title: Th0 0.1uM tofa_donor4

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description:
RNA with spikein
RNA-seq
hg19

data_processing:
ChIP libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions. ChIP libraries were aligned to mm9 or hg19 reference genomes using bowtie2 with bowtie indexes derived based on UCSC annotations and Phred+33 selected for qualities.
Peak-calling for all transcription factors and p300 binding was performed by macs141 using p-value=1e-7. Control library for all peak-calling libraries was the input DNA performed under Th0 condition. Peaks with FDR values more than 30% were further excluded. Peaks intensities (‘tags’ column) were normalized as tag-per-million.
The spike-in RNA-Seq libraries were subsequently sequenced on Illumina HiSeq 2000 and then trimmed using ‘cutadapt’ with “TruSeq Indexed Adapters”. The sequences of the ERCC synthetic spike-in RNAs (http://tools.invitrogen.com/downloads/ERCC92.fa) had been added to both mouse and human genomes (genome.fa).
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bigwig files

source_name: whole blood from healthy donor

growth_protocol:
Naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured with plate-bound anti-CD3 and anti-CD28 (10 ug/ml each)either under: Th1conditions (IL-12 (20 ng ml) and anti-IL-4 neutralizing antibodies (10 μgml-1); Th17 conditions (IL-6 (20 ng ml-1) plus human TGF-β1 (2 ng ml-1) and anti-IFN-γ neutralizing antibodies (10 μg ml-1) and anti-IL-4 neutralizing antibodies (10 μg ml-1))
Wildtype and Bach2KO cells:  Naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured with plate-bound anti-CD3 and anti-CD28 (10 ug/ml each)either under: Th1conditions (IL-12 (20 ng ml) and anti-IL-4 neutralizing antibodies (10 μgml-1); Th17 conditions (IL-6 (20 ng ml-1) plus human TGF-β1 (2 ng ml-1) and anti-IFN-γ neutralizing antibodies (10 μg ml-1) and anti-IL-4 neutralizing antibodies (10 μg ml-1)) or iTreg conditions(IL-2 (100 IU ml-1) plus human TGF-β1 (5 ng ml-1) for 3 days.

extract_protocol:
RNA-seq: Total RNA wasprepared from approximately 1 million cells by using mirVana miRNA Isolation Kit(AM1560, ABI). 200 ng of total RNA was subsequently used to prepare RNA-seq library byusing TruSeq SRRNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s6protocol.The resulted libraries are sequenced using the Illumina HiSeq 2000. Only unique reads of 50 bp were mapped to the mouse genome (mm9) using Tophat and Cufflinks.
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow celland sequenced on HiSeq 2000.

value: in vitro activated Th0 condition for 3 days

tag: culture condition

value: Naïve CD4+CD45RA+CD45RO- T cell population was sorted using FACS Aria II

value: 0.1uM tofacitinib

tag: genotype

tag: strain


title: GPA-147_HumanDC_smallRNA_RNAseq

status: Public on Feb 18 2015

type: SRA

city: Paris

first: Katherine

last: Siddle

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

library_source: transcriptomic

data_processing:
Reads were trimmed to remove 3' adaptor
Read quality was assessed and reads were filtered using the R bioconductor package ShortRead. We removed reads (i) reads containing a mononucleotide repeat longer than 10nt, (ii) reads containing >75% mono, di or tri-nucleotide repeat, (iii) reads containing >20% "N" bases, (iv) reads shorter than 16nt or longer than 26nt
Reads were mapped to the human genome using bowtie (version 0.12.7) with parameters -v 2 -m 50 -a --best --strata
Cross-mapping correction (de Hoon et al., 2010) was applied to handle reads that mapped to multiple genomic locations
Reads aligning to mature miRNAs (miRBase v20, minimum overlap 75%) were extracted using BEDTools.
miRNA expression levels were calculated as the sum of the read counts of all sequences aligning to the mature miRNA
miRNA expression levels were normalised across samples by scaling counts of all miRNAs by a sizeFactor calculated using the function calculateSizeFactor from the bioconductor package DESeq (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of scaled, unfiltered expression levels for all detected mature miRNAs (miRBase v20) in all 116 samples (txt)

molecule: total RNA

organism: Homo sapiens

source_name: monocyte-derived Dendritic Cells

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation. Monocytes were purified from peripheral blood mononuclear cells by positive selection with magnetic CD14 MicroBeads (Miltenyi Biotech). Monocytes were then cultured for 5 days in RPMI-1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned.

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen).
Indexed sequencing libraries were prepared using the Illumina TruSeq protocol following isolation of low molecular weight (small) RNA fragments. Once prepared, indexed cDNA libraries were pooled (8 or 12 libraries per pool) in equimolar amounts and sequenced with single-end 50-bp reads on the Illumina HiSeq2000.

treatment_protocol: Monocyte-derived DCs were infected (~2x10^6 cells per condition) at an MOI of 1:1 with one of a panel of bacteria (Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis Beijing strain GC1237, Mycobacterium bovis BCG, Salmonella typhimurium strain Keller, Staphloccocus epidermidis and Yersinia pseudotuberculosis), or left uninfected, for 1h at 37c. Next the cells were washed and cultured for a further hour with 50ug/ml gentamycin. The cells were then washed a second time and cultured in complete medium with 5ug/ml gentamycin for an additional 4h, 18h and 48h.

tag: cell type

value: monocyte-derived Dendritic Cells

tag: donor

tag: infection agent

value: Non-infected

tag: time point


title: Th0 0.3uM tofa_donor4

city: Bethesda

state: MD

country: USA

description:
RNA with spikein
RNA-seq
hg19

tag: treatment

value: 0.3uM tofacitinib

tag: chip antibody


title: CUTLL1_CON_24HR_R2

city: New York

first: Tharu

middle: M

last: Fernando

state: NY

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.0 software used for basecalling.
Reads that passed filter were aligned to hg19 using TopHat (Trapnell et al., 2009).
Gene expression expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/ HTSeq/).
Differentially expressed genes were identified with the edgeR package (Robinson et al., 2010).  Genes with a p-value < 0.01 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count is provided as a .txt file.

source_name: CUTLL1 cells

growth_protocol: Cells were grown in RPMI 1640 medium with 10% FBS, 2mM glutamine, and pen/strep.

extract_protocol:
Total RNA was harvested with Trizol reagent (Life Technologies).
Genomic DNA was eliminate with Dnase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.

treatment_protocol: Cells were treated with agarose alone or T3- and T4-bound agarose (Sigma) for 24 hours.

value: Agarose alone, 24hrs


title: GPA-76_HumanDC_smallRNA_RNAseq


title: Th0 0.3uM tofa_donor3

description:
RNA with spikein
RNA-seq
hg19


title: Th0 0 tofa_donor3

description:
RNA with spikein
RNA-seq
hg19

value: 0 tofacitinib


title: Th0 0.3uM tofa_donor2

description:
RNA with spikein
RNA-seq
hg19


title: NANOG MNChIP-seq in cell type dEC Nanog_120312_ecto

status: Public on Feb 19 2015

city: Cambridge

first: Alexander

last: Tsankov

state: MA

address: 7 Divinity Drive

institute: Harvard University

description: NANOG MNChIP-seq in cell type dEC

library_source: genomic

data_processing:
Reads were aligned to the hg19 reference assembly using bwa version 0.5.7 (Li et al., Bioinformatics 2009) with default parameter settings. Subsequently, reads were filtered for duplicates and extended by 200bp. For the bigWig files, extended reads were summed at each base and normalized for sequencing depth by scaling the y-axis to represent cumulative reads per 1 million reads sequenced. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing the normalized occupancy (extended read count) across all genomic coordinates for each MNChIP-seq profile.
Supplementary_files_format_and_content: BED format file which contains the peak locations.
Supplementary_files_format_and_content: bigBed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column

molecule: genomic DNA

source_name: dEC

growth_protocol: When human ES cells reached 60-70% confluency on MEFs, the cells were plated as clumps on 6-well plates coated with Matrigel (Life Technologies) in mTeSR1 basal medium (Stem Cell Technologies). We maintained the cells for three days in feeder-free culture and then induced directed differentiation towards mesendoderm (dMS), endoderm (dEN), mesoderm (dME), and ectoderm (dEC) using different media conditions. For mesendoderm and endoderm differentiation cells were cultured for 12 and 120 hours, respectively, in Roswell Park Memorial Institute (RPMI) medium (Life Technologies) supplemented with 100ng/ml Activin A (R&D Systems), 50nM/ml WNT3A (R&D Systems), 0.5% FBS (Hyclone), 200mM GlutaMax (Life Technologies), .2X MEM Non-Essental Amino Acids Solution (Life Technologies), and 55µM b-mercaptoethanol. For the first 24 hours of mesoderm differentiation, cells were cultured in DMEM/F12 medium supplemented with 100ng/ml Activin A (R&D Systems), 10 ng/ml bFGF (Millipore), 100ng/ml BMP4 (R&D Systems), 100ng/ml VEGF (R&D Systems), 0.5% FBS (Hyclone), 200mM GlutaMax (Life Technologies), 0.2X MEM Non-Essental Amino Acids Solution (Life Technologies), and 55µM b-mercaptoethanol. From 24 to 120 hours of mesoderm differentiation, Activin A was removed from the culture. For ectoderm differentiation cells were cultured in DMEM/F12 medium supplemented with 2µM TGFb inhibitor (Tocris, A83-01), 2µM WNT3A inhibitor (Tocris, PNU-74654), 2uM Dorsomorphin BMP inhibitor (Tocris), 15% KOSR (Life Technologies), .2X MEM Non-Essental Amino Acids Solution (Life Technologies), and 55µM b-mercaptoethanol. Media was changed daily.

extract_protocol:
Cells were grown to a final count of 10 million, resuspended in PBS, and crosslinked in 10% formaldehyde solution for 10 minutes at room temperature.  Following quenching with 0.125M glycine and two PBS washes, we isolated nuclei using cell lysis buffer (20 mM Tris-HCl ph8, 85mM KCl, 0.5% NP40). Nuclei were then digested using MNase (Worthington, LS004797) as done in (Henikoff et al., PNAS 2011). Digestion was stopped with 0.05M EGTA and chromatin was aliquoted into 1-2 million cells per ChIP. Antibodies were added and immunoprecipitation was carried out overnight at 4°C as done in1. The next day, protein G beads (Life Technology, 10009D) were added for 2 hours at 4°C to isolate the protein bound DNA and washed twice using Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1,), and TE Buffer pH 8 (10mM Tris-HCl, pH 8, 1mM EDTA pH 8). DNA was eluted twice using 100µL of ChIP Elution Buffer (1% SDS, 0.1M NaHCO3) at 65°C for 15 minutes. Crosslinking was reversed by addition of 32µl reverse crosslinking salt mixture (250 mM Tris-HCl pH 6.5, 62.5 mM EDTA pH 8, 1.25 M NaCl, 5mg/ml Proteinase K) for 5-18 hours at 65°C. DNA was isolated using phenol/chloroform extraction and treated with DNase-free RNase for 30 minutes at 37°C. The whole cell extract (WCE) control was generated using MNase treated material that was then reverse crosslinked and phenol chloroform extracted, skipping the immunoprecipitation and washing steps.
MNChIP-seq library construction was performed as in (Henikoff et al., PNAS 2011) with gel size selection from 140bp to 720bp as described in (Gu et al., 2010). RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010).

tag: cell line

value: dEC

value: NANOG(R&D Systems,AF1997,KKJ0512051)


title: Th0 0.1uM tofa_donor1

description:
RNA
RNA-seq
hg19


title: Th0 0.3uM tofa_donor1

description:
RNA
RNA-seq
hg19


title: Th0 0 tofa_donor2

description:
RNA with spikein
RNA-seq
hg19


title: Th0 0 tofa_donor1

description:
RNA
RNA-seq
hg19


title: Periphery, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 12

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the D. melanogaster genome (dm3) with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis
Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq)
Genome_build: dm3
Supplementary_files_format_and_content: Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9 to the end) FPKM

molecule: polyA RNA

organism: Drosophila melanogaster

growth_protocol: Flies were raised on standard cornmeal molasses agar medium at 25C. TRF flies were alternated with a medium that contained agar and water.

extract_protocol:
Total RNA of all samples was extracted using Rneasy Mini Kit (Qiagen) per manufacturer's instructions
RNA libraries were prepared for sequencing using Illumina TruSeq kits per the manufacturer's instructions
unstranded polyA+ RNA-Seq

treatment_protocol: Flies were snap frozen using liquid nitrogen and stored at -80C before extraction.

value: Oregon R

tag: Sex

value: male

tag: age

value: 7 Weeks

tag: feeding type

value: Time Restricted Fed (TLF)

value: ZT12; Zeitgeber Time 12

tag: tissue

value: Periphery (entire body except head)


title: Periphery, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 18

value: ZT18; Zeitgeber Time 18


title: Periphery, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 06

value: ZT06; Zeitgeber Time 06


title: Th0 0.1uM tofa_donor3

description:
RNA with spikein
RNA-seq
hg19

value: in vitro activated Th0 condition for 3 days

value: Naïve CD4+CD45RA+CD45RO- T cell population was sorted using FACS Aria II


title: Hi-C, Thymus STL001, replicate one

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description: Sample 1

data_processing:
library strategy: HaploSeq
fastq:  Illumina's HiSeq Control Software
For Hi-C read alignment, we aligned Hi-C reads to the hg18 (human) genome. We masked any bases in the genome that were genotyped as SNPs in the individual genome. These bases were masked to “N” in order to reduce reference bias mapping artifacts. Hi-C reads were aligned as single end reads using Novoalign. After mapping was finished, read pairs were re-constructed from single reads using an in house pipeline.  Unmapped reads were filtered out and PCR duplicate reads were removed.
Haplotypes were generated from the final aligned bam file using the HapCUT algorithm.  The details of HapCUT are described previously (Bansal and Bafna, Bioinformatics 24, i153-159, 2008).
The final processed haplotypes were generateds after removing local biases through following three steps. First the alignment biases were removed by aligning simulated reads spanning surrounding variants location. If there is more than 5% difference between alleles those variant loci were considered to subject an inherent mapping bias. Second, we removed alleles located in copy number variable regions and allelic biased copy number variable regions by comparing the coverage between two alleles based on WGS data. Any variants that had more coverage than three standard deviation above the mean of each haplotype were excluded. Any variants showing biased WGS coverage between two alleles were also excluded (binomial test p-value 0.05 after Benjamini correction). Lastly, we remove erroneously called as heterozygous variant during genotyping. We calculated the probability of each heterozygous variants were actually homozygous from the likelihood of observing the coverage on each allele from whole genome sequencing. Only heterozygous SNPs that had a FDR of less than 0.5% were included in downstream analysis.
HaploSeq generates two haplotypes for each chromosome, one for the maternal allele and one for the paternal allele. One allele is named as P1 (parent1) and another allele is named as P2 (parent2) since we do not have information regarding the parent of origin in each donor genome. For the chr9 we can generate haplotypes in each chromosome arm. The haplotypes in chrX STL002 was independtly generated based on hg19 genome build.
Genome_build: hg18
Supplementary_files_format_and_content: The processed haplotypes for the individual genome ("*_haps.vcf") are available in VCF format.

source_name: Thymus STL001

growth_protocol: Tissues samples were obtained from deceased donors at the time of organ procurement at the Barnes-Jewish Hospital (St. Louis, USA).  Samples were flash frozen and pulverized prior to formaldehyde cross-linking.  Research consent from family was obtained, and this study was approved by Mid-American Transplant Services.

extract_protocol:
Hi-C experiments were conducted using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).
Sequencing libraries were constructed according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

value: Thymus


title: Periphery, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 00

value: ZT00; Zeitgeber Time 00


title: Periphery, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 18

value: Ad Libitum Fed (ALF)


title: Th0 0 tofa_donor4

description:
RNA with spikein
RNA-seq
hg19


title: Periphery, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 12


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 15

value: 5 Weeks

value: ZT15; Zeitgeber Time 15


title: Periphery, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 00


title: Periphery, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 06


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 09

value: ZT09; Zeitgeber Time 09


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 12


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 00


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 06


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 21

value: ZT21; Zeitgeber Time 21


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 21

value: Oregon R


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 03

value: male

value: ZT03; Zeitgeber Time 03


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 15


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 12


title: Th0 0.1uM tofa_donor2

description:
RNA with spikein
RNA-seq
hg19

value: 0.1uM tofacitinib


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 09


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 06


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 03


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 00


title: Periphery, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 18

value: 3 Weeks

value: Time Restricted Fed (TLF)


title: Periphery, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 06

value: Periphery (entire body except head)


title: Periphery, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 00


title: Periphery, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 18

value: ZT18; Zeitgeber Time 18


title: Heart, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 18

value: heart


title: Periphery, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 06

value: ZT06; Zeitgeber Time 06


title: Periphery, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 00


title: Periphery, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 12

value: ZT12; Zeitgeber Time 12


title: Periphery, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 18


title: Heart, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 06


title: Heart, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 12


title: Heart, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 06


title: Head, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 06

value: 7 Weeks

value: head


title: Head, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 18


title: Head, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 12


title: Heart, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 18

value: 5 Weeks

value: Ad Libitum Fed (ALF)


title: CKp25_6wk_DNA_WCE

first: Andreas

middle: R

last: Pfenning

address: Computer Science and Artificial Intelligence Laboratory

department: CSAIL

institute: Massachusetts Institute of Technology

data_processing:
The reads from RNA-Seq experiment were aligned to the genome using the Bowtie alignment tool, producing BAM format files. A number of quality scores, including proportion of aligned reads and read length distribution were calucated using PICARD, and no outlier samples were detected (http://picard.sourceforge.net/)
RNA-Seq reads that overlapped each ensembl gene models in GFF format (NCBIM37,Ensembl release 67) were counted using HT-Seq v0.6.1 (http://www-huber.embl.de/users/anders/HTSeq/).
ChIP-Seq reads were mapped to the mm9 reference mouse genome using MAQ v0.7.1-9 using default parameters.  Reads mapping to multiple locations were discarded.  Duplicates were marked and filtered using PICARD (http://picard.sourceforge.net/). Datasets passed quality control based on ENCODE ChIP-seq data standards based on read quality, read mapping statistics, library complexity and strand cross-correlation analysis (to measure signal-to-noise ratios)
For each histone modification in each condition, mapped reads were pooled across ChIP-seq replicates and regions of enrichment (peaks) were identified for the pooled ChIP-seq dataset relative to the pooled control using the MACS2 peak caller (version 2.0.10.20130712; https://github.com/taoliu/MACS/) using a relaxed p-value of 0.01.  For each histone modification, overlapping peaks (at least 1 bp overlap) were merged across all conditions to obtain a non-redundant master list of regions of enrichment.
Master lists of broad domains of enrichment for the diffused marks H3K27me3, H3K9me3, H3K36me3 and H4K20me1 were obtained by allowing merging peaks across conditions that were within 1kb of each other.
Genome-wide signal coverage tracks representing per-base fold enrichment and the likelihood ratio of ChIP relative to control were also computed using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: big wig files (.bw) were generated using MACS2; narrow peak files (extended bed format) were also generated using MACS2

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Mouse hippocampus was harvested immediately after euthanasia. Upon dissection tissue was flash-frozen in liquid nitrogen.
Tissues were minced and crosslinked in 1% formaldehyde (Thermo Scientific) for 15 min at room temperature and quenched with glycine for 5 min (Sigma).  The samples were homogenized in cell lysis buffer containing proteinase inhibitors (complete, Roche) and chromatin was then fragmented to a size range of ~200-500 bp using a Branson 250 digital sonifier.  Solubilized chromatin was then diluted and incubated with ~1 μg antibody at 4C overnight.  Immune complexes were captured with Protein A-sepharose beads, washed and eluted.  Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65C, phenol-chloroform extraction and ethanol precipitation.  Isolated ChIP DNA was resuspended and quantified using the Qubit assay (Invitrogen). Sequencing libraries were prepared from ~1-5 ng ChIP (or input) DNA.  Gel electrophoresis was used to retain library fragments between 300 and 600 bp.  Prior to sequencing, libraries were quantified using Qubit (Invitrogen) and quality-controlled using Agilent’s Bioanalyzer. 36 bp single end sequencing was performed using the Illumina HiSeq 2000 platform according to standard operating procedures.

treatment_protocol: Adult (3-months-old) female double-transgenic CK-p25 mice and their respective control littermates were used for the experiments.  Brain tissue was collected at either 2 or 6 weeks following p25 induction.

tag: genotype/variation

tag: time since treatment

value: 6 weeks

value: brain (hippocampus)

tag: measurement

value: WCE


title: Heart, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 00

value: Oregon R

value: male

value: ZT00; Zeitgeber Time 00


title: CKp25_2wk_DNA_WCE

value: 2 weeks


title: CK_6wk_DNA_WCE

value: CK


title: Head, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 18


title: CK_2wk_DNA_WCE


title: Heart, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 12


title: Periphery, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 12

value: 3 Weeks

value: Time Restricted Fed (TLF)

value: Periphery (entire body except head)


title: Head, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 12


title: CK_6wk_DNA_H4K20me1

value: H4K20me1 (Abcam, catalog# ab9051, lot# GR4867-1)


title: CKp25_2wk_DNA_H4K20me1


title: Head, 7 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 00


title: Periphery, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 18

value: ZT18; Zeitgeber Time 18


title: CK_2wk_DNA_H4K20me1


title: Head, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 06

value: 7 Weeks

value: ZT06; Zeitgeber Time 06


title: Heart, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 00

value: 5 Weeks

value: heart


title: CKp25_6wk_DNA_H3K9me3

value: 6 weeks

value: H3K9me3 (Abcam, catalog# ab8898, lot# GR79978-1 and also 960144 earlier)


title: CKp25_2wk_DNA_H3K9me3

value: brain (hippocampus)


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 21

value: Oregon R

value: ZT21; Zeitgeber Time 21

value: head


title: Head, 7 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 00

value: male

value: Ad Libitum Fed (ALF)

value: ZT00; Zeitgeber Time 00


title: CK_6wk_DNA_H3K9me3

value: CK


title: CK_2wk_DNA_H3K9me3

value: 2 weeks


title: CKp25_6wk_DNA_H3K4me3

value: H3K4me3 (Millipore, catalog# 07-473, lot# DAM1817678)


title: CKp25_2wk_DNA_H3K4me3


title: CK_6wk_DNA_H3K4me3


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 18

value: Time Restricted Fed (TLF)

value: ZT18; Zeitgeber Time 18


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 15

value: ZT15; Zeitgeber Time 15


title: Sox2 ChIP 1

city: Boston

first: David

middle: P

last: Corey

address: 220 Longwood Ave.

department: Neurobiology

institute: Harvard Medical School

description: Sox2 ChIP biological replicate 1

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using cloud service at GenomeQuest using default parameters
peaks were called using GenomeQuest ChIP-Seq workflow to obtain peak sites using the MACS algorithm
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak sites, p-value, and folds of enrichment for each ChIPseq sample relative to input DNA

source_name: iMOP cells

growth_protocol: Cells were cultured in the DMEM/F12 containing B27 and 20 ng/ml of bFGF in suspension as floating otospheres

extract_protocol:
iMOP cells were harvested by gravity sedimentation. Cells were lysed and nuclei enriched.  Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iMOP cells grown in suspension with DMEM/F12 containing B27 and 20 ng/ml of bFGF. Depending on treatments, small molecules were added to the cultures.

value: immortalized multipotent otic progenitor

value: Sox2 clone 6F1.2 EMD Millipore Cat# 17-656


title: Sox2 ChIP 2

description: Sox2 ChIP biological replicate 2


title: CKp25_6wk_DNA_H3K4me1

value: 6 weeks

value: H3K4me1 (Abcam, catalog# ab8895, lot# GR61280-1)


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 12

value: 5 Weeks

value: ZT12; Zeitgeber Time 12


title: CKp25_2wk_DNA_H3K4me1

value: brain (hippocampus)


title: CK_2wk_DNA_H3K4me3


title: cMyc ChIP 2

description: N-termianl cMyc ChIP biological replicate 2

value: c-Myc (N-262) Santa Cruz Cat# sc-764


title: CKp25_6wk_DNA_H4K20me1

value: H4K20me1 (Abcam, catalog# ab9051, lot# GR4867-1)


title: cMyc ChIP 1

description: N-termianl cMyc ChIP biological replicate 1


title: CK_6wk_DNA_H3K4me1


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 09

value: Oregon R

value: male

value: ZT09; Zeitgeber Time 09

value: head


title: CK_2wk_DNA_H3K4me1

value: CK

value: 2 weeks


title: CKp25_2wk_DNA_H3K36me3

value: H3K36me3 (Abcam, catalog# ab9050, lot# GR82518-1 and also 750267 earlier)


title: CK_6wk_DNA_H3K36me3


title: PolII ChIP 2

description: RNA polymerase II ChIP biological replicate 2

value: RNA polymerase II clone 4H8 (Abcam Cat#ab5408)


title: CK_2wk_DNA_H3K36me3


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 03

value: Time Restricted Fed (TLF)

value: ZT03; Zeitgeber Time 03


title: CKp25_6wk_DNA_H3K27me3

value: 6 weeks

value: H3K27me3 (Millipore, catalog# 07-449, lot# 1999681)


title: CKp25_2wk_DNA_H3K27me3


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 00

value: 5 Weeks

value: ZT00; Zeitgeber Time 00


title: B27_2

description: iMOP w/o bFGF biological replicate 2

data_processing:
Raw reads were aligned to mouse reference genome using the cloud server at DNAnexus.
Assignment of non-unique alignments were weighed by the posterior probability of their mapping. The read counts of RefSeq mouse genes were calculated using the RNA-Seq / Transcriptome-based quantification analysis pipeline.
Custom scripts were developed to generate raw read-counts tables.
The data were summarized, normalized, and statistically tested for differential gene expression for each gene under various comparison schemes using the DESeq package in R/BioConductor
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read couts of mouse RefSeq genes for each sample

source_name: iMOP

extract_protocol:
Inner ears were removed and trypsinized to dissociate cells.  Cells that form otospheres were harvested and RNA obtained from these cells using Trizol reagent. RNA-Seq was done using protocol from Marioni et al. 2008.  RNA-Seq from otospheres were done using Ovation RNA-Seq System v2 kit (NuGEN).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For growth factor withdrawal experiments cells were switched to DMEM/F12 containing B27

value: immortalized multipotent otic progenitor


title: PolII ChIP 1

description: RNA polymerase II ChIP biological replicate 1


title: CK_6wk_DNA_H3K27me3

value: brain (hippocampus)


title: B27_1

description: iMOP w/o bFGF biological replicate 1


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 21

value: Ad Libitum Fed (ALF)

value: ZT21; Zeitgeber Time 21


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 18

value: Oregon R

value: male

value: ZT18; Zeitgeber Time 18


title: CKp25_2wk_DNA_H3K27ac

value: H3K27ac (Abcam, catalog# ab4729, lot# GR87165-1)


title: CK_6wk_DNA_H3K27ac

value: CK


title: CK_2wk_DNA_H3K27ac

value: 2 weeks


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 15

value: ZT15; Zeitgeber Time 15

value: head


title: CKp25_6wk_DNA_H3K36me3

value: H3K36me3 (Abcam, catalog# ab9050, lot# GR82518-1 and also 750267 earlier)


title: Otosphere6

description: Otosphere biological replicate 3

source_name: Otosphere

value: Otosphere


title: CKp25_6wk_RNA

description: CKp25_6wk_3937.bam, CKp25_6wk_3940.bam, CKp25_6wk_4008.bam

extract_protocol:
Mouse hippocampus was harvested immediately after euthanasia. Upon dissection tissue was flash-frozen in liquid nitrogen.
Total RNA was quality-controlled using Agilent’s Bioanalyzer and prepared for sequencing using Illumina’s TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero. High-throughput sequencing was performed on an Illumina HiSeq 2000 platform.  Roughly 15 million 76 pair-end reads were generated for each dataset.

value: 6 weeks

value: RNA


title: Head, 5 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 06

value: 5 Weeks

value: Time Restricted Fed (TLF)

value: ZT06; Zeitgeber Time 06


title: Input DNA

description: Input DNA

value: immortalized multipotent otic progenitor


title: CKp25_2wk_RNA

description: CKp25_2wk_4518.bam, CKp25_2wk_4890.bam, CKp25_2wk_4894.bam

extract_protocol:
Mouse hippocampus was harvested immediately after euthanasia. Upon dissection tissue was flash-frozen in liquid nitrogen.
Total RNA was quality-controlled using Agilent’s Bioanalyzer and prepared for sequencing using Illumina’s TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero.

value: brain (hippocampus)


title: CK_6wk_RNA

description: CK_6wk_3936.bam, CK_6wk_3938.bam, CK_6wk_4009.bam


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 09

value: Oregon R

value: Ad Libitum Fed (ALF)

value: ZT09; Zeitgeber Time 09


title: CK_2wk_RNA

description: CK_2wk_4520.bam, CK_2wk_4891.bam, CK_2wk_4893.bam


title: Otosphere5

description: Otosphere biological replicate 2


title: CK_2wk_DNA_H3K27me3

value: H3K27me3 (Millipore, catalog# 07-449, lot# 1999681)


title: Otosphere2

description: Otosphere biological replicate 1


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 06

value: male


title: Just ERCC spikeins

city: Los Angeles

last: Hoffmann

state: CA

address: 570 Boyer Hall

department: MIMG

institute: UCLA

description: Negative

data_processing:
Reads were aligned to the ENSEMBL NCBI m37 genome (Church et al, 2009) using rna-STAR(Dobin et al, 2013) using default settings.
To compute spikein concentrations for normalization purposes, the 23 most abundant RNA spikein concentrations (at least one read in all samples) were compared to the expected concentrations in log-log space, and the y-intercept in log-space was used to compute a normalized spike in concentrations for each sample.
A constant count of 100 was added because spikeins with counts < 100 were variable across samples.
To assess the overall quality of each cell, we correlated their transcriptomes to the average across all cells as well as to the positive tube control. We found that one large cell had significantly lower correlation, so we omitted it from further analysis.
To determine if a particular gene was upregulated/downregulated in big cells, we computed an expression score: Escore=Sum(Big cells with count>300)/#Big-Sum(Small cells with count>300)/#Small
Differential gene expression was computed using WebGestalt (Want et al, 2013) using FDR correction and a p-value of 0.05. Significant transcription factors were further filtered to remove non-NFkB downstream targets as defined in Table E1 of the manuscript.
Genome_build: ENSEMBL NCBI m37
Supplementary_files_format_and_content: Excel matrix tables of features/gene counts for each sample, and other post-processing analyses

source_name: Primary B cell from mouse spleen

growth_protocol: 6-8 week old wildtype mice were maintained in ventilated cages. Animal studies were approved by the Institutional Animal Care and Use Committee of the University of California, San Diego.

extract_protocol:
Primary splenocytes were isolated from 6-8 week old mice, naïve B cells purified using magnetic bead separation (Miltenyi Biotec), and stimulated with 250 ng/mL CpG ODN 1668 (Invivogen). B cells were grown in fresh media with 1% penicillin streptomycin solution (Mediatech Inc.), 5 mM L-glutamine (Mediatech Inc.), 25 mM HEPES buffer (Mediatech Inc.), 10% FCS and 55 uM 2-ME (Fisher Scientific) at a concentration of 5x10^4 cells/mL in 48 well plates at 37oC for a 24 h period. Stimulated wildtype B cells were collected at 24 h post stimulation and concentrated to 5x10^5 cells per mL. Cells were loaded onto a 10-17 uM primed C1 single-cell auto prep array IFC (Fluidigm), and phase contrast images were taken of all viable cells as determined by the Live/Dead® Viability/Cytotoxicity Kit (Invitrogen). ERCC RNA spikein controls (LifeTechnologies) were added to the lysis mix at a 1:200 dilution. Tube controls (bulk cell positive control, and no cell negative control) were also prepared according to the Fluidigm protocol. Lysis, reverse transcription, and PCR were performed using the SMARTer Ultra Low RNA Kit (CloneTech) and Advantage® 2 PCR Kit (CloneTech) on individual cells using the C1 Single-Cell Auto Prep System (Fluidigm). Cell size was manually determined from images using ImageJ software.
Sample libraries for the five smallest and five largest cells along with the controls were prepared using the Nextera XT DNA Sample Preparation (Illumina), and library quality was assayed using the Quant-iT PicoGreen dye (Life Technologies) quantification on a Qubit® 2.0 Fluorometer (LifeTechnologies) and by gel electrophoresis.

treatment_protocol: Mice were not treated prior to B cell purification

value: wild type

value: 6-8 weeks

value: spleen

value: primary B cells

tag: stimulated with

value: 250 nM CpG ODN 1668

tag: time after stimulation

tag: sample group

value: Just ERCC spikeins


title: Bulk sample diluted (24 h)

description: Positive

tag: strain

tag: cell type

value: Bulk sample diluted (24 h)


title: Bulk sample from 0 h

description: 0h ctrl

value: 0 h

value: Bulk sample_unstimulated (0h)


title: Large cell from well G2

value: Large cell


title: ChIP CTCF Th1

description:
genomic DNA
ChIP-seq
mm9

source_name: primary CD4+ T cells from spleen and lymph nodes

value: in vitro polarized T helper1 cells for 7 days

tag: culture condition

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition

value: C57BL/6J (wild type)

value: chip antibody:anti-CTCF


title: bFGF_1

description: iMOP with bFGF biological replicate 1

value: immortalized multipotent otic progenitor


title: ChIP p300 Th17

description:
genomic DNA
ChIP-seq
mm9

value: in vitro polarized T helper17 cells for 3 days

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th17 condition

value: chip antibody:anti-p300, antibody vendor/catalog#:sc-585, Santa Cruz Biotechnology


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 00

value: Oregon R

value: male

value: 5 Weeks

value: Ad Libitum Fed (ALF)

tag: time point

value: ZT00; Zeitgeber Time 00

value: head


title: bFGF_2

description: iMOP with bFGF biological replicate 2

tag: treatment


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 03

value: ZT03; Zeitgeber Time 03


title: Large cell from well E3

value: wild type

value: 6-8 weeks

value: spleen

value: primary B cells

value: 250 nM CpG ODN 1668


title: CKp25_6wk_DNA_H3K27ac

value: 6 weeks

value: brain (hippocampus)

tag: chip antibody

value: H3K27ac (Abcam, catalog# ab4729, lot# GR87165-1)


title: Large cell from well E1

value: Large cell


title: Small cell from well F7

value: Small cell


title: Head, 5 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 12

value: Oregon R

value: ZT12; Zeitgeber Time 12


title: Head, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 12

value: male

value: 3 Weeks

value: Time Restricted Fed (TLF)


title: Head, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 18

value: ZT18; Zeitgeber Time 18

value: head


title: Large cell from well C1

value: wild type


title: Head, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 06

value: ZT06; Zeitgeber Time 06


title: Small cell from well H1

value: 6-8 weeks

value: spleen


title: Small cell from well C12

value: primary B cells

value: 250 nM CpG ODN 1668


title: RNA WT Treg rep3

description:
RNA with spikein
RNA-seq
mm9

value: in vitro polarized inducible regulatory cells for 3 days

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under iTreg condition

tag: genotype

value: C57BL/6J (wild type)


title: Small cell from well C7

value: Small cell


title: Small cell from well A2


title: Head, 3 Weeks Old Male Drosophila, Time Restricted Fed, Zeitgeber Time 00

value: Oregon R

tag: Sex

value: ZT00; Zeitgeber Time 00


title: RNA Bach2KO Treg rep2

description:
RNA with spikein
RNA-seq
mm9

value: C57BL/6J (Bach2KO)


title: RNA Bach2KO Treg rep1

description:
RNA with spikein
RNA-seq
mm9


title: Large cell from well C3

tag: age

value: Large cell


title: RNA WT Treg rep2

description:
RNA with spikein
RNA-seq
mm9


title: Head, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 18

value: male

value: 3 Weeks

tag: feeding type

value: Ad Libitum Fed (ALF)


title: RNA WT Treg rep1

description:
RNA with spikein
RNA-seq
mm9

value: wild type


title: Head, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 06

value: ZT06; Zeitgeber Time 06

tag: tissue

value: head


title: RNA Th0_no_tofa

description:
RNA
RNA-seq
mm9

value: in vitro activated Th0 condition for 3 days

value: FACS sorted naive CD4+T cells treated with anti-CD3/CD28 for 3 days

value: C57BL/6J (stat5 fl/fl OT2)


title: RNA Th0_tofa

description:
RNA
RNA-seq
mm9

value: tofacitinib


title: 249

first: Mark

last: Cookson

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

description: Sample 11

data_processing:
Basecalls performed using CASAVA version 1.7.1
Tophat v2.0.6/ Bowtie v2.0.2.0
htseq v0.5.3p9
DESeq v1.14.0
DEXSeq v1.8.0
Genome_build: mm9
Supplementary_files_format_and_content: Polg_processed_data_RNA-seqQC.txt
Supplementary_files_format_and_content: PolG_rawcounts_wMT.csv contains the read counts at gene level which were input into DESEQ.
Supplementary_files_format_and_content: The exoncount.txt files contain the exon level data that was input into DEXSEQ
Supplementary_files_format_and_content: Polg_processed_data_DESEQ.txt contains the data comparing expression levels between the two groups (Con = 3 WT/WT and 1 WT/D257A, Mut = 7 D257A/D257A) at the gene level. Base_Mean is the average normalized read count for all 11 samples.  DESEQ provides information about expression levels of entire genes.
Supplementary_files_format_and_content: Polg_processed_data_DEXSEQ.txt contains the data comparing expression levels between the two groups ( Con = 3 WT/WT, Mut = 7 D257A/D257A) at the exon level. DEXSEQ provides information about alternative exon usage.

source_name: Cerebrum

extract_protocol:
Total RNA was extracted from frozen cerebral tissue with TRIzol (Invitrogen) using a tissue homogenizer. RNA quality was determined using the Agilent 2100 Bioanalyzer RNA Nano Chip (Mean RIN = 9.22, RIN Range = 7.8-9.6). We purified poly(A)+ RNA from 4 μg total RNA using poly-T oligo attached magnetic beads and synthesized cDNA libraries using the TruSeq RNA sample preparations kit with random priming (Illumina cat. no. RS-122-2001) as per the manufacturer’s protocol. The 11 libraries were multiplexed (6 samples per pool) and 3.5 pmol of pooled cDNA was run on a single flowcell lane. 100-bp paired end sequences were generated using an Illumina Hi-Seq sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Cerebrum

value: 1 year

tag: genotype/variation

value: Mutator


title: 211

description: Sample 3


title: 217

description: Sample 4


title: 239

description: Sample 7

value: WT/WT


title: 246

description: Sample 9


title: 240

description: Sample 8


title: 236

description: Sample 5


title: 237

description: Sample 6


title: 207

description: Sample 2


title: 205

description: Sample 1


title: ΔVpacspD

city: Shanghai

first: Lanming

last: Chen

address: 999 Hu Cheng Huan Road

department: College of Food Science and Technology

country: China

institute: Shanghai Ocean University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to Vibrio parahemolyticus CHN25 whole genome using bowtie (version: 2-2.0.5).
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Mortazavi et al., Nature methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Vibrio parahemolyticus CHN25
Supplementary_files_format_and_content: tab-delimited text files include count and RPKM values for each Sample

organism: Vibrio parahaemolyticus

source_name: mid-logarithmic phase RNA,10 °C

extract_protocol:
Total RNA was extracted using RNeasy Protect bacterial mini kit 74524(Qiagen, Hilden, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell

tag: temperature

value: 10 °C

value: cspD gene knockout


title: ΔVpacspAD

value: cspA and cspD genes knockout


title: ΔVpacspA

value: cspA gene knockout


title: Head, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 12

value: Oregon R

value: male

value: 3 Weeks

value: Ad Libitum Fed (ALF)

value: ZT12; Zeitgeber Time 12


title: 4C-seq, GCLM bait, H1 mesenchymal stem cells, replicate two

first: Jesse

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

description:
GCLM_rep2_read1.fastq.gz
GCLM_rep2_read2.fastq.gz

data_processing:
fastq:  Illumina's HiSeq Control Software
For 4C read alignment, sequences were aligned to an H1 variant masked version of the hg18 genome.  Data was aligned and normalized using the 4cseqpipe software.
Normalized fragment level interactions were averaged over sliding windows with a 1kb step size surrounding the bait region of interest.
Genome_build: hg18
Supplementary_files_format_and_content: Normalized interaction frequency files are in bedGraph format.

source_name: H1 mesenchymal stem cells

growth_protocol: Growth and differentiation of H1 hESCs was performed as previously described in Xie et al., 2013, Cell 153 (1134-1148)

extract_protocol:
4C experiments were performed as described previously (van de Werken et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions, Nature Methods 9, 969-972 2012).  Primer design for allelic 4C-seq was performed as previously described (Holwerda et al., Allelilc exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells. Nucleic Acids Research 41, 6905-6916 2013).
Sequencing libraries were constructed according to previous publication (van de Werken et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions, Nature Methods 9, 969-972 2012).

value: H1 embryonic stem cells


title: 4C-seq, MAN1C1 bait, H1 mesenchymal stem cells, replicate one

description:
MAN1C1_rep1_read1.fastq.gz
MAN1C1_rep1_read2.fastq.gz


title: 4C-seq, MAN1C1 bait, H1 mesenchymal stem cells, replicate two

description:
MAN1C1_rep2_read1.fastq.gz
MAN1C1_rep2_read2.fastq.gz


title: 4C-seq, GCLM bait, H1 mesenchymal stem cells, replicate one

description:
GCLM_rep1_read1.fastq.gz
GCLM_rep1_read2.fastq.gz


title: Head, 3 Weeks Old Male Drosophila, Ad Libitum Fed, Zeitgeber Time 00

value: ZT00; Zeitgeber Time 00

value: head


title: 248

description: Sample 10

value: Cerebrum


title: 4C-seq, PXK bait, H1 mesenchymal stem cells, replicate one

description:
PXK_rep1_read1.fastq.gz
PXK_rep1_read2.fastq.gz


title: 4C-seq, HAPLN1 bait, H1 mesenchymal stem cells, replicate two

description:
HAPLN1_rep2_read1.fastq.gz
HAPLN1_rep2_read2.fastq.gz


title: 4C-seq, HAPLN1 bait, H1 mesenchymal stem cells, replicate one

description:
HAPLN1_rep1_read1.fastq.gz
HAPLN1_rep1_read2.fastq.gz


title: 4C-seq, MT2A bait, H1 embryonic stem cells, replicate two

description:
MT2A_rep2_read1.fastq.gz
MT2A_rep2_read2.fastq.gz

source_name: H1 embryonic stem cells


title: 4C-seq, MT2A bait, H1 embryonic stem cells, replicate one

description:
MT2A_rep1_read1.fastq.gz
MT2A_rep1_read2.fastq.gz


title: 4C-seq, FAM65B bait, H1 embryonic stem cells, replicate two

description:
FAM65B_rep2_read1.fastq.gz
FAM65B_rep2_read2.fastq.gz


title: WT(G)

value: wild type


title: 4C-seq, FAM65B bait, H1 embryonic stem cells, replicate one

description:
FAM65B_rep1_read1.fastq.gz
FAM65B_rep1_read2.fastq.gz


title: 4C-seq, PXK bait, H1 mesenchymal stem cells, replicate two

description:
PXK_rep2_read1.fastq.gz
PXK_rep2_read2.fastq.gz


title: Brg1 ChIP-Seq No Dex

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: Brg1-ChIP in untreated cells

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%.   Peaks with the maximum tag density lower than 10 were eliminated.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots.

source_name: 3134 cells

growth_protocol: For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, and penicillin-streptomycin cocktail.

extract_protocol: NEB Chip-Seq Prep Kit was used and lysates were clarified from sonicated nuclei and p300-DNA complexes or BRG1-DNA complexes were isolated with antibody and prepared for sequencing according to the manufacturer (Illumina).

treatment_protocol: Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran treated serum 48 hours prior to conducting the experiment.  Cells were untreated or induced with 600nM Corticosterone, 100nM dexamethasone

tag: cell line

value: mouse mammary cells

value: 0 min Dex

tag: replicate

value: replicate 1

tag: chip antibodies

value: anti-BRG1 (SMARCA4) antibody

tag: chip antibody vendor

value: Epitomics


title: p300 ChIP-Seq 60m Dex

description: p300-ChIP in cells with Dex for 60 min

tag: cell type

value: 60 min Dex

value: anti-p300 (EP300)] antibody

value: a kind gift from Dr. K. Gardner, NCI


title: ocu.br.2

status: Public on Feb 17 2015

city: Seoul

first: Alexey

last: Fushan

state: Seodaemun-gu

address: 52, Ewhayeodae-gil

institute: EWHA

description: biological replicate 2

data_processing:
The RNA-seq libraries were each sequenced (76 cycles) in at least one lane of the Illumina Genome Analyser IIx platform.
Samples were demultiplexed and the indexed adapter sequences were trimmed using the CASAVA v1.8.2 software (Illumina, Inc.).
The fluorophore intensity files were analyzed with the standard Illumina base-calling algorithms.
51-bp paired-end reads that passed the chastity filter threshold were mapped using TopHat4 2.0 with default parameter values, except for distance between mature pairs (r=200) and the number of allowable mismatches between read and genomic sequences (n=3) to ensure possible genetic heterogeneity between populations. The anchor size (i.e. the minimum aligned length spanning each of the two exons that deﬁne a splice junction) was set at 8 bp, and we allowed 1 mismatch on the anchor region. The transcript isoform abundance and averaged gene expression levels were calculated and FPKM normalized using Cufflinks.
Genome_build: Bos taurus Ensembl genome build 62,
Capra hircus de novo transcriptome assembly (PRJNA182763); see GSE43013_chi.rna.gtf.
Sus scrofa Ensembl genome build 62
Canis familiaris Ensembl genome build 62
Felis catus Ensembl genome build 62
Meles meles de novo transcriptome assembly (PRJNA182767)
Ursus americanus de novo transcriptome assembly (PRJNA182773)
Murina leucogaster de novo transcriptome assembly (PRJNA182766)
Tadarida brasiliensis de novo transcriptome assembly (PRJNA182772)
Petaurus breviceps de novo transcriptome assembly (PRJNA182769)
Erinaceus europaeus Ensembl genome build 62
Oryctolagus cuniculus Ensembl genome build 62
Equus caballus Ensembl genome build 62
Chlorocebus aethiops de novo transcriptome assembly (PRJNA182762)
Acomys cahirinus de novo transcriptome assembly (PRJNA182705)
Cavia porcellus Ensembl genome build 62
Mesocricetus auratus de novo transcriptome assembly (PRJNA182765)
Meriones unguiculatus de novo transcriptome assembly (PRJNA182768)
Mus musculus Ensembl genome build 62
Peromyscus leucopus de novo transcriptome assembly (PRJNA182770)
Rattus norvegicus Ensembl genome build 62
Tamias sibiricus de novo transcriptome assembly (PRJNA183188)
Suncus murinus de novo transcriptome assembly (PRJNA182771).
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Oryctolagus cuniculus

source_name: Oryctolagus cuniculus_brain

extract_protocol:
Total RNA was extracted using RNAeasy (Qiagen) purification kit according to the manufacturer’s instructions. RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina, Inc.) in accordance with the manufacturer' instructions. Polyadenylated RNA was isolated using a poly-dT bead procedure, chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 300-bp fragments were excised and then PCR-amplified (20 cycles). After column purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalysers.

tag: strain (source)

value: in-house colony

value: adult

value: normal brain

tag: organ part

value: frontal parts of brain


title: ocu.br.1

description: biological replicate 1


title: CTCF CHIP-Seq, H1 Trophectoderm cells, replicate one

data_processing:
fastq:  Illumina's HiSeq Control Software
For Hi-C read alignment, we aligned Hi-C reads to the hg18 (human) genome. We masked any bases in the genome that were genotyped as SNPs in the H1 genome. These bases were masked to “N” in order to reduce reference bias mapping artifacts. Hi-C reads were aligned iteratively as single end reads using Novoalign. Specifically, for iterative alignment, we first aligned the entire sequencing read to either the mouse or human genome. Unmapped reads are then trimmed by 5 base pairs and realigned. This process is repeated until the read successfully aligns to the genome or until the trimmed read is less than 25 base pairs long.  After iterative mapping was finished, read pairs were re-constructed from single reads using an in house pipeline.  Unmapped reads were filtered out and PCR duplicate reads were removed.  Final alignment files were then processed using the GATK pipeline, specifically using Indel Realignment and Variant Recalibration.  A similar pipeline was used for alignment of the other high-throughput sequencing datasets without the iterative alignment step.
Haplotypes were generated from the final aligned bam file after merging the two biological replicats using the HapCUT algorithm.  The details of HapCUT are described previously (Bansal and Bafna, Bioinformatics 24, i153-159, 2008).
Genome_build: hg18
Supplementary_files_format_and_content: Reads are listed in bed format with one line for each sequencing read.  The reads have been split by haplotype into the "A" and "B" (alternatively, "p1" and "p2") alleles according to which haplotype the bases within each sequencing read correspond.  For paired end Hi-C data, each line lists a single read, and paired infomration can be obtained from the read names.  The original fastq files for data other than the Hi-C and CTCF ChIP-seq are available in the GSE16256 dataset.
Supplementary_files_format_and_content: The processed haplotypes for the H1 genome ("H1_haps.vcf") are available in VCF format.

source_name: H1 Trophectoderm cells

extract_protocol: Sequencing libraries were constructed according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

value: H1 Trophectoderm cells


title: CTCF CHIP-Seq, H1 Mesendoderm cells, replicate one

source_name: H1 Mesendoderm cells

value: H1 Mesendoderm cells


title: CTCF CHIP-Seq, H1 Mesenchymal stem cells, replicate one

source_name: H1 Mesenchymal stem cells

value: H1 Mesenchymal stem cells


title: CTCF CHIP-Seq, H1 Neuronal Progenitor cells, replicate one

source_name: H1 Neuronal Progenitor cells

value: H1 Neuronal Progenitor cells


title: cpo.br.1

description: biological replicate 1

organism: Cavia porcellus

source_name: Cavia porcellus_brain

value: wild type


title: cpo.br.3

description: biological replicate 3


title: cpo.br.2

description: biological replicate 2


title: Hi-C, H1 Mesenchymal stem cells, replicate two

description:
MS_R2_T1_read1.fastq.gz
MS_R2_T1_read2.fastq.gz
MS_R2_T2_read1.fastq.gz
MS_R2_T2_read2.fastq.gz
MS_R2_T3_read1.fastq.gz
MS_R2_T3_read2.fastq.gz

data_processing:
Library strategy: Hi-C
fastq:  Illumina's HiSeq Control Software
For Hi-C read alignment, we aligned Hi-C reads to the hg18 (human) genome. We masked any bases in the genome that were genotyped as SNPs in the H1 genome. These bases were masked to “N” in order to reduce reference bias mapping artifacts. Hi-C reads were aligned iteratively as single end reads using Novoalign. Specifically, for iterative alignment, we first aligned the entire sequencing read to either the mouse or human genome. Unmapped reads are then trimmed by 5 base pairs and realigned. This process is repeated until the read successfully aligns to the genome or until the trimmed read is less than 25 base pairs long.  After iterative mapping was finished, read pairs were re-constructed from single reads using an in house pipeline.  Unmapped reads were filtered out and PCR duplicate reads were removed.  Final alignment files were then processed using the GATK pipeline, specifically using Indel Realignment and Variant Recalibration.  A similar pipeline was used for alignment of the other high-throughput sequencing datasets without the iterative alignment step.
Haplotypes were generated from the final aligned bam file after merging the two biological replicats using the HapCUT algorithm.  The details of HapCUT are described previously (Bansal and Bafna, Bioinformatics 24, i153-159, 2008).
Genome_build: hg18
Supplementary_files_format_and_content: Reads are listed in bed format with one line for each sequencing read.  The reads have been split by haplotype into the "A" and "B" (alternatively, "p1" and "p2") alleles according to which haplotype the bases within each sequencing read correspond.  For paired end Hi-C data, each line lists a single read, and paired infomration can be obtained from the read names.  The original fastq files for data other than the Hi-C and CTCF ChIP-seq are available in the GSE16256 dataset.
Supplementary_files_format_and_content: The processed haplotypes for the H1 genome ("H1_haps.vcf") are available in VCF format.


title: ocu.kd.2

description: biological replicate 2

source_name: Oryctolagus cuniculus_kidney

value: normal kidney

value: whole kidney


title: ocu.kd.1

description: biological replicate 1


title: Hi-C, H1 Mesendoderm cells, replicate two

description:
Me_R2_T1_read1.fastq.gz
Me_R2_T1_read2.fastq.gz
Me_R2_T2_read1.fastq.gz
Me_R2_T2_read2.fastq.gz
Me_R2_T3_read1.fastq.gz
Me_R2_T3_read2.fastq.gz
Me_R2_T4_read1.fastq.gz
Me_R2_T4_read2.fastq.gz


title: Hi-C, H1 Trophectoderm cells, replicate two

description:
Tr_R2_T1_read1.fastq.gz
Tr_R2_T1_read2.fastq.gz
Tr_R2_T2_read1.fastq.gz
Tr_R2_T2_read2.fastq.gz
Tr_R2_T3_read1.fastq.gz
Tr_R2_T3_read2.fastq.gz


title: Hi-C, H1 Neuronal Progenitor cells, replicate one

description:
NP_R1_T1_read1.fastq.gz
NP_R1_T1_read2.fastq.gz
NP_R1_T2_read1.fastq.gz
NP_R1_T2_read2.fastq.gz
NP_R1_T3_read1.fastq.gz
NP_R1_T3_read2.fastq.gz
NP_R1_T4_read1.fastq.gz
NP_R1_T4_read2.fastq.gz
NP_R1_T5_read1.fastq.gz
NP_R1_T5_read2.fastq.gz
NP_R1_T6_read1.fastq.gz
NP_R1_T6_read2.fastq.gz
NP_R1_T7_read1.fastq.gz
NP_R1_T7_read2.fastq.gz
NP_R1_T8_read1.fastq.gz
NP_R1_T8_read2.fastq.gz


title: ocu.lv.1

description: biological replicate 1

source_name: Oryctolagus cuniculus_liver

value: normal liver

value: whole liver


title: ocu.lv.2

description: biological replicate 2


title: Hi-C, H1 Trophectoderm cells, replicate one

description:
Tr_R1_T1_read1.fastq.gz
Tr_R1_T1_read2.fastq.gz
Tr_R1_T2_read1.fastq.gz
Tr_R1_T2_read2.fastq.gz
Tr_R1_T3_read1.fastq.gz
Tr_R1_T3_read2.fastq.gz
Tr_R1_T4_read1.fastq.gz
Tr_R1_T4_read2.fastq.gz
Tr_R1_T5_read1.fastq.gz
Tr_R1_T5_read2.fastq.gz
Tr_R1_T6_read1.fastq.gz
Tr_R1_T6_read2.fastq.gz
Tr_R1_T7_read1.fastq.gz
Tr_R1_T7_read2.fastq.gz


title: Hi-C, H1 Mesendoderm cells, replicate one

description:
Me_R1_T1_read1.fastq.gz
Me_R1_T1_read2.fastq.gz
Me_R1_T2_read1.fastq.gz
Me_R1_T2_read2.fastq.gz
Me_R1_T3_read1.fastq.gz
Me_R1_T3_read2.fastq.gz
Me_R1_T4_read1.fastq.gz
Me_R1_T4_read2.fastq.gz
Me_R1_T5_read1.fastq.gz
Me_R1_T5_read2.fastq.gz
Me_R1_T6_read1.fastq.gz
Me_R1_T6_read2.fastq.gz
Me_R1_T7_read1.fastq.gz
Me_R1_T7_read2.fastq.gz


title: Hi-C, H1 Neuronal Progenitor cells, replicate two

description:
NP_R2_T1_read1.fastq.gz
NP_R2_T1_read2.fastq.gz
NP_R2_T2_read1.fastq.gz
NP_R2_T2_read2.fastq.gz
NP_R2_T3_read1.fastq.gz
NP_R2_T3_read2.fastq.gz


title: cpo.kd.3

description: biological replicate 3

source_name: Cavia porcellus_kidney


title: CTCF CHIP-Seq, H1 embryonic stem cells, replicate one

value: H1 embryonic stem cells


title: cpo.kd.2

description: biological replicate 2


title: cpo.kd.1

description: biological replicate 1


title: Hi-C, H1 Mesenchymal stem cells, replicate one

description:
MS_R1_T1_read1.fastq.gz
MS_R1_T1_read2.fastq.gz
MS_R1_T2_read1.fastq.gz
MS_R1_T2_read2.fastq.gz
MS_R1_T3_read1.fastq.gz
MS_R1_T3_read2.fastq.gz


title: cpo.lv.3

description: biological replicate 3

source_name: Cavia porcellus_liver


title: cpo.lv.2

description: biological replicate 2


title: p300 ChIP-Seq No Dex

description: p300-ChIP in untreated cells

value: mouse mammary cells

tag: treatment

value: 0 min Dex

value: replicate 1


title: caf.kd.1

description: biological replicate 1

organism: Canis lupus familiaris

source_name: Canis familiaris_kidney

value: in-house colony


title: caf.br.2

description: biological replicate 2

source_name: Canis familiaris_brain

value: adult


title: aca.lv.2

description: biological replicate 2

organism: Acomys cahirinus

source_name: Acomys cahirinus_liver


title: aca.lv.1

description: biological replicate 1


title: caf.br.1

description: biological replicate 1

value: normal brain


title: cpo.lv.1

description: biological replicate 1


title: aca.lv.3

description: biological replicate 3


title: caf.kd.2

description: biological replicate 2


title: caf.lv.1

description: biological replicate 1

source_name: Canis familiaris_liver


title: B1H assay using TTCT as bait, replicate 2

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Reads were trimmed at the 3’ end, so that for each read the minimum Phred quality score of any base of the remaining part was 12, there were no more than 10 bases with Phred quality scores <20, and the reads, after removing the constant vector region and amplification adapters, were not longer than 80 bases. The trimmed reads were further filtered to remove those shorter than 50 bases.
Reads were mapped to the library using Bowtie, allowing a maximum of 2 mismatches at the first 28 bases and a maximum of 70 for the sum of quality values at all mismatched read positions, retaining only reads that were uniquely mapped. The number of reads that mapped to each Egr1 variant was recorded.
Genome_build: Custom library
Supplementary_files_format_and_content: Text files containing the number of reads that were uniquely mapped to each Egr1 variant

organism: synthetic construct

source_name: B1H assay using TTCT as bait

growth_protocol: We performed B1H screens essentially as described before (PMID 17406209), with the modification that we first transformed the bacterial selection strain with the bait plasmid, then made electrocompetent cells, then transformed these with the prey library of C2H2 variants.  We plated ~10^7 transformants on three μM medium plates (150 mm) containing 1 mM 3-Amino-1,2,4-triazole (3-AT), 100 μg/ml ampicillin, 25 μg/ml kanamycin, 10 μM IPTG, no histidine, and 0.2 mM uracil.  We incubated the plates at 37C for 2 days, or more if needed to obtain colonies (typically hundreds to thousands of visible colonies of varying size).

extract_protocol:
We scraped the colonies from the plates, and prepared plasmid DNA.
We PCR-amplified F3 from the plasmid DNA using Illumina barcoded primers.

tag: bait

value: TTCT

tag: ols

tag: molecule type

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using TTTT as bait, replicate 1

source_name: B1H assay using TTTT as bait

value: TTTT


title: B1H assay using TGTG as bait, replicate 2

source_name: B1H assay using TGTG as bait

value: TGTG


title: B1H assay using TTTG as bait, replicate 1

source_name: B1H assay using TTTG as bait

value: TTTG


title: B1H assay using TTCC as bait, replicate 1

source_name: B1H assay using TTCC as bait

value: TTCC


title: B1H assay using TGTG as bait, replicate 1


title: B1H assay using TTTG as bait, replicate 2


title: B1H assay using TTGT as bait, replicate 2

source_name: B1H assay using TTGT as bait

value: TTGT


title: caf.lv.2

description: biological replicate 2

value: wild type

tag: age


title: B1H assay using TTCC as bait, replicate 2


title: B1H assay using TCTG as bait, replicate 2

source_name: B1H assay using TCTG as bait

value: TCTG


title: B1H assay using TGAG as bait, replicate 2

source_name: B1H assay using TGAG as bait

value: TGAG


title: B1H assay using TTCG as bait, replicate 2

source_name: B1H assay using TTCG as bait

value: TTCG


title: B1H assay using TGAG as bait, replicate 1


title: B1H assay using TTCA as bait, replicate 2

source_name: B1H assay using TTCA as bait

value: TTCA


title: B1H assay using TTCA as bait, replicate 1


title: B1H assay using TTCT as bait, replicate 1


title: B1H assay using TTTT as bait, replicate 2


title: B1H assay using TTGT as bait, replicate 1


title: Effector 14h

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

data_processing:
RNA-Seq data analysis was performed using the Wardrobe Experiment Management System (http://www.biorxiv.org/content/early/2014/12/18/012799; https://code.google.com/p/genome-tools/).
Briefly, reads were mapped to the hg19 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.0c and assigned to the RefSeq genes  using the Wardrobe algorithm.
STAR PARAMS:
--clip3pNbases 0      --seedSearchStartLmax 15   --alignSJDBoverhangMin 1
--outFilterMultimapNmax 1   --outFilterMismatchNmax 5   --clip5pNbases 0
Genome_build: hg19
Supplementary_files_format_and_content: csv file includes RPKM values for each sample

source_name: T cells

growth_protocol: Blood samples were obtained from Hoxworth Blood bank. Samples were de-identified and the study was done under an exemption provided by CCHMC IRB. PBMCs were depleted of CD45RO+, CD8+, and CD25+ cells using biotinylated antibodies (BioLegend) and IMagTM streptavidin beads (BD Biosciences) and stimulated in 6-well plates at 8x106 cells/2 ml with soluble aCD3 (2 mg/ml, OKT-3, BioXCell) and aCD28 (Effector samples; 1 mg/ml, BD Biosciences) or CTLA4-Ig (Anergic samples; 7.5 mg/ml, BioXCell) in RPMI 1640 supplemented with 10% FBS, penicillin/streptomycin, L-glutamine, and b-mercapethanol. At specified timepoints CD4 T cells were purified using Invitrogen positive selection kit.

extract_protocol:
RNA was extracted with Aurum™ Total RNA Mini Kit (Bio-Rad)
A modified dUTP method was used for preparation of RNA-Seq libraries[27]. Briefly, mRNA was purified from total RNA by Dynabeads® mRNA Purification Kit (Invitrogen) and reverse-transcribed with SuperScript® III (Invitrogen). The second strand was created by DNA Polymerase 1 (NEB) in the presence of RNase H and a dNTP mix containing dUTP instead dTTP. The cDNA was fragmented on a Covaris sonicator, and end repair and A-tailing were performed using the Quick Blunting kit and exo- Klenow fragment of DNA polymerase I, respectively (NEB). Illumina genomic adapters were ligated, and the sample was size-fractionated (~170–400 bp) on E-Gel EX 2% agarose (Invitrogen). After uracil-dna glycosylase (UDG) treatment (NEB) and a final PCR amplification step with Illumina primers (18 cycles), the cDNA libraries were size-fractionated (~175-400 bp) on a 2% agarose gel, quantified using a Qubit 2.0 fluorometer and dsDNA HS kit (Invitrogen), and sent to sequencing on a Illumina HiSeq 2500 sequencing system

treatment_protocol: Cells were stimulated in 6-well plates at 8x106 cells/2 ml with soluble aCD3 (2 mg/ml, OKT-3, BioXCell) and aCD28 (1 mg/ml, BD Biosciences) or CTLA4-Ig (7.5 mg/ml, BioXCell).

tag: cell state

value: Effector 14h


title: Anergic 14h

value: Anergic 14h


title: Anergic 7h

value: Anergic 7h


title: Effector 7h

value: Effector 7h


title: B1H assay using TCTA as bait, replicate 2

source_name: B1H assay using TCTA as bait

value: TCTA


title: Anergic 3h

value: Anergic 3h


title: Effector 3h

value: Effector 3h


title: B1H assay using TCTG as bait, replicate 1

value: Plasmid extracted from bacteria after selection in B1H assay


title: Resting

value: Resting


title: B1H assay using TTCG as bait, replicate 1


title: B1H assay using TCTA as bait, replicate 1


title: B1H assay using TCCG as bait, replicate 2

source_name: B1H assay using TCCG as bait

value: TCCG


title: B1H assay using TATG as bait, replicate 1

source_name: B1H assay using TATG as bait

value: TATG


title: B1H assay using TCCG as bait, replicate 1


title: B1H assay using TCAG as bait, replicate 1

source_name: B1H assay using TCAG as bait

value: TCAG


title: B1H assay using TAGA as bait, replicate 1

source_name: B1H assay using TAGA as bait

value: TAGA


title: B1H assay using TAGA as bait, replicate 2


title: B1H assay using TACG as bait, replicate 1

source_name: B1H assay using TACG as bait

value: TACG


title: B1H assay using GGCG as bait, replicate 2

source_name: B1H assay using GGCG as bait

value: GGCG


title: B1H assay using TAGC as bait, replicate 2

source_name: B1H assay using TAGC as bait

value: TAGC


title: B1H assay using TACG as bait, replicate 2


title: B1H assay using GCTG as bait, replicate 2

source_name: B1H assay using GCTG as bait

value: GCTG


title: B1H assay using GCTG as bait, replicate 1


title: B1H assay using GCCG as bait, replicate 2

source_name: B1H assay using GCCG as bait

value: GCCG


title: B1H assay using GGCG as bait, replicate 1


title: B1H assay using GCCG as bait, replicate 1


title: B1H assay using GCCC as bait, replicate 2

source_name: B1H assay using GCCC as bait

value: GCCC


title: B1H assay using TAGC as bait, replicate 1


title: B1H assay using TCAG as bait, replicate 2


title: B1H assay using TATG as bait, replicate 2


title: B1H assay using GCAG as bait, replicate 1

source_name: B1H assay using GCAG as bait

value: GCAG


title: B1H assay using GCAG as bait, replicate 2


title: B1H assay using CTTG as bait, replicate 1

source_name: B1H assay using CTTG as bait

value: CTTG


title: B1H assay using CTTT as bait, replicate 2

source_name: B1H assay using CTTT as bait

value: CTTT


title: B1H assay using CTTC as bait, replicate 2

source_name: B1H assay using CTTC as bait

value: CTTC


title: B1H assay using CTTT as bait, replicate 1


title: B1H assay using GCCC as bait, replicate 1


title: B1H assay using CTCT as bait, replicate 2

source_name: B1H assay using CTCT as bait

value: CTCT


title: B1H assay using CTCT as bait, replicate 1

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using CTTC as bait, replicate 1


title: B1H assay using CTAG as bait, replicate 2

source_name: B1H assay using CTAG as bait

value: CTAG


title: B1H assay using CTCA as bait, replicate 2

source_name: B1H assay using CTCA as bait

value: CTCA


title: B1H assay using CTCG as bait, replicate 2

source_name: B1H assay using CTCG as bait

value: CTCG


title: B1H assay using CTCA as bait, replicate 1


title: B1H assay using CTAG as bait, replicate 1


title: B1H assay using CTCG as bait, replicate 1


title: B1H assay using CGTC as bait, replicate 1

source_name: B1H assay using CGTC as bait

value: CGTC


title: B1H assay using CGTC as bait, replicate 2


title: B1H assay using CGCT as bait, replicate 1

source_name: B1H assay using CGCT as bait

value: CGCT


title: B1H assay using CGCT as bait, replicate 2


title: B1H assay using CGCG as bait, replicate 1

source_name: B1H assay using CGCG as bait

value: CGCG


title: B1H assay using CGCG as bait, replicate 2


title: B1H assay using CGCC as bait, replicate 1

source_name: B1H assay using CGCC as bait

value: CGCC


title: B1H assay using CGCA as bait, replicate 2

source_name: B1H assay using CGCA as bait

value: CGCA


title: B1H assay using CTTG as bait, replicate 2


title: B1H assay using CGCA as bait, replicate 1


title: B1H assay using CCTT as bait, replicate 2

source_name: B1H assay using CCTT as bait

value: CCTT


title: B1H assay using CGAG as bait, replicate 1

source_name: B1H assay using CGAG as bait

value: CGAG


title: B1H assay using CGAG as bait, replicate 2


title: B1H assay using CCGT as bait, replicate 2

source_name: B1H assay using CCGT as bait

value: CCGT


title: B1H assay using CCGT as bait, replicate 1


title: B1H assay using CCGA as bait, replicate 2

source_name: B1H assay using CCGA as bait

value: CCGA


title: B1H assay using CCGA as bait, replicate 1


title: B1H assay using CCCG as bait, replicate 2

source_name: B1H assay using CCCG as bait

value: CCCG


title: B1H assay using CCTT as bait, replicate 1


title: B1H assay using CCCG as bait, replicate 1


title: B1H assay using CCAG as bait, replicate 2

source_name: B1H assay using CCAG as bait

value: CCAG


title: B1H assay using CCCC as bait, replicate 1

source_name: B1H assay using CCCC as bait

value: CCCC


title: B1H assay using CCCC as bait, replicate 2


title: B1H assay using CCAC as bait, replicate 1

source_name: B1H assay using CCAC as bait

value: CCAC


title: B1H assay using CAGG as bait, replicate 1

source_name: B1H assay using CAGG as bait

value: CAGG

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using CCAC as bait, replicate 2


title: B1H assay using CAGC as bait, replicate 2

source_name: B1H assay using CAGC as bait

value: CAGC


title: B1H assay using CCAG as bait, replicate 1


title: B1H assay using CAGG as bait, replicate 2


title: B1H assay using CAGA as bait, replicate 2

source_name: B1H assay using CAGA as bait

value: CAGA


title: B1H assay using CAGC as bait, replicate 1


title: B1H assay using CGCC as bait, replicate 2


title: B1H assay using CACG as bait, replicate 2

source_name: B1H assay using CACG as bait

value: CACG


title: B1H assay using CACG as bait, replicate 1


title: B1H assay using CAGA as bait, replicate 1


title: B1H assay using ATCG as bait, replicate 1

source_name: B1H assay using ATCG as bait

value: ATCG


title: B1H assay using ATCG as bait, replicate 2


title: B1H assay using ATCA as bait, replicate 2

source_name: B1H assay using ATCA as bait

value: ATCA


title: B1H assay using ATAG as bait, replicate 1

source_name: B1H assay using ATAG as bait

value: ATAG


title: B1H assay using ATCA as bait, replicate 1


title: B1H assay using AGTT as bait, replicate 2

source_name: B1H assay using AGTT as bait

value: AGTT


title: B1H assay using AGTT as bait, replicate 1


title: B1H assay using AGGC as bait, replicate 2

source_name: B1H assay using AGGC as bait

value: AGGC


title: B1H assay using AGTC as bait, replicate 1

source_name: B1H assay using AGTC as bait

value: AGTC


title: B1H assay using ATAG as bait, replicate 2


title: B1H assay using AGGC as bait, replicate 1


title: B1H assay using AGCT as bait, replicate 2

source_name: B1H assay using AGCT as bait

value: AGCT


title: B1H assay using AGCG as bait, replicate 2

source_name: B1H assay using AGCG as bait

value: AGCG


title: B1H assay using AGCA as bait, replicate 2

source_name: B1H assay using AGCA as bait

value: AGCA


title: B1H assay using AGCT as bait, replicate 1


title: B1H assay using AGCG as bait, replicate 1


title: B1H assay using AGCC as bait, replicate 2

source_name: B1H assay using AGCC as bait

value: AGCC


title: B1H assay using AGCC as bait, replicate 1


title: B1H assay using ATCT as bait, replicate 1

source_name: B1H assay using ATCT as bait

value: ATCT


title: B1H assay using ATCT as bait, replicate 2


title: B1H assay using AGCA as bait, replicate 1


title: B1H assay using AGAC as bait, replicate 1

source_name: B1H assay using AGAC as bait

value: AGAC


title: B1H assay using AGAT as bait, replicate 1

source_name: B1H assay using AGAT as bait

value: AGAT


title: B1H assay using ACTG as bait, replicate 2

source_name: B1H assay using ACTG as bait

value: ACTG

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using AGAC as bait, replicate 2


title: B1H assay using ACTG as bait, replicate 1


title: B1H assay using ACGC as bait, replicate 1

source_name: B1H assay using ACGC as bait

value: ACGC


title: B1H assay using ACGC as bait, replicate 2


title: B1H assay using ACGA as bait, replicate 2

source_name: B1H assay using ACGA as bait

value: ACGA


title: B1H assay using ACGT as bait, replicate 1

source_name: B1H assay using ACGT as bait

value: ACGT


title: B1H assay using AGTC as bait, replicate 2


title: B1H assay using ACGA as bait, replicate 1


title: B1H assay using ACAG as bait, replicate 2

source_name: B1H assay using ACAG as bait

value: ACAG


title: B1H assay using AAGA as bait, replicate 2

source_name: B1H assay using AAGA as bait

value: AAGA


title: B1H assay using ACAG as bait, replicate 1


title: B1H assay using AAGA as bait, replicate 1


title: B1H assay using AGAT as bait, replicate 2


title: B1H assay using TTAC as bait, replicate 2

data_processing:
Reads were trimmed at the 3’ end, so that for each read the minimum Phred quality score of any base of the remaining part was 12, there were no more than 10 bases with Phred quality scores <20, and the reads, after removing the constant vector region and amplification adapters, were not longer than 80 bases. The trimmed reads were further filtered to remove those shorter than 50 bases.
Reads were mapped to the library using Bowtie, allowing a maximum of 2 mismatches at the first 28 bases and a maximum of 70 for the sum of quality values at all mismatched read positions, retaining only reads that were uniquely mapped. The number of reads that mapped to each Egr1 variant was recorded.
*count.txt contains unique ID given to each sequence in the library and its abundance count. The 'OLS.info.xlsx' file contains the mapping of these IDs to different sequences.
Genome_build: Custom library
Supplementary_files_format_and_content: Text files containing the number of reads that were uniquely mapped to each Egr1 variant

source_name: B1H assay using TTAC as bait

value: TTAC


title: B1H assay using TTTC as bait, replicate 1

source_name: B1H assay using TTTC as bait

value: TTTC


title: B1H assay using TTGA as bait, replicate 1

source_name: B1H assay using TTGA as bait

value: TTGA


title: B1H assay using TTAT as bait, replicate 1

source_name: B1H assay using TTAT as bait

value: TTAT


title: B1H assay using TTAT as bait, replicate 2


title: B1H assay using TTTC as bait, replicate 2


title: B1H assay using TTAG as bait, replicate 2

source_name: B1H assay using TTAG as bait

value: TTAG


title: B1H assay using TTGC as bait, replicate 1

source_name: B1H assay using TTGC as bait

value: TTGC


title: B1H assay using TTTA as bait, replicate 1

source_name: B1H assay using TTTA as bait

value: TTTA


title: B1H assay using TTGC as bait, replicate 2


title: B1H assay using TTGG as bait, replicate 2

source_name: B1H assay using TTGG as bait

value: TTGG


title: B1H assay using TTGA as bait, replicate 2


title: B1H assay using TTAG as bait, replicate 1


title: B1H assay using TTAC as bait, replicate 1


title: B1H assay using TTAA as bait, replicate 1

source_name: B1H assay using TTAA as bait

value: TTAA


title: B1H assay using TTAA as bait, replicate 2


title: B1H assay using ACGT as bait, replicate 2


title: B1H assay using TGTA as bait, replicate 2

source_name: B1H assay using TGTA as bait

value: TGTA


title: B1H assay using TGTA as bait, replicate 1


title: B1H assay using TGGG as bait, replicate 1

source_name: B1H assay using TGGG as bait

value: TGGG


title: B1H assay using TGGG as bait, replicate 2

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using TGGA as bait, replicate 2

source_name: B1H assay using TGGA as bait

value: TGGA


title: B1H assay using TGCT as bait, replicate 2

source_name: B1H assay using TGCT as bait

value: TGCT


title: B1H assay using TGGA as bait, replicate 1


title: B1H assay using TTTA as bait, replicate 2


title: B1H assay using TGCA as bait, replicate 2

source_name: B1H assay using TGCA as bait

value: TGCA


title: B1H assay using TTGG as bait, replicate 1


title: B1H assay using TGCA as bait, replicate 1


title: B1H assay using TGAC as bait, replicate 2

source_name: B1H assay using TGAC as bait

value: TGAC


title: chi.br.2

description: biological replicate 2

organism: Capra hircus

source_name: Capra hircus_brain

value: in-house colony

value: wild type

value: adult

tag: tissue

value: normal brain

value: frontal parts of brain


title: chi.kd.1

description: biological replicate 1

source_name: Capra hircus_kidney

value: normal kidney

value: whole kidney


title: B1H assay using TGAC as bait, replicate 1


title: B1H assay using TGCT as bait, replicate 1


title: B1H assay using TCGC as bait, replicate 1

source_name: B1H assay using TCGC as bait

value: TCGC


title: chi.br.1

description: biological replicate 1


title: chi.kd.2

description: biological replicate 2


title: B1H assay using TCGC as bait, replicate 2


title: chi.lv.2

description: biological replicate 2

source_name: Capra hircus_liver

value: normal liver

value: whole liver


title: ple.br.2

description: biological replicate 2

organism: Peromyscus leucopus

source_name: Peromyscus leucopus_brain


title: B1H assay using TCCT as bait, replicate 1

source_name: B1H assay using TCCT as bait

value: TCCT


title: B1H assay using TCCT as bait, replicate 2


title: chi.lv.1

description: biological replicate 1


title: B1H assay using TAAC as bait, replicate 1

source_name: B1H assay using TAAC as bait

value: TAAC


title: B1H assay using TAAA as bait, replicate 2

source_name: B1H assay using TAAA as bait

value: TAAA

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using TAAG as bait, replicate 2

source_name: B1H assay using TAAG as bait

value: TAAG


title: B1H assay using TAAC as bait, replicate 2


title: B1H assay using TAAG as bait, replicate 1


title: ple.kd.1

description: biological replicate 1

source_name: Peromyscus leucopus_kidney


title: B1H assay using TAAA as bait, replicate 1


title: ple.br.1

description: biological replicate 1


title: B1H assay using TAGG as bait, replicate 2

source_name: B1H assay using TAGG as bait

value: TAGG


title: B1H assay using GTTT as bait, replicate 2

source_name: B1H assay using GTTT as bait

value: GTTT


title: ple.kd.2

description: biological replicate 2

value: in-house colony


title: B1H assay using TATA as bait, replicate 2

source_name: B1H assay using TATA as bait

value: TATA


title: B1H assay using TATA as bait, replicate 1


title: ple.lv.2

description: biological replicate 2

source_name: Peromyscus leucopus_liver

value: wild type

value: adult


title: B1H assay using TCAC as bait, replicate 2

source_name: B1H assay using TCAC as bait

value: TCAC


title: B1H assay using TCAC as bait, replicate 1


title: B1H assay using TAGG as bait, replicate 1


title: B1H assay using GTTT as bait, replicate 1


title: mun.br.3

description: biological replicate 3

organism: Meriones unguiculatus

source_name: Meriones unguiculatus_brain

value: normal brain

value: frontal parts of brain


title: B1H assay using GTTG as bait, replicate 2

source_name: B1H assay using GTTG as bait

value: GTTG


title: B1H assay using GTGG as bait, replicate 2

source_name: B1H assay using GTGG as bait

value: GTGG


title: mun.br.2

description: biological replicate 2


title: B1H assay using GTGG as bait, replicate 1


title: mun.kd.2

description: biological replicate 2

source_name: Meriones unguiculatus_kidney

value: normal kidney

value: whole kidney


title: mun.kd.3

description: biological replicate 3


title: mun.br.1

description: biological replicate 1


title: B1H assay using GTGC as bait, replicate 2

source_name: B1H assay using GTGC as bait

value: GTGC


title: B1H assay using GTGA as bait, replicate 1

source_name: B1H assay using GTGA as bait

value: GTGA


title: mun.lv.2

description: biological replicate 2

source_name: Meriones unguiculatus_liver

value: normal liver

value: whole liver


title: mun.lv.3

description: biological replicate 3


title: B1H assay using GTGA as bait, replicate 2

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using GTCG as bait, replicate 1

source_name: B1H assay using GTCG as bait

value: GTCG


title: B1H assay using GTGC as bait, replicate 1


title: B1H assay using GTCG as bait, replicate 2


title: mun.kd.1

description: biological replicate 1

value: in-house colony


title: mun.lv.1

description: biological replicate 1


title: B1H assay using GTCA as bait, replicate 2

source_name: B1H assay using GTCA as bait

value: GTCA


title: B1H assay using GTCA as bait, replicate 1


title: B1H assay using GTCC as bait, replicate 1

source_name: B1H assay using GTCC as bait

value: GTCC


title: eeu.br.1

description: biological replicate 1

organism: Erinaceus europaeus

source_name: Erinaceus europaeus_brain

value: wild type

value: adult


title: eeu.br.2

description: biological replicate 2

value: normal brain


title: eeu.kd.1

description: biological replicate 1

source_name: Erinaceus europaeus_kidney


title: eeu.lv.2

description: biological replicate 2

source_name: Erinaceus europaeus_liver


title: ple.lv.1

description: biological replicate 1


title: B1H assay using GTTG as bait, replicate 1


title: eeu.lv.1

description: biological replicate 1


title: B1H assay using GTAT as bait, replicate 1

source_name: B1H assay using GTAT as bait

value: GTAT


title: cae.br.1

description: biological replicate 1

organism: Chlorocebus aethiops

source_name: Chlorocebus aethiops_brain

value: frontal parts of brain


title: cae.kd.1

description: biological replicate 1

source_name: Chlorocebus aethiops_kidney


title: eeu.kd.2

description: biological replicate 2


title: B1H assay using GTCC as bait, replicate 2


title: B1H assay using GTAC as bait, replicate 2

source_name: B1H assay using GTAC as bait

value: GTAC


title: B1H assay using GGTT as bait, replicate 2

source_name: B1H assay using GGTT as bait

value: GGTT


title: B1H assay using GTAC as bait, replicate 1


title: B1H assay using GGGG as bait, replicate 2

source_name: B1H assay using GGGG as bait

value: GGGG


title: B1H assay using GTAG as bait, replicate 1

source_name: B1H assay using GTAG as bait

value: GTAG


title: B1H assay using GGTT as bait, replicate 1


title: B1H assay using GGGC as bait, replicate 2

source_name: B1H assay using GGGC as bait

value: GGGC


title: B1H assay using GGGC as bait, replicate 1


title: B1H assay using GGGA as bait, replicate 1

source_name: B1H assay using GGGA as bait

value: GGGA


title: B1H assay using GGGA as bait, replicate 2


title: B1H assay using GGCC as bait, replicate 2

source_name: B1H assay using GGCC as bait

value: GGCC


title: B1H assay using GGCC as bait, replicate 1

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using GGAT as bait, replicate 2

source_name: B1H assay using GGAT as bait

value: GGAT


title: B1H assay using GGAG as bait, replicate 2

source_name: B1H assay using GGAG as bait

value: GGAG


title: B1H assay using GGAG as bait, replicate 1


title: B1H assay using GGGG as bait, replicate 1


title: B1H assay using GTAG as bait, replicate 2


title: B1H assay using GGCA as bait, replicate 2

source_name: B1H assay using GGCA as bait

value: GGCA


title: B1H assay using GGAC as bait, replicate 2

source_name: B1H assay using GGAC as bait

value: GGAC


title: B1H assay using GGCA as bait, replicate 1


title: B1H assay using GTAT as bait, replicate 2


title: B1H assay using GGAC as bait, replicate 1


title: B1H assay using GGAA as bait, replicate 2

source_name: B1H assay using GGAA as bait

value: GGAA


title: cae.lv.1

description: biological replicate 1

source_name: Chlorocebus aethiops_liver

value: in-house colony

value: wild type

value: adult

value: normal liver

value: whole liver


title: B1H assay using GCTC as bait, replicate 1

source_name: B1H assay using GCTC as bait

value: GCTC


title: B1H assay using GCGT as bait, replicate 2

source_name: B1H assay using GCGT as bait

value: GCGT


title: B1H assay using GCGT as bait, replicate 1


title: B1H assay using GGAT as bait, replicate 1


title: B1H assay using GCGC as bait, replicate 2

source_name: B1H assay using GCGC as bait

value: GCGC


title: B1H assay using GCGG as bait, replicate 2

source_name: B1H assay using GCGG as bait

value: GCGG


title: B1H assay using GCCT as bait, replicate 2

source_name: B1H assay using GCCT as bait

value: GCCT


title: B1H assay using GCGA as bait, replicate 1

source_name: B1H assay using GCGA as bait

value: GCGA


title: B1H assay using GCCA as bait, replicate 1

source_name: B1H assay using GCCA as bait

value: GCCA

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using GCAT as bait, replicate 1

source_name: B1H assay using GCAT as bait

value: GCAT


title: B1H assay using GCGC as bait, replicate 1


title: B1H assay using GCCT as bait, replicate 1


title: B1H assay using GCAC as bait, replicate 2

source_name: B1H assay using GCAC as bait

value: GCAC


title: B1H assay using GCGA as bait, replicate 2


title: B1H assay using GCCA as bait, replicate 2


title: B1H assay using GCAA as bait, replicate 1

source_name: B1H assay using GCAA as bait

value: GCAA


title: B1H assay using GCAA as bait, replicate 2


title: B1H assay using GATG as bait, replicate 1

source_name: B1H assay using GATG as bait

value: GATG


title: B1H assay using GATT as bait, replicate 2

source_name: B1H assay using GATT as bait

value: GATT


title: B1H assay using GGAA as bait, replicate 1

value: GGAA


title: B1H assay using GAGG as bait, replicate 1

source_name: B1H assay using GAGG as bait

value: GAGG


title: B1H assay using GCTC as bait, replicate 2


title: B1H assay using GATG as bait, replicate 2


title: B1H assay using GCAT as bait, replicate 2


title: B1H assay using GAGG as bait, replicate 2


title: B1H assay using GACT as bait, replicate 1

source_name: B1H assay using GACT as bait

value: GACT


title: B1H assay using GACG as bait, replicate 2

source_name: B1H assay using GACG as bait

value: GACG


title: B1H assay using GACG as bait, replicate 1


title: B1H assay using GACT as bait, replicate 2


title: B1H assay using GCGG as bait, replicate 1


title: B1H assay using GACC as bait, replicate 2

source_name: B1H assay using GACC as bait

value: GACC


title: B1H assay using GACC as bait, replicate 1


title: B1H assay using GACA as bait, replicate 2

source_name: B1H assay using GACA as bait

value: GACA


title: B1H assay using GACA as bait, replicate 1


title: B1H assay using GCAC as bait, replicate 1


title: B1H assay using GAAC as bait, replicate 1

source_name: B1H assay using GAAC as bait

value: GAAC


title: B1H assay using GAAG as bait, replicate 1

source_name: B1H assay using GAAG as bait

value: GAAG


title: B1H assay using GAAT as bait, replicate 2

source_name: B1H assay using GAAT as bait

value: GAAT


title: B1H assay using CTGT as bait, replicate 1

source_name: B1H assay using CTGT as bait

value: CTGT


title: B1H assay using GAAG as bait, replicate 2


title: B1H assay using CTGT as bait, replicate 2


title: B1H assay using CTGG as bait, replicate 2

source_name: B1H assay using CTGG as bait

value: CTGG


title: B1H assay using GAAT as bait, replicate 1

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using CTGG as bait, replicate 1


title: B1H assay using CTGC as bait, replicate 2

source_name: B1H assay using CTGC as bait

value: CTGC


title: B1H assay using GATT as bait, replicate 1


title: B1H assay using CTAT as bait, replicate 2

source_name: B1H assay using CTAT as bait

value: CTAT


title: B1H assay using CTAT as bait, replicate 1


title: B1H assay using CTGC as bait, replicate 1


title: B1H assay using CTAC as bait, replicate 2

source_name: B1H assay using CTAC as bait

value: CTAC


title: B1H assay using CGTT as bait, replicate 2

source_name: B1H assay using CGTT as bait

value: CGTT


title: B1H assay using CTAC as bait, replicate 1


title: B1H assay using CTAA as bait, replicate 2

source_name: B1H assay using CTAA as bait

value: CTAA


title: B1H assay using CGTA as bait, replicate 1

source_name: B1H assay using CGTA as bait

value: CGTA


title: B1H assay using CGGT as bait, replicate 2

source_name: B1H assay using CGGT as bait

value: CGGT


title: B1H assay using CGGT as bait, replicate 1


title: B1H assay using CGTT as bait, replicate 1


title: B1H assay using CGGC as bait, replicate 2

source_name: B1H assay using CGGC as bait

value: CGGC


title: B1H assay using GAAC as bait, replicate 2


title: B1H assay using CGGG as bait, replicate 1

source_name: B1H assay using CGGG as bait

value: CGGG


title: B1H assay using CGGG as bait, replicate 2


title: B1H assay using CGGC as bait, replicate 1


title: B1H assay using CGAT as bait, replicate 2

source_name: B1H assay using CGAT as bait

value: CGAT


title: B1H assay using CGAT as bait, replicate 1


title: B1H assay using CCTG as bait, replicate 2

source_name: B1H assay using CCTG as bait

value: CCTG


title: B1H assay using CGAC as bait, replicate 2

source_name: B1H assay using CGAC as bait

value: CGAC


title: B1H assay using CGAA as bait, replicate 1

source_name: B1H assay using CGAA as bait

value: CGAA


title: B1H assay using CTAA as bait, replicate 1


title: B1H assay using CCTC as bait, replicate 1

source_name: B1H assay using CCTC as bait

value: CCTC


title: B1H assay using CGAC as bait, replicate 1


title: B1H assay using CGAA as bait, replicate 2


title: B1H assay using CCTA as bait, replicate 2

source_name: B1H assay using CCTA as bait

value: CCTA