title: MGM62362

city: New York

first: Michael

middle: S

last: Glickman

state: NY

address: 408 East 69th street, Z1531

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
basecalling made with Illumina CASAVA2
paired sequence read files were trimmed for adapter sequence and low quality sequence using cutadapt -q 3,3 --minimum length 30 --pair-filter=any and assessed for overall quality using fastqc
trimmed reads were mapped to MC2 155 (NC_008596.1) using bwa mem -M -t 12, resulting SAM files were sorted and merged using samtools view -u | samtools sort -O bam, samtools merge
gene counts were obtained using featureCounts -a MC2155.gff -t gene -g Name -s 2 -Q 5 -o counts.txt -R -B -C -P -p
Normalized expression values and log2 fold changes were obtained using R package DESeq2 with design= ~strain using strains WT, BLSID, and CDBLSID; pairwise comparisons were obtained using contrast, csv files were written for each comparison and merged together along with the DESeq normalized counts for each sample and exported to a .txt file
Genome_build: MC2 155 (NC_008596.1)
Supplementary_files_format_and_content: tab delimited .txt file with gene name, mean expression, log2 fold change, standard error, Wald statistic, pvalue and Benjamini-Hochberg adjusted pvalues for each pairwise comparison along with normalzed counts for each sample

organism: Mycolicibacterium smegmatis

source_name: ΔrbpA attB::rbpA(72-114aa) kan, bacterial cells

growth_protocol: 50 ml bacterial log phase culture in LBsmeg normalized to an OD600 of 0.4

extract_protocol:
Pellets collected by centrifugation were washed in 1 ml 10 mM Tris, pH 8.0. Pellets were then resuspended in 100 µl TE80 with 1 mg/ml lysozyme and disrupted by bead beating with a FastPrep120 2 times at 5.0 m/sec for 25 seconds. This lysate was used for RNA purification with a GeneJet RNA purification kit (Thermoscientific) following the manufacturer's protocol. RNA was eluted in 85 µl elution buffer and then treated with DNase I (Thermoscientific) for 30 minutes at 37°C. GeneJet purification columns were used to clean RNA from DNaseI reactions.
Sample libraries were prepared for RNA-seq using the Ribo-Zero Magnetic Bacterial kit (Epicentre) in connection with TruSeq Stranded Total RNA kit (Illumina)

treatment_protocol: Pellets were resuspended in RNALater (Invitrogen) and stored overnight at 4°C

tag: strain

tag: genotype

value: {delta}rbpA attB::rbpA(72-114aa) kan


title: H9_pxMARGI_rep2_1

status: Public on Jan 26 2017

type: SRA

city: La Jolla

first: Marcelo

last: Rivas

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

country: USA

institute: University of California San Diego

description:
Chimeric fragments from RNA-DNA interactions were retrieved. R1 and R2 reads correspond to RNA and DNA fragments, respectively. Thus, the paired-end files are not characterized by average insert size or standard deviation.
Processed data file: HEK_P_pqvalues.poisson.txt

library_source: transcriptomic

data_processing:
The first two bases of R1 reads were removed.
Duplicated paired-end reads were removed.
Reads containing linker sequences (found using FastQC) were trimmed.
Using only non-protein-coding genes (GTF from ENSEMBL GRCh38 release 84), we counted the RNA ends (R1 reads) per gene. For every gene, we determined the statistical significance of its RNA count under the null hypothesis that RNA ends are distributed proportionally to gene lengths. For a given gene x, we modeled the distribution of RNA counts with a Poisson function with parameter lambda=(count of RNA reads overlapping all genes)*(length of gene x)/(sum of all gene lengths). For each gene, P-values were computed as the probability of the gene RNA count being equal to or greater than its observed gene RNA count. The corresponding q-values were computed using the Bioconductor package qvalue.
Genome_build: GRCh38
Supplementary_files_format_and_content: *pqvalues.poisson.txt: Tab-delimited text files include raw counts. The files contain 7 columns: gene_id, gene_name (extracted from ENSEMBL GTF), biotype (extracted from ENSEMBL GTF), rna (observed RNA count), dna (observed DNA count), p-value (of observed RNA count), and q-value (of observed RNA count).

molecule: other

organism: Homo sapiens

source_name: H9 cells

growth_protocol: HEK cells were cultured in Dulbecco's modified Eagle medium (DMEM; GIBCO 11960044) supplemented with 10% FBS, 2 mM Glutamax (GIBCO 35050061), and 5,000 U/ml penicillin/streptomycin (GIBCO 15070063), at 37 ºC with 5% CO2. H9 cells were cultured on matrigel (Corning 354277) coated plates and maintained in Essential 8 medium (GIBCO A1517001) at 37 ºC with 5% CO2.

extract_protocol:
The major steps of MARGI technologies are: crosslinking, isolation of nuclear material, protein biotinylation, genome fragmentation, RNA fragmentation, stabilization of proteins on streptavidin beads, end modification and RNA ligation, DNA ligation, reverse crosslinking, purification of RNA and DNA, removal of biotin from non-ligated linkers, pulldown of ligation products, reverse transcription, DNA denaturation, circularization and re-linearization, generation of sequencing library, and paired-end sequencing. See Extended Materials and Methods in published paper for details.
Sequencing library was generated by amplifying material using NEBnext Hi-fidelity PCR enzyme (New England Biolabs M0541S) with NEBnext multiplex oligos for Illumina sequencing (New England Biolabs E7335S) as the primers. Multiple test PCRs with 1 μL of sample and 10 μL reaction volume were run to identify the correct cycle number for the production run. The production PCR was run in a 50 μL reaction volume with 5 μL sample. After the PCR, size selection was performed using Ampure XP beads (Beckman Coulter A63880). Library between 200-2000 bp was selected. Library was run on a Bioanalyzer to determine the size distribution and then paired-end sequenced for 100 cycles at each end on Illumina HiSeq 2500 (PE100) or MiniSeq sequencers (PE150).

tag: cell line

tag: cell type

value: embryonic stem (ES) cells

tag: protocol

value: pxMARGI


title: H9_pxMARGI_rep1_2


title: MGM62342

molecule: total RNA

source_name: ΔrbpA attB::rbpA(28-114aa) kan, bacterial cells

value: {delta}rbpA attB::rbpA(28-114aa) kan


title: MGM62343


title: H9_diMARGI_rep1_2

description:
Chimeric fragments from RNA-DNA interactions were retrieved. R1 and R2 reads correspond to RNA and DNA fragments, respectively. Thus, the paired-end files are not characterized by average insert size or standard deviation.
Processed data file: HEK_I_pqvalues.poisson.txt

value: diMARGI


title: MDAMB134_genomic_input_DNA_3

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

library_source: genomic

data_processing:
Sequences were aligned to the human reference genome (GRCh37) using BWA version 0.7.12.
Duplicates were removed using Picard Tool version 1.47
Overlapping reads were clipped using clipOverlap tool from bamUtil repository version 1.0.14 with default parameters
SNPs were identified from gDNA samples using the Genome Analysis ToolKit 3.4-46 software across all gDNA samples simultaneously.
As per GATK recomendations, duplicated reads were removed and local realignment and base quality recalibration were employed prior to SNP  calling.
Called SNPs were filtered using a hard filtering criteria (QD < 2.0, FS > 60.0, MQ < 30.0, MQRankSum < -12.5, ReadPosRankSum < -8.0).
Allele-specific analysis was performed with BaalChIP R package (version 0.1.9) with the default parameters and options.
VariantAnnotaion (version 1.8.13) package in R was used to annotate ASB SNPs with respect to gene annotations
Genome_build: GRCh37
Supplementary_files_format_and_content: Information about the allele-specific SNPs identified in FAIRE-seq samples. The data contains SNP identifiers and chromosome coordinates according to dbSNP137 (columns "ID", "CHROM" and "POS"), the reference and alternative allele of each SNP (REF, ALT), information about which allele is specifically bound ("ASB_allele"), degree of the allele-specific imbalance as given by BaalChIP pipeline ("Allelic Imbalance"). The columns "GeneName" and "Location" correspond to SNP annotations relative to gene features (intron, coding, intergenic, etc).

molecule: genomic DNA

source_name: MDAMB134 cells

growth_protocol: MDAMB134 and T47D human breast cancer cells were cultured in RPMI (Invitrogen) supplemented with 10% FBS and antibiotics. All cells were maintained at 37C, 5% CO2. All cell lines were from the CRUK Cambridge Institute biorepository collection. Cell lines were authenticated by short tandem repeat genotyping using the GenePrint 10 (Promega) system and confirmed to be mycoplasma free.

extract_protocol:
Cells were fixed for 10 mins in 1% formaldehyde in FCS-free medium, washed and frozen. Nuclei were isolated and sonicated in Diagenode Bioruptor using 300ul volumes in 1.5ml eppendorfs. MDAMB134 (3x107 cells/tube) and T47D (1.5x107 cells/tube). Sonication was performed for 20 cycles of 30s on/off. Sonicate was subjected to three consecutive phenol–chloroform–isoamyl alcohol (25:24:1) extractions and reverse cross-linked overnight. DNA was purified by ethanol precipitation and quantified by Quanti-iT. Genomic DNA was isolated using Qiagen DNeasy Blood and tissue Kit according to protocol.
DNA fragments are prepped for sequencing using the recommended protocol available for Angilent SureSelect-Illumina sequencing.

value: breast cancer cell line MDAMB134


title: HEK_pxMARGI_rep1_2

description:
Chimeric fragments from RNA-DNA interactions were retrieved. R1 and R2 reads correspond to RNA and DNA fragments, respectively. Thus, the paired-end files are not characterized by average insert size or standard deviation.
Processed data file: H9_P_pqvalues.poisson.txt

source_name: HEK cells

value: HEK


title: MGM62363


title: MGM62341


title: VenusPos3

city: San Francisco

first: Brian

middle: J

last: Laidlaw

address: 513 Parnassus Avenue, HSE 1001

institute: University of California, San Francisco

data_processing:
Sequences reported as fastq files
Fastq files alligned to mm10 genome with STAR
Mappable reads counted with HTseq and imported into RStudio
DESeq2 used  to analyze differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet with normalized counts for all samples

organism: Mus musculus

extract_protocol:
Cells were isolated by sorting using an Aria sorter and total RNA purified using the RNeasy Mini kit (Qiagen). RNA quality was assessed with an Agilent 2100 Bioanalyzer (RNA integrity number>9 for all samples)
Barcoded sequencing libraries were generated with 100ng of RNA with an Ovation RNAseq System V2 (Nugen), KAPA Hyper Prep Kit for Illumina (KAPA Biosystems), and NEXTflex DNA barcodes (Bioo Scientific). Single-end sequencing was performed on an Illumina HiSeq 2500 (UCSF Center for Advanced Technology)

treatment_protocol: LCMV Armstrong day 11

tag: infection

value: LCMV Armstrong day 11

tag: tissue

value: Spleen

tag: markers


title: MGM62361


title: MGM62323

source_name: ΔrbpA attB::rbpA kan, bacterial cells

value: {delta}rbpA attB::rbpA kan


title: RNA-seq_UCLA1_cardiac_p15_rep2

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

description: UCLA1 cardiac p15 rep2

data_processing:
RNA-seq library reads were mapped to the hg19 reference genome and gene annotation using tophat-2.0.4 (Trapnell et al., 2009) calling bowtie-0.12.8 (Langmead et al., 2009)
HTSeq (Anders et al., 2014) was used to perform gene counts
Genome_build: hg19
Supplementary_files_format_and_content: Tab seperated value spreadsheet of reads counts per gene (rows) for each sample (columns)

source_name: Differentiated female human embryonic stem cells

extract_protocol:
as described in paper
as described in paper

value: Cardiomyocytes differentiated from human embryonic stem cells


title: MGM62321


title: MDAMB134_genomic_input_DNA_1


title: MDAMB134_FAIRESeq_2


title: VenusNeg3


title: MGM62322


title: MDAMB134_FAIRESeq_1


title: VenusPos2


title: VenusNeg2


title: MDAMB134_FAIRESeq_3


title: Mem2


title: T47D_genomic_input_DNA_3

source_name: T47D cells

value: breast cancer cell line T47D


title: Mem1


title: T47D_genomic_input_DNA_2


title: VenusPos1


title: chrr_merr_KO_Dark_rep2

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

data_processing:
Illumina data processing pipeline (v1.5) was used for base calling.
FastQC (v0.11.5) was used to evaluate the initial quality of the raw reads.
The following steps were performed to obtain high quality clean reads using Trimmomatic (v0.32) tool: (1) removing the reads with adaptor contamination; (2) filtering the low-quality reads with ambiguous sequences ‘N’; (3) removing the low-quality bases (quality score < Q30).
Data resulting from the above RNA-seq experiments was analyzed with the tool Rockhopper. Reads were aligned to the V. cholera O1 biovar El Tor str. N16961 genome with the parameters: minimum seed length 0.33 and allowed mismatches 15%. Following alignment of the sequencing reads to the genome, reads from each experiment were normalized by upper quartile normalization [17]. A Pearson correlation analysis was conducted to obtain the transcript-level R2 between replicates.
We used the q-value < 0.01 (FDR) and the absolute value of |Fold change| ≥ 2 as the threshold to judge the significant differences of gene expression.
Genome_build: ASM674v1
Supplementary_files_format_and_content: Microsoft Office Open XML Spreadsheet with abundance measurements

organism: Vibrio cholerae O1 biovar El Tor str. N16961

growth_protocol: V. cholerae  cultures were grown in Luria-Bertani (LB) broth (1% tryptone, 0.5% yeast extract, and 1% NaCl) with supplemented streptomycin (100 μg/ml) at 37°C with agitation (250 rpm).

extract_protocol:
Total RNA was extracted from OD600=1.0, 500 µl cell culture by using TRIzol reagent according to the manufacturer’s instructions.
After quality and quantity measurements of RNA by using 2100 BioAnalyzer, RNA was treated with RNase-free DNase I at a concentration of 1 U/µg to remove residual genomic DNA. In order to remove the rRNA, 2.5 µg total RNA was treated with Ribo-Zero™ bacterial rRNA removal kit  following the manufacturer instructions. The rRNA depleted RNA pellets obtained after the ethanol precipitation step was re-suspended in 10 μl of RNase free water. After that, RNA samples were fragmented using fragmentation buffer by using TruSeq mRNA Sample Preparation Kit . The cleaved short RNA fragments were used for the first-strand cDNA synthesis using random hexamer-primer, and then the second strand was synthesized by using DNA polymerase I and RNase H. The double strand cDNAs were purified with AMPure XP beads and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. Paired-end sequencing of the two cDNA libraries (dark and blue-light exposed) of each wild type and mutant V. cholerae cells was performed using the Illumina MiSeq sequencing platform.  All sequence data are PE 2x75 bp.  Image processing, base calling, and quality calue calculation were performed by the Illumina data processing pipeline (v1.5). High quality reads were saved in FASTQ format.

treatment_protocol: For blue-light experiments, V.cholerae cells were inoculated into 5 mL streptomycin supplemented LB and grown overnight under complete darkness by covering the tubes with aluminum foil.  Then, dark kept cells were diluted (1:50) in 15 mL streptomycin supplemented LB and grown until OD600=0.8-1.0. After that, cells were harvested by centrifugation at 4000 rpm for 5 minutes, washed once with PBS and resuspended in 15 mL PBS buffer . Cells were then exposed to blue-light (50 µmole m-2s-1) for 45 minutes.

value: O1 biovar eltor str. N16961

value: delta_VCA0056, delta_VC2301 (MerR,ChrR)

tag: light status

value: dark


title: chrr_merr_KO_BL_rep1

value: blue light


title: Brain microvessel endothelial cells #2

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
Raw data was aligned using LifeScope Genomic Analysis to human genome hg19
Aligned reads were then assembled and used to estimate gene expression using Cufflinks
For slice junction analysis, data was realigned with Bowtie to a custom reference transcriptome generated with all known and putative splice junctions in approximately 900 genes chosen for their potential involvement with pharmacogenomics including all SLC and ABC transporters
Reads containing at least 8 bases of overhang into each exon, as well as having at least 2 unique read start sites (i.e. not duplicate reads) were used to define putative splice junctions.  For read counting, we relax this criteria and require reads with at least 4 bases of overhang.  The ratio of junction counts from BMEC and whole tissue samples was normalized to the total counts for the gene to determine if splicing is occurring more or less often in the enriched samples.
Genome_build: hg19
Supplementary_files_format_and_content: BBB_GeneExpr.txt contains FPKM for each gene and each sample as generated by Cufflinks.

source_name: enriched for microvessel endothelial cells

extract_protocol:
Brain microvessel endothelial cells (BMEC) from human cerebral cortex were enriched through a homogenization and centrifugation procedure
An RNA-seq cDNA library was produced from RNA isolated from enriched Brain microvessel endothelial cells (BMECs) and whole tissue using Nugen Ovation V2 cDNA preparation and the SOLiD library preparation kit.


title: T47D_FAIRESeq_3


title: cry1_cry2_phr_KO_BL

value: delta_VCA0057, delta_VC1392, delta_VC1814 (phr,cry1,cry2)


title: T47D_FAIRESeq_1


title: VenusNeg1


title: cry1_cry2_phr_KO_dark


title: IP8-control

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters were removed with Tagdust. We added the next adapter sequence to the default library file : TCGTATGCCGTCTTCTGCTTG
Bad quality reads extremities were trimmed using Sickle (https://github.com/najoshi/sickle). We used the Phred quality threshold 20 (-q 20). Reads shorter than 18 (IP7-9) or 15 (IP1-2) were removed.
Reads were mapped on the Legionella pneumophila strain Paris genome sequence with Bowtie 2 software
Duplicate reads were removed from mapping results with samtools rmdup, and separated BAM files for forward and reverse mapped reads were built using samtools.
For sample and control, coverage files (wig) were generated for the forward and the reverse strand and normalized according to the number of mapped base pairs. For each couple treatment/control, a scale factor was applied to scale the small sample up to the bigger sample.
Genome_build: Legionella pneumophila strain Paris, NCBI Acc.-No : NC_006368.1
Supplementary_files_format_and_content: For sample and control, coverage files (wig) were generated for the forward and the reverse strand and normalized according to the number of mapped base pairs. For each couple treatment/control, a scale factor was applied to scale the small sample up to the bigger sample. These WIG files represent the normalized coverage (in mapped reads) by position of the reference genome. There are two files (forward/reverse) for each sample (treatment or control).

organism: Legionella pneumophila str. Paris

source_name: bacterial cells

growth_protocol: L. pneumophila expressing CsrA+2xFlagTag and L. pneumophila expressing CsrA without Flag-Tag as negative control were grown in AYE broth until exponential growth (OD 2).

extract_protocol:
Cell pellets were resuspended in lysis buffer (50mM HEPES-KOH pH7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, protease inhibitor), sonicated and total protein concentrations were adjusted to 1mg/ml. The total protein of both samples, CsrA+2xFlagTag and negative control, was cleared separately by BSA-blocked Dynabeads protein G (Invitrogen) and subsequently incubated with Dynabeads protein G coupled to Anti-Flag antibodies (Sigma) over night at 4°C on a rotating platform. Samples and negative control were washed twice with Lysis buffer containing 350mM NaCl and 5 times with wash buffer (10mM Tris-HCl pH 7.5, 250 mM NaCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA). Subsequently beads were washed with TE buffer, resuspended in elution buffer (50mM Tris-HCl pH 8.0, 1mM EDTA, 1% SDS) and incubated at 65°C for 30 min. Crosslinking was reversed and DNA and protein were digested to get purified RNA.
The RNA was metal-catalyzed heat fragmented to a size around 100-200nt using the RNA fragmentation kit and the RNA of both independent samples was purified and further processed according to the TruSeq stranded mRNA sample preparation guide of Illumina. The two parallel processed samples were ligated with adaptor 6 (positive CsrA+2xFlagTag library) and adaptor 12 (negative control, minus FlagTag), respectively, the quantity was determined using a Qubit 2.0 (Invitrogen) and the quality was checked using a Bioanalyzer. High quality libraries were sequenced using an Illumina HiSeq platform. This experiment was done in 5 replicates.

treatment_protocol: Cells were cross linked with formaldehyde (final concentration 1,1%) over night at 4°C on a rotating platform, then formaldehyde was quenched by adding 125 mM glycine and pellets were rinsed twice with PBS.

value: Paris

tag: growth

value: exponential phase OD 2

tag: rip antibody

value: monoclonal anti-FLAG MS2 #F3165 Sigma

tag: expressing

value: plasmid pMMB-CsrA without FLAG-tag


title: IP9-control


title: Brain microvessel endothelial cells #1

value: enriched for microvessel endothelial cells


title: chrr_merr_KO_Dark_rep1


title: whole tissue #2

source_name: whole brain tissue

value: whole brain tissue


title: chrr_KO_BL_rep2

value: delta_VC2301 (ChrR)


title: IP7-control


title: IP2-control


title: DangsuB miRNA-seq

city: beijing

first: zhengqin

last: rong

address: Chaoqian Rd,Changping Science Park of Zhongguancun Science Park

country: China

institute: hornortech

description: Small RNA

data_processing:
reads were aligned to Rfam(v12) to remove tRNA、rRNA.
Using mirdeep(v2) to analysis Known microRNA with default parameter
Using mireap  to predict novel microRNA and miRpara(v6.3) to check them
Using edgeR to nomalize the expression of miRNA
Genome_build: Pyrus_bretschneideri (V121010)

organism: Pyrus x bretschneideri x Pyrus pyrifolia

source_name: fruit

extract_protocol:
libraries were prepared according to a version of Illumina's mRNA-Seq protocol adapted for small sample inputs
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: parent

value: Pyrus pyrifolia Nakai

value: Pyrus x bretschneideri cv. Dangshansu


title: DangsuA miRNA-seq

description: Small RNA

organism: Pyrus x bretschneideri

value: Pyrus x bretschneideri Rehder


title: T47D_genomic_input_DNA_1


title: whole tissue #1


title: chrr_merr_KO_BL_rep2


title: sc35-sclC

city: Shanghai

first: Qing

middle: qing

last: Yan

address: 300 Feng Lin Road

institute: Yuda Fang

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2 2.0.1-beta release mapping to reference genome
count counting
Genome_build: tair10
Supplementary_files_format_and_content: xls file contain counts for each sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: All seeds were germinated in MS-medium (1% sucrose and 0.8% agar), after vernalizing at 4°C for 3d or 4d.  Plants were grown in a greenhouse under a 16h light/8h dark photoperiod for 12 days.

extract_protocol:
Total RNAs were extracted from 12 d seedlings of WT and quintuple mutant (scl28 scl30 scl30a scl33 sc35) using the RNeasy plant mini kit (Qiagen).
The total RNAs were treated with DNase I followed by mRNA isolation using magnetic beads with Oligo (dT). Fragmented mRNAs were used as templates for the PCR amplification and the construction of the RNA-seq library construction.

value: seedling

tag: age

value: 12 day after vernalization

tag: genome type

tag: ecotype


title: sc35-sclB


title: IP8-treat

value: plasmid pMMB-CsrA+2xFLAG-tag


title: HEK_pxMARGI_rep1_1

value: HEK

value: diMARGI


title: chrr_KO_Dark_rep2

value: O1 biovar eltor str. N16961

value: dark


title: chrr_KO_Dark_rep1


title: T47D_FAIRESeq_2

value: breast cancer cell line T47D


title: HEK_diMARGI_rep1_1

description:
Chimeric fragments from RNA-DNA interactions were retrieved. R1 and R2 reads correspond to RNA and DNA fragments, respectively. Thus, the paired-end files are not characterized by average insert size or standard deviation.
Processed data file: H9_I_pqvalues.poisson.txt


title: chrr_KO_BL_rep1

value: blue light


title: IP9-treat

value: Paris

value: exponential phase OD 2

value: monoclonal anti-FLAG MS2 #F3165 Sigma


title: IP2-treat


title: WT_BL_rep1

value: wild type


title: WT_BL_rep2


title: sc35-sclA

value: 16 day after vernalization


title: ColB

value: WT


title: HEK_pxMARGI_rep2_1

value: pxMARGI


title: H9_pxMARGI_rep1_1

value: embryonic stem (ES) cells


title: ColC

value: seedling

value: 14 day after vernalization


title: IP1-treat

value: plasmid pMMB-CsrA+2xFLAG-tag


title: WT_Dark_rep1


title: H9_diMARGI_rep1_1


title: IP1-control

value: plasmid pMMB-CsrA without FLAG-tag


title: Col_K14

status: Public on Jan 25 2017

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline
ChIP-seq reads were aligned to the Arabidopsis genome (TAIR10) using BOWTIE.
Perfect and unique reads from the mapping were processed for further analysis. Wiggle (WIG) files of the alignments were generated using bam2wig and visualized using IGV. Using the SICER program, ChIP-enriched peaks were identified, and qualitative comparisons of binding levels in wild-type and mutant plants were determined.
Genome_build: TAIR10
Supplementary_files_format_and_content: peaks bed files

source_name: Young seedlings

growth_protocol: Seeds were surface-sterilized and sown on MS-agar plates. After two days of cold treatment, the plated seeds were transferred to 23°C under long-day (16 h light, 8 h dark) condition.

extract_protocol:
Seedlings were ground in liquid nitrogen and cross-linked with 1% formaldehyde in M1 buffer [10 mM phosphate buffer pH 7.0, 0.1 M NaCl, 10 mM mercaptoethanol, 1 M hexylene glycol, protease inhibitor cocktail (Roche)] for 10 min. The cross-linking reaction was quenched by adding glycine. The suspension was filtered through four layers of Miracloth, and the filtrate was centrifuged at 12,000 rpm for 10 min. The pelleted chromatin was washed three times with M2 buffer (M1 buffer plus 10 mM MgCl2 and 0.5% Triton X-100) and one time with M3 buffer [10 mM phosphate buffer pH 7.0, 0.1 M NaCl, 10 mM mercaptoethanol, protease inhibitor cocktail (Roche)]. The chromatin was resuspended in nuclei lysis buffer and sonicated to generate DNA fragments approximately 200bp in length. The lysate was pre-cleared by incubation with 50 µl protein-A agarose beads/salmon sperm DNA (Millipore) for 1 h then incubated with anti-H3K9ac (Abcam, ab10812) and anti-H3K14ac antibodies (Abcam, ab52946) overnight. The beads were washed two times with each of the following solutions: low salt, high salt, LiCl and TE. The bound DNA fragments were recovered and purified using columns from the Qiagen Plasmid Extraction Kit according to the manufacturer’s instructions.
ChIP DNA was quantified using a fluorescence-based quantification method (Qubit, Invitrogen). ChIP-seq libraries were prepared according to the manufacturer’s instructions (Illumina TruSeq ChIP sample prep kit). Input ChIP DNA was blunt-ended and phosphorylated, and a single adenine base was added to the 3' ends of the fragments in preparation for ligation to an adapter with a single thymine base overhang. The products of this ligation reaction were purified and size-selected (300 to 400 bp fragments) by 2% agarose gel electrophoresis. The size-selected DNA was purified and PCR-amplified to enrich for fragments with adapters on both ends. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent). After qPCR using SYBR Green PCR Master Mix (Applied Biosystems), the index-tagged libraries were combined in equimolar amounts within a single pool. Sequencing was performed using an Illumina NextSeq 500 system following the provided protocols for 1x75 sequencing.

value: Seedling

tag: developmental stage

tag: antibody

value: H3K14ac (Abcam, ab52946)

tag: genotype/variation

value: Col


title: WT_Dark_rep2

tag: strain

value: O1 biovar eltor str. N16961

tag: genotype

value: dark


title: pwr2_input


title: HEK-dm_pxMARGI_rep1

description:
Chimeric fragments from RNA-DNA interactions were retrieved. R1 and R2 reads correspond to RNA and DNA fragments, respectively. Thus, the paired-end files are not characterized by average insert size or standard deviation.
This sample does not have processed data as it was used only to count how many interspecies chimeric reads were generated by the protocol (the count was done directly from the BAM files).

organism:
Drosophila melanogaster
Homo sapiens

source_name: HEK and DM cells

tag: cell line

value: HEK

value: DM

tag: protocol


title: hdac_input

tag: tissue


title: hdac_K14


title: IP7-treat

value: Paris

value: exponential phase OD 2

value: monoclonal anti-FLAG MS2 #F3165 Sigma


title: hiPSC-RPE 3 (Control 3) vehicle

city: Rensselaer

first: Thomas

middle: R

last: Kiehl

address: One Discovery Drive

institute: Neural Stem Cell Institute

description: Gene expression data from hiPSC-RPE sample Control 3 treated with vehicle.

data_processing:
Mapped with STAR Aligner to HG19
Bedtools used to filter out reads that map to ribosomal regions
DESeq2 was used to normalize reads and gauge differential expression
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing normalized reads and computed fold changes/pvalues for each gene between control and NAM treatment.

source_name: hiPSC-RPE 7 treated with vehicle for 3 weeks

growth_protocol: hiPSC derived RPE lines were cultured in NAM-containing RPE culture medium.

extract_protocol:
To extract RNA, hiPSC-RPE cells were scraped from the culture wells and collected in RNA protect. Total RNA was purified using the RNeasy plus micro kit (Qiagen) according to manufacturer's instructions.
10ng total RNA was used to generate libararies using the  SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clontech) as per standard protocol. Final libraries are pooled at 1.6pM final concentration for sequencing (1x75 cycle) on an Illumina Nextseq500 instrument

treatment_protocol: Upon formation of monolayers of RPE, for assesing the effect of NAM by microarray, hiPSC derived RPE were treated with NAM or vehicle (cell culture grade water) for 3 weeks and then collected in RNA protect (Qiagen).

tag: gender

value: Female

tag: disease status

value: Control

tag: treatment

value: Vehicle

tag: tissue of origin

value: Cornea


title: hiPSC-RPE 3 (Control 3) NAM

description: Gene expression data from hiPSC-RPE sample Control 3 treated with Nicotinamide.

source_name: hiPSC-RPE 7 treated with Nicotinamide for 3 weeks

value: Nicotinamide


title: hiPSC-RPE 1 (Control 1) NAM

description: Gene expression data from hiPSC-RPE sample Control 1 treated with Nicotinamide.

source_name: hiPSC-RPE 52 treated with Nicotinamide for 3 weeks


title: hiPSC-RPE 2 (Control 2) NAM

description: Gene expression data from hiPSC-RPE sample Control 2 treated with Nicotinamide.

source_name: hiPSC-RPE 6 treated with Nicotinamide for 3 weeks

value: RPE


title: hiPSC-RPE 2 (Control 2) vehicle

description: Gene expression data from hiPSC-RPE sample Control 2 treated with vehicle.

source_name: hiPSC-RPE 6 treated with vehicle for 3 weeks


title: hiPSC-RPE 1 (Control 1) vehicle

description: Gene expression data from hiPSC-RPE sample Control 1 treated with vehicle.

source_name: hiPSC-RPE 5 treated with vehicle for 3 weeks


title: ColA

value: seedling

value: 12 day after vernalization

value: WT


title: hiPSC-RPE 4 (AMD 4) NAM

description: Gene expression data from hiPSC-RPE sample AMD 4 treated with Nicotinamide.

source_name: hiPSC-RPE 4 treated with Nictinamide for 3 weeks

value: Male

value: Age related Macular degeneration (AMD)


title: hiPSC-RPE 4 (AMD 4) vehicle

description: Gene expression data from hiPSC-RPE sample AMD 4 treated with vehicle.

source_name: hiPSC-RPE 4 treated with vehicle for 3 weeks


title: hiPSC-RPE 3 (AMD 3) NAM

description: Gene expression data from hiPSC-RPE sample AMD 3 treated with Nicotinamide.

source_name: hiPSC-RPE 3 treated with Nicotinamide for 3 weeks


title: hiPSC-RPE 2 (AMD 2) NAM

description: Gene expression data from hiPSC-RPE sample AMD 2 treated with Nicotinamide.

source_name: hiPSC-RPE 2 treated with Nicotinamide for 3 weeks


title: pwr2_K14

value: Seedling

value: H3K14ac (Abcam, ab52946)

value: Col


title: hiPSC-RPE 3 (AMD 3) vehicle

description: Gene expression data from hiPSC-RPE sample AMD 3 treated with vehicle.

source_name: hiPSC-RPE 3 treated with vehicle for 3 weeks


title: hiPSC-RPE 1 (AMD 1) vehicle

description: Gene expression data from hiPSC-RPE sample AMD 1 treated with vehicle.

source_name: hiPSC-RPE 1 treated with vehicle for 3 weeks


title: hiPSC-RPE 1 (AMD 1) NAM

description: Gene expression data from hiPSC-RPE sample AMD 1 treated with Nicotinamide.

source_name: hiPSC-RPE 1 treated with Nictinamide for 3 weeks


title: GSC4_RNAseq_rep1

city: Boston

first: Cem

last: Sievers

address: 165 Cambridge Street

department: Molecular Pathology

institute: MGH

data_processing:
Paired-end reads were aligned to UCSC transcriptome (hg19) using Bowtie (version 0.12.7) with the following parameters: --chunkmbs 512 -q --phred33-quals -n 0 -l 25 -I 1 -X 2000 -p 6 -a -m 15.
Gene expression, quantified as transcript per million (TPM), was estimated using RSEM with the following parameters: --fragment-length-max 1000 --estimate-rspd --paired-end.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

growth_protocol: Neurosphere cultures were maintained in Neurobasal media supplemented with 20 ng/mL recombinant EGF (R and D Systems), 20ng/mL FGF2 (R and D Systems), 1X B27 supplement (Invitrogen), 0.5X N2 supplement (Invitrogen), 3mM L-glutamine,  and penicillin/ streptomycin.

extract_protocol:
Whole RNA was extracted from 1-3×10e6 cells using the QIAGEN RNeasy kit according to the manufacturer’s protocol.
For RNA-seq library preparation, Poly(A)+ RNA was enriched using magnetic oligo(dT)-beads (Life Technologies) and fragmented to 200–600 base pairs and then ligated to RNA adaptors using T4 RNA Ligase (NEB).

treatment_protocol: Cells were treated with drugs with a final DMSO concentration of either 0.1 or 0.15% DMSO.

value: Patient-derived neurosphere line GSC4

tag: drug treatment


title: GSC4_RNAseq_rep2


title: GSC8Per_RNAseq_rep3

data_processing:
Paired-end reads were aligned to UCSC transcriptome (hg19) using Bowtie (version 0.12.7) with the following parameters: --chunkmbs 512 -q --phred33-quals -n 0 -l 25 -I 1 -X 2000 -p 6 -a -m 15.
Gene expression, quantified as transcript per million (TPM), was estimated using RSEM with the following parameters: --fragment-length-max 1000 --estimate-rspd --paired-end.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig density files
Supplementary_files_format_and_content: .tab-delimited text files include TPM values for each Sample

value: Patient-derived neurosphere line GSC8

value: chronic 1 µM dasatinib


title: Col_input


title: GSC8Per_RNAseq_rep1


title: GSC8_12d-das_RNAseq_rep1

value: 12 day 1 µM dasatinib


title: GSC8_RNAseq_rep3


title: GSC8_RNAseq_rep1


title: GSC8_12d-das_RNAseq_rep3


title: mRNA sequencing of HCT116 cells upon eIF1 knockdown

city: Gent

first: Petra

middle: Van

last: Damme

state: East Flanders

address: Albert Baertsoenkaai 3

department: Department of Biochemistry

country: Belgium

institute: University of Gent

description: total RNA depleted of rRNA

data_processing:
Ribosome profiling sequenced reads were processed using the PROTEOFORMER pipeline (Crappe et al 2015). PROTEOFORMER performs the quality control, mapping onto a reference genome, identification of TIS and generation of a protein database.
The sequenced mRNA-seq and ribo-seq reads were trimmed for adaptor sequences (CTGTAGGCACCATCAAT and AGATCGGAAGAGCACAC, respectively) using fastx_clipper 0.0.14.
The PROTEOFORMER pipeline sequentially mapped the ribo-seq trimmed reads onto the rRNA, snRNA and tRNA. All reads mapping to these indices were discarded.
The trimmed mRNA-seq and the remaining ribo-seq reads were then aligned human GRCh38 reference genome (Ensembl annotation bundle 82) using STAR v2.5.1b and allowing only unique mapping with a maximum of 2 mismatches.
Ribosome occupancy position was determined by using only reads of length 26-34bps. An offset  of +12, +13 and +14 from the 5' end of the reads were  used for reads of length 26-30bps, 31-33 bps and 34bps respectively. The positional scores from represent the number of reads alignment attributed to each genomic position.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: Bedgraph files were generated by PROTEOFORMER for the sense and antisense seperately. The positional scores represent the number of reads aligned to each genomic position. Bedgraphs were adjusted for difference in sequencing depth.

source_name: colorectal carcinoma cell line

growth_protocol: The human colon cancer HCT116 cells were cultivated in McCoy’s medium (Gibco, Thermo Fisher Scientific Inc.)supplemented with 10% fetal bovine serum (FBS, HyClone, Thermo Fisher Scientific Inc.), 2 mM alanyl-L-glutamine dipeptide (GlutaMAX, Gibco, Thermo Fisher Scientific Inc.), 50 units/ml penicillin (Gibco, Thermo Fisher Scientific Inc.) and 50 µg/ml streptomycin (Gibco, Thermo Fisher Scientific Inc.) in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
For mRNA-sequencing (RNA-seq), total RNA was isolated from 400ul cell lysate with TRIzol reagent (Invitrogen, Thermo Fisher Scientific Inc.) according to manufacturer’s instructions. RNA quality was assessed by Agilent Bioanalyzer RNA 600 Nano Kit and RIN values above 9 were accepted.
For mRNA-seq, rRNA depletion with Ribo-Zero probes, random fragmentation, cDNA synthesis and library generation were performed according to TruSeq Stranded Total RNA Sample Preparation protocol (Illumina). mRNA-seq and ribo-seq libraries were subjected to sequencing on a NextSeq 500 instrument (Illumina) to yield 75 bp single-end reads.

treatment_protocol: For knockdown experiments, HCT116 cells were transferred to serum-free McCoy’s medium and seeded at a density of 2.4*10E6 cells per 10 cm2 plate. Cells were transfected with either 10nM control si-RNA (si-Ctrl, ON-TARGETplus Non-targeting Control siRNAs: D-001810-01-05, Dharmacon, GE Healthcare Life Sciences) or 10nM si-RNAs targeting eIF1 (si-eIF1, SMARTpool: M-015804-01-0005, Dharmacon, GE Healthcare Life Sciences) using 63ul of HiPerFect (QIAGEN) per 10 cm2 plate. 5 hours post-transfection, cells were supplemented with FBS at a final concentration (f.c.) of 10%. Overall, 4 x 10 cm2 plates of si-Ctrl and 4 x 10 cm2 plates of si-eIF1 treated HCT116 cells were obtained. Subsequently, 2 plates per condition were incubated with either 50 µM lactimidomycin (LTM) or 100 µg/ml cycloheximide (CHX) (Sigma, USA) in a total volume of 5 ml per plate for 30 min at 37°C.

value: colon

tag: phenotype

value: colorectal carcinoma


title: mRNA sequencing of control HCT116 cells

description: total RNA depleted of rRNA


title: hiPSC-RPE 2 (AMD 2) vehicle

description: Gene expression data from hiPSC-RPE sample AMD 2 treated with vehicle.

source_name: hiPSC-RPE 2 treated with vehicle for 3 weeks

value: Female

tag: age

value: Vehicle


title: Ribosome profiling of control HCT116 cells treated with cycloheximide

description: ribosome-associated mRNA

data_processing:
Library strategy: Ribo-seq
Ribosome profiling sequenced reads were processed using the PROTEOFORMER pipeline (Crappe et al 2015). PROTEOFORMER performs the quality control, mapping onto a reference genome, identification of TIS and generation of a protein database.
The sequenced mRNA-seq and ribo-seq reads were trimmed for adaptor sequences (CTGTAGGCACCATCAAT and AGATCGGAAGAGCACAC, respectively) using fastx_clipper 0.0.14.
The PROTEOFORMER pipeline sequentially mapped the ribo-seq trimmed reads onto the rRNA, snRNA and tRNA. All reads mapping to these indices were discarded.
The trimmed mRNA-seq and the remaining ribo-seq reads were then aligned human GRCh38 reference genome (Ensembl annotation bundle 82) using STAR v2.5.1b and allowing only unique mapping with a maximum of 2 mismatches.
Ribosome occupancy position was determined by using only reads of length 26-34bps. An offset  of +12, +13 and +14 from the 5' end of the reads were  used for reads of length 26-30bps, 31-33 bps and 34bps respectively. The positional scores from represent the number of reads alignment attributed to each genomic position.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: Bedgraph files were generated by PROTEOFORMER for the sense and antisense seperately. The positional scores represent the number of reads aligned to each genomic position. Bedgraphs were adjusted for difference in sequencing depth.

extract_protocol:
Cells were harvested by trypsinitation (Trypsin/EDTA solution, Thermo Fisher Scientific Inc.), collected by centrifugation (5 min at 300g), washed with ice-cold PBS with 100 µg/ml CHX added and recovered again by centrifugation. Cells were re-suspended in 1 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 2 mM dithiothreitol (DTT), 100 µg/ml CHX, 1 × complete and EDTA-free protease inhibitor cocktail (Roche)), lysed by incubation on ice for 10 min and subsequently passed through QIAshredder spin columns (Qiagen). The flow-through was clarified by centrifugation for 10 min at 16,000 × g and 4°C. The supernatant was recovered and protein concentration was measured. For ribosome profiling (ribo-seq), 600 µl of each lysate was subjected to RNase I (Thermo Fisher Scientific Inc.) digestion using 3000 U of enzyme for every 7 mg protein. Digestion of polysomes proceeded for 45 min at room temperature  and was stopped with SUPERase.In RNase Inhibitor (Life Technologies). Next, monosomes were recovered by ultracentrifugation at 75,000 RPM in a cooled TLA-120.2 rotor over a 1 M sucrose cushion in 20 mM HEPES-KOH pH 7.4, 5 mM MgCl2, 100 mM KCl, 2 mM DTT, 100 µg/ml CHX and 100 U/ml Superase.In. RNA was extracted from the samples using a heated acid phenol; chloroform; isoamyl alcohol (125:24:1) procedure.
For ribo-seq, ribosome protected fragments (RPFs) of 26-34 nucleotides were extracted from 22 µg of RNA subjected to electrophoresis under denaturing conditions in 15% TBE-Urea polyacrylamide gel (Life Technologies). Extraction from gel was performed in RNase-free water for 10 min at 70°C and precipitated with 1/10 volume of 3 M sodium acetate pH 5.2, 1.5 µl GlycoBlue (Life Technologies) and 1 volume of isopropanol overnight at − 80 °C. Following a dephosphorylation reaction (end-repair) with 10 U of T4 polynucleotide kinase (New England Biolabs), the RPFs were ligated to a 1.5 µg of Universal cloning linker using 200 U of T4 RNA ligase II (both New England Biolabs). The ligated product was size-selected using denaturing gel electrophoresis and purified from gel as described above. Subsequently, reverse transcription (RT) was performed with 200 U of SuperScript III (Life Technologies) according to (Ingolia et al, 2011), followed by a size-selection of the RT product (described above). Ribosomal RNA derived contaminants were depleted from reverse transcribed samples using a custom set of 20 biotynylated deoxyoligonucleotides. 100 pmol of mixed probes with 60ul MyOne Streptavidin C1 DynaBeads (Thermo Fisher Scientific Inc.) were used each time. Next, samples were subjected to circular ligation using 100 U of CircLigase (Illumina), diluted and amplified by PCR using Phusion polymerase (New England Biolabs) for 12 cycles of denaturation (10 s at 98°C), annealing (10 s of 65°C) and elongation (5 s at 72°C) using primer pairs compatible with the Illumina sequencing platform. The resulting ribosome-profiling libraries were duplexed (samples treated with the same inhibitor, LTM or CHX, were joined).


title: Ribosome profiling of HCT116 cells upon eIF1 knockdown treated with cycloheximide

description: ribosome-associated mRNA


title: Ribosome profiling of control HCT116 cells treated with lactimidomycin

description: ribosome-associated mRNA


title: H3K27me3_GSC8_4d-GSKJ4_ChIPseq

data_processing:
Reads were aligned to hg19 using BWA.
Resulting alignment files were filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq BigWig tracks were generated using the 'BEDTools' tool 'genomeCoverageBed' and the UCSC tool 'bedGraphToBigWig'
Genome_build: hg19
Supplementary_files_format_and_content: BigWig density files were generated by BEDTools and UCSC tools

extract_protocol:
Cells was fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of crosslinked cells was calibrated such that DNA was sheared to between 400bp and 2000bp.
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

value: 4 day 1.5 µM GSKJ4

tag: chip-antibody


title: H3K27ac_GSC8Per_ChIPseq


title: Ribosome profiling of HCT116 cells upon eIF1 knockdown treated with lactimidomycin

description: ribosome-associated mRNA


title: H3K27ac_GSC8_12d-das_ChIPseq


title: H3K27me3_GSC8_8d-GSKJ4_ChIPseq

value: 8 day 1.5 µM GSKJ4


title: H3K27ac_GSC8_ChIPseq


title: H3K27me3_GSC8_PD0325901_ChIPseq

value: chronic 2 µM PD0325901


title: H3K27me3_GSC8_12d-das_ChIPseq


title: H3K27me3_GSC8_4d-das_ChIPseq

value: 4 day 1 µM dasatinib


title: H3K27me3_GSC8_12d-das_8d-GSKJ4_ChIPseq

value: 12 day 1 µM dasatinib, 8 day 1.5 µM GSKJ4


title: GSC8Per_RNAseq_rep2


title: H3K27me3_GSC8_4d-das_4d-GSKJ4_ChIPseq

value: 4 day 1 µM dasatinib, 4 day 1.5 µM GSKJ4


title: H3K27me3_GSC8Per_ChIPseq


title: H3K4me3_GSC8_4d-KDM5C70_ChIPseq

value: 4 day 2.5 µM KDM5C70


title: GSC8_12d-das_RNAseq_rep2


title: GSC8_RNAseq_rep2


title: H3K4me3_GSC8_ChIPseq


title: H3K4me3_GSC8_12d-das_ChIPseq


title: H3K4me3_GSC8_12d-das_8d-GSKJ4_ChIPseq


title: H3K4me3_GSC8_4d-das_4d-KDM5C70_ChIPseq

value: 4 day 1 µM dasatinib, 4 day 2.5 µM KDM5C70


title: H3K4me3_GSC8_4d-das_ChIPseq


title: H3K4me3_GSC8_4d-das_4d-GSKJ4_ChIPseq


title: H3K4me3_GSC8Per_ChIPseq


title: H3K27me3_GSC8_ChIPseq


title: NICD_GSC8_12d-das_ChIPseq

value: cleaved Notch1 (Val1744) (CST, 4147, lot 4)


title: NICD_GSC8Per_ChIPseq


title: NICD_GSC8_ChIPseq


title: RBPJ_GSC8_12d-das_ChIPseq


title: RBPJ_GSC8Per_ChIPseq


title: H3K4me3_GSC8_4d-GSKJ4_ChIPseq


title: Input_GSC8_ChIPseq


title: Input_GSC8_4d-das_ChIPseq


title: H3K4me3_GSC8_8d-GSKJ4_ChIPseq


title: Input_GSC8Per_ChIPseq


title: Light fraction; control; rep2

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Removed the GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC adaptor using cutadapt -a GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC -m 17
Mapped to the mm9 mouse genome using STAR --outSAMstrandField intronMotif --readFilesCommand zcat --runThreadN 16 --outFileNamePrefix 2-Free_-GS
Reduced the BAM file to keep just the 1st base of the alignment
Counted the number of reads mapping to each FANTOM promoter using htseq-count -s yes
Genome_build: mm9
Supplementary_files_format_and_content: bigWig coverage files for each strand

source_name: Light fraction; control

extract_protocol:
RNA was isolated for each fraction using Trizol and Direc-Zol RNA mini-prep kits (Zymo Research).
RNA spikes (0.25ng GFP and 1pg Luciferase) that were transcribed (P1300, Promega) and capped (S1407, NEB) in-vitro using T7 RNA Polymerase were added into each fraction. Equivalent RNA volume was taken from each fraction for the library preparation for TSSs sequencing using the CapSeq method (with modifications) as previously described (Gu et al. 2012). Specifically, the RNA samples were treated with Terminator 5´-Phosphate-Dependent Exonuclease (TER51020, Epicenter). Then, reaction volume was enlarged and CIP (M0290, NEB) was added to dephosphorylate non-mRNA RNAs (tRNA and 5S rRNA). DNaseI was added in this step. In order to remove mRNA 5’Cap, the samples were treated with TAP (T19050, Epicenter) and then RNA linker was ligated at the 5’end of the formerly capped mRNA by T4 RNA ligase (M0204, NEB). cDNA was prepared from each RNA sample by using hexamer random primers linked to illumina 3’ Rd2 seq primer, index (unique barcode for each sample), 4nt-long UMI and P7 illumina adaptor. To increase the cDNA quantity, a linear PCR amplification (second strand synthesis) was performed with forward primer containing the ligated linker sequence and carry P5 illumina adaptor. Final library amplification PCR step was performed after calibrating the numbers of PCR cycles. Size selection with magnetic beads (Ampure XP, according to the manufacturer guidelines) was performed after cDNA for removal of fragments <~150 nt and after linear amplification and final PCR steps, in which sizes of >200 bp and < 500 bp were selected. The deep sequencing was performed with HiSeq High-Throughput Sequencing System.

treatment_protocol: Untreated and 8h glucose starved MEFs were incubated with 100 μg/ml Cycloheximide (Sigma) for 5 minutes and then washed twice with cold buffer containing 20mM Tris pH 8, 140mM KCl, 5mM MgCl2 and 100 μg/ml Cycloheximide. The cells were collected and lyzed with 500 μl of same buffer that also contains 0.5% Triton, 0.5% DOC, 1.5mM DTT, 150 units RNAse inhibitor (Eurx) and 5μl of protease inhibitor (Sigma). The lyzed samples were centrifuged at 12,000g at 4°C for 5 minutes. The cleared lysates were loaded onto 10-50% sucrose gradient and centrifuged at 41,000 RPM in a SW41 rotor for 90 minutes at 4°C. Gradients were fractionated and the optical density at 254 nm was continuously recorded using ISCO absorbance detector UA-6. The collected samples were then merged to create three fractions: Polysome-free (F), Light (L) and Heavy (H). The use of three pools is sensitive to large changes in translation but relatively insensitive to smaller changes.

value: control

tag: replicate

tag: polysomal fraction

value: Light

tag: cell type

value: Mouse Embryonic Fibroblasts (MEFs)


title: Light fraction; glucose stravation; rep2

source_name: Light fraction; glucose stravation

value: glucose stravation


title: Heavy fraction; glucose stravation; rep2

source_name: Heavy fraction; glucose stravation

value: Heavy


title: IgG Run 1 and 2

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
Basecalls performed using CASAVA 1.7, ChIP-seq reads were aligned to the mm9 genome assembly using ELANDv2 with default parameters. Two technical replicates of each sample were pooled, because each sample was sequenced twice due to insufficient read depth obtained in the first sequencing run. Peaks were called relative to IgG as a control. Coverages estimates were generated using MACS 1.4 with p value cuff off set at 1e-5. Peaks in bed files and coverage in wig files are converted to bigbed and bigwig using bedToBigBed and wigToBigWig respectively.
Genome_build: mm9
Supplementary_files_format_and_content: Bigbed for peaks, bigwig for coverage

source_name: IgG

growth_protocol: Mouse TS cells were routinely cultured under stem condition utilising standard protocol consists of MEF conditioned media in the presence of FGF4 & heparin.

extract_protocol:
Cells were trypsinized and washed with PBS before fixing them with 1% paraformaldehyde. Fixed cells were used to prepare genomic DNA fargments using a sonicator. Sonicated fragments were immunoprecipitated using either anti-GATA2 or anti-GATA3 antibodies or non-specific IgG. Samples from three independent experiments were poooled and genomic libraries were sequenced in Illumina Genome  Analyzer II and in Illumina HiSeq platforms to generate 35 bp single end reads.
Libraries were prepared by Illumina. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

value: Mouse trophoblast stem cells

tag: antibody

value: IgG


title: Heavy fraction; control; rep1

source_name: Heavy fraction; control


title: Free fraction; glucose stravation; rep2

source_name: Free fraction; glucose stravation

value: Free


title: Light fraction; control; rep1


title: Free fraction; glucose stravation; rep1


title: Heavy fraction; control; rep2


title: Free fraction; control; rep2

source_name: Free fraction; control


title: Heavy fraction; glucose stravation; rep1


title: Light fraction; glucose stravation; rep1


title: Free fraction; control; rep1


title: GATA3 Run 1 and 2


title: RBPJ_GSC8_ChIPseq

value: Patient-derived neurosphere line GSC8


title: CVLH  rep2

city: Macau

first: Beixian

last: Zhou

address: Av. Wai Long, Taipa, Macau

institute: Macau University of Science and Technology

data_processing:
bcl2fastq-2.17 software uesed  for basecaling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.13
Reads counts were caculated using gfold v1.1.2
differentially expression genes were determined with DEGseq
Genome_build: hg19

source_name: A549 cells infected with A/PR8/34/(H1N1) at the high concentration of lariciresinol-4-β-D-glucopyranoside treatment (800 ug/ml)

growth_protocol: A549 human lung adenocarcinoma cells that were purchased from ATCC were cultured in MDEM/DF12 (1:1, V/V), with 10% foetal bovine serum (FBS), 100 U/ml penicillin, and 100 ug/ml streptomycin under standard conditions at 37℃ in 5% CO2 humidified air.

extract_protocol:
Total RNA extracts from each sample were obtained following the manufacturer’s instructions (Life technologies). The total RNA quality was assessed by 1.5% agarose gel electrophoresis. The A260/A280 ratio was determined using a NanoDrop ND-200 spectrophotometer (NanoDrop Technologies, USA). RNA integrity was assessed by Agilent 2200 TapeStation analysis (Agilent Technologies, Santa Clara, CA, USA). A A260/A280 ratio between 1.8 to 2.0 and RIN > 7 were considered acceptable. RNA sequencing was performed on an Illumina HiSeq-2000 RNA-seq sequence production system.
RNA sequencing was performed on an Illumina HiSeq-2000 RNA-seq sequence production system.

value: lung epithelial cells

tag: passages


title: CVLL  rep2

source_name: A549 cells infected with A/PR8/34/(H1N1) at the low concentration of lariciresinol-4-β-D-glucopyranoside treatment (400 ug/ml)


title: GATA2 Run 1 and 2


title: Input_GSC8_PD0325901_ChIPseq

value: chronic 2 µM PD0325901


title: Input_GSC8_12d-das_ChIPseq

value: 12 day 1 µM dasatinib


title: CVLL  rep1


title: PANC-1_H3K27ac-ChIPseq_NS

city: Tokyo

first: Tsuyoshi

last: Osawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

country: Japan

institute: The University of Tokyo

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
ChIP-seq and FAIRE-seq reads were trimmed into 36b and aligned to the NCBI Build #37 (UCSC hg19) reference human genome, using ELAND (Illumina mapping program)
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: NCBI Build #37 (UCSC hg19)
Supplementary_files_format_and_content: bigWig

source_name: PANC-1 nutrient starvation H3K27ac ChIP

growth_protocol: Human pancreatic carcinoma, epithelial-like cell line PANC-1 and adenocarcinoma ascites metastasis AsPC-1 were maintained in RPMI1640 or Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 atmosphere, respectively.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA or SREBP2-DNA complexes were isolated.  For FAIRE-seq, sonicated nuclear fructions were subjected to phenol/chloroform extraction twice followed by ethanol precipitation.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were treated for 24 h under control (pH7.4), low pH (pH6.8), nutrient starvation (all nutrients 1/100) and hypoxia (pO2 = 1%) condition.

tag: culture condition

value: Nutrient Starvation (all nutrients 1/1000

tag: ChIP


title: CV

source_name: A549 cells with IAV infection

tag: cell line


title: PANC-1_H3K27ac-ChIPseq_Con

source_name: PANC-1 control H3K27ac ChIP

value: Control (pH 7.4)


title: PANC-1_H3K27ac-ChIPseq_pH

source_name: PANC-1 low pH H3K27ac ChIP

value: low pH (pH 6.8)


title: PANC-1_H3K27ac-ChIPseq_H

source_name: PANC-1 hypoxia H3K27ac ChIP

value: Hypoxia (pO2 = 1%)


title: PANC-1_FAIREseq_H

source_name: PANC-1 hypoxia FAIRE

value: FAIRE


title: PANC-1_FAIREseq_NS

source_name: PANC-1 nutrient starvation FAIRE


title: C

source_name: A549 cells without IAV infection


title: CVLH  rep1


title: PANC-1_FAIREseq_pH

source_name: PANC-1 low pH FAIRE


title: PANC-1_FAIREseq_Con

source_name: PANC-1 control FAIRE


title: AsPC-1_RNA-seq_H

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
RNA-seq reads were trimmed into 100bp and algined to human transcriptome (UCSC gene) and genome (GRCh37/hg19) references respectively using Burrows-Wheeler Aligner.  After transcript coordinate was converted to genomic positions, an optimal mapping result was selected either from transcript or genome mapping by comparing the minimal edit distance to the reference.
Local realignment was performed within in-house short reads aligner with smaller k-mer size (k=11).
Fragments per kilobase of exon per million fragment mapped (fpkm) values were calculated for each UCSC gene while considering strand-specific information.
Genome_build: NCBI Build #37 (UCSC hg19)
Supplementary_files_format_and_content: fpkm

source_name: AsPC-1 hypoxia

extract_protocol:
Total RNA was extracted from cells using the Isogen reagent (Nippon Gene, Toyama, Japan). TruSeq RNA sample Preparation Kits v2 (Illumina, #RS-122) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions.


title: Double Knock Out (DKO) mTS

description: FPKM.txt

data_processing:
base calling was performed using Illumina’s Real Time Analysis (RTA) software
Sequence reads were mapped to the mouse reference genome (GRCm38) using STAR with default parameters
Transcript abundance estimates were generated using Cufflinks and differential gene expression calculated using Cuffdiff with default parameters.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files of FPKM values for each Sample

source_name: Cell line

growth_protocol: Gata2f/f;Gata3f/f;UBC-cre/ERT2 mTS cells were routinely cultured under stem condition utilising standard protocol consists of 20% FBS in the presence of FGF4 & heparin (1 microgram/ml) in MEF conditioned media.

extract_protocol:
Total RNA from the whole cell-extract was isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol with on column DNase digestion.  RNA concentrations were quantified using a NanoDrop Spectrophotometer at a  wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) and the samples with RNA integrity values above 7.0 were used for the sequencing experiments.
Total RNA was used to construct RNA-seq libraries using the Illumina TruSeq RNA Sample Preparation Kit v3 according to manufacturer's instructions

treatment_protocol: DKO cells were treated with  1 μg/ml 4-hydroxytamoxifen (4-OHT) for 48 hours.

tag: genotype/variation

value: double knock out


title: Control mTS

description: FPKM.txt

value: control


title: AsPC-1_RNA-seq_NS

source_name: AsPC-1 nutrient starvation


title: AsPC-1_RNA-seq_Con

source_name: AsPC-1 control


title: PANC-1_RNA-seq_NS

source_name: PANC-1 nutrient starvation


title: PANC-1_RNA-seq_H

source_name: PANC-1 hypoxia


title: AGO10IP-Mock-br1

city: Riverside

first: Brandon

last: Le

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

data_processing:
Raw reads were processed by first trimming 3’ adapter sequence using custom Perl script. Reads without 3’ adapter sequence or less than 18 nucleotides after trimming were discarded from further analysis.
Trimmed reads were aligned against a custom database containing rRNA, tRNA, snoRNA, and snRNAs using Bowtie 0.12.8 to filter out rRNA reads.
Trimmed reads were collapsed into unique sequences with counts (tag count files) and processed as described in Zhao et al. Curr Biol 2012 for determining 3' end truncation and tailing.
Genome_build: TAIR10
Supplementary_files_format_and_content: tag count files contain raw reads (after adapter-trimming) collapsed into unique sequences with the corresponding read count in the library. This file is used to analyze the modifications of miRNA 3'ends as described in Zhao et al. Curr Biol 2012.

source_name: 13-day-old seedlings, with AGO10-IP

growth_protocol: 13-day-old seedlings grown on ½ Murashige and Skoog (MS) plates under 16h light/8h dark cycle

extract_protocol:
RNA was extracted with TRIzol reagent (Life Technologies, USA, 15596018)
Libraries were made using the NEBNext Small RNA Library Prep kit (NEB, USA) according to manufacturer’s instructions. Briefly, 3' and 5' adapters were ligated sequentially to the small RNAs. Ligated small RNAs were converted to cDNA by reverse transcription followed by PCR amplification for 15 cycles. The barcoded libraries were sequenced on the Illumina NextSeq500.

treatment_protocol: AGO1- and AGO10-RISC were immunoprecipitated (IP) from His-FLAG-AGO10 transgenic plants using anti-AGO1 (Agrisera) and anti-FLAG (Sigma) antibodies, respectively. Beads containing AGO1- or AGO10-IP were resuspended in reaction buffer (50 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT, 2.5 mM MnCl2, 1mM ATP) and then incubated with SDN1 or SDN1-D283A catalytic mutant for one hour. Mock treatment included buffer only (no SDN). Beads were collected after incubation for RNA extraction.

value: His-FLAG-AGO10 transgenic

tag: ip

tag: rip antibody

value: anti-FLAG (Sigma, F1804)

tag: biological replicate

value: 13 days old

tag: developmental stage

value: seedling


title: AGO1IP-Mock-br2

source_name: 13-day-old seedlings, with AGO1-IP

value: anti-AGO1 (Agrisera, AS09 527)

tag: treatment

value: Mock treatment included buffer only (no SDN)


title: AGO10IP-Mock-br2


title: AsPC-1_RNA-seq_pH

source_name: AsPC-1 low pH


title: pwr rep3

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline
The raw reads were aligned to the Arabidopsis genome (TAIR10) using hisat2. The reads mapped to more than one positions were removed.
The raw counts of gene were generated by perl script.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel files of raw counts

source_name: Young seedlings

extract_protocol:
Total RNA was extracted from 10-day old seedlings using the Trizol reagent (Invitrogen)
mRNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit). mRNA was purified and fragmented from total RNA (1 µg) using poly-T oligo-attached magnetic beads and two rounds of purification. Cleaved RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase, random primers and dUTP in place of dTTP. (The incorporation of dUTP quenches the second strand during amplification because the polymerase does not incorporate past this nucleotide.) A single adenine base was added to these cDNA fragments, followed by adapter ligation. The products were purified and amplified with PCR to create the final strand-specific cDNA library. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent). After qPCR using SYBR Green PCR Master Mix (Applied Biosystems), the index-tagged libraries were combined in equimolar amounts within a single pool.

tag: tissue

value: Seedling

tag: ecotype

value: Col


title: PANC-1_RNA-seq_Con

source_name: PANC-1 control


title: pwr rep2


title: AGO1IP-Mock-br1

tag: age


title: pwr rep1


title: PANC-1_RNA-seq_pH

source_name: PANC-1 low pH


title: PANC-1_SREBP2-ChIPseq_pH

source_name: PANC-1 low pH SREBP2 ChIP


title: PANC-1_SREBP2-ChIPseq_Con

source_name: PANC-1 control SREBP2 ChIP


title: hdac rep2


title: hdac rep3


title: hdac rep1


title: Col rep1

value: WT


title: Col rep2


title: Col rep3


title: pwr2_input_rep2


title: pwr2_K9_rep2

value: H3K9ac (Abcam, ab10812)


title: pnh-2_1

description: Illumina Truseq kit

data_processing:
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences.
The reads were mapped to the Arabidopsis genome using SOAP2 v2.21 (M4v0r1)
Bioinformatics analyses to categorize miRNA reads into the “full-length”, “3’ truncated-only”, “3’ tailed-only”, and “3’ truncated-and-tailed” categories
Genome_build: tair10
Supplementary_files_format_and_content: txt file, which has two columns: small RNA sequence, counts

source_name: RNA from pnh-2 seedlings

growth_protocol: all the seedling tissue are grown on MS plates under continuous light in the growth chamber

extract_protocol:
Total RNA was extracted using TRI-reagent (Molecular Research Center, Inc.) as per manufacturer's instructions. Contaminating DNA was removed by DNase I (Promega, Cat# M610A; Roche, Cat# 04716728001) digestion. cDNA was synthesized from 2 µg total RNAs using reverse transcriptase (Fermentas, Cat# EP0441) and an oligo-dT primer. Quantitative PCR was performed in triplicates on a Bio-Rad IQ cycler apparatus with the iQ SYBR green supermix (Bio-Rad, Cat# 170-8882).Values were obtained by normalizing to UBIQUITIN5.
Small RNA libraries were prepared using the Illumina Tru-Seq kit and sequenced with Illumina's HiSeq2000 platform at the UCR Institute for Integrative Genome Biology (IIGB) genomic core facility.


title: pnh-2_3

description: Illumina Truseq kit


title: ler3

description: Illumina Truseq kit

source_name: RNA from Ler seedlings


title: hdac_K9_rep2


title: hdac_input_rep2


title: ler1

description: Illumina Truseq kit


title: Col_input_rep2


title: Col_K9_rep2


title: ago10_2

description: Illumina Truseq kit

source_name: RNA from ago10-13 seedlings


title: pwr2_K9_rep1


title: ago10_3

description: Illumina Truseq kit


title: ler2

description: Illumina Truseq kit


title: ago10_1

description: Illumina Truseq kit


title: sdn1sdn2-2

description: Illumina Truseq kit

source_name: RNA from sdn1-1 sdn2-1 seedlings


title: hdac_K9_rep1


title: hen1sdn1sdn2-2

description: Illumina Truseq kit

source_name: RNA from hen1-8 sdn1-1 sdn2-1 seedlings


title: pwr2_input_rep1


title: hdac_input_rep1


title: sdn1sdn2-1

description: Illumina Truseq kit


title: hen1sdn1sdn2-1

description: Illumina Truseq kit


title: hen1-2

description: Illumina Truseq kit

source_name: RNA from hen1-8 seedlings


title: pnh-2_2

description: Illumina Truseq kit


title: Col_input_rep1


title: Col_K9_rep1


title: hen1-1

description: Illumina Truseq kit


title: AGO10IP-SDN-D283A-br1

treatment_protocol: AGO1- and AGO10-RISC were immunoprecipitated (IP) from His-FLAG-AGO10 transgenic plants using anti-AGO1 (Agrisera) and anti-FLAG (Sigma) antibodies, respectively. Beads containing AGO1- or AGO10-IP were resuspended in reaction buffer (50 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT, 2.5 mM MnCl2, 1mM ATP) and then incubated with SDN1 or SDN1-D283A catalytic mutant for one hour. Beads were collected after incubation for RNA extraction.


title: AGO10IP-SDN-D283A-br2


title: col-2_ct4hen1_sdn

description: Illumina Truseq kit

source_name: RNA from Col seedlings


title: AGO10IP-SDN-br1

value: SDN


title: AGO10IP-SDN-br2


title: AGO1IP-SDN-D283A-br1


title: AGO1IP-SDN-br1


title: AGO10 OE (I_s)

description:
Total RNA
Illumina Truseq kit

data_processing:
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences.
The reads were mapped to the Arabidopsis Ler genome using SOAP2 v2.21 (M4v0r1)
Genome_build: tair10
Supplementary_files_format_and_content: txt file, which has two columns: small RNA sequence, counts

source_name: AGO10 OE seedlings

value: AGO10 OE


title: AGO1IP-SDN-br2


title: sdn1 sdn2 AGO10 OE (I_s)

description:
Total RNA
Illumina Truseq kit

source_name: sdn1 sdn2 AGO10 OE seedlings

value: sdn1 sdn2 AGO10 OE


title: AGO10 OE (II_f)

description:
Total RNA
Illumina Truseq kit

source_name: AGO10 OE inflorescence

value: inflorescence


title: wildtype_with_ATc

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: GD-E

data_processing:
Sequencing data were processed using the Illumina Pipeline Software version 1.84.
Reads were right-trimmed for the Illumina adapter sequence using Flexbar (https://sourceforge.net/projects/flexbar/) and aligned with Bowtie2. Counting reads over annotated features was done with featureCounts. Annotation was taken from Tuberculist release R27 (http://tuberculist.epfl.ch/). To avoid the influence of transcripts deriving from the original 5’ fragment of mmpL3, a truncated version of mmpL3 was added to the annotation.
Differential gene expression (DGE) analysis was done using DESeq2 .
Genome_build: NC_000962.3

organism: Mycobacterium tuberculosis

source_name: cell culture, with ATc

growth_protocol: M. tuberculosis H37Rv strains were cultured at 37°C in either Middlebrook 7H9 (liquid medium) or 7H10 (solid medium, Difco), supplemented with 0.05% v/v Tween 80 (Sigma-Aldrich), 0.2% v/v glycerol (Sigma-Aldrich) and 10% ADN (2% glucose, 5% BSA, 0,85% NaCl). When required, antibiotics were added at the following concentrations: kanamycin (Sigma-Aldrich), 50 μg/ml; hygromycin (Invitrogen), 200 μg/ml; streptomycin (Sigma-Aldrich), 50 μg/ml (E. coli); streptomycin, 20 μg/ml; hygromycin, 50 μg/ml (M. tuberculosis).

extract_protocol:
Exponential phase M. tuberculosis cultures were pelleted and cells were flash frozen in liquid nitrogen and stored at -80°C until use. Bacteria were re-suspended in 1 ml Trizol (Ambion) and added to a 2-ml screw-cap tube containing 0.5 ml zirconia beads (BioSpec Products) for disruption by bead-beating (twice for 1 minute with a 2-minute interval on ice). The cell suspension was then transferred to a new tube, where chloroform-isoamylalcohol (24:1) extraction was performed. RNA was precipitated by adding 1/10 volume of sodium acetate (2 M, pH 5.2) and 0.7 volume of isopropanol, washed with 70% ethanol, air-dried and resuspended in DEPC-treated water. DNase treatment was carried out using TURBO DNA-free™ Kit (Ambion), following the manufacturer’s recommendations, and the reactions were subsequently cleaned up by phenol-chloroform extraction and ethanol precipitation. RNA was stored at -80°C in DEPC-treated water. Amount and purity of RNA were determined spectrophotometrically; integrity of RNA was assessed on 1% agarose gel.
Total RNA was extracted as previously described, and used for the preparation of strand-specific Illumina libraries, with an additional ribosomal RNA depletion step. Ribosomal transcript depletion was performed on 1 µg of total RNA using the Ribo-Zero rRNA Removal Kit for Gram-Positive Bacteria (Catalog Number MRZGP126; Illumina, San Diego, USA) according to the protocol provided by the supplier.  Sequencing libraries were then generated using the resulting ribosomal transcript-depleted RNA and the Illumina TruSeq Stranded mRNA Library Prep Kit reagents (Catalog Number RS-122-2101) according to the protocol provided by the supplier.

treatment_protocol: Anhydrotetracycline (ATc, Sigma) was added, when required, at a final concentration of 500 ng/ml.

tag: strain

tag: genotype

value: wild type


title: TB416_no_ATc_rep2

description: GD-D

source_name: cell culture, no Atc

value: pL3 conditional mutant (TB416)


title: AGO10OE-W1-AGO1-IP

source_name: 13-day-old seedlings, with AGO1-IP

extract_protocol:
RNA was extracted with TRIzol reagent (Life Technologies, USA, 15596018)
For samples without AGO1-IP, small RNA fragments (~15–30 nucleotides) were selected and recovered from 10 µg of total RNAs by 15% urea-polyacrylamide gel electrophoresis. RNAs isolated from AGO1-IP RISC were used directly for making libraries without size selection. Libraries were made using the NEBNext Small RNA Library Prep kit (NEB, USA) according to manufacturer’s instructions. Briefly, 3' and 5' adapters were ligated sequentially to the small RNAs. Ligated small RNAs were converted to cDNA by reverse transcription followed by PCR amplification for 15 cycles. The barcoded libraries were sequenced on the Illumina NextSeq500.

treatment_protocol: Anti-AGO1 antibody (Agrisera) was used to immunoprecipitate AGO1-RISC

tag: line

value: AGO10 overexpression


title: wildtype_no_ATc

description: GD-F


title: TB416_no_ATc_rep1

description: GD-C


title: AGO10 OE_2

description:
Total RNA
Illumina Truseq kit


title: AGO10OE-M2-AGO1-IP


title: TB416_with_ATc_rep2

description: GD-B


title: AGO10 OE_3

description:
Total RNA
Illumina Truseq kit


title: AGO10OE-S2-AGO1-IP


title: AGO10OE-M1-AGO1-IP


title: AGO10 OE_1

description:
Total RNA
Illumina Truseq kit


title: TB416_with_ATc_rep1

description: GD-A


title: col-1_ct4hen1_sdn

description: Illumina Truseq kit


title: Col_3

description:
Total RNA
Illumina Truseq kit

source_name: Col seedlings

value: control (Col)


title: AGO10OE-W1

source_name: 13-day-old seedlings, without AGO1-IP


title: Col_2

description:
Total RNA
Illumina Truseq kit


title: AGO1IP-SDN-D283A-br2

value: His-FLAG-AGO10 transgenic


title: sdn1 sdn2 AGO10 OE (II_f)

description:
Total RNA
Illumina Truseq kit

source_name: sdn1 sdn2 AGO10 OE inflorescence


title: AGO10OE-M1

value: 13 days old


title: Col_1

description:
Total RNA
Illumina Truseq kit

value: seedling


title: AGO10OE-M2


title: Primary_HsESF_218S-2_undecidualized

city: West Haven

first: Gunter

last: Wagner

state: CT

address: 300 Heffernan Drive, ISTC 108

department: Systems Biology Institute, EEB

institute: Yale University

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the human (GRCh37.69) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci. 131:218
Genome_build: human (GRCh37.69)
Supplementary_files_format_and_content: .txt files include TPMs and read counts for each sample.

source_name: endometrial biopsy

growth_protocol: Cells were grown in DMEM supplemented with 10% charcoal stripped fetal bovine serum, 0.1% ITS, and 1% antibiotic/antimycotic.

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini Kit followed by on-column treatment with DNase-1 treatment
RNA libraries were prepared for sequencing using standard illumina protocols.

treatment_protocol: To induce decidualization cells were treated with 0.5mM 8-Br-cAMP and 0.5mM of the progesterone analog, medroxy-progesterone acetate for 48 hours in Dulbeccos Modified Eagle Medium supplemented with 2% fetal bovine serum.

tag: cell type

value: Endometrial Stromal Fibroblast

tag: menstrual cycle

value: Day 9


title: Primary_HsESF_218S-1_undecidualized


title: AGO10OE-S2


title: AGO10 IP_3

description:
RNA from IP
Illumina Truseq kit

source_name: IP with anti-GFP antibody from AGO10 OE seedling tissue

value: YFP-AGO10 (Clontech, catalog#:632460, lot#:1301021)


title: Primary_HsESF_217S-2_undecidualized

value: Day 3


title: AGO1 IP (Col)

description:
RNA from IP
Solexa method, barcoded

source_name: IP with anti-AGO1 antibody from Col seedling tissue

value: AGO1 (generated in-house)


title: 12 h

city: Stockton

first: Douglas

middle: D

last: Risser

state: California

address: 3601 Pacific Ave

department: Biology

institute: University of the Pacific

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence at the University of California Berkeley QB3 Vincent J. Coates Genomics Sequencing Laboratory prior to dissemination of data to the end user
Alignment, normalization, and transcript abundance was performed using the Rockhopper software package with default settings
Genome_build: ASM2002v1
Supplementary_files_format_and_content: .txt file reports abundance measurements

organism: Nostoc punctiforme PCC 73102

source_name: N. punctiforme

growth_protocol: Nostoc punctiforme strains were cultured in Allan and Arnon medium diluted four fould (AA/4), as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) with the exception that cultures were supplemented with 30mM fructose

extract_protocol:
RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256)
Total RNA was ribodepleted using the Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, Inc.). cDNA was synthesized from the rRNA depleted samples, sheared to a library size of 200 bp, and appended with adapters following standard protocols at the University of California Berkeley QB3 Vincent J. Coates Genomics Sequencing Laboratory .

treatment_protocol: For hormogonium induction cultures supplemented with 2.5 mM NH4Cl at a chlorophyl a concentration of 2-3 ug/ml were harvested at 1000xg for 5 min, washed 3x with AA/4 and resuspended in AA/4 supplemented with 2.5 mM NH4Cl and containing the Anthoceros punctatus derived hormogonium inducing factor (HIF) (see materials and methods of Risser and Meeks. 2013. Molecular Microbiology. 87:884-893)

tag: filament type

value: developing hormogonia

tag: time following hormogonium induction


title: Primary_HsESF_218S-2_decidualized

value: in vitro decidualized stromal fibroblasts


title: Primary_HsESF_217S-1_undecidualized


title: 18 h


title: Primary_HsESF_218S-1_decidualized


title: AGO10 IP_1

description:
RNA from IP
Illumina Truseq kit

value: AGO10 OE


title: AGO1 IP_3

description:
RNA from IP
Illumina Truseq kit

source_name: IP with anti-AGO1 antibody from AGO10 OE seedling tissue


title: AGO1 IP_2

description:
RNA from IP
Illumina Truseq kit


title: Primary_HsESF_217S-1_decidualized


title: 1 h

value: 1 h


title: AGO1 IP_1

description:
RNA from IP
Illumina Truseq kit


title: Primary_HsESF_217S-2_decidualized


title: TH+ D50 anti-MED1-seq

status: Public on Jan 24 2017

city: Bozeman

first: Ninuo

last: Xia

state: Montana

address: 3114 annie street

department: cell biology and neurosciences

institute: Montana State University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v2.0 with the following configurations…
Data were filtered using thefastq filter in Galaxy …
peaks were called using MACS version1.0.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig generated using wig to bigwig converter in Galaxy

source_name: D50 TH+ DA neurons

growth_protocol: This differentiation is based on Kirks protocol (Kriks et al., 2011) with following modifications: first, we control our differentiation seeding density at 1.8x105 per cm2, this optimized seeding density ensures cell survival during the first 10 days of differentiation; second, opposed to the original protocol which passages cells at day 11, we do not do any cell passaging until differentiation day 20; third, during the “floor plate” induction, we used small molecules SAG and purmorphamine instead of SHH.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: TH+ Dopamine neurons


title: TH+ D50 H3K27ac-seq


title: TH+ D50 5hmC-seq

data_processing:
Library strategy: 5hmC-seq
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v2.0 with the following configurations…
Data were filtered using thefastq filter in Galaxy …
peaks were called using MACS version1.0.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig generated using wig to bigwig converter in Galaxy


title: 6 h

value: 6 h


title: AGO10 OE 4mAGO1

description:
Total RNA
Illumina Truseq kit

source_name: AGO10 OE 4mAGO1 seedlings

value: AGO10 OE 4mAGO1


title: TH+ D50 input seq


title: 751-NC_RNASeq

city: Beijing

first: Qinong

last: Ye

address: Taiping Rd.27

institute: Beijing Institute of Biotechnology

description: control

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat with parameters -a 8 -m 0 -i 50 -I 500000 -N 2 --read-gap-length 2 --read-edit-dist 2 -g 20 --library-type fr-unstranded -p 8 -r 130 --microexon-search
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample...

source_name: ZR75-1 cells stably infected with lentivirus carrying control shRNA

growth_protocol: DMEM containing 10% Newborn Calf Serum

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

tag: cell line

tag: tissue type

value: breast cancer

tag: passages


title: 751-Six1-si_RNASeq

description: treatment

source_name: ZR75-1 cells stably infected with lentivirus carrying Six1 shRNA


title: 0 h

value: vegetative

value: 0 h


title: WT

description: Col-WT

tag: genotype/variation

value: WT

value: 13 days old


title: AGO1 IP (AGO10 OE)

description:
RNA from IP
Solexa method, barcoded

value: seedling

tag: rip antibody


title: AGO10 IP_2

description:
RNA from IP
Illumina Truseq kit


title: F_TN_LPS_2

city: Ames

first: Angelica

middle: G

last: Van Goor

state: Iowa

address: 1221 Kildee Hall

institute: USDA-NIFA

data_processing:
Clipped barcode adapter sequences -FASTX Clipper, Version 0.0.13. Discard sequences shorter than: 30 bp, minimum quality score: 30, and minimum percent of bases that must have this quality: 80.
Mapped reads to GalGal 4.0  -TopHat, Version 2.0.9.  Bowtie version: 2.1.0. Quality scale: phredd, Anchor length: 8, Maximum number of mismatches: 0, Minimum intron length: 70, Maximum intron length: 5000, Minimum isoform fraction: 0.15, Maximum number of alignments: 20, Minimum intron length that may be found during split-segment: 50, Maximum intron length that may be found during split-segment: 500000, Number of mismatches allowed in each segment: 2, Minimum length of read segments: 20, Bowtie 2 speed and sensitivity: sensitive (slower)
Count reads to chicken genome -HTSeq, Version 0.6.1. Use acceptedhits.bam from tophat2 output, Minimum mapping quality 0 because of only high quality data phred 30 going in, Bed file for overlap is output from tophat junctions.bed, GFF file was downloaded from NCBI Gallus_gallus.Galgal4.78.gtf, Mode: intersection-nonempty for stringency, Strandspecificity: none because sequencing wasn’t strand specific, Minimum quality: default 0, Feature type: exon, Feature attribute: gene_id, Feature counts output file: name of samplefeaturecounts.txt

organism: Gallus gallus

source_name: Chicken splenic tissue

growth_protocol: Chickens were raised with ad libitim access to feed and water that met all NRC requirements.

extract_protocol:
The total RNA was isolated from 4 chicken spleens per treatment group (32 birds total) with the RNAqueous kit (Ambion) using all manufacturers recommendations as previously described (Cheeseman et al. 2007), and treated with DNA-free kit (Ambion).
Only samples with an RNA Integrity Number (RIN) greater than 9 were used for cDNA library construction using the TruSeq RNA Library preparation kit v2 (Illumina) that preferentially amplifies PolyA mRNA. The cDNA libraries created from the spleen of 32 chickens were run on the HiSeq 2500 machine (Illumina) with the option of 100 bp single end reads at the Iowa State University DNA Facility. Four lanes were used for RNA-sequencing with 8 multiplexed samples per lane (one sample per each treatment).
Individually barcoded samples with 8 different bar codes per lane for multiplexing.

treatment_protocol: Chickens were treated with a themal stimulation (heat stress or thermoneutral) and/or an inflammatory stimulus (LPS or PBS).

tag: chicken breed

value: Fayoumi

tag: thermal treatment

value: Thermoneutral

tag: inflammatory stimulus treatment

value: LPS


title: F_TN_PBS_1

value: PBS


title: C419_DMSO_24hr_rep2

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2)
Reads were aligned to hg19 geneome assembly and transcript assembly was performed using tophat (v.2.0.13)
RPKM calculation and differential expression analysis was performed using cufflinks (v.2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: C419 celles treated with DMSO for 24hrs

growth_protocol: C419 cells were maintained in neurosphere culture using neuronal stem cell medium (DMEM F12 50:50 medium, with 20 ng/ml EGF, 20 ng/ml FGF, 20 ng/ml progesterone, 2% B27 serum, 1% insulin-transferrin-selenium-ethanolamine, 1% penicillin/streptomycin, 4 µg/ml doxycycline, 0.1% fungizone)

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: C419 cells were treated for 24 or 48 hours with either DMSO (vehicle) or 50 nM mithramycin.

tag: histology

value: Glioblastoma (GBM)


title: C419_50nm_MTM_48hr_rep2

source_name: C419 celles treated with MTM for 48hrs


title: C419_DMSO_24hr_rep1


title: C419_50nm_MTM_24hr_rep2

source_name: C419 celles treated with MTM for 24hrs


title: C419_DMSO_48hr_rep1

source_name: C419 celles treated with DMSO for 48hrs


title: C419_DMSO_48hr_rep2


title: C419_50nm_MTM_48hr_rep1


title: C419_50nm_MTM_24hr_rep1


title: TH+ D50 H3K4me1-seq


title: F_TN_PBS_3


title: F_HS_PBS_1

value: Heat stress


title: F_TN_LPS_3


title: F_HS_PBS_3

value: Broiler


title: B_HS_LPS_3


title: B_HS_PBS_3


title: B_HS_LPS_1


title: B_TN_PBS_4


title: E70 rep3

first: Fu

last: Wang

address: Tian Tan Xi Li No.4, P. R. China

institute: Capital Medical University

data_processing:
We used the spliced read aligner TopHat[1] version V1.31 to map all sequencing reads to domestic pig ( ftp://ftp.ensembl.org/pub/release-69/fasta/sus_scrofa/dna/),mini-pig (http://gigadb.org/wuzhishan-inbred-pig/).
Two rounds of TopHat mapping were used to maximize the splice junction information derived from all samples. In the first round, all reads were mapped with TopHat using the following parameters: multi hits = 1 and the rest set as default; in the second round of TopHat mapping, all splice junctions produced by the initial mapping were collected and fed into TopHat to re-map each sample with the following parameters: raw-juncs, no-novel-juncs, multi hits = 1. Biological replicates of mapped reads from the same sample were merged into a single BAM file to facilitate the transcript assembly and quantification.
Aligned reads from TopHat were assembled into transcriptome for each sample separately by Cufflinks (V1.0.3) with default parameters (and‘min-frags-per-transfrag = 0’) and gave out transcripts information in gtf format and expression value in FPKM (fragments per kilobase of exons per million fragments mapped).
aligned reads filtered from TopHat were assembled into transcriptome by Cufflinks (V1.0.3) running with default parameters. The assembled transcripts were merged by running Cuffcompare. Calculation and statistical analysis of the gene expression levels from the RNA-Seq data were performed using Cuffdiff for Pathway and Go analysis.
The transcripts from E50, E60 and E70 with low expression and a length<200bp or exon number equals one from input ﬁles were removed to avoid noise data. The remaining transcripts were merged with Cuffmerge, and then subjected to CNCI to get the lncRNA candidates. The lncRNA candidates overlapping with known protein-coding regions of WZSP, pig, human, cow and mouse using Cuffcompare were filtered, the remaining transcripts with length of >=200bp and exon number>1 were considered as putative lncRNAs. The lncRNA was functional annotated using ncFANs and then maped to WZSP resulting in known and novel lncRNA transcripts. The novel transcripts were then blased to lncRNA database of mouse, human (NONCODEv4 database) and cow (ftp://ftp.ensembl.org/pub/release-72/fasta/bos_taurus/dna/) for annotation in turn.
Genome_build: sscrofa10, WZSP
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Sus scrofa

source_name: additional molar germs

extract_protocol:
The additional molar germs, attached the dental lamina from the mandibles of the staged miniature pig embryos were isolated and immerged in 5–10 volumes of RNAlater solution (Ambion, USA) overnight at 4°C. Total RNA was extracted from samples at specific stages using TRIZOL Reagent (Life technologies, CA, US) following the manufacturer’s instructions, and then checked for integrity using an Agilent Bioanalyzer 2100 (Agilent technologies, CA US).  Total RNA was further purified using the RNeasy mini kit and RNase-Free DNase Set (QIAGEN, GmBH, Germany).Pools of samples with RNA integrity numbers (RIN) ≥7.0 was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: miniature pig

tag: tissue

value: additional molar germs

tag: age

value: embryonic day 70

value: wild type


title: E70 rep1

tag: strain

tag: genotype


title: E50

value: embryonic day 50


title: B_TN_LPS_4


title: E70 rep2


title: E60

value: embryonic day 60


title: B_HS_PBS_2


title: B_TN_LPS_1


title: B_TN_PBS_1


title: F_TN_LPS_4


title: F_HS_LPS_1


title: F_HS_LPS_3


title: F_TN_PBS_4


title: F_HS_LPS_4


title: F_TN_PBS_2


title: F_HS_PBS_2


title: B_TN_PBS_2


title: F_TN_LPS_1


title: F_HS_PBS_4


title: F_HS_LPS_2


title: B_TN_PBS_3


title: B_HS_PBS_1


title: B_HS_PBS_4


title: B_TN_LPS_3


title: Whole WAT H3K27ac rep2

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

data_processing:
ChIP-seq data were aligned using Bowtie2 to the mm9 mouse genome
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. Low signal peaks (log2 CPM<2) were removed, and differential peaks were defined at log2 FC≥1 and log2 FDR≤0.25.
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files

source_name: epididymal WAT

growth_protocol: Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual.
Extracted DNA (1-10ng, or all if less) was used to generate sequencing libraries by following the “on-bead” sequencing library preparation method. Briefly, DNA was processed through end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment (NEB M0212) and index adaptor ligation using the Quick Ligase (NEB M2200). AMPure XP beads were left in all the reactions to clean up the DNA using PEG(Polyethylene Glycol 8000)/NaCl solution. After ligation, DNA was eluted from AMPure XP beads and then PCR-amplified using the PfuUltra II Hotstart PCR Master Mix (Agilent 600850). Gel electrophoresis/extraction was performed using the E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction (Qiagen) to select library fragments between 250 and 600bp. Quantity and quality of the libraries were analyzed by Qubit and Agilent Bioanalyzer, respectively, and the libraries were pooled at a final concentration of 12pM and sequenced by HiSeq2500 or NextSeq 500 systems.

value: adipose

tag: chip antibody

value: H3K27ac (Active Motif, 39133)


title: B_HS_LPS_4


title: Whole WAT H3K27ac rep1


title: WAT_adipocyte_H3K4me3


title: Non-hepatocyte_H3K27ac

source_name: Liver

value: Liver


title: WAT Adipocyte H3K4me1 rep2

source_name: inguinal WAT