title: AGS5 MethylC-seq

extract_protocol:
Genomic DNA was extracted, sonicated and bisulfite treated (Zymo EZ DNA methylation-direct kit).
standard illumina protocol


title: Rph1- Old (S4O, Exp 4)

status: Public on Jul 17 2015

type: SRA

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

library_source: transcriptomic

data_processing:
Base-Calling: bases were called using CASAVA
Trimming: tags were trimmed to 35bp before alignment.
Alignment: RNA-seq tags were aligned using tophat v2.0.5 and bowtie indices for the sacCer2 assembly. RNA spike-in sequences were included in the assembly (see sacCer2.SPIKE.fa, available on series record). Libraries were stranded and tophat was run using the parameter --library-type fr-firststrand to reflect this. Additionally, only the optimal alignment for each tag was recorded (-g 1).
Masking: tags mapping to rDNA loci were filtered out.
Track Generation: masked BED files were split into two files containing tags aligned to the + reference strand and the - reference strand. Each was passed through the BEDtools utility genomeCoverageBed (-bg) to make bedGraphs. These were then normalized to the RPKM coefficient for the sample and then run through bedGraphToBigWig from the UCSC Genome Browser utilities package. Tags on the + strand are in *.P.bw and tags on the - strand are in *.M.bw.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Standard YPD medium was used in all experiments.

extract_protocol:
mRNA was purified from 5ug total RNA using the Dynabeads mRNA Direct kit (Ambion).
Since yeast genes are relatively short (average gene size ~1.3Kb), we chose to fragment the mRNA to ~40-50bp rather than the conventional 200-300bp size using RNA fragmentation reagents from Ambion. We believe that this gives better resolution over gene bodies to quantify 5’ and 3’ reads for estimation of cryptic transcripts. To do this, the fragmented RNA was phosphorylated by T4 PNK (NEB) and then size selected on a 15% polyacrylamide gel containing urea. Following size selection, the entire RNA was used as input in the TruSeq small RNA sample preparation protocol (Illumina). Final size selection of amplified library was done using 6% polyacrylamide gels.

treatment_protocol: Up to 4 X 10^8 replicatively aged yeast mother cells (20-25 generations old on average) for RNA-seq were purified as described in S. Tsuchiyama, E. Kwan, W. Dang, A. Bedalov, B. K. Kennedy, Methods in molecular biology 1077, 11 (2013).

tag: experiment

tag: age

value: Old

tag: sort

tag: genotype

tag: strategy

value: Small Fragment


title: Rph1- Old (S3O, Exp 4)


title: AGS2 P1 rep 2 RNA-seq

city: Davis

first: Yoong Wearn

last: Lim

state: CA

address: One Shields Avenue

department: Molecular and Cellular Biology

institute: University of California, Davis

data_processing:
DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf and custom Perl script before mapping.
DRIP-seq: Trimmed fastq reads were mapped to hg19 using BWA 0.6.1. Peak calling was first performed by MACS 1.4.2 using input library as control. DRIP peaks were further assigned onto restriction fragments using custom Perl script. DRIP peaks from 2 AGS2 and 2 AGS4 cells were merged into one sample, respectively.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5. Count table was generated using HTSeq using the "intersection-nonempty" option.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
RRBS: Fastq files were trimmed with Trim Galore before mapping to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
Genome_build: hg19

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary fibroblast

extract_protocol:
Total RNA was extracted using Trizol for downstream processing with the Illumina Truseq kit.
Illumina TruSeq protocol

tag: mutation

tag: sample type

value: Primary fibroblast


title: WT Old (S4O, Exp 5)

value: WT


title: Rph1- Old (S2O, Exp 2) Input

library_source: genomic

data_processing:
Base-Calling: CASAVA was used to call bases for experiment 1 and BCL2FASTQ v2 was used to call bases for experiment 2.
Merge: experiment 2 data are merged from four lanes and two flowcells, or eight lanes each. Raw files correspond to merged data with internal labeling in tag headers.
Alignment: ChIP-seq data were aligned using bowtie v0.12.7 and v0.12.5 in the case of the first and second replicate of H3K36me3 data respectively. ChIP-seq data were aligned with parameters -m 1 --best, to guarantee a single optimal alignment for each tag and to remove tags mapping optimally to multiple loci.
Track Generation: aligned tags were expressed as bedGraphs using the BEDtools utility genomeCoverageBed (-bg) and adjusted for total tags sequenced. H3 bedGraphs were subtracted from H3K36me3 bedGraphs to normalize for sonication efficiency, then tracks for the two replicates were combined by unweighted average.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

extract_protocol:
Chromatin immunoprecipitation was performed as described previously from 4 X 10^8 cells (W. Dang et al., Nature 459, 802 (Jun 11, 2009)). Briefly, cross-linked cells were lyzed by bead beating in FA lysis buffer (50mM HEPES-KOH, pH 7.5, 500mM NaCl, 1mM EDTA, 0.1% Triton X-100) and the chromatin sheared using a Diagenode Bioruptor or Covaris Ultrasonicator to achieve an average size of <500bp. Equal aliquots of sonicated chromatin were used per immunoprecipitation (IP) reaction (H3K36me3 (Active Motif 61101) and H3 (Abcam ab1791)) and 10% of the amount was saved as input. IP was performed using protein A Dynabeads (Life Technologies). ChIP-qPCR was performed against standards made from a dilution series of an input DNA mix. Enrichment was ascertained by calculating signal over IgG. To ensure that we were getting H3K4me3 and H3K36me3 enrichment at 5’ ends and 3’ ends respectively, ChIP-qPCR validation was performed with 5’ and 3’ end primer sets over long genes before library preparation for ChIP-seq. Primer sequences are available upon request.
For ChIP-seq, 1ng of DNA from IP and input was used to prepare libraries using the Microplex library preparation kit (Diagenode). Twelve multiplexed libraries were sequenced in a single lane on the Illumina HiSeq or NextSeq 500 platform.

tag: ChIP

value: Input

tag: antibody


title: AGS4 P1 MethylC-seq


title: WT Old (S4O, Exp 4)


title: Rph1- Young (S2Y, Exp 4)

value: Young


title: WT Old (S3O, Exp 4)


title: Rph1- Old (S3O, Exp 2) Input


title: Rph1- Old (S3O, Exp 2) H3

value: Abcam ab1791


title: AGS1 MethylC-seq


title: AGS2 P1 MethylC-seq


title: Control 2 MethylC-seq


title: WT Old (S2O, Exp 4)


title: Rph1- Old (S2O, Exp 2) H3


title: Rph1- Young (S2Y, Exp 2) H3


title: Control 1 MethylC-seq


title: FUDR-Treated Old (Day 12)

data_processing:
Base-Calling: bases were called using BCL2FASTQ v2
Trimming: tags were trimmed to 35bp before alignment.
Alignment: RNA-seq tags were aligned using tophat v2.0.5 and bowtie indices for the ce10 assembly.  Libraries were stranded and tophat was run using the parameter --library-type fr-firststrand to reflect this. Additionally, only the optimal alignment for each tag was recorded (-g 1).
Track Generation: BED files were split into two files containing tags aligned to the + reference strand and the - reference strand. Each was passed through the BEDtools utility genomeCoverageBed (-bg) to make bedGraphs. These were then normalized to the RPKM coefficient for the sample and then run through bedGraphToBigWig from the UCSC Genome Browser utilities package. Tags on the + strand are in *.P.bw and tags on the - strand are in *.M.bw.
Genome_build: ce10
Supplementary_files_format_and_content: bigWig

organism: Caenorhabditis elegans

source_name: Worm

growth_protocol: N2 (C. elegans var Bristol), obtained from the Caenorhabditis Genetics Center, was used in the aging experiment. Worms were staged by bleaching gravid adults and synchronized to L1 in the M9 buffer.

extract_protocol:
Worms were lysed in QIAzol (QIAGEN) by beadbeating with 1.0 mm dia. zirconia/silica beads (BioSpec), four times, 1 min each time, with 2 minute pauses on ice. Total RNA was then extracted and purified with miRNeasy Mini Kit (QIAGEN).
To generate libraries for RNA-seq, mRNA was purified from 5ug total RNA using the Dynabeads mRNA Direct kit (Ambion). We chose to fragment the mRNA to ~40-50bp rather than the conventional 200-300bp size using RNA fragmentation reagents from Ambion. To do this, the fragmented RNA was phosphorylated by T4 PNK (NEB) and then size selected on a 15% polyacrylamide gel containing urea. Following size selection, the entire RNA was used as input in the TruSeq small RNA sample preparation protocol (Illumina). Final size selection of amplified library was done using 6% polyacrylamide gels.

treatment_protocol: L1 worms were grown on NGM plates seeded with OP50 E. coli until L4, which corresponds to day 0, when they were transferred to NGM plates supplemented with 100 µM 5-Fluoro-2’-deoxyuridine (FUDR), seeded with OP50. At day 1, 8, and 12 of adulthood, 500-1,000 worms and 10,000 worms were washed in the M9 buffer and collected for RNA-seq and ChIP experiments, respectively.

tag: strain

tag: developmental stage (days)

tag: treatment

value: FUDR

tag: age (days)


title: FUDR-Treated Old (Day 8)


title: AGS5 P1 DRIP-seq

extract_protocol:
Genomic DNA was extracted from primary fibroblasts and fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
standard illumina protocol


title: WT Young (S2Y, Exp 4)


title: Rph1- Old (S4O, Exp 3)


title: AGS4 P2 DRIP-seq


title: FUDR-Treated Young (Day 1)


title: Rph1- Old (S3O, Exp 2) H3K36me3

value: Active Motif 61101


title: Rph1- Old (S2O, Exp 2) H3K36me3


title: Untreated Young (Day 1)

value: No FUDR


title: AGS4 P1 DRIP-seq


title: Rat 12 Olanzapine 24h

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

description: Olanzapine IV infused 24 h

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter trimmed fastq files were generated.
Merged fastq files from lane 1 and lane 2. Fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using Rnor_5.0 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1 using -u and -N option. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used Enemble (release 77) gtf file as guided annotation file.
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: FPKM gene expression data

organism: Rattus norvegicus

source_name: gastrocnemius muscle

growth_protocol: Male Sprague Dawley rats (150-175g) from Charles River Laboratories (Cambridge, MA, USA) were acclimated to single housing for several weeks while being maintained on a 12:12 h light dark cycle at ~21°C and provided free access to water and a standard rodent chow (2018, Harlan Laboratories, Madison, WI)

extract_protocol:
Gastrocnemius was then surgically removed under isoflurane anesthesia (carried with 100% O2), and frozen between two aluminum blocks cooled to the temperature of liquid nitrogen and then stored at -80oC until RNA was isolated. Frozen muscle tissue was pulverized in liquid nitrogen using mortar and pestle, followed by bead mill homogenization (Bullet Blender, Next Advance) using stainless steel beads (Next Advance, cat# SSB14B) and mirVana RNA isolation kit (Life Technologies). Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RIN was determined for each sample using Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies).
The cDNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Six libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).

treatment_protocol: For the olanzapine group, the venous catheter was attached to a New Era Pump Systems syringe pump (Model NE-300) filled with olanzapine (Dr. Reddy’s Laboratories Ltd, Hyderabad, India) in sterile saline (infusion: 1mg/100g BW loading dose for 0.5h and then 0.04mg/100g/h continuously for 23.5h). Control rats were infused with vehicle at the same rate and volume.

tag: charlers river strain code

tag: body weight gms


title: Rph1- Young (S2Y, Exp 2) H3K36me3


title: Rph1- Young (S2Y, Exp 2) Input


title: Rph1- Old (S2O, Exp 3)


title: AGS2 P2 DRIP-seq


title: WT Old (S3O, Exp 2) Input


title: Rph1- Young (S2Y, Exp 3)


title: Rat 11 Vehicle

description: Vehicle Control


title: Rat 10 Olanzapine 24h

description: Olanzapine IV infused 24 h


title: WT Young (S2Y, Exp 2) Input


title: AGS1 P1 DRIP-seq


title: Rat 9 Vehicle

description: Vehicle Control


title: AGS2 P1 DRIP-seq


title: WT Old (S3O, Exp 3)


title: WT Old (S3O, Exp 2) H3


title: WT Old (S2O, Exp 3)


title: Control 1 DRIP-seq


title: Rat 3 Vehicle

description: Vehicle Control


title: Rph1- Old (S3O, Exp 3)


title: Digested input

extract_protocol:
Genomic DNA was extracted from primary fibroblasts and fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.
standard illumina protocol


title: WT Young (S2Y, Exp 2) H3


title: WT Old (S2O, Exp 2) H3


title: WT Old (S4O, Exp 2)


title: 15dd_DOX_shRNA_plus_Rep1

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
Custom perl software was used to analyze the resulting fastq sequencing files. Each read harbors a unique variable sequence that corresponds to one of the hairpin sequences listed in the processed data table. We simply counted the number of reads harboring individual hairpin sequences and then normalized by the total number of reads in each sample.
Supplementary_files_format_and_content: tab-delimited text file: TRC hairpin ID, hairpin sequence, target genes, sequencing depth normalized read counts for each sample

source_name: reprogramming of shRNA infected hiF-T cell

growth_protocol: Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript. http://www.cell.com/cell/pdf/S0092-8674(15)00700-X.pdf

extract_protocol:
Genomic DNA was extracted with the QIAamp DNA Mini Kit (QIAGEN)
shRNA sequences were retrieved by PCR from genomic DNA with the direct inclusion of illumina sequencing adapters. Strezoska et al., 2012

tag: surface antigen enrichment

value: DOX days 0-15

tag: cell type


title: Rat 4 Olanzapine 24h

description: Olanzapine IV infused 24 h


title: WT Old (S3O, Exp 2) H3K36me3

tag: experiment


title: WT Old (S2O, Exp 2) Input

tag: age


title: Q119

city: Shenzhen

first: Wuxian

last: Li

state: Guangdong

address: 1017, North road, Dongmen

country: China

institute: the Second Clinical Medical College of Jinan University

description:
Small RNA
Control group

data_processing:
Illumina Casava 1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Homo sapiens whole genome using SOAP(2.0) with parameters soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap
The mapped sequences were aligned against miRBase17.0, Rfam 10.0 (http://rfam.sanger.ac.uk/), piRNABank (NCBI) and the human genes UCSC annotation hg19 (http://genome.ucsc.edu/). Overlapping annotation sequences from these data were classified as miRNA, tRNA, rRNA, mRNA, snoRNA, snRNA, piRNA or other non-coding RNAs.
Before expression analysis of known miRNAs, the miRNA expression level was normalized by calculating its transcripts parts per million (TPM). The total clone count is the sum of the frequencies of all unique sequences remaining after filtering.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values or identified novel miRNAs for each Sample.
Supplementary_files_format_and_content: *txt: abundance measurements
Supplementary_files_format_and_content: *nov.txt: identified novel miRNAs

source_name: Fetal cord blood, control

extract_protocol: Cord blood mononuclear cells (CBMCs) were separated by a Ficoll-Paque. Total RNA was harvested using Trizol reagent. The 18-30nt small RNA population was isolated by separating 10 μg of total RNA using denaturing polyacrylamide gel electrophoresis (PAGE). The Illumina Small RNA Sample Prep Kit (Cat# FC-102-1009) was used to construct the sequencing libraries.

value: cord blood mononuclear cells

tag: developmental stage

value: 18-22 weeks of gestation

tag: karyotype

value: 46,XX and 46,XY

value: pool of 3 samples


title: 15dd_DOX_shRNA_plus_Rep2

treatment_protocol: Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript. http://www.cell.com/cell/pdf/S0092-8674(15)00700-X.pdf

value: reprogramming of shRNA infected hiF-T cell


title: WT Old (S4O, Exp 3)

tag: sort

tag: genotype

tag: strategy


title: Q058

description:
Small RNA
DS group

source_name: Fetal cord blood, Down syndrome

tag: sample type


title: shRNA_hiF-T_Rep2

source_name: shRNA infected hiF-T cell

value: shRNA infected hiF-T cell


title: WT Old (S2O, Exp 2) H3K36me3

tag: ChIP

value: Old

tag: antibody


title: WT Young (S2Y, Exp 2) H3K36me3


title: WT Young (S2Y, Exp 2)

value: Small Fragment


title: shRNA_hiF-T_Rep1


title: WT Young (S2Y, Exp 1)


title: WT Young (S2Y, Exp 3)


title: DsrA

status: Public on Jul 16 2015

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

description: rne131 ΔdsrA

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010 (i.e. divided by total number of proof reads for each sample)
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and MS2-DsrA/DsrA ratio

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterium

growth_protocol: Cells were harvested in exponential (OD600nm=0.5; 100 mL LB medium) and in stationary phase (OD600nm=1; 100 mL LB medium).

extract_protocol:
Cells were resuspended in 3 mL of buffer A and lysed using a French Press (430 psi, four times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 100 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 200 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 8 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA libraries were prepared with ScriptSeq™ v3 RNA-Seq Library Preparation Kit (Epicentre)

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-DsrA/DsrA during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

tag: genotype/variation

value: rne131 delta dsrA

tag: growth phase

value: exponential and stationary phases


title: pBAD-MS2

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010 (i.e. divided by total number of proof reads for each sample)
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and pBAD-MS2/pNM12 ratio

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2 aptamer (fused to RyhB terminator) during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.


title: MS2-DsrA

description: rne131 ΔdsrA


title: WT Old (S4O, Exp 1)

value: WT


title: H3.3-YFP Daxx WT1 ESC

city: Bethesda

first: Gernot

last: Wolf

state: Maryland

address: 6 Center Drive

department: NICHD

institute: NIH

data_processing:
The first 3 nucleotides were trimmed from each read
Reads were aligned to the mm9 genome using Bowtie with standard parameters and --best mode activated
Genome_build: mm9
Supplementary_files_format_and_content: tdf coverage files

organism: Mus musculus

source_name: Daxx fl/- Embryonic stem cell

growth_protocol: ES cells were grown on mitomycin C inactivated feeder cells in DMEM supplemented with 16% FBS, 104 U/mL LIF, HEPES, NEAA, L-glutamine, b-ME, and antibiotics

extract_protocol:
Lysates were clarified from Micrococcal Nuclease (MNase) treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina)

tag: strain

tag: chip antibody

value: GFP (A-6455, life technologies)

value: Daxx fl/- ESC (control for KO1)

tag: treatment

value: Daxx fl/- subclone picked after transient Cre transfection


title: H3.3-YFP Daxx KO1 ESC

source_name: Daxx -/- Embryonic stem cell

value: Daxx -/- ES cells

value: Daxx -/- subclone picked after transient Cre transfection


title: H3.3-YFP Daxx WT2 ESC

source_name: Daxx fl/fl Embryonic stem cell_DMSO-treated

value: Daxx fl/fl; RosaCreERT (control for KO2)


title: Wdr61 LPS  4 hours+ Brefeldin

city: Cambridge

first: Oren

last: Parnas

state: MA

address: 415 main street

department: Biology

institute: BROAD INSTITUTE

data_processing:
We created a Bowtie index based on the mm9 mouse reference genome, and then aligned paired-end reads directly to this index using Bowtie v 0.12.7 (Trapnell et al., 2009). Next, we ran RSEM v1.11 (Li and Dewey 2011) with default parameters on these alignments to estimate expression levels. RSEM’s gene level expression estimates (tau) were multiplied by 1,000,000 to obtain transcript per million (TPM) estimates for each gene. To transform expression levels to log-space, we took the log2(TPM+1). Sequencing libraries that correlated poorly (Pearson r<0.8) with the majority of samples or had fewer than 500,000 expected counts across the transcriptome were removed from further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The log2(TPM+1) values were then quantile normalized, which reduced the coefficient of variation for each gene across samples. Without batch correction, samples separated strongly according to the experiment and plate in the first two principal components within a given time point. Batch correction was performed using the SVA package in R (Leek et al., n.d.). The primary known batch covariate was the plate on which the sample was processed. After batch correction, the effects associated with batch were attenuated.

growth_protocol: RPMI medium (Invitrogen) supplemented with 10% heat inactivated FBS (Invitrogen), β-mercaptoethanol (50uM, Invitrogen), L-glutamine (2mM, VWR), penicillin/streptomycin (100U/ml, VWR), MEM non-essential amino acids (1X, VWR), HEPES (10mM, VWR), sodium pyruvate (1mM, VWR), and GM-CSF (20 ng/ml; Peprotech) was used throughout the study. At day 0, cells were collected from femora and tibiae and plated in 100mm non tissue culture treated plastic dishes using 10ml medium per plate at concentration of 2 × 105/ml. At day 2, cells were fed with another 10ml of medium per dish. At day 5, 12ml of the medium were carefully removed (to avoid removal of cells) and 10ml of fresh medium were added back to the original dish. Cells were fed with another 5ml medium at day 7. At day 8, all non-adherent and loosely bound cells were collected and harvested by centrifugation. Cells were then re-suspended with medium, plated at a concentration of 10x106 cells in 10ml medium per 100mm dish.

extract_protocol:
RNA was purified using Qiagen RNAeasy 96 Kit according to the manufacturer’s instructions. The RNA was eluted in a volume of 50ml.
For library construction we used the SMART-seq2 protocol (Picelli et al., 2013) in a 96 well plate format and with several modifications. 2 μl of RNA sample per well were mixed with 2ml RT primer (10mM 5 ́-AAGCAGTGGTATCAACGCAGAGTACT30VN-3 ́), 2ml dNTP mix (10mM each, Agilent Technologies) and 2ml Recombinant RNase Inhibitor (RRI-Clontech). This mix was incubated for 3min at 72°C and immediately placed on ice. To perform reverse transcription (RT) we added a mix of 1.5ml H2O, 4 ml Maxima buffer (ThermoFisher Scientific), 4 ml Betaine (5M SIGMA-ALDRICH), 1.8 ml MgCL2, 2ml TSO (10mM AAGCAGTGGTATCAACGCAGAGTACrGrG+G), 0.5 RRI and 0.2ml Maxima H Minus Reverse Transcriptase enzyme (ThermoFisher Scientific). We incubated the RT reaction mix at 42°C for 90 min followed by 10 cycles of 50°C for 2 min, 42°C for 2 min, afterwards heat inactivated the enzyme for 15 min at 70°C. We used 11ml of the RT reaction for the PCR reaction by adding 12.5 ml KAPA HiFi Hotstart (KAPA Biosystems), 1ml H2O and 0.5 ml of (10mM 5’-AAGCAGTGGTATCAACGCAGAGT-3 ́) primer under the following conditions: 98°C for 3 min, 14 cycles of (98°C for 15 sec, 67°C for 20 sec, 72°C for 6 min), final extension at 72°C for 5 min. The PCR product was used for library preparation with Nextera XT DNA Sample Preparation (Illumina) according to the manufacturer’s instructions. Samples were combined and purified using Ampure XP Agencourt beads (Beckman Coulter) and sequenced on a Hi-Seq 2500 (Illumina), to generate paired-end 25bp reads. Each sample was sequenced to an average depth of four million reads (IQR-2.3 -5.5 million).

treatment_protocol: At day 9, cells were stimulated for various time points with LPS (100ng/ml, rough, ultrapure E. coli K12 strain, Invitrogen),  30 min later Brefeldin was added and than the cells were harvested.

tag: knockout

tag: tissue/cell line

value: BMDC

tag: condition

value: Brefeldin 30 min after activation

value: LPS  4 hours


title: pNM12


title: Wdr61 LPS  2 hours+ Brefeldin

value: LPS  2 hours


title: Tnf LPS  4 hours+ Brefeldin

value: Tnf


title: Traf6 LPS  2 hours+ Brefeldin


title: Tnf LPS  2 hours+ Brefeldin


title: Tirap LPS  2 hours+ Brefeldin

value: Tirap


title: Ticam2 LPS  2 hours+ Brefeldin


title: Tmem258 LPS  2 hours+ Brefeldin


title: Ticam1 LPS  4 hours+ Brefeldin


title: Srp54c LPS  4 hours+ Brefeldin


title: Tirap LPS  4 hours+ Brefeldin


title: Ticam2 LPS  4 hours+ Brefeldin


title: Srpr LPS  2 hours+ Brefeldin

value: Srpr


title: Srpr LPS  4 hours+ Brefeldin


title: Sgms1 LPS  2 hours+ Brefeldin


title: Ticam1 LPS  2 hours+ Brefeldin


title: Sgms1 LPS  4 hours+ Brefeldin


title: Srp54c LPS  2 hours+ Brefeldin


title: Rpn1 LPS  4 hours+ Brefeldin


title: Rbx1 LPS  2 hours+ Brefeldin


title: Rbck1 LPS  4 hours+ Brefeldin


title: Rpn1 LPS  2 hours+ Brefeldin


title: Rbx1 LPS  4 hours+ Brefeldin


title: Tmem258 LPS  4 hours+ Brefeldin


title: Polr2j LPS  2 hours+ Brefeldin


title: Rbck1 LPS  2 hours+ Brefeldin


title: Polr2g LPS  4 hours+ Brefeldin


title: Rpn2 LPS  2 hours+ Brefeldin


title: Polr2j LPS  4 hours+ Brefeldin


title: Rpn2 LPS  4 hours+ Brefeldin


title: Polr2g LPS  2 hours+ Brefeldin


title: Paf1 LPS  4 hours+ Brefeldin


title: H3.3-YFP Daxx KO2 ESC

source_name: Daxx fl/fl Embryonic stem cell_tamoxifen-treated to induce Daxx -/-

value: Daxx fl/fl; RosaCreERT

value: 1 µM 4-hydroxytamoxifen for 48 hours followed by 3 days recovery


title: Pabpc1 LPS  2 hours+ Brefeldin


title: Myd88 LPS  4 hours+ Brefeldin


title: Pabpc1 LPS  4 hours+ Brefeldin


title: Kcnc1 LPS  4 hours+ Brefeldin


title: Ly96 LPS  2 hours+ Brefeldin


title: Myd88 LPS  2 hours+ Brefeldin


title: Kcnc1 LPS  2 hours+ Brefeldin


title: Gtf2h1 LPS  2 hours+ Brefeldin


title: Ikbkb LPS  2 hours+ Brefeldin

value: Ikbkb


title: Ly96 LPS  4 hours+ Brefeldin


title: Ikbkb LPS  4 hours+ Brefeldin


title: Gtf2b LPS  4 hours+ Brefeldin


title: Gpkow LPS  4 hours+ Brefeldin

value: Gpkow


title: Gtf2h1 LPS  4 hours+ Brefeldin


title: Gtf2b LPS  2 hours+ Brefeldin


title: Fam96b LPS  4 hours+ Brefeldin


title: Gabpb1 LPS  4 hours+ Brefeldin


title: Gabpb1 LPS  2 hours+ Brefeldin


title: Gpkow LPS  2 hours+ Brefeldin


title: Dmrta1 LPS  4 hours+ Brefeldin


title: Fam96b LPS  2 hours+ Brefeldin


title: Dhx15 LPS  4 hours+ Brefeldin


title: Dhx15 LPS  2 hours+ Brefeldin


title: Ddx39b LPS  4 hours+ Brefeldin


title: Paf1 LPS  2 hours+ Brefeldin


title: Ddx39b LPS  2 hours+ Brefeldin


title: Ddost LPS  4 hours+ Brefeldin

value: Ddost


title: Dmrta1 LPS  2 hours+ Brefeldin


title: Ddost LPS  2 hours+ Brefeldin


title: Dad1 LPS  4 hours+ Brefeldin


title: Dad1 LPS  2 hours+ Brefeldin


title: Ctr9 LPS  4 hours+ Brefeldin


title: Ctcf LPS  4 hours+ Brefeldin

value: Ctcf


title: Cd14 LPS  4 hours+ Brefeldin


title: Ash2l LPS  4 hours+ Brefeldin


title: Ctr9 LPS  2 hours+ Brefeldin


title: Ctcf LPS  2 hours+ Brefeldin


title: Alg2 LPS  2 hours+ Brefeldin


title: Alg2 LPS  4 hours+ Brefeldin


title: Akirin2 LPS  4 hours+ Brefeldin


title: 0610009D07Rik LPS  2 hours+ Brefeldin


title: 0610009D07Rik LPS  4 hours+ Brefeldin


title: P3_H10

data_processing:
Paired reads were used for analysis if all sixteen bases of the first read had quality scores of at least 10 and the first six bases corresponded exactly to a designed well-barcode. All second sequence reads were aligned to a reference database consisting of all human RefSeq mRNA sequences (hg19) and the ERCC RNA spike-in reference sequences using bwa version 0.7.4 4 with non-default parameter “-l 24”. Reads mapped to multiple genes were excluded from further analysis. Digital gene expression (DGE) profiles were then generated by counting, for each microplate well and RefSeq gene, the number of unique molecular identifiers (UMIs) associated with alignments to that gene in that well.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes UMI values for each sample.

source_name: unrelated murine random control

growth_protocol: Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript.

extract_protocol:
Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
The 3’-DGE libraries were prepared from 20ng of total RNA according to the Single Cell RNA Barcoding and Sequencing method originally developed for single cell RNA-seq (SCRB-seq (Soumillon et al., 2014) and adapted to extracted total RNA. Briefly, Poly(A)+ mRNA from extracted total RNA are converted to cDNA decorated with universal adapters, sample-specific barcodes and unique molecular identifiers (UMIs) using a template-switching reverse transcriptase. Decorated cDNA from multiple samples are then pooled, amplified and prepared for multiplexed sequencing using a modified transposon-based fragmentation approach that enriches for 3’ ends and preserves strand information.

value: negative control


title: Akirin2 LPS  2 hours+ Brefeldin


title: P3_H12


title: mmu_mir_466c_2 LPS 6 hours (mmu_mir_466c_2..MGLibA_64110nnT6)

treatment_protocol: At day 9, cells were stimulated for various time points with LPS (100ng/ml, rough, ultrapure E. coli K12 strain, Invitrogen) and harvested.

value: LPS  6 hours


title: non_trgetauh LPS 4 hours (non_trgetauhsnnT4)


title: non_trgetauh LPS 2 hours (non_trgetauhsnnT2)


title: mmu_mir_106a LPS 6 hours (mmu_mir_106a..MGLibA_66132nnT6)


title: mmu_mir_466c_2 LPS 4 hours (mmu_mir_466c_2..MGLibA_64110nnT4)


title: mmu_mir_106a LPS 4 hours (mmu_mir_106a..MGLibA_66132nnT4)


title: auh LPS 2 hours (auhp5g3snnT2)

value: auh


title: auh LPS 2 hours (auhp5f3snnT2)


title: auh LPS 4 hours (auhp5f3snnT4)


title: Cd14 LPS  2 hours+ Brefeldin


title: Ash2l LPS  2 hours+ Brefeldin


title: Zfp36 LPS 4 hours (Zfp36..MGLibB_60667T4)


title: Zfp36 LPS 6 hours (Zfp36..MGLibB_60667T6)


title: Zfp36 LPS 2 hours (Zfp36..MGLibB_60667T2)


title: Zfp36 No LPS (Zfp36..MGLibB_60667T0)

value: No LPS


title: Zfp36 LPS 6 hours (Zfp36..MGLibA_60687T6)

value: BMDC


title: Zfp36 LPS 4 hours (Zfp36..MGLibA_60687T4)


title: P3_H11


title: Xab2 LPS 6 hours (Xab2..MGLibB_59663T6)


title: Xab2 LPS 4 hours (Xab2..MGLibB_59663T4)


title: Zfp36 No LPS (Zfp36..MGLibA_60687T0)


title: Xab2 LPS 2 hours (Xab2..MGLibB_59663T2)


title: Wdr61 LPS 6 hours (Wdr61..MGLibB_59338T6)


title: Wdr61 LPS 4 hours (Wdr61..MGLibB_59338T4)


title: Xab2 No LPS (Xab2..MGLibB_59663T0)


title: Wdr61 No LPS (Wdr61..MGLibB_59338T0)


title: Wdr61 LPS 2 hours (Wdr61..MGLibB_59338T2)


title: Wdr61 LPS 4 hours (Wdr61..MGLibA_59357T4)


title: Wdr61 LPS 6 hours (Wdr61..MGLibA_59357T6)


title: Wdr61 LPS 2 hours (Wdr61..MGLibA_59357T2)


title: Tti2 LPS 6 hours (Tti2..MGLibB_56474nnT6)


title: Wdr61 No LPS (Wdr61..MGLibA_59357T0)


title: Tti2 LPS 4 hours (Tti2..MGLibB_56474nnT4)


title: Tti2 LPS 2 hours (Tti2..MGLibB_56474nnT2)


title: Traf6 LPS 6 hours (Traf6..MGLibB_55541T6)


title: Traf6 LPS 4 hours (Traf6..MGLibB_55541T4)


title: Traf6 LPS 2 hours (Traf6..MGLibB_55541T2)


title: Zfp36 LPS 2 hours (Zfp36..MGLibA_60687T2)


title: Traf6 No LPS (Traf6..MGLibB_55541T0)


title: Traf6 LPS 6 hours (Traf6..MGLibA_55559T6)


title: Traf6 LPS 4 hours (Traf6..MGLibA_55559T4)


title: Tnf LPS 6 hours (Tnf..MGLibB_55163T6)


title: Tnf No LPS (Tnf..MGLibB_55163T0)


title: Tnf LPS 4 hours (Tnf..MGLibB_55163T4)


title: Tnf LPS 4 hours (Tnf..MGLibB_55162T4)


title: Traf6 No LPS (Traf6..MGLibA_55559T0)


title: Tnf LPS 2 hours (Tnf..MGLibB_55163T2)


title: Tnf LPS 6 hours (Tnf..MGLibB_55162T6)


title: Tmem258 LPS 6 hours (Tmem258..MGLibB_54678T6)


title: Tnf LPS 2 hours (Tnf..MGLibB_55162T2)


title: Tti2 No LPS (Tti2..MGLibB_56474nnT0)


title: Tmem258 LPS 2 hours (Tmem258..MGLibB_54678T2)


title: Tmem258 LPS 4 hours (Tmem258..MGLibB_54678T4)


title: Tmem258 LPS 4 hours (Tmem258..MGLibA_54693T4)


title: Tmem258 LPS 6 hours (Tmem258..MGLibA_54693T6)


title: Tmem258 No LPS (Tmem258..MGLibB_54678T0)


title: Tmem258 No LPS (Tmem258..MGLibA_54693T0)


title: Tmem258 LPS 2 hours (Tmem258..MGLibA_54693T2)


title: Tmem186 LPS 6 hours (Tmem186..MGLibB_54470T6)


title: Tnf No LPS (Tnf..MGLibB_55162T0)


title: Tmem186 LPS 2 hours (Tmem186..MGLibB_54470T2)


title: Traf6 LPS 2 hours (Traf6..MGLibA_55559T2)


title: Tmem186 No LPS (Tmem186..MGLibB_54470T0)


title: Tlr4 LPS 6 hours (Tlr4..MGLibA_54043T6)


title: Tlr4 LPS 2 hours (Tlr4..MGLibA_54043T2)


title: Tlr4 No LPS (Tlr4..MGLibA_54043T0)


title: Tlr4 LPS 4 hours (Tlr4..MGLibA_54043T4)


title: Tlr4 LPS 6 hours (Tlr4..MGLibA_54041T6)


title: Tlr4 LPS 2 hours (Tlr4..MGLibA_54041T2)


title: Tlr4 LPS 4 hours (Tlr4..MGLibA_54041T4)


title: Tlr4 No LPS (Tlr4..MGLibA_54041T0)


title: Tirap LPS 6 hours (Tirap..MGLibA_53950T6)


title: Tirap No LPS (Tirap..MGLibA_53950T0)


title: Tirap LPS 6 hours (Tirap..MGLibA_53948T6)


title: Tirap LPS 4 hours (Tirap..MGLibA_53950T4)


title: Tirap LPS 2 hours (Tirap..MGLibA_53950T2)


title: Tirap LPS 2 hours (Tirap..MGLibA_53948T2)


title: Tirap No LPS (Tirap..MGLibA_53948T0)


title: Tipin LPS 4 hours (Tipin..MGLibB_53927nnT4)

value: Tipin


title: Tmem186 LPS 4 hours (Tmem186..MGLibB_54470T4)

value: LPS  4 hours


title: Ticam2 LPS 4 hours (Ticam2..MGLibB_53819T4)


title: Ticam2 No LPS (Ticam2..MGLibB_53819T0)


title: Ticam2 LPS 2 hours (Ticam2..MGLibB_53818T2)

value: LPS  2 hours


title: Ticam2 LPS 4 hours (Ticam2..MGLibB_53818T4)


title: Ticam2 No LPS (Ticam2..MGLibB_53818T0)


title: Ticam1 LPS 6 hours (Ticam1..MGLibB_53816T6)


title: Ticam1 LPS 4 hours (Ticam1..MGLibB_53816T4)


title: Ticam1 No LPS (Ticam1..MGLibB_53816T0)


title: Ticam1 LPS 6 hours (Ticam1..MGLibA_53833T6)


title: Ticam1 LPS 4 hours (Ticam1..MGLibA_53833T4)


title: Tirap LPS 4 hours (Tirap..MGLibA_53948T4)


title: Ticam1 No LPS (Ticam1..MGLibA_53833T0)


title: Ticam1 LPS 2 hours (Ticam1..MGLibA_53833T2)


title: Suz12 LPS 4 hours (Suz12..MGLibB_52162nnT4)


title: Tipin LPS 6 hours (Tipin..MGLibB_53927nnT6)


title: Stat5b LPS 6 hours (Stat5b..MGLibB_51687T6)


title: Stat5b LPS 4 hours (Stat5b..MGLibB_51687T4)


title: Suz12 LPS 2 hours (Suz12..MGLibB_52162nnT2)


title: Stat5b LPS 2 hours (Stat5b..MGLibB_51687T2)


title: Stat5b No LPS (Stat5b..MGLibB_51687T0)


title: Ticam2 LPS 2 hours (Ticam2..MGLibB_53819T2)


title: Ticam2 LPS 6 hours (Ticam2..MGLibB_53819T6)


title: Suz12 No LPS (Suz12..MGLibB_52162nnT0)


title: Ticam2 LPS 6 hours (Ticam2..MGLibB_53818T6)


title: Stat5b LPS 4 hours (Stat5b..MGLibA_51703T4)


title: Stat5b LPS 2 hours (Stat5b..MGLibA_51703T2)


title: Stat5b No LPS (Stat5b..MGLibA_51703T0)


title: Srpr LPS 6 hours (Srpr..MGLibB_51325nnT6)


title: Stat5b LPS 6 hours (Stat5b..MGLibA_51703T6)


title: Srpr LPS 4 hours (Srpr..MGLibB_51325nnT4)


title: Srp54c LPS 4 hours (Srp54c..MGLibB_51301T4)


title: Srpr LPS 2 hours (Srpr..MGLibB_51325nnT2)


title: Srpr No LPS (Srpr..MGLibB_51325nnT0)


title: Ticam1 LPS 2 hours (Ticam1..MGLibB_53816T2)


title: Srp54c LPS 6 hours (Srp54c..MGLibB_51301T6)


title: Srp54c No LPS (Srp54c..MGLibB_51301T0)


title: Suz12 LPS 6 hours (Suz12..MGLibB_52162nnT6)


title: Srp54c LPS 2 hours (Srp54c..MGLibB_51301T2)


title: Sgms1 LPS 6 hours (Sgms1..MGLibB_48173T6)


title: Sgms1 LPS 2 hours (Sgms1..MGLibB_48173T2)


title: Sgms1 LPS 4 hours (Sgms1..MGLibB_48173T4)


title: Sgms1 No LPS (Sgms1..MGLibB_48173T0)


title: Traf6 LPS  4 hours+ Brefeldin

value: Brefeldin 30 min after activation


title: Sgms1 LPS 4 hours (Sgms1..MGLibA_48189T4)


title: Sgms1 LPS 6 hours (Sgms1..MGLibA_48189T6)


title: Sgms1 LPS 2 hours (Sgms1..MGLibA_48189T2)


title: Sec13 LPS 4 hours (Sec13..MGLibB_47504T4)


title: Sec13 LPS 6 hours (Sec13..MGLibB_47504T6)


title: Sec16a No LPS (Sec16a..MGLibA_47534T0)


title: Sec13 LPS 2 hours (Sec13..MGLibB_47504T2)


title: Ruvbl2 LPS 6 hours (Ruvbl2..MGLibB_46746nnT6)


title: Ruvbl2 LPS 4 hours (Ruvbl2..MGLibB_46746nnT4)


title: Sec16a LPS 4 hours (Sec16a..MGLibA_47534T4)


title: Ruvbl2 No LPS (Ruvbl2..MGLibB_46746nnT0)


title: Rtf1 LPS 4 hours (Rtf1..MGLibA_46666T4)


title: Rtf1 LPS 6 hours (Rtf1..MGLibA_46665T6)


title: Rtf1 LPS 4 hours (Rtf1..MGLibA_46665T4)


title: Rtf1 LPS 2 hours (Rtf1..MGLibA_46666T2)


title: Rtf1 No LPS (Rtf1..MGLibA_46666T0)


title: Ruvbl2 LPS 2 hours (Ruvbl2..MGLibB_46746nnT2)


title: Rtf1 No LPS (Rtf1..MGLibA_46665T0)


title: Rtf1 LPS 2 hours (Rtf1..MGLibA_46665T2)


title: Rpn2 LPS 6 hours (Rpn2..MGLibB_46294T6)


title: Rpn2 LPS 4 hours (Rpn2..MGLibB_46294T4)


title: Sec16a LPS 2 hours (Sec16a..MGLibA_47534T2)


title: Sec16a LPS 6 hours (Sec16a..MGLibA_47534T6)


title: Rpn2 No LPS (Rpn2..MGLibB_46294T0)


title: Sgms1 No LPS (Sgms1..MGLibA_48189T0)


title: Rpn2 LPS 6 hours (Rpn2..MGLibA_46307T6)


title: Rpn2 LPS 2 hours (Rpn2..MGLibA_46307T2)


title: Sec13 No LPS (Sec13..MGLibB_47504T0)


title: Rpn2 No LPS (Rpn2..MGLibA_46307T0)


title: Rtf1 LPS 6 hours (Rtf1..MGLibA_46666T6)


title: Rpn1 LPS 4 hours (Rpn1..MGLibB_46290T4)


title: Rpn1 LPS 6 hours (Rpn1..MGLibA_46306T6)


title: Rpn1 LPS 4 hours (Rpn1..MGLibA_46306T4)


title: Rpn1 No LPS (Rpn1..MGLibB_46290T0)


title: Rpn1 LPS 2 hours (Rpn1..MGLibB_46290T2)


title: Rpn1 LPS 2 hours (Rpn1..MGLibA_46306T2)


title: Rpn1 No LPS (Rpn1..MGLibA_46306T0)


title: Rpl35 LPS 6 hours (Rpl35..MGLibA_46238T6)


title: Rpl35 LPS 4 hours (Rpl35..MGLibA_46238T4)


title: Rpl35 No LPS (Rpl35..MGLibA_46238T0)


title: Rpl35 LPS 2 hours (Rpl35..MGLibA_46238T2)


title: Rpl23a LPS 6 hours (Rpl23a..MGLibA_46192T6)


title: Rpl23a LPS 4 hours (Rpl23a..MGLibA_46192T4)


title: Rpn2 LPS 2 hours (Rpn2..MGLibB_46294T2)


title: Rpl23a LPS 2 hours (Rpl23a..MGLibA_46192T2)


title: Rpl23a LPS 2 hours (Rpl23a..MGLibA_46191T2)


title: Rpl23a LPS 4 hours (Rpl23a..MGLibA_46191T4)


title: Rpn2 LPS 4 hours (Rpn2..MGLibA_46307T4)


title: Rpl23a LPS 6 hours (Rpl23a..MGLibA_46191T6)


title: Rpl23a No LPS (Rpl23a..MGLibA_46191T0)


title: Rnf31 LPS 6 hours (Rnf31..MGLibB_45943T6)


title: Rnf31 LPS 4 hours (Rnf31..MGLibB_45943T4)


title: Rnf31 No LPS (Rnf31..MGLibB_45943T0)


title: Rpn1 LPS 6 hours (Rpn1..MGLibB_46290T6)


title: Rnf31 LPS 4 hours (Rnf31..MGLibB_45942nnT4)


title: Rnf31 LPS 2 hours (Rnf31..MGLibB_45942nnT2)


title: Rnf31 No LPS (Rnf31..MGLibB_45942nnT0)


title: Rnf31 LPS 6 hours (Rnf31..MGLibB_45941T6)


title: Rnf31 LPS 2 hours (Rnf31..MGLibB_45943T2)


title: Rnf31 LPS 4 hours (Rnf31..MGLibB_45941T4)


title: Rnf31 LPS 2 hours (Rnf31..MGLibB_45941T2)


title: Rnf128 No LPS (Rnf128..MGLibA_45802T0)


title: Rnf128 LPS 4 hours (Rnf128..MGLibA_45802T4)


title: Rnf31 No LPS (Rnf31..MGLibB_45941T0)


title: Rnf128 LPS 6 hours (Rnf128..MGLibA_45802T6)


title: Rnf128 LPS 2 hours (Rnf128..MGLibA_45802T2)


title: Rfwd2 LPS 6 hours (Rfwd2..MGLibA_45219T6)


title: Rfwd2 LPS 2 hours (Rfwd2..MGLibA_45219T2)


title: Rfwd2 LPS 4 hours (Rfwd2..MGLibA_45219T4)


title: Rfwd2 LPS 6 hours (Rfwd2..MGLibA_45221nnT6)


title: Rela LPS 6 hours (Rela..MGLibB_45061T6)

value: Rela


title: Rela LPS 4 hours (Rela..MGLibB_45061T4)


title: Rfwd2 No LPS (Rfwd2..MGLibA_45219T0)


title: Rela LPS 2 hours (Rela..MGLibB_45061T2)


title: Rela LPS 6 hours (Rela..MGLibA_45073T6)


title: Rela LPS 4 hours (Rela..MGLibA_45073T4)


title: Rnf31 LPS 6 hours (Rnf31..MGLibB_45942nnT6)


title: Rela No LPS (Rela..MGLibB_45061T0)


title: Rela No LPS (Rela..MGLibA_45073T0)


title: Rela LPS 2 hours (Rela..MGLibA_45073T2)


title: Rc3h1 LPS 4 hours (Rc3h1..MGLibA_44912T4)


title: Rc3h1 No LPS (Rc3h1..MGLibA_44912T0)


title: Rc3h1 LPS 6 hours (Rc3h1..MGLibA_44912T6)


title: Rc3h1 LPS 6 hours (Rc3h1..MGLibA_44910T6)


title: Rc3h1 LPS 2 hours (Rc3h1..MGLibA_44912T2)


title: Rfwd2 LPS 4 hours (Rfwd2..MGLibA_45221nnT4)


title: Rc3h1 LPS 2 hours (Rc3h1..MGLibA_44910T2)


title: Rbx1 LPS 4 hours (Rbx1..MGLibB_44894T4)


title: Rbm27 LPS 6 hours (Rbm27..MGLibA_44791T6)


title: Rbx1 No LPS (Rbx1..MGLibB_44894T0)


title: Rbx1 LPS 6 hours (Rbx1..MGLibB_44894T6)


title: Rbm27 No LPS (Rbm27..MGLibA_44791T0)


title: Rbm27 LPS 2 hours (Rbm27..MGLibA_44791T2)


title: Rc3h1 No LPS (Rc3h1..MGLibA_44910T0)


title: Rbm27 LPS 4 hours (Rbm27..MGLibA_44791T4)


title: Rbck1 LPS 2 hours (Rbck1..MGLibB_44707snnT2)


title: Rbck1 LPS 4 hours (Rbck1..MGLibB_44707snnT4)


title: Rbck1 No LPS (Rbck1..MGLibB_44707snnT0)


title: Rbck1 No LPS (Rbck1..MGLibB_44706T0)


title: Rbck1 LPS 4 hours (Rbck1..MGLibB_44706T4)


title: Rara LPS 6 hours (Rara..MGLibB_44539T6)

value: Rara


title: Rara LPS 4 hours (Rara..MGLibB_44539T4)


title: Rbck1 LPS 2 hours (Rbck1..MGLibB_44706T2)


title: Rara LPS 2 hours (Rara..MGLibB_44539T2)


title: Rara No LPS (Rara..MGLibB_44539T0)


title: Rara LPS 6 hours (Rara..MGLibB_44538T6)


title: Rc3h1 LPS 4 hours (Rc3h1..MGLibA_44910T4)


title: Rara No LPS (Rara..MGLibB_44538T0)


title: Rara LPS 4 hours (Rara..MGLibB_44538T4)


title: Rara LPS 2 hours (Rara..MGLibB_44538T2)


title: Prpf40a LPS 4 hours (Prpf40a..MGLibB_43005nnT4)


title: Prpf40a LPS 6 hours (Prpf40a..MGLibB_43005nnT6)


title: Polr2j LPS 6 hours (Polr2j..MGLibA_41911snnT6)


title: Polr2j LPS 4 hours (Polr2j..MGLibA_41911snnT4)


title: Polr2j LPS 2 hours (Polr2j..MGLibA_41911snnT2)


title: Rbck1 LPS 6 hours (Rbck1..MGLibB_44707snnT6)


title: Rbck1 LPS 6 hours (Rbck1..MGLibB_44706T6)


title: Rbx1 LPS 2 hours (Rbx1..MGLibB_44894T2)


title: Polr2g LPS 2 hours (Polr2g..MGLibA_41904nnT2)


title: Polr2j No LPS (Polr2j..MGLibA_41911snnT0)


title: Polr2g LPS 4 hours (Polr2g..MGLibA_41904nnT4)


title: Polr2g LPS 4 hours (Polr2g..MGLibA_41903T4)


title: Polr2g LPS 6 hours (Polr2g..MGLibA_41903T6)


title: Polr2g LPS 2 hours (Polr2g..MGLibA_41903T2)


title: Paf1 LPS 6 hours (Paf1..MGLibB_39314T6)


title: Pla2g7 No LPS (Pla2g7..MGLibB_41260T0)


title: Polr2g LPS 6 hours (Polr2g..MGLibA_41904nnT6)


title: Paf1 LPS 4 hours (Paf1..MGLibB_39314T4)


title: Paf1 No LPS (Paf1..MGLibB_39314T0)


title: Paf1 LPS 6 hours (Paf1..MGLibA_39326T6)


title: Paf1 LPS 2 hours (Paf1..MGLibA_39326T2)


title: Paf1 LPS 2 hours (Paf1..MGLibB_39314T2)


title: Paf1 LPS 4 hours (Paf1..MGLibA_39326T4)


title: Pabpc1 LPS 4 hours (Pabpc1..MGLibA_39265T4)


title: Pabpc1 LPS 6 hours (Pabpc1..MGLibA_39265T6)


title: Paf1 No LPS (Paf1..MGLibA_39326T0)


title: Pabpc1 LPS 2 hours (Pabpc1..MGLibA_39265T2)


title: Pabpc1 No LPS (Pabpc1..MGLibA_39265T0)


title: NonTargetingControlGuideForMouse_9 LPS 2 hours (NonTargetingControlGuideForMouse_9..MGLibA_66458T2)


title: NonTargetingControlGuideForMouse_9 LPS 4 hours (NonTargetingControlGuideForMouse_9..MGLibA_66458T4)


title: NonTargetingControlGuideForMouse_9 LPS 6 hours (NonTargetingControlGuideForMouse_9..MGLibA_66458T6)


title: NonTargetingControlGuideForMouse_9 No LPS (NonTargetingControlGuideForMouse_9..MGLibA_66458T0)


title: Polr2g No LPS (Polr2g..MGLibA_41904nnT0)


title: NonTargetingControlGuideForMouse_9 LPS 6 hours (NonTargetingControlGuideForMouse_9..MGLibA_66456T6)


title: NonTargetingControlGuideForMouse_9 No LPS (NonTargetingControlGuideForMouse_9..MGLibA_66456T0)


title: NonTargetingControlGuideForMouse_9 LPS 4 hours (NonTargetingControlGuideForMouse_9..MGLibA_66456T4)


title: NonTargetingControlGuideForMouse_9 LPS 2 hours (NonTargetingControlGuideForMouse_9..MGLibA_66456T2)


title: NonTargetingControlGuideForMouse_9 LPS 6 hours (NonTargetingControlGuideForMouse_9..MGLibA_66454T6)


title: NonTargetingControlGuideForMouse_9 No LPS (NonTargetingControlGuideForMouse_9..MGLibA_66454T0)


title: NonTargetingControlGuideForMouse_9 LPS 4 hours (NonTargetingControlGuideForMouse_9..MGLibA_66454T4)


title: NonTargetingControlGuideForMouse_9 LPS 2 hours (NonTargetingControlGuideForMouse_9..MGLibA_66454T2)


title: NonTargetingControlGuideForMouse_68 LPS 2 hours (NonTargetingControlGuideForMouse_68..MGLibA_66813T2)


title: NonTargetingControlGuideForMouse_68 LPS 6 hours (NonTargetingControlGuideForMouse_68..MGLibA_66813T6)


title: NonTargetingControlGuideForMouse_68 No LPS (NonTargetingControlGuideForMouse_68..MGLibA_66813T0)


title: NonTargetingControlGuideForMouse_68 LPS 4 hours (NonTargetingControlGuideForMouse_68..MGLibA_66811T4)


title: NonTargetingControlGuideForMouse_68 LPS 6 hours (NonTargetingControlGuideForMouse_68..MGLibA_66811T6)


title: NonTargetingControlGuideForMouse_68 LPS 2 hours (NonTargetingControlGuideForMouse_68..MGLibA_66811T2)


title: NonTargetingControlGuideForMouse_68 No LPS (NonTargetingControlGuideForMouse_68..MGLibA_66811T0)


title: NonTargetingControlGuideForMouse_64 LPS 6 hours (NonTargetingControlGuideForMouse_64nnT6)


title: NonTargetingControlGuideForMouse_64 LPS 4 hours (NonTargetingControlGuideForMouse_64nnT4)


title: NonTargetingControlGuideForMouse_64 LPS 4 hours (NonTargetingControlGuideForMouse_64..MGLibA_66784T4)


title: NonTargetingControlGuideForMouse_64 LPS 2 hours (NonTargetingControlGuideForMouse_64snnT2)


title: NonTargetingControlGuideForMouse_100 LPS 4 hours (NonTargetingControlGuideForMouse_100nnT4)


title: NonTargetingControlGuideForMouse_100 LPS 2 hours (NonTargetingControlGuideForMouse_100nnT2)


title: NonTargetingControlGuideForMouse_64 LPS 2 hours (NonTargetingControlGuideForMouse_64..MGLibA_66784T2)


title: NonTargetingControlGuideForMouse_100 LPS 4 hours (NonTargetingControlGuideForMouse_100..MGLibA_67005T4)


title: NonTargetingControlGuideForMouse_64 No LPS (NonTargetingControlGuideForMouse_64..MGLibA_66784T0)


title: NonTargetingControlGuideForMouse_100 LPS 6 hours (NonTargetingControlGuideForMouse_100..MGLibA_67005T6)


title: NonTargetingControlGuideForMouse_100 No LPS (NonTargetingControlGuideForMouse_100nnT0)


title: NonTargetingControlGuideForMouse_100 LPS 6 hours (NonTargetingControlGuideForMouse_100nnT6)


title: NonTargetingControlGuideForMouse_100 LPS 6 hours (NonTargetingControlGuideForMouse_100..MGLibA_67004T6)


title: NonTargetingControlGuideForMouse_100 LPS 2 hours (NonTargetingControlGuideForMouse_100..MGLibA_67005T2)


title: NonTargetingControlGuideForMouse_100 No LPS (NonTargetingControlGuideForMouse_100..MGLibA_67005T0)


title: NonTargetingControlGuideForMouse_100 LPS 6 hours (NonTargetingControlGuideForMouse_100..MGLibA_67001T6)


title: NonTargetingControlGuideForMouse_100 No LPS (NonTargetingControlGuideForMouse_100..MGLibA_67004T0)


title: NonTargetingControlGuideForMouse_100 LPS 4 hours (NonTargetingControlGuideForMouse_100..MGLibA_67004T4)


title: NonTargetingControlGuideForMouse_100 LPS 2 hours (NonTargetingControlGuideForMouse_100..MGLibA_67001T2)


title: NonTargetingControlGuideForMouse_100 LPS 4 hours (NonTargetingControlGuideForMouse_100..MGLibA_67001T4)


title: NonTargetingControlGuideForMouse_100 LPS 2 hours (NonTargetingControlGuideForMouse_100..MGLibA_67004T2)


title: NonTargetingControlGuideForMouse_100 LPS 2 hours (NonTargetingControlGuideForMouse_100..MGLibA_67000T2)


title: NonTargetingControlGuideForMouse_100 LPS 4 hours (NonTargetingControlGuideForMouse_100..MGLibA_67000T4)


title: NonTargetingControlGuideForMouse_100 LPS 6 hours (NonTargetingControlGuideForMouse_100..MGLibA_67000T6)


title: NonTargetingControlGuideForMouse_64 LPS 6 hours (NonTargetingControlGuideForMouse_64..MGLibA_66784T6)


title: NonTargetingControlGuideForMouse_100 No LPS (NonTargetingControlGuideForMouse_100..MGLibA_67000T0)


title: NonTargetingControlGuideForMouse_100 No LPS (NonTargetingControlGuideForMouse_100..MGLibA_67001T0)


title: Nf1 LPS 2 hours (Nf1..MGLibA_33836T2)


title: Nf1 LPS 6 hours (Nf1..MGLibA_33836T6)


title: Nf1 No LPS (Nf1..MGLibA_33836T0)


title: Myd88 LPS 4 hours (Myd88..MGLibB_32799T4)


title: Nf1 LPS 4 hours (Nf1..MGLibA_33836T4)


title: Myd88 LPS 6 hours (Myd88..MGLibA_32810T6)


title: Myd88 No LPS (Myd88..MGLibB_32799T0)


title: Myd88 LPS 6 hours (Myd88..MGLibB_32799T6)


title: Myd88 LPS 4 hours (Myd88..MGLibA_32810T4)


title: Myd88 LPS 2 hours (Myd88..MGLibA_32810T2)


title: Mapkapk2 LPS 6 hours (Mapkapk2..MGLibA_30388T6)


title: Mapkapk2 No LPS (Mapkapk2..MGLibA_30388T0)


title: Mapkapk2 LPS 4 hours (Mapkapk2..MGLibA_30388T4)


title: Mapkapk2 LPS 2 hours (Mapkapk2..MGLibA_30388T2)


title: Map3k8 LPS 6 hours (Map3k8..MGLibB_30280nnT6)


title: Map3k8 LPS 4 hours (Map3k8..MGLibB_30280nnT4)


title: Map3k8 No LPS (Map3k8..MGLibB_30280nnT0)


title: Map3k8 LPS 2 hours (Map3k8..MGLibB_30280nnT2)


title: Ly96 LPS 6 hours (Ly96..MGLibB_29810T6)


title: Ly96 LPS 4 hours (Ly96..MGLibB_29810snnT4)


title: Ly96 No LPS (Ly96..MGLibB_29810T0)


title: Ly96 No LPS (Ly96..MGLibB_29809T0)


title: Ly96 LPS 2 hours (Ly96..MGLibB_29809T2)


title: Ly96 LPS 4 hours (Ly96..MGLibB_29809T4)


title: Ly96 LPS 6 hours (Ly96..MGLibB_29809T6)


title: Lrrc63 LPS 6 hours (Lrrc63..MGLibB_29514T6)


title: Lrrc63 LPS 4 hours (Lrrc63..MGLibB_29514T4)


title: Lrrc63 LPS 2 hours (Lrrc63..MGLibB_29514T2)


title: Lrrc63 No LPS (Lrrc63..MGLibB_29513T0)


title: Lrrc63 LPS 6 hours (Lrrc63..MGLibB_29513T6)


title: Lrrc63 No LPS (Lrrc63..MGLibB_29514T0)


title: Lmbrd1 LPS 6 hours (Lmbrd1..MGLibB_29075T6)


title: Lrrc63 LPS 2 hours (Lrrc63..MGLibB_29513T2)


title: Lmbrd1 LPS 2 hours (Lmbrd1..MGLibB_29075T2)


title: Myd88 LPS 2 hours (Myd88..MGLibB_32799T2)


title: Lmbrd1 No LPS (Lmbrd1..MGLibB_29075T0)


title: Leo1 LPS 4 hours (Leo1..MGLibB_28750T4)


title: Ly96 LPS 2 hours (Ly96..MGLibB_29810T2)


title: Lmbrd1 LPS 4 hours (Lmbrd1..MGLibB_29075T4)


title: Leo1 No LPS (Leo1..MGLibB_28750T0)


title: Kcnc1 LPS 6 hours (Kcnc1..MGLibB_26880snnT6)


title: Leo1 No LPS (Leo1..MGLibA_28761T0)


title: Leo1 LPS 6 hours (Leo1..MGLibA_28761T6)


title: Leo1 LPS 2 hours (Leo1..MGLibA_28761T2)


title: Leo1 LPS 4 hours (Leo1..MGLibA_28761T4)


title: Leo1 LPS 6 hours (Leo1..MGLibB_28750T6)


title: Myd88 No LPS (Myd88..MGLibA_32810T0)


title: Lrrc63 LPS 4 hours (Lrrc63..MGLibB_29513T4)


title: Kcnc1 LPS 2 hours (Kcnc1..MGLibB_26880snnT2)


title: Jak2 LPS 6 hours (Jak2..MGLibA_26654T6)


title: Jak2 LPS 4 hours (Jak2..MGLibA_26654T4)


title: Jak2 LPS 2 hours (Jak2..MGLibA_26654T2)


title: Ikzf1 LPS 6 hours (Ikzf1..MGLibA_25669T6)


title: Ikzf1 LPS 4 hours (Ikzf1..MGLibA_25669T4)


title: Ikzf1 No LPS (Ikzf1..MGLibA_25669T0)


title: Ikzf1 LPS 2 hours (Ikzf1..MGLibA_25669T2)


title: Ikbkg No LPS (Ikbkg..MGLibA_25667T0)

value: Ikbkg


title: Ikbkg LPS 6 hours (Ikbkg..MGLibA_25667T6)


title: Ikbkg LPS 2 hours (Ikbkg..MGLibA_25667T2)


title: Ikbkg LPS 4 hours (Ikbkg..MGLibA_25667T4)


title: Ikbkb LPS 6 hours (Ikbkb..MGLibB_25653T6)


title: Ikbkb LPS 2 hours (Ikbkb..MGLibB_25653T2)


title: Ikbkb LPS 4 hours (Ikbkb..MGLibB_25653T4)


title: Kcnc1 LPS 4 hours (Kcnc1..MGLibB_26880snnT4)


title: Ikbkb No LPS (Ikbkb..MGLibB_25653T0)


title: Ikbkb LPS 6 hours (Ikbkb..MGLibA_25660T6)


title: Ikbkb LPS 2 hours (Ikbkb..MGLibA_25660T2)


title: Ikbkb No LPS (Ikbkb..MGLibA_25660T0)


title: Ikbkb LPS 4 hours (Ikbkb..MGLibA_25660T4)


title: Hsp90b1 LPS 6 hours (Hsp90b1..MGLibB_25001T6)


title: Hsp90b1 LPS 4 hours (Hsp90b1..MGLibB_25001T4)


title: Jak2 No LPS (Jak2..MGLibA_26654T0)


title: Hsp90b1 LPS 6 hours (Hsp90b1..MGLibA_25010T6)


title: Hsp90b1 LPS 2 hours (Hsp90b1..MGLibB_25001T2)


title: Hsp90b1 LPS 4 hours (Hsp90b1..MGLibA_25010T4)


title: Hsp90b1 No LPS (Hsp90b1..MGLibB_25001T0)


title: Hsp90b1 LPS 2 hours (Hsp90b1..MGLibA_25010T2)


title: Hsp90b1 No LPS (Hsp90b1..MGLibA_25010T0)


title: Gtf2h1 LPS 6 hours (Gtf2h1..MGLibB_23250snnT6)


title: Gtf2h1 LPS 4 hours (Gtf2h1..MGLibB_23250snnT4)


title: Leo1 LPS 2 hours (Leo1..MGLibB_28750T2)


title: Gtf2h1 LPS 2 hours (Gtf2h1..MGLibB_23250snnT2)


title: Gtf2h1 No LPS (Gtf2h1..MGLibB_23250snnT0)


title: Gtf2b LPS 4 hours (Gtf2b..MGLibB_23236snnT4)


title: Gpkow LPS 4 hours (Gpkow..MGLibB_22495snnT4)


title: Gtf2b LPS 2 hours (Gtf2b..MGLibB_23236snnT2)


title: Gpkow No LPS (Gpkow..MGLibB_22495snnT0)


title: Gpkow LPS 2 hours (Gpkow..MGLibB_22495snnT2)


title: Git2 LPS 6 hours (Git2GPP1snnT6)


title: Gpkow LPS 6 hours (Gpkow..MGLibB_22495snnT6)


title: Git2 LPS 2 hours (Git2GPP1snnT2)


title: Git2 No LPS (Git2GPP1snnT0)


title: Gabpb1 LPS 6 hours (Gabpb1..MGLibB_19241T6)


title: Gabpb1 No LPS (Gabpb1..MGLibB_19241T0)


title: Gabpb1 LPS 4 hours (Gabpb1..MGLibB_19241T4)


title: Gabpb1 LPS 6 hours (Gabpb1..MGLibA_19247snnT6)


title: Gabpb1 LPS 2 hours (Gabpb1..MGLibB_19241T2)


title: Gabpb1 LPS 2 hours (Gabpb1..MGLibA_19247snnT2)


title: Gtf2b LPS 6 hours (Gtf2b..MGLibB_23236snnT6)


title: Fam96b LPS 6 hours (Fam96b..MGLibA_17729nnT6)


title: Fam96b LPS 4 hours (Fam96b..MGLibA_17729nnT4)


title: Fam96b No LPS (Fam96b..MGLibA_17729nnT0)


title: Fam96b LPS 2 hours (Fam96b..MGLibA_17729nnT2)


title: Gabpb1 LPS 4 hours (Gabpb1..MGLibA_19247snnT4)


title: Eif5 LPS 6 hours (Eif5..MGLibB_15898T6)


title: Eif5 LPS 4 hours (Eif5..MGLibB_15898T4)


title: Eif5 No LPS (Eif5..MGLibB_15898T0)


title: Git2 LPS 4 hours (Git2GPP1snnT4)


title: Eif5 LPS 2 hours (Eif5..MGLibA_15906T2)


title: Dnttip1 LPS 4 hours (Dnttip1..MGLibB_14644T4)


title: Dnttip1 LPS 6 hours (Dnttip1..MGLibA_14650T6)


title: Dnttip1 No LPS (Dnttip1..MGLibB_14644T0)


title: Dnttip1 LPS 2 hours (Dnttip1..MGLibA_14650T2)


title: Dnttip1 LPS 4 hours (Dnttip1..MGLibA_14650T4)


title: Dmrta1 LPS 6 hours (Dmrta1..MGLibB_14349snnT6)


title: Dhx15 LPS 6 hours (Dhx15..MGLibB_14095T6)


title: Eif5 LPS 2 hours (Eif5..MGLibB_15898T2)


title: Dmrta1 No LPS (Dmrta1..MGLibB_14349snnT0)


title: Dmrta1 LPS 2 hours (Dmrta1..MGLibB_14349snnT2)


title: Dhx15 LPS 4 hours (Dhx15..MGLibB_14095T4)


title: Dhx15 LPS 2 hours (Dhx15..MGLibB_14095T2)


title: P3_H8

molecule: other

organism: synthetic construct

source_name: empty well

value: empty well (negative control)


title: Dhx15 LPS 4 hours (Dhx15..MGLibB_14094snnT4)


title: P3_H9


title: P3_H7


title: Dhx15 LPS 6 hours (Dhx15..MGLibB_14094snnT6)


title: Eif5 No LPS (Eif5..MGLibA_15906T0)


title: Dmrta1 LPS 4 hours (Dmrta1..MGLibB_14349snnT4)


title: Dhx15 LPS 6 hours (Dhx15..MGLibA_14101T6)


title: Eif5 LPS 4 hours (Eif5..MGLibA_15906T4)


title: Dhx15 LPS 4 hours (Dhx15..MGLibA_14101T4)


title: P3_G12


title: Dhx15 No LPS (Dhx15..MGLibB_14095T0)


title: Dnttip1 LPS 6 hours (Dnttip1..MGLibB_14644T6)


title: P3_G10


title: P3_G11


title: Dnttip1 LPS 2 hours (Dnttip1..MGLibB_14644T2)


title: Dnttip1 No LPS (Dnttip1..MGLibA_14650T0)


title: P3_G9


title: Dhx15 No LPS (Dhx15..MGLibA_14101T0)


title: P3_G8


title: P3_G7


title: Ddx39b LPS 4 hours (Ddx39b..MGLibA_13615snnT4)


title: Dhx15 No LPS (Dhx15..MGLibB_14094snnT0)


title: Ddx10 LPS 6 hours (Ddx10..MGLibB_13565T6)


title: P3_F12


title: Ddx39b No LPS (Ddx39b..MGLibA_13615snnT0)


title: Ddx39b LPS 2 hours (Ddx39b..MGLibA_13615snnT2)


title: P3_F9


title: P3_F8


title: P3_F7


title: Ddx10 No LPS (Ddx10..MGLibB_13565T0)


title: Ddost LPS 2 hours (Ddost..MGLibB_13547T2)


title: Ddost No LPS (Ddost..MGLibB_13545T0)


title: Ddx10 LPS 2 hours (Ddx10..MGLibB_13565T2)


title: Ddx10 LPS 4 hours (Ddx10..MGLibB_13565T4)


title: Ddost LPS 6 hours (Ddost..MGLibB_13547T6)


title: Ddost No LPS (Ddost..MGLibB_13547T0)


title: Ddost LPS 2 hours (Ddost..MGLibA_13550nnT2)


title: Ddost LPS 2 hours (Ddost..MGLibB_13545T2)


title: Ddost LPS 4 hours (Ddost..MGLibB_13545T4)


title: Ddost LPS 6 hours (Ddost..MGLibA_13550nnT6)


title: Ddost LPS 4 hours (Ddost..MGLibA_13550nnT4)


title: Dhx15 LPS 2 hours (Dhx15..MGLibA_14101T2)


title: Ddost No LPS (Ddost..MGLibA_13550nnT0)


title: Ddx39b LPS 6 hours (Ddx39b..MGLibA_13615snnT6)


title: P3_F10


title: Dad1 LPS 2 hours (Dad1..MGLibB_13229T2)


title: P3_F11


title: Dad1 No LPS (Dad1..MGLibB_13229T0)


title: Dad1 LPS 6 hours (Dad1..MGLibB_13228T6)


title: Dad1 LPS 4 hours (Dad1..MGLibB_13228T4)


title: Dad1 No LPS (Dad1..MGLibB_13228T0)


title: Cyp2c40 LPS 6 hours (Cyp2c40..MGLibB_12784T6)


title: Cyp2c40 LPS 2 hours (Cyp2c40..MGLibB_12784T2)


title: Cyp2c40 No LPS (Cyp2c40..MGLibB_12784T0)


title: Cyp2c40 LPS 4 hours (Cyp2c40..MGLibB_12784T4)


title: DNaseHiC-WG-brain-rep1

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: DNase Hi-C experiment in F1 hybrid mouse brain cells

data_processing:
First, we performed an exhaustive search and cleaning of the Illumina primer and adaptor sequences in the full-length reads and extracted the remaining read fragments of various lengths from 25-80 bp.
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger) into the BL6 reference genome.
We then mapped each end of these cleaned paired-end reads separately to the C57BL/6J genome (mm9 assembly) and the pseudo-spretus genome using BWA/v0.5.9. We only retained the reads that mapped uniquely, allowing at most 3 mismatches and requiring mapping quality MAPQ >= 30. Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
To eliminate the bias due to the PCR duplication step, we removed redundant paired-end reads. We define two reads as redundant if both ends of the reads are mapped to identical locations in the genome.
Genome_build: mm9
Supplementary_files_format_and_content: txt files, containing uniquely mapped and non-redundent read pairs. The files are tab-delimited. The columns are #1 read identifier, #2 strand of the 1st end, #3 mapped chr of the 1st end, #4 mapped coordinate of the 1st end, #5 allele of 1st read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #6 sequence of 1st end, #7 strand of the 2nd end, #8 mapped chr of the 2nd end, #9 mapped coordinate of the 2nd end, #10 allele of 2nd read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #11 sequence of 2nd end.

organism: Mus musculus x Mus spretus

source_name: brain cells

extract_protocol: DNase Hi-C or in situ DNase Hi-C:  Cells are cross-linked with formaldehyde; chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor; and proximity ligation is carried out inside individual nuclei to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is created by shearing the DNA and selecting the biotin-containing fragments with streptavidin magnetic beads. After linear library amplification, a DNase Hi-C library is generated and can be sequenced to identify whole-genome chromatin contacts.

tag: experiment

value: DNase Hi-C

tag: replicate


title: xenograft lung adenocarcinoma tissue

city: Seoul

first: Kyu-Tae

last: Kim

address: Irwon-Ro 81

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

data_processing:
RNA-Seq reads were filtered out according to the read quality less than Q33 by using Trimmomatic (Bolger et al., Bioinformatics 2014) and then aligned to the human genome reference (hg19) using Tophat2 (Kim et al., Genome Biology 2013).
FPKM (fragments per kilo bases of exons for per million mapped reads) was estimated from Cufflinks (Trapnell et al., Nature Biotechnology 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Each processed file was originally named as genes.fpkm_tacking from running Cufflinks.

source_name: PDX, LADC_tissue

growth_protocol: Animal experiments were conducted in accordance with the Institute for Laboratory Animal Research Guide for the Care and Use of Laboratory Animals and within the protocols approved by the appropriate IRB at the Samsung Medical Center. Xenograft tumor specimens were dissociated into single cells. Dissociated cells were cultured in neurobasal media-A supplemented with N2 (×1/2), B27 (×1/2) (GIBCO, Carlsbad, CA), bFGF/EGF (25ng/ml each), neuregulin 1 (hNRG1, 10ng/ml), and long-insulin growth factor 1 (IGF1, 100ng/ml) (R&D Systems, Minneapolis, MN). As spheres appeared in suspension culture conditions, they were dissociated with accutase (PAA Laboratories GmbH, Cölbe, Germany) and expanded by reseeding.

extract_protocol:
Bulk RNA was extracted from each tissue using RNeasy Mini kit (QIAGEN, CA, USA) and amplified using a SMARTer kit (Clontech, CA, USA) with 10 ng of starting material.
Libraries were prepared using the Nextera XT DNA Sample Prep Kit (Illumina, CA, USA) following the manufacturer’s instruction, assayed the quantity and quality, pooled, and then sequenced on the HiSeq 2500 (Illumina) using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina) at the Samsung Genome Institute (Seoul, Korea).

tag: tissue

value: lung

tag: disease status

value: adenocarcinoma

tag: host

value: mouse


title: Cyp2c40 No LPS (Cyp2c40..MGLibA_12787T0)


title: P3_H6

source_name: hiF-T cells

tag: reprogramming time point (day)

value: 1 uM ROCK inhibitor


title: Cyp2c40 LPS 4 hours (Cyp2c40..MGLibA_12787T4)


title: Cul3 LPS 2 hours (Cul3..MGLibB_12472T2)


title: Cul3 No LPS (Cul3..MGLibB_12472T0)


title: Cyp2c40 LPS 6 hours (Cyp2c40..MGLibA_12787T6)

value: LPS  6 hours


title: Cul3 LPS 6 hours (Cul3..MGLibB_12472T6)


title: Cul3 LPS 4 hours (Cul3..MGLibB_12472T4)


title: Cyp2c40 LPS 2 hours (Cyp2c40..MGLibA_12787T2)


title: matched normal lung tissue from a patient

source_name: Pt, normal_tissue

value: normal


title: Dad1 LPS 6 hours (Dad1..MGLibB_13229T6)


title: Dad1 LPS 4 hours (Dad1..MGLibB_13229T4)


title: P3_H5

value: 0.1 uM LSD1 inhibitor


title: Cul3 LPS 4 hours (Cul3..MGLibA_12475T4)

value: BMDC


title: P3_H4

value: control


title: Cul3 LPS 2 hours (Cul3..MGLibA_12475T2)


title: P3_H3


title: Dad1 LPS 2 hours (Dad1..MGLibB_13228T2)


title: P3_H2


title: Cul3 No LPS (Cul3..MGLibA_12475T0)

value: No LPS


title: Ctr9 LPS 6 hours (Ctr9..MGLibB_12353T6)


title: Ctr9 LPS 4 hours (Ctr9..MGLibB_12353T4)

value: LPS  4 hours


title: P3_H1


title: Ctr9 No LPS (Ctr9..MGLibB_12353T0)


title: P3_G6


title: Cul3 LPS 6 hours (Cul3..MGLibA_12475T6)


title: P3_G5


title: Ctr9 LPS 6 hours (Ctr9..MGLibA_12357T6)


title: P3_G2


title: P3_G3


title: P3_G1


title: P3_G4


title: P3_F4


title: Ctcf No LPS (Ctcf..MGLibA_12273T0)

value: Ctcf


title: Ctr9 LPS 4 hours (Ctr9..MGLibA_12357T4)


title: P3_F3


title: Ctcf LPS 2 hours (Ctcf..MGLibA_12273T2)

value: LPS  2 hours


title: Ctcf LPS 6 hours (Ctcf..MGLibA_12273T6)


title: P3_F5


title: Ctcf LPS 4 hours (Ctcf..MGLibA_12273T4)


title: P3_F6


title: P3_F2


title: Ctr9 LPS 2 hours (Ctr9..MGLibA_12357T2)


title: P3_F1


title: Cebpb LPS 4 hours (Cebpb..MGLibB_09726T4)

value: Cebpb


title: Cldn7 LPS 2 hours (Cldn7..MGLibB_10673T2)


title: Cebpb LPS 2 hours (Cebpb..MGLibB_09726T2)


title: Cebpb LPS 6 hours (Cebpb..MGLibB_09726T6)


title: Ctr9 LPS 2 hours (Ctr9..MGLibB_12353T2)


title: P3_E11


title: Cebpb No LPS (Cebpb..MGLibB_09726T0)


title: Cebpb LPS 6 hours (Cebpb..MGLibA_09728T6)


title: Ctr9 No LPS (Ctr9..MGLibA_12357T0)


title: P3_E9


title: P3_E8


title: Cebpb No LPS (Cebpb..MGLibA_09728T0)


title: Cd14 LPS 4 hours (Cd14..MGLibB_08998T4)


title: P3_E7


title: Cd14 LPS 6 hours (Cd14..MGLibB_08998T6)


title: Cebpb LPS 2 hours (Cebpb..MGLibA_09728T2)


title: P3_E5


title: P3_E6


title: Cd14 No LPS (Cd14..MGLibB_08998T0)


title: Cd14 LPS 6 hours (Cd14..MGLibA_08997T6)


title: P3_E4


title: P3_E1


title: P3_E2


title: Cd14 LPS 2 hours (Cd14..MGLibB_08998T2)


title: P3_E12


title: P3_E3


title: Cd14 LPS 4 hours (Cd14..MGLibA_08997T4)


title: P3_D12


title: Cd14 No LPS (Cd14..MGLibA_08997T0)


title: Cd14 LPS 2 hours (Cd14..MGLibA_08997T2)


title: P3_D10


title: P3_D11


title: P3_E10


title: BC023829 LPS 6 hours (BC023829..MGLibA_06281T6)


title: Cebpb LPS 4 hours (Cebpb..MGLibA_09728T4)


title: P3_D7


title: BC023829 LPS 2 hours (BC023829..MGLibA_06281T2)


title: P3_D8


title: BC023829 LPS 4 hours (BC023829..MGLibA_06281T4)


title: P3_D6


title: Atp2b3 LPS 6 hours (Atp2b3..MGLibA_05779T6)


title: BC023829 No LPS (BC023829..MGLibA_06281T0)


title: Atp2b3 LPS 2 hours (Atp2b3..MGLibA_05779T2)


title: P3_D5


title: P3_D4


title: Atp2b3 No LPS (Atp2b3..MGLibA_05779T0)


title: Ash2l No LPS (Ash2l..MGLibB_05467snnT0)


title: Ash2l LPS 4 hours (Ash2l..MGLibB_05467snnT4)


title: Ash2l LPS 2 hours (Ash2l..MGLibB_05467snnT2)


title: Ash2l LPS 6 hours (Ash2l..MGLibB_05467snnT6)


title: P3_D1


title: P3_C11


title: P3_D2


title: P3_C12


title: P3_C9


title: Ash2l LPS 4 hours (Ash2l..MGLibA_05466T4)


title: P3_C10


title: Ash2l LPS 4 hours (Ash2l..MGLibA_05467T4)


title: Ash2l LPS 2 hours (Ash2l..MGLibA_05466T2)


title: P3_C8


title: P3_C7


title: P3_D9


title: P3_C6


title: Ash2l No LPS (Ash2l..MGLibA_05466T0)


title: P3_C5


title: Alg2 LPS 6 hours (Alg2..MGLibB_03837snnT6)


title: P3_C4


title: P3_D3


title: P3_C3


title: Alg2 LPS 2 hours (Alg2..MGLibB_03837snnT2)


title: Alg2 LPS 4 hours (Alg2..MGLibB_03837snnT4)


title: Alg2 No LPS (Alg2..MGLibB_03837snnT0)


title: P3_C1


title: Akirin2 LPS 4 hours (Akirin2..MGLibA_03653snnT4)


title: P3_B12


title: P3_B11


title: Akirin2 LPS 2 hours (Akirin2..MGLibA_03653snnT2)


title: Actb LPS 6 hours (Actb..MGLibB_02797T6)

value: Actb


title: Akirin2 No LPS (Akirin2..MGLibA_03653snnT0)


title: Actb LPS 2 hours (Actb..MGLibB_02797T2)


title: P3_B7


title: P3_B9


title: P3_B10


title: Actb LPS 6 hours (Actb..MGLibB_02796T6)


title: Actb LPS 4 hours (Actb..MGLibB_02797T4)


title: P3_B5


title: P3_B6


title: Ash2l LPS 6 hours (Ash2l..MGLibA_05467T6)


title: P3_B8


title: P3_B4


title: P3_C2


title: Actb LPS 2 hours (Actb..MGLibB_02796T2)


title: Actb No LPS (Actb..MGLibB_02797T0)


title: Actb LPS 4 hours (Actb..MGLibB_02796T4)


title: P3_B3


title: P3_B2


title: Akirin2 LPS 6 hours (Akirin2..MGLibA_03653snnT6)


title: A20 LPS 6 hours (A20T6)


title: Actb No LPS (Actb..MGLibB_02796T0)


title: P3_A12


title: A20 LPS 4 hours (A20T4)


title: A20 No LPS (A20T0)


title: P3_B1


title: P3_A9


title: A20 LPS 2 hours (A20T2)


title: P3_A10


title: P3_A5


title: P3_A11


title: A20 LPS 6 hours (A20-1T6)


title: P3_A7


title: P3_A8


title: P3_A3


title: A20 No LPS (A20-1T0)


title: P3_A6


title: A20 LPS 4 hours (A20-1T4)


title: 0610009D07Rik LPS 4 hours (0610009D07Rik..MGLibA_00009snnT4)


title: P3_A4


title: 0610009D07Rik LPS 2 hours (0610009D07Rik..MGLibA_00009snnT2)


title: P3_A1


title: WT_Nbs1_Exp1_ChIPSeq

city: Worcester

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND in the CASAVA pipeline. Unaligned reads were aligned by Bowtie (v1.0.0) using the options -n2 -strata -m 1 --chunkmbs 128, and combined with the ELAND alignments.
Duplicate reads were removed.
Peaks were called using using HOMER findPeaks in factor mode, using fragment lengths estimated by the makeTagDirectory program. findPeaks was run with the corresponding aidko library as control using a window size of 500 bp and a fold change threshold of 2.0. An empirical filtering scheme based on total peak tag counts was applied to eliminate questionable calls. The filtering thresholds were (tag count, WT/aidko threshold, local background threshold): ≥18, 2.0, 6.0; ≥16, 2.5, 4.0; ≥14, 3.6, 4.0; ≥13, 9.0, 8.0.  For subsequent downstream analyses, the peak coordinates were extended 1000 bp from the center.
Coverage track was generated by the ReadCoverage program of the USeq suite after extending reads to the fragment length estimated by the fragment-size-estimation.sh utility of SICER  (336 bp).  Stranded coverage tracks were generated by the makeUCSCfile program of HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: Values in coverage tracks are reads per million total reads (RPM).

source_name: splenic B cells

growth_protocol: B cells were isolated from spleens by depletion of RBCs by lysis in Gey's solution for 5 min on ice and by depletion of T cells with a cocktail of anti-T cell reagents, anti-CD4 (GK1.5), anti-CD8 (3.168), and anti-Thy1 (HO13.4 and J1J10), followed by anti–rat κ chain mAb (MAR18.5) and guinea pig complement (Pelfreeze Biochem).Viable cells were isolated by flotation on Ficoll/Hypaque gradients (δ = 1.09) and cultured in RPMI 1640 (BioWhittaker), with 10% FCS (Hyclone), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (all from GIBCO BRL), 50 µM 2-ME (Sigma Chemical Co.), and 50 ng/ml human BAFF/BLyS (Human Genome Sciences).

extract_protocol:
2 × 10e7 live cells were resuspended in SBSS and cross-linked with 1% formaldehyde for 5 min at 37°C. Cross-linking was quenched by addition of glycine to 125 mM and incubating for 5 min at room temperature. Cross-linked cells were sonicated on ice for twenty 10-sec bursts, cooling on ice for 15 sec between bursts. A total of 2 × 10e6 cell equivalents were used per ChIP. Lysates were incubated with the appropriate antibodies overnight at 4°C. Protein A or G Dynabeads (Invitrogen) were added to samples for 2 h,followed by washing with low-salt (150 mM NaCl), high-salt (500 mM NaCl), and LiCl salt buffers, and finally with TE. The complexes were then eluted overnight at 65°C in the presence of 1 mg/ml RNAse A (Sigma-Aldrich). The following day, the samples were incubated with 10 mg/ml proteinase K (Sigma-Aldrich) at 55 °C overnight. Following phenol:chloroform and chloroform extractions, DNA was precipitated using 1 mg/ml glycogen (Roche) and 95% ethanol overnight at −20°C.
DNA fragments were made blunt using the END-IT DNA repair kit (Epicentre) and a 3'-dA overhang added using Exo-Minus Klenow DNA Polymerase (Epicentre). Illumina paired-end (PE) adapters were added using the Fast-Link DNA Ligation kit (Epicentre), and the fragments were amplified twice using Illumina PE primers and PfuUltra II Fusion HS DNA polymerase (Stratagene). Each round of PCR was followed by gel purification and sizing of the fragments.

treatment_protocol: LPS (25 μg/ml) (Sigma-Aldrich) and anti–δ-dextran (10 ng/ml) was added to induce switching to IgG3.

value: spleen

tag: cell type

value: B cells

value: anti-Nbs1 (Abcam, ab32074)

tag: genotype

value: wildtype


title: q52_0

data_processing:
Data processing was performed using the Tuxedo RNAseq suite (Trapnell et al., 2012). 52 single cells displayed more than 50% alignment rate and 100,000 reads per sample and were therefore considered for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

extract_protocol:
The single-cell RNA-seq libraries were prepared from MEF-depleted hiF-T cells at day 10 of reprogramming directly sorted in lysis buffer at single cell using an ARIA facs sorter (BD).
Library preparation was performed using SMART-seq2 protocol with minor modifications (Trombetta et al., 2014) on 96 cells

tag: well number


title: dCas9_KRAB_HS2_CR10_rep3

city: Durham

last: Crawford

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
First 20 bp of Dnase-seq raw reads were mapped to hg19 with BWA, with 2 mismatches allowed, to generate bam files, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using fseq (PMID: 18784119).
Genome_build: hg19
Supplementary_files_format_and_content: peak

source_name: Cultured K562 cells

growth_protocol: K562 cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cel Culture Facilities and were maintained in RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Cells were Lysed and nuclei were digested according to the publication PMID: 20150147.
Libraries were prepared according to the publication PMID: 20150147.

treatment_protocol: K562 cells were transduced with lentivirus to stably express dCas9 or dCas9-KRAB and HS2 targeted gRNA.  To facilitate transduction, the cationic polymer polybrene was added at a concentration of 4 µg/mL to the viral media.  The lentivirus contained a puromycin resistance gene, and 1 µg/ml puromycin was used to initiate selection for transduced cells approximately 96 hours after transduction.

tag: transduced gene

tag: grna target

value: globin HS2 enhancer

tag: cell line


title: dCas9_HS2_CR10_rep3


title: 0610009D07Rik LPS 6 hours (0610009D07Rik..MGLibA_00009snnT6)


title: P3_A2


title: aidko_Nbs1_Exp1_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND in the CASAVA pipeline. Unaligned reads were aligned by Bowtie (v1.0.0) using the options -n2 -strata -m 1 --chunkmbs 128, and combined with the ELAND alignments.
Duplicate reads were removed.
Coverage track was generated by the ReadCoverage program of the USeq suite after extending reads to the fragment length estimated by the fragment-size-estimation.sh utility of SICER  (336 bp).
Genome_build: mm9
Supplementary_files_format_and_content: Values in coverage tracks are reads per million total reads (RPM).

tag: strain

tag: chip antibody

value: aid-/-


title: q50_0

source_name: MEF-depleted hiF-T cells at day 10 of reprogramming


title: q48_0


title: q45_0


title: dCas9_KRAB_HS2_CR4_rep3


title: dCas9_KRAB_HS2_CR10_rep2


title: q43_0


title: q51_0


title: A20 LPS 2 hours (A20-1T2)

tag: knockout

tag: treatment


title: dCas9_HS2_CR4_rep3


title: dCas9_KRAB_HS2_CR10_rep1


title: q47_0


title: dCas9_HS2_CR10_rep1


title: q46_0


title: q38_0


title: dCas9_KRAB_HS2_CR4_rep2


title: dCas9_KRAB_HS2_CR4_rep1


title: q37_0


title: dCas9_KRAB_rep1


title: 0610009D07Rik No LPS (0610009D07Rik..MGLibA_00009snnT0)

tag: tissue/cell line


title: q42_0


title: q41_0


title: q40_0


title: dCas9_KRAB_rep2


title: dCas9_HS2_CR4_rep1


title: RNA-seq: Gastric Carcinoma Biopsy 2 - Bioserve

city: New Orleans

first: Erik

middle: K

last: Flemington

state: Louisiana

address: 1430 Tulane Avenue, SL-79

department: Tulane Cancer Center/Pathology and Laboratory Medicine

institute: Tulane University

description: ribodepleted RNAs

data_processing:
Read alignment to transcriptome, and expression calculation using RSEMv1.2.20
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file generated using RSEMv1.2.20 containing RPKM values for each gene

source_name: Gastric Carcinoma Biopsy 2 - Bioserve

extract_protocol:
RNA extracted using Trizol protocol
100 base single end sequenced reads, Truseq stranded library preparation

value: EBV-positive gastric carcinoma


title: RNA-seq: Gastric Carcinoma Biopsy 1 - Bioserve

description: ribodepleted RNAs

source_name: Gastric Carcinoma Biopsy 1 - Bioserve


title: dCas9_HS2_CR4_rep2


title: q39_0


title: hIPSC29e hIPSC

data_processing:
Reads were mapped with TopHat version 2.0.7 and Bowtie version 2.1.0 with default parameters against build hg19 of the human genome, and build 13 of the GENCODE human genome annotation. Samples were quantified with the Cufflinks package version 2.2.0. Differential expression was performed using Cuffdiff 2.2.0 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: reference hIPSC line

extract_protocol:
Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
RNA-Seq Illumina libraries for mRNA profiling were prepared from 100 ng total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).
TruSeq RNA Sample Prep Kit v2 (Illumina)


title: q34_0


title: q33_0


title: dCas9_KRAB_rep3


title: q32_0


title: RNA-seq: Gastric Cancer Cell Line 1 - YCCEL1

description: ribodepleted RNAs

source_name: Gastric Cancer Cell Line 1 - YCCEL1

growth_protocol: Cultured in RPMI plus 10% FBS in 5% CO2 incubator at 37C


title: hIPSC27b hIPSC


title: hIPSC27e hIPSC


title: q36_0


title: RNA-seq: Gastric Cancer Cell Line 1 - NCC24

description: ribodepleted RNAs

source_name: Gastric Cancer Cell Line 1 - NCC24


title: q35_0


title: q31_0


title: hIPSC18c hIPSC


title: q30_0


title: q28_0


title: hIPSC20b hIPSC


title: hIPSC18b hIPSC


title: q27_0


title: hIPSC18 hIPSC


title: q25_0


title: q26_0


title: q23_0


title: hIPSC15b hIPSC


title: hIPSC17a hIPSC


title: q24_0


title: q22_0


title: hIPSC11c hIPSC


title: dCas9_HS2_CR10_rep2


title: q21_0


title: HUES65 hESC

source_name: reference hESC line


title: q20_0


title: HUES66 hESC


title: q19_0


title: q29_0


title: q18_0


title: HUES63 hESC


title: HUES53 hESC


title: HUES62 hESC


title: q17_0


title: q16_0


title: q14_0


title: q15_0


title: HUES49 hESC


title: HUES45 hESC


title: HUES48 hESC


title: hIPSC17b hIPSC


title: q9_0


title: q10_0


title: HUES9 hESC


title: HUES28 hESC


title: q13_0


title: HUES64 hESC


title: HUES13 hESC


title: q8_0


title: HUES8 hESC


title: q6_0


title: q12_0


title: HUES1 hESC


title: q4_0


title: q1_0


title: H1 hESC


title: H9 hESC


title: HUES3 hESC


title: Uninjected - rep 3

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped with Tophat with standard parameters
Read counts were obtained using Htseq-count and ENSEMBL gene models
Differentation expression and subsequent analyses were conduced in the R package using DESeq2 library
Genome_build: JGI 4.2/xenTro3
Supplementary_files_format_and_content: files containing read counts by gene models

organism: Xenopus tropicalis

source_name: Whole embryos

growth_protocol: standard Xenopus embryo culture

extract_protocol:
RNA was extracted with Tri-reagent (Sigma) and cleaned on Qiagen RNAeasy colmun according to manufacturer specification
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 20 ng MO per embryo (or 6.67ng for each MO for the triple) was injected at the 1- or 2-cell stage, in a total volume of 10 nL divided between each cell

tag: developmental stage

value: Stage 14 (early neurula)

tag: morpholino

value: whole embryo


title: q2_0


title: GSM1378015_NT2_2

city: La Jolla

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description: re-accessioned sample

data_processing:
RNA-Seq reads were trimmed and mapped to the GRCh37 reference using STAR (version 2.3.0.1). Four previously published IVF-ESC samples and four NT-ESC were added to increase statistical power and for quality control.
Samtools (version 0.1.17) was then used to sort, merge, and eliminate duplicate reads
Expression levels for each gene were quantified using the python script rpkmforgenes and annotated using Ensembl GRCh37 refGene. Genes that did not have at least one sample with at least five reads were removed from the analysis.
The data was normalized using the R (version 3.1.1) package DESeq2 (version 1.4.5). Eight samples were added for comparison: Four IVF-ESC samples: GSM1282324, GSM1378018,GSM1282325 and GSM1378019 and four NT-ESC samples: GSM1282320,GSM1378014, GSM1282321, GSM1378015. These have been re-accessioned and are included in this record.
DESeq2 uses negative binomial generalized linear models and shrinkage estimation for dispersions and fold changes to improve stability and interpretability of the estimates. It reports a p-value and an adjusted p-value using the Benjamini-Hochberg procedure.
Transcripts with an adjusted P-Value less than 0.05 were considered differentially expressed.
All enrichment analysis was performed using GREAT (v. 2.0.2).
Genome_build: GRCH37
Supplementary_files_format_and_content: .txt file including DESeq2 normalized counts filtered for genes with at least 5 reads in at least one sample

source_name: Nuclear Transfer Stem Cell

growth_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Cells were transduced by retro virus-based iPSC vectors as previously reported (Lowry, W. E. et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proceedings of the National Academy of Sciences of the United States of America 105, 2883-2888, doi:10.1073/pnas.0711983105 (2008)). Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)).

extract_protocol:
RNA was isolated (TRIzol Reagent, Life Technologies, Inc.) quantified (Qubit RNA Assay Kit, Life Technologies, Inc.) and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent).
Approximately 500 ng was used as input for the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented and copied into first strand cDNA using random primers and reverse transcriptase. Second strand cDNA synthesis was then done using DNA Polymerase I and RNase H. The cDNA was then ligated to adapters and enriched with PCR to create the final cDNA library. The library was then pooled and sequenced on a HiSeq 2000 (Illumina, Inc.) instrument as per manufacturer’s instructions. Sequencing was performed up to 2 X 101 cycles.

treatment_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Genetically matched iPSCs were generated by transductions of the same HDF culture with  retroviral or Sendai virus vectors carrying OCT4, SOX2, KLF4, and MYC. Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols.

value: Human Pluripotent Stem Cell

value: Nuclear Transfer Derived

tag: sequenced molecule

value: polyA RNA


title: q3_0


title: q11_0


title: HUES44 hESC


title: hIPSC11b hIPSC


title: mock MO - rep 3

value: standard control MO

tag: tissue


title: GSM1282321_NT2

description: re-accessioned sample


title: GSM1378014_NT1_2

description: re-accessioned sample


title: TET1-A_-DOX

city: Essen

first: Bernhard

last: Horsthemke

address: Hufelandstrasse 55

department: Universitaetsklinikum Essen

country: Germany

institute: Institut fuer Humangenetik

description: 5hmC data from TET1-A clone (TET1#1), not induced

data_processing:
Library strategy: RRHP library
Sequence reads from RRHP libraries were first processed to trim off the low quality bases and the P7CG adapter at the 3’ end of the reads. Reads were then aligned to the hg19 reference genome using the Bowtie default parameters and --best. Aligned reads with the MspI tag (CCGG) were counted.
Genome_build: hg19
Supplementary_files_format_and_content: bigBed files with 5hmC tracks

source_name: Flp-In™ T-REx™ 293

growth_protocol: Cells were cultured in DMEM supplemented with 10% FCS, 1% Pen/Strep and appropriate concentrations of selective antibiotics.

extract_protocol:
DNA was extracted using the AllPrep DNA/RNA/Protein Mini kit (Qiagen)
Genomic DNA was fragmented overnight at 37°C with a hydroxymethyl-insensitive enzyme, MspI, and purified using the DNA Clean and Concentrator kit (Zymo Research). Modified Illumina TruSeq P5 and P7 adapters containing 5’-CG overhangs were ligated onto the digested DNA using T4 DNA ligase (2 hours at 16°C). Libraries were then strand extended at 72°C with Taq DNA Polymerase. The adapters were designed to regenerate the 5’-CCGG site at the P5 junction while the P7 adapter generates a 5’-TCGG junction, making it insensitive to MspI digestion. Adapterized libraries were treated with ß-glucosyltransferase to label 5-hmC modifications and purified using the DNA Clean and Concentrator kit. The glucosylated libraries were then subjected to an overnight MspI digestion at 37°C, cutting any fragments not containing a glucosyl-5hmC site at the P5 CCGG junction. After incubation, the libraries were size-selected from 100bp to 500bp and purified using the ZymoClean Gel DNA Recovery Kit (Zymo Research). The fragments were amplified using OneTaq 2X Master Mix (NEB), and the PCR conditions include an initial denaturation of 94°C for 30 sec followed by 12 cycles of 94°C for 30 sec, 58°C for 30 sec, and 68°C for 1 min. Fragments containing 5-hmC were positively selected during PCR amplification with adapter-specific indexing primers whereas fragments lacking glucosylated-5-hmC at the P5 junction were cleaved and, therefore, not amplified by PCR. Amplified libraries were purified using the DNA Clean and Concentrator kit, and multiplexed using equal volume of the libraries. All adapters and primers used were synthesized by Integrated DNA Technologies.

treatment_protocol: Doxycycline was used to induce the expression of the integrated TET1 copy.

tag: transgene

value: uninduced


title: TET1-G_-DOX

description: 5hmC data from TET1-G clone (TET1#3), not induced


title: GSM1282320_NT1

description: re-accessioned sample


title: q44_0

tag: reprogramming time point (day)


title: q7_0


title: Sample_1123-03_23_1_31_006

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were mapped to the hg19 reference genome and GencdeV7 reference transcriptome using Tophat 1.3.1with parameters : -g 1 -p 4 -r 150 --coverage-search --no-novel-indels --microexon-search -G GFFfile --solexa-quals hg19 FASTQFILE1 FASTQFILE2
Gene expression estimates: Counts were calculated using the BEDTools 2.12.0 function coverageBed with parameters: -abam BAMfilename -b BEDfilename
BAM files were sorted using the samtols 0.1.18 function: samtools sort -n
BAM files were converted to SAM format using the samtols 0.1.18 function: samtools view -h
SAM files were converted to MRF format using the RSEQtools 0.6 function: sam2mrf
Gene expression estimates in RPKM were calculated using the RseqTools function mrfQuantifier with parameters: INTERVALfile multipleOverlap MRFfile
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include gene expression estimates in RPKM (.rpkm) and COUNTS (.counts.txt) for each sample.

source_name: iPSC-derived neural progenitors, day 31, ASD

growth_protocol: Neuronal differentiation of iPSCs: iPSC colonies were dissociated and plated on AggrewellTM 800 plates (STEMCELL Technologies) in DMEM/F12-GLUTAMAX medium containing 4% B27 supplement without vitamin A (Invitrogen), 1% N2 supplement (Invitrogen), and 55 uM 2-mercaptoethanol, 5μM Y-27632 and 200ng/ml recombinant mouse Noggin (R&D Systems). After 2 days, embryoid bodies (EBs) were collected and plated onto 10-cm bacterial Petri dishes in neuronal medium as above. After two days (day 4), free-floating EBs were collected and plated in neuronal medium, supplemented with only Noggin, onto tissue culture dishes coated with growth factor-reduced Matrigel (BD Bioscience) to allow neural rosette formation. The neuronal medium was changed the next day and supplemented with 20 ng/ml FGF2, 200 ng/ml Noggin, and 200 ng/ml rhDkk1 (R&D Systems). After two or three days, the neural rosettes were manually dissected and replated as free-floating aggregates in 10-cm bacterial Petri dishes in neuronal medium supplemented with FGF2 (10ng/ml) and EGF (10ng/ml). After five days in suspension, free-floating aggregates were plated onto ultra low-attachment 96-well plates (Corning) in neuronal medium supplemented with FGF2 and EGF. Terminal differentiation was started the next day, using a NEUROBASAL-type medium supplemented with 1% N2, 2% B27, 15 mM HEPES, 1X Glutamax, 1X nonessential amino acids (NEAA) and 55 uM 2-mercaptoethanol, supplemented with 200 nM ascorbic acid, 10 ng/ml BDNF (R&D), 10 ng/ml GDNF (R&D) and 1 mM dibutyryl-cAMP (Sigma). Half of the medium was changed twice a week.

extract_protocol:
Cells were treated with Accutase and pelleted. Total RNA was extracted using the PicoPure kit (Life Technologies catalog # KIT0204).
RNA sequencing was performed using 50ng of total RNA with the SMARTer® Ultra Low RNA kit for Illumina® Sequencing according to the manufacturer's instructions. Samples were barcoded. Multiplex Paired-End RNA sequencing (2x75) was performed on an IIllumina HiSeq 2000 to an average depth of 30M reads per sample.

tag: donor's disease state

value: autism spectrum disorder with macrocephaly

tag: donor's gender

value: male

tag: cell type

value: iPSC-derived neural progenitors

tag: number of days in vitro in terminal differentiation conditions

tag: donor id


title: mock MO - rep 2


title: 12dd_DOX_plus_SSEA3_plus_Rep1 (hiF)

source_name: reprogramming intermediates of hiF cells

tag: cell line


title: Uninjected - rep 2


title: Sample_1123-01_23_4_31_004

source_name: iPSC-derived neural progenitors, day 31, non-ASD

value: unaffected


title: TET1-A_+DOX

description: 5hmC data from TET1-A clone (TET1#1), 48 h after induced expression of the integrated TET1 gene

value: induced


title: Sample_1123-01_23_4_11_002

source_name: iPSC-derived neural progenitors, day 11, non-ASD


title: CdxA MO - rep 1

value: Cdx1 + Cdx2 + Cdx4


title: Uninjected - rep 1


title: Sample35_NT2_fib2

description: wt mtDNA

data_processing:
RNA-Seq reads were trimmed and mapped to the GRCh37 reference using STAR (version 2.3.0.1). Four previously published IVF-ESC samples and four NT-ESC were added to increase statistical power and for quality control.
Samtools (version 0.1.17) was then used to sort, merge, and eliminate duplicate reads
Expression levels for each gene were quantified using the python script rpkmforgenes and annotated using Ensembl GRCh37 refGene. Genes that did not have at least one sample with at least five reads were removed from the analysis.
The data was normalized using the R (version 3.1.1) package DESeq2 (version 1.4.5). Eight samples were added for comparison: Four IVF-ESC samples: GSM1282324, GSM1378018,GSM1282325 and GSM1378019 and four NT-ESC samples: GSM1282320,GSM1378014, GSM1282321, GSM1378015. These have been re-accessioned and are included in this record.
DESeq2 uses negative binomial generalized linear models and shrinkage estimation for dispersions and fold changes to improve stability and interpretability of the estimates. It reports a p-value and an adjusted p-value using the Benjamini-Hochberg procedure.
Transcripts with an adjusted P-Value less than 0.05 were considered differentially expressed.
All enrichment analysis was performed using GREAT (v.2.0.2)
genome build: GRCH37
processed data files format and content: .txt file including DESeq2 normalized counts filtered for genes with at least 5 reads in at least one sample

source_name: Differentiated Nuclear Transfer Stem Cell

growth_protocol: Leigh patient fibroblasts were acquired from Coriell Cell Repositories (catalogue no. GM13411) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated as described previously (Ma, H. et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177-183, doi:10.1038/nature13551 (2014)). NT-ESC lines were produced from Leigh patient fibroblasts as described previously (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)). iPSC and NT-ESC lines were differentiated into fibroblasts as described previously (Paull, D. et al. Nuclear genome transfer in human oocytes eliminates mitochondrial DNA variants. Nature 493, 632-637, doi:10.1038/nature11800 (2013)).

treatment_protocol: Sendai virus-based reprogramming was carried out using sendai virus vectors carrying OCT4, SOX2, KLF4, and MYC. Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated as described previously (Ma, H. et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177-183, doi:10.1038/nature13551 (2014)). NT-ESC lines were produced from Leigh patient fibroblasts as described previously (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)). iPSC and NT-ESC lines were differentiated into fibroblasts as described previously (Paull, D. et al. Nuclear genome transfer in human oocytes eliminates mitochondrial DNA variants. Nature 493, 632-637, doi:10.1038/nature11800 (2013)).

value: Fibroblast

value: Differentiated NT-ESC


title: Cdx4 MO - rep 3


title: Sample_1123-03_23_1_11_005

source_name: iPSC-derived neural progenitors, day 11, ASD


title: TET1-G_+DOX

description: 5hmC data from TET1-G clone (TET1#3), 48 h after induced expression of the integrated TET1 gene


title: CdxA MO - rep 3


title: mock MO - rep 1


title: Sample_1120-03_23_5_11_007


title: CdxA MO - rep 2


title: Cdx4 MO - rep 2


title: Sample34_NT2_fib1

description: wt mtDNA


title: Sample33_NT1_fib2

description: wt mtDNA


title: q49_0

tag: well number


title: Sample_1120-01_23_7_31_006


title: Sample_1120-01_23_9_31_004


title: Cdx2 MO - rep 1


title: Cdx2 MO - rep 2


title: Sample_1120-01_23_9_11_002


title: Cdx1 MO - rep 3


title: Sample31_Melas_iPS4_fib2

description: mutant mtDNA

source_name: Differentiated induced Pluripotent Stem Cell

value: Differentated iPSC


title: Sample_1120-01_23_7_11_005


title: Sample_07-03_23_3_31_004


title: Sample30_Melas_iPS4_fib1

description: mutant mtDNA


title: Sample_1120-03_23_5_31_012


title: Cdx1 MO - rep 2


title: Sample_07-03_23_3_11_002


title: Cdx4 MO - rep 1


title: Sample28_Melas_iPS3_fib1

description: mutant mtDNA


title: Sample_07-02_23_5_31_012

value: female


title: Sample25_Leigh_iPS2_fib2

description: mutant mtDNA


title: Sample26_Leigh_iPS3_fib1

description: mutant mtDNA


title: Sample32_NT1_fib1

description: wt mtDNA


title: Sample_07-01_23_2_31_007


title: Sample_07-01_23_1_31_006


title: Cdx2 MO - rep 3

value: Stage 14 (early neurula)


title: Sample27_Leigh_iPS3_fib2

description: mutant mtDNA