title: HPM4-A2

city: Burlington

first: Julie

last: Dragon

state: VT

address: 95 Carrigan Dr

department: MMG

institute: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

description: 2x100 paired-end sequence reads

data_processing:
Illumina HiSeq 1000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of Partek Genomics Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq release 2013-5-10). Exclusions included a minimum RPKM value of 1.0 in at least two of the 16 samples (potentially duplicates of one sample group). RPKM values were log2-transformed with an offset value of 1.0.
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: ProcessedDataMatrix_Final.txt: Tab-delimited text file includes RPKMs (log2-transformed with an offset value of 1.0) for each sample.

source_name: Primary mesothelial cell line HPM4, crocidolite asbestos exposure, 8hrs

growth_protocol: LP9 cells were grown in 50:50 DMEM/F-12 medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml), hydrocortisone (100 mg/ml), insulin (2.5 mg/ml), transferrin (2.5 mg/ml), and selenium (2.5 mg/ml); all other cells were grown in 50:50 M199:MCDB106 medium supplemented with 15% FBS, 10 ng/mL EGF, 0.4 µg/mL hydrocortisone, 50 units/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of crocidolite asbestos fibers prepared and added (5 μg/cm2 or 75 x 10^6 μm2/cm2 for 8 h) to cell culture medium. After sterilization under ultraviolet light overnight to avoid endotoxin and microbial contamination, fibers were suspended in HBSS at 1 mg/ml, sonicated for 15 minutes in a water bath sonicator, and triturated five times through a 22-gauge needle. This suspension was added to cells in medium.

value: primary mesothelial cells

tag: cell source

value: pleural cavity

tag: treatment

value: 5 μg/cm2 of crocidolite asbestos exposure for 8 hrs


title: Sample4_C24A9XCol-0_Rep2

status: Public on Mar 02 2015

type: SRA

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

department: Genome Center

country: USA

institute: UC Davis

description:
Samples 1-4 were standard RNA-seq. Samples 5-9: mRNA amplicons, PCR sequence data for validation
Seed from 3 DAP C24A9 X Col-0 crosses

library_source: transcriptomic

data_processing:
All sequence preprocessing was done with custom python scripts available at the Comai lab wiki (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). Sequences were divided according to barcodes and barcodes were removed. The Illumina 1.5+ format (fastq) reads were trimmed for adaptor contamination and bases with a quality score lower than Phred 20 were also excluded using a custom python script. Reads that were shorter than 40 base pairs (for 80-bp or 100-bp). The Illumina quality scores were converted to Sanger, which is compatible with most aligners. Biological replicates were pooled for greater sequence depth.
Processed and pooled sequences were aligned to A. thaliana TAIR10 cDNA all gene models using Burrows-Wheeler Aligner (BWA) version 0.5.8c and SAM files and parsed pileups were generated using Samtools version 0.1.7 [58] as well as custom python scripts..
Read counts were generated using a custom python script available for download at http://comailab.genomecenter.ucdavis.edu/index.php/Hybrid_Transcriptome.
Supplementary_files_format_and_content: .txt (count file)
The N libraries are normalized libraries of the Sample 1 and Sample 3

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seeds

growth_protocol: Wild type Col-0 (CS6673) and C24 (CS22620), as well as male sterile lines that were hemizygous for a male sterility construct, were grown in 16 hours of light at 21°C and 8 hours of dark at 18°C in a controlled environment fascility. The male-sterile A. thaliana lines (ColA9 and C24A9) were pollinated by either wild type Col-0 or C24. Two biological replicates for each condition (ColA9 X C24 or C24A9 X Col-0) were used in these experiments. No emasculation was needed because all egg donors had a sterility construct.

extract_protocol: RNA processing for Illumina sequencing was performed using a homemade kit (see Burkart-Waco et al. 2013 for technical details). RNA was sequenced according to Illumina's specifications on HiSeq2000 (Illumina, San Diego) (100-bp paired-end reads).

treatment_protocol: Seeds were harvested fresh from ColA9 X C24 and C24A9 X Col-0 and frozen on dry ice. RNA isolation using Invitrogen's Plant RNA Reagent was described by Burkart-Waco et al. (2013).

tag: ecotype

value: A. thaliana eco. C24A9 X Col-0

tag: tissue

value: whole seeds

tag: time

value: 3 days after pollination


title: HPM4-C1

description: 2x100 paired-end sequence reads

organism: Homo sapiens

source_name: Primary mesothelial cell line HPM4, untreated

tag: cell line

tag: cell type

value: no exposure for 8 hrs


title: HPM4-C2

description: 2x100 paired-end sequence reads


title: HPM4-A1

description: 2x100 paired-end sequence reads


title: HPM3-C1

description: 2x100 paired-end sequence reads

source_name: Primary mesothelial cell line HPM3, untreated


title: HPM3-A1

description: 2x100 paired-end sequence reads

source_name: Primary mesothelial cell line HPM3, crocidolite asbestos exposure, 8hrs


title: HPM3-C2

description: 2x100 paired-end sequence reads


title: LP-A2

description: 2x100 paired-end sequence reads

source_name: Immortalized mesothelial cell line LP9, crocidolite asbestos exposure, 8hrs

value: immortalized mesothelial cells

value: peritoneal cavity


title: HM3-C1

description: 2x100 paired-end sequence reads

source_name: Primary mesothelial cell line HM3, untreated


title: HM3-C2

description: 2x100 paired-end sequence reads


title: HM3-A2

description: 2x100 paired-end sequence reads

source_name: Primary mesothelial cell line HM3, crocidolite asbestos exposure, 8hrs


title: LP-A1

description: 2x100 paired-end sequence reads


title: LP-C1

description: 2x100 paired-end sequence reads

source_name: Immortalized mesothelial cell line LP9, untreated


title: Hsa N replicate 1

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

country: Germany

institute: TUD Dresden University of Technology

description:
Hsa_N_1
hsa_fpkm_matrix.txt

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were trimmed with cutadapt (-m 20 -q 25)
Trimmed Reads were mapped using tophat v2.0.11 (-G $gtfFile -g1)
Abundance estimation was performed using cuffdiff (v2.2.1)
Genome_build: mm10, hg19
Supplementary_files_format_and_content: FPKM normalized expressoin score tables as provided by cummerbund::countMatrix

source_name: Neuron

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions.
Complete cDNA was synthesized from half of the isolated mRNA with SmartScribe reverse transcriptase (Clontech) using a universally tailed poly-dT primer and template switching oligos. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase (12 cylces). After ultrasonic shearing of the amplified cDNA (Covaris S2), samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs), in brief: fragments were end repaired, A-tailed and ligated to indexed Illumina Truseq adapters. Subsequently, the NGS libraries were finalized by a universally primed PCR amplification (15 cycles). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75-bp single end sequencing on the Illumina HiSeq 2000 platform providing on average 35 Mio reads per sample.

tag: age


title: LP-C2

description: 2x100 paired-end sequence reads


title: Hsa N replicate 0

description:
Hsa_N_0
hsa_fpkm_matrix.txt


title: Hsa bRG replicate 3

description:
Hsa_bRG_3
hsa_fpkm_matrix.txt

source_name: bRG


title: mRNA_wild-type DED1 replicate 2_37 deg

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 CENTER DR Room 230, MSC 0609

institute: NICHD

description:
Experiment 2
processed data file: ded1-ts.csv

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Read quantitation using custom scripts
Analysis of reads using DESeq
Genome_build: sacCer2
Supplementary_files_format_and_content: processed  txt (csv) files per experiment show a matrix (with columns: yORF name, gene name, WT ribosome occupancy, mutant ribosome occupancy, WT mRNA occupancy, mutant mRNA occupancy, ribosome occupancy change, mRNA occupancy change, TE change). All numerical columns have log values with base 2

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD600 of ~  0.7 in synthetic complete medium and subjected to temperature shifts as indicated

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill.
Ribosome profiling (Rnase I footprinting, size selection,RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223

treatment_protocol: All cultures were treated  with cycloheximide (100 ug / ml) for 2 min prior to harvesting

tag: strain (genetic background)

value: wild-type DED1 (NSY10)

tag: temperature

value: 37 deg

tag: molecule type

value: mRNA


title: Hsa bRG replicate 1

description:
Hsa_bRG_1
hsa_fpkm_matrix.txt


title: mRNA_wild-type DED1 replicate 1_37 deg


title: Hsa bRG replicate 0

description:
Hsa_bRG_0
hsa_fpkm_matrix.txt


title: ribo_ded1-ts replicate 2_37 deg

value: ded1-ts (NSY11)

value: Ribosome-protected RNA


title: HPM3-A2

description: 2x100 paired-end sequence reads


title: ribo_ded1-ts replicate 1_37 deg


title: Hsa aRG replicate 3

description:
Hsa_aRG_3
hsa_fpkm_matrix.txt

source_name: aRG


title: mRNA_tif1-ts replicate 2_37 deg

description:
Experiment 4
processed data file: tif1-ts_37_deg.csv

value: tif1-ts (NSY21)


title: Hsa aRG replicate 2

description:
Hsa_aRG_2
hsa_fpkm_matrix.txt


title: ribo_wild-type DED1 replicate 2_37 deg


title: HM3-A1

description: 2x100 paired-end sequence reads


title: Time-course_Ago2_FLAG-IP_mut_72hr

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: Ago2-associated RNA

data_processing:
For each read, the 3′ adaptor TGGAATTCTCGGGTGCCAAGG was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least seven or ten bases, respectively. Reads with Low-complexity were filtered out based on their dinucleotide entropy (removing <1% of the reads). Only reads with a minimum length of 14nt were retained. Alignments to the rat miRNA database miRBase release 20 (http://www.mirbase.org/) were performed by the software bowtie (version 0.9.9.1) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Reads that mapped to a miRNA but at the same time also mapped with fewer mismatches to the genome (rn4) were filtered out. The expression of each miRNA was determined by counting the number of associated reads. To compensate for differences in the read depths of the individual libraries, each sample was divided by its total number of counts and multiplied by the ave  rage sample size. The resulting values were log2 transformed using a pseudocount of 8 (y=log2(x+8)). The two experiments “Syn-Target” and “Time-course” were normalized separately.
genome build: rn4 (UCSC)
Supplementary_files_format_and_content:MiRNA expression table (all samples)

organism: Rattus norvegicus

source_name: Primary hippocampal neurons

growth_protocol: Primary dissociated hippocampal neurons were routinely generated by removing hippocampi from embryonic day 18.5 (E18.5) rats and treated with 0.05 % trypsin (Sigma) for 15 min at 37 °C, followed by washing and trituration. Dissociated cells were plated at 30,000 cells/cm2 on poly-D-lysine coated plates (BD biosciences) and cultured in Neurobasal medium (Gibco) supplemented with 2 mM Glutamax (Invitrogen), and 2% B-27 supplement (Invitrogen).

extract_protocol:
Total RNA and Ago-associated RNA (FLAG-IP fraction) were extracted using Trizol reagent.
Small RNA libraries were prepared for sequencing using Illumina TruSeq Small RNA Sample Prep Kits (Cat # RS-200-0024).

treatment_protocol: Neurons were transduced with lentiviruses 9 days after plating (DIV9) at a multiplicity of infection (MOI) of 1-5, and analyzed 5-6 days after infection (DIV15-16). Immunoprecipitation of FLAG/HA-Ago2 was performed with Anti-FLAG M2 Magnetic Beads (Sigma. Cat # M8823).

tag: strain

value: Sprague Dawley

tag: embryo stage for culture prep

tag: days of in vitro culture (div)

tag: antibody

value: FLAG/HA-Ago2 (Sigma. Cat # M8823)


title: ribo_wild-type DED1 replicate 1_37 deg


title: Time-course_Ago2_FLAG-IP_mut_24hr

description: Ago2-associated RNA


title: Hsa aRG replicate 0

description:
Hsa_aRG_0
hsa_fpkm_matrix.txt


title: mRNA_tif1-ts replicate 1_37 deg


title: mRNA_ded1-ts replicate 2_37 deg


title: mRNA_wild-type TIF1 replicate 2_37 deg

value: wild-type TIF1 (NSY20)


title: Hsa aRG replicate 1

description:
Hsa_aRG_1
hsa_fpkm_matrix.txt


title: Time-course_Ago2_FLAG-IP_mut_4hr

description: Ago2-associated RNA


title: Hsa bRG replicate 2

description:
Hsa_bRG_2
hsa_fpkm_matrix.txt


title: Time-course_Ago2_FLAG-IP_mut_8hr

description: Ago2-associated RNA


title: mRNA_ded1-ts replicate 1_37 deg


title: mRNA_wild-type TIF1 replicate 1_37 deg


title: si DGCR8_HeLa_nuclear polyA+

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology,  University of Oxford

description:
Nuclear RNA
si_DGCR8_HeLa_nuclear_polyA+

data_processing:
Paired-end reads for each sample were mapped to the human genome reference assembly GRh37/hg19 (build 37.2, Feb 2009) using the Bowtie2 alignment software. Prior to alignment, the first 12 nucleotides were trimmed from all the reads owing to the low quality of the bases. Uniquely mapped reads with no more than two mismatches were retained for further analysis. For nuclear polyA+ data, we filtered out reads that had 8 or more genomically encoded A-stretch at their 3’ ends.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

molecule: nuclear RNA

source_name: HeLa

extract_protocol:
Chromatin-associated RNA Isolation:  siRNA treated HeLa cells from one ~80% confluent 10 cm plate were scraped into 10 ml of cold PBS followed by centrifugation at 1500 rpm in 15 ml conical tubes. The cell pellets were resuspended in 500 µl cold cytoplasmic lysis buffer (0.15% NP-40,10mM Tris pH 7.5, 150mM NaCl) using wide orifice tips and incubated on ice for 5 min. The lysate was under layered with 500 µl cold sucrose buffer (10mM Tris pH7.5,150mM NaCl, 24% sucrose w/v), and centrifuged in microfuge tubes at 13,000 rpm for 10 min at 4°C. The supernatant from this spin represented the cytoplasmic fraction and was discarded The nuclear pellet was gently resuspended into 200 µl of cold glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50%glycerol, 0.85 mM DTT). An additional 10 volumes (2 ml) of cold nuclei lysis buffer (20 mM HEPES pH 7.6, 7.5 mM MgCl2,0.2mM EDTA, 0.3M NaCl, 1M urea, 1% NP-40, 1mM DTT) was added to the samples, followed by a pulsed vortexing and incubation on ice for 10 min. The chromatin was sedimented by centrifugation for 10 min at 14,000 rpm and at 4°C. The supernatant from this spin was discarded. The chromatin pellet fraction was incubated in 200 µl high salt buffer (10 mM Tris HCl pH 7.5, 500 mM NaCl, and 10mM MgCl2) + 20U of DNaseI for 20 min at 37ºC, extracted with Trizol reagent, and isopropanol precipitated. The precipitate was twice treated with DNaseI treated and incubated for 20 min at 37ºC, then extracted with Trizol reagent followed by isopropanol precipitation. Chromatin pellet RNAs were eluted in 50 µl RNase-free water.
Nuclear RNA preparation:  Nuclear RNA preparation was carried out from nuclear pellet obtained as above. The nuclear pellet was resuspended in 200 µl high salt buffer (10 mM Tris HCl pH 7.5, 500 mM NaCl, and 10mM MgCl2) + 20U of DNaseI for 20 min at 37ºC, extracted with Trizol reagent, and isopropanol precipitated. The precipitate was twice treated with DNaseI treated and incubated for 20 min at 37ºC, then extracted with Trizol reagent followed by isopropanol precipitation. Nuclear RNAs were eluted in 50 µl RNase-free water. DNase I-treated nuclear RNA was incubated with oligo(dT) magnetic beads (Dynabeads mRNA purification kit, Invitrogen) to isolate either poly(A)+ RNA, which was bound to beads, or poly(A)- RNA, which was present in the flowthrough after incubation. Oligo(dT) magnetic bead selection was performed twice to ensure pure polyA+ or polyA- populations. The poly(A)- RNA population was further processed with the Ribo-Zero Magnetic Kit (Human/Mouse/Rat, Epicentre) to deplete most of the abundant ribosomal RNAs.
RNA-seq was performed by the High‐Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, University of Oxford. RNA Samples were ribodepleted using Ribo-Zero rRNA removal kit (Human/Mouse/Rat, EpiCentre RZH110424). Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, v1.0 (cat # E7420) using manufacturer's guidelines with an exception of using our own 8bp tags for indexing according to5. Libraries were sequenced on an Illumina HiSeq-2000 using 100bp and 50bp paired end reads, v3 chemistry.

value: HeLa

tag: genotype/variation

value: si DGCR8

tag: rna prep

value: polyA+ nuclear fraction


title: ribo_tif1-ts replicate 2_37 deg


title: si DGCR8_HeLa_nuclear polyA-

description:
Nuclear RNA
si_DGCR8_HeLa_nuclear_polyA-

value: polyA- nuclear fraction


title: Time-course_Ago2_FLAG-IP_mut_2hr

description: Ago2-associated RNA


title: si cntrl_HeLa_nuclear polyA+

description:
Nuclear RNA
si_cntrl_HeLa_nuclear_polyA+

value: si cntrl


title: Time-course_Ago2_FLAG-IP_mut_0hr

description: Ago2-associated RNA


title: si DGCR8_chromatin_Huh7

description:
Chromatin RNA
si_DGCR8_chromatn_Huh7

value: chromatin-associated RNA fraction


title: ribo_wild-type TIF1 replicate 2_37 deg


title: si cntrl_HeLa_nuclear polyA-

description:
Nuclear RNA
si_cntrl_HeLa_nuclear_polyA-


title: Time-course_Ago2_FLAG-IP_WT_72hr

description: Ago2-associated RNA


title: si cntrl_chromatin_Huh7

description:
Chromatin RNA
si_cntrl_chromatn_Huh7


title: si Dicer_chromatin_HeLa

description:
Chromatin RNA
si_Dicer_chromatn_HeLa

data_processing:
Paired-end reads were mapped to the human genome reference assembly GRh37/hg19 (build 37.2, Feb 2009) using the Bowtie2 alignment software. Prior to alignment, the first 12 nucleotides were trimmed from all the reads owing to the low quality of the bases. Uniquely mapped reads with no more than two mismatches were retained for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

extract_protocol:
Chromatin-associated RNA Isolation:  siRNA treated HeLa cells from one ~80% confluent 10 cm plate were scraped into 10 ml of cold PBS followed by centrifugation at 1500 rpm in 15 ml conical tubes. The cell pellets were resuspended in 500 µl cold cytoplasmic lysis buffer (0.15% NP-40,10mM Tris pH 7.5, 150mM NaCl) using wide orifice tips and incubated on ice for 5 min. The lysate was under layered with 500 µl cold sucrose buffer (10mM Tris pH7.5,150mM NaCl, 24% sucrose w/v), and centrifuged in microfuge tubes at 13,000 rpm for 10 min at 4°C. The supernatant from this spin represented the cytoplasmic fraction and was discarded The nuclear pellet was gently resuspended into 200 µl of cold glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50%glycerol, 0.85 mM DTT). An additional 10 volumes (2 ml) of cold nuclei lysis buffer (20 mM HEPES pH 7.6, 7.5 mM MgCl2,0.2mM EDTA, 0.3M NaCl, 1M urea, 1% NP-40, 1mM DTT) was added to the samples, followed by a pulsed vortexing and incubation on ice for 10 min. The chromatin was sedimented by centrifugation for 10 min at 14,000 rpm and at 4°C. The supernatant from this spin was discarded. The chromatin pellet fraction was incubated in 200 µl high salt buffer (10 mM Tris HCl pH 7.5, 500 mM NaCl, and 10mM MgCl2) + 20U of DNaseI for 20 min at 37ºC, extracted with Trizol reagent, and isopropanol precipitated. The precipitate was twice treated with DNaseI treated and incubated for 20 min at 37ºC, then extracted with Trizol reagent followed by isopropanol precipitation. Chromatin pellet RNAs were eluted in 50 µl RNase-free water.
Nuclear RNA preparation:  Nuclear RNA preparation was carried out from nuclear pellet obtained as above. The nuclear pellet was resuspended in 200 µl high salt buffer (10 mM Tris HCl pH 7.5, 500 mM NaCl, and 10mM MgCl2) + 20U of DNaseI for 20 min at 37ºC, extracted with Trizol reagent, and isopropanol precipitated. The precipitate was twice treated with DNaseI treated and incubated for 20 min at 37ºC, then extracted with Trizol reagent followed by isopropanol precipitation. Nuclear RNAs were eluted in 50 µl RNase-free water. DNase I-treated nuclear RNA was incubated with oligo(dT) magnetic beads (Dynabeads mRNA purification kit, Invitrogen) to isolate either poly(A)+ RNA, which was bound to beads, or poly(A)- RNA, which was present in the flowthrough after incubation. Oligo(dT) magnetic bead selection was performed twice to ensure pure polyA+ or polyA- populations. The poly(A)- RNA population was further processed with the Ribo-Zero Magnetic Kit (Human/Mouse/Rat, Epicentre) to deplete most of the abundant ribosomal RNAs.
RNA-seq was performed by the High‐Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, University of Oxford. RNA Samples were ribodepleted using Ribo-Zero rRNA removal kit (Human/Mouse/Rat, EpiCentre RZH110424). Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, v1.0 (cat # E7420) using manufacturer's guidelines with an exception of using their own 8bp tags for indexing. Libraries were sequenced on an Illumina HiSeq2000 using 100bp and 50bp paired end reads, v3 chemistry.

value: si Dicer


title: ribo_wild-type TIF1 replicate 1_37 deg


title: Time-course_Ago2_FLAG-IP_WT_24hr

description: Ago2-associated RNA


title: si DGCR8_chromatin_HeLa

description:
Chromatin RNA
si_DGCR8_chromatn_HeLa


title: si Drosha_chromatin_HeLa

description:
Chromatin RNA
si_Drosha_chromatn_HeLa

value: si Drosha


title: mRNA_tif1-ts replicate 2_30 deg

description:
Experiment 3
processed data file: tif1-ts_30_deg.csv

value: 30 deg


title: Time-course_Ago2_FLAG-IP_WT_8hr

description: Ago2-associated RNA


title: mRNA_wild-type TIF1 replicate 2_30 deg


title: mRNA_tif1-ts replicate 1_30 deg


title: Time-course_Ago2_FLAG-IP_WT_4hr

description: Ago2-associated RNA


title: Time-course_Ago2_FLAG-IP_WT_2hr

description: Ago2-associated RNA


title: mRNA_wild-type TIF1 replicate 1_30 deg


title: Time-course_Ago2_FLAG-IP_WT_0hr

description: Ago2-associated RNA


title: Scramble ShRNA control replicate 2

city: Copenhagen

first: Anders

middle: H

last: Lund

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Base Calling using BGI Pipeline
Alignments were performed with STAR with the following parameters: --outFilterMismatchNoverLmax 0.04 --outFilterMatchNmin 16
Abundance Measurement was performed with HTSeq-count v0.5.4p5 with the following parameters: -s no -m intersection-nonempty
Differential Expression was performed with DESeq v. 1.14.0
Genome_build: hg19

source_name: U2932 cell line

growth_protocol: The U2932 cell line was maintained in RPMI1640 supplemented with 10% FCS (Biochrom), 100 U/ml penicillin and 100 g/ml streptomycin (Invitrogen)

extract_protocol:
RNA was extracted with RNeasy Plus kit and on-column DNAse digestion (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U2932 cells were infected with ShScramble or ShPRDM11 and selected with puromycin for 3 days.

tag: plasmid

value: pLKO-puro-scramble shRNA (Addgene 1864)


title: Scramble ShRNA control replicate 3


title: ribo_tif1-ts replicate 2_30 deg


title: ribo_tif1-ts replicate 1_37 deg

value: 37 deg


title: Time-course_Ago2_input_mut_72hr


title: Scramble ShRNA control replicate 1


title: ribo_tif1-ts replicate 1_30 deg


title: ribo_wild-type TIF1 replicate 2_30 deg


title: Time-course_Ago2_input_mut_24hr


title: Knockdown of PRDM11 replicate 3


title: Time-course_Ago2_input_mut_8hr


title: ribo_wild-type TIF1 replicate 1_30 deg


title: Time-course_Ago2_input_mut_4hr


title: Knockdown of PRDM11 replicate 1


title: mRNA_ded1-cs replicate 2_15 deg

description:
Experiment 1
processed data file: ded1-cs.csv

value: ded1-cs (NSY5)

value: 15 deg

value: mRNA


title: Time-course_Ago2_input_mut_2hr

value: Sprague Dawley


title: si cntrl_chromatin_HeLa

description:
Chromatin RNA
si_cntrl_chromatn_HeLa


title: U2932_Input

description: Sample 5

library_source: genomic

data_processing:
No filtering of the raw reads were performed prior to alignment.
Raw sequence reads were mapped to the human genome using the the BOWTIE tool (version 0.12.7) with default parameters except:  -S -m 1
SAM format alignment files were converted to BAM format using “samtools view”. BAM files contain both aligned and unaligned reads.
Peak calling was performed on U2932_Ab1, U2932_Ab2 and U2932_RNAPII using either IgG or Input as control, thus producing two peak sets for each non-control sample.
The program MACS2  (2.0.9 20111102 (tag:alpha) was used for calling peaks and run with default parameters except: --format=BAM -g hs -q 0.1 --nomodel –shiftsize=X. Shiftsize X was estimated using the tool Phantom Peak.
Genome_build: hg19
Supplementary_files_format_and_content: The .bed files report called peaks.

molecule: genomic DNA

source_name: U2932 human lymphoma cell line

extract_protocol:
U2932 cells were collected, cross-linked, sonicated and lyzed. Samples were immunoprecipitated with polyclonal antibodies specific for PRDM11, RNA polII (sc-899X, Santa Cruz) or rabbit IgG (Sigma). Eluted DNA was de-crosslinked and extracted using the QIAquick PCR Purification Kit (Qiagen) or MinElute PCR purification Kit (Qiagen)
DNA libraries were build using NEBNext DNA Library Prep (NEB) according to manufacturer’s instructions

treatment_protocol: non-treated

value: U2932 lymphoma cell line

tag: chip antibody


title: mRNA_ded1-cs replicate 1_15 deg


title: Time-course_Ago2_input_mut_0hr


title: U2932_IgG

description: Sample 4

value: rabbit IgG (Sigma, catalog# I8140, lot# 115K7551)


title: Time-course_Ago2_input_WT_72hr


title: U2932_RNAPII

description: Sample 3

value: RNA polymerase II (Santa Cruz, catalog# sc-899X, lot#B2713)


title: mRNA_wild-type DED1 replicate 1_15 deg

value: wild-type DED1 (NSY4)


title: mRNA_wild-type DED1 replicate 2_15 deg


title: Time-course_Ago2_input_WT_24hr


title: Time-course_Ago2_input_WT_8hr


title: U2932_Ab2

description: Sample 2

value: rabbit polyclonal anti-PRDM11 antibody 2 (non-commercial)


title: ribo_ded1-cs replicate 2_15 deg

value: Ribosome-protected RNA


title: ribo_ded1-cs replicate 1_15 deg


title: Time-course_Ago2_input_WT_4hr


title: Time-course_Ago2_input_WT_2hr


title: Checkpoint IMR90 p53 r2 HiSeq 2000

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: 24 hour Etoposide treated IMR90 anti p53 mouse monoclonal antibody (DO-1) ChIP Seq

data_processing:
Single-end reads were aligned against the Human Reference Genome (assembly hg18, NCBI Build 36) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Principle Component Analysis (PCA) was used to assess the prevalence and quality of read data in TSS regions. Counts were normalized between samples by dividing by effective library size (bin count sums).
The MACS algorithm version 1.4.1 was used together with hg18 aligned, sequence read BAM files for identifying peak regions representing p53 binding sites.
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format

source_name: diploid fibroblast

growth_protocol: cultured in 5%O2 in DMEM with 10% FBS and Pen/Strep and Glutamine

extract_protocol: immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 4 sequencing on an Illumina Genome Analyzer according to the manufacturer’s recommendationas described in Chandra, T. et al. Independence of Repressive Histone Marks and ChromatinCompaction during Senescent Heterochromatic Layer Formation. Mol Cell 47, 203–214 (2012)

treatment_protocol: 24 hours Etoposide (100microM),pBabe-Puro H-RasG12V, pWXL-Hygro E2A, H-RasG12V, pLNCX-Neo ER:H-RasG12V overexpression

tag: factor

tag: condition

value: DDR

value: anti p53 mouse monoclonal (DO-1) Sigma


title: Time-course_Ago2_input_WT_0hr


title: C1 Large live cell 74

status: Public on Mar 01 2015

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 210 S. 33rd St., Ste. 240 Skirkanich Hall

department: Bioengineering

institute: University of Pennsylvania

description:
sample id: Live-PL2-H12
processed data file: singlecellseq_star_HTSeqCounts.tsv

data_processing:
Aligned reads to genome using STAR
Assigned counts per gene using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts for all genes and samples. All single-cell data is compiled into a single .tsv file, and there is a separate .txt file for the bulk data from each cell line.

molecule: polyA RNA

source_name: Primary foreskin fibroblast cells

extract_protocol:
Cells were added to the Fluidigm C1 Single Cell Auto Prep System at 200K cells/ml. ERCC control mix 1 was added at a dilution of 1:10,000.
First- and second-strand synthesis were performed on the C1 Single Cell Auto Prep System. Final library prep was performed using the Illumina Nextera XT DNA sample preparation kit, using the modified protocol in the C1 manual.

value: large live


title: Knockdown of PRDM11 replicate 2


title: ribo_wild-type DED1 replicate 1_15 deg


title: C1 Large live cell 71

description:
sample id: Live-PL2-H08
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: Checkpoint IMR90 p53 r1 HiSeq 2000


title: C1 Large live cell 72

description:
sample id: Live-PL2-H09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 73

description:
sample id: Live-PL2-H10
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 70

description:
sample id: Live-PL2-H07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 69

description:
sample id: Live-PL2-H06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 68

description:
sample id: Live-PL2-H03
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 66

description:
sample id: Live-PL2-H01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 64

description:
sample id: Live-PL2-G11
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 65

description:
sample id: Live-PL2-G12
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 63

description:
sample id: Live-PL2-G10
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 61

description:
sample id: Live-PL2-G08
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 67

description:
sample id: Live-PL2-H02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: U2932_Ab1

description: Sample 1

value: rabbit polyclonal anti-PRDM11 antibody 1 (non-commercial)


title: ribo_wild-type DED1 replicate 2_15 deg


title: C1 Large live cell 59

description:
sample id: Live-PL2-G06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 57

description:
sample id: Live-PL2-G02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 60

description:
sample id: Live-PL2-G07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 56

description:
sample id: Live-PL2-F11
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 54

description:
sample id: Live-PL2-F09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 58

description:
sample id: Live-PL2-G04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 55

description:
sample id: Live-PL2-F10
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 53

description:
sample id: Live-PL2-F07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 51

description:
sample id: Live-PL2-F05
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 48

description:
sample id: Live-PL2-F01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 50

description:
sample id: Live-PL2-F04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 44

description:
sample id: Live-PL2-E09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 47

description:
sample id: Live-PL2-E12
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 46

description:
sample id: Live-PL2-E11
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 45

description:
sample id: Live-PL2-E10
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 43

description:
sample id: Live-PL2-E08
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 41

description:
sample id: Live-PL2-E04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 42

description:
sample id: Live-PL2-E06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 62

description:
sample id: Live-PL2-G09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 40

description:
sample id: Live-PL2-E03
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 37

description:
sample id: Live-PL2-D11
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 33

description:
sample id: Live-PL2-D04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 39

description:
sample id: Live-PL2-E01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 38

description:
sample id: Live-PL2-D12
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 35

description:
sample id: Live-PL2-D07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 52

description:
sample id: Live-PL2-F06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 36

description:
sample id: Live-PL2-D09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 34

description:
sample id: Live-PL2-D05
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 28

description:
sample id: Live-PL2-C11
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 30

description:
sample id: Live-PL2-D01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 31

description:
sample id: Live-PL2-D02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 29

description:
sample id: Live-PL2-C12
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 25

description:
sample id: Live-PL2-C07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 24

description:
sample id: Live-PL2-C06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 27

description:
sample id: Live-PL2-C10
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 23

description:
sample id: Live-PL2-C05
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 32

description:
sample id: Live-PL2-D03
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 21

description:
sample id: Live-PL2-C03
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 49

description:
sample id: Live-PL2-F02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 20

description:
sample id: Live-PL2-B12
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 18

description:
sample id: Live-PL2-B09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 17

description:
sample id: Live-PL2-B07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 22

description:
sample id: Live-PL2-C04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 16

description:
sample id: Live-PL2-B06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 15

description:
sample id: Live-PL2-B05
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 13

description:
sample id: Live-PL2-B03
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 14

description:
sample id: Live-PL2-B04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 12

description:
sample id: Live-PL2-B02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 11

description:
sample id: Live-PL2-B01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 26

description:
sample id: Live-PL2-C09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 9

description:
sample id: Live-PL2-A09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 10

description:
sample id: Live-PL2-A10
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 8

description:
sample id: Live-PL2-A08
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 7

description:
sample id: Live-PL2-A07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 6

description:
sample id: Live-PL2-A06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 4

description:
sample id: Live-PL2-A04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 3

description:
sample id: Live-PL2-A03
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 2

description:
sample id: Live-PL2-A02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Large live cell 1

description:
sample id: Live-PL2-A01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Med live cell 2

description:
sample id: Live-PL1-A03
processed data file: singlecellseq_star_HTSeqCounts.tsv

value: med live


title: C1 Large live cell 19

description:
sample id: Live-PL2-B11
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Med live cell 1

description:
sample id: Live-PL1-A02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 12

description:
sample id: Fixed-PL3-G09
processed data file: singlecellseq_star_HTSeqCounts.tsv

extract_protocol:
Fixed cells were added to the Fluidigm C1 Single Cell Auto Prep System at 200K cells/ml. ERCC control mix 1 was added at a dilution of 1:10,000.
First- and second-strand synthesis were performed on the C1 Single Cell Auto Prep System. Final library prep was performed using the Illumina Nextera XT DNA sample preparation kit, using the modified protocol in the C1 manual.

value: fixed cell


title: C1 Fixed cell 13

description:
sample id: Fixed-PL3-H01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 10

description:
sample id: Fixed-PL3-F04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 9

description:
sample id: Fixed-PL3-F02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 6

description:
sample id: Fixed-PL3-D07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 8

description:
sample id: Fixed-PL3-E09
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 4

description:
sample id: Fixed-PL3-C08
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 5

description:
sample id: Fixed-PL3-D02
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 2

description:
sample id: Fixed-PL3-A07
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 3

description:
sample id: Fixed-PL3-C01
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 Fixed cell 1

description:
sample id: Fixed-PL3-A05
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 No-cell control 5

description:
sample id: Ctrl-PL3-F08
processed data file: singlecellseq_star_HTSeqCounts.tsv

value: no cell


title: C1 Large live cell 5

description:
sample id: Live-PL2-A05
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 No-cell control 1

description:
sample id: Ctrl-PL2-D10
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 No-cell control 2

description:
sample id: Ctrl-PL2-F12
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 No-cell control 4

description:
sample id: Ctrl-PL3-B06
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: C1 No-cell control 3

description:
sample id: Ctrl-PL2-H04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: embryos 34-48h_smallRNA

city: Pasadena

first: Maria

last: Ninova

state: CA

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

description: small RNA library

data_processing:
For small RNA sequencing, adaptor sequences were removed using the cutadapt tool
Small RNA sequencing reads were mapped to the T. castaneum genome using Bowtie v1.0 allowing one mismatch; read counts per microRNA gene were calculated by a custom script accounting for multiple mapping positions
RNA-seq reads were mapped to the T. castaneum genome using Tophat, followed by htseq-count using Tcas 4.0 gene annotations
Genome_build: Tcas 4.0
Supplementary_files_format_and_content: tab-delimited file of genes/microRNAs and read counts

organism: Tribolium castaneum

source_name: embryos 34-48h

growth_protocol: Mixed sex adults (for embryonic samples) or virgin females (for oocytes) were maintained on whole grain flour and allowed to lay on white flour for the desired periods of time at 25°C.

extract_protocol:
Standard Trizol RNA extraction
Small RNA libraries were constructed according to the TruSeq Small RNA Sample Prep Kit instructions, and transcriptome libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Flour debri were manually, removed and embryos were dechorionated in 1% hypochlorite solution and washed with distilled water prior RNA extraction

tag: developmental stage

value: embryos 34-48h


title: embryos 48-144h_smallRNA

description: small RNA library

source_name: embryos 48-144h

value: embryos 48-14h


title: embryos 24-34h_smallRNA

description: small RNA library

source_name: embryos 24-34h

value: embryos 24-34h


title: C1 Fixed cell 14

description:
sample id: Fixed-PL3-H02
processed data file: singlecellseq_star_HTSeqCounts.tsv

tag: cell line


title: embryos 8-16h_smallRNA

description: small RNA library

source_name: embryos 8-16h

value: embryos 8-16h


title: embryos 0-5h_smallRNA_rep2

description: small RNA library

source_name: embryos 0-5h

value: embryos 0-5h


title: C1 Fixed cell 11

description:
sample id: Fixed-PL3-G07
processed data file: singlecellseq_star_HTSeqCounts.tsv

tag: cell type


title: embryos 0-5h_smallRNA_rep1

description: small RNA library


title: C1 Med live cell 3

description:
sample id: Live-PL1-A04
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: embryos 16-20h_smallRNA

description: small RNA library

source_name: embryos 16-20h

value: embryos 16-20h


title: C1 Fixed cell 7

description:
sample id: Fixed-PL3-E08
processed data file: singlecellseq_star_HTSeqCounts.tsv


title: Cytosolic Hsp60 normal and TNF-alpha positive

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

description: Hsp60 sense-ODN treated and TNF-alpha positive

data_processing:
Quality trimming using Trimmomatic-v0.30
Alignment using Tophat v2.0.12 to GRCh37
Differential expression analysis using Cuffdiff v2.2.1
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM txt files and differential expression test

growth_protocol: Human aortic vascular smooth muscle cells (HASMC) were purchased from Clonetics-Bio Whittaker (Venders, Belgium) and grown at 37°C in a humidified incubator containing 5% CO2 in Smooth Muscle Cell Basal Medium (SmBMTM) SingleQuotes with 10% fetal bovine serum (FBS) and full supplements (Clonetics-BioWhittaker; Cat no. cc-4149).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) from the HASMC cells.
The mRNA library (insert size of ~300 bp) was created using the TruSeq RNA Library Preparation kit v2 (Illumina).

treatment_protocol: HASMCs were transfected with Hsp60 sense oligodeoxynucleotides (AS-ODN at 200 nM) for 24 hrs using Oligofectamine™ reagent (Invitrogen, USA) and then stimulated with or without TNF-alpha (10 ng/ml).

tag: treatment

value: aortic vascular smooth muscle cells


title: Cytosolic Hsp60 normal and TNF-alpha negative

description: Hsp60 sense-ODN treated and TNF-alpha negative

source_name: Human aortic vascular smooth muscle cells


title: Cytosolic Hsp60 depletion and TNF-alpha negative

description: Hsp60 antisense-ODN treated and TNF-alpha negative

treatment_protocol: HASMCs were transfected with Hsp60 antisense oligodeoxynucleotides (AS-ODN at 200 nM) for 24 hrs using Oligofectamine™ reagent (Invitrogen, USA) and then stimulated with or without TNF-alpha (10 ng/ml).


title: Cytosolic Hsp60 depletion and TNF-alpha positive

description: Hsp60 antisense-ODN treated and TNF-alpha positive


title: Day4_Brg1_ChIPexo_Rep2

city: San Francisco

first: Jeffrey

middle: Michael

last: Alexander

address: 1650 Owens St

institute: Gladstone Institutes

description: ChIP-exo-enriched genomic DNA

data_processing:
The 50bp single-end reads were trimmed for quality using fastq-mcf (Aronesty et al 2011), and were them aligned to the mm9 genome assembly using Bowtie2 (Langmead et al 2012).
Reads were extended 200 bp and grouped into 25-bp bins.  Extended sequences were processed into Wiggle/BigWig format for visualization, allowing one repeat read.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig values are read depth per 25 bp bin scaled per million mapped reads.

organism: Mus musculus

source_name: Differentiated embryonic stem cells

growth_protocol: Mouse ES cells were cultured in feeder-free conditions under standard conditions.  Mouse ES cells were aggregated into embryoid bodies (EB) and differentiated for two days in serum free media (Day2).  Embryoid bodies were dissociated and reaggregated for 40 hours in the presence of VEGF, Activin A, and BMP4 to promote mesoderm differentiation (Day4).

extract_protocol:
Frozen pellets of cross-linked cells (8-10x106) were thawed in cold lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors) and gently rocked at 4°C for 10 minutes in 15 mL conical tubes. Cells were pelleted at 1350 x g at 4°C and resuspended in cold lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitors) and gently rocked at 4°C for 10 minutes in 15 mL conical tubes.  Cells were pelleted at 1350 x g at 4°C in a table top centrifuge and resuspended in 0.5 mL cold ChIP lysis buffer (50 mM HEPES-NaOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) and sonicated to 200-1000 bp fragments using a VirSonic sonicator.  Sonicated lysates were cleared by pelleting insoluble material at 13,000 RPM at 4°C followed by incubation with 5 ug antibody overnight.  Next, Protein G magnetic beads (45 uL) were added to the lysate and incubated at 4°C for 7 hrs.
ChIPExo was performed on Brg1 ChIP material while still on protein G magnetic dynabeads. After incubation with the antibody, the beads were washed six times with RIPA buffer (50mM HEPES, pH7.6, 1mM EDTA, pH8.0, 0.7% Sodium deoxycholate, 1% NP-40 and 500mM Lithium chloride) and two times with Tris (10mM Tris.Cl, pH 8.0). The bead bound DNA were end polished at 30°C for 30mins in using T4 DNA polymerase, Klenow fragment of DNA polymerase and T4 polynucleotide kinase. From this point each subsequent enzymatic steps were followed by two washes with each of RIPA and 10mM Tris. P7 adapter was ligated to the DNA ends using T4 DNA ligase at 25°C for 60 mins followed by nick repair using Phi29 polymerase at 30°C for 20 mins. Samples were periodically vortexed at 900rpm in a thermomixure during enzymatic reaction. DNA was digested with lambda and RecJf exonucleases at 37°C for 30 mins each. Samples were then eluted off the beads with 100ml of Elution buffer (50mM Tris.Cl, pH 8.0, 10mM EDTA, 1% SDS) by incubating at 65°C for 30mins with periodic shaking. RNase A was added to the samples for 30min at 37°C. Proteinase K was added to degrade proteins, crosslink was reversed by overnight incubation at 65°C and using Ampure beads ChIP DNA was purified. The purified DNA was denatured at 95°C for 5 mins before synthesis of the 2nd strand by P7 primer extension in presence of Phi29 polymerase. Then, P5 adapters were ligated to the DNA ends and the DNA fragments were PCR amplified for 18 cycles using universal primers containing the index sequences. PCR products were purified using Ampure beads, size selected using 2% agarose gels in an E-Gel Electrophoresis system (Invitrogen), gel purified using minielute gel extraction columns (Qiagen) and eluted in 20microlitre of TE. Samples were quantified and analysed on Qubit and Bioanalyser before sequencing on a Illumina Hi-Seq 2500 sequencing machine.

treatment_protocol: On Day2, cultures were treated with either 200 nM 4-OHT in tetrahydrofuran (THF) or THF alone. 4-OHT induces CreER mediated deleted of Brg1 floxed alleles.

tag: timepoint

value: Day 4

value: anti-BRG1 (Abcam, catalog# 110641, lot#YG081901C)

tag: brg1 levels

value: Normal


title: Day4_Brg1_ChIPexo_Rep1

description: ChIP-exo-enriched genomic DNA


title: Sequencing of input DNA from human monocytes [patient 1]

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the  hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup ( version 0.1.18) function.
Samtools was used to convert aligned reads to BAM format.
Genome_build: hg19
Supplementary_files_format_and_content: Smoothed and normalized coverage vectors were produced in 25 bp steps using custom software. Data was subsequently converted into indexed binary wiggle (bigwig) files using wigToBigWig utility downloaded from UCSC genome browser homepage.

source_name: CD14++ CD16- monocytes from patient 1

extract_protocol:
A blood sample of 30 ml was taken and peripheral blood mononuclear cells were isolated using ficoll-based density gradient centrifugation. Further isolation of CD14++ CD16- monocytes was conducted using magnetic cell sorting to deplete CD16++ monocytes and separate CD14++ monocytes. Purity of isolation was checked by flow cytometric analysis of the CD14+ cell fraction. Cells were cross-linked for 10 min using formaldehyde (final concentration 1%). Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris/HCl, pH8.1, 1x concentrated protease inhibitors) and sonciated using a Branson-250 Sonicator (http.www.bransonultrasonics.com) using the microtip setting. Fragment size of the obtained chromatin was checked to be between 100 bp and 300 bp. Sheared chromatin was diluted 1/10 with dilution buffer (SDS 0.01%, Triton X-100 1%, EDTA 1.2 mM, Tris/HCl, pH 8.1 16.7 mM, NaCl 167 mM). Chromatin was precleared using a protein A/G-sepharose mixture for 1 hr at 4°C and incubated with apprpriate antibodies over night. Immune complexes were precipitated with protein A/G-sepharose and washed with low salt (SDS 0.1%, Triton X-100 1%, EDTA 2 mM, Tris/HCl, pH8.1 20 mM, NaCl 150 mM), high salt (SDS 0.1%, Triton X-100 1%, EDTA 2 mM, Tris/HCl, pH8.1 20 mM, NaCl 500 mM), LiCl buffer (LiCl 0.25 M, NP40 1%, Deoxycholat 1%, EDTA 1 mM, Tris/HCl, pH8.1 10 mM) and twice with TE. After crosslink reversal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare).
ChIP-seq library preparation using MicroPlex kit from Diagenode

tag: disease

value: septic disease


title: ChIP-seq analysis of H3K9Ac  in human monocytes [patient 2]

description: ChIP-seq

source_name: CD14++ CD16- monocytes from patient 2

value: H3K9Ac [Abcam ab4441]


title: ChIP-seq analysis of H3K27me3 in human monocytes [patient 2]

description: ChIP-seq

value: H3K27me3 [Abcam ab6002]


title: ChIP-seq analysis of H3K4me3  in human monocytes [patient 2]

description: ChIP-seq

value: H3K4me3 [Abcam ab8580]


title: Day4_Brg1_ChIPexo_4OHT_Rep1

description: ChIP-exo-enriched genomic DNA

value: Brg1f/f; Actin-CreER

tag: agent

value: Deleted


title: Day4_Brg1_ChIPexo_THF_Rep1

description: ChIP-exo-enriched genomic DNA

value: THF


title: ChIP-seq analysis of H3K4me3  in human monocytes [patient 1]

description: ChIP-seq


title: ChIP-seq analysis of H3K27me3 in human monocytes [patient 1]

description: ChIP-seq


title: s23N24Veh

city: Ann Arbor

first: Yongsheng

last: Huang

state: MI

address: 100 Washtenaw Ave

department: Bioinformatics

institute: University of Michigan

data_processing:
Omicsoft sequence aligner (OSA) (Pubmed ID: 22592379) is used for alignment
Alignment to Genome Library with known Gene Model (Human B37.3 and Refseq 2012/12/07)
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.
Reads were filtered to remove rRNA, tRNA, Illumina adapters, ERCC reads, etc.
Genome_build: Refseq 2012/12/07
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample in log10 scale

source_name: ALI trachae-bronchial epithelial cells

growth_protocol: ALI cultures (0.6 cm2 insert devices from Millipore cultured in 6 well plates) were changed to hydrocortisone-free media for 24 hours (37ºC, 5% CO2)

extract_protocol:
Cells were washed three times with PBS, followed by adding 175 uL RLT buffer to each ALI device  ALI cell lysates were transferred to tubes on ice, and  were further rinsed and samples were pooled with an additional 175 uL aliquot of RLT (350 uL total/sample). Total RNA was isolated from RLT cell lysates using the QIAGEN RNeasy mini kit, and quantified via Nanodrop (Thermo Scientific, Wilmington, DE) Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The apical surface of ALI cultures was washed twice with room temperature PBS to remove accumulated mucus prior to apical treatment application of HRV16 at MOI=10 or culture media.  Treated cultures were shifted to a 34ºC incubator (5% CO2) with gentle shaking on a Bellco orbital shaker until 24 hours.

value: Isolated from human trachea-bronchial tissues

tag: passages

tag: disease state

value: non-asthmatic

value: Vehicle


title: s11N24Veh


title: s20N24Veh


title: s30N24Veh


title: s20N24HRV


title: s21N24Veh


title: s21N24HRV


title: s11N24HRV


title: s22N24HRV


title: s23N24HRV


title: s14A24Veh

value: asthmatic


title: s18A24Veh


title: s30N24HRV


title: s15A24Veh


title: s12A24Veh


title: Sequencing of input DNA from human monocytes [patient 2]

description: ChIP-seq

tag: antibody


title: s26A24Veh


title: s28A24Veh


title: s15A24HRV


title: ChIP-seq analysis of H3K9Ac  in human monocytes [patient 1]

description: ChIP-seq


title: s26A24HRV


title: s18A24HRV


title: s28A24HRV


title: s14A24HRV


title: s12A24HRV


title: s22N24Veh


title: Delta_8aa_Dox+_1

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description: srsf2-shRNA + Delta_8aa srsf2 + dox rep1

data_processing:
library strategy: RASL-Seq
The sequenced 40 bases were mapped to the oligo pool sequences with Bowtie by allowing 1 mismatch in each of the donor and acceptor sequences.
Genome_build: hg18
Supplementary_files_format_and_content: The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.

source_name: MDS-L

growth_protocol: MDS-L cells transduced with pTRIPZ vectors containing shRNA against endogenous SRSF2 with/without wild type (WT), P95H or 8-amino-acid deletion (Delta_8aa) mutant of human SRSF2 cDNA were cultured in triplicate in RPMI supplemented with 10% fetal bovine serum, penicillin/streptomycin and 10 ng/ml human IL-3

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Life technologies).
RASL library was constructed according to Li H, et al protocol published Current Protocols in Molecular Biology.

treatment_protocol: Doxycycline 2.5 ug/ml (for sh only cells) or 1.0 ug/ml (for other cells) were added (Dox+) or not added (Dox-) to the cells every day for 3 days.

tag: individual

value: MDS patient

tag: tissue

value: bone marrow

value: MDS-derived cell line (MDS-L)

value: srsf2-shRNA + Delta_8aa srsf2 +dox


title: Delta_8aa_Dox+_3

description: srsf2-shRNA + Delta_8aa srsf2 + dox rep3


title: Delta_8aa_Dox+_2

description: srsf2-shRNA + Delta_8aa srsf2 + dox rep2


title: Delta_8aa_Dox-_2

description: srsf2-shRNA + Delta_8aa srsf2 without dox rep2

value: srsf2-shRNA + Delta_8aa srsf2


title: Delta_8aa_Dox-_3

description: srsf2-shRNA + Delta_8aa srsf2 without dox rep3


title: Delta_8aa_Dox-_1

description: srsf2-shRNA + Delta_8aa srsf2 without dox rep1


title: P95H_Dox+_3

description: srsf2-shRNA + P95H srsf2 + dox rep3

value: srsf2-shRNA + P95H srsf2 +dox


title: P95H_Dox+_2

description: srsf2-shRNA + P95H srsf2 + dox rep2


title: WT_Dox-_3

description: srsf2-shRNA + WT srsf2  without dox rep3

value: srsf2-shRNA + WT srsf2


title: WT_Dox+_3

description: srsf2-shRNA + WT srsf2 +dox rep3

value: srsf2-shRNA + WT srsf2 +dox


title: P95H_Dox-_2

description: srsf2-shRNA + P95H srsf2 without dox rep2

value: srsf2-shRNA + P95H srsf2


title: P95H_Dox-_3

description: srsf2-shRNA + P95H srsf2 without dox rep3


title: WT_Dox+_1

description: srsf2-shRNA + WT srsf2 +dox rep1


title: WT_Dox-_2

description: srsf2-shRNA + WT srsf2  without dox rep2


title: P95H_Dox-_1

description: srsf2-shRNA + P95H srsf2 without dox rep1


title: shRNA_only_Dox+_3

description: srsf2-shRNA +dox rep3

value: srsf2-shRNA +dox


title: shRNA_only_Dox-_1

description: srsf2-shRNA without dox rep1


title: P95H_Dox+_1

description: srsf2-shRNA + P95H srsf2 + dox rep1


title: shRNA_only_Dox-_3

description: srsf2-shRNA without dox rep3


title: WT_Dox+_2

description: srsf2-shRNA + WT srsf2 +dox rep2


title: shRNA_only_Dox-_2

description: srsf2-shRNA without dox rep2


title: shRNA_only_Dox+_2

description: srsf2-shRNA +dox rep2


title: shRNA_only_Dox+_1

description: srsf2-shRNA +dox rep1


title: Input for 2x50

city: Singapore

first: Ricardo

middle: Cruz-Herrera

last: del Rosario

address: 60 Bipolis St, #02-01 Genome

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: technique: RegVAR-seq

data_processing:
Illumina Casava1.7 software was used for basecalling 2x100 and 1x100 libraries;  Illumina Casava1.8 software was used for basecalling 2x50 libraries
ChIP-seq reads were aligned to hg19 reference genome with bwa 0.6.2.r126 (-q 10 option)
Peaks were called using Dfilter (Kumar et al., Nature Biotech 2013)
Genome_build: hg19
Supplementary_files_format_and_content: wig files of uniquely mapped reads were created using custom perl scripts and converted to bigWig using wigToBigWig

source_name: Lymphoblastoid cell lines

growth_protocol: Cell lines were purchased from Coriell Institute for Medical Research and grown and maintained according to the provided Coriell protocols. Briefly, cells were grown in RPMI 1640 media (15% FBS, 2mM L-glutamine) to approximately 1 million cells per ml and then collected for ChIP-seq or snap-frozen in liquid nitrogen and stored at -80C.

extract_protocol:
Excess formaldehyde was quenched by addition of glycine (0.625M). Cells were washed with cold PBS and spun down (3,000 rpm for 10 minutes at 4°C; Kubota 3500). The pellet was re-suspended in FA lysis buffer (0.25% Triton X-100, 10 mM EDTA, 10 mM Tris HCl [pH 8.0], 100 mM NaCl, Roche 1X cOmplete protease inhibitor) and incubated for 15 minutes. Nuclei were collected (3,000 rpm for 10 minutes at 4°C; Kubota 3500) and re-suspended in 300 μl SDS lysis buffer (1% SDS, 1% Triton X 100, 2 mM EDTA, 50 mM Hepes-KOH [pH 7.5], 0.1% Na dodecyl sulfate, Roche 1X cOmplete protease inhibitor). Nuclei were lysed for 15 minutes, after which sonication was used to fragment chromatin to an average size of 200–500 bp (Bioruptor Next gen, Diagenode). Cellular debris was removed by centrifugation at 15,000 rpm at 4°C (Kubota 3500). Next, 300 μl of nuclear lysate was diluted 1:10 with a dilution buffer (1% Triton X 100, 2 mM EDTA, 50 mM Hepes-KOH [pH 7.5], 0.1% Na dodecyl sulfate, Roche 1X cOmplete protease inhibitor) and  protein-DNA complexes were immuno-precipitated using  3 μg of H3K27acetyl antibody (AB4729,  Lot number 730178, Abcam) coupled to 50μl protein G Dynal beads (Invitrogen)  overnight. The beads were washed and protein-DNA complexes were eluted with 150 μl of elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris.HCl [pH 8]), followed by protease treatment and de-crosslinking at 65°C overnight. After phenol/chloroform extraction, DNA was purified by ethanol precipitation.
80% of ChIP material was used for library preparation using the Biooscientific library preparation kit with the following modification. The provided adapters were diluted down 40-fold in order to prevent adapter dimer formation that would affect enrichment. Libraries were then enriched for 15 cycles with PFX polymerase (Invitrogen) followed by gel size selection (300-500bp). The ChIP libraries were then sequenced on the Illumina Hiseq 2000 platform in three batches

treatment_protocol: Approximately ten million cells from each cell line were cross-linked with 1% formaldehyde for 15 minutes.

value: None (input)


title: Input for 2x100

description: technique: RegVAR-seq


title: GM19114 H3K27ac_rep2

description: technique: RegVAR-seq

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: GM19147 H3K27ac_rep1

description: technique: RegVAR-seq


title: Input for 1x100

description: technique: RegVAR-seq


title: GM19114 H3K27ac_rep1

description: technique: RegVAR-seq


title: GM18916 H3K27ac

description: technique: RegVAR-seq


title: GM18909 H3K27ac

description: technique: RegVAR-seq


title: GM18520 H3K27ac

description: technique: RegVAR-seq


title: GM18511 H3K27ac

description: technique: RegVAR-seq


title: GM18510 H3K27ac

description: technique: RegVAR-seq


title: GM19119 H3K27ac

description: technique: RegVAR-seq


title: GM18498 H3K27ac

description: technique: RegVAR-seq


title: GM19171 H3K27ac

description: technique: RegVAR-seq


title: GM18486 H3K27ac

description: technique: RegVAR-seq


title: GM19201 H3K27ac

description: technique: RegVAR-seq


title: GM19138 H3K27ac

description: technique: RegVAR-seq


title: GM19222 H3K27ac

description: technique: RegVAR-seq


title: GM19137 H3K27ac

description: technique: RegVAR-seq


title: GM18913 H3K27ac

description: technique: RegVAR-seq


title: GM19159 H3K27ac

description: technique: RegVAR-seq


title: GM19160 H3K27ac

description: technique: RegVAR-seq


title: GM19147 H3K27ac_rep2

description: technique: RegVAR-seq


title: GM18912 H3K27ac

description: technique: RegVAR-seq


title: GM18852 H3K27ac

description: technique: RegVAR-seq


title: GM18522 H3K27ac

description: technique: RegVAR-seq


title: GM18855 H3K27ac

description: technique: RegVAR-seq


title: GM18516 H3K27ac

description: technique: RegVAR-seq


title: GM18517 H3K27ac

description: technique: RegVAR-seq


title: GM18519 H3K27ac

description: technique: RegVAR-seq


title: GM19193 H3K27ac

description: technique: RegVAR-seq


title: GM19239 H3K27ac

description: technique: RegVAR-seq


title: GM19099 H3K27ac

description: technique: RegVAR-seq


title: GM19098 H3K27ac

description: technique: RegVAR-seq


title: GM19143 H3K27ac

description: technique: RegVAR-seq


title: GM19101 H3K27ac

description: technique: RegVAR-seq


title: GM19152 H3K27ac

description: technique: RegVAR-seq


title: GM19144 H3K27ac

description: technique: RegVAR-seq


title: GM19127 H3K27ac

description: technique: RegVAR-seq


title: GM18853 H3K27ac

description: technique: RegVAR-seq


title: GM19140 H3K27ac

description: technique: RegVAR-seq


title: GM19128 H3K27ac

description: technique: RegVAR-seq


title: GM19130 H3K27ac

description: technique: RegVAR-seq


title: GM19131 H3K27ac

description: technique: RegVAR-seq


title: GM18523 H3K27ac

description: technique: RegVAR-seq


title: GM19209 H3K27ac

description: technique: RegVAR-seq


title: GM19200 H3K27ac

description: technique: RegVAR-seq


title: GM19093 H3K27ac

description: technique: RegVAR-seq


title: GM19116 H3K27ac

description: technique: RegVAR-seq


title: GM19102 H3K27ac

description: technique: RegVAR-seq


title: GM19210 H3K27ac

description: technique: RegVAR-seq


title: GM19172 H3K27ac

description: technique: RegVAR-seq


title: GM18862 H3K27ac

description: technique: RegVAR-seq


title: GM18870 H3K27ac

description: technique: RegVAR-seq


title: GM18508 H3K27ac

description: technique: RegVAR-seq


title: GM18499 H3K27ac

description: technique: RegVAR-seq


title: GM18507 H3K27ac

description: technique: RegVAR-seq


title: GM18856 H3K27ac

description: technique: RegVAR-seq


title: GM18504 H3K27ac

description: technique: RegVAR-seq


title: GM19153 H3K27ac

description: technique: RegVAR-seq


title: GM18502 H3K27ac

description: technique: RegVAR-seq


title: 918_N

city: Taipei

first: King-Jen

last: Chang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Surgery

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
All SOLiD small RNA reads generated from ligation sequencing were screened to filter out any reads containing ribosomal RNA, transfer RNA, and adaptor sequences (AB Small RNA Analysis Tool V0.5).
The remaining reads were aligned to human miRNA reference (AB Small RNA Analysis Tool V0.5). The reference databases used for alignment were miRBase (version 17.0) and human genome RefSeq Hg19.
One mismatch was allowed for the first 16 sequences of a SOLiD read and up to 4 maximum mismatches were allowed for a miRNA read count.
Reads that were not uniquely mapped to miRBase reference were disregarded to eliminate ambiguous alignments.
miRNA reads derived from each sample were normalized using the quantile-quantile scaling method. A miRNA mean expression profile obtained from 38 samples was used as the reference for quantile-quantile linear scaling. A scaling factor was determined for each sample dataset to vertically shift all miRNA expression data close to the diagonal line in each log10-scaled quantile-quantile plot.
Genome_build: human genome hg 19
Supplementary_files_format_and_content: tab-delimited text files include miRNA ID, mapped miRNA read counts, RNA strand direction, and genomic coordinates.

source_name: Adjacent normal tissue

extract_protocol: Each small RNA library was constructed from total RNA of each sample using the SOLiD Total RNA-Seq Kit (Applied Biosystems, Foster City, CA, USA). Integrity of each small RNA library was examined by using RNA 6000 Nano Chip (Agilent, Santa Clara, CA, USA), Small RNA Chip (Agilent), and Bioanalyzer (Agilent) following the standard protocol.

tag: age (years)

tag: Stage

tag: grade

tag: tumor size

tag: recurrence

tag: lymph node metastasis

tag: recurrence-free time (years)


title: 922_N


title: 887_N


title: 881_N


title: 673_N


title: 574_N


title: 477_N


title: 602_N


title: 291_N


title: 357_N


title: 941_T

source_name: Triple-negative breast cancer (Invasive ductal carcinoma)

value: IIA


title: 507_N


title: 582_N


title: GM18861 H3K27ac

description: technique: RegVAR-seq

tag: cell line


title: 922_T

value: I


title: 887_T


title: 918_T


title: 893_T

value: IIB


title: 894_T


title: 677_T


title: 673_T


title: 621_T


title: 602_T


title: 593_T


title: 677_N


title: 582_T


title: 557_T


title: 881_T


title: 574_T


title: 507_T


title: 477_T


title: 557_N


title: 417_T


title: 452_T


title: 357_T

value: IIIC


title: Green tomato

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Basecalls performed using CASAVA 1.8.1 (use only Illumin'a passed filter)
Reads were aligned to the Solanum lycopersicu (tomato) genome and to Colletotrichum gloeosporioides contigs (SUB133583, PRJNA176412)  release SL2.40 using TopHat V1.3.0 with the option --segment-mismatches 1
Transcripts were defined using cufflinks 1.1.0
Transcripts were quantified using Partek Genomics Suite V6.6 beta

organism: Solanum lycopersicum

source_name: Fruit cuticle and parenchyma

growth_protocol: Tomato (Solanum lycopersicum) wild-type cultivars Motelle were grown in pots filled with a peat-vermiculite (4:1, v/v) mixture containing slow-release high-N Multicote 4 with microelements (0.3% w/w; Haifa Chemicals, Haifa Bay, Israel). Average temperatures in the greenhouse during the growth period fluctuated from 18 to 25˚C.

extract_protocol:
RNA was extracted from 100mg (dry weight) of C. gloeosporioides colonizing tomato fruit. Samples were ground into fine powder and were extracted using Tri-reagent 100 mg/ml (38% water saturated phenol, 0.8M Guanidine thiocyanate, 0.4M Ammonium thiocyanate, 0.1MSodium acetate pH=5, 5% glycerol). Aqueous phase was subsequently extracted twice with chloroform. Follow by isopropanol precipitation and two 70% ethenol washes, the RNA pellet was resuspended in DDW. The RNA was treated with DNase, Amplification Grade (Sigma, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tomato fruits cv. Mottel were inoculated with 7 µl, 106 conidia/ml at 30 inoculation spots per fruit on 5 different fruits per biological replicate with seven biological replicates per treatment. For necrotrophic stage growth a 10 mm2 of ripe tomato fruit cuticle was removed and inoculated with 70 µl of a conidial suspension (106 conidia/ml). Three inoculation spots on each of 10 different fruits were inoculated per biological replicate with seven biological replicate per treatment.

tag: cultivar/strain

value: Sl-Motelle


title: Red tomato

source_name: Fruit  parenchyma


title: 291_T

value: IIIA


title: 917_T


title: Purified Atoh1-GFP- cells from mouse cochlea_2

city: Houston

first: Andrew

last: Groves

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: mRNA enriched ds cDNA was sequenced paired end

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm9) using TopHat (v1.4.0) with default parameters except -G Ensembl GTF gene annotation.
Read counts for each gene were determined using htseq -count (python) function.
Reads were normalized across samples using DESeq Bioconductor package (v1.9.2).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Cochlea GFP- rep 2

growth_protocol: Cells were sorted from neonatal mouse cochlea.

extract_protocol:
Total RNA was extracted from FACS-purified cells using an RNeasy Plus Micro kit (Qiagen).
RNA-seq libraries of FACS purified cells were generated as previously described: Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB (2011) Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol 9:e1000590.

treatment_protocol: Whole inner ears were dissected from homozygous P0 Atoh1A1GFP/A1GFP mice and incubated in Ca2+, Mg2+-free (CMF) PBS. The cochleas were isolated and the spiral ganglia and Reissner’s membrane removed to expose the organ of Corti. Isolated cochleas were washed with CMF-PBS and then incubated in 0.1% Trypsin-EDTA (Sigma) diluted in CMF-PBS for 10 minutes at 37°C. The trypsin solution was removed and the tissue rinsed in DMEM with 5% fetal calf serum (FCS). The tissue was then gently triturated with an 1000μl pipette tip in CMF-PBS containing 5% FCS for ~100 times to generate a single cell suspension. Hair cells were purified on a BD FACSAria Cell Sorting Flow Cytometer using a 100 µm nozzle and 488-nm excitation. Gates were set each time using small number of cells from the same sample to identify the viable cells and GFP fluorescence. GFP+ and GFP- cells were individually collected in CMF-PBS with 5% FCS. Sorted cells were spun down at 1000g for 10 minutes at 4°C. The supernatant was carefully removed and pellets were suspended in cell lysis buffer from an RNeasy Plus Micro kit (Qiagen) and stored at -80 °C for future RNA extraction.

tag: genotype

value: Atoh1-GFP Knock-in  Mouse (Atoh1tm4.1Hzo)

tag: background strain

value: outbred (ICR)

value: P0 Mouse cochlea


title: Macrophages from Normal Spleen

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

country: China

institute: Chinese Academy of Medical Science& Peking Union  Medical College

description: Macrophages from Normal Spleen

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 mouse genes.
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: n/a
Supplementary_files_format_and_content: RPKM

source_name: Macrophage

extract_protocol:
sorted Macrophages were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GFP+ leukemia cells were isolated from leukemia mice and transplanted into 6-8 weeks old C57BL/6J mice (1×106 cells/mouse) without irradiation. All mice suffered T-ALL with a survival time of 35 to 40 days. Macrophages were sorted from BM and spleen of leukemia mice at 0d and 21d.

tag: cell type

value: macrophage

tag: strain

value: Spleen

tag: age


title: Purified Atoh1-GFP+ cells from mouse cochlea_2

source_name: Cochlea GFP+ rep 2

tag: tissue


title: Purified Atoh1-GFP- cells from mouse cochlea_1

source_name: Cochlea GFP- rep 1


title: DEC_rep2

city: Naples

first: Piergiuseppe

last: De Berardinis

state: Italy

address: Via P. Castellino, 111

department: Institute of Protein Biochemistry

country: Italy

institute: National Research Council

data_processing:
Reads quality assessment with FastQC
Reads alignment with Tophat version 2 (parameters: --bowtie1 -p 12 -N 2 -g 10 -r 200 -a 15 -m 1 -i 100 --library-type fr-unstranded --segment-mismatches 3 --read-edit-dist 2 --transcriptome-index)
Samtools and BedTools for sam/bam/bed conversions and Bedgraph generation
Differential gene expression analysis with Cuffdiff version 2 (with default paramenters)
Genome_build: mm9
Supplementary_files_format_and_content: Normalized expression values, FPKM (tab delimited file with "gene symbol" and "FPKM" columns respectively).

source_name: dendritic cells

growth_protocol: Bone marrow cells from tibias of C57BL/6 mice were collected by flushing with RPMI 1640 ( medium supplemented with 50 μM 2-mercaptoethanol, 1 mM sodium pyruvate, 100 U/ml penicillin, 100 μg/ml streptomycin, and 10% FCS . Washed cells were seeded in bacteriological petri dishes in complete medium supplemented with 200 U/ml of recombinant murine GM-CSF .

extract_protocol:
Total RNA was extracted from BMDCs using Tri Reagent  according to manufacturer's protocol. The integrity and quantity of RNAs were assessed by denaturing agarose gel electrophoresis and digital electophoresis on Experion platform (Bio-rad)
Paired-end libraries (unstranded) were prepared according to Illumina's protocol.

treatment_protocol: Immature cells were harvested and incubated or not for 24 hours  with 50 μg/ml of LPS-free E2wt, 100μg/ml of fd bacteriophage or 100μg/ml of scDEC fd bacteriophage at a final concentration of 2.5 x 106 cells/ml.

tag: treatment

value: scDEC fd bacteriophage


title: Purified Atoh1-GFP+ cells from mouse cochlea_1

source_name: Cochlea GFP+ rep 1


title: 619_T


title: E2_rep1

value: E2 scaffold


title: E2_rep2


title: Macrophages form 21Day T-all  BM

description: LAMs form 21Day T-ALL BM

value: leukemia associated macrophage

value: BM


title: Macrophages form Normal BM

description: Macrophages form Normal BM


title: WT_rep2

value: fdwt bacteriophage


title: 545_T


title: DC_rep2

value: untreated (replicate 2)


title: Day4_Suz12_4OHT_Rep2

data_processing:
Reads were aligned using Bowtie.
Reads were extended 200 bp and grouped into 25-bp bins.  Extended sequences were processed into Wiggle/BigWig format for visualization, allowing one repeat read.
Experimentally matched Input sequences were used to estimate background signal.  A Poissonian model was used to determine statistically enriched bins with a p value threshold set at 1 X 10^-12 as described previously (Marson et al., 2008) and a 5-fold enrichment over input cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig values are read depth per 25 bp bin scaled per million mapped reads.

extract_protocol:
Chromatin immunoprecipitation of histone modifications were performed according to the Young lab protocol (Lee et al. 2006) with minor modification in biological duplicate per experimental condition, except for H3K27me3 and BRG1-FLAG- ChIP-seq, which were performed in biological triplicate.  Briefly, frozen pellets of cross-linked cells (10x106) were thawed in cold lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors) and gently rocked at 4°C for 10 minutes in 15 mL conical tubes.    Cells were pelleted at 1350 x g at 4°C and resuspended in cold lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitors) and gently rocked at 4°C  for 10 minutes in 15 mL conical tubes.  Cells were pelleted at 1350 x g at 4°C  in a table top centrifuge and resuspended in 0.5 mL cold ChIP lysis buffer (50 mM HEPES-NaOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) and sonicated to 200-1000 bp fragments using a VirSonic sonicator.  Sonicated lysates were cleared by pelleting insoluble material at 13,000 RPM at 4°C  followed by incubation with 5 ug antibody overnight.  Next, Protein A magnetic beads (45 uL) were added to the lysate and incubated at 4°C for 7 hrs.  Prior to addition, magnetic beads were washed 3 times with block (0.5% BSA/PBS).  Immunoprecipitated material was washed 2 times each with ChIP lysis buffer, high salt lysis buffer (50 mM HEPES-NaOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate), and LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) and one time with TE plus NaCl, followed by elution and reverse crosslinking in 210 uL of 1% SDS in TE overnight at 65°C.  200 uL of uncrosslinked material was treated with RNase A for 2 hours, proteinase K for 2 hours, and extracted 2 times with phenol chloroform isoamyl alcohol.  This was followed by ethanol precipitation with a glycogen coprecipitant, 80% ethanol wash and final resuspension in TE.  Nucleic acid yield was determined via PicoGreen (Invitrogen). Adapter ligation and size selection (200-400 bp) were performed using a Beckman Coulter SPRI TE nucleic acid extractor, or, in some cases, performed by hand.  Fragments were PCR amplified for 13 cycles followed by sequencing on an Illumina HiSeq 2000 system.
Adapter ligation and size selection (200-400 bp) were performed using a Beckman Coulter SPRI TE nucleic acid extractor, or, in some cases, performed by hand.  Fragments were PCR amplified for 13 cycles followed by sequencing on an Illumina HiSeq 2000 system.  For hand prepared libraries, libraries were made using the Ovation Library Prep kit according the manufacturer's instructions (NuGen).  Briefly, DNA samples were end repaired, ligated to adaptors, and purified using AMPure beads.  Purified samples were amplified by PCR for 18 cycles, purified, and sequenced on an Illumina HiSeq 2000 system.

value: Brg1f/f; Actin-CreER

tag: timepoint

value: Day 4

tag: antibody

value: anti-SUZ12 (Bethyl A302-407A)

tag: brg1 levels

value: Deleted


title: DEC_rep1


title: DC_rep1

value: untreated (replicate 1)


title: WT_rep1


title: Day4_Suz12_THF_Input_Rep1

value: Normal


title: Day4_Suz12_4OHT_Rep1


title: Day4_Suz12_THF_Rep1


title: Day4_H3K27me3_4OHT_Rep3

value: anti-H3K27me3(Millipore 17-622)


title: Day4_H3K27me3_4OHT_Rep1


title: Day4_Suz12_4OHT_Input_Rep1


title: Day4_Suz12_THF_Rep2


title: Macrophages form 21Day T-all  Spleen

description: LAMs form 21Day T-ALL  Spleen


title: Day4_H3K27me3_THF_Input_Rep1


title: Day4_H3K27me3_THF_Rep1


title: Day4_H3K27me3_4OHT_Input_Rep2


title: Day4_H3K27me3_4OHT_Rep2


title: Day4_H3K27me3_THF_Rep2


title: Day4_H3K27me3_THF_Rep3


title: Day4_H3K27me3_THF_Input_Rep2


title: Day4_Brg1Flag_Rep3

description: For BRG1-FLAG ChIP-seq, the protocol described below was followed except 8-10x107 cells were used as starting material and 10 ug anti-FLAG (Sigma F1804) were incubated with Protein G magnetic beads for roughly 6 hours prior to washing and addition of the bead/antibody complex to chromatin lysate for immunoprecipitation overnight.  BRG1-FLAG ChIP-seq enriched regions were identified with a p value threshold of 1 x 10^-6 and a fold cutoff of 2-fold enriched over input.

value: anti-FLAG (Sigma M2 F1804)


title: Day4_H3K27ac_4OHT_Rep1

value: anti-H3K27ac (ActiveMotif #39134)


title: Day4_H3K27ac_THF_Rep2


title: Day4_H3K27ac_4OHT_Rep2


title: Day4_Brg1Flag_Rep1


title: Day4_Brg1Flag_Input_Rep3


title: Day4_Brg1Flag_Input_Rep1


title: Day4_4OHT_Rep2

data_processing:
Reads were aligned using Bowtie reporting uniquely aligned reads and allowing 2 bp mismatches
Generated .useq files using (USeq Version 8) Application Sam2USeq
USeq files were converted to BigWig format via GnomEx (https://hci-as3.hci.utah.edu/gnomex/gnomex.html)
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig values are per base read depth scaled per million mapped reads.

extract_protocol:
RNA was extracted using TRIzol according to the manufacturer's instructions.
8 ug of total RNA was used as input material for the preparation of the RNA-Seq libraries, according to Illumina RNA Seq library kit with minor modifications.  Briefly, mRNA was isolated using Dynabeads® mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation.  First and second strand synthesis were performed followed by end repair, A-tailing, adapter ligation and size selection on a Beckman Coulter SPRI TE nucleic acid extractor.  200-400 bp dsDNA was enriched by 13 cycles of PCR with Phusion® High-Fidelity DNA Polymerase (NEB).  Amplified libraries were sequenced on an Illumina HiSeq 2000 system.


title: Day4_H3K27me3_4OHT_Input_Rep1


title: Day4_H3K27ac_4OHT_Input_Rep1


title: Day4_H3K27ac_THF_Rep1


title: Day4_THF_Rep2


title: Day4_THF_Rep1


title: Day4_H3K27ac_THF_Input_Rep1


title: Day4_Brg1Flag_Rep2


title: Day2_Rep1

value: Day 2


title: Day4_4OHT_Rep1


title: Day2_Rep2


title: RCH350_LL_rep_2

city: Seattle

first: Caroline

last: Harwood

state: WA

address: 1705 NE Pacific Street

department: Microbiology

institute: University of Washington

description: low-light condition

data_processing:
All cDNA libraries were sequenced with an Illumina HiSeq at the University of Washington High Throughput Genomics Center
Raw sequencing data were processed by with the Xpression pipeline, as described in Phattarasukol, S., Radey, M. C., Lappala, C. R., Oda, Y., Hirakawa, H., Brittnacher, M. J., and Harwood, C. S. (2012) Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris by Xpression, an integrated tool for prokaryotic RNA-seq data processing. Appl. Environ. Microbiol. 78, 6812–8.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene

organism: Rhodopseudomonas palustris

growth_protocol: Cells were grown anaerobically in light at 30°C in 10 ml non-nitrogen-fixing medium (PM) or nitrogen-fixing medium (NF and LL) containing 20 mM acetate, 10 μl VCl3, and Wolfe's vitamin solution (5 ml/l).

extract_protocol:
RNA was extracted and purified from 5 ml of the same cell suspensions and time points used for tracking the biomass composition.
The R. palustris-specific selective primers v2 were based on the genome sequences of six R. palustris strains (CGA009, TIE-1, HaA2, BisB5, BisB18, and BisA53). We used a pool of 1,203 selective primers with no perfect match to any rRNA genes (e.g., 5S, 16S, and 23S rRNA). An additional set of 200 primers that were responsible for the majority of rRNA-priming events in test libraries, was further removed, leaving a final set of 1,003 R. palustris-specific selective primers v2 (Table S1). For first strand cDNA synthesis, 500 ng of total RNA was mixed with 1 μl of 100 μM of R. palustris-specific selective primers v2 in 5 μl reaction volume, and incubated at 65 °C for 5 min. After snap chilling on ice, 2 μl of 5X First-Strand Buffer (Invitrogen, Carlsbad, CA), 2 μl of 10 mM dNTP mix (New England BioLabs, Ipswich, MA), 0.5 μl of 0.1 M DTT, 0.5 μl of SuperScript III Reverse Transcriptase (Invitrogen) were added, and the mixture was further incubated at 40°C for 90 min. To generate the second strand, 45.5 μl of water, 15 μl of 5X Second Strand Buffer (Invitrogen), 1.5 μl of 10 mM dNTP mix, 0.5 μl of Escherichia coli DNA Ligase (Invitrogen, 10 U/μl), 2 μl of DNA Polymerase I (Invitrogen, 10 U/μl), and 0.5 μl of RNase H (Invitrogen, 2 U/μl) were added to the reaction, and incubated at 16 °C for 2 h. The reaction was stopped by adding 25 μl of 20 mM EDTA, pH8.0.  Double stranded cDNA was then purified by using the MinElute PCR Purification Kit (QIAGEN, Valencia, CA) using 12 μl of Buffer EB. Finally, the cDNA library was constructed using the Ovation Ultralow DR Multiplex System (NuGEN, San Carlos, CA) following the manufacture’s instructions.

value: low-light condition


title: RCH350_PM_rep_1

description: non-hydrogen-producing condition

value: non-hydrogen-producing condition


title: RCH350_NF_rep_1

description: hydrogen-producing condition

value: hydrogen-producing condition


title: RCH350_LL_rep_1

description: low-light condition


title: RCH350_PM_rep_2

description: non-hydrogen-producing condition


title: NCIB8288_PM_rep_2

description: non-hydrogen-producing condition


title: NCIB8288_NF_rep_1

description: hydrogen-producing condition


title: NCIB8288_PM_rep_1

description: non-hydrogen-producing condition


title: NCIB8288_LL_rep_2

description: low-light condition


title: Day4_Brg1Flag_Input_Rep2


title: NCIB8288_LL_rep_1

description: low-light condition


title: NCIB8288_NF_rep_2

description: hydrogen-producing condition


title: KD1_PM_rep_1

description: non-hydrogen-producing condition


title: KD1_PM_rep_2

description: non-hydrogen-producing condition


title: KD1_NF_rep_1

description: hydrogen-producing condition


title: KD1_LL_rep_1

description: low-light condition


title: DSM8283_NF_rep_2

description: hydrogen-producing condition


title: DSM8283_PM_rep_2

description: non-hydrogen-producing condition


title: DSM8283_LL_rep_2

description: low-light condition


title: DSM126_PM_rep_2

description: non-hydrogen-producing condition


title: DSM8283_PM_rep_1

description: non-hydrogen-producing condition


title: DSM8283_NF_rep_1

description: hydrogen-producing condition


title: DSM126_PM_rep_1

description: non-hydrogen-producing condition


title: DSM8283_LL_rep_1

description: low-light condition


title: RCH350_NF_rep_2

description: hydrogen-producing condition


title: DSM126_NF_rep_2

description: hydrogen-producing condition


title: DSM126_NF_rep_1

description: hydrogen-producing condition


title: KD1_NF_rep_2

description: hydrogen-producing condition


title: DCP3_LL_rep_2

description: low-light condition


title: DCP3_PM_rep_2

description: non-hydrogen-producing condition


title: DCP3_NF_rep_1

description: hydrogen-producing condition


title: DCP3_PM_rep_1

description: non-hydrogen-producing condition


title: DSM126_LL_rep_1

description: low-light condition


title: DSM126_LL_rep_2

description: low-light condition


title: DCP3_LL_rep_1

description: low-light condition


title: KD1_LL_rep_2

description: low-light condition


title: CGA010_LL_rep_1

description: low-light condition


title: CGA010_PM_rep_2

description: non-hydrogen-producing condition


title: CGA009_PM_rep_2

description: non-hydrogen-producing condition


title: CGA010_NF_rep_1

description: hydrogen-producing condition


title: CGA010_NF_rep_2

description: hydrogen-producing condition


title: CGA010_PM_rep_1

description: non-hydrogen-producing condition


title: CGA009_NF_rep_2

description: hydrogen-producing condition


title: CGA009_PM_rep_1

description: non-hydrogen-producing condition


title: CGA009_LL_rep_2

description: low-light condition


title: CGA009_LL_rep_1

description: low-light condition


title: CGA009_NF_rep_1

description: hydrogen-producing condition


title: CEA001_PM_rep_2

description: non-hydrogen-producing condition


title: CEA001_PM_rep_1

description: non-hydrogen-producing condition


title: CEA001_NF_rep_2

description: hydrogen-producing condition


title: CEA001_NF_rep_1

description: hydrogen-producing condition


title: CEA001_LL_rep_1

description: low-light condition


title: DCP3_NF_rep_2

description: hydrogen-producing condition


title: BIS3_PM_rep_2

description: non-hydrogen-producing condition


title: CEA001_LL_rep_2

description: low-light condition


title: CGA010_LL_rep_2

description: low-light condition


title: BIS3_PM_rep_1

description: non-hydrogen-producing condition


title: BIS3_NF_rep_1

description: hydrogen-producing condition


title: BIS3_NF_rep_2

description: hydrogen-producing condition


title: ATCC17007_NF_rep_1

description: hydrogen-producing condition


title: BIS3_LL_rep_2

description: low-light condition


title: ATCC17007_PM_rep_1

description: non-hydrogen-producing condition


title: ATCC17007_PM_rep_2

description: non-hydrogen-producing condition


title: ATCC17007_NF_rep_2

description: hydrogen-producing condition


title: ATCC17007_LL_rep_2

description: low-light condition


title: AP1_NF_rep_2

description: hydrogen-producing condition


title: BIS3_LL_rep_1

description: low-light condition


title: AP1_NF_rep_1

description: hydrogen-producing condition


title: AP1_LL_rep_2

description: low-light condition


title: ATCC17007_LL_rep_1

description: low-light condition


title: AP1_PM_rep_1

description: non-hydrogen-producing condition


title: 1a1_PM_rep_2

description: non-hydrogen-producing condition


title: AP1_LL_rep_1

description: low-light condition


title: 1a1_NF_rep_1

description: hydrogen-producing condition


title: 1a1_LL_rep_1

description: low-light condition


title: 1a1_LL_rep_2

description: low-light condition


title: 0001L_PM_rep_1

description: non-hydrogen-producing condition


title: 0001L_PM_rep_2

description: non-hydrogen-producing condition


title: 0001L_NF_rep_2

description: hydrogen-producing condition


title: 0001L_NF_rep_1

description: hydrogen-producing condition


title: TIE1_PM_rep_2

description: non-hydrogen-producing condition


title: TIE1_PM_rep_1

description: non-hydrogen-producing condition


title: RSP24_PM_rep_2

description: non-hydrogen-producing condition


title: TIE1_LL_rep_2

description: low-light condition


title: RSP24_PM_rep_1

description: non-hydrogen-producing condition


title: AP1_PM_rep_2

description: non-hydrogen-producing condition


title: 1a1_PM_rep_1

description: non-hydrogen-producing condition


title: TIE1_NF_rep_2

description: hydrogen-producing condition


title: RCH500_PM_rep_2

description: non-hydrogen-producing condition


title: RSP24_LL_rep_2

description: low-light condition


title: TIE1_NF_rep_1

description: hydrogen-producing condition


title: RCH500_PM_rep_1

description: non-hydrogen-producing condition


title: RCH500_LL_rep_2

description: low-light condition


title: RSP24_NF_rep_1

description: hydrogen-producing condition


title: RCH500_NF_rep_2

description: hydrogen-producing condition


title: TIE1_LL_rep_1

description: low-light condition


title: RSP24_NF_rep_2

description: hydrogen-producing condition


title: RSP24_LL_rep_1

description: low-light condition


title: RCH500_LL_rep_1

description: low-light condition