title: T22 Dorsal rep2

city: Zurich

first: Steven

last: Brown

state: Switzerland

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

description: immunoprecipitated DNA

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Burrows-Wheeler Alignment tool (BWA).
Mapped reads were than analyzed using the MEDIPS package (Lienhard et al., 2014). Methylation score was calculated for each region of 500bp across the genome.  CpG density-dependent normalization was incorporated.  Pairwise correlation analysis of the genome wide coverage profile between MEDIP replicate samples was performed using the MEDIPS.correlation function. Pearson correlation coefficient r varied between 0.85 and 0.92, indicating good reproducibility of MEDIP-seq signal. Differential methylation analysis was performed using MEDIPS in 500bp widows excluding regions with less than 8 unique mapped reads. DMR were than identified by filtering for a widows associated with a p ≤0.001.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and the fold change (Differential methylation measurements)

source_name: SCN

extract_protocol:
Brains were isolated at the circadian time CT4 and then sliced immediately using vibratome, one coronal SCN slice of ~250μM was collected from the middle part of the SCN. Using ophthalmic knife vSCN and dSCN sub-regions were separated.  Genomic DNA was extracted from SCN slices by overnight Proteinase K digestion, followed by phenol-chloroform and ethanol precipitation. After RNase treatment, genomic DNA was sonicated to generate small fragments (average of 300bp), using a Covaris sonicator (BioRuptor). DNA immunoprecipitation was performed using Epiquik™ MeDIP Ultra Kit (EPIGENTEK™), following manufacturer's instructions.
The methylated enriched DNA was then used for library preparation using Accel-NGS™ DNA Library Kits (Swift Biosciences), following manufacturer's instructions

treatment_protocol: Six-week-old wild-type mice (C57BL/6Cr1) were entrained to light:dark cycles either 22, 24, or 26 hours in length (T22, T24, or T26) for six weeks. After 6 weeks, we recorded wheel-running behavior in constant darkness. After 3 days in DD, we used Clocklab software to predict time of activity onset for each mouse.

value: brain

tag: tissue compartment

value: suprachiasmatic nuclei (SCN)

tag: scn subregion

value: Dorsal

tag: age

value: post natal day 90

value: wild type


title: T24 Ventral rep2

status: Public on Oct 28 2016

type: SRA

description: immunoprecipitated DNA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue

value: Ventral

tag: genotype


title: T26 Dorsal rep1

description: immunoprecipitated DNA


title: MTP12

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

description: library of 96 >4c FSL-1 treated cells

library_source: transcriptomic

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The 65bp right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The 25bp left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for quantification.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

molecule: total RNA

source_name: Bone marrow derived macrophage precursors

growth_protocol: Bone marrow cells were flushed from the femurs of mice and cultured with murine M-CSF (20 ng/ml) on petri dishes in DMEM supplemented with 10% FBS for 4-5 days. The adherent cell population (referred to as ‘macrophage precursors’) was then recovered and plated at 2x104 cells/ml in OptiMEM medium containing 10% FBS and 50ng/ml M-CSF.

extract_protocol:
Hoechst staining was performed on control and FSL-1 treated cells to quantify the DNA content and single cells were FACS-sorted using BD Influx in 384-well plates.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: Cells were re-plated in OptiMEM medium and stimulated with M-CSF (50ng/ml) ('control') or M-CSF (50ng/ml) and (FSL-1 20ng/ml) for 6 days.

value: Bone marrow

tag: condition

value: 6 days M-CSF+ FSL-1 treatment

tag: dna content

value: greater than 4c


title: MTP11

description: library of 96 >4c FSL-1 treated cells


title: T22 Ventral rep2

description: immunoprecipitated DNA


title: T22 Dorsal rep1

description: immunoprecipitated DNA


title: T22 Ventral rep1

description: immunoprecipitated DNA


title: T26 Ventral rep2

description: immunoprecipitated DNA


title: T24 Ventral rep1

description: immunoprecipitated DNA


title: RWPE1 ERG-WT with EWS shRNA replicate 1

city: Bloomington

first: Vivekananda

last: Kedage

state: IN

address: 1001 E. third Street

country: USA

institute: Indiana University

data_processing:
Casava1.8.2 software was used for basecalling
Differential gene expression analysis was carried out with Tuxedo Suite RNA sequencing pipeline (Trapnell et al., Nature Protocol 2012). Sequence reads obtained from illumina sequencer was mapped to the human genome (hg19, UCSC) using Bowtie2. Differential gene expression was determined using Cuffdiff.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: Tab delimited text file of differential gene expression analysis. Output from CuffDiff

molecule: polyA RNA

organism: Homo sapiens

source_name: RWPE1 ERG-WT with EWS shRNA

growth_protocol: RWPE1 cells were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract,  human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)

extract_protocol:
Total RNA from three biological replicates of RWPE1 cells expressing either vector, ERG-WT, ERG-P436A or ERG-WT with EWS knockdown shRNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol. Total RNA was DNase treated with RNase-Free DNase set (Qiagen) according to manufacturer’s protocol.
polyA containing RNA was purified using oligo(dT) beads (Invitrogen). cDNAs of polyA selected RNA was generated with SuperScript III reverse transcriptase enzyme using random hexamers (Invitrogen). Second strand synthesis from cDNAs was carried out with E. coli DNA ligase and E. coli DNA polymerase I (New England BioLabs). The double-stranded cDNAs were sheared to ~150 nucleotide fragments using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis.Sheared DNA was end-repaired and ligated to indexing primers provided in Truseq sample preparation kit (Illumina). DNA libraries were pooled and sequenced in Illumina NextSeq 500 according to manufacturers protocol.

tag: cell line

tag: cell type

value: human prostatic epithelial cell line

tag: genotype/variation

value: expressing ERG-WT with EWS shRNA


title: MTP9

description: library of 96 >4c FSL-1 treated cells


title: MTD7

description: library of 96 2c FSL-1 treated cells


title: MTP10

description: library of 96 >4c FSL-1 treated cells


title: MTD8

description: library of 96 2c FSL-1 treated cells


title: MC4

description: library of 96 2c M-CSF treated cells

value: 6 days M-CSF treatment


title: MC2

description: library of 96 2c M-CSF treated cells


title: MTD6

description: library of 96 2c FSL-1 treated cells


title: T26 Dorsal rep2

description: immunoprecipitated DNA


title: MTD5

description: library of 96 2c FSL-1 treated cells


title: MC3

description: library of 96 2c M-CSF treated cells


title: MC1

description: library of 96 2c M-CSF treated cells


title: T26 Ventral rep1

description: immunoprecipitated DNA


title: linc2025-pAS-151214-H2

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

institute: Stanford University

description: poly(A)+ RNA-seq with hybrid selection

data_processing:
DNA sequencing (ATAC-Seq) and RNA sequencing (PRO-Seq and RNA-seq) analyses were performed as previously described (Engreitz et al. Cell 2014) except that data were initially aligned to both the 129S1 and Castanets genomes and reads were merged using pysuspenders. For RNA-seq experiments, reads mapping to specifically to the 129 or Castaneus alleles were counted for each gene (including any read overlapping an intron or exon)
Genome_build: mm9
Supplementary_files_format_and_content: TDF: Coverage at 5bp resolution across genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/)
Supplementary_files_format_and_content: BED: Read counts mapping specifically to the 129 or Castaneus alleles. Columns: chromosome, start, end, gene, count-129, count-castaneus

source_name: F1 2-1 129/Castaneus Female mESCs

growth_protocol: Male ES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).

extract_protocol: p(A)+ RNA-seq with hybrid selection: We generated RNA sequencing libraries as   described in Engreitz et al. Cell 2014. We performed hybrid selection after barcoding of DNA libraries on a combined pool as described in Gnirke et al. Nature Biotech 2009.    ATAC-Seq:  We performed ATAC-Seq as previously described (Buenrostro JD et al. Nature Methods 2013) using 50,000 mESCs.    PRO-Seq:  We performed PRO-Seq essentially as described in Kwak H et al. Science 2013.    ChIP-Seq: We performed ChIP-Seq as described in Busby M et al. biorXiv 2016.

value: embryonic stem cell

tag: gender

value: female


title: linc2025-pAS-151214-H1

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-PromoterDeletion-150126-C3

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-pAS-151214-G7

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-PromoterDeletion-150126-B5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-H7

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-pAS-151214-G6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-C8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-C6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-C5

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-PromoterDeletion-150126-F2

description: poly(A)+ RNA-seq with hybrid selection


title: T24 Dorsal rep1

description: immunoprecipitated DNA


title: linc2025-PromoterDeletion-150126-E10

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-PromoterDeletion-150126-E2

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-PromoterDeletion-150126-D6

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-PromoterDeletion-150126-C7

description: poly(A)+ RNA-seq with hybrid selection


title: linc2025-PromoterDeletion-150126-B11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-E10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-G10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-D6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1547-PromoterDeletion-141107-B5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-PromoterDeletion-150126-E4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-pAS-150416-B6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1509-PromoterDeletion-150126-H3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-pAS-150416-G2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1509-PromoterDeletion-150126-E4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1509-PromoterDeletion-150126-D7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1509-PromoterDeletion-150126-E11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1509-PromoterDeletion-150126-F11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-G5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-D10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-pAS-150416-F9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-pAS-150416-F7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-pAS-150416-F10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-pAS-150416-E11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-pAS-150416-A1

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-B7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-A7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-PromoterDeletion-150126-H5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-PromoterDeletion-150126-E6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-F9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-PromoterDeletion-150126-E11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1509-PromoterDeletion-150126-G7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-PromoterDeletion-150126-D9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1509-PromoterDeletion-150126-D6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-F6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-E11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-D4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-C2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-B6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-D8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1399-PromoterDeletion-150126-S1-E3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-H3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-D7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-C4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1399-PromoterDeletion-150126-S1-A9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1423-PromoterDeletion-150126-B8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1399-PromoterDeletion-150126-S1-C10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1399-PromoterDeletion-150126-S1-A10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1386-PromoterDeletion-141107-G9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-pAS-151214-S1-E5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1536-PromoterDeletion-150126-C10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-B2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-B8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-pAS-151214-S1-E7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-C4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1405-PromoterDeletion-141107-F5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1399-PromoterDeletion-150126-S1-D8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1399-PromoterDeletion-150126-S1-E5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1329-pAS-151214-D4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1329-pAS-151214-B9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1329-pAS-151214-A9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-4kb-151214-S1-H8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-4kb-151214-S1-H7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-4kb-151214-S1-G4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-4kb-151214-S1-F3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-4kb-151214-S1-F2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1386-PromoterDeletion-141107-C11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-2kb-151214-S1-F6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1386-PromoterDeletion-141107-B6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-2kb-151214-S1-F2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-2kb-151214-S1-C10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1399-PromoterDeletion-150126-S1-A6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1329-pAS-151214-A7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1329-pAS-151214-A3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-4kb-151214-S1-G3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-2kb-151214-S1-B4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-G9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-0.5kb-150216-E2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-H5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-2kb-151214-S1-D11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-40bp-150216-C2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-40bp-150216-A6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-0.5kb-150216-A7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-0.5kb-150216-A8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-15kb-151214-S1-H2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-G8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-G4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-4kb-151214-S1-F4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-B9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1386-PromoterDeletion-141107-G3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-40bp-150216-B4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterDeletion-141107-F1

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-pAS-0.5kb-150216-C11

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-B8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterDeletion-141107-B1

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron3Deletion-150801-B6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron3Deletion-150801-C1

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterDeletion-141107-G6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-B10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterDeletion-141107-C1

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron3Deletion-150801-A9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron3Deletion-150801-E1

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-H4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron3Deletion-150801-B3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron3Deletion-150801-A7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterInsertion-150216-G10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron2Deletion-150801-B6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron2Deletion-150801-A8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron2Deletion-150801-B3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron1Deletion-150801-C4

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-PromoterDeletion-141107-G7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-H6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-D9

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron1Deletion-150801-B7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-A5

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-D3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-B10

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-A6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon2KO-151101-G3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon3Deletion-150801-A3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon2KO-151101-B7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon2KO-151101-D6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon3Deletion-150801-B7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron2Deletion-150801-B8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon3Deletion-150801-H2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Intron1Deletion-150801-H6

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-5ssDeletion-151101-F10

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-E8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-5ssDeletion-151101-B2

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-E11

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-H5

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-H3

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon2KO-151101-A9

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-F7

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-D8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-B5

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-C8

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-C6

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg17-PromoterDeletion-150126-B3

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg17-PromoterDeletion-150126-B2

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg17-PromoterDeletion-150126-A5

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-pAS-151214-E3

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg17-PromoterDeletion-150126-A2

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-pAS-151214-C2

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-pAS-151214-D2

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-pAS-151214-D3

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-pAS-151214-C1

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg3-PromoterDeletion-150126-H4

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-pAS-151214-A7

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-H8

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon4Deletion-150801-D8

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-G6

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-D5

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-C6

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-B3

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-B7

description: poly(A)+ RNA-seq with hybrid selection


title: Snhg17-PromoterDeletion-150126-C9

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-G6

description: poly(A)+ RNA-seq with hybrid selection


title: Sfmbt2-PromoterDeletion-141107-D10

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-A4

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-F9

description: poly(A)+ RNA-seq with hybrid selection


title: Sfmbt2-PromoterDeletion-141107-B11

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-G7

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-H8

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-A11

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-F5

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-C9

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-B2

description: poly(A)+ RNA-seq with hybrid selection


title: Meg3-PromoterDeletion-150126-S1-D5

description: poly(A)+ RNA-seq with hybrid selection


title: Meg3-PromoterDeletion-150126-S1-D3

description: poly(A)+ RNA-seq with hybrid selection


title: Slc30a9-PromoterDeletion-150126-F11

description: poly(A)+ RNA-seq with hybrid selection


title: Meg3-PromoterDeletion-150126-S1-C9

description: poly(A)+ RNA-seq with hybrid selection


title: Meg3-PromoterDeletion-150126-S1-B7

description: poly(A)+ RNA-seq with hybrid selection


title: Meg3-PromoterDeletion-150126-S1-B8

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-151214-H9

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-151214-G8

description: poly(A)+ RNA-seq with hybrid selection


title: Meg3-PromoterDeletion-150126-S1-A2

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-151214-G5

description: poly(A)+ RNA-seq with hybrid selection


title: Rcc1-PromoterDeletion-150126-E5

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-151214-F8

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-151214-G1

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-151214-F4

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-150416-G4

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-150416-C4

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-150416-D8

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-150416-H1

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-150416-A1

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-PromoterDeletion-150126-H5

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-150416-E7

description: poly(A)+ RNA-seq with hybrid selection


title: linc1319-Exon3Deletion-150801-B4

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-150416-D5

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-PromoterDeletion-150126-D11

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-PromoterDeletion-150126-G8

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-PromoterDeletion-150126-A3

description: poly(A)+ RNA-seq with hybrid selection


title: Dicer1-PromoterDeletion-150126-S1-G9

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-H10

description: poly(A)+ RNA-seq with hybrid selection


title: Dicer1-PromoterDeletion-150126-S1-E5

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-pAS-151214-H6

description: poly(A)+ RNA-seq with hybrid selection


title: Dicer1-PromoterDeletion-150126-S1-G3

description: poly(A)+ RNA-seq with hybrid selection


title: Gpr19-PromoterDeletion-150126-A5

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-F9

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-H3

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-E6

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-D5

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-E7

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P9-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P9-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-D4

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-G5

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P9-141107-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P8-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P9-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P9-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: EL4_Rep2

city: Boston

first: James

middle: John

last: Kaminski

state: MA

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Boston Children's Hospital

description:
ATAC-Seq data for EL4 T Cells
EL4-Rep3_L_006305_peaks.bed

data_processing:
We used the FASTQC pipeline (Babraham Bioinformatics) on our reads, and aligned them to the reference genome (mm9) with bowtie version 1.1.1, retaining only reads that mapped to a unique position in the genome [“–m 1”]. We marked duplicate reads in the bam files using PICARD and checked for contamination of primer sequences. [Please note that the bam files in this accession are the raw data returned from the sequencing facility, prior to our alignment and processing.]
For each of our five replicate pairs, we merged the two replicates using samtools, and then called peaks using MACS2 version 2.1.0, setting the FDR to 0.001 with the “nomodel” option and default mouse genome size.
Genome_build: mm9
Supplementary_files_format_and_content: bed files of ATAC-Seq peaks

source_name: T Cells (EL4 Line)

growth_protocol: Wild type C57/BL/6N (CD45.2+) and congenic B6.SJL-Ptprca Pepcb/BoyJ (CD45.1+) mice were obtained from the US National Cancer Institute. C57BL/6N P14 mice (LCMV-specific T cell receptor transgenic) were bred in-house. Male mice were used at between 6 and 10 weeks of age. All animal experiments were done in accordance with the Animal Care and Use guidelines for the University of Pennsylvania.

extract_protocol:
All donor P14 cells were prepared from naive spleen using CD8 negative selection (Miltenyi Biotec). To generate effector, memory and exhausted CD8+ T cells, approximately 1-2 x 103 P14 cells were transferred into recipient mice, followed by LCMV infection one day later. Target effector/memory/exhausted P14 cells were harvested only from recipient spleens at d8 or d27 p.i. After enrichment using CD45.2 FITC Ab and anti-FITC microbes (Miltenyi), cells were stained and sorted by Aria II (BD). Naïve and effector/memory/exhausted CD8+ T (P14) cells were sorted by gating on CD8+ TCRVa2+ CD62L+ CD44lo and CD8+ TCRVa2+ CD45.2+ CD45.1- population, respectively. The following fluorochrome-conjugated antibodies from Biolegend were used for flow-cytometry: anti–TCR Vα2 (B20.1), anti-CD8α (53-6.7), anti-CD44 (IM7), anti-CD45.1 (A20), anti-CD45.2 (104), and anti-CD62L (MEL14).
We sorted 40-50,000 cells per biological replicate (Naïve, Acute d8, Acute d27, Chronic d8, Chronic d27 and EL4), which were then washed once in cold PBS and lysed in 50μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Lysed nuclei were incubated in Tn5 transposition reaction mix as described in (Buenrostro et al 2013) and purified using MinElute Reaction Cleanup kit (Qiagen). ATAC-seq fragments from one set of replicates for Acute d8, Acute d27, Chronic d8 and Chronic d27, as well as both biological replicates for Naïve cells and EL4 cells, were size selected for fragments between 115 and 600 bp using Pippin Prep 2% Agarose Gel Cassettes and the Pippin Prep DNA Size Selection System (Sage Science). Post size-selection, ATAC libraries were amplified and Nextera sequencing primers ligated using Polymerase Chain Reaction (PCR). Finally, PCR primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and library quality was verified using a Tapestation machine. High quality ‘multiplexed’ DNA libraries were sequenced on the Illumina HiSeq2000.
ATAC-Seq

treatment_protocol: LCMV strains were produced and titred as described in Kurachi et al  [Nature immunology 15, 373-383 (2014)10.1038/ni.2834)] and P. M. Odorizzi et al [The Journal of experimental medicine,  (2015)10.1084/jem.20142237)]. Two cohorts of mice were infected by intraperitoneal injection of LCMV Armstrong (2 × 105 plaque-forming units) or intravenous injection of LCMV Clone 13 (4 × 106 plaque-forming units).

value: T Cell

tag: viral infection


title: Control-P8-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P8-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Dicer1-PromoterDeletion-150126-S1-D10

description: poly(A)+ RNA-seq with hybrid selection


title: Crlf3-PromoterDeletion-150126-G3

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P8-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Chronic-d27_Rep2

description:
ATAC-Seq data for CD8+ T Cells Responding to Chronic LCMV (Clone 13) Infection, 27 days after infection
Mouse_ChronicD27_peaks.bed

source_name: CD8+ T Cells

value: CD8+ T Cell [CD8+ TCRVa2+ CD45.2+ CD45.1-]

value: C57BL/6N P14 mice (LCMV-specific T cell 4 receptor transgenic)

value: LCMV Clone 13


title: Control-P8-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P8-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P8-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Chronic-d8_Rep2

description:
ATAC-Seq data for CD8+ T Cells Responding to Chronic LCMV (Clone 13) Infection, 8 days after infection
Mouse_ChronicD8_peaks.bed


title: Control-P9-150126-H12

description: poly(A)+ RNA-seq with hybrid selection


title: EL4_Rep1

description:
ATAC-Seq data for EL4 T Cells
EL4-Rep2_L_006304_peaks.bed


title: CD8_Chronic-d8_Rep1


title: Control-P7-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P7-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Acute-d27_Rep2

description:
ATAC-Seq data for CD8+ T Cells Responding to Acute LCMV (Armstrong) Infection, 27 days after infection
Mouse_AcuteD27_peaks.bed

value: LCMV Armstrong


title: Control-P9-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P8-141107-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P7-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P7-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Acute-d27_Rep1


title: Control-P7-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P6-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P6-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P6-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P7-141107-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P8-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Acute-d8_Rep1

description:
ATAC-Seq data for CD8+ T Cells Responding to Acute LCMV (Armstrong) Infection, 8 days after infection
Mouse_AcuteD8_peaks.bed


title: CD8_Naive_Rep1

description:
ATAC-Seq data for Naive CD8+ T Cells
Mouse_Naive_peaks.bed

value: CD8+ T Cell [CD8+ TCRVa2+ CD62L+ CD44 lo]


title: Control-P6-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Chronic-d27_Rep1


title: Control-P6-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P6-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P6-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P6-141107-A12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-4_Treg (11466x24)

city: Saskatoon

first: Peter

middle: Dion

last: Pioli

state: SK

address: 107 Wiggins Rd

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Saskatchewan

description: processed data file: cDKO_Treg_vs_WT_Treg.fpkm.txt

data_processing:
Reads were aligned to mm10 chromosome sequence + splice junction sequences using Novoalign (v2.08.03), allowing up to 50 alignments for each read. Splice junctions were created by running USeq (v8.8.8) MakeTranscriptome application using Ensembl transcript annotations.
The resulting alignment file was processed with the USeq (v8.8.8) application SamTranscriptomeParser, which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities.  SamTranscriptomeParser also converts splice junction alignment coordinates back to genomic space.
USeq's DefinedRegionDifferentialSeq application was used to calculate FPKMs
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing FPKMs

source_name: cDKO splenic GFP- CD3e+ CD8a- CD4+ CD25+ T cells

extract_protocol:
Total RNA was isolated from cells using the Qiagen miRNeasy Micro Kit (Cat. #: 217084) according to the manufacturer's instructions.
Isolated RNA was utilized for RNA-seq library preparation using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold treatment to eliminate ribosomal RNAs.

value: cDKO

tag: time of isolation

value: 9 weeks post bone marrow transplant

value: spleen

value: T cells


title: Control-P5-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-3_Treg (11466x23)


title: Control-P5-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-4_Treg (11466x20)

source_name: WT splenic GFP- CD3e+ CD8a- CD4+ CD25+ T cells

value: wildtype


title: Control-P7-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-2_Treg (11466x18)


title: WT-3_Treg (11466x19)


title: Control-P6-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P6-141107-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-150126-S1-G12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Acute-d8_Rep2


title: Control-P5-150126-S1-F12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-1_Treg (11466x17)


title: Control-P5-150216-B12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-3_Tconv (11466x15)

description: processed data file: cDKO_Tcov_vs_WT_Tcov.fpkm.txt

source_name: cDKO splenic GFP- CD3e+ CD8a- CD4+ CD25- T cells


title: Control-P5-150126-S1-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-4_Tconv (11466x16)


title: Control-P5-150126-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-150126-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P7-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: CD8_Naive_Rep2


title: cDKO-2_Tconv (11466x14)


title: Control-P5-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-150216-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-150216-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P5-141107-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-151101-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-151101-F12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-4_Tconv (11466x12)

source_name: WT splenic GFP- CD3e+ CD8a- CD4+ CD25- T cells


title: WT-2_Tconv (11466x10)


title: Control-P4-151101-E12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-1_Tconv (11466x13)


title: Control-P4-150416-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150416-C12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-3_Tconv (11466x11)


title: cDKO-3_CD8 (11466x7)

description: processed data file: cDKO_CD8_vs_WT_CD8.fpkm.txt

source_name: cDKO splenic GFP- CD3e+ CD8a+ CD4- T cells


title: Control-P4-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150126-S1-G12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-1_Tconv (11466x9)


title: cDKO-2_CD8 (11466x6)


title: Control-P4-150126-S1-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-4_CD8 (11466x4)

source_name: WT splenic GFP- CD3e+ CD8a+ CD4- T cells


title: Control-P4-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-4_CD8 (11466x8)


title: Control-P4-150216-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-141107-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150216-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150126-S1-D12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-1_CD8 (11466x5)


title: Control-P4-151101-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-141107-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-3_CD8 (11466x3)


title: WT-2_CD8 (11466x2)


title: Control-P3-151101-H12

description: poly(A)+ RNA-seq with hybrid selection


title: cDKO-2_Treg (11466x22)


title: Control-P4-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150216-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150126-S1-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-151101-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P4-150216-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150126-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150216-E12

description: poly(A)+ RNA-seq with hybrid selection


title: WT-1_CD8 (11466x1)


title: Control-P3-151101-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-151101-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150416-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P25-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150126-S1-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P24-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P24-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P25-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150126-S1-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-150801-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P23-150126-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P25-150126-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P3-141107-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P24-150126-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P22-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P21-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P21-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P21-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P22-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P21-150126-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P21-150126-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P22-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P20-141107-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P20-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P20-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P20-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-151101-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P23-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P20-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P20-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-151101-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150801-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150801-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P23-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-151101-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150216-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150416-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150216-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150416-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150126-S1-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150126-S1-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150126-S1-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P19-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P19-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150416-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P18-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P18-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P19-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P18-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P19-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P18-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P17-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P18-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P18-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P17-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P19-141107-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P17-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P17-150126-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P16-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P16-150126-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P16-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P17-141107-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P2-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-150126-H12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P16-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P19-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P16-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P17-150126-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-141107-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P15-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P14-150126-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P13-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P14-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P13-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P14-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P14-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P12-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P14-141107-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P13-150126-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P14-150126-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P12-150126-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P13-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P13-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P12-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P11-150126-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P12-141107-G12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P11-150126-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P12-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P12-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P16-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P11-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P11-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-150801-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P11-141107-F12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P11-141107-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P13-150126-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-141107-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-141107-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-150126-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-151101-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-151101-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-151101-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150416-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150126-S1-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150416-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150216-E12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150216-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150126-S1-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150126-S1-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Input

city: Nijmegen

first: Simon

last: van Heeringen

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

data_processing:
Basecalling and demultiplexing was performed using the default Illumina software.
Reads were mapped to the Xenopus laevis genome (J-Strain v9.1) using bwa mem (version 0.7.10-r789) with default settings. Duplicate reads were marked using bamUtil v1.0.2.
Where applicable (H3K4me3, p300) peaks were called using MACS (version 2.1.0.20140616) relative to the Input track using the options --broad -g 2.3e9 -q 0.001. --buffer-size 1000
Peaks were combined for replicates using bedtools intersect (version v.2.20.1).
Genome_build: J-Strain v9.1 (http://www.xenbase.org)
Supplementary_files_format_and_content: .bed files report peaks

organism: Xenopus laevis

source_name: whole embryo

extract_protocol:
Embryos (n= 35-90) were fixed in 1% formaldehyde for 30 minutes at the indicated developmental stage. Embryos were washed once in 125 mM glycine / 25% Marc's modified Ringer's medium (MMR) and twice in 25% MMR, homogenized on ice in sonication buffer (20 mM Tris•HCl, pH 8/10 mM KCl/1mM EDTA/10% glycerol/5 mM DTT/0.125% Nonidet P-40, and protease inhibitor cocktail (Roche)). Homogenized embryos were sonicated for 20 minutes using a Bioruptor sonicator (Diagenode). Sonicated extract was centrifuged at top speed in a cold table-top centrifuge and supernatants (ChIP extracts) were snap frozen in liquid nitrogen and stored at -20 degree C until used. Prior to assembling the ChIP reaction, the ChIP extract was diluted with IP buffer (50 mM Tris•HCl, pH 8/100 mM NaCl/2mM EDTA/1 mM DTT/1% Nonidet P-40, and protease inhibitor cocktail) and then incubated with 1-5 µg of antibody and 12.5 µl Prot A/G beads (Santa Cruz)  for an overnight  binding reaction on the rotating wheel in the cold room. The beads were sequentially washed, first with ChIP1 buffer (IP buffer plus 0.1% sodium deoxycholate),  then ChIP2 buffer (ChIP1 buffer with 500 mM NaCl final concentration), then ChIP3 buffer (ChIP1 buffer with 250 mM LiCl), then again with ChIP1 buffer, and lastly with TE buffer (10 mM Tris, pH 8/1 mM EDTA). The material was eluted in 1% SDS in 0.1M  sodium bicarbonate. Cross-linking was reversed by adding 16 µl  of 5M NaCl and incubating at 65°C for 4-5 hours. DNA was extracted using the Qiagen QIAquick PCR purification kit. ~ 10 ng input DNA was used  for sample preparation for high-throughput sequencing (according to manufacturer’s protocol).
Libraries were prepared using the Kapa Hyper Prep kit (Kapa Biosystems) according to manufacturer's protocol and sequenced on an Illumina HiSeq 2000 or an Illumina NextSeq.

tag: developmental stage

value: NF stage 10.5

value: whole embryo

tag: chip antibody

value: none (input)


title: Control-P10-150801-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150126-C12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150126-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150126-A12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-150801-A12

description: poly(A)+ RNA-seq with hybrid selection


title: RNAPII_replicate1

value: RNA polymerase II (Diagenode, catalog# C15200004, lot# #001-11)


title: H3K36me3_replicate2

value: H3K36me3 (Abcam, catalog# ab9050)


title: Control-P1-141107-C12

description: poly(A)+ RNA-seq with hybrid selection

value: embryonic stem cell

value: female


title: Control-P1-151101-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-150416-D12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P10-150126-B12

description: poly(A)+ RNA-seq with hybrid selection


title: Control-P1-141107-B12

description: poly(A)+ RNA-seq with hybrid selection


title: PROSeq-linc1536-pAS-150416-E11

description: precision run-on sequencing (PRO-Seq)

data_processing:
Library strategy: PRO-Seq
DNA sequencing (ATAC-Seq) and RNA sequencing (PRO-Seq and RNA-seq) analyses were performed as previously described (Engreitz et al. Cell 2014) except that data were initially aligned to both the 129S1 and Castanets genomes and reads were merged using pysuspenders. For RNA-seq experiments, reads mapping to specifically to the 129 or Castaneus alleles were counted for each gene (including any read overlapping an intron or exon)
Genome_build: mm9
Supplementary_files_format_and_content: TDF: Coverage at 5bp resolution across genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/)
Supplementary_files_format_and_content: BED: Read counts mapping specifically to the 129 or Castaneus alleles. Columns: chromosome, start, end, gene, count-129, count-castaneus


title: PROSeq-linc1536-PromoterDeletion-150126-E11

description: precision run-on sequencing (PRO-Seq)


title: PROSeq-linc1319-pAS-2kb-151214-S1-C10

description: precision run-on sequencing (PRO-Seq)


title: p300_replicate1

value: p300 (C-20, Santa Cruz , catalog# sc-585, lot# #A0914)


title: H3K4me1_replicate2

value: H3K4me1 (Abcam, catalog# ab8895, lot# GR193555-1)


title: p300_replicate2


title: H3K4me1_replicate1


title: H3K4me3_replicate2

value: H3K4me3 (Abcam, catalog# ab8580, lot# GR164207-1)


title: PROSeq-linc1319-pAS-15kb-151214-S1-H2

description: precision run-on sequencing (PRO-Seq)


title: Control-P1-141107-D12

description: poly(A)+ RNA-seq with hybrid selection


title: H3K4me3_replicate1


title: PROSeq-ControlClone2-Rep2

description: precision run-on sequencing (PRO-Seq)


title: H3K4me3-linc1319-PromoterDeletion-141107-C1

description: H3K4me3 ChIP-Seq


title: PROSeq-linc1319-PromoterDeletion-141107-C1

description: precision run-on sequencing (PRO-Seq)


title: H3K4me3-linc1319-5ssDeletion-151101-F10

description: H3K4me3 ChIP-Seq


title: LPS 1

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 970 Washington Street

institute: Virginia Tech

description: upregulated miRNA by LPS

data_processing:
Sequences were assayed to ensure high quality for all samples using a custom R script.
Reads were first trimmed for adaptor and quality using a combination of custom perl scripts and Btrim64
Trimmed fastq sequences were imported into mirAnalyzer for mapping with mouse genome build MM9, miRNA assembly, and quantitation.
Genome_build: mm9
Supplementary_files_format_and_content: txt files reporting mirAnalyzer quantitation results

source_name: monocytes

growth_protocol: Murine bone marrow monocytes were cultured in complete DMEM medium

extract_protocol:
microRNAs were extracted with the miRNAeasy extraction kit following the manufacture's protocol.
Small RNA-seq libraries were prepared using Illumina TruSeq Small kit with standard Illumina protocol.

treatment_protocol: Cultured monocytes were treated with or without 5 pg/ml LPS

tag: cells

value: bone marrow monocytes

tag: agent

value: LPS

value: wild type


title: Control 3

value: Control


title: LPS 3

description: upregulated miRNA by LPS


title: PROSeq-ControlClone

description: precision run-on sequencing (PRO-Seq)

value: ControlClone


title: PROSeq-ControlClone2-Rep1

description: precision run-on sequencing (PRO-Seq)


title: H3K27me3-linc1319-PromoterDeletion-141107-C1

description: H3K27me3 ChIP-Seq


title: PROSeq-linc1319-5ssDeletion-151101-F10

description: precision run-on sequencing (PRO-Seq)


title: LPS 2

description: upregulated miRNA by LPS


title: H3K4me3-ControlClone

description: H3K4me3 ChIP-Seq


title: H3K27me3-linc1319-5ssDeletion-151101-F10

description: H3K27me3 ChIP-Seq


title: H3K36me3_replicate1

value: H3K36me3 (Abcam, catalog# ab9050 )


title: H3K27me3-ControlClone

description: H3K27me3 ChIP-Seq


title: Control 2


title: Control 1


title: ATAC-linc1319-pAS-2kb-151214-S1-B4-Rep2

description: ATAC-Seq

data_processing:
Library strategy: ATAC-Seq
DNA sequencing (ATAC-Seq) and RNA sequencing (PRO-Seq and RNA-seq) analyses were performed as previously described (Engreitz et al. Cell 2014) except that data were initially aligned to both the 129S1 and Castanets genomes and reads were merged using pysuspenders. For RNA-seq experiments, reads mapping to specifically to the 129 or Castaneus alleles were counted for each gene (including any read overlapping an intron or exon)
Genome_build: mm9
Supplementary_files_format_and_content: TDF: Coverage at 5bp resolution across genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/)
Supplementary_files_format_and_content: BED: Read counts mapping specifically to the 129 or Castaneus alleles. Columns: chromosome, start, end, gene, count-129, count-castaneus


title: Ssb2 ChIP-exo, Rnh1 overexp., Induced, Rep2

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

data_processing:
Demultiplexing and removal of adapter conatmination was done in one step.
Reads were mapped to modified S. pombe genome, with Bowtie2 software. (v2.2.5)
PCR duplicates were filtered out and genome-wide coverage was calculated using R Bioconductor packages.
Datasets were normalised for coverage over Chr I.
Genome_build: ASM294v2.29 with insertion at position 1231078. Insert length is 1842 bases. Insert sequence (txt file), modified genome (fasta format) and modified annotations (bedfile) are included in the upload.
Supplementary_files_format_and_content: BigWig format containing normalised genome-wide coverage for forward (.fw) and for reverse (.rev) strands separately

organism: Schizosaccharomyces pombe

source_name: Yeast DNA

growth_protocol: Cultures were grown in full media (YEA) at 30ºC to O.D. of 0.8.

extract_protocol:
For extraction and library preparation protocol please refer to the Materials and Methods. (ChIP-exo)
For extraction and library preparation protocol please refer to the Materials and Methods. (ChIP-exo)

treatment_protocol: For treatment protocol please refer to the Materials and Methods.

value: DSB-PpoI system, pNmt1::Rnh1

tag: ppoi induction

value: ON

tag: antibody

value: a-Flag

tag: protein tag

value: Flag tag

tag: beads


title: Ssb2 ChIP-exo, Rnh1del-Rnh201del, Induced, Rep1

tag: strain

value: DSB-PpoI system, Rnh1del-Rnh201del


title: Ssb2 ChIP-exo, WT, Induced, Rep2

value: DSB-PpoI system


title: ATAC-linc1319-PromoterDeletion-141107-C1-Rep1

description: ATAC-Seq

value: embryonic stem cell


title: Ssb2 ChIP-exo, Rnh1del-Rnh201del, Induced, Rep2


title: ATAC-linc1319-PromoterDeletion-141107-C1-Rep2

description: ATAC-Seq

value: female


title: Ssb2 ChIP-exo, WT, Uninduced, Rep2

value: OFF


title: ATAC-linc1319-pAS-2kb-151214-S1-B4-Rep1

description: ATAC-Seq


title: Ssb2-Flag ChIP-exo, Rnh1 overexp. , Induced, Rep1


title: ATAC-linc1319-5ssDeletion-151101-F10-Rep1

description: ATAC-Seq


title: Ssb2 ChIP-exo, WT, Induced, Rep1


title: RNA-DNA hybrid ChIP-exo, Induced, Rep2

value: Protein A-G mix


title: Sin3B KO rep2

city: New York

first: David

last: Cantor

state: New York

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to the mm9 genome with bowtie.
RPKM values and differential expresssion was determined using DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values for each Sample and FoldChange

source_name: Sin3B KO

extract_protocol:
HSCs were sorted directly into RLT (Qiagen) lysis buffer and RNA extracted with micro Rneasy columns. RNA quality and quantity was determined by a Bioanalyzer and normalized for library construction.
Libraries were prepared with the SMARTER method for low-input RNA using standard Illumina procedures.

tag: age

value: 8-12 weeks

value: HSC

tag: hsc markers

value: LSK CD34- FLk2-

value: Sin3B KO


title: RNA-DNA hybrid ChIP-exo, Induced, Rep1


title: WT rep2

source_name: WT

value: WT


title: RNA-DNA hybrid ChIP-exo, Uninduced, Rep1


title: ATAC-ControlClone-Rep2

description: ATAC-Seq

tag: cell line

value: ControlClone


title: Cytoplasm-Total

description: cytoplasmic total RNA

data_processing:
Align to repetitive mm9 RNA sequences from RefSeq and RepeatMasker
Align remaining reads to mm9 genome with Tophat-2.0.8
Remove duplicate reads with Picard
Remove reads with MAPQ < 30
Genome_build: mm9
Supplementary_files_format_and_content: BigWig: Coverage at 5bp resolution across genome

extract_protocol:
We first lysed 5 million cells in 200 µl cold cell lysis buffer (10 mM Tris-HCl pH 7.5, 0.05% IGEPAL CA-630, 150 mM NaCl), incubating on ice for 5 minutes. We layered the cell lysate over 2.5 volumes of chilled sucrose cushion (24% sucrose in cell lysis buffer) and centrifuged at 15,000 × g for 10 minutes. The supernatant from this spin became the cytoplasmic fraction. After washing the pellet of nuclei with PBS (pH 7.5) + 1 mM EDTA, we resuspended the pellet in 100 µl of cold glycerol buffer (20 mM Tris-HCl pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) by gently flicking the tube. We added 100 µl of cold nuclei lysis buffer (10 mM HEPES pH 7.5, 1 mM DTT, 7.5 MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% IGEPAL CA-630), then vortexed for four seconds. After 2 minutes on ice, we spun the nuclear lysate at 15,000 × g for 2 minutes. This supernatant was collected as the soluble nuclear (nucleoplasm) fraction. We rinsed the remaining pellet (chromatin fraction) in PBS + 1 mM EDTA, then resuspended the chromatin in 300 µl chromatin DNase buffer (20 mM Tris-HCl pH 7.5, 50 mM KCl, 4 mM MgCl2, 0.5 mM CaCl2, 2 mM TCEP, 0.5 mM PMSF, 0.4% sodium deoxycholate, 1% IGEPAL CA-630, 0.1% N-lauroylsarcosine) plus 15 µl murine RNase inhibitor (NEB) and 30 µl TURBO DNase (Ambion). The DNase digestion proceeded for 20 minutes at 37°C and was halted by adding 10 mM EDTA and 5 mM EGTA. Protein was digested with proteinase K for 1 hour at 37°C. RNA was isolated using Zymo RNA Concentrator-25 columns (two columns for the cytoplasmic fraction).
From each cellular fraction, we sequenced total RNA and polyadenylated RNA (selected using oligo d(T)25 magnetic beads, NEB) using a strand-specific RNA-sequencing protocol for Illumina instruments described in Engreitz et al. Cell 2014.

tag: cell type

value: male

tag: cellular fraction

value: cytoplasmic total RNA


title: Sin3B KO rep1

tag: genotype/variation


title: Nucleoplasm-Total

description: soluble nuclear total RNA

tag: gender

value: soluble nuclear total RNA


title: WT rep1


title: RNA-DNA hybrid ChIP-exo, Uninduced, Rep2


title: ATAC-ControlClone-Rep1

description: ATAC-Seq


title: Control 3

city: Houston

first: Zhandong

last: Liu

state: TEXAS

address: 1250 Moursund St., STE NR-1325

institute: Baylor College of Medicine

description:
ribosome-bound RNA, BacTRAP technique
ZL37887

data_processing:
Alignment: TopHat v2.1.0 using --mate-inner-dist of 200 and rest default settings
Counts: Htseq version 0.6.0 using default settings
Genome_build: mm10
Supplementary_files_format_and_content: Counts_Matrix.txt: Read count matrix from Htseq.
Supplementary_files_format_and_content: bed: Junction bed files from Tophat output.

source_name: Cerebellar Purkinje neurons

extract_protocol:
BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment.
Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.

tag: tissue

value: brain

value: Pcp2-BacTrap; Rbm17 f/+


title: cKO1

description:
ribosome-bound RNA, BacTRAP technique
ZL37880

value: Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-


title: Cytoplasm-PolyA

description: cytoplasmic polyA RNA

value: cytoplasmic polyA RNA


title: J93_RNA-seq

status: Public on Oct 27 2016

city: Stockholm

first: Nigel

last: Kee

address: Nobels vag 3

country: Sweden

institute: LICR Stockholm

data_processing:
reads were aligned to the mm10 genome using default settings of STAR v2.3.0
RPKM values were derived using rpkmforgenes, and the Ensemble v75 annotation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and raw counts for each sample. RPKM values occupy the first half of the columns. Raw counts occupy the second half of the columns

source_name: E11.5 Single Cell

extract_protocol:
Smart-seq2
Nextera XT DNA library preparation kits (FC-131-1024) using dual indexes (i5 + i7), then sequenced on an Illumina HiSeq 2000

value: C57BL/6 Heterozygous Lmx1a-EGFP

tag: developmental stage

value: developing ventral midbrain cells


title: J94_RNA-seq


title: J88_RNA-seq


title: J96_RNA-seq


title: J86_RNA-seq


title: Nucleoplasm-PolyA

description: soluble nuclear polyA RNA

value: embryonic stem cell

value: soluble nuclear polyA RNA


title: J89_RNA-seq


title: J95_RNA-seq


title: ATAC-linc1319-5ssDeletion-151101-F10-Rep2

description: ATAC-Seq

value: female


title: cKO3

description:
ribosome-bound RNA, BacTRAP technique
ZL37885


title: Chromatin-Total

description: chromatin-associated total RNA

value: chromatin-associated total RNA


title: cKO2

description:
ribosome-bound RNA, BacTRAP technique
ZL37884


title: Control 1

description:
ribosome-bound RNA, BacTRAP technique
ZL37881


title: Ssb2 ChIP-exo, WT, Uninduced, Rep1

value: DSB-PpoI system

value: OFF

value: a-Flag

value: Flag tag


title: J85_RNA-seq


title: J92_RNA-seq


title: J91_RNA-seq


title: J84_RNA-seq


title: Phaw_male

city: London

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: bisulfite treated

data_processing:
Bisulfite sequencing data was preprocessed using the BisMark software
P. hawaiensis assembly Genome Contigs were artificially joined together using a custom Perl script (Perl v5.12) and used to build a genome for BisMark using the bismark_genome_preparation program.
The data was aligned using Bismark to the prepared genome, using the bismark align program.  The bowtie2 option was specified
The alignment files were used to extract a coverage file reporting on each cytosine in the genome using the bismark_methylation_extractor program using the options --counts --CX
The alignment coordinates were converted back to the original Phawaiensis coordinates using a custom Perl script.  Only sites with >10 reads were retained
Genome_build: Parhyale hawaiensis genome sequuence in SRA as SRP066767
Supplementary_files_format_and_content: Bismark output format with additional columns reqpresenting the original coordinates and the coordinates on the artificial joined genome.
Supplementary_files_format_and_content: phaw_30.fa_info_joining_.txt links the coordinates of the assembly to the synthetic  joined  chromosomes, part of the analysis pipeline for bisulfite sequencing data but not part of the assembly itself

organism: Parhyale hawaiensis

source_name: Parhyale hawaiensis

growth_protocol: P. hawaiensis was cultured according to standard methods

extract_protocol:
DNA was extracted using standard techniques
100ng DNA was bisulfite treated using the EZ-methylation Gold Kit (Zymo) according to manufacturer's instructions.  The DNA was then used as input for the Illumina Truseq Bisulfite sequencing kit (Illumina) prepared according to manufacturers instructions
Whole genome bisulfite sequenicng

tag: Sex

value: Male

tag: Stage

value: Adult


title: Chromatin-PolyA

description: chromatin-associated polyA RNA

value: male

value: chromatin-associated polyA RNA


title: J79_RNA-seq


title: J80_RNA-seq


title: J83_RNA-seq


title: J97_RNA-seq


title: J78_RNA-seq


title: Control 2

description:
ribosome-bound RNA, BacTRAP technique
ZL37883

value: brain

value: Pcp2-BacTrap; Rbm17 f/+


title: J87_RNA-seq


title: J77_RNA-seq


title: J75_RNA-seq


title: J74_RNA-seq


title: J72_RNA-seq


title: J73_RNA-seq


title: J67p_RNA-seq

source_name: 100 cell pools - E13.5 GFP-ve


title: J69p_RNA-seq


title: J71_RNA-seq


title: J66p_RNA-seq


title: J68p_RNA-seq


title: J62p_RNA-seq

source_name: 100 cell pools - E13.5 GFP+ve


title: J65p_RNA-seq


title: J54p_RNA-seq

source_name: 100 cell pools - E10.5 GFP-ve


title: J57p_RNA-seq


title: J59p_RNA-seq


title: J58p_RNA-seq


title: J61p_RNA-seq


title: J60p_RNA-seq


title: J53p_RNA-seq


title: J50p_RNA-seq


title: J46p_RNA-seq

source_name: 100 cell pools - E10.5 GFP+ve


title: J48p_RNA-seq


title: J51p_RNA-seq


title: J49p_RNA-seq


title: J45p_RNA-seq


title: J76_RNA-seq


title: J44p_RNA-seq


title: J43p_RNA-seq


title: J70p_RNA-seq


title: J42p_RNA-seq


title: J175_RNA-seq


title: J173_RNA-seq


title: J174_RNA-seq


title: J171_RNA-seq


title: J170_RNA-seq


title: J169_RNA-seq


title: J172_RNA-seq


title: J168_RNA-seq


title: J52p_RNA-seq


title: J161_RNA-seq


title: J164_RNA-seq


title: J166_RNA-seq


title: J158_RNA-seq


title: J162_RNA-seq


title: J163_RNA-seq


title: J165_RNA-seq


title: J159_RNA-seq


title: J154_RNA-seq


title: J157_RNA-seq


title: J156_RNA-seq


title: J152_RNA-seq


title: J153_RNA-seq


title: J151_RNA-seq


title: J148_RNA-seq


title: J150_RNA-seq


title: J147_RNA-seq


title: J146_RNA-seq


title: J145_RNA-seq


title: J167_RNA-seq


title: J144_RNA-seq


title: J149_RNA-seq


title: J143_RNA-seq


title: J142_RNA-seq


title: J140_RNA-seq


title: J160_RNA-seq


title: J141_RNA-seq


title: J115_RNA-seq


title: J134_RNA-seq


title: J133_RNA-seq


title: J136_RNA-seq


title: J119_RNA-seq


title: J129_RNA-seq


title: J123_RNA-seq


title: J127_RNA-seq


title: J137_RNA-seq


title: J118_RNA-seq


title: J121_RNA-seq


title: J128_RNA-seq


title: J138_RNA-seq


title: J116_RNA-seq


title: J114_RNA-seq


title: J139_RNA-seq


title: J111_RNA-seq


title: J112_RNA-seq


title: J110_RNA-seq


title: J108_RNA-seq


title: J113_RNA-seq


title: J107_RNA-seq


title: J106_RNA-seq


title: J104_RNA-seq


title: J105_RNA-seq


title: J103_RNA-seq


title: J126_RNA-seq


title: J102_RNA-seq


title: J125_RNA-seq


title: J124_RNA-seq


title: G96_RNA-seq

source_name: E13.5 Single Cell


title: G95_RNA-seq


title: G99_RNA-seq


title: G89_RNA-seq


title: J101_RNA-seq


title: G98_RNA-seq


title: G80_RNA-seq


title: G85_RNA-seq


title: G97_RNA-seq


title: G92_RNA-seq


title: G93_RNA-seq


title: G8_RNA-seq


title: G79_RNA-seq


title: G88_RNA-seq


title: G9_RNA-seq


title: G84_RNA-seq


title: G87_RNA-seq


title: G94_RNA-seq


title: G91_RNA-seq


title: G76_RNA-seq


title: G90_RNA-seq


title: G72_RNA-seq


title: G73_RNA-seq


title: G75_RNA-seq


title: G74_RNA-seq


title: G71_RNA-seq


title: G81_RNA-seq


title: G78_RNA-seq


title: G82_RNA-seq


title: G77_RNA-seq


title: G70_RNA-seq


title: G7_RNA-seq


title: G67_RNA-seq


title: G66_RNA-seq


title: G63_RNA-seq


title: G64_RNA-seq


title: G68_RNA-seq


title: G6_RNA-seq


title: G62_RNA-seq


title: G61_RNA-seq


title: G60_RNA-seq


title: G59_RNA-seq


title: G55_RNA-seq


title: G53_RNA-seq


title: G57_RNA-seq


title: G56_RNA-seq


title: G50_RNA-seq


title: G51_RNA-seq


title: G45_RNA-seq


title: G47_RNA-seq


title: G48_RNA-seq


title: G46_RNA-seq


title: G54_RNA-seq


title: G5_RNA-seq


title: G49_RNA-seq


title: G44_RNA-seq


title: G43_RNA-seq


title: G69_RNA-seq


title: G65_RNA-seq


title: G42_RNA-seq


title: G4_RNA-seq


title: G52_RNA-seq


title: G40_RNA-seq


title: G37_RNA-seq


title: G35_RNA-seq


title: G33_RNA-seq


title: G36_RNA-seq


title: G32_RNA-seq


title: G31_RNA-seq


title: G3_RNA-seq


title: G29_RNA-seq


title: G28_RNA-seq


title: G27_RNA-seq


title: G26_RNA-seq


title: G39_RNA-seq


title: G25_RNA-seq


title: G2_RNA-seq


title: G20_RNA-seq


title: G24_RNA-seq


title: G19_RNA-seq


title: G23_RNA-seq


title: G152_RNA-seq


title: G17_RNA-seq


title: G21_RNA-seq


title: G18_RNA-seq


title: G151_RNA-seq


title: G16_RNA-seq


title: G41_RNA-seq


title: G15_RNA-seq


title: G30_RNA-seq


title: G149_RNA-seq


title: G148_RNA-seq


title: G147_RNA-seq


title: G146_RNA-seq


title: G145_RNA-seq


title: G144_RNA-seq


title: G142_RNA-seq


title: G14_RNA-seq


title: G141_RNA-seq


title: G140_RNA-seq


title: G139_RNA-seq


title: G143_RNA-seq


title: G137_RNA-seq


title: G138_RNA-seq


title: G136_RNA-seq


title: G128_RNA-seq


title: G133_RNA-seq


title: G150_RNA-seq


title: G127_RNA-seq


title: G135_RNA-seq


title: G129_RNA-seq


title: G125_RNA-seq


title: G13_RNA-seq


title: G130_RNA-seq


title: G134_RNA-seq


title: G126_RNA-seq


title: G131_RNA-seq


title: G124_RNA-seq


title: G120_RNA-seq


title: G122_RNA-seq


title: G121_RNA-seq


title: G119_RNA-seq


title: G12_RNA-seq


title: G117_RNA-seq


title: G115_RNA-seq


title: G114_RNA-seq


title: G123_RNA-seq


title: G118_RNA-seq


title: G116_RNA-seq


title: G110_RNA-seq


title: G132_RNA-seq


title: G111_RNA-seq


title: G11_RNA-seq


title: G109_RNA-seq


title: G106_RNA-seq


title: G102_RNA-seq


title: G107_RNA-seq


title: G101_RNA-seq


title: G100_RNA-seq


title: G10_RNA-seq


title: G103_RNA-seq


title: F99_RNA-seq

source_name: E12.5 Single Cell


title: G1_RNA-seq


title: F96_RNA-seq


title: F97_RNA-seq


title: G113_RNA-seq


title: F92_RNA-seq


title: F94_RNA-seq


title: G112_RNA-seq


title: F90_RNA-seq


title: F89_RNA-seq


title: F91_RNA-seq


title: F9_RNA-seq


title: F93_RNA-seq


title: F88_RNA-seq


title: F87_RNA-seq


title: F86_RNA-seq


title: G105_RNA-seq


title: G108_RNA-seq


title: F85_RNA-seq


title: F83_RNA-seq


title: F82_RNA-seq


title: F80_RNA-seq


title: F8_RNA-seq


title: F81_RNA-seq


title: F77_RNA-seq


title: F79_RNA-seq


title: F98_RNA-seq


title: F76_RNA-seq


title: F78_RNA-seq


title: F75_RNA-seq


title: F71_RNA-seq


title: F73_RNA-seq


title: F72_RNA-seq


title: F70_RNA-seq


title: F68_RNA-seq


title: F7_RNA-seq


title: F65_RNA-seq


title: F74_RNA-seq


title: F63_RNA-seq


title: F69_RNA-seq


title: F62_RNA-seq


title: F66_RNA-seq


title: F67_RNA-seq


title: F64_RNA-seq


title: F61_RNA-seq


title: F84_RNA-seq


title: F60_RNA-seq


title: F6_RNA-seq


title: F58_RNA-seq


title: F57_RNA-seq


title: F56_RNA-seq


title: F54_RNA-seq


title: F55_RNA-seq


title: F51_RNA-seq


title: F52_RNA-seq


title: F5_RNA-seq


title: F50_RNA-seq


title: F49_RNA-seq


title: F48_RNA-seq


title: F46_RNA-seq


title: F45_RNA-seq


title: F42_RNA-seq


title: F43_RNA-seq


title: F40_RNA-seq


title: F37_RNA-seq


title: F35_RNA-seq


title: F32_RNA-seq


title: F31_RNA-seq


title: F3_RNA-seq


title: F30_RNA-seq


title: F29_RNA-seq


title: F28_RNA-seq


title: F27_RNA-seq


title: F26_RNA-seq


title: F21_RNA-seq


title: F23_RNA-seq


title: F20_RNA-seq


title: F2_RNA-seq


title: WT_E3.5_blastocyst_1

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

country: China

institute: Peking University

description: processed data file: Blastocyst_E3.5_ncount.txt.gz

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling.
Adaptor contamination and low-quality reads were discarded from the raw data.
For RNA-Seq Illumina paired-end reads, TopHat (version 2.0.10) were used for sequence alignment, and nCount values were generated by HTSeq(version 0.6.1) and then normalized by DESeq2(version 1.6.1).
For PBAT DNA illumina paired-end reads,Bismark(version 0.7.6) were use for sequence alignment, and SingleC data were generated by SAMtools(version 0.1.19-44428cd)
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly mm9. Bisulfite conversion rate was estimated by the lambda genome, which was built as the extra chromosome.
Supplementary_files_format_and_content: nCount data were generated by DESeq2 and SingleC data were generated by SAMtools (version 0.1.19-44428cd)

growth_protocol:
For collection of mature oocytes, oviducts were removed from the female mice 13–15h after human chorionic gonadotropin injection. Cumulus–oocyte complexes were released into HCZB containing 0.1% bovine testicular hyaluronidase (300 USP units per mg; ICN Biomedicals Inc.).
Cavitated E3.5 blastocysts were flushed from the uteri of naturally mated mice into M2 or DMEM followed by sequential washing in KSOM.

extract_protocol:
Total RNA was extracted using Rneasy Micro Kit (QIAGEN, Cat No. 74004), and treated with Rnase-Free Dnase Set (QIAGEN, Cat No. 79254).
Total RNA was purified from isolated blastocysts by using the Qiagen AllPrep DNA/RNA Mini Kit, treated with DNase.
Then libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat No. E7530L) following the manual. Then libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat No. E7530L) following the manual.
About 1 ng of extracted RNA was first amplified 18 cycles according to the protocol for single-cell RNA-seq published previously. Briefly, 1 ng of extracted RNA was reverse translated into cDNA, then the free primers were removed by the ExoSAP-IT. TdT was used to add PolyA to the 3’ end of cDNA, the second strand were synthesized, and the double-stranded DNA product were amplified 18 cycles to obtain enough product for DNA library construction. The amplified DNA product was purified by DNA Clean & Concentrator™-5 (Zymo Research), and further purified by Zymoclean™ Gel DNA Recovery Kit (Zymo Research) for the 0.5-8 kb size DNA products. The gel purified products were sheared by Covaris S2 for the generation of fragments about 250 bp in length, and purified with DNA Clean & Concentrator™-5 (Zymo Research). Then NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, Catalog #E7370L) was used to construct a cDNA library, with reagent amount reduced to half of the reactions. The cDNA libraries were sequenced on Illumina HiSeq 2500 instrument with 100-bp reads and paired-end parameter.

treatment_protocol:
A pool of 200 (x 2) WT and 200 (x 2) Tet-null fresh oocytes were disrupted and homogenized in Buffer RLT Plus respectively, then snap-frozen in liquid nitrogen and stored at -80 ºC.
A pool of 46 WT and 46 Tet-null fresh blastocysts were disrupted and homogenized in Buffer RLT Plus respectively, then snap-frozen in liquid nitrogen and stored at -80 ºC.

tag: strain background

value: Embryonic day 3.5

value: Blastocyst


title: WT_E3.5_blastocyst_3


title: F19_RNA-seq

value: C57BL/6 Heterozygous Lmx1a-EGFP

value: developing ventral midbrain cells


title: F39_RNA-seq


title: TKO_E3.5_blastocyst_3


title: F41_RNA-seq


title: WT_E3.5_blastocyst_2


title: F36_RNA-seq


title: TKO_E3.5_blastocyst_1


title: F38_RNA-seq


title: F17_RNA-seq


title: TKO_E3.5_blastocyst_2


title: F16_RNA-seq


title: F18_RNA-seq


title: F34_RNA-seq


title: F14_RNA-seq


title: eYFP low, three miR-92 sites, rep 2

city: South San Francisco

first: Vikram

last: Agarwal

address: 1130 Veterans Blvd

institute: Calico Life Sciences

description:
mRNA
eYFP_Lo_NoSite_vs_miR92_3sites.txt

data_processing:
A genome index was built for the latest build of the mouse genome (mm10) using STAR v. 2.4 (options --runMode genomeGenerate --genomeFastaFiles mm10.fa --sjdbGTFfile Ensembl72.gtf --sjdbOverhang 125 --sjdbGTFtagExonParentTranscript Parent) (Dobin et al. 2013), with “Ensembl72.gtf” referring to mouse transcript models annotated in Ensembl release 72. For ES cell libraries, the mCherry and eYFP sequences were also included in the --genomeFastaFiles parameter.
Raw reads were aligned to this genome index using STAR v. 2.4 (options --outFilterType BySJout --outFilterMultimapScoreRange 0 --readMatesLengthsIn Equal --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --outStd SAM) (Dobin et al., 2013). For ES cell libraries, reads were also mapped to mCherry and eYFP sequences, which were included in the genome index.
Pooling all biological replicates of a particular sample, differential expression analysis was performed between two samples of interest using cuffdiff v. 2.2.1 (options --library-type fr-firststrand -b mm10.fa -u --max-bundle-frags 100000000) (Trapnell et al., 2013), using mouse transcript models of protein-coding and long non-coding RNA genes annotated in Ensembl release 72. For ES cell libraries, mCherry and eYFP sequences were also quantified.
For each biological replicate, expression level data (measured in Fragments Per Kilobase Million, or FPKM) was computed using cufflinks v. 2.2.1 (options --library-type fr-firststrand -b mm10.fa -u --max-bundle-frags 100000000 --compatible) (Trapnell et al., 2010), using mouse transcript models of protein-coding and long non-coding RNA genes annotated in Ensembl release 72. For ES cell libraries, mCherry and eYFP sequences were also quantified.
For small RNA-seq data, we initially trimmed the first 8 nucleotides from the 5' end, which were added to each sequence to minimize the effect of ligation bias. We then counted the number of occurrences in which the first 20 nucleotides of the trimmed sequence matched a known mature Mus musculus miRNA sequence deposited in miRBase version 20.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression measurements (FPKM), log2(fold changes), and statistical significance values for differential expression comparisons. Separate tab-delimited text file containing gene expression measurements (FPKM) for individual biological replicates, with upper and lower confidence intervals for FPKM values. For small RNA seq data, a tab-delimited text file consisting of the name of the miRNA, the miRNA seed sequence, the observed number of reads detected, and Reads Per Million (RPM) normalized abundance measurement.

source_name: E14 cell line

growth_protocol: Male embryonic stem cell line E14 was cultured in DMEM (4.5 g/l glucose, 15% heat-inactivated fetal bovine serum, 1000 U/ml recombinant mouse LIF, 0.1 mM 2-mercaptoethanol, 1% Penicillin-Streptomycin, 1% Glutamax, and 1mM sodium pyruvate) on a 0.1% gelatin-coated plated in the absence of feeder cells.

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's instructions and the RNA treated with DNase prior to library preparation.
For RNA-seq, total RNA was treated with the DNA-free Kit (Life Technologies), cleaned up with an RNAeasy MinElute Cleanup Kit (Qiagen) and the quality controlled with an Agilent 2100 Bioanalyzer. Library preparation and sequencing were performed by Fasteris SA (Switzerland) or by the Functional Genomics Centre Zürich (FGCZ), using an Illumina HiSeq 2500 machine. For small RNA-seq total RNA was size fractionated (18–35 nt), followed by ligation of 3’ preadenylated adapter (AppNNNNAGATCGGAAGAGCACACGTCTddC) and 5’ adapter (Truseq small RNA 5’ adapter RA5 + 8Ns, GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNN), reverse transcription, PCR amplification, and Solexa sequencing. The 8 and 4 random nucleotides (Ns) on the 5' and 3' ends, respectively, were added to minimize the effect of ligation bias during the quantification step.

treatment_protocol: Plates with ~80% confluence were trypsinized and plated at 2 x 10^5 cells/well in gelatin-coated Nucleon Delta Surface 12-well plates. 16 to 24 hours after plating cells were transfected in Opti-MEM with 5ul Lipofectamine 2000, together with 250 ng pTRE-Tight-BI dual-fluorescent (eYFP and mCherry) plasmid, 250 ng rtTA plasmid, 1000 ng pWhitescript. Six hours after transfection the media was changed to ESC media containing 1ug/ml Doxycycline, incubated for 18 hours, and then harvested for downstream flow cytometry analysis.

value: ES cells


title: F13_RNA-seq


title: Embryonic Stem Cells small RNA profile, rep 1

description: small RNA

treatment_protocol: No treatment


title: F25_RNA-seq


title: Primary hepatocytes small RNA profile, rep 1

description: small RNA

source_name: Primary hepatocytes

growth_protocol: Primary hepatocytes were isolated from liver as reported by Zhang et al. (PLoS One, 2012; also see http://www.mouselivercells.com/), grown for 4-6 hours in DMEM 1g/l glucose (1% Penicillin-Streptomycin, 1% Glutamax and 10% fetal bovine serum) and grown for 24 hours in HepatoZYME-SFM (1% Penicillin-Streptomycin and 1% Glutamax) at 300,000 cells per 6-well and lysed 30 hours post isolation.

value: cells derived from liver


title: F128_RNA-seq


title: eYFP intermediate, three miR-92 sites, rep 2

description:
mRNA
eYFP_In_NoSite_vs_miR92_3sites.txt


title: eYFP low, three miR-92 sites, rep 1

description:
mRNA
eYFP_Lo_NoSite_vs_miR92_3sites.txt


title: F127_RNA-seq


title: eYFP intermediate, three miR-92 sites, rep 1

description:
mRNA
eYFP_In_NoSite_vs_miR92_3sites.txt


title: F126_RNA-seq


title: eYFP high, three miR-92 sites, rep 2

description:
mRNA
eYFP_Hi_NoSite_vs_miR92_3sites.txt


title: F125_RNA-seq


title: eYFP high, three miR-92 sites, rep 1

description:
mRNA
eYFP_Hi_NoSite_vs_miR92_3sites.txt


title: F122_RNA-seq


title: Embryonic Stem Cells small RNA profile, rep 2

description: small RNA


title: eYFP low, three miR-293 sites, rep 2

description:
mRNA
eYFP_Lo_NoSite_vs_miR293_3sites.txt


title: eYFP low, three miR-293 sites, rep 1


title: F120_RNA-seq


title: eYFP intermediate, three miR-293 sites, rep 2

description:
mRNA
eYFP_In_NoSite_vs_miR293_3sites.txt


title: F15_RNA-seq


title: eYFP intermediate, three miR-293 sites, rep 1


title: F123_RNA-seq


title: F118_RNA-seq


title: F119_RNA-seq


title: F12_RNA-seq


title: F121_RNA-seq


title: eYFP low, no site, rep 2

description: mRNA


title: eYFP high, three miR-293 sites, rep 2

description:
mRNA
eYFP_Hi_NoSite_vs_miR293_3sites.txt


title: eYFP low, no site, rep 1

description: mRNA


title: F115_RNA-seq


title: F114_RNA-seq


title: eYFP intermediate, no site, rep 2

description: mRNA


title: eYFP intermediate, no site, rep 1

description: mRNA


title: eYFP high, no site, rep 2

description: mRNA


title: eYFP high, three miR-293 sites, rep 1


title: F113_RNA-seq


title: F112_RNA-seq


title: F110_RNA-seq


title: F11_RNA-seq


title: F109_RNA-seq


title: F108_RNA-seq


title: MOI120 Ad-AldoA, one miR-192 8-mer site, rep 1

treatment_protocol: Adenovirus were added 4-6 hours after isolation and left on the cells for 24 hours


title: MOI120 Ad-AldoA, one miR-192 8-mer site, rep 2


title: MOI120 Ad-AldoA, one miR-194 8-mer site, rep 1

description:
mRNA
MOI120_NoSite_vs_miR194_8mer.txt


title: MOI120 Ad-AldoA, no sites, rep 2

description: mRNA


title: F105_RNA-seq


title: F106_RNA-seq


title: MOI120 Ad-AldoA, one miR-194 8-mer site, rep 2

description:
mRNA
MOI120_NoSite_vs_miR194_8mer.txt


title: MOI120 Ad-AldoA, no sites, rep 1

description: mRNA


title: MOI80 Ad-AldoA, one miR-122 8mer site and one let-7 8mer site, rep 1

description:
mRNA
MOI80_let7_8mer_vs_miR122_8mer_let7_8mer.txt


title: MOI80 Ad-AldoA, one miR-122 8mer site and one let-7 8mer site, rep 2


title: F117_RNA-seq


title: F104_RNA-seq


title: F102_RNA-seq


title: MOI80 Ad-AldoA, one let-7 8-mer site, rep 1

description: mRNA


title: F101_RNA-seq


title: MOI63 Ad-AldoA, one let-7 8-mer site, rep 2

description:
mRNA
MOI63_NoSite_vs_let7_8mer.txt


title: F10_RNA-seq


title: MOI63 Ad-AldoA, one let-7 8-mer site, rep 1

description:
mRNA
MOI63_NoSite_vs_let7_8mer.txt


title: F1_RNA-seq


title: eYFP high, no site, rep 1

description: mRNA

treatment_protocol: Plates with ~80% confluence were trypsinized and plated at 2 x 10^5 cells/well in gelatin-coated Nucleon Delta Surface 12-well plates. 16 to 24 hours after plating cells were transfected in Opti-MEM with 5ul Lipofectamine 2000, together with 250 ng pTRE-Tight-BI dual-fluorescent (eYFP and mCherry) plasmid, 250 ng rtTA plasmid, 1000 ng pWhitescript. Six hours after transfection the media was changed to ESC media containing 1ug/ml Doxycycline, incubated for 18 hours, trypsin downstream flow cytometry analysis. Cells were sorted into three bins(low, intermediate, and high) based on their eYFP fluorescence.


title: E99_RNA-seq

source_name: E10.5 Single Cell


title: MOI63 Ad-AldoA, no sites, rep 2

description: mRNA


title: REH-SPLAT

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

institute: Uppsala University

data_processing:
Base calling: RTA 1.18.61
Quality and adapter trimming; TrimGalore v0.37 --paired , --trim1
Alignment: Bismark v0.14 (bowtie2)
Deduplication: Bismark v0.14
Methylation calling: Bismark v0.14
Genome_build: GRCh37
Supplementary_files_format_and_content: bedgraph: 4th column is methylation level
Supplementary_files_format_and_content: bigWig: data value is number of reads covering position

source_name: ALL cell line

extract_protocol:
SPLAT
QIAGEN All Prep protocol

value: REH

value: ALL cell line

tag: library preparation protocol

value: SPLAT


title: E98_RNA-seq


title: REH-NEB

extract_protocol:
NEBNextUltra
QIAGEN All Prep protocol

value: NEBNextUltra


title: F107_RNA-seq


title: MOI63 Ad-AldoA, no sites, rep 1

description: mRNA


title: E95_RNA-seq


title: E96_RNA-seq