yorkshire

tag: gender

value: male

value: Thymus

tag: infection

value: PCMV Sichuan (SC) strain


title: 8754A


title: chr11_LacR_Suv39h1_4C-Seq_R2

tag: strain


title: 8751I


title: chr11_LacR_Suv39h1_4C-Seq_R1


title: 888uI


title: chr8_LacR_Suv39h1_4C-Seq_R1


title: Spleen PCMV-infected

source_name: Porcine Spleen-PCMV infected

value: Spleen


title: chr11_LacR_Ezh2_4C-Seq_R1


title: chr11_reciprocal_Asic2_vp_LacR_Suv39h1_4C-Seq_R2


title: chr11_reciprocal_Asic2_vp_LacR_Suv39h1_4C-Seq_R1


title: Spleen Control

source_name: Porcine Spleen-Control


title: chr11_LacR_4C-Seq_R2


title: chr11_reciprocal_HoxB_vp_LacR_Ezh2_4C-Seq_R2


title: chr11_reciprocal_HoxB_vp_LacR_Ezh2_4C-Seq_R1


title: Lung PCMV-infected

source_name: Porcine Lung-PCMV infected

value: Lung


title: Liver PCMV-infected

source_name: Porcine Liver-PCMV infected

value: Liver


title: chr11_reciprocal_Asic2_vp_LacR_4C-Seq_R2

value: LacO transgenic embryonic stem cells

value: cell line


title: Lung Control

source_name: Porcine Lung-Control


title: chr11_reciprocal_Asic2_vp_LacR_4C-Seq_R1

value: F1s from 129/Sv x C57BL/6


title: Liver Control

source_name: Porcine Liver-Control

value: control


title: chr11_LacO_Untransduced_4C-Seq_R1


title: chr11_reciprocal_HoxB_vp_LacR_4C-Seq_R1


title: Kidney PCMV-infected

source_name: Porcine Kidney-PCMV infected

value: Kidney


title: Thymus Control

source_name: Porcine Thymus-Control


title: H3K4me3_sh-ets1

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
For the HiSeq 2000 system, basecalls were performed using the Sequencing Analysis Viewer Software v1.9.1 and converted to fastq files using bcl2fastq 1.8.4
Alignment of reads to the mm9 genome was conducted using bowtie, using --all --best --strata -v 2 -m 1. Only reads with a unique best scoring alignment were retained. Clonal artifacts were filtered out retaining the longer reads.
Aligned reads were processed using a previously described in-house ChIP-Seq analysis pipeline (Koch, Fenouil et al 2011).  Using a stepwise tag size extension in 10bp increments, fragment size was estimated in silico for DN and DP ChIPs.
Tags were then elongated to the estimated mean fragment size and converted to wig format using a binning window of 50bp. Replicate tracks were subsequently merged by addition. To account for differences in tag counts between DN and DP experiments, tag count normalization was performed by scaling DP datasets to DN tag counts. Visual inspection of invariant targets (e.g. Eβ for Ets1, β-actin for Pol II, H3K4me1/2, Mnase, the Hoxa locus for H3K27me3) allowed further fine tuning and scaling of DP tag-counts to reflect potential differences in signal to noise ratios between DN and DP experiments.
Peak detection was carried out with CoCAS using averaged into 50bp windows and converted to general feature format (GFF). Thresholds were 7.5 x SD + mean for the main window and 5 x SD + mean for the extension window. Artifacts were detected and removed by performing peak detection in CoCAS (using 2 X SD + mean and SD + mean as main and extension window thresholds, respectively) in reads originating from the Input treatment. Peaks were annotated to the nearest TSS, except in the case of intragenic peaks which were assigned to the surrounding gene. Peaks outside of [-5kb; +5kb] around known TSSs (refSeq, miRNA, rRNA, scRNA, snRNA, snoRNA and tRNA) were considered to be distal, while those falling within [-5kb; +5kb] around known TSSs were considered proximal. Distal peaks within a gene body were considered intragenic and those outside of gene bodies were considered intergenic.
Genome_build: mm9
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Fixed-step 50bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Peaks were called using CoCAS

source_name: P5424 thymic cell line

growth_protocol: P5424 cells were grown in RPMI-1640 with 100 units/mL penicillin, 100 mg/mL streptomycin, and 2 mM L-glutamine at 37°C and with 5% CO2

extract_protocol:
Phenol-chroloform
Library preparation was carried out as per manufacturer’s instructions (Illumina) using 10ng material. Samples were subsequently size-selected via gel migration and extraction,. Sequencing was carried out on an Illumina HiSeq 2000. The quality of libraries was checked with the Bioanalyser DNA High sensitivity and by Q-PCR.

treatment_protocol: P5424 cells were transfected with sh-scr, sh-Ets1 with an Neon electroporator using manufacturer's instructions and grown for 48 hours

tag: treatment

tag: cells used

value: Abcam (ab8580)

tag: antibody quantity

value: 2 µg

tag: magnetic beads

value: Protein G dynabeads

tag: bead volume

tag: estimated fragment size


title: H3K4me1_sh-ets1

value: Abcam (ab8895)

tag: cell line


title: Macrophage PCMV-infected

source_name: Porcine PCMV infected macrophage

value: macrophage


title: H3K4me1_sh-scr

value: sh-scr

tag: antibody


title: chr8_LacO_Neomycin_vp_4C-Seq_R1


title: chr11_LacR_Nanog_4C-Seq_R1


title: Ets1_P5424

value: WT

value: Santa Cruz (sc-350x)

value: 10 µg

value: Sheep anti-rabbit IgG dynabeads


title: Kidney Control

source_name: Porcine Kidney-Control

value: Yorkshire

value: male


title: Macrophage control

source_name: Porcine macrophage


title: RNR3 OE relicate 2 Input (Total)

status: Public on Dec 18 2015

city: Los Angeles

first: Jared

middle: M

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

description:
Total genomic DNA from galactose induced culture arrested in early S-phase
processed data file: RNR_HU.txt

data_processing:
library strategy: Quantitative BrdU-IP Seq (QBU)
fastq-multx by ea-utils was used to split barcodes (QBU_501_305_swap.txt)
Barcode split PE files were aligned to S. cerevisiae reference genome R64-1-1 using Bowtie2
Aligned files were sorted and binned into 50 bp non-overlapping bins using Samtools/Bedtools (QBU_HU.txt)
For QBU samples, IP bins were divided by their corresponding Input (Total) Sample Bins to yield normalized data (QBU_Time_Course.txt)
Genome_build: R64-1-1
Supplementary_files_format_and_content: txt files

organism: Saccharomyces cerevisiae

source_name: RNR3 OE Input (Total)

growth_protocol: For late G1 block, induction, and release, cells (pre-selected on SD-URA for plasmid as appropriate) were inoculated into YEP+2% raffinose at 25°C and grown to mid-log phase

extract_protocol:
Genomic DNA was isolated with standard phenol chloroform extraction
Genomic DNA isolation and shearing by sonication has been described previously (Knott et al., 2012) 1 µg total genomic DNA (sheared to ~300 bp average) was end-repaired and ligated with a barcoded, Illumina-compatible adapter using NEBNext Ultra End Repair/dA-Tailing Module (E7442) and NEBNext Ultra Ligation Module (E7445) (Dunham and Friesen, 2013).  AMPure beads (Beckman Coulter Cat#A63880) were used to isolate the genomic DNA and its concentration was determined by spectroscopy (Nanodrop).  Equal amounts of multiple such barcoded DNA samples were pooled; 20 ng was set aside as “Input” and 1 µg of this pool was subject to BrdU-IP as described previously (Knott et al., 2012).  The IP and Input DNA samples were PCR-amplified separately with indexed Illumina-compatible primers.  Amplified DNA was isolated using AMPure beads and validated and quantified on a Bioanalyzer, and pooled.

treatment_protocol: Cells were blocked in G1 by resuspension (at O.D. ~0.5) in fresh YEP+2% raffinose +7.5 nM α-factor at 25°C for 3 hrs.  For induction, cells were resuspended in YEP+2% galactose +7.5 nM α-factor at 25°C for 2 hrs. Cultures were released into S-phase by resuspension (at O.D. ~1.0) in fresh YEP+2% galactose +200 µg/mL Pronase E (Sigma-Aldrich, P5147) and sonicated to disperse cells.  Early S-phase analysis of replication was performed by including 0.2M HU (Sigma-Aldrich, H8627) and BrdU at 400 µg/mL (Sigma-Aldrich, B5002) for 60 min at 25°C.  For the time course experiment, BrdU was used at 800 µg/mL.

tag: genotype/variation

value: RNR3 OE (WT pGAP-RNR3)

tag: drug

value: Hydroxyurea

tag: time point

value: HU arrest (60 min post release)

tag: barcode (5')

tag: chip antibody


title: chr11_LacR_4C-Seq_R1

source_name: LacO transgenic embryonic stem cells

tag: cell type

value: LacO transgenic embryonic stem cells

tag: tissue/cell line

value: cell line

value: F1s from 129/Sv x C57BL/6


title: chr11_LacO_Untransduced_4C-Seq_R2


title: no OE replicate 2 Input (Total; control for RNR3 OE)

source_name: no OE Input (Total; control for RNR3 OE)

value: no OE (WT)


title: RNR3 OE relicate 1 Input (Total)


title: chr8_LacO_Untransduced_4C-Seq_R1


title: RNR3 OE relicate 1 IP

description:
BrdU labeled genomic DNA immunoprecipitated from galactose induced culture arrested in early S-phase
processed data file: RNR_HU.txt

source_name: RNR3 OE  IP

value: BrdU antibody (Invitrogen, catalog#033900)


title: no OE replicate 2 IP (control for RNR3 OE IP)

source_name: no OE IP (control for RNR3 OE IP)


title: no OE replicate 1 IP (control for RNR3 OE IP)


title: no OE replicate 1 Input (Total; control for RNR3 OE)


title: Fkh1 OE replicate 1 RNA-Seq

description:
polyA isolated RNA from galactose induced culture arrested in G1
genes_G1.txt

data_processing:
QBU Samples:
fastq-multx by ea-utils was used to split barcodes
Barcode split PE files were aligned to S. cerevisiae reference genome R64-1-1 using Bowtie2
Aligned files were sorted and binned into 50 bp non-overlapping bins using Samtools/Bedtools
For QBU samples, IP bins were divided by their corresponding Input (Total) Sample Bins to yield normalized data
RNA-Seq Samples:
Samples were aligned to S. cerevisiae reference genome R64-1-1 with Tophat2 using a known transcript file (.gtf)
Samples were next subjected to the Cufflinks transcript assembly and differential experession pipeline including Cuffdiff to call differentially expressed transcripts (FDR <= 0.01)
Genome_build: R64-1-1
Supplementary_files_format_and_content: .bed file

source_name: S. cerevisiae

extract_protocol:
Genomic DNA was isolated with standard phenol chloroform extraction
Genomic DNA isolation and shearing by sonication has been described previously (Knott et al., 2012) 1 µg total genomic DNA (sheared to ~300 bp average) was end-repaired and ligated with a barcoded, Illumina-compatible adapter using NEBNext Ultra End Repair/dA-Tailing Module (E7442) and NEBNext Ultra Ligation Module (E7445) (Dunham and Friesen, 2013).  AMPure beads (Beckman Coulter Cat#A63880) were used to isolate the genomic DNA and its concentration was determined by spectroscopy (Nanodrop).  Equal amounts of multiple such barcoded DNA samples were pooled; 20 ng was set aside as “Input” and 1 µg of this pool was subject to BrdU-IP as described previously (Knott et al., 2012).  The IP and Input DNA samples were PCR-amplified separately with indexed Illumina-compatible primers.  Amplified DNA was isolated using AMPure beads and validated and quantified on a Bioanalyzer, and pooled.
Quantitative BrdU-IP Seq (QBU)

value: Fkh1 OE (WT pGAL-Fkh1)

value: No Drug

value: G1 Arrest

value: No BC


title: Fkh2 OE replicate 1 RNA-Seq

value: Fkh2 OE (WT pGAL-Fkh2)


title: Fkh2 OE replicate 2 RNA-Seq


title: Fkh1 OE replicate 2 RNA-Seq


title: DM replicate 1Input (Total)

description:
Total genomic DNA from galactose induced culture released into early S-phase at the indicated timepoint
QBU_501_305_swap.txt

value: fkh1delta fkh2delta ars501delta::ARS305 (pGAL)


title: no OE replicate 2  RNA-Seq

value: no OE ( WT pGAL)


title: DM replicate 2 Input (Total)


title: no OE replicate 1 RNA-Seq


title: DM Fkh1 OE replicate 2 Input (Total)

value: fkh1delta fkh2delta ars501delta::ARS305 Fkh1OE (pGAL-Fkh1)


title: DM Fkh1 OE replicate 1 Input (Total)


title: DM replicate 1 IP

description:
BrdU labeled genomic DNA immunoprecipitated from galactose induced culture arrested in early S-phase
QBU_501_305_swap.txt


title: DM replicate 2 IP


title: RNR3 OE relicate 2 IP


title: H3K4me3_sh-scr

value: sh-scr

value: Abcam (ab8580)

value: 2 µg

value: Protein G dynabeads


title: no OE 45 min replicate 2 IP

description:
BrdU labeled genomic DNA immunoprecipitated from galactose induced culture released into early S-phase at the indicated timepoint
QBU_Time_Course.txt

value: S-phase pulse 30-45 min


title: no OE 35 min replicate 2 IP

value: S-phase pulse 20-35 min


title: DM Fkh1 OE replicate 1 IP

value: Hydroxyurea

value: HU arrest (60 min post release)


title: DM Fkh1 OE replicate 2 IP

value: BrdU antibody (Invitrogen, catalog#033900)


title: Fkh1 OE 45 min replicate 2 IP

value: Fkh1 OE (WT pGAL-Fkh1)


title: no OE 55 min replicate 2 IP

value: No Drug

value: S-phase pulse 40-55 min


title: Fkh1 OE 55 min replicate 2 IP


title: no OE 45 min replicate 2 Input (Total)

description:
Total genomic DNA from galactose induced culture released into early S-phase at the indicated timepoint
QBU_Time_Course.txt


title: no OE 55 min replicate 2 Input (Total)


title: no OE 35 min replicate 2 Input (Total)


title: Fkh1 OE 35 min replicate 2 IP


title: Fkh1 OE 55 min replicate 1 IP


title: Fkh1 OE 55 min replicate 2 Input (Total)


title: Fkh1 OE 35 min replicate 2 Input (Total)


title: Fkh1 OE 45 min replicate 2 Input (Total)


title: Fkh1 OE 45 min replicate 1 IP


title: no OE 55 min replicate 1 IP


title: no OE 35 min replicate 1 IP


title: Fkh1 OE 45 min replicate 1 Input (Total)


title: no OE 45 min replicate 1 IP


title: Fkh2 OE replicate 2 Input (Total)

description:
Total genomic DNA from galactose induced culture arrested in early S-phase
QBU_HU.txt


title: no OE 45 min replicate 1 Input (Total)


title: Fkh1 OE 35 min replicate 1 Input (Total)


title: Fkh2 OE replicate 1 Input (Total)


title: Fkh2 OE replicate 3 Input (Total)


title: Fkh1 OE replicate 3 Input (Total)


title: no OE 35 min replicate 1 Input (Total)


title: no OE replicate 2 Input (Total)


title: Fkh1 OE replicate 2 Input (Total)


title: Fkh1 OE replicate 1 Input (Total)


title: Fkh1 OE 35 min replicate 1 IP


title: no OE replicate 1 Input (Total)


title: Fkh2 OE replicate 3 IP

description:
BrdU labeled genomic DNA immunoprecipitated from galactose induced culture arrested in early S-phase
QBU_HU.txt


title: Fkh2 OE replicate 2 IP


title: Fkh1 OE replicate 3 IP


title: Fkh2 OE replicate 1 IP


title: no OE replicate 3 IP


title: Fkh1 OE replicate 1 IP


title: Fkh1 OE replicate 2 IP


title: no OE replicate 1 IP


title: no OE replicate 2 IP


title: Fkh1 OE 55 min replicate 1 Input (Total)


title: Jurkat_Gata3_ChIP-seq

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1.

source_name: T-ALL

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

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

value: Jurkat

tag: antibody vendor

value: Santa Cruz

tag: antibody cat. #

tag: antibody lot


title: Jurkat_Runx1_ChIP-seq

value: Abcam


title: IIS3

city: Guangzhou

first: Ji-Long

address: 483 Wushan Rd

institute: South China Agricultural University

description:
New Zealand White
mRNA(polyA+)

data_processing:
After sequencing, a computational pipeline was used to process RNA-seq data. Raw sequence data in fastq format were filtered to remove reads with more than 10% unknown nucleotides. Clean reads were mapped to rabbit reference genome OryCun2 with Tophat v1.4.0 allowing no more than two mismatches. Transcript isoforms were assembled using Cufflinks v1.3.0 and combined with the gene annotations from ENSEMBL database release 81. Gene expression levels were measured using reads per Kilobase of transcript per million mapped reads (RPKM). To compare profile differences between two groups, a t-test with Benjamini-Hochberg multiple test correction was employed. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.01.
Genome_build: OryCun2
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. The first column is gene name, the second column is ENSEMBL ID, and the third column is RPKM value.

organism: Oryctolagus cuniculus

source_name: Uterine tissues from the inter-implantation site (IIS) on day 7.25 of pregancy

growth_protocol: Adult New Zealand White rabbits, aged 3~4 mo and weighted 2.5~3.1 kg, were used for this study. Female rabbits were mated with males and the time of mating was designated as day 0 of pregnancy. Animals (n=3) were euthanased on day 7.25 (6 h after day 7) of pregnancy by injecting 20 ml air into the auricular veins. Uterine tissues from the implantation site (IS) and the inter-implantation site (IIS) were collected separately. All samples were flash-frozen in liquid nitrogen and stored at -80 °C for further analysis. All animal procedures were approved by the Institutional Animal Care and Use Committee of South China Agricultural University.

extract_protocol: Total RNA from uterine samples was extracted using TRIzol reagent (invitrogen). RNA purity was assessed using the ND-1000 Nanodrop and RNA integrity was evaluated using the Agilent 2200 TapeStation. The following RNA quality control parameters were used: A260/A280 ratio ≥ 1.8, A260/A230 ratio ≥ 2.0 and RIN value ≥ 7.0. The mRNA-Seq sample preparation kit (Illumina) was used for the preparation of RNA-Seq libraries. Briefly, poly-(A)+ mRNA was purified with oligo-(dT) magnetic beads and fragmented to approximately 200 bp in fragmentation buffer. The obtained cleaved RNA fragments were reverse transcribed to first-strand cDNA, followed by second-strand cDNA synthesis. The double-stranded cDNA fragments were purified, end-repaired and then ligated to sequencing adapters. After purification, suitable fragments were amplified through 15 cycles of PCR to generate the final sequencing libraries. Finally, PCR products were purified and quantified for high-throughput sequencing using the Illumina HiSeq™ 2500.

tag: tissue

value: uterus

tag: group

value: inter-implantation site


title: IIS2

description:
New Zealand White
mRNA(polyA+)


title: no OE replicate 3 Input (Total)

tag: strain

value: no OE ( WT pGAL)


title: IIS1

description:
New Zealand White
mRNA(polyA+)


title: IS2

description:
New Zealand White
mRNA(polyA+)

source_name: Uterine tissues from the implantation site (IS) on day 7.25 of pregancy

value: implantation site


title: IS3

description:
New Zealand White
mRNA(polyA+)


title: Diabetic liver

city: Shanghai

first: Qiwei

last: Zhai

address: 294 Taiyuan Road

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

description: small RNAs (18-30 nucleotides)

data_processing:
We filtered the Solexa small RNA sequencing dataset by eliminating low quality reads and trimming 3' primer adaptor sequences and adaptor contaminants to generate clean reads.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: Diabetic liver

extract_protocol:
About 3 h after the beginning of light cycle, 9-week-old mice were sacrificed, and the livers were immediately removed and snap-frozen in liquid nitrogen. Total RNA was extracted from liver samples with Trizol reagent (Invitrogen), according to the manufacturer's instruction.
The Solexa sequencing procedure was conducted by using the manufacturer’s protocol. Briefly, after gel purification of small RNAs sized at 18-30 nt, a pair of Solexa proprietary adaptors was ligated to their 5’ and 3’ ends. Ligation products were gel-purified, reverse transcribed, and amplified by PCR using Illumina’s small RNA primer set complementary to the linker sequences. The generated cDNA library was utilized for sequencing analysis using the Illumina Genome Analyzer according to the manufacturer’s instructions.

tag: genotype

value: db/db

value: liver

tag: developmental stage

value: adult, 9 weeks

tag: gender

value: male


title: Normal liver

description: small RNAs (18-30 nucleotides)

source_name: Normal liver

value: wild type


title: IS1

description:
New Zealand White
mRNA(polyA+)


title: CFTR knockout Mouse Colon Tumor rep 2 tech rep 2 in run2

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence quality was accessed via FastQC, and none of the preprocessing (trimming, filtering or masking) is necessary.
Raw paired-reads were mapped to mouse genome (mm10) using Tophat 2.0.13 with iGenome (mm10) reference and following parameters: -p 8 -r 0 --no-novel-juncs.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following the nature protocol
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements (output from Cuffnorm)

source_name: CFTR knockout Mouse Colon Tumor

growth_protocol: Apc+/+ Cftr+/+ and Apc+/+ Cftrfl/fl-Villin-Cre mice were maintained in colonies at the University of Minnesota-Medical School Duluth until the age of 12 weeks.

extract_protocol:
All samples were processed in Qiagen RNAlater, and total RNA was isolated using a Qiagen RNA Easy kit. Total RNA was quantitated with a Nanodrop Spectrophotometer.
RNA samples passed the quality control (RIN>8) were used to create a polyA barcoded RNAseq libraries using standard Illumina TruSeq protocols.

treatment_protocol: Mouse small intestine and colon tissues were removed, opened longitudinally, and rinsed in PBS.

tag: strain background

value: CFTR knockout; Apc-CFTR-

tag: age

value: 3 month

tag: tissue type

value: Mouse Tumor

value: Colon Tumor


title: CFTR knockout Mouse Colon Tumor rep 2 tech rep 1 in run2

tag: genotype/variation


title: CFTR knockout Mouse Ileum Tumor rep 1 tech rep 1 in run2

source_name: CFTR knockout Mouse Ileum Tumor

value: Ileum Tumor


title: CFTR knockout Mouse Ileum Tumor rep 2 tech rep 1 in run2


title: no OE 55 min replicate 1 Input (Total)

tag: drug

value: No Drug

tag: time point

value: S-phase pulse 40-55 min

tag: barcode (5')


title: CFTR knockout Mouse Colon Tumor rep 1 tech rep 1 in run2


title: CFTR knockdown Mouse Colon Tumor rep 2 tech rep 2 in run1

source_name: CFTR knockdown Mouse Colon Tumor

value: CFTR knockdown; Apc-CFTRhet


title: CFTR knockdown Mouse Colon Tumor rep 2 tech rep 1 in run1


title: CFTR knockout Mouse Colon Tumor rep 1 tech rep 2 in run2


title: CFTR knockdown Mouse Colon Tumor rep 1 tech rep 2 in run1


title: CFTR wildtype Mouse Ileum Tumor rep 2 tech rep 2 in run2

source_name: CFTR wildtype Mouse Ileum Tumor

value: CFTR wildtype; Apc-CFTR+


title: CFTR knockdown Mouse Duodenum Tumor rep 1 tech rep 2 in run1

source_name: CFTR knockdown Mouse Duodenum Tumor

value: Duodenum Tumor


title: CFTR knockdown Mouse Duodenum Tumor rep 2 tech rep 1 in run1


title: CFTR wildtype Mouse Ileum Tumor rep 2 tech rep 1 in run2


title: CFTR wildtype Mouse Ileum Tumor rep 1 tech rep 2 in run2


title: CFTR wildtype Mouse Ileum Tumor rep 1 tech rep 1 in run2


title: CFTR wildtype Mouse Colon Tumor rep 2 tech rep 2 in run2

source_name: CFTR wildtype Mouse Colon Tumor


title: CFTR knockdown Mouse Duodenum Tumor rep 1 tech rep 1 in run1


title: CFTR wildtype Mouse Colon Tumor rep 1 tech rep 1 in run2


title: CFTR wildtype Mouse Colon Tumor rep 2 tech rep 1 in run2


title: CFTR knockout Mouse Ileum Tumor rep 2 tech rep 2 in run2


title: CFTR knockout Mouse Ileum Tumor rep 1 tech rep 2 in run2


title: CFTR knockout Mouse Duodenum Tumor rep 2 tech rep 2 in run2

source_name: CFTR knockout Mouse Duodenum Tumor

value: CFTR knockout; Apc+CFTR-


title: CFTR wildtype Mouse Colon Tumor rep 1 tech rep 2 in run2


title: CFTR knockout Mouse Duodenum Tumor rep 2 tech rep 1 in run2


title: CFTR knockout Mouse Colon Tumor tech rep 2 in run1


title: mRNA_Hb9:gfp_WT_rep_6

city: La Jolla

first: Neal

middle: D

last: Amin

state: CA

address: 10010 N Torrey Pines Road

department: Gene Expression Laboratory

institute: Salk Institute for Biological Studies

data_processing:
Raw FASTQ reads were processed for gene expression levels using Sailfish against the mouse mm10 Refgene database (downloaded from UCSC). For paired-end samples only the left reads were quantified.  All reads were trimmed to 50bp prior to quantification.
Estimated counts per transcript from all samples were normalized using median normalization (DESeq method) and scaled per kilobase of transcript length to generate normalized reads per kilobase (NRPK) expression levels.
Bedgraph files were generated from corresponding FASTQ samples aligned to Mouse mm9 and processed to bedgraph format using bedtools.
Supplementary_files_format_and_content: NRPK expression values for gene and isoform level quantifications.

growth_protocol: Embryos or differentiated mES were collected at the indicated developmental stage.  Spinal cords were microdissected and dissociated with papain before performing FACS to isolate fluorescently labelled cell populations.  Floor plate cells were dissected without FACS-isolation.  mES cells were differentiated into neural progenitors in the presence of retinoic acid and sonic hedghog agonist before FACS-isolation or collection.

extract_protocol:
Isolated cells were collected directly into RNA lysis buffer (miRvana kit) and the total RNA isolation protocol was followed.
mRNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA+ tails was selected using oligo-dT beads. mRNA was then fragmented and reverse-transcribed into cDNA. cDNA was end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acids after each step.

tag: background mutation

tag: genetic reporter

tag: sorted fraction

value: GFP positive

tag: cell type

value: motoneurons


title: CFTR knockdown Mouse Colon Tumor rep 1 tech rep 1 in run1

tag: tissue


title: mRNA_Hb9:gfp_WT_rep_5


title: CFTR knockout Mouse Duodenum Tumor rep 2 tech rep 2 in run1


title: CFTR knockout Mouse Colon Tumor tech rep 1 in run1


title: CFTR knockout Mouse Duodenum Tumor rep 1 tech rep 2 in run2


title: CFTR knockout Mouse Colon Tumor tech rep 1 in run2


title: mRNA_Floor_Plate_rep_1

value: unsorted

value: floor plate glial cells


title: mRNA_Hb9:gfp_WT_rep_4


title: CFTR knockdown Mouse Duodenum Tumor rep 2 tech rep 2 in run1


title: CFTR knockout Mouse Duodenum Tumor rep 1 tech rep 1 in run2


title: CFTR knockout Mouse Colon Tumor tech rep 2 in run2


title: CFTR wildtype Mouse Duodenum rep 2 tech rep 2 in run2

source_name: CFTR wildtype Mouse Duodenum

value: CFTR wildtype; Apc+CFTR+

value: Mouse Epithelium

value: Duodenum


title: CFTR wildtype Mouse Duodenum rep 2 tech rep 1 in run2

value: 3 month


title: CFTR knockout Mouse Duodenum Tumor rep 1 tech rep 1 in run1

value: Mouse Tumor


title: mRNA_Hb9:gfp_WT_rep_1

value: wild type


title: CFTR wildtype Mouse Colon rep 2 tech rep 2 in run2

source_name: CFTR wildtype Mouse Colon

value: Mouse whole tissue

value: Colon


title: CFTR wildtype Mouse Duodenum rep 2 tech rep 1 in run1


title: CFTR wildtype Mouse Colon rep 2 tech rep 2 in run1


title: CFTR knockout Mouse Duodenum Tumor rep 2 tech rep 1 in run1


title: CFTR wildtype Mouse Colon rep 2 tech rep 1 in run2


title: CFTR wildtype Mouse Duodenum rep 1 tech rep 1 in run1


title: CFTR wildtype Mouse Duodenum rep 1 tech rep 1 in run2


title: CFTR wildtype Mouse Duodenum rep 1 tech rep 2 in run2


title: CFTR wildtype Mouse Duodenum rep 1 tech rep 2 in run1


title: CFTR wildtype Mouse Colon rep 1 tech rep 1 in run2


title: CFTR wildtype Mouse Colon rep 1 tech rep 2 in run1


title: CFTR wildtype Mouse Colon rep 1 tech rep 1 in run1


title: CFTR knockout Mouse Duodenum rep 2 tech rep 2 in run2

source_name: CFTR knockout Mouse Duodenum


title: CFTR knockout Mouse Duodenum Tumor rep 1 tech rep 2 in run1


title: CFTR knockout Mouse Colon rep 2 tech rep 1 in run2

source_name: CFTR knockout Mouse Colon


title: CFTR knockout Mouse Duodenum rep 2 tech rep 1 in run1


title: CFTR knockout Mouse Colon rep 2 tech rep 2 in run2


title: CFTR knockout Mouse Duodenum rep 2 tech rep 2 in run1


title: CFTR knockout Mouse Colon rep 2 tech rep 2 in run1


title: CFTR knockout Mouse Colon rep 2 tech rep 1 in run1


title: CFTR wildtype Mouse Duodenum rep 2 tech rep 2 in run1


title: CFTR knockout Mouse Duodenum rep 1 tech rep 1 in run2


title: CFTR knockout Mouse Duodenum rep 1 tech rep 2 in run1


title: CFTR knockout Mouse Colon rep 1 tech rep 2 in run2


title: CFTR wildtype Mouse Colon rep 2 tech rep 1 in run1


title: CFTR knockout Mouse Duodenum rep 1 tech rep 2 in run2


title: CFTR knockout Mouse Colon rep 1 tech rep 2 in run1


title: CFTR knockout Mouse Colon rep 1 tech rep 1 in run2


title: E12_5_Chx10_V2a

description: processed data file: Amin_et_al_sRNA_E12_5.txt

data_processing:
Reads containing the adapter sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were trimmed and aligned to the mature miRNA database for mouse (downloaded from miRBase) with bowtie2.
Reads mapping equally well to multiple targets were downweighted by 1/N where N is the number of targets.
Read counts were converted to TPM (transcripts per million mapped reads)
Supplementary_files_format_and_content: Tab delim table of TPM expression levels

source_name: V2a interneurons

growth_protocol: Embryos were collected at the indicated developmental stage.  Spinal cords were microdissected and dissociated with papain before performing FACS to isolate fluorescently labelled cell populations.

extract_protocol:
FACS-isolated cells were collected directly into RNA lysis buffer (miRvana kit) and the total RNA isolation protocol was followed.
Small RNA-sequencing libraries were prepared using NEBNext Small RNA Library Prep for Illumina. Libraries were then quantified, pooled and sequenced using either the Illumina HiSeq 2500 or Illumina HiSeq 2000 platforms.

value: tdTomato positive

value: V2a spinal interneurons

tag: molecule subtype

value: small RNAs


title: CFTR knockout Mouse Colon rep 1 tech rep 1 in run1


title: CFTR wildtype Mouse Colon rep 1 tech rep 2 in run2


title: CFTR knockout Mouse Duodenum rep 1 tech rep 1 in run1


title: E12_5_Sim1_V3

source_name: V3 interneurons

value: V3 spinal interneurons


title: E10_5_Hb9:gfp_neg_rep_2

description: processed data file: Amin_et_al_sRNA_E10_5.txt

source_name: Non-motoneurons

value: GFP negative

value: non-motoneuron spinal cells


title: E10_5_Hb9:gfp_neg_rep_1


title: CFTR knockout Mouse Duodenum rep 2 tech rep 1 in run2

value: CFTR knockout; Apc+CFTR-


title: E10_5_Hb9:gfp_pos_rep_2

source_name: Motoneurons

value: GFP positive

value: spinal motoneurons


title: mRNA_mES_NP

value: unsorted

value: spinal neuronal progenitors


title: E10_5_Hb9:gfp_pos_rep_1


title: mRNA_mES_pMN

value: motoneuron progenitors


title: mRNA_En1_V1

value: V1 spinal interneurons


title: mRNA_Chx10_V2a


title: mRNA_Hb9:gfp_218DKO_rep_2

value: motoneurons


title: mRNA_Hb9:gfp_WT_rep_2

value: wild type


title: mRNA_Sim1_V3


title: mRNA_Hb9:gfp_218DKO_rep_1


title: RNAseq_EP400KD

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description: RNA.FPKM

data_processing:
EP400_IP fastq files (I, II and III) were merged together and a single fastq file for EP400IP was generated. Corresponding EP400_Input fastq files (I, II and III) were also merged together and the resultant EP400Input file was used for EP400 peak calling.
All Mock IPs were analysed with EP400Input_I.fastq.gz, and all IPs under EP400 knock-down condition were analysed with Input_EP400KD.
Fastq files were used to map reads to human genome (hg19) with bowtie-0.12.9 for ChIP-seq or TopHat v2.0.8 for RNA-seq
An in-house MATLAB script was used for ChIP-seq peak-calling. CEAS was used to plot metagene profiles. poissP values were plotted to generate heatmaps.  FPKM was calculated using accepted bam file from cuffdiff v2.0.2 for mRNA-Seq.
Genome_build: hg19_2009
Supplementary_files_format_and_content: ChIP: peak .bed; RNA-Seq: FPKM

growth_protocol: U2OS cells were grown in DMEM with Tet-approved FBS

extract_protocol:
Total RNA was extracted with Trizol, digested with DNaseI and further purified by acid phenol. For ChIP-Seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with respective antibodides.
Libraries for ChIP-seq were prepared with KAPA LTP kit and RNA-seq Illumina TruSeq RNA Sample Prep Kits v2 according to the manufacturer’s protocol

treatment_protocol: Cells were transfected either with EP400 or mock siRNA (GFP) for 72 hr prior to harvest

tag: antibody

tag: cell line


title: Input_EP400KD

description: Input for EP400 siRNA treated cells


title: H3K4me1_Mock

description: H3K4me1_IP in Mock siRNA treated cells

value: anti-H3K4me1 antibody is from Abcam, ab8895


title: RNAseq_Mock

description: RNA.FPKM


title: MED26_Mock

description: MED26_IP in Mock siRNAtreated cells

value: anti-MED26 antibody is from Santa Cruz Biotechnology, sc-48776


title: H3K18ac_Mock

description: H3K18ac_IP in Mock siRNA treated cells

value: Anti-H3K18ac antibody is from Kurdistani lab


title: H2AZ_Mock

description: H2AZ_IP in Mock siRNAtreated cells

value: anti-H2AZ antibody is from Abcam, ab4174


title: H2AZ_EP400KD

description: H2AZ_IP in EP400 siRNAtreated cells


title: MED26_EP400KD

description: MED26_IP in EP400 siRNAtreated cells


title: E12_5_Hb9:gfp_pos

tag: developmental stage

tag: genotype

value: small RNAs


title: H3.3_EP400KD

description: H3.3_IP in EP400 siRNAtreated cells

value: anti-H3.3 antibody is from Abnova,H00003021-M01


title: H3.3_Mock

description: H3.3_IP in Mock siRNAtreated cells


title: PolII_Mock

description: PolII_IP in Mock siRNAtreated cells

value: anti-Pol II antibody is from (QED Bioscience)


title: EP400_Input_III

description: Input_III for EP400


title: PolII_EP400KD

description: PolII_IP in EP400 siRNAtreated cells


title: EP400_IP_III

description: EP400_IP_III in U2OS cells

value: anti-EP400 antibody is from Abcam, ab70301


title: EP400_Input_II

description: Input_II for EP400


title: EP400_IP_II

description: EP400_IP_II in U2OS cells


title: EP400_Input_I

description: Input_I for EP400


title: unc_WW_input_2

status: Public on Dec 17 2015

city: Happy Valley

first: Alex

last: Chitsazan

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

description:
diffReps_output_mll_WW.txt
unc_mll_WW_H3K4me3_2_peaks.bed

data_processing:
Base calls were performed using CASAVA-1.8.2
Single-end 51 base reads were mapped to version 3.1 of the S. mediterranea genome using bowtie with the following parameters:    best --strata    v 2    m 2 .
H3K4me3 difference peaks between control (unc22(RNAi)) and knockdown (set1(RNAi) or mll1/2(RNAi)) were called using diffReps (Shen et al., 2013) with the following parameters: --btr --bco --nsd sharp --frag 250. Peaks were mapped to genes and all further quantitative analysis was carried out using R and Bioconductor.
Peaks were found using macs2 with the following parameters: -g 895484558 -q 0.01 --model.   The "v31.xxxxxx" identifiers represent contigs.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: diffReps output files.
Supplementary_files_format_and_content: MACS2 peaks files.

organism: Schmidtea mediterranea

source_name: WholeWorm

extract_protocol:
Chromatin-immunoprecipitation was performed as previously described (Lee et al., 2006) with some modifications. Briefly, worms were snap-frozen in liquid nitrogen, homogenized with a clean razor, resuspended in freshly cracked 4% PFA (EMS)/calcium- and magnesium-free buffer with 1% BSA (CMFB) and rocked for 10 minutes at room temperature to cross-link and dissociate. Samples were then quenched with 0.125M glycine, filtered with 100μm cell strainers (Corning), pelleted by centrifugation at 700*g, and washed twice with ice-cold 0.4XPBS + 10% FBS + 1X Roche Complete protease inhibitors. FACS-isolated planarian cells and Drosophila S2 cells were cross-linked in suspension in collection buffer + 10% FBS or Schneider’s media + 10% FBS, respectively. Pellets were then either snap-frozen or resuspended in lysis buffer (1% SDS, 50mM Tris pH 8, 10mM EDTA) and incubated on ice for 10 min. Samples were then sheared for 12 min in the S220 Focused Ultrasonicator (Covaris) in milliTubes (Covaris) with either the AFA fiber or 100μl glass beads (for volumes < 1ml). Samples were then cleared by centrifugation (10K*g, 10 min) and used for immunoprecipitations. H3K4me3 antibody (Millipore 07-473) was used at 0.5-1μl antibody/μg chromatin (as estimated by Qubit measurement of dsDNA in IP inputs) and incubated 4hrs - overnight at 4°C. Antibody-chromatin complexes were then captured with a mix of ProteinA/G magnetic beads (Life Technologies; 2hrs, 4°C), washed, eluted and incubated overnight at 65°C to reverse cross-links. Samples were then digested with RNase and ProteinaseK, and DNA was isolated by column purification (Qiagen).
DNAseq libraries were made using an optimized protocol with reagents from the Illumina TruSeq RNA kit and data was collected for ChIP Seq analysis on an Illumina HiSeq 2500.

treatment_protocol: dsRNA-containing food for RNAi treatment was generated as previously described (Gurley et al., 2008); briefly, cloned genes were transformed into bacterial strain Ht115, induced to express dsRNA with 1mM (final) IPTG, incubated with shaking at 37C for 2 hours, then pelleted, rinsed, and mixed with calf liver paste for ingestion. Live worms images were captured using a Leica M205-FA; movies were captured using a Zeiss Lumar V12 equipped with an Axiocam HRc. Worms were subjeted to RNAi for 6 days for set RNAI and 9 days from mll RNAi

value: whole worm

tag: replicate

tag: RNAi treatment

value: unc

tag: chip antibody

value: None (Input)


title: EP400_IP_I

description: EP400_IP_I in U2OS cells


title: unc_WW_input_1

description:
diffReps_output_mll_WW.txt
unc_mll_WW_H3K4me3_1_peaks.bed


title: unc_mll_WW_H3K4me3_2

value: anti-H3K4me3 (Millipore, catalog# 07-473, lot# 2459618)


title: unc_mll_WW_H3K4me3_1


title: X1_input

data_processing:
Base calls were performed using CASAVA-1.8.2
Single-end 51 base reads were mapped to version 3.1 of the S. mediterranea genome using bowtie with the following parameters: —best --strata –v 2 –m 2.
H3K4me3 difference peaks between control (unc22(RNAi)) and knockdown (set1(RNAi) or mll1/2(RNAi)) were called using diffReps (Shen et al., 2013) with the following parameters: --btr --bco --nsd sharp --frag 250. Peaks were mapped to genes and all further quantitative analysis was carried out using R and Bioconductor.
Peaks where found using macs2 with the following parameters: -g 895484558 -q 0.01 --model. For H3K36me3, the previous parameters were used with the addition of: --broad.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: broadPeak file (the "v31.xxxxxx" identifiers represent contigs).

source_name: X1 Cells

tag: RNAi

value: None (WT)


title: X1_K36m3

value: H3K36me3 (Abcam, catalog#  ab9050, lot# GR75636-2)


title: mll_WW_input_1

description:
diffReps_output_mll_WW.txt
mll_WW_H3K4me3_1_peaks.bed

value: mll


title: mll_WW_input_2

description:
diffReps_output_mll_WW.txt
mll_WW_H3K4me3_2_peaks.bed


title: mll_WW_H3K4me3_2


title: mll_WW_H3K4me3_1


title: unc_Xins_input_1

description:
diffReps_output_mll_Xins.txt
unc_mll_Xins_H3K4me3_1_peaks.bed

source_name: Xins cells

value: Xins


title: unc_Xins_input_2

description:
diffReps_output_mll_Xins.txt
unc_mll_Xins_H3K4me3_2_peaks.bed


title: unc_mll_Xins_H3K4me3_2


title: unc_mll_Xins_H3K4me3_1


title: unc_mll_X1_H3K4me3_2

description:
diffReps_output_mll_X1.txt
unc_mll_X1_H3K4me3_2_peaks.bed

source_name: X1 cells


title: unc_X1_input_2


title: unc_mll_X1_H3K4me3_1

description:
diffReps_output_mll_X1.txt
unc_mll_X1_H3K4me3_1_peaks.bed


title: mll_Xins_input_2

description:
diffReps_output_mll_Xins.txt
mll_Xins_H3K4me3_2_peaks.bed


title: mll_Xins_input_1

description:
diffReps_output_mll_Xins.txt
mll_Xins_H3K4me3_1_peaks.bed


title: mll_Xins_H3K4me3_2


title: mll_Xins_H3K4me3_1


title: mll_X1_input_2

description:
diffReps_output_mll_X1.txt
mll_X1_H3K4me3_2_peaks.bed


title: mll_X1_input_1

description:
diffReps_output_mll_X1.txt
mll_X1_H3K4me3_1_peaks.bed


title: unc_WW_tc_1

description:
diffReps_output_set1_WW.txt
unc_set_WW_H3K4me3_1_peaks.bed


title: mll_X1_H3K4me3_2


title: mll_X1_H3K4me3_1


title: unc_WW_tc_2

description:
diffReps_output_set1_WW.txt
unc_set_WW_H3K4me3_2_peaks.bed


title: unc_set_WW_H3K4me3_2


title: set1_WW_tc_2

description:
diffReps_output_set1_WW.txt
set1_WW_H3K4me3_2_peaks.bed


title: unc_set_WW_H3K4me3_1


title: set1_WW_H3K4me3_2


title: set1_WW_H3K4me3_1

description:
diffReps_output_set1_WW.txt
set1_WW_H3K4me3_1_peaks.bed


title: WholeWorm_input


title: unc_Xins_tc_1

description:
diffReps_output_set1_Xins.txt
unc_set_Xins_H3K4me3_1_peaks.bed


title: WholeWorm_H3K4me3


title: unc_Xins_tc_2

description:
diffReps_output_set1_Xins.txt
unc_set_Xins_H3K4me3_2_peaks.bed


title: unc_set_Xins_H3K4me3_2


title: unc_X1_input_1


title: unc_X1_tc_2

description:
diffReps_output_set1_X1.txt
unc_set_X1_H3K4me3_2_peaks.bed


title: unc_set_Xins_H3K4me3_1


title: unc_X1_tc_1

description:
diffReps_output_set1_X1.txt
unc_set_X1_H3K4me3_1_peaks.bed


title: unc_set_X1_H3K4me3_2


title: set1_Xins_tc_1

description:
diffReps_output_set1_Xins.txt
set1_Xins_H3K4me3_1_peaks.bed


title: set1_Xins_H3K4me3_1


title: set1_Xins_H3K4me3_2

description:
diffReps_output_set1_Xins.txt
set1_Xins_H3K4me3_2_peaks.bed


title: set1_X1_tc_2

description:
diffReps_output_set1_X1.txt
set1_X1_H3K4me3_2_peaks.bed


title: unc_set_X1_H3K4me3_1


title: set1_X1_tc_1

description:
diffReps_output_set1_X1.txt
set1_X1_H3K4me3_1_peaks.bed


title: set1_X1_H3K4me3_2


title: tc_Xins_1

description:
diffReps_output_X1_Xins.txt
Xins_1_peaks.bed


title: set1_WW_tc_1


title: tc_Xins_2

description:
diffReps_output_X1_Xins.txt
Xins_2_peaks.bed


title: tc_X1_2

description:
diffReps_output_X1_Xins.txt
X1_2_peaks.bed


title: tc_X1_1

description:
diffReps_output_X1_Xins.txt
X1_1_peaks.bed


title: set1_X1_H3K4me3_1


title: H3K4me3_ip_Xins_1


title: H3K4me3_ip_X1_2


title: H3K4me3_ip_X1_1


title: H3K4me3_ip_Xins_2


title: WW_unc_9_3

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614 defined in GEO submission: GSE72389
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt  files contain tab-delimited RPKM values for each sample.

source_name: Wholeworm Tissue

extract_protocol:
To isolate stem cells, we used a well-established method to isolate planarian stem cells by Hoechst blue staining and flow cytometry. Sorted cells were homogenized in Trizol reagent and RNA was isolated per the manufacturer-supplied protocol. Isolated RNA from whole worm tissue was treated with RNase-free DNase on QIagen RNeasy columns and eluted in nuclease-free water.
500ng-1μg RNA per whole worm sample or 100ng of sorted cell RNA was used for generation of RNAseq libraries using the Illumina TruSeq kit.

treatment_protocol: dsRNA-containing food for RNAi treatment was generated as previously described (Gurley et al., 2008); briefly, cloned genes were transformed into bacterial strain Ht115, induced to express dsRNA with 1mM (final) IPTG, incubated with shaking at 37C for 2 hours, then pelleted, rinsed, and mixed with calf liver paste for ingestion. set1 was treated with RNAi for 6 and 9 days. and mll1/2 was treated with RNAi for 9 and 12 days

tag: days exposed to rnai


title: WW_unc_9_1


title: set1_Xins_tc_2


title: WW_unc_12_4


title: WW_unc_12_2


title: WW_unc_12_1


title: WW_mll_9_4


title: WW_unc_12_3


title: WW_mll_9_2


title: WW_mll_9_3


title: WW_mll_12_2


title: WW_mll_12_3


title: WW_mll_9_1


title: WW_mll_12_1


title: unc_X1_d9_4


title: unc_X1_d9_3


title: unc_X1_d9_2


title: unc_X1_d12_4


title: unc_X1_d12_2


title: WW_unc_9_4


title: WW_unc_9_2


title: unc_9_X1_2


title: unc_9_X1_4


title: unc_9_X1_3


title: unc_9_X1_1


title: unc_9_3


title: WW_mll_12_4


title: unc_6_X1_3


title: unc_6_X1_2


title: unc_6_X1_1


title: unc_X1_d9_1


title: unc_9_2


title: unc_6_X1_4


title: unc_6_4


title: unc_6_1


title: unc_6_3


title: set1_9_X1_3


title: unc_6_2


title: set1_9_X1_4


title: unc_X1_d12_1


title: set1_9_X1_2


title: set1_9_X1_1


title: unc_X1_d12_3


title: set1_9_4


title: set1_9_3


title: set1_9_1


title: set1_9_2


title: unc_9_4


title: set1_6_X1_4


title: unc_9_1


title: set1_6_4


title: set1_6_X1_1


title: set1_6_X1_2


title: mRNA_Hb9:gfp_WT_rep_3

value: wild type

value: GFP positive

value: motoneurons


title: set1_6_2


title: set1_6_1


title: mll_X1_d9_4


title: mll_X1_d12_4


title: mll_X1_d9_1


title: mll_X1_d12_3


title: mll_X1_d9_2


title: mll_X1_d12_1


title: mll_X1_d12_2


title: set1_6_X1_3


title: X1_3

description: rpkm.txt

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614.fa (same .fa linked to GSE72389).
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.
Supplementary_files_format_and_content: smed_20140614.fa contains the sequences of the 36,035 alignment targets described above. Each sequence defline contains a unique identifier for the sequence, the originating transcriptome identifier, and the source of the sequence.

value: adult


title: X1_1

description: rpkm.txt


title: Xins_1

description: rpkm.txt

source_name: Xins Cells


title: X1_4

description: rpkm.txt


title: Xins_4

description: rpkm.txt


title: Xins_3

description: rpkm.txt


title: X1_2

description: rpkm.txt


title: xylulose evo 12a

first: Zvi

last: Tamari

state: California

address: 5531 Boelter Hall

description: evolved

data_processing:
Illumina Casava1.8 software used for basecalling.
Adaptor and UMI barcodes were trimmed off and reads were aligned to the S288C_reference_sequence_R64-1-1_20110203 reference genome using Bowtie
Genome_build: S288C_reference_sequence_R64-1-1_20110203
Supplementary_files_format_and_content: Processed read count per gene per sample. Each column corresponds to one of twelve strains, either before or after evolution, grown on either glucose or xylulose. Each row corresponds to a gene. Data was averaged over two repeats. Samples containing less than 400,000 reads were not included in the analysis.

source_name: cell population

growth_protocol: Cells were inoculated into either YPD or YP-xylulose media with initial OD of 0.1

extract_protocol:
Log phase cells were harvested and frozen in liquid Nitrogen. Total RNA was extracted using a NucleoSpin® 96 RNA kit (Macherey-Nagel), substituting β-mercaptoethanol with DTT
RNA extracts were fragmented and polyadenylation was selected using PolydT beads. cDNA was prepared using Smartscribe and UMI-containing barcoded primers, and subjected to RNnase H treatment. A second adaptor was subsequently ligated.

tag: strain

tag: repetition

value: repetition 1


title: xylulose evo 12b

description: evolved

value: repetition 2


title: xylulose evo 10a

description: evolved


title: xylulose evo 8a

description: evolved


title: xylulose evo 11b

description: evolved


title: xylulose evo 11a

description: evolved


title: xylulose evo 9a

description: evolved


title: xylulose evo 10b

description: evolved


title: mll_X1_d9_3


title: xylulose evo 8b

description: evolved


title: xylulose evo 7b

description: evolved


title: xylulose evo 7a

description: evolved


title: xylulose evo 6a

description: evolved


title: xylulose evo 5b

description: evolved


title: xylulose evo 4b

description: evolved


title: xylulose evo 5a

description: evolved


title: Xins_2

description: rpkm.txt


title: xylulose evo 4a

description: evolved


title: xylulose evo 3b

description: evolved


title: xylulose evo 2b

description: evolved


title: xylulose evo 3a

description: evolved


title: xylulose evo 2a

description: evolved


title: xylulose evo 9b

description: evolved


title: xylulose evo 1b

description: evolved


title: xylulose wt  12b

description: wild type


title: xylulose wt  8b

description: wild type


title: xylulose wt  10a

description: wild type


title: xylulose evo 6b

description: evolved


title: xylulose wt  10b

description: wild type


title: xylulose wt  9b

description: wild type


title: xylulose wt  7b

description: wild type


title: xylulose wt  11a

description: wild type


title: set1_6_3


title: xylulose wt  8a

description: wild type


title: xylulose wt  6b

description: wild type


title: xylulose wt  7a

description: wild type


title: xylulose wt  12a

description: wild type


title: xylulose evo 1a

description: evolved


title: xylulose wt  9a

description: wild type


title: xylulose wt  4b

description: wild type


title: xylulose wt  11b

description: wild type


title: xylulose wt  6a

description: wild type


title: xylulose wt  5a

description: wild type


title: xylulose wt  2b

description: wild type


title: xylulose wt  3a

description: wild type


title: xylulose wt  2a

description: wild type


title: xylulose wt  3b

description: wild type


title: xylulose wt  5b

description: wild type


title: xylulose wt  4a

description: wild type


title: xylulose wt  1a

description: wild type


title: glucose evo 12a

description: evolved


title: glucose evo 11b

description: evolved


title: glucose evo 12b

description: evolved


title: glucose evo 9b

description: evolved


title: glucose evo 10a

description: evolved


title: glucose evo 10b

description: evolved


title: glucose evo 6b

description: evolved


title: glucose evo 7b

description: evolved


title: glucose evo 8a

description: evolved


title: glucose evo 7a

description: evolved


title: glucose evo 6a

description: evolved


title: glucose evo 5a

description: evolved


title: glucose evo 5b

description: evolved


title: glucose evo 4a

description: evolved


title: glucose evo 4b

description: evolved


title: glucose evo 3b

description: evolved


title: HF19

city: Worcester

first: Alper

last: Kucukural

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

description: WGBS

data_processing:
bsmap, v2.73, default
Genome_build: Illumina NextSeq:mm10, Illumina HiSeq 2500: mm9
Supplementary_files_format_and_content: Methylation calls could not be located. Processed data are not available for this study.

source_name: Spermatozoa_WGBS_13weeks_high fat

growth_protocol: Sibling male mice were split at weaning (3 weeks) onto control or low protein, or control or high fat diets. Mice were maintained on these diets until sacrifice at 10 weeks.

extract_protocol:
Cauda epididymis and vas deferens was rapidly dissected and punctured, and was incubated in 500 ¼L of human tubule fluid (HTF - Millipore MR-070-D) at 37 C for 30 minutes. Supernatant was removed, sperm were pelleted at 2000 g for 5 minutes, washed once with 1 mL water and then pelleted. Sperm were washed again with 1 mL PBS, and pelleted again. Sperm were resuspended in 400 ¼L DNA Lysis Buffer (10mM Tris, 5mM EDTA, 0.5% SDS, and 200mM NaCl) with 10mM DTT, and incubated at 37oC for 30 minutes. Sperm were subjected to needle homogenization. 20 ¼g/mL Proteinase K was added to the homogenate and incubated at 55oC for 16 hours.  DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol and precipitated with 100% EtOH.
DNA was sheared to an average length of ~100-500 bp with a Covaris sonicator, fragment ends were cleaned up and A-tailed. Fragments were ligated to pre-methylated Illumina paired-end adaptors, bisulfite converted, and PCR-amplified.

tag: age

value: 13 weeks

value: FVB/NJ

value: Cauda epididymis and vas deferens

value: Spermatozoa


title: glucose evo 3a

description: evolved


title: HF33

description: WGBS

source_name: Spermatozoa_WGBS_12weeks_high fat

treatment_protocol: Sibling male mice were split at weaning (3 weeks) onto control or low protein, or control or high fat diets. Mice were maintained on these diets until sacrifice at 10 weeks.

value: 12 weeks


title: HF49

description: WGBS


title: SEM ATACSeq

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital

department: Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

data_processing:
Library strategy: ATAC-Seq
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk

source_name: Leukaemia cell line (SEM)

growth_protocol: SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5

extract_protocol:
Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040).

value: SEM

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: LP33

description: WGBS

source_name: Spermatozoa_WGBS_12weeks_low protein


title: xylulose wt  1b

description: wild type


title: glucose evo 2b

description: evolved


title: HF43

description: WGBS

source_name: Spermatozoa_WGBS_13.5weeks_high fat

value: 13.5 weeks


title: glucose evo 2a

description: evolved


title: LP19

description: WGBS

source_name: Spermatozoa_WGBS_13weeks_low protein


title: glucose evo 11a

description: evolved


title: glucose evo 1b

description: evolved


title: glucose evo 8b

description: evolved


title: glucose evo 9a

description: evolved


title: LP49

description: WGBS


title: glucose wt  12b

description: wild type


title: R8 rep2

first: Lawrence

middle: S.

last: Zipursky

address: Howard Hughes Medical Institu675 Charles E. Young Drive South 5-784 MacDonald Research Laboratories

institute: University of California, Los Angeles

data_processing:
Illumina Casava1.7 software used for basecalling.
After filtering out reads with low quality and reads containing sequencing adapters, we mapped raw reads to the D. melanogaster reference genome (release FB2013_01) with the gapped aligner Tophat, allowing up to two mismatches. The Drosophila melanogaster gene model annotation (i.e. Drosophila_melanogaster.BDGP5.73.gtf) was downloaded from the Ensembl database and supplied to Tophat. Only reads uniquely aligned were collected.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using customized scripts written in Perl.
Genome_build: Release 5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Drosophila melanogaster

source_name: Photoreceptor neurons

extract_protocol:
For tissue dissociation, pupal brain tissue dissected at 40hrs after pupal formation was incubated with a Papain (Worthington) and Liberase TM protease cocktail (Roche) at 250C for 15 min in a microfuge shaker at 1000rpm. At 5 and 10 min into this incubation, the tissue was pipetted up and down with a P200. At 15 min the sample was passed through a 25G 5/8-gauge needle until the tissue was completely dissociated. Digestion was inactivated by the addition of rich media with serum, and the cell suspension was passed through a 70μm filter. To concentrate the cells, the suspension was spun down at 1600rpm for 8 min at 40C. After decanting the supernatant, cells were re-suspended in approximately 500ul of rich media and sorted in a BD FACSAria II.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Photoreceptor neurons

value: optical lobe

value: 96 hrs APF


title: LP43

description: WGBS

source_name: Spermatozoa_WGBS_13.5weeks_low protein


title: C19

description: WGBS


title: glucose wt  12a

description: wild type


title: C49

description: WGBS


title: glucose wt  11a

description: wild type


title: R8 rep1

value: wild type


title: C43

description: WGBS


title: R7 rep2

value: 65 hrs APF


title: glucose wt  10a

description: wild type


title: R7 rep1


title: glucose wt  10b

description: wild type


title: L5 rep2

source_name: Lamina neurons

value: Lamina neurons

value: 53 hrs APF


title: glucose wt  9b

description: wild type


title: AF4_ENL Input DNA

data_processing:
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk

value: none (input)


title: L4 rep1

value: 45 hrs APF


title: glucose wt  9a

description: wild type

value: repetition 1


title: glucose evo 1a

description: evolved


title: ENL_ChIPSeq


title: L4 rep2


title: L3 rep4

value: 40 hrs APF


title: AF4_ChIPSeq


title: glucose wt  8b

description: wild type

value: repetition 2


title: MLL Input DNA


title: C33

description: WGBS

value: FVB/NJ

value: Cauda epididymis and vas deferens

value: Spermatozoa


title: glucose wt  7b

description: wild type


title: L3 rep3


title: glucose wt  8a

description: wild type


title: L3 rep2


title: MLL_ChIPSeq

value: SEM

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

value: MLL (Bethyl, A300-086A)


title: glucose wt  7a

description: wild type


title: Histone Input DNA


title: L3 rep1

value: optical lobe


title: glucose wt  6b

description: wild type


title: glucose wt  11b

description: wild type


title: L5 rep1


title: H3K79me3_ChIPSeq


title: L2 rep2

value: 35 hrs APF


title: L2 rep1

value: wild type


title: glucose wt  5b

description: wild type


title: H3K79me2_ChIPSeq


title: L1 rep2

value: 24 hrs APF


title: glucose wt  5a

description: wild type


title: H3K4me1_ChIPSeq


title: glucose wt  4b

description: wild type


title: dcl1/2/3/4

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
sRNAseq: After removing bacodes, adapters and low-quality reads, clean reads of size 18-30 nt or 30-60 nt were mapped to the Arabidopsis genome (TAIR10 version) with Bowtie (Langmead et al., Genome Biology, 2009, 10, R25) allowing no mismatches.sRNA abundance was calculated as reads per million (RPM) or reads per 10 million (RP10M).
BS-Seq: Bisulfite sequencing reads were mapped to Arabidopsis genome (TAIR10) by BRAT-BW (Harris et al., 2012) with parameters -m 3 -i 0 -a 1000, allowing up to three mismatches. Only uniquely mapped reads were retained for further methylation analysis. Copy-duplicates were removed by Remove-dupl command of BRAT-BW package. Acgt-count command of BRAT-BW was used to calculate fractional DNA methylation levels.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq processed data, our provided files were generated by acgt-count command of BRAT-BW and their format is 'Chr,Start,End,Context:Coverage,Methylation level,Strand'. Small RNA-seq samples are associated with files containing genome-matched unique sequence and the read count.

organism: Arabidopsis thaliana

source_name: Three-wks-old seedlings

growth_protocol: plants were grown under a 16-hlight/ 8-h-dark photoperiod

extract_protocol:
Genomic DNA was isolated by CTAB method
Bisulfite sequencing libraries were constructed using the NEXTflex Bisulfite-Seq kit (BIOO SCIENTIFIC) according to the manufacturer’s instructions.

tag: ecotype background

value: Columbia

tag: genotype/variation

value: Three-weeks-old

value: seedlings


title: L1 rep1

tag: cell type

value: Lamina neurons


title: glucose wt  4a

description: wild type

value: repetition 1


title: atrimmer2 Rep3

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen) followed by PEG precipitation to enrich low molecular-weight sRNAs. The resulting sRNAs were resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-30nt were excised, and the RNAs were eluted and purified for small RNA library contruction.
Small RNA libraries were constructed as previously described (Mi et al., Cell, 2008, 133, 116-127).

tag: tissue

value: Small RNA


title: OVCAR8_BRD4-KDM4C_rep2

first: Gabriela

last: Pregernig

state: Massachusetts

address: 1325 Boylston Street, Suite 500

institute: Decibel Therapeutics

data_processing:
Basecalls were performed using standard Illumina software.
Trimmed reads were aligned to the human transcriptome (hg19, refFlat GTF given with -G option) using TopHat2 (v 2.0.9) with the options --no-novel-juncs --library-type fr-firststrand.
Cufflinks (v 2.1.1) was used for evaluating gene expression levels in individual samples (hg19, refFlat GTF given with -G option). Options used were --frag-bias-correct --library-type fr-firststrand and masking mitochondrial and rRNA transcripts with -M.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing FPKM (Fragments per Kilobase per Million Reads) values for each sample.

source_name: Human ovarian cancer cell line

growth_protocol: OVCAR8-ADR-Cas9 was cultured in RPMI supplemented with 10% heat-inactivated fetal bovine serum and 1X antibiotic-antimycotic at 37 oC with 5% CO2.

extract_protocol:
RNA were extracted from cells using TRIzol Plus RNA Purification Kit (Life Technologies) according to manufacturer’s protocol and treated with PureLink on-column DNase kit (Life Technologies). RNA quality and concentration was determined using NanoDrop Spectrophotometer. RNA samples were reverse-transcribed using SuperScript III Reverse Transcriptase (Life Technologies), Random Primer Mix (New England Biolabs) and RNAse OUT (Invitrogen). Sequencing libraries were prepared using the Illumina Library Prep Kit, starting with an input amount of 1 µg total RNA and following the manufacturer’s recommendations.
Strand-specific libraries were prepared using the Illumina Library Prep Kit according to the manufacturer's instructions. After PCR amplification, the libraries were size-selected to 300 +/- 25 bp on a 2% agarose gel (E-Gel EX, Invitrogen).

treatment_protocol: OVCAR8-ADR-Cas9 cells infected with the indicated sgRNAs for 15 days.

tag: infected with sgrna


title: glucose wt  3a

description: wild type


title: atrimmer2 Rep2

tag: molecule subtype


title: glucose wt  3b

description: wild type

value: repetition 2


title: OVCAR8_BRD4-KDM4C_rep1

tag: cell line


title: glucose wt  2b

description: wild type