title: Tx5MEMpos

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI37) using BWA package ( mem –t 7 –c 100 –M –R ).
The RPKM values and the raw read numbers were calculated using the rnaseq_countgeneread function from Cisgenome v2
Genome_build: hg19
Supplementary_files_format_and_content: *.rna raw read counts
Supplementary_files_format_and_content: *.rna.RPKM RPKM values

source_name: memory (CD45RA+) CD4 T cell, thymectomy 5

extract_protocol:
Total RNA was purified from sorted CD31+ and CD31- naïve CD4+ T cells using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) as according to manufacturer’s instructions. RNA was stored at -80C until further processing
mRNA was isolated using the Poly(A) Beads (NEXTflex). Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

tag: cell subtype

value: memory (CD45RA+) CD4

tag: group

value: thymectomy

tag: cell type

value: T cells (FACSsorted)


title: worker_3pm_1

status: Public on Oct 18 2016

type: SRA

city: Urbana

first: Amy

last: Cash

state: IL

address: 1206 W. Gregory Dr

department: Biology

country: USA

institute: University of Illinois

library_source: transcriptomic

data_processing:
Each pool of 8 samples was quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000 using a TruSeq SBS sequencing kit version 3.
FastQ files were generated and demultiplexed with Casava 1.8.2
Each sample's pair of fastq files were run through trimmomatic 0.30 to first remove any remaining standard Illumina PE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove individual reads shorter than 30 bp and their paired read, regardless of length (parameters ILLUMINACLIP:/home/apps/trimmomatic/trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10 TRAILING:28 LEADING:28 MINLEN:30)
Paired reads per samples were aligned to Amel 4.5 genome and OGS 3.2 gene models using Tophat2 2.0.10 with parameters --library-type fr-firststrand --mate-inner-dist 150 --mate-std-dev 40. Alignment bam files were sorted by read name using "samtools sort -n".
Fragment counts for each gene were obtained using htseq-count (htseq 0.5.4) with parameters -s reverse -m union -a 0 -t gene -i ID
Genome_build: Amel 4.5
Supplementary_files_format_and_content: tab-delimited text files of raw fragment counts per gene per sample were used directly in edgeR 3.4.2 for statistical analysis and thus are the "normalized" data.
Supplementary_files_format_and_content: Those identifiers are from Beebase.org's OGSv3.2, which is the official gene set for Apis mellifera genome assembly Amel_4.5. It is available for download from here:
http://hymenopteragenome.org/beebase/?q=download_sequences

molecule: total RNA

organism: Apis mellifera

source_name: active worker bees collected in the afternoon as they prepared to forage

growth_protocol: Three colonies used in these experiments was headed by a naturally mated queen (unrelated to each other), contained 8,000-10,000 workers and several hundred drones, and were maintained according to standard methods at the University of Illinois Bee Research Facility, Urbana, Illinois, USA

extract_protocol:
Bees were flash frozen on liquid nitrogen, heads were incubated in RNAlater ICE, and mushroom bodies were dissected from the brain.  Total RNA was extracted using Picopure RNA isolation kits and poly-adenylated RNA was enriched using Oligo(dT)25 dynabeads
Libraries were constructed using the NEXTflex Directional RNA-Seq Kit from Bioo Scientific

treatment_protocol: Behavioral observations and marking were used to identify active drones and workers

tag: sex type

value: worker

tag: collection time

tag: tissue

value: mushroom body (dissected from brain)

tag: colony

tag: pool


title: RT rep2 - 4m_MNase-seq

city: Princeton

first: Tess

last: Jeffers

state: NJ

address: 165 Carl Icahn Laboratory

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: sequencing of mononucleosomal DNA liberated at 4 minute timepoint

library_source: genomic

data_processing:
Paired end reads were mapped to ce10 genome release using Bowtie (v1.1.2) with stringent multimapping parameters: bowtie -q -X 2000 --fr -p 1 -S -n 2 -e 70 -l 28 --pairtries 100 --maxbts 125 -k 1 -m 1 --un /Unmapped_Reads.fastq --phred33-quals /ce10 -1 /read1.fastq -2 /read2.fastq
Reads with insert sizes between 100 and 250 bp were kept for downstream analysis.
Replicates were first processed individually, then pooled after confirming a high degree of correlation between replicates.
Nucleosome analysis was performed as described previously {Kaplan:2010we, Gossett:2012hw}.
Scaled Coverage: Nucleosome coverage was calculated by extending the filtered mapped reads to their fragment length and measuring the sum of reads covering each bp. To normalize for variation between samples, nucleosome coverage was scaled by 1/(mean coverage), yielding a mean nucleosome coverage of 1.0.
Smooth Dyads: Dyads are approximated as the center of a paired-end fragment. The number of dyads at each base pair was scaled by 1/(mean dyad density), then Gaussian smoothed with a standard deviation of 20 bp.
Nucleosome calls: Nucleosome positions were identified from dyad density maps using a previously reported greedy algorithm {Albert:2007cb, Gossett:2012hw}. Using the local maxima of the dyad density as the nucleosome center p, the size of the nucleosome (the nucleosome-protected region) was determined by measuring the average length of all reads that covered the nucleosome center. The standard deviation of the nucleosome center (the nucleosome “fuzziness”) was calculated for each called nucleosome as the standard deviation of dyads around the mean. Nucleosome occupancy was defined as the number of dyads that fell within 50 bp of the nucleosome center.
RNA-seq reads were mapped to the C. elegans WS220 Gene Annotation Model using Tophat2 (v0.7) {Trapnell:2012kp}.
HTSeq-counts: The resulting alignment files were quantified using HT-Seq (v0.4.1) and the RefSeq gene annotations for WS220 {Anders:2015gf}.
Total read counts per gene were normalized for differential expression using DESeq2 (v1.0.19) in R (v3.0.1) {Love:2014eo}.
Genome_build: UCSC C. elegans October 2010 release (ce10/WS220)
Supplementary_files_format_and_content: Scaled Coverage: wig file containing normalized signal for every basepair in the genome.
Supplementary_files_format_and_content: SmoothDyads: wig file containing normalized & smoothed dyad signal for every basepair in the genome.
Supplementary_files_format_and_content: CalledNucleosomes: bed file containing chr, start, stop, length, lengthStdev, dyad position, dyad Stdev, conditionalPosition, dyadMean, and occupancy for every nucleosome in the genome.
Supplementary_files_format_and_content: HTSeq-counts: tabular file containing total number of read counts mapping to every gene in the genome

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Embryo

growth_protocol: Wild type N2 worms were maintained at 20degC in liquid culture in S-medium supplemented daily with concentrated HB101 bacteria. Mixed-stage embryos were isolated from gravid adults by bleach hypochlorite treatment.

extract_protocol:
Cross-linked embryos were incubated with chitinase, washed, and dounced in dounce buffer to extract nuclei. Nuclei were pelleted and washed with MNase digestion buffer. Chromatin was digested with MNase, and at each timepoint (0, 2, 4, 8, 15, or 30 minutes after enzyme addition) a fraction of the reaction was removed, quenched with EDTA, and stored on ice. Samples were treated with Proteinase K for 2 hours at 55 degC, then incubated overnight at 65 degC to reverse crosslinks. DNA was isolated from RNA and proteins using phenol:chloroform extraction and RNase A treatment for 1 hour at 37 degC. Mononucleosome-sized fragments (100 to 200 bp) were extracted from a 2% agarose gel and purified using a Qiagen gel extraction kit.
Libraries were prepared from 100 ng of gel-extracted DNA using the Illumina TruSeq DNA library preparation kit v2 (FC-121-2001) according to manufacturer instructions. Ampure beads were used for the final purification in lieu of gel purification. Individual samples were barcoded with unique 6bp index sequences contained within the sequencing adapters.  Individual libraries were then pooled at equimolar ratios for paired-end multiplex sequencing.

treatment_protocol: Control. After hypochlorite treatment, embryos were incubated at 20 degC for 20 minutes. Embryos were then cross-linked for 30 minutes in M9 + 2% formaldehyde

tag: developmental stage

value: Mixed-stage

tag: strain


title: RT rep1 - 2m_MNase-seq

description: sequencing of mononucleosomal DNA liberated at 2 minute timepoint


title: RT rep1 - 30m_MNase-seq

description: sequencing of mononucleosomal DNA liberated at 30 minute timepoint


title: drone_9am_12

source_name: inactive drone bees collected in the morning

value: drone


title: Tx4Npos

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

organism: Homo sapiens

source_name: naive CD31+ CD4+ T cell, thymectomy 4

value: naive CD31+ CD4+


title: glp1_rege1RNAi_2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
The RNA-seq data were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/3.1/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression (ce_mRNA_rege1RNAi_rawCounts.txt) was quantified by counting the number of reads that started within any of the exons belonging to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same") which counts the reads on the same strand as the gene. To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8)). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts (ce_mRNA_rege1RNAi_normalized.txt). Intronic expression for each gene (ce_intron_rege1RNAi_rawCounts.txt, ce_intron_rege1RNAi_normalized.txt) was quantified by subtracting the reads that fall within exons from the reads that cover the whole gene body. Exon coordinates were extended by 10bp on both sides to ensure that exonic reads close to the junctions are not counted as intronic reads. Intronic and exonic read tables were normalized the same way but the procedure was performed separately for the two tables.
Genome_build: ce6
Supplementary_files_format_and_content: ce_mRNA_rege1RNAi_rawCounts.txt, ce_mRNA_rege1RNAi_normalized.txt, ce_intron_rege1RNAi_rawCounts.txt, ce_intron_rege1RNAi_normalized.txt

source_name: Whole animal

growth_protocol: Animals were synchronized by hypochloride treatment and allowed to hatch in M9 over night.

extract_protocol:
Animals were grown to young adulthood, frozen in liquid nitrogen and RNA was extracted by Trizol treatment.
ScriptSeq v2 RNA-Seq Library Preparation Kit

treatment_protocol: Synchronized L1 larvae were put on RNAi plates to facilitate knock down by feeding dsRNA directed against rege-1 or mock. Glp-1 animals were grown on 25°C (restrictive temperature).

value: young adults

tag: genotype

value: rege-1 knock down


title: Tx3Npos

source_name: naive CD31+ CD4+ T cell, thymectomy 3


title: glp1_mock_2

description: mock RNAi

value: control


title: glp1_mock_1

description: mock RNAi


title: glp1_rege1RNAi_1


title: Tx3Nneg

source_name: naive CD31- CD4+ T cell, thymectomy 3

value: naive CD31- CD4+


title: Tx3MEMneg

source_name: memory (CD45RA-) CD4 T cell, thymectomy 3

value: memory (CD45RA-) CD4


title: U2OS_ChIPseq_vector_+Dox_HA

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Wiggle files were generated using MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6.
hg19
Fixed step wiggle files with a resolution of 10bp.
Fastq files were generated using Illumina's CASAVA software.

source_name: U2OS cells

growth_protocol: U2OS and KPC cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma). The U2OS tet-on-MYC cell line was generated as described previously (Walz et al., 2014). For constitutive expression, N-terminally HA-tagged OmoMYC or various mutants (generated using site-directed mutagenesis) were cloned into SFFV-driven lentiviral expression vectors. Lentiviruses were produced by co-transfection with the packaging plasmid psPAX.2, and the envelope plasmid pMD2.G into HEK293 cells using the PEI method. Cells were infected with lentiviral supernatants in the presence of 4 mg/ml polybrene (Sigma) for 24 h and selected with 2 µg/ml Puromycin (InvivoGen).

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-sepharose or Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using Qiagen PCR purification columns.
Libraries were constructed following manufacturer's instructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay.

treatment_protocol: U2OS cells were treated with doxycycline (1µg/ml) for 30h (RNA-seq) or 8h (ChIP-seq) to induce MYC expression. For the shRNA screen, KPC cells were infected with doxycycline inducible lentiviral shRNA vectors and shRNA expression was induced with 1µg/ml doxycycline for 5 days.

tag: cell line

tag: treatment1(constitutive ha-omomyc or empty vector)

value: vector

tag: treatment2 (doxycycline to induce myc expression)

value: Doxycycline

tag: antibody

value: HA (ab9110 , Abcam)


title: N2_rege1RNAi_2


title: drone_9am_9


title: Tx2Npos

source_name: naive CD31+ CD4+ T cell, thymectomy 2


title: Tx2Nneg

source_name: naive CD31- CD4+ T cell, thymectomy 2


title: drone_9am_7


title: N2_mock_1

description: mock RNAi


title: Tx2MEMneg

source_name: memory (CD45RA-) CD4 T cell, thymectomy 2


title: drone_9am_6


title: rrr13_ets4RNAi_2

data_processing:
The RNA-seq data were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/3.1/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression (ce_mRNA_ets4RNAi_rawCounts.txt) was quantified by counting the number of reads that started within any of the exons belonging to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same") which counts the reads on the same strand as the gene. To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8)). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts (ce_mRNA_ets4RNAi_normalized.txt).
Genome_build: ce6
Supplementary_files_format_and_content: ce_mRNA_ets4RNAi_rawCounts.txt and ce_mRNA_ets4RNAi_normalized.txt

treatment_protocol: Synchronized L1 larvae were put on RNAi plates to facilitate knock down by feeding dsRNA directed against ets-4 or mock.

value: ets-4 knockdown


title: Tx1Nneg

source_name: naive CD31- CD4+ T cell, thymectomy 1


title: drone_9am_5


title: rrr13_ets4RNAi_1


title: Tx1Npos

source_name: naive CD31+ CD4+ T cell, thymectomy 1


title: drone_9am_10


title: rrr13_mock_2

description: mock RNAi


title: drone_9am_2


title: mESC_3C-seq (PacBio)

city: Rehovot

first: Pedro

last: Olivares-Chauvet

address: 234 Hertzl Street

department: Department of Computer Science and Applied Mathematics/Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

description: Direct sequencing of raw 3C template

data_processing:
Cwalks from PacBio reads were assembled using the cwalk pipeline with default parameters although the shotgun assembly step was not necessary. Components were directly transformed from fenchain files into cadj format
Hi-C reads were processed using the same Cwalk pipeline with the difference that adj files can directly represent the pair-wise information of genome contacts.
reads were mapped using bowtie2 with --reorder --local for cwalks and HiC
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: cadj.annot: tab separated text file with adjacency information, linked to cwalks, annotated by the epigenomic features of TADs who are visited by the cwalk; 38 fields  [chr1]: chromosome of side 1  [start1]: chrosomal coordinate of side 1  [chr2]: chromosome of side 2  [start2]: chromosomal coordinate of side 2  [comp]: component (cwalk) id  [amp_i]: phi29 amplification well id  [fid1]: restriction fragment id of side 1  [fid2]: restriction fragment id of side 2  [span1]: span of component 1  [span2]: span of component 2  [seq_batch]: sequencing batch  [n]: number of hops  [trans_n]: number of trans interfaces  [cmer_doms.dist.x]: distance to closest TAD for side 1  [cmer_doms.id.x]: id of domain hosting side 1  [cmer_doms.k4me3.x]: signal of k4me3 in domain side 1  [cmer_doms.size.x]: size of domain side 1  [cmer_doms.tor.x]: time of replication for domain side 1  [cmer_doms.mode.x]: classification of active or inactive for domain side 1  [cmer_doms.dist.y]: distance to closest TAD for side 2  [cmer_doms.id.y]: id of domain hosting side 2  [cmer_doms.k4me3.y]: signal of k4me3 in domain side 2  [cmer_doms.size.y]: size of domain side 2  [cmer_doms.tor.y]: time of replication for domain side 2  [cmer_doms.mode.y]: classification of active or inactive for domain side 2  [dom_n]: number of domains visited by cwalk  [tss_1]: distance to the closest tss from side 1  [k4me3_1]: distance to the closest peak of k4me3 from side 1   [k27me3_1]: distance to the closest peak of k27me3 from side 1  [actenh_1]: distance to the closest active enhancer from side 1  [ctcf_1]: distance to the closest ctcf from side 1  [border_1]: distance to the closest domain border for side 1  [tss_2]: distance to the closest tss from side 2  [k4me3_2]: distance to the closest peak of k4me3 from side 2   [k27me3_2]: distance to the closest peak of k27me3 from side 2  [actenh_2]: distance to the closest active enhancer from side 2  [ctcf_2]: distance to the closest ctcf from side 2  [border_2]: distance to the closest domain border for side 2
Supplementary_files_format_and_content: adj file: adjacency file ; 7 fields  [chrom1]: chromosome side 1  [start1]: start coordinate side 1  [end1]: end coordinate side 1  [chrom2]: chromosome side 2  [start2]: start coordinate side 2  [end2]: end coordinate side 2  [count]: number of molecules supporting this pair

organism: Mus musculus

source_name: v6.5 mESC

extract_protocol:
Between 25 to 50 x 10e7 cells were used to perform in-nucleus ligation 3C; biotin fill-in was omitted. Briefly, adherent cells (mES) were incubated in the presence of trypsin (Biological Industries 03-053-1) for 8-10 minutes max at 37°C and passed through a cell strainer after harvesting to ensure a single-cell suspension. Cells (including K562 from now on) were washed 1x with phosphate-buffered saline (PBS) and resuspended PBS/FBS 10% and cross-linked in formaldehyde final concentration of 2% for 5 minutes at room temperature. After quenching with 0.125 M glycine and wash with PBS, cells were incubated in permeabilization buffer (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2 % NP-40 alternative (CALBIOCHEM 492016), Protease Inhibitor Cocktail (P8340 Sigma)) for 60 minutes at 4°C while slowly mixing. Cells were split into 5 M cell aliquots and washed 2x with cold PBS. After the second wash, cell pellets were then flash frozen on liquid nitrogen. Pellets were resuspended on 175.5 µl H2O and 24.5 µl DpnII RE buffer 10x. After addition of 3 µl of 20% SDS (final concentration of 0.3%), cells were incubated for 60 minutes at 37°C while agitating (750 RPM). Triton X-100 20% was added to a final concentration of 1.8% and incubated for 60 min at 37°C. Aliquots were then digested with 15 µl HC DpnII (NEB 50,000 U/ml) ON. Cells were centrifuged for 5 minutes at 600 g and washed 1x with PBS. Incubation of pellets for 20 minutes at 65°C was performed in order to heat-inactivate any DpnII residue. In-nucleus ligation was then performed incubating cells on ligation mix (415 µl H2O, 5 µl BSA (10mg/ml NEB) and 5 µl T4 ligation enzyme NEB (2x106 U/ml)) ON at 16°C.  Cross-link was reversed by incubating aliquots with 10 mg/ml proteinase K (Roche) at 65°C ON followed by the addition of 15 µl of RNase A (Roche) for 45 minutes at 37°C. DNA was purified with AmpureXP SPRI beads 1x (Beckman Coulter; A63881) with two elution rounds of 100 µl each with the aim of size selecting for the high molecular weight portion of the sample.
Hi-C: Bioruptor Microtubes (C30010015) to reach a DNA fragment size between 400-500 bp. The sonicated DNA  was then subjected to end-repair reaction (5 µl 10x end-repair buffer + 2.5 µl end-repair mix (NEB E6050L)) at 20 °C for 30 minutes. The DNA was cleaned up with 2.2x SPRI beads and eluted in 38 µl EB. A-tailing reaction was performed with 5 µl NEB buffer 2, 4 µl Klenow fragment -3′-5′ exo (NEB M0212M) and 10 µl dATP 10 nM for 30 minutes at 37 °C, cleaned up with 2.2 x SPRI beads and eluted in 30 µl EB. DNA template was ligated with 5 µl Illumina indexed adapters 0.75 µM with 5 µl T4 quick ligase (NEB M2200) and 40 µl 10x ligase buffer for 15 minutes at 25 °C. Ligated template was then cleaned up with 1.3x SPRI beads and eluted in 41 µl.

value: Embryonic Stem Cells

tag: lineage

value: Embryonic


title: rrr13_mock_1

description: mock RNAi


title: Tx1MEMneg

source_name: memory (CD45RA-) CD4 T cell, thymectomy 1

value: thymectomy

value: T cells (FACSsorted)


title: drone_9am_11

value: mushroom body (dissected from brain)


title: drone_9am_8


title: N2_mock_2

description: mock RNAi


title: N2_rege1RNAi_1


title: drone_3pm_11

source_name: active drone bees collected in the afternoon just prior to taking flight


title: drone_9am_1


title: drone_3pm_12


title: HC3Nneg

source_name: naive CD31- CD4+ T cell, healthy control 3

value: healthy control


title: HC2Npos

source_name: naive CD31+ CD4+ T cell, healthy control 2


title: HC3MEMneg

source_name: memory (CD45RA-) CD4 T cell, healthy control 3


title: HC2Nneg

source_name: naive CD31- CD4+ T cell, healthy control 2


title: HC2MEMneg

source_name: memory (CD45RA-) CD4 T cell, healthy control 2


title: drone_3pm_10

value: drone


title: drone_3pm_9


title: drone_3pm_8


title: HC1Npos

source_name: naive CD31+ CD4+ T cell, healthy control 1

value: naive CD31+ CD4+


title: drone_9am_4

source_name: inactive drone bees collected in the morning


title: drone_3pm_6


title: HC1Nneg

source_name: naive CD31- CD4+ T cell, healthy control 1


title: HC3Npos

source_name: naive CD31+ CD4+ T cell, healthy control 3


title: drone_9am_3


title: HC1MEMneg

source_name: memory (CD45RA-) CD4 T cell, healthy control 1


title: drone_3pm_4


title: drone_3pm_5


title: WT_RAd1_mRNA

city: Shanghai

first: Li

last: Wenjing

address: DongAn Road 130, Mingdao Building Room 509, Shanghai 200032, P.R.China

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

data_processing:
base_calling: CASAVA package (Illumina v1.7)
alignment: tophat (version 2.0.12)
FPKM_calculating: cufflinks (version 2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: .fpkm_tracking

molecule: polyA RNA

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% Glutamine, 1% NEAA and LIF. For ES cell maintenance dishes were coated with 0.2% gelantin and irradiated CF1 mouse embryonic fibroblasts (MEFs) were plated as confluent layer of feeder cells. ESCs were seeded in a density of 50000 cells/ 6well and were splitted every 2-3 days.

extract_protocol:
mRNA purification was carried as manual (61011, Iife technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nono was knocked out in Mouse embryonic stem cells.

value: mESC

value: WT


title: NonoKO_RAd1_mRNA

value: Nono knockout


title: WTplus2i_mRNA


title: WTplusPD03_mRNA


title: drone_3pm_2


title: NonoKO_mRNA


title: EF_6-8hr_FAIRE_Rep2

city: Chapel Hill

first: Daniel

middle: J

last: McKay

state: NC

address: 3344 Genome Sciences Building

department: Biology, Genetics

institute: The University of North Carolina at Chapel Hill

data_processing:
Library strategy: FAIRE-seq
Basecalls were performed with CASAVA version 1.8.2
reads were aligned to the dm3 Drosophila reference genome using Bowtie2 and the following flags: –trim5 8, –sensitive, –end-to-end
reads with a MAPQ score less than 10 were removed using samtools view –q 10
aligned reads were converted to bed format using BEDTools bamToBed, and FAIRE signal files were generated by extending each read to 110bp. The number of reads overlapping each base in the genome was counted.
FAIRE data were normalized by subtracting input signal from FAIRE at each base, and z-scores were generated using the mean and standard deviation for each chromosome arm.
FAIRE peaks were called on individual replicates or pooled data using MACS2 with Input as control, and a shift size of 125bp.
Genome_build: dm3
Supplementary_files_format_and_content: processed data files are in wig format, and contain Input-subtracted FAIRE z-scores, smoothed with a 200bp sliding window average and 10bp step size.

organism: Drosophila melanogaster

source_name: 6-8 hour embryos

growth_protocol: Following a pre-clearing step, embryos were collected for 2 hours and aged at 25C until the designated time.

extract_protocol:
FAIRE-enriched DNA was ethanol precipitated, heated at 65C, treated with Rnase, and column purified.
DNA was prepared for sequencing using custom internal barcodes on an Illumina Hi-Seq machine at the UNC High-Throughput Sequencing Facility

treatment_protocol: staged samples were fixed for 10 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex. Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.

value: OregonR

value: 6-8 hours after egg laying

value: whole embryo


title: drone_3pm_1


title: WT_mRNA


title: MF_6-8hr_FAIRE_Rep2

treatment_protocol: staged embryos were Dounce homogenized and resuspended in HL buffer. GFP+ cells were FACS sorted into cold HL buffer, fixed for 5 minutes at 25C, quenched with glycine, pelleted, washed and frozen. Nuclei were resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.

value: sim3.7-Gal4 UAS-mCD8::GFP

value: sorted midline cells


title: mES_Nono_KO1_H3K27me3

data_processing:
base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0
peaks were called using macs14 with the following setting:--pvalue=1e-5
normalized abundance on gene features is generated using home-made softwares
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: *peaks.bed: peaks bed files generated by Macs14, monoExt*.bed:mapped reads files in bed format, monoExt*.bg:ChIP-seq density files in bedgraph format.

extract_protocol:
mES cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 108 cells and fragmented to 200 to 400 bp by sonication.Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.3% SDS) overnight at 4℃. The antibody-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

value: mES

tag: genotype/variation

value: NONO KO


title: MF_6-8hr_FAIRE_Rep1


title: JMJD3c-MYOD1-myocytes

city: Tokyo

first: Tomohiko

last: Akiyama

address: 35 Shinanomachi

department: School of Medicine

country: Japan

institute: Keio University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.13.
Fragments of exon per Megabase of library size (FPM) were calculated
Genome_build: hg19
Supplementary_files_format_and_content: Text files include FPM values for each Sample

source_name: Embryonic stem cells

growth_protocol: JMJD3c-hESCs were maintained in feeder-free conditions using StemFit AK-03 medium, and HSMM cells were mantained in SkGM-2 medium.

extract_protocol:
Total RNA was extracted using Trizol solution following the manufacture’s instruction. The quality of total RNA was checked by Nanodrop (260/280=1.9-2.1, 260/230>2.0) and BioAnalyzer 2000 (RIN>7).
The cDNA library from Poly(A) RNA for massive parallel sequencing was prepared from each 500 ng total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra Directional RNA Library Prep Kit for Illumina. The produced cDNA library was in 400-1000 bp size range including the adaptor sequences.

treatment_protocol: JMJD3c-hESCs were differentiated in alphaMEM containing 5% KSR, and HSMM cells were differentiated in DMEM-F12 supplemented with 2% horse serum


title: mES_Nono_KO1_H3K4me3


title: Myotubes

source_name: Skeletal myoblasts

value: HSMM


title: H3K4me3-Dox-minus

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were mapped to the human genome (hg19) using Bowtie2
K27me3 or K4me3 enrichment values were calculated using ngs.plot
Genome_build: hg19
Supplementary_files_format_and_content: Text files include normalized K27me3 or K4me3 values in +-3Kb from TSS

growth_protocol: JMJD3c-hESCs were maintained in feeder-free conditions using StemFit AK-03 medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIPed DNA libraries were constructed using NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB).

treatment_protocol: Doxycycline (1 μg/ml) was added to the medium to induce JMJD3c.

tag: chip antibody

value: H3K4me3 (Millipore, 07-473)

tag: treatment


title: H3K4me3-Dox-plus

value: Doxycycline (1 ug/ml)


title: H3K27me3-Dox-minus

value: H3K27me3 (Millipore, 07-449)


title: mES_WT_PolI

value: PolI, Abcam, ab817

tag: cell type


title: mES_NonoKO_PolII


title: drone_3pm_3

tag: sex type

value: drone

value: mushroom body (dissected from brain)


title: mES_NonoKO_PolIIS5P

value: PolIIS5P, Abcam, ab5131


title: D3_INPUT

city: Gif sur Yvette

first: isabelle

last: Vallet-Gely

address: avenue de la Terrasse

country: France

institute: CNRS

description: Processed data files are available on the ChIP samples.

data_processing:
The Illumina CASAVA software was used for basecalling
Reads were aligned on the PAO1 genome using Bowtie 2
Wig files were then generated
Analyzes were performed as described in El Sahhyed et al., 2016 (PMID:27171414) using homemade matlab functions.
Genome_build: PAO1
Supplementary_files_format_and_content: Enrichments fold were calculated for each base as the ratio of the number of reads in the IP fraction and the number of reads in the input fraction. The processed data files do not contain chromosome coordinates but the data are listed continuously from base 1 to 6275464 of the PAO1 genome represented in the fasta file on the series record.

organism: Pseudomonas aeruginosa

growth_protocol: Strains were grown in Minimal medium supplemented with Citrate to an OD600 of 0.1, at 30 degres.

extract_protocol:
Chromosomal DNA was sheared by sonication to an average size of 0.5-1 kb. After the removal of cell debris by centrifugation, 50 μl of each sample was removed to serve as an input control. The remaining samples were added to 50 μl of ANTI-FLAG M2 affinity resin (Sigma A2220) previously washed twice with TBS and twice with lysis buffer. After incubation at 4°C overnight, beads were pelleted and washed twice with TBS Tween 0.5% and three times with TBS. Elution was performed using the 3X FLAG peptide (Sigma F4799), as recommended. The recovered supernatants were placed at 65°C overnight to reverse the cross-links. The input samples were also incubated at 65°C overnight after the addition of 200 μl of TBS.
Libraries preparation and sequencing were performed by the IMAGIF facility (I2BC, Gif sur Yvette), according to Illumina recommendations.

treatment_protocol: Formaldehyde was added to 150 ml of culture (Minimal Medium A supplemented with 0.25% citrate, OD600 approximately 0.1) to a final concentration of 1% and samples were incubated at room temperature for 30 min. To quench cross-linking reaction, glycine was added to a final concentration of 125 mM and followed by a 10 min incubation at room temperature. Cell pellets were washed three times with 10ml of PBS and then resuspended in 1 ml of lysis buffer (50 mM Tris-HCl pH 7.4; 150 mM NaCl; 1 mM EDTA; Triton X-100 1%; and Roche Protease Inhibitor Cocktail).

value: delta_parS123 ParB-3xflag


title: NOFLAG_INPUT


title: Hhex-/fl leukemia cell line rep 2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Reads were mapped to the GRCm37/mm9 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained. Mapped reads were assigned to mouse RefSeq genes using the featureCounts program. NCBI RefSeq mouse annotation build 37.2 was used. Genes were removed from analysis if they failed to achieve a CPM (counts per million assigned reads) value of 1 or greater in at least one library.
Read counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. P-values were adjusted to control the global false discovery rate across all comparisons with the ‘global’ option of the limma package. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 or less.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.

source_name: Cell line

extract_protocol:
RNA was extracted from sorted LSKs, GFP+ LICs and GFP+ leukemia cells using the RNeasy Kit (Qiagen, Valencia CA).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

value: Cell line

tag: celltype

value: MLL-ENL leukemia

value: Hhex-/fl


title: mES_Nono_KO_Input


title: mES_WT_PolIIS5P

value: WT


title: JMJD3c-mut-plus

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.13.
FPKM was calculated using Cufflinks v2.1.1.
Genome_build: hg19

growth_protocol: The ES cells were maintained in feeder-free conditions using StemFit AK-03 medium on iMatrix-511-coated plates.

treatment_protocol: Doxycycline (1 μg/ml) was added to the medium to induce JMJD3c or JMJD3c mutant.


title: JMJD3c-mut-minus


title: JMJD3c-D4


title: JMJD3c-D3


title: D4_ChIP

value: delta_parS1234 ParB-3xflag

value: ANTI-FLAG M2 affinity resin (Sigma A2220)


title: Hhex-/fl tumor rep 2

source_name: Bone marrow

tag: tissue

value: Bone marrow


title: Hhex-/fl leukemia cell line rep 1


title: D3_ChIP


title: WT2_INPUT

value: PAO1 ParB-3xflag


title: JMJD3c-D2


title: WT1_INPUT


title: Hhex-/fl tumor rep 1


title: NOFLAG_ChIP


title: H3K27me3-Dox-plus


title: JMJD3c-D1


title: D4_INPUT


title: Hhex+/fl leukemia cell line rep 2

value: Hhex+/fl


title: WT1_ChIP


title: JMJD3c-D0


title: WT2_ChIP


title: Hhex+/fl tumor rep 2


title: Hhex+/fl leukemia cell line rep 1


title: drone_3pm_7

source_name: active drone bees collected in the afternoon just prior to taking flight

tag: collection time

tag: colony


title: Hhex+/fl tumor rep 1


title: Fourth instar Culex quinquefasciatus Time 24h – Permethrin treatment LC50

city: Auburn

first: Nannan

last: Liu

state: AL

address: 301 Funchess Hall

department: Entomology

institute: Auburn University

description: mRNA seq

data_processing:
Base-calling, filtering, and conversion to fastq files were conducted by the Hudson Alpha Institute of Biotechnology using CASAVA version 1.8.
Paired end fastq data were trimmed for adapter using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic)
Cleaned reads were mapped to the Cx. quinquefasciatusburg v1.3 (www.vectorbase.org) using Tophat as paired end reads with no novel junction discovery, an average insert size of 200 nt and a standard deviation of 50 (http://www.cbcb.umd.edu/).
Gene expression and differential gene expression estimations were performed using the Cufflinks-Cuffdiff pipeline as a time series (http://www.cbcb.umd.edu/).
Genome_build: Culex quinquefasciatus strain Johannesburg version 1.3 (www.vectorbase.org)
Supplementary_files_format_and_content: Tab-delimited text file of FPKM values of all gene expression by time point

organism: Culex quinquefasciatus

source_name: Fourth instar larvae, Time 24h – Permethrin treatment LC50

growth_protocol: Cx. quinquefasciatus were reared under a 12:12 (L:D) photoperiod and fed a diet consisting of brewer's yeast.

extract_protocol:
A total of 200 larvae were pooled for each sample, homogenized in quanidinium isothiocyanate buffer and extracted using the hot acid phenol extraction method as outlined by Chomczynski and Sacchi (1987). RNA was extracted over 1:1 acid phenol twice, precipitated over two volumes of 100% ethanol, then resuspended in buffer and treated with Proteinase K to remove remaining protein, re-extracted over 1:1 phenol:chloroform, extracted 1x over chloroform and precipitated over two volumes of ethanol and 0.3M sodium acetate. From this, a total of 30 micrograms of RNA was used for DNase I treatment using the Ambion DNA-Free kit to remove residual DNA. DNA-free RNA was then re-extracted over 1:1 phenol:chloroform followed by final extraction over chloroform, precipitation over two volumes of 100% ethanol and 0.3M sodium acetate. The precipitated pellet was washed two times over 80% ethanol, resuspended in sterile deionized water and sent for sequencing.
Paired end libraries were prepared according to Illumina's instructions accompanying the mRNA Seq 8-sample kit by the Hudson Alpha Institute of Biotechnology, Huntsville, AL. Libraries were then sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols. Lengths of 51 nucleotides were sequenced for each of the paired ends and the average insert size was 200 nucleotides.

treatment_protocol: Untreated or 24h exposure to either acetone, permethrin (at the LC50 rate), or permethrin (at the LC70 rate)

tag: developmental stage

value: larval (fourth instar)

value: whole body

value: LC50 permethrin


title: Fourth instar Culex quinquefasciatus Time 0 untreated

description: mRNA seq

source_name: Fourth instar larvae, Time 0 untreated

value: Untreated


title: Fourth instar Culex quinquefasciatus Time 24h – Permethrin treatment LC70

description: mRNA seq

source_name: Fourth instar larvae, Time 24h – Permethrin treatment LC70

value: LC70 permethrin


title: Fourth instar Culex quinquefasciatus Time 24h – Acetone treatment

description: mRNA seq

source_name: Fourth instar larvae, Time 24h – Acetone treatment

value: Acetone


title: mES_WT_Input

data_processing:
base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0
peaks were called using macs14 with the following setting:--pvalue=1e-5
normalized abundance on gene features is generated using home-made softwares
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: *peaks.bed: peaks bed files generated by Macs14, monoExt*.bedGraph:ChIP-seq density files in bedgraph format.

value: mES


title: mES_WT_Nono

value: Nono, Abcam, ab70335


title: s_RCC351_4

status: Public on Oct 17 2016

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
Sample name: s_RCC351_4
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt

data_processing:
Raw output BAMs were converted back to FASTQ using PICARD Sam2Fastq. Reads were then mapped to the human genome using rnaStar. The genome used was hg19 with junctions from ENSEMBL (GRCh37.69_ENSEMBL) and a read overhang of 49. Gene level counts were computed using htseq-count and the same gene models as used in the mapping step.
HTSeq v0.5.4 is used for feature counting.
Counts were normalized and rescaled into log2 counts using the limma R package.
Genome_build: hg19
Supplementary_files_format_and_content: run_RNASTAR_pipe.txt: Tab-delimited text file includes normalized count tables from each experiment.

source_name: clear cell RCC tumor, CD16+ NK cells

extract_protocol:
Tumors were homogenized in Trizol and processed according to instructions with reagent.
Follow Ion Torrent protocol, start with 2ng RNA for SMARTer Clontech kit v3, then library starts with 10ng SMARTer amplified cDNA, using Ion ampliseq library builder protocol.

tag: disease status

value: clear cell renal cell carcinoma (RCC)

value: clear cell RCC tumor

value: CD16+ natural killer (NK) cells

tag: sorting marker

tag: patient identifier


title: s_RCC343_4

description:
Sample name: s_RCC343_4
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt

source_name: clear cell RCC tumor, macrophages

value: macrophages


title: s_RCC344hg_2

description:
Sample name: s_RCC344hg_2
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt

source_name: clear cell RCC tumor, CD8+ T cells

value: CD8+ T cells


title: s_RCC343_2

description:
Sample name: s_RCC343_2
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: s_RCC344cc_2

description:
Sample name: s_RCC344cc_2
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: mES_WT_H3K4me3

value: WT


title: s_RCC290_2

description:
Sample name: s_RCC290_2
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: s_RCC344cc_3

description:
Sample name: s_RCC344cc_3
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: mES_WT_H3K27me3


title: s_RCC351_2

description:
Sample name: s_RCC351_2
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: s_RCC290_4

description:
Sample name: s_RCC290_4
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt

source_name: clear cell RCC tumor, CD45- non-immune cells

value: CD45- non-immune cells


title: s_RCC351_1

description:
Sample name: s_RCC351_1
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt

source_name: clear cell RCC tumor, CD4+ T cells

value: CD4+ T cells


title: s_RCC344hg_1

description:
Sample name: s_RCC344hg_1
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: s_RCC290_1

description:
Sample name: s_RCC290_1
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: s_RCC344cc_1

description:
Sample name: s_RCC344cc_1
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: Sample_9-Lymphnode-Tcell-WT5

city: San Francisco

first: Rachel

last: Gate

state: CA

address: 533 Parnassus Ave

institute: UCSF

data_processing:
Library strategy: ATAC-seq
alignment with BWA
Filter mitochondrial and duplicate reads
Remove reads aligning to centromers and telomers
Call peaks using MACS2(FDR=0.05)
Genome_build: mm9
Supplementary_files_format_and_content: bedfile

source_name: Lympnode Tcell WT ATAC

growth_protocol: CD4+ T cells were isolated from the lymph nodes mice using negative selection (Thermo Fisher Dynabeads) and cultured in plates pre-coated with anti-CD3ε and anti-CD28 (BD Pharmingen) under standard Th2 polarization conditions for four days, as described29.  On day 5 the supernatants were removed for cytokine measurement and the cells were washed and analyzed for 4get (GFP) allele expression.

extract_protocol:
Cells were lysed in 100 μl of mild detergent (100mM Tris-HCL pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice for 5 minutes to release the nuclei.  Pelleted nuclei were then incubated for 90 minutes with Tagment DNA Enzyme transposase from the Nextera DNA Library Preparation kit (Illumina).  The reaction was stopped and DNA was purified using the MinElute Reaction Cleanup kit (Qiagen)
The eluted DNA was amplified with the NEBNext High-Fidelity 2x PCR Master Mix using Nextera index primers (Illumina).  The indexed libraries were purified using the MinElute PCR Reaction Cleanup (Qiagen) before sequencing on an Illumina HiSeq 2500 with 25 bp paired-end reads.

treatment_protocol: Briefly, 50,000 – 75,000 cells were sorted into PBS, washed once, and then lysed in 100 μl of mild detergent (100mM Tris-HCL pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice for 5 minutes to release the nuclei.  Pelleted nuclei were then incubated for 90 minutes with Tagment DNA Enzyme transposase from the Nextera DNA Library Preparation kit (Illumina)

tag: strain background

value: Balb/c

value: Lymphnode

value: T cell


title: Sample_8-Lymphnode-Tcell-WT4


title: Sample_7-Lymphnode-Tcell-KO4

source_name: Lympnode Tcell KO ATAC

value: cytokine KO


title: Sample_3-Lymphnode-Tcell-WT3


title: Sample_5-Lymphnode-Tcell-KO2


title: Sample_6-Lymphnode-Tcell-KO3


title: s_RCC356_1

description:
Sample name: s_RCC356_1
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: s_RCC344hg_4

description:
Sample name: s_RCC344hg_4
SMARTer RNA-Seq
Processed data file: run_RNASTAR_pipe.txt


title: Sample_2-Lymphnode-Tcell-WT2


title: Sample_15-Lung-Tcell-KO3

source_name: Lung Tcell KO  ATAC

value: Lung


title: Sample_1-Lymphnode-Tcell-WT1


title: Sample_13-Lung-Tcell-KO1


title: Sample_20-Lung-ILC2-WT3

source_name: Lung ILC2 WT ATAC


title: Sample_14-Lung-Tcell-KO2

source_name: Lung TcellKO  ATAC


title: Sample_17-Lung-Tcell-WT4

source_name: Lung Tcell WT  ATAC


title: RNA-seq for BRD4 knockdown cells

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: RNA-seq for BRD4 knockdown cells

data_processing:
RNA-Seq data analysis was done with rsem(ver. 1.2.3) and hg19 genome with UCSC known gene set.
EdgeR was used for differential expression was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed file contains raw counts for all genes

source_name: PEO1 ovarian cancer cells

growth_protocol: Human ovarian cancer cell line PEO1 were cultured in RPMI1640 medium (Corning) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were passaged every 3-4 days to complete growth medium.

extract_protocol:
Total RNA was extracted using Trizol
The sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA sequencing library preparation kit (SKU:015.24) for Illumina sequencing platform compatible libraries. All 12 libraries were pooled in equal molar amounts and run on the Illumina Nextseq500 using the Mid Output V2 (150 cycles) kit (cat # FC-404-2001)

treatment_protocol: PEO1 cells were treated with or without 200 nM JQ1 for 72 hours or PEO1 cells were infected with lentivirus encoding short hairpin RNA to the human BRD4 gene (shBRD4) or control

tag: experiment type

value: RNAseq


title: TH2_IL5_6

first: Jesse

last: Nussbaum

state: California

address: 513 Parnassus Ave., Campus Box 0795

department: Medicine

institute: University of California San Francisco

description: Lung IL-5-reporter positive Th2s

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed of the first 11 bp for quality reasons, then mapped to mm10 whole genome using tophat v2.0.11 with parameters -q -p 10 --no-coverage-search --segment-length 20
Raw reads were aggregated across all isoforms on a per-gene basis, using only reads mapping to exons, using htseq-count. S Anders, T P Pyl, W Huber: HTSeq — A Python framework to work with high-throughput sequencing data. bioRxiv 2014. doi: 10.1101/002824.
Raw reads were normalized using DESeq: Anders S and Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, pp. R106.
Genome_build: GRCm37.63 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include raw per-gene values for each sample

source_name: IL-5-positive Th2s Rep6

extract_protocol:
Qiagen RNEasy Micro Plus, according to manufacturer's guidelines
NuGen Ovation RNA-Seq System V2 and Ultralow Library System V2 kits
SE 50bp RNAseq

treatment_protocol: Infection with 500 L3 larvae of Nippostrongylus brasiliensis subcutaneously on day 0; cell harvest on day 14

tag: strain

tag: infection

value: Nippostrongylus brasiliensis

tag: source tissue

value: lung

tag: sorting criteria

value: CD4/CD5-pos; Thy1-pos; Red5 reporter-pos

tag: date of sort

tag: sorted cell type

value: IL-5-positive Th2s


title: TH2_IL5_2

description: Lung IL-5-reporter positive Th2s

source_name: IL-5-positive Th2s Rep2


title: TH2_IL5_5

description: Lung IL-5-reporter positive Th2s

source_name: IL-5-positive Th2s Rep5


title: ILC2_IL5_7

description: Lung IL-5-reporter positive ILC2s

source_name: IL-5-positive ILC2s Rep7

value: Lineage-neg; CD4/CD5-neg; Thy1-pos; Red5 reporter-pos

value: IL-5-positive ILC2s


title: Sample_22-Lung-ILC2-KO2

source_name: Lung ILC4 KO ATAC

tag: genotype/variation

tag: cell type


title: ILC2_IL5_2

description: Lung IL-5-reporter positive ILC2s

source_name: IL-5-positive ILC2s Rep2


title: TH2_IL5_4

description: Lung IL-5-reporter positive Th2s

source_name: IL-5-positive Th2s Rep4


title: TH2_IL5_1

description: Lung IL-5-reporter positive Th2s

source_name: IL-5-positive Th2s Rep1


title: L10-09-Control_RNA-seq

city: Bronx

first: Neil

middle: Ari

last: Wijetunga

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Before sequencing, libraries were tested using the BioAnalyzer to assure library quality, in terms of size and primer-dimer depletion and indexed libraries were multiplexed for 100 bp single-end sequencing on the Illumina HiSeq 2000 platform.
FASTQ files of past filter reads were obtained and aligned to a composite reference exome of human (hg19), mirBase and HCV using GSNAP.
Next, alignments were associated with genes using HTSeq.
We scaled gene counts using DESeq implemented in R to estimate effective library size.
Genome_build: hg19
Supplementary_files_format_and_content: Combined_processed_RNAseq_data.txt.gz: Matrix with columns corresponding to each sample and rows corresponding to each gene/

source_name: Biopsy of Uninfected Non-neoplastic

extract_protocol:
We extracted total RNA from homogenized liver samples with 0.2 ml of chloroform and 1 ml of TRIZOL Reagent. After precipitation and washing, the RNA was dissolved in RNase-free water and given DNase treatment.
DNase-treated,   rRNA-depleted   (Ribozero,   Epicentre)   RNA   was used   as   a   template   for SuperScript  III  first-strand  cDNA synthesis  (Invitrogen),  using  oligo-dT  as  well  as  random hexamers. Actinomycin D was added to the reaction to prevent any possible amplification from contaminating  genomic  DNA.  During  second-strand synthesis,  a  dU/VTP  mix  was  used  to create  directional  libraries. cDNA  samples  were  fragmented  with  Covaris  to  300-bp  fragments. The samples  were  then  end-filled,  3     terminal  A  extended  and  ligated to  preannealed  TruSeq-indexed Illumina adapters. Uracil-DNAglycosylase UDG) treatment preceded the PCR reaction to  amplify  exclusively  the originally  oriented  transcripts.  Libraries  were  amplified  using  P5 and P7  Illumina  primers and  gel-extracted  for  size  selection  and primer-dimer  removal.  Before sequencing, libraries were tested using the BioAnalyzer to assure library quality, in terms of size and primer-dimer   depletion.   Indexed   libraries   were   multiplexed for   100-bp   single-end sequencing on the Illumina HiSeq 2000 platform.

tag: tissue

value: liver

tag: disease state

value: Control

tag: Sex

value: M

tag: age

tag: staging

tag: cea

tag: afp

tag: sgot

tag: sgpt

tag: batch

tag: race

value: NB

tag: differentiation


title: RNA-seq for DMSO treated cells

description: RNA-seq for DMSO treated cells

tag: experiment type

tag: treatment

value: DMSO


title: ILC2_IL5_5

description: Lung IL-5-reporter positive ILC2s

source_name: IL-5-positive ILC2s Rep5

tag: strain

tag: infection

tag: source tissue

tag: sorting criteria

tag: date of sort

tag: sorted cell type


title: L12-07-NonTumor_RNA-seq

source_name: Biopsy of HCV+ Non-neoplastic

tag: tissue

tag: disease state

value: Non-Tumor

tag: Sex

tag: age

value: B


title: L10-06-Control_RNA-seq

tag: staging

tag: cea

tag: afp

tag: sgot


title: ILC2_IL5_4

description: Lung IL-5-reporter positive ILC2s

source_name: IL-5-positive ILC2s Rep4


title: ILC2_IL5_3

description: Lung IL-5-reporter positive ILC2s

source_name: IL-5-positive ILC2s Rep3


title: ILC2_IL5_1

description: Lung IL-5-reporter positive ILC2s

source_name: IL-5-positive ILC2s Rep1


title: L10-08-Tumor_RNA-seq

source_name: Biopsy of HCV+ HCC tumor

value: Tumor

tag: sgpt

tag: batch

tag: race

tag: differentiation


title: RNA-seq for JQ1 treated cells

description: RNA-seq for JQ1 treated cells

tag: experiment type

tag: treatment


title: RNA-seq for BRD4 wild type cells

description: RNA-seq for BRD4 wild type cells


title: Sample_12-Lung-Tcell-WT3

source_name: Lung Tcell WT ATAC

tag: strain background

value: Balb/c

tag: genotype/variation

value: WT

tag: cell type

value: T cell


title: L10-08-NonTumor_RNA-seq

tag: tissue


title: L12-07-Tumor_RNA-seq

tag: disease state


title: L11-33-Tumor_RNA-seq

tag: Sex

value: F


title: L11-26-Tumor_RNA-seq

tag: age


title: L10-22-Control_RNA-seq

tag: staging


title: L10-20-Control_RNA-seq

tag: cea


title: L10-18-Control_RNA-seq

tag: afp


title: L10-23-NonTumor_RNA-seq

tag: sgot


title: L11-26-NonTumor_RNA-seq

tag: sgpt


title: L11-25-NonTumor_RNA-seq

tag: batch


title: L11-25-Tumor_RNA-seq

tag: race


title: L10-21-Control_RNA-seq

tag: differentiation


title: L10-15-Control_RNA-seq


title: L10-14-Tumor_RNA-seq


title: L10-10-Tumor_RNA-seq


title: L12-07-Tumor

data_processing:
Library strategy: HELP-tagging
Libraries were multiplexed for 50 bp single-end sequencing on the Illumina HiSeq 2000 platform.  Illumina CASAVA pipeline 1.8 was used to generate fastq files.
Alignment was completed with ELAND allowing at most 3 mismatches. Reads flanking HpaII sites were quantified with a custom script.
The read counts were log transformed and normalized before taking the ratio of the normalized HpaII count to normalized MspI count at each assayed HpaII site.  The CDF of the Cauchy distribution was used to obtain methylation probabilities.
Mixture modeling of the distribution assuming three composite distributions was performed to scale the probabilities between 0 and 1.  HpaII sites with less than 5 read counts were removed from the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Combined_processed_HELP_tagging_data.txt.gz: Matrix with columns corresponding to each sample and rows corresponding to assayed HpaII sites.
Supplementary_files_format_and_content: Hcount files: Quantification of the number reads with an end located at a HpaII site for the positive strand, negative strand, and total.

extract_protocol:
We extracted genomic DNA using proteinase K and RNase A digestion followed by phenol/chloroform extraction and ethanol precipitation.
We characterized DNA methylation patterns using the HELP-tagging assay, a massively parallel sequencing-based restriction enzyme approach described previously.  To minimize potential batch effects, HELP-tagging libraries were processed in batches that balanced by patient age, disease grade, HIV viral load, and HPV genotype. Genomic DNA was digested with the methylation sensitive restriction enzyme, HpaII for comparison with a reference genome digested with the methylation insensitive restriction enzyme, MspI.  Digested DNA was ligated to a custom Illumina sequencing adapter containing a T7 transcriptional promoter and an EcoP15I restriction site at the 3’ end, allowing digestion with EcoP15I.  A second Illumina sequencing adapter with a unique sequencing index was then added and after in vitro transcription, reverse transcription, and PCR amplification, the library was sequenced on the Illumina HiSeq 2000 platform.

value: Moderately


title: L10-14-NonTumor_RNA-seq


title: L10-12-Control_RNA-seq


title: L10-16-Control_RNA-seq


title: L11-11-Tumor_RNA-seq


title: L11-27-Control_RNA-seq


title: L11-32-NonTumor

value: NonTumor

value: Minimally


title: L10-10-NonTumor_RNA-seq


title: L11-11-NonTumor_RNA-seq


title: L11-26-NonTumor

value: Mildly


title: L11-33-NonTumor_RNA-seq


title: L12-07-NonTumor


title: L11-27-Control


title: L11-33-NonTumor

value: Severely


title: L11-33-Tumor

value: liver


title: L11-29-Control

value: Control


title: L11-11-NonTumor

value: M


title: L11-25-NonTumor

value: NB


title: L11-26-Tumor


title: L10-20-Control


title: L10-23-NonTumor


title: L10-22-Control


title: L11-25-Tumor


title: L10-18-Control


title: L10-21-Control


title: L10-16-Control


title: L10-15-Control


title: L11-32-Tumor


title: L10-14-Tumor

value: Mildly to moderately


title: L10-10-Tumor


title: L10-12-Control


title: L10-14-NonTumor


title: L10-10-NonTumor


title: L10-09-Control


title: L10-06-Control


title: L10-08-Tumor


title: 51_U87_8

city: Stockholm

first: Ilgar

last: Abdullayev

address: Nobels väg 3

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing raw reads: The sequence in FastQ file corresponding to UMIs were removed from sequence reads and appended to the read name (for later analyses). Adapter and polyA sequences were removed from reads using cutadapt v1.8.1, with minimum overlap between adapter and the 3’ of the read set to 1 nt. Reads shorter than 18 nt after adaptor trimming were discarded.
Alignment: Trimmed reads were aligned to the human genome (hg38) using STAR v2.4.0 with parameters --outSAMstrandField intronMotif --outFilterMismatchNoverLmax 0.04 --outFilterMatchNmin 18 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1. We did not allow any mismatches within the first 25 nucleotides and allowed only 1 mismatch in the remaining part of the sequence reads (25 – 41 nts). Spliced alignments were disabled and hard/soft-clipping was disabled for the 5’ of the read. Soft-clipping of up to 3 nts were allowed at the 3’ end of the read in order to account for RNA editing and 3’ tRNA modifications such as addition of CCA. Reads mapping with insertions or deletions were removed.
Counting unqiue molecules: We collapsed PCR amplicons and counted RNA molecules using the adjacency network approach (dedup_umi.py at https://github.com/CGATOxford/UMI-tools), where reads with UMIs having a single Hamming distance from another UMI were collapsed. We separated RNA molecule counts into two categories based on the extent of the alignment of our sequenced read with the human genome. Reads aligning over the full sequence (41 nts) were assigned as precursor molecules, whereas reads aligning with 40 or less nts were assigned as a potential small RNA. Potential small RNAs were further scrutinized to find instances were trimmed 3’ ends matched the genomic sequence after the alignment (cases where actual RNA sequence matched adapter sequence, false positive adapter trimming). Consequently, these molecules were instead assigned to the precursor RNA.
Annotating molecules: We estimated expression for annotation transcripts in the following databases (Gencode V22, Mirbase V21 and GtRNAdb).  During the quantification procedure, molecules were hierarchical assigned to annotated biotypes in the following order: Mirbase miRNAs, tRNAs from GtRNAdb, small RNA biotypes from Gencode (such as snoRNAs, snRNAs, rRNAs etc.), and lastly the remaining of Gencode transcripts such as protein coding and lincRNAs. We counted molecules from both intronic and exonic regions of the protein coding and lincRNAs in an attempt to capture small RNAs transcribed from these regions. We used a weighing approach to assign molecules of sequences mapping to multiple genomic location, by divided by number of annotated location the sequence aligned to. Finally, for miRNAs we collapsed molecules supporting the same miRNA that were expressed from different genomic loci (i.e. where the microRNAs gene was present in multiple genomic locations).
Filtering samples: We excluded libraries with fewer than one million reads (before alignment) and if the number of expressed transcripts were more than two standard deviations of the median number of expressed transcripts obtained within the cell population (to filter out potential doublets and low-quality libraries). All analyses in the manuscript was carried out on small RNA molecule counts (i.e. amplicon corrected values), except otherwise noted.
Genome_build: hg38
Supplementary_files_format_and_content: Tabular expression matrix

source_name: Glioblastoma

growth_protocol: HEK293T and glioblastoma cells (U87, KS4, JM3, JM4) were mycoplasma tested. Naïve Stem Cell Culture: Human ESC line WA09 (female) (WiCell, Madison, WI) was transitioned from conventional primed conditions to 5iAF naïve state by closely following the conversion protocol described in Theunissen et al., 2014. Naïve hESCs were maintained and expanded in a medium containing 50:50 N2B27/Neurobasal (GIBCO) with 1mM glutamine (Invitrogen), 1% NEAA (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), and freshly supplemented with 10 µM Y-27632 ROCKi (Stemgent), 1 µM PD0325901 MEKi (Sigma), 1 µM IM-12 GSK3i (Sigma), SB590885 BRAFi (Sigma), 1 µM WH-4-023 SRCi (Sigma), 20 ng/ml Activin A (R&D), 0.5 % KOSR (Invitrogen), 8 ng/ml bFGF (R&D), 50 ug/ml BSA (Sigma), and 20 ng/ml hLIF (Millipore) (Theunissen et al. 2014). Cells were propagated on irradiated E12.5 MEFs (GIBCO) seeded at 250 k cells/well of a 6 well (9.5 cm2), and once colonies reached confluence they were dissociated and expanded by single cell using Accutase (GIBCO). WA09 (H9) has been mycoplasma tested and validated for pluripotency by teratoma assay (in primed state) as well as immunocytochemistry (for both naive and primed). Based on our Smart-seq2 data, our cells exhibit a transcriptional profile that are indicative of the previously reported works that we aimed to reproduce. This cell line was obtained from WiCell Research Institute, Inc. from which we hold the MTA (license). Primed Stem Cell Culture: Conventional primed human hESC line WA09 (WiCell, Madison, WI) was maintained on a layer of mouse embryonic fibroblasts (MEF), in media consisting of: DMEM: F12 (Invitrogen), 20 % KSR (Invitrogen), 4 ng/ml bFGF (R&D), 2 mM glutamine (GIBCO), 0.1 mM non-essential amino acids (Invitrogen), 0.1 mM ß-Mercaptoethanol (Sigma). Once colonies reached confluence they were mechanically passaged through dissociation using a 26-gauge needle (VWR).

extract_protocol:
Cells were lysed directly into the reaction tube. No RNA extraction was performed.
Plates were pre-deposited with 3 µl of lysis buffer (0.13 % Triton-X-100, 4 u recombinant RNase Inhibitor, Takara). After single cell sorting, the plates were transferred to -80 °C for long storage. After thawing the plate, 1 µl of 5.8 S rRNA masking oligo (5 pmol) was added and the whole plate was incubated at 72 °C for 20 minutes.  Then, 2 µl of 3’ adaptor ligation reaction was added (20 pmol 3’ adaptor oligo, 8.33 % PEG 8000, 50 u T4 RNA Ligase 2, truncated KQ, NEB, 0.83 X T4 RNA ligase buffer, NEB, 4 u recombinant RNase Inhibitor, Takara) and reaction was incubated at 30 °C for 6 h followed by 4 °C for 10 hours.  Next, 3 µl of RT primer and free adaptor removal enzymes were added (200 pmol RT primer, 2.5 u Lambda exonuclease, NEB, 10 u 5’ deadenylase, NEB) and the reaction was incubated at 30 °C for 15 minutes followed by 37 °C for 15 minutes. Next, 2 µl of 5’ adaptor ligation reaction was added (45 pmol 5’ adaptor oligo, 0.68 mM Tris-buffered ATP, Thermo Fisher, 4 u T4 RNA ligase, Thermo Fisher,  0.23 X T4 RNA ligase buffer, NEB ) and the mix was incubated at 37 °C for 1 hour. Reverse transcription reaction was performed by adding 7 µl of RT reaction (1.28 X Taq DNA Polymerase PCR Buffer, Thermo Fisher, 8.33 mM DTT, 0.42 mM/each dNTP, 4 u recombinant RNase Inhibitor, 150 u Superscript II reverse transcriptase, Thermo Fisher). The PCR amplification is carried out by adding 35 µl of the reagents (0.94 X Phusion HF buffer, 1 u Phusion Hot Start II DNA Polymerase, Thermo Fisher, 0.12 mM/each dNTP,  1.89 µM RP1 primer) and incubating at 98 °C for 30 seconds followed by 13 cycles of 98 °C for 10 seconds, 60 °C for 30 seconds and 72 °C for 30 seconds and a final incubation at 72 °C for 5 minutes. At last, 1 µl of the amplified product is transferred to a fresh tube and the second PCR reaction is added (2 µM indexed primers, 0.2 µM RP1 primer, 1 X Phusion HF buffer, 0.5 u Phusion Hot Start II DNA Polymerase, Thermo Fisher,  0.2 mM/each dNTP) and incubating at 98 °C for 30 seconds followed by 13 cycles of 98 °C for 10 seconds, 67 °C for 30 seconds and 72 °C for 30 seconds and a final incubation at 72 °C for 5 minutes. The amplified libraries of single cells are then pooled and purified with DNA Clean & Concentrator™-5, Zymo research. All samples have been sequenced 1x 43 bp or 1x 51 bp using Illumina HiSeq 2500 instrument.

value: GBM


title: 51_U87_9


title: L10-08-NonTumor

value: B


title: 51_U87_6


title: 51_U87_7


title: 51_U87_1


title: 51_U87_3


title: L11-11-Tumor

value: Tumor


title: 51_U87_10


title: 51_primed2_6

source_name: Embryonic stem cells

value: ES


title: 51_U87_4


title: 51_primed2_3


title: 51_primed2_4


title: 51_U87_5


title: 51_primed2_11


title: 51_primed2_12


title: 51_U87_2


title: 51_naive_2_8


title: 51_U87_11


title: 51_naive_2_9


title: 51_U87_12


title: 51_primed2_9


title: 51_primed2_7


title: 51_primed2_8


title: 51_primed2_2


title: 51_naive_1_7


title: 51_primed2_1


title: 51_naive_1_9


title: 51_primed2_10


title: 51_naive_1_2


title: 51_naive_1_12


title: 51_naive_2_6


title: 51_naive_2_7


title: 51_naive_1_11


title: 51_naive_2_5


title: 51_KS4_9


title: 51_naive_2_4


title: 51_naive_2_1


title: 51_naive_2_2


title: 51_naive_2_3


title: 51_KS4_7


title: 51_naive_2_12


title: 51_KS4_15


title: 51_KS4_14


title: 51_primed2_5


title: 51_naive_2_11


title: 51_naive_2_10


title: 51_naive_1_8


title: 51_naive_1_4


title: 51_naive_1_3


title: 51_KS4_13


title: 51_KS4_12


title: 51_JM4_8


title: 51_JM4_4


title: 51_naive_1_10


title: 51_JM4_5


title: 51_naive_1_1


title: 51_JM4_14


title: 51_JM4_13


title: 51_JM4_16


title: 51_JM4_1


title: 51_JM4_10


title: 51_JM4_3


title: 51_JM3_7


title: 51_JM4_11


title: 51_KS4_6


title: 51_KS4_8


title: 51_naive_1_5


title: 51_naive_1_6


title: 51_JM3_11


title: 51_JM3_14


title: 51_KS4_5


title: 51_KS4_16


title: 51_KS4_4


title: 51_KS4_10


title: 51_JM4_9


title: 51_KS4_11


title: 51_JM4_6


title: 51_HEK_6

value: HEK292T cell line


title: 51_HEK_8


title: 51_JM4_2


title: 51_HEK_1


title: 51_JM4_15


title: 51_HEK_12


title: 51_JM4_12


title: 51_HEK_10


title: 51_JM4_7


title: 51_JM3_9


title: Smartseq2_primed_8


title: Smartseq2_primed_6


title: Smartseq2_primed_2


title: Smartseq2_primed_3


title: Smartseq2_primed_21


title: 51_JM3_5


title: Smartseq2_primed_5


title: Smartseq2_primed_1


title: Smartseq2_primed_17


title: Smartseq2_primed_16


title: 51_JM3_16


title: Smartseq2_primed_15


title: 51_JM3_4


title: 51_JM3_15


title: 51_JM3_8


title: 51_JM3_6


title: 51_JM3_13


title: 51_JM3_10


title: 51_HEK_7


title: 51_JM3_12


title: 51_HEK_9


title: 51_HEK_4


title: 51_HEK_3


title: 51_HEK_5


title: 51_HEK_11


title: 51_HEK_2


title: Smartseq2_primed_7


title: Smartseq2_primed_4


title: Smartseq2_primed_20


title: Smartseq2_primed_9


title: Smartseq2_naive_9


title: Smartseq2_primed_18


title: Smartseq2_primed_19


title: Smartseq2_primed_12


title: Smartseq2_primed_11


title: Smartseq2_primed_10


title: Smartseq2_primed_14


title: Smartseq2_naive_8


title: Smartseq2_naive_7


title: Smartseq2_naive_19


title: Smartseq2_naive_3


title: Smartseq2_primed_13


title: Smartseq2_naive_2


title: Smartseq2_naive_6


title: Smartseq2_naive_17


title: Smartseq2_naive_21


title: Smartseq2_naive_15


title: Smartseq2_naive_20


title: Smartseq2_naive_1


title: Smartseq2_naive_18


title: Smartseq2_naive_11


title: Smartseq2_naive_16


title: Smartseq2_naive_4


title: Smartseq2_HEK_8


title: Smartseq2_naive_5


title: Smartseq2_naive_13


title: Smartseq2_naive_12


title: Smartseq2_naive_10


title: Smartseq2_naive_14


title: Smartseq2_HEK_9


title: Smartseq2_HEK_4


title: Smartseq2_HEK_3


title: Smartseq2_HEK_6


title: Smartseq2_HEK_16


title: Smartseq2_HEK_2


title: Smartseq2_HEK_15


title: Smartseq2_HEK_13


title: Smartseq2_HEK_18


title: Smartseq2_HEK_1


title: Smartseq2_HEK_14


title: Smartseq2_HEK_12


title: NEBNext_1ug_HEKRNA_3


title: Smartseq2_HEK_11


title: Smartseq2_HEK_10


title: NEBNext_1ug_HEKRNA_2


title: HEK_dilution_10ng_3


title: HEK_dilution_1ng_1


title: HEK_dilution_1ng_3


title: HEK_dilution_1ng_2


title: Smartseq2_HEK_5


title: Smartseq2_HEK_17


title: HEK_dilution_10ng_2


title: HEK_dilution_10ng_1


title: HEK_dilution_100ng_3


title: HEK_dilution_100ng_1


title: HEK_dilution_100ng_2


title: HEK_dilution_1000ng_3


title: HEK_dilution_1000ng_2


title: HEK_dilution_1000ng_1


title: HEK_dilution_0.1ng_3


title: HEK_dilution_0.01ng_3


title: HEK_dilution_0.1ng_1


title: HEK_dilution_0.01ng_2


title: HEK_dilution_0.01ng_1


title: Smartseq2_HEK_7


title: HEK_35


title: HEK_33


title: NEBNext_1ug_HEKRNA_1


title: HEK_34


title: HEK_dilution_0.1ng_2


title: HEK_29


title: HEK_32


title: HEK_31


title: HEK_30


title: HEK_24


title: HEK_23


title: HEK_27


title: HEK_26


title: HEK_22


title: HEK_20


title: HEK_21


title: HEK_25


title: U87_8


title: U87_6


title: U87_9


title: HEK_36


title: HEK_19


title: U87_7


title: U87_4


title: U87_23


title: U87_2


title: U87_24


title: U87_22


title: U87_3


title: HEK_28


title: U87_21


title: U87_20


title: U87_1


title: U87_19


title: U87_17


title: U87_15


title: U87_16


title: U87_14


title: U87_12


title: U87_13


title: U87_11


title: U87_10


title: U87_5


title: JM4_D_2


title: JM4_D_7


title: JM4_D_3


title: JM4_D_22


title: JM4_D_20


title: JM4_D_23


title: JM4_D_15


title: JM4_D_16


title: JM4_D_4


title: JM4_D_17


title: JM4_D_18


title: JM4_D_21


title: U87_18


title: JM4_D_12


title: JM4_D_24


title: JM4_D_1


title: JM4_D_5


title: JM4_D_10


title: JM4_D_19


title: JM4_D_11


title: JM4_D_13


title: JM4_D_9


title: JM4_9


title: JM4_7


title: JM4_D_8


title: JM4_8


title: JM4_5


title: JM4_2


title: JM4_3


title: JM4_24


title: JM4_4


title: JM4_D_6


title: JM4_23


title: JM4_18


title: JM4_22


title: JM4_20


title: JM4_19


title: JM4_21


title: JM4_1


title: JM4_17


title: JM4_6


title: JM4_13


title: JM4_16


title: JM4_14


title: JM4_15


title: KS4_D_9


title: KS4_D_8


title: KS4_D_6


title: JM4_11


title: JM4_10


title: KS4_D_4


title: KS4_D_5


title: JM4_D_14


title: KS4_D_3


title: KS4_D_2


title: KS4_D_23


title: KS4_D_22


title: KS4_D_20


title: KS4_D_1


title: KS4_D_21


title: KS4_D_19


title: JM4_12


title: KS4_D_18


title: KS4_D_7


title: KS4_D_12


title: KS4_D_14


title: KS4_D_15


title: KS4_D_24


title: KS4_D_10


title: KS4_9


title: KS4_5


title: KS4_D_17


title: KS4_8


title: KS4_4


title: KS4_6


title: KS4_3


title: KS4_7


title: KS4_24


title: KS4_2


title: KS4_22


title: KS4_23


title: KS4_D_16


title: KS4_21


title: KS4_1


title: KS4_19


title: KS4_D_11


title: KS4_D_13


title: KS4_18


title: JM3_8


title: KS4_17


title: KS4_15


title: KS4_16


title: KS4_10


title: KS4_12


title: KS4_14


title: KS4_11


title: KS4_13


title: JM3_9


title: JM3_3


title: JM3_4


title: JM3_5


title: JM3_6


title: JM3_2


title: JM3_23


title: JM3_24


title: JM3_22


title: JM3_20


title: JM3_1


title: JM3_21


title: JM3_19


title: KS4_20


title: JM3_15


title: JM3_18


title: JM3_16


title: JM3_7


title: JM3_14


title: JM3_13


title: HEK_9


title: HEK_8


title: JM3_10


title: HEK_7


title: HEK_5


title: JM3_12


title: HEK_6


title: JM3_11


title: HEK_4


title: HEK_3


title: HEK_2


title: HEK_18


title: HEK_16


title: HEK_1


title: HEK_14


title: HEK_17


title: HEK_15


title: HEK_13


title: JM3_17


title: HEK_11


title: HEK_12


title: HEK_10


title: naivecell_82


title: naivecell_81


title: naivecell_83


title: naivecell_84


title: naivecell_79


title: naivecell_77


title: naivecell_78


title: naivecell_76


title: naivecell_69


title: naivecell_71


title: naivecell_68


title: naivecell_73


title: naivecell_80


title: naivecell_72


title: naivecell_74


title: naivecell_70


title: naivecell_75


title: naivecell_67


title: naivecell_63


title: naivecell_65


title: naivecell_59


title: naivecell_66


title: naivecell_58


title: naivecell_56


title: naivecell_57


title: naivecell_55


title: naivecell_54


title: naivecell_51


title: naivecell_52


title: naivecell_50


title: naivecell_53


title: naivecell_9


title: naivecell_8


title: naivecell_6


title: naivecell_48


title: naivecell_62


title: naivecell_64


title: naivecell_46


title: naivecell_5


title: naivecell_60


title: naivecell_61


title: naivecell_47


title: naivecell_43


title: naivecell_41


title: naivecell_4


title: naivecell_3


title: naivecell_39


title: naivecell_44


title: naivecell_38


title: naivecell_35


title: naivecell_36


title: naivecell_37


title: naivecell_49


title: naivecell_34


title: naivecell_33


title: naivecell_7


title: naivecell_31


title: naivecell_30


title: naivecell_32


title: naivecell_45


title: naivecell_2


title: naivecell_40


title: naivecell_42


title: naivecell_28


title: naivecell_27


title: naivecell_29


title: naivecell_26


title: H3K23me2_N2_2_ChIPSeq

city: Copenhagen

first: Anna Elisabetta

last: Salcini

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: bam file contains all unaligned and aligned (ce10) reads

data_processing:
Reads were checked for quality using FastQC.
Reads were mapped to C. elegans genome (ce10) using Bowtie2 (version 2.0.6) (Langmead and Salzberg, 2012).
bam files were converted to bed format using 'bedtools bamtobed'.
Bed files were filtered allowing only one read per chromosomal position and extended (bedExtendRanges, Kent tools) from 5' -end to a total length of 250 bp, converted to bedGraph format (bedItemOverlapCount, Kent tools), scaled to tags per million (unique, mapped reads) and finally converted to bigWig format (bedGraphToBigWig, Kent tools). Kent tools URL: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER
Genome_build: ce10
Supplementary_files_format_and_content: bigWig files are ce10 genome assembly

source_name: whole embryo

growth_protocol: C. elegans strains were cultured using standard growth conditions at 20°C on Escherichia coli OP50 (Brenner, 1974).

extract_protocol:
ChIP was performed as described in Rechtsteiner, A. et al., 2010. Lysates were clarified from sonicated chromatin and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the ChIP-seq DNA sample prep kit (Illumina) with a protocol adapted from Meyer and Kircher, 2010.

tag: developmental stage

value: mixed stage (embryonic)

tag: strain

value: Bristol N2

value: wild type

tag: chip antibody

value: H3K23me2 (Active Motif, catalog# 39653, lot# 28209001)


title: IgG_N2_2_ChIPSeq

tag: genotype/variation

value: IgG (Sigma-Aldrich, catalog# I8140)


title: naivecell_23

tag: cell type


title: naivecell_24


title: H3K23me2_N2_1_ChIPSeq


title: naivecell_21


title: naivecell_25


title: naivecell_20


title: IgG_N2_1_ChIPSeq


title: naivecell_19


title: vivo_MII_oocyte_rep3

city: Fukuoka

first: Nobuhiko

last: Hamazaki

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku,

department: Department of Developmental Stem Cell Biology

institute: Kyushu University

data_processing:
RNA-seq reads were processed with the FASTX tool kit (v0.0.14, Patel and Jain, 2012) to remove short (<20 bp) and low quality (quality score <20) reads, followed by trimming of the adaptor sequence.
Processed reads were mapped to the mouse mm10 genome using TopHat2/Bowtie2 (v2.0.13, Kim et al., 2013).
Cufflinks and Cuffdiff (v2.2.1, Trapnell et al., 2012) were used for the fragments per kb of exon model per million mapped reads (FPKM) calculation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample.

source_name: MII oocytes collected from 8 weeks female mice

growth_protocol: The ESCs used in all experiments were maintained under a 2i+LIF condition. PGCLCs were differentiated from ESCs or iPSCs as described previously (Hayashi et al., 2013), purified by FACSAriaTM II (BD Bioscience). 5,000 PGCLCs were cultured with 50,000 gonadal somatic cells to produce one reconstituted ovary. Reconstituted ovaries were placed on Transwell®-Col membranes (Coaster) soaked in IVDi-aMEM medium: aMEM supplemented with 10% FCS, 150 µM ascorbic acid (Sigma), 1x Glutamax, 1x penicillin/streptomycin and 55 µM 2-mercaptoethanol (Life Technologies). At 4 days of culture, the culture medium was changed to IVDi-SP medium: StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 µM ascorbic acid, 1x Glutamax, 1x penicillin/streptomycin and 55 µM 2-mercaptoethanol. From 7 days to 10 days of culture, 500 nM ICI182780 was added to the IVDi-SP medium. At 21 days of culture, oocytes embedded in 2FLs were obtained and sequenced.  The single 2FLs on the Transwell®-Col membranes were soaked in IVG-aMEM medium: aMEM supplemented with 5% FCS, 2% polyvinylpyrrolidone (Sigma), 150 µM ascorbic acid, 1x Glutamax, 1x penicillin/streptomycin, 100 µM 2-mercaptoethanol, 55 µg/ml sodium pyruvate (Nacalai Tesque), 0.1IU/ml FSH (Follistim; MSD), 15 ng/ml BMP15 and 15 ng/ml GDF9 (R&D Systems). At 2 days of culture, BMP15 and GDF9 were withdrawn from the medium and then follicles were incubated in 0.1% TypeIV Collagenase (MP Biomedicals). After washing with aMEM supplemented with 5% FCS several times, follicles were cultured in IVG-aMEM without BMP15 and GDF9. At 11 days of culture, COCs grown on the membrane were picked up by a fine glass capillary. COCs were transferred to IVM medium: aMEM supplemented with 5% FCS, 25 µg/ml sodium pyruvate, 1x penicillin/streptomycin, 0.1 IU/ml FSH, 4 ng/ml EGF, and 1.2 IU/ml hCG (Gonadotropin®; ASKA). At 16 hours of culture, swollen cumulus cells were stripped from the oocytes by treating with hyaluronidase (Sigma), and then MII oocytes were determined by 1st polar body extrusion.

extract_protocol:
Directional RNA-seq library was constructed, as described previously (Hamazaki et al. 2015). Briefly, poly(A)+ RNA were purified from 100-15,000 cells or oocytes (ESCs; 10,000-13,200, PGCLCs day 6; 10,000, PGCLCs re-agg day 3; 5,300-15,000, secondary follicle oocyte; 337-812, MII oocyte; 99-134), using the Dynabeads mRNA DIRECT Micro Kit (Invitrogen).
Purified RNAs were subjected to library construction using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). cDNA were enriched by 12-cycles PCR. Sequencing of the libraries was performed with HiSeq2000 (Illumina).

value: MII oocyte


title: vivo_MII_oocyte_rep2


title: vivo_MII_oocyte_rep1


title: naivecell_17


title: vivo_2nd_fol._oocyte_rep3

source_name: Secondary follicle oocytes sorted with BVSC transgenes from 8 d.p.p. ovaries

value: Secondary follicle oocyte


title: naivecell_16


title: naivecell_14


title: naivecell_15


title: vivo_2nd_fol._oocyte_rep2


title: naivecell_13


title: vivo_E12.5_PGCs_rep3

source_name: E12.5 PGCs sorted with BVSC transgenes

value: E12.5 PGCs


title: naivecell_22


title: vivo_2nd_fol._oocyte_rep1


title: vivo_E12.5_PGCs_rep2


title: naivecell_1


title: naivecell_11


title: primedcell_84


title: naivecell_10


title: naivecell_18


title: vitro_MII_oocyte_rep2

source_name: Secondary follicle oocytes derived from PGCLCs

value: in vitro cultured MII oocyte


title: vivo_E12.5_PGCs_rep1


title: vitro_MII_oocyte_rep3


title: primedcell_83


title: vitro_2nd_fol._oocyte_rep1

source_name: PGCLCs were re-aggregated with female E12.5 gonadal somatic cells for 21 days

value: in vitro cultured secondary follicle oocyte


title: primedcell_81


title: primedcell_78


title: PGCLCs_agg3_rep2

source_name: Re-aggregated PGCLCs with female E12.5 gonadal somatic cells for 3 days

value: PGCLCs agg 3


title: PGCLCs_d6_rep2

source_name: PGCLCs induced from female EpiLCs for 6 days

value: PGCLCs d6


title: PGCLCs_agg3_rep1


title: primedcell_77


title: primedcell_79


title: vitro_MII_oocyte_rep1


title: primedcell_76


title: vitro_2nd_fol._oocyte_rep3


title: PGCLCs_d6_rep1


title: ESCs_rep3

source_name: Mouse female ESCs cultured in 2i+LIF medium.

value: ES cells


title: primedcell_75


title: naivecell_12


title: primedcell_74


title: vitro_2nd_fol._oocyte_rep2


title: ESCs_rep1


title: primedcell_80


title: PGCLCs_agg3_rep3


title: primedcell_73


title: ESCs_rep2


title: primedcell_82


title: primedcell_72


title: primedcell_69


title: primedcell_71


title: Sample 4547; CC Strain IL-1513

city: Tel Aviv

first: Irit

last: Gat-Viks

department: Cell Research and Immunology

institute: Tel-Aviv University

data_processing:
The alignment and the expression quantification was done by using RSEM (version 1.2.18) with the mouse genome UCSC, mm9, NCBI37, and annotation file Ensembl version 37.67.
Genome_build: mm9
Supplementary_files_format_and_content: Includes the 2 output files of RSEM which are isoforms.results and genes.results. These are tab delimited files with the expression levels of the isoforms and genes.

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-1513

growth_protocol: Animals were housed on hardwood chip bedding in open top cages at the animal facility of Tel-Aviv University (TAU) under a 12-hour light/dark cycle. Mice were given tap water and rodent chow ad libitum throughout the experiment

extract_protocol:
The liver tissues were dissected and then were stored in sterilized tubes at -150°C (in liquid nitrogen). The RNA was extracted using the RNeasy Plus kit procedure (Qiagen).
The libraries were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina).

tag: age (w)

tag: body weight (g)

tag: tissue

value: liver


title: Sample 4546; CC Strain IL-1513


title: primedcell_70


title: Sample 4475; CC Strain IL-670

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-670


title: Sample 4474; CC Strain IL-670


title: primedcell_66


title: primedcell_65


title: Sample 4477; CC Strain IL-785

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-785


title: Sample 4468; CC Strain IL-611

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-611


title: primedcell_68


title: Sample 4469; CC Strain IL-611


title: primedcell_67


title: Sample 4473; CC Strain IL-670


title: primedcell_60


title: primedcell_64


title: primedcell_63


title: primedcell_58


title: primedcell_59


title: Sample 4466; CC Strain IL-557

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-557


title: primedcell_57


title: primedcell_56


title: Sample 4415; CC Strain IL-2146

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2146


title: Sample 4414; CC Strain IL-2146


title: primedcell_55


title: primedcell_61


title: primedcell_54


title: Sample 4464; CC Strain IL-4032

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-4032


title: Sample 4458; CC Strain IL-2693

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2693


title: Sample 4319; CC Strain IL-1452

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-1452


title: Sample 4457; CC Strain IL-2689

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2689


title: Sample 4434; CC Strain IL-785


title: Sample 4431; CC Strain IL-2750

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2750


title: primedcell_51

source_name: Embryonic stem cells


title: Sample 4318; CC Strain IL-1061

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-1061


title: Sample 4317; CC Strain IL-1061


title: primedcell_9


title: primedcell_53


title: Sample 4429; CC Strain IL-2750


title: primedcell_8


title: Sample 4467; CC Strain IL-611


title: primedcell_52


title: primedcell_7


title: primedcell_6


title: Sample 4297; CC Strain IL-3575

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-3575


title: Sample 4299; CC Strain IL-72

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-72


title: Sample 4283; CC Strain IL-3575


title: Sample 4280; CC Strain IL-3438

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-3438


title: Sample 4281; CC Strain IL-3438


title: primedcell_62


title: primedcell_48


title: Sample 4303; CC Strain IL-1052

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-1052


title: Sample 4277; CC Strain IL-2156

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2156


title: primedcell_50


title: Sample 4276; CC Strain IL-2156


title: rrm3D_rnh1D_rnh201D_replicate1

first: Duncan

last: Smith

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

data_processing:
bowtie2 (version 2.2.3) was used to align paired-end fastq files to the S. cerevisiae reference genome
sam files were converted to bam files using samtools. Reads were sorted and filtered to exclude reads with mapq score <30
Remove PCR duplicates: Use MarkDuplicates function in picard tools to mark PCR duplicates in bam file. Used options -Xmx4g , REMOVE_DUPLICATES=false, ASSUME_SORTED=true. Remove reads in bam file marked as PCR duplicates using samtools view using option -F 0x400
Sort bam file by read name using samtools sort using option -n. Convert sorted bam file to a bedpe file using bedtools bamtobed using options -i, -bedpe, - mate1
An in-house python script was used to convert the bedpe file from a zero-based bedpe file to a one-based bedpe. In Bedpe files, starts are zero-based and ends are one-based.
An in-house python script was used to convert the bedpe file to a bed file where it records the 3’ or 5’ ends of the mates depending on whether the first mate is watson or crick. A fragment length limit of 1000 is also imposed.
Linux command sort is used to sort the bed file by chromosome, then base. The options used were -k1n,1 -k2n,2 -t $'\t'
Two sgr files for watson and crick fragments are created from the bed file using bedtools genomecov. The options used are -i, -g with a genome size file containing the sizes of each chromosome, -d, -strand with either ‘+’ or ‘-‘.
Percent Watson and percent Crick strand files were calculated from the sgr files, adding 1 to all values to avoid zeros
Genome_build: Genome_build: Yeast S288C, build R64-1-1, released Feb 2011
Supplementary_files_format_and_content: [.sgr] Percent Watson strand hit files calculated per chromosome and per base.  Three columns: chromosome, base,Percent Watson strand hits

organism: Saccharomyces cerevisiae

growth_protocol: YPD, 30˚C

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)

treatment_protocol: All cells were treated with doxycycline for 2.5h to deplete DNA ligase. For HU-treated cultures, HU was added to 25 mM 1h before the addition of doxycycline.

tag: strain background

value: rrm3delta ; rnh1delta ; rnh201delta

tag: construct

value: Doxycycline-repressible CDC9 allele

tag: molecule subtype

value: DNA; Okazaki Fragments

tag: treatment

value: doxycycline for 2.5h


title: primedcell_43

value: ES


title: primedcell_44


title: Sample 4305; CC Strain IL-1141

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-1141


title: primedcell_42


title: primedcell_41


title: Sample 4275; CC Strain IL-2011

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2011


title: primedcell_40


title: Sample 4430; CC Strain IL-2750


title: rnh1D_rnh201D_replicate3

value: rnh1delta ; rnh201delta


title: Sample 4274; CC Strain IL-2011


title: rnh1D_rnh201D_replicate2


title: primedcell_38


title: Sample 4272; CC Strain IL-785

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-785


title: Sample 4302; CC Strain IL-1052


title: rnh1D_rnh201D_replicate1


title: primedcell_5


title: Sample 4300; CC Strain IL-72


title: primedcell_4


title: primedcell_35


title: Sample 4270; CC Strain IL-521

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-521


title: primedcell_47


title: Sample 4269; CC Strain IL-519

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-519


title: primedcell_31


title: primedcell_33


title: primedcell_46


title: Sample 4278; CC Strain IL-2156


title: primedcell_45


title: rrm3D_rnh1D_rnh201D_replicate3


title: rrm3D_gal_rnh1_gal_replicate1

value: rrm3delta ; Gal1,10 promoter upstream of RNH1

tag: growth protocol

value: grown in Galactose


title: primedcell_49


title: rrm3D_gal_rnh1_glu_replicate3

value: grown in Glucose


title: rrm3D_rnh1D_rnh201D_replicate2


title: primedcell_37


title: primedcell_36


title: primedcell_3


title: Sample 4271; CC Strain IL-521


title: primedcell_26


title: primedcell_34


title: primedcell_39


title: Sample 4265; CC Strain IL-4457

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-4457


title: Sample 4264; CC Strain IL-4141

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-4141


title: gal_rnh1_gal_replicate3

value: Gal1,10 promoter upstream of RNH1

value: grown o/n in Galactose


title: rrm3D_gal_rnh1_gal_replicate3


title: rrm3D_gal_rnh1_gal_replicate2


title: primedcell_25


title: primedcell_22


title: Sample 4247; CC Strain IL-4052

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-4052


title: primedcell_32


title: gal_rnh1_gal_replicate1


title: primedcell_30


title: Sample 4268; CC Strain IL-519


title: Sample 4266; CC Strain IL-4457


title: primedcell_2


title: primedcell_29


title: primedcell_28


title: rrm3D_gal_rnh1_glu_replicate2


title: primedcell_27


title: gal_rnh1_glu_replicate3


title: primedcell_1


title: rrm3D_gal_rnh1_glu_replicate1


title: primedcell_23


title: primedcell_24


title: Sample 4244; CC Strain IL-3912

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-3912


title: gal_rnh1_glu_replicate2


title: primedcell_17


title: primedcell_16


title: gal_rnh1_glu_replicate1


title: primedcell_15


title: Sample 4243; CC Strain IL-3912


title: primedcell_21


title: primedcell_20


title: Sample 4246; CC Strain IL-4052


title: primedcell_19


title: pif1-m2_rrm3D_hu_replicate3

value: pif1-m2 ; rrm3delta

value: HU for 2.5h, doxycycline for 2h


title: primedcell_13


title: primedcell_18


title: Sample 4241; CC Strain IL-3348

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-3348


title: pif1-m2_rrm3D_hu_replicate2


title: primedcell_14

source_name: Embryonic stem cells


title: primedcell_12


title: FL_HSPC

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

institute: WEHI

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling
The raw reads were mapped to the human genome (hg19) using the STAR aligner version 2.4.0h1 in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.4.6 using GENCODE Release 19 comprehensive annotation
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with Gene symbol and Gene length in the first two columns, followed by 26 columns containing counts for each sample

source_name: 17 week humn fetal liver sorted form haematopoietic stem/progenitor cells

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

tag: cell population

value: primary tissue

tag: culture medium

value: not cultured


title: A.08.AGM90

source_name: 5 week human aorta gonad mesonephros (AGM)


title: primedcell_11


title: primedcell_10


title: Sample 4239; CC Strain IL-2680

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2680


title: rrm3D_hu_replicate2


title: A.06.AGM90


title: Sample 4236; CC Strain IL-219

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-219


title: rrm3D_hu_replicate3


title: Sample 4240; CC Strain IL-3348


title: rrm3D_hu_replicate1


title: X66.2_S10

source_name: d18 differentiated SOX17mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells

value: d2 SB & CHIR plus BMP4, VEGF,SCF,ACTIVIN A, FGF (BVSAF)

value: APEL cell culture medium


title: X66.4_S12


title: Sample 4234; CC Strain IL-2126

source_name: mRNA of liver tissue of CC mouse. Strain ID : IL-2126

value: liver


title: pif1-m2_hu_replicate2

value: Doxycycline-repressible CDC9 allele


title: X66.1_S9


title: pif1-m2_hu_replicate3

value: DNA; Okazaki Fragments


title: X61.2.Elef

source_name: d22 differentiated SOX17mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells


title: EN_39_d10P.8

description: RawCountsCellPops.txt

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling.
The raw reads were mapped to the human genome (hg19) using the STAR aligner version 2.4.0h1 in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.4.6 using GENCODE Release 19 comprehensive annotation
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with Gene symbol and Gene length in the first two columns, followed by 26 columns containing counts for each sample

source_name: day 10 differentiated SOX17 mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells

value: d2 SB & CHIR plus BVSAF


title: X61.4.Elef


title: EN_39_d10P.9

description: RawCountsCellPops.txt


title: WT_hu_replicate3

value: WT


title: pif1-m2_rrm3D_hu_replicate1


title: A.07.AGM90


title: EN_39_d10P.7

description: RawCountsCellPops.txt


title: pif1-m2_hu_replicate1


title: EN_39_d10P.6

description: RawCountsCellPops.txt


title: EN_39_d10P.3

description: RawCountsCellPops.txt

value: BMP4, VEGF,SCF,ACTIVIN A, FGF (BVSAF)


title: Sample 4235; CC Strain IL-219


title: EN_39_d10P.5

description: RawCountsCellPops.txt


title: Sample 4238; CC Strain IL-2680


title: EN_39_d10.9

description: RawCountsCellPops.txt


title: EN_39_d10P.2

description: RawCountsCellPops.txt


title: EN_39_d10.7

description: RawCountsCellPops.txt


title: EN_39_d10P.4

description: RawCountsCellPops.txt


title: WT_hu_replicate1


title: EN_39_d10.4

description: RawCountsCellPops.txt


title: rrm3D_replicate3

value: doxycycline for 2.5h


title: EN_39_d10P.10

description: RawCountsCellPops.txt


title: EN_39_d10P.1

description: RawCountsCellPops.txt


title: rrm3D_replicate2


title: pif1-m2_rrm3D_replicate3


title: EN_39_d10.5

description: RawCountsCellPops.txt


title: pif1-m2_rrm3D_replicate2


title: pif1-m2_rrm3D_replicate1


title: EN_39_d10.8

description: RawCountsCellPops.txt


title: UMI_7

organism: synthetic construct

source_name: Artificial

tag: sample type

value: Artificial


title: EN_30_d11P.8

description: RawCountsCellPops.txt

source_name: day 11 differentiated SOX17 mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells


title: pif1-m2_replicate3


title: WT_hu_replicate2

value: if using Dox-repressible CDC9 construct)


title: EN_39_d10.3

description: RawCountsCellPops.txt


title: UMI_6


title: UMI_5


title: EN_39_d10.2

description: RawCountsCellPops.txt


title: EN_39_d10.6

description: RawCountsCellPops.txt


title: pif1-m2_replicate2


title: pif1-m2_replicate1


title: rrm3D_replicate1


title: EN_30_d11P.7

description: RawCountsCellPops.txt


title: UMI_4