title: ChIP Seq H4ac Control

city: Berlin

first: Annalisa

last: Marsico

address: Ihnestraße 63-73

department: Computational Biology

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using the Bowtie Software (v1) with default options, except that we allowed a maximum of two mismatches.
Gene promoters were defined as +/- 1000 bp around the transcription start site. For each sample, the read counts per promoter were determined and corrected for the input.
Genome_build: hg19
Supplementary_files_format_and_content: Alignment files in bam format were converted to bedgraph format using the genomeCoverageBed command from the bedtools. The read coverage was scaled by the median of promoters' read counts in each sample. Bedgraph files were then converted to BigWig by using the bedGraphToBigWig command. Sample-specific raw read count promoter files contain, for each gene promoter, the number of aligned reads in the =/- 1000 bp region around the gene TSS (last column).

source_name: Human blood-derived macrophages

growth_protocol: Human monocytes were isolated from buffy coats by CD14 positive selection. Cell were maintained for 6 days in RPMI 1640 (plus 1 % glutamine and 1 % Human Serum Type AB).

extract_protocol:
Cells were fixed in 1 % v/v formaldehyde/PBS solution. Cells were taken up in 1 % w/v SDS/RIPA solution and sonicated to shear DNA.
Library preparation was conducted with the Tru-Seq ChIP Sample KIT (Illumina, San Diego) according to the manufacturer's recommendation. Sequencing was done on an Illumina HiSeq2000 with read length 51 bp.

treatment_protocol: On day 6, human blood-derived macrophages (BDM) were infected with L. pneumophila Corby for 1 h at multiplicity of infection of 10.

value: primary monocyte-derived macrophage

value: Anti-acetyl-Histone H4 (06-598, Millipore)


title: input DNA Control

status: Public on Apr 18 2016

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: chip antibody


title: Zebrafish 28-30hpf embryo Bio-CAP

city: Oxford

first: Hannah

middle: Katherine

last: Long

state: Oxfordshire

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Library strategy: Bio-CAP
Tc1 and Tc0 mouse Bio-CAP reads were aligned to the appropriate reference genome using Bowtie version 1.0.0 allowing a maximum of two mismatches in the entire read, and retaining only uniquely mapping reads.
PCR duplicates were removed uisng Picard-Tools MarkDuplicates version 1.105(1632).
Peaks were called using MACS version 14 against an input file, with tag size 50, bandwidth 300, mfold 10,30 and pvalue cutoff of 1e-5.
Peaks closer than 200bp apart were merged.
Peaks from biological replicates were merged and only peaks found in both replicated were retained
Peaks overlapping a deleted region or breakpoint on human chromosome 21 in the Tc1 mouse were removed from further analysis.
To identify differentially hypomethylated loci, total normalised read count was compared for human and Tc1 mouse at all peaks identified in the two species, peaks with over a 2-fold changes in read density were determined to be differentially methylated between human and mouse. Peaks found at a duplicated region in Tc1 mouse were compensated for during the differential peak-calling.
Zebrafish embryo Bio-CAP reads were aligned to the zebrafish and mouse genome using  version 2.1.0 bowtie2 default settings.
Genome_build: Genome_build: Tc1 (composite mm9 chromosomes and hg19 chr21), mm9, hg19 and danRer7.

organism: Danio rerio

source_name: 28-30hpf embryo

extract_protocol:
Samples were obtained either as fresh-frozen samples or were dissected in-house and fresh-frozen. Samples were subjected to manual homogenisation followed by DNA purification by phenol chloroform extraction or using the QIAGEN 100/G genomic tip kit. For each individual Bio-CAP experiment, 25 μl of NeutrAvidin Agarose Resin (Thermo Scientific, 29200) was washed with BC100 buffer and then incubated with 50 μl of 0.5 μg/μl biotinylated hKDM2b-CxxC protein diluted in BC100 buffer for 1 hour at 4°C. The conjugated resin/CxxC protein was then washed with CAP100 buffer (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 100 mM NaCl). Genomic DNA was sonicated to an average size of 150-250 bp using a Diagenode Bioruptor. Sonicated DNA was then diluted in CAP100 buffer to a concentration of 16 μg/ml and a 100 μl Input sample was retained. For each Bio-CAP experiment, 500 μl of diluted sonicated DNA, corresponding to approximately 8 μg of DNA, was added to the conjugated CxxC resin. The DNA and resin were incubated at 4°C for 1 hour with gentle mixing. The resin was then collected by centrifugation at 1500 x g for 3 minutes at 4°C, and the unbound flowthrough (FT) material was removed. The resin and any associated DNA was washed twice with 1 ml of CAP100 buffer, before the first elution was performed by adding 50 μl of CAP300 (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 300 mM NaCl) to the resin and incubating at room temperature for 10 minutes. Following centrifugation a 50 μl elution fraction was carefully collected. The elution process was repeated using another 50 μl of CAP300 and the 300 mM elution fractions were pooled (giving a total volume of 100 μl). Subsequent elutions were performed in the same way using buffers with 500 mM, 700 mM and 1 M NaCl sequentially. Each 100 μl elution fraction, together with 100 μl of both the Input and FT samples, was purified using a PCR purification column (Qiagen) and DNA was eluted in a volume of 50 μl. The 700 mM and 1 M fractions were pooled for sequencing.
Bio-CAP material was quantified using the High Sensitivity Qubit system (Invitrogen) and the fragmentation profile was assessed using a DNA HS Agilent 2200 TapeStation chip or a DNA HS Agilent 2100 Bioanalyzer chip. Bio-CAP material was then prepared for Solexa sequencing using the NEBNextTM DNA Sample Prep Master Mix Set 1, according to manufacturer's specifications.   Next generation sequencing was performed using two Illumina sequencing platforms: HiSeq and NextSeq Systems yielding 51bp and 80bp single-end reads respectively. Sequencing was carried out according to the manufacturer’s instructions.

tag: developmental stage

value: 28-30hpf embryo


title: ChIP Seq H4ac Lp infection


title: CH3 0uM

city: Chicago

first: Paul

middle: W

last: Burridge

state: IL

address: 320 E Superior St Searle 8-525

department: Pharmacology

country: USA

institute: Northwestern

library_source: transcriptomic

data_processing:
Tuxedo suite
Supplementary_files_format_and_content: FPKM

molecule: total RNA

source_name: hiPSC-CM d30

growth_protocol: hiPSC-CM plated on Matrigel in CDM3, grown to d30

extract_protocol:
RNA extraction performed by Macrogen
Library prep performed by Macrogen
Library prep performed by Macrogen, sequencing performed on HiSeq 2000

treatment_protocol: Treated with 0uM or 1uM doxorubicin

value: hiPSC-CM d30

tag: passages


title: input DNA Lp infection


title: CH1 0uM


title: CON4 0uM


title: CON3 1uM


title: CH4 1uM


title: CON4 1uM


title: CH3 1uM


title: CH4 0uM


title: CON1 1uM


title: CH1 1uM


title: CON1 0uM


title: CON3 0uM


title: pachytene rnp wt rep2

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using TOPHAT
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated and isoforms were assembled by using a protocol from Cufflinks
Genome_build: mm9

organism: Mus musculus

source_name: testis

extract_protocol:
Large RNAs were isolated using the AquaRNA RNA Purification Kit
RNA libraries were prepared for sequencing using illumina stranded RNA library kit

tag: strain

tag: tissue

value: pachytene spermatocyte

tag: age

value: adult

tag: genotype

value: wild type


title: elongating rnp wt rep3

value: elongating spermatid


title: elongating rnp wt rep2


title: round rnp wt rep2

value: round soermatid


title: round polysome wt rep3


title: pachytene rnp wt rep1


title: round rnp wt rep3


title: round polysome wt rep1


title: round polysome wt rep2


title: elongating rnp wt rep1


title: pachytene rnp wt rep3


title: elongating polysome wt rep3


title: pachytene polysome wt rep1


title: pachytene polysome wt rep2


title: elongating polysome wt rep2


title: NPC2 rep2 RNA expression

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description: processed data file: npc2.RNAseq.av.bedGraph.gz

data_processing:
Mnase-seq and ChIP-seq:  The sequenced paired-end reads were mapped to dm3, hg19, and mm9 genomes in the cases of D. melanogaster, H. sapiens and M. musculus data respectively using Bowtie aligner v. 0.12.939. Only uniquely mapped reads with no more than two mismatches were retained.  The reads with the insert sizes less than 50 bp or larger than 500 bp were filtered out. Genomic positions with the numbers of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded. Read frequencies were computed in 300-bp non-overlapping bins in the case of fly data and in 500-bp bins in the case of human data for each titration point independently. The read frequencies were normalized by the corresponding library sizes to represent values per one million of mapped reads. To facilitate the comparison of the results between different genomes, the frequencies were additionally scaled by the factors representing ratios between the corresponding genome size and 100 Mb, similarly to the approach described in Kasinathan et al. (Nat Methods 2014).
s2 RNA-seq:
Tags were aligned using Tophat software package with default parameters. RNA-Seq tag frequencies were normalized for GC-content using bioconductor package EDASeq and then the expression estimates for each gene were obtained using bioconductor package DESeq.
esc2 and npc2 RNA-seq:
Tags were aligned using Tophat software package with default parameters. Cufflinks  tool was used to compute average FPKM values.
Genome_build: dm3, mm9 and hg19
Supplementary_files_format_and_content: bedGraph files representing either tag occupancy profiles normalized to library sizes or MNase accessibility (MACC) profiles

source_name: Embryonic neural progenitors

extract_protocol:
s2 MNase-seq:
Cells were grown in Schneider’s medium supplemented with 10% heat inactivated FBS at 28C. For fixation, 107 S2 cells were pelleted and rinsed twice in PBS. Cells were crosslinked in 1.1% formaldehyde in PBS for 10 minutes at room temperature, tumbling end over end in a volume of 10 mL. After addition of 50 uL of 2.5M glycine, the cells were tumbled at room temperature for 2 minutes to quench the reaction. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, the cell pellet was resuspended in PBS with 0.1% Triton-X100 (PBS-TX). Digestion of 106 cells per titration point took place in a volume of 400uL PBS-TX supplemented with 1mM CaCl2. Either 1.5U, 6.25U, 25U, or 100U of MNase (Worthington Biochemical) were added to pre-warmed cells and incubated at 37C for 3 minutes. Digestion was halted by moving to ice and adding 10 uL of 250 mM EDTA, 250 mM EGTA. Prior to DNA clean-up, the digestions were adjusted to 0.5% SDS and 10 mM Tris pH 8. For DNA cleanup, digestions were incubated with RNase (Roche) for 30 minutes at 37C, with proteinase K (Roche) for 60 minutes at 55C, and incubated at 65C for 60 minutes to reverse crosslinks. This was followed by phenol-chloroform extraction and ethanol precipitation. For size selection, digestion products in a volume of 100 uL of water were incubated for 5 minutes at room temperature with 60uL of Agencourt AMPure XP beads (Beckman Coulter). After bead separation, the supernatant was moved to a new tube and 120uL of new bead suspension was added. DNA was eluted from these beads and used as input into the library preparation protocol described in Bowman et al. (BMC Genomics 2013).  For histone ChIP, after halting the MNase digestion, adding EDTA/EGTA, and adding SDS, 135 uL was removed from the 400 uL digestion as an input fraction and kept overnight at 4C. The remainder of each digestion was split in half (135uL each). Each chromatin aliquot was independently adjusted to ChIP buffer conditions in a volume of 500 uL (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.5% sarkosyl, 1% Triton X-100, and 1X COMPLETE protease inhibitors (Roche)). After adding 1 mL additional ChIP buffer to each chromatin aliquot (total volume of 1.5ml), this was tumbled end over end for 10 min at 4C and then subjected to a high-speed spin in a microcentrifuge for 10 min at 4C. Supernatant was taken to a new tube for precipitation. 2 uL of antibody was added to each tube (histone H3 ChIP, ab1791, Abcam).
s2 ChIP-seq:
After halting the MNase digestion, adding EDTA/EGTA, and adding SDS, 135 uL was removed from the 400 uL digestion as an input fraction and kept overnight at 4C. The remainder of each digestion was split in half (135uL each). Each chromatin aliquot was independently adjusted to ChIP buffer conditions in a volume of 500 uL (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.5% sarkosyl, 1% Triton X-100, and 1X COMPLETE protease inhibitors (Roche)). After adding 1 mL additional ChIP buffer to each chromatin aliquot (total volume of 1.5ml), this was tumbled end over end for 10 min at 4C and then subjected to a high-speed spin in a microcentrifuge for 10 min at 4C. Supernatant was taken to a new tube for precipitation. 2 uL of antibody was added to each tube (histone H3 ChIP, ab1791, Abcam; histone H4 ChIP, ab10158, Abcam).
esc and npc MNase-seq:
J1 ESCs (ESC1) and E14-derived ESCs (ESC2) were maintained on mitomycin-C inactivated embryonic fibroblast feeder layers in DMEM supplemented with 15% fetal bovine serum (Hyclone) and 1000U/ml of leukemia inhibitory factor (EMD Millipore). ESC cultures were depleted of feeder cells prior to use in experiments. Neural progenitors (NPC1) were derived by in vitro differentiation from J1 ESC and maintained using previously described methods38. Embryonic NPCs (NPC2) were isolated from the brains of E13.5 embryos and maintained on poly-l-ornithine coated plates in DMEM:F12 containing B-27 and N-2 supplements (Gibco) and EGF+FGF-2 (10ng/ml). One million Cells were cross-linked at room temperature for 10 minutes with 1% formaldehyde and cross-linking stopped by the addition of 125mM glycine. Nuclei were isolated and MNase digestion performed on either 200,000 or 250,000 nuclei per reaction. Digestions were performed using 64U, 16U, 4U or 1U MNase (Worthington) in 10mM Tris pH 7.4, 15mM NaCl, 60mM KCl, 1mM CaCl2 for 10 minutes (250,000 nuclei reactions) or 15 minutes (200,000 nuclei reactions) at 25C. Reactions were stopped with EDTA/EGTA and 0.5% SDS and 125mM NaCl added to the samples. RNase A and proteinase K treatment along with cross-link reversal at 65C were performed. DNA was purified by phenol-chloroform extraction and column purification. MNase digestion was evaluated and the recovered DNA from 1 -64U MNase digested samples was used to generate sequencing libraries
k562 Mnase-seq:
Human K562 cells were grown in Iscove's Modified Dulbecco's Medium supplemented with 10% heat inactivated FBS at 37C. Human cells were expanded to yield approximately 4 million cells/reaction and cross-linked with 1.1% formaldehyde for 10 minutes at room temperature. Cells were lysed and nuclei were isolated using a sucrose cushion and treated with a range of 18 MNase concentrations in buffer containing 10mM Tris pH 7.4, 15mM NaCl, 60mM KCl and protease inhibitors for 15 minutes at room temperature. EDTA and EGTA were added to stop the digestion. Cross-link reversal was performed at 65 degrees C for 16 hours followed by RNase treatment for 30 minutes at 37 degrees C, followed by the addition of SDS to a final concentration of 1% and proteinase K digestion overnight, at 55C. DNA was purified by phenol- chloroform extraction and ethanol precipitation. Ampure SPRI beads (Beckman Coulter) were used in a double size selection with ratios of 0.7X and 1.7X to obtain a range of fragment sizes from approximately 100 bp to 1000 bp.
s2 RNA-seq:
107 Drosophila S2 cells were harvested on ice, washed in cold PBS and their RNA was extracted using the RNeasy Kit (Qiagen) with on column DNAse digestion according to the manufacturer’s protocol. Ribosomal RNA was depleted from the total RNA (5ug) by using the RiboZero gold magnetic kit (Epicentre/Illumina) according to manufacturer’s instructions. cDNA was generated with the TruSeq non–stranded kit (Illumina) according to manufacturer’s instructions.
esc2 and npc2 RNA-seq protocol:
mESC and NPC were harvested and ESC were depleted of feeders. RNA was extracted from whole cells using Trizol (Thermo Fisher Cat. No. 15596026). RNA was treated with DNase (Promega Cat. No. M6101) at 37 deg C for 30 minutes. Ribosomal RNA was depleted from the total RNA (5ug) by using the RiboZero gold magnetic kit (Epicentre/Illumina) according to manufacturer’s instructions. cDNA was generated with the TruSeq non–stranded kit (Illumina) according to manufacturer’s instructions.
All libraries were prepared as described in Bowman et al.  (BMC Genomics 2013)

value: Embryonic neural progenitors


title: NPC2 rep1 RNA expression


title: round rnp wt rep1


title: ESC2 rep2 RNA expression

description: processed data file: esc2.RNAseq.av.bedGraph.gz

source_name: J1 ESC

value: J1 ESC


title: elongating polysome wt rep1


title: ESC2 rep1 RNA expression


title: NPC2 whole chromatin rep2 16U MNase

description:
processed data file:
npc2.Pooled_WholeChromatin.ReplicateSet_bin500.bedGraph.gz;
npc2.MACC_WholeChromatin.ReplicateSet_bin500.bedGraph.gz

data_processing:
Mnase-seq and ChIP-seq: The sequenced paired-end reads were mapped to dm3, hg19, and mm9 genomes in the cases of D. melanogaster, H. sapiens and M. musculus data respectively using Bowtie aligner v. 0.12.939. Only uniquely mapped reads with no more than two mismatches were retained.  The reads with the insert sizes less than 50 bp or larger than 500 bp were filtered out. Genomic positions with the numbers of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded. Read frequencies were computed in 300-bp non-overlapping bins in the case of fly data and in 500-bp bins in the case of human data for each titration point independently. The read frequencies were normalized by the corresponding library sizes to represent values per one million of mapped reads. To facilitate the comparison of the results between different genomes, the frequencies were additionally scaled by the factors representing ratios between the corresponding genome size and 100 Mb, similarly to the approach described in Kasinathan et al. (Nat Methods 2014).
RNA-seq: Tags were aligned using Tophat software package with default parameters. RNA-Seq tag frequencies were normalized for GC-content using bioconductor package EDASeq and then the expression estimates for each gene were obtained using bioconductor package DESeq.
Genome_build: dm3, mm9 and hg19
Supplementary_files_format_and_content: bedGraph files representing either tag occupancy profiles normalized to library sizes or MNase accessibility (MACC) profiles

extract_protocol:
s2 MNase-seq:
Cells were grown in Schneider?s medium supplemented with 10% heat inactivated FBS at 28C. For fixation, 107 S2 cells were pelleted and rinsed twice in PBS. Cells were crosslinked in 1.1% formaldehyde in PBS for 10 minutes at room temperature, tumbling end over end in a volume of 10 mL. After addition of 50 uL of 2.5M glycine, the cells were tumbled at room temperature for 2 minutes to quench the reaction. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, the cell pellet was resuspended in PBS with 0.1% Triton-X100 (PBS-TX). Digestion of 106 cells per titration point took place in a volume of 400uL PBS-TX supplemented with 1mM CaCl2. Either 1.5U, 6.25U, 25U, or 100U of MNase (Worthington Biochemical) were added to pre-warmed cells and incubated at 37C for 3 minutes. Digestion was halted by moving to ice and adding 10 uL of 250 mM EDTA, 250 mM EGTA. Prior to DNA clean-up, the digestions were adjusted to 0.5% SDS and 10 mM Tris pH 8. For DNA cleanup, digestions were incubated with RNase (Roche) for 30 minutes at 37C, with proteinase K (Roche) for 60 minutes at 55C, and incubated at 65C for 60 minutes to reverse crosslinks. This was followed by phenol-chloroform extraction and ethanol precipitation. For size selection, digestion products in a volume of 100 uL of water were incubated for 5 minutes at room temperature with 60uL of Agencourt AMPure XP beads (Beckman Coulter). After bead separation, the supernatant was moved to a new tube and 120uL of new bead suspension was added. DNA was eluted from these beads and used as input into the library preparation protocol described in Bowman et al. (BMC Genomics 2013).  For histone ChIP, after halting the MNase digestion, adding EDTA/EGTA, and adding SDS, 135 uL was removed from the 400 uL digestion as an input fraction and kept overnight at 4C. The remainder of each digestion was split in half (135uL each). Each chromatin aliquot was independently adjusted to ChIP buffer conditions in a volume of 500 uL (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.5% sarkosyl, 1% Triton X-100, and 1X COMPLETE protease inhibitors (Roche)). After adding 1 mL additional ChIP buffer to each chromatin aliquot (total volume of 1.5ml), this was tumbled end over end for 10 min at 4C and then subjected to a high-speed spin in a microcentrifuge for 10 min at 4C. Supernatant was taken to a new tube for precipitation. 2 uL of antibody was added to each tube (histone H3 ChIP, ab1791, Abcam).
s2 ChIP-seq:
After halting the MNase digestion, adding EDTA/EGTA, and adding SDS, 135 uL was removed from the 400 uL digestion as an input fraction and kept overnight at 4C. The remainder of each digestion was split in half (135uL each). Each chromatin aliquot was independently adjusted to ChIP buffer conditions in a volume of 500 uL (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.5% sarkosyl, 1% Triton X-100, and 1X COMPLETE protease inhibitors (Roche)). After adding 1 mL additional ChIP buffer to each chromatin aliquot (total volume of 1.5ml), this was tumbled end over end for 10 min at 4C and then subjected to a high-speed spin in a microcentrifuge for 10 min at 4C. Supernatant was taken to a new tube for precipitation. 2 uL of antibody was added to each tube (histone H3 ChIP, ab1791, Abcam; histone H4 ChIP, ab10158, Abcam).
esc and npc MNase-seq:
J1 ESCs (ESC1) and E14-derived ESCs (ESC2) were maintained on mitomycin-C inactivated embryonic fibroblast feeder layers in DMEM supplemented with 15% fetal bovine serum (Hyclone) and 1000U/ml of leukemia inhibitory factor (EMD Millipore). ESC cultures were depleted of feeder cells prior to use in experiments. Neural progenitors (NPC1) were derived by in vitro differentiation from J1 ESC and maintained using previously described methods38. Embryonic NPCs (NPC2) were isolated from the brains of E13.5 embryos and maintained on poly-l-ornithine coated plates in DMEM:F12 containing B-27 and N-2 supplements (Gibco) and EGF+FGF-2 (10ng/ml). One million Cells were cross-linked at room temperature for 10 minutes with 1% formaldehyde and cross-linking stopped by the addition of 125mM glycine. Nuclei were isolated and MNase digestion performed on either 200,000 or 250,000 nuclei per reaction. Digestions were performed using 64U, 16U, 4U or 1U MNase (Worthington) in 10mM Tris pH 7.4, 15mM NaCl, 60mM KCl, 1mM CaCl2 for 10 minutes (250,000 nuclei reactions) or 15 minutes (200,000 nuclei reactions) at 25C. Reactions were stopped with EDTA/EGTA and 0.5% SDS and 125mM NaCl added to the samples. RNase A and proteinase K treatment along with cross-link reversal at 65C were performed. DNA was purified by phenol-chloroform extraction and column purification. MNase digestion was evaluated and the recovered DNA from 1 -64U MNase digested samples was used to generate sequencing libraries
k562 Mnase-seq:
Human K562 cells were grown in Iscove's Modified Dulbecco's Medium supplemented with 10% heat inactivated FBS at 37C. Human cells were expanded to yield approximately 4 million cells/reaction and cross-linked with 1.1% formaldehyde for 10 minutes at room temperature. Cells were lysed and nuclei were isolated using a sucrose cushion and treated with a range of 18 MNase concentrations in buffer containing 10mM Tris pH 7.4, 15mM NaCl, 60mM KCl and protease inhibitors for 15 minutes at room temperature. EDTA and EGTA were added to stop the digestion. Cross-link reversal was performed at 65 degrees C for 16 hours followed by RNase treatment for 30 minutes at 37 degrees C, followed by the addition of SDS to a final concentration of 1% and proteinase K digestion overnight, at 55C. DNA was purified by phenol- chloroform extraction and ethanol precipitation. Ampure SPRI beads (Beckman Coulter) were used in a double size selection with ratios of 0.7X and 1.7X to obtain a range of fragment sizes from approximately 100 bp to 1000 bp.
s2 RNA-seq:
10^7 Drosophila S2 cells were harvested on ice, washed in cold PBS and their RNA was extracted using the RNeasy Kit (Qiagen) with on column DNAse digestion according to the manufacturer?s protocol. Ribosomal RNA was depleted from the total RNA (5ug) by using the RiboZero gold magnetic kit (Epicentre/Illumina) according to manufacturer?s instructions. cDNA was generated with the TruSeq non?stranded kit (Illumina) according to manufacturer?s instructions

tag: mnase concentration (u)


title: NPC2 whole chromatin rep2 64U MNase


title: Soybean root nodules containing B. japonicum USDA 110 bacteroids - with TEX treatment

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping  (READemption 0.0.1)
Size filtering: discarding reads shorter than 12 nt (READemption 0.0.1)
Read mapping (READemption 0.0.1 and segemehl version 0.1.3)
Coverage calculation and normalisation (READemption 0.0.1)
Genome_build: NC_004463.1 (Bradyrhizobium japonicum USDA 110)
Genome_build: GCA_000004515.1 (Glycine max)

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: bacteria

growth_protocol:
Grown in liquid cultures in PSY medium at 30°C and 140 rpm with spectinomycin (100 μg μl-1) till OD (at 600 nm) of 0.5 as described by 1. Mesa S, Hauser F, Friberg M, Malaguti E, Fischer HM, Hennecke H. J Bacteriol. 2008 Oct;190(20):6568-79
Grown in symbiosis with soybean as described by Pessi G, Ahrens CH, Rehrauer H, Lindemann A, Hauser F, Fischer HM, Hennecke H. Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules. Mol Plant Microbe Interact. 2007;20:1353-63

extract_protocol:
total RNA was isolated with hot phenol
The cDNA libraries were constructed as previously described (Dugar et al. 2013). For Illumina sequencing (GAIIx) of cDNA molecules, the libraries were constructed by vertis Biotechnology AG, Germany.

treatment_protocol: Cells were rapidly cooled on ice; nodules were frozen in liquid nitrogen

tag: sample type

value: soybean root nodules

tag: treatment

value: with terminator exonuclease


title: NPC2 whole chromatin rep1 64U MNase


title: NPC2 whole chromatin rep2 4U MNase


title: NPC2 whole chromatin rep1 16U MNase


title: NPC2 whole chromatin rep1 4U MNase


title: Soybean root nodules containing B. japonicum USDA 110 bacteroids - without TEX treatment

value: without terminator exonuclease


title: NPC2 whole chromatin rep2 1U MNase


title: Free-living B. japonivum USDA 110 cells - with TEX treatment

value: free living


title: NPC2 whole chromatin rep1 1U MNase


title: NPC1 whole chromatin rep2 16U MNase

description:
processed data file:
npc1.Pooled_WholeChromatin.ReplicateSet_bin500.bedGraph.gz;
npc1.MACC_WholeChromatin.ReplicateSet_bin500.bedGraph.gz

source_name: Neuronal progenitors

value: Neuronal progenitors


title: Free-living B. japonivum USDA 110 cells - without TEX treatment


title: NPC1 whole chromatin rep2 64U MNase


title: NPC1 whole chromatin rep2 4U MNase


title: NPC1 whole chromatin rep1 64U MNase


title: NPC1 whole chromatin rep2 1U MNase


title: NPC1 whole chromatin rep1 16U MNase


title: NPC1 whole chromatin rep1 1U MNase


title: ESC2 whole chromatin rep2 64U MNase

description:
processed data file:
esc2.Pooled_WholeChromatin.ReplicateSet_bin500.bedGraph.gz;
esc2.MACC_WholeChromatin.ReplicateSet_bin500.bedGraph.gz

source_name: E14-derived ESC

value: E14-derived  ESC


title: RS

city: Montpellier Cedex 5

first: Stephane

last: Jouannic

address: 911 Avenue Agropolis BP 64501

department: UMR DIADE

country: France

institute: IRD

data_processing:
Clustering in Perl and Bash
BLAST alignment, 85 % size (min 16), 85% identity
Genome_build: Oryza sativa ssp japonica cv NipponBare MSU v7.0
Supplementary_files_format_and_content: Xslx – position and number of reads per clusters, plus information on the pahsed state and miR2118 motif

organism: Oryza barthii

source_name: panicles

growth_protocol: Plants  were grown in greenhouse for 7 weeks in long day conditions (14-10 hours light-dark) and flowering was induced by short day conditions (10-14 hours light-dark). For Illumina sequencing, the panicles were collected from 4 to 15 days after induction, corresponding to stage In1 (i.e. rachis and primary branch meristems) to stage In6/In7 (i.e beginning of floral meristem differentiation) of panicle development (Itoh et al., 2005) for the individual accessions.

extract_protocol:
Total RNA (including small RNAs) from rice panicles were extracted using a modified RNeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq SBS v5)

value: from rachis meristem stage to spikelet differentiation stage

value: mix of 10 accessions

tag: rna subtype

value: small RNAs


title: RC

organism: Oryza glaberrima


title: pachytene polysome wt rep3


title: ESC2 whole chromatin rep2 16U MNase


title: ESC2 whole chromatin rep2 1U MNase


title: ESC2 whole chromatin rep1 64U MNase


title: ESC2 whole chromatin rep2 4U MNase


title: ESC2 whole chromatin rep1 16U MNase


title: ESC2 whole chromatin rep1 4U MNase


title: ESC1 whole chromatin rep1 64U MNase

description:
processed data file:
esc1.Pooled_WholeChromatin.ReplicateSet_bin500.bedGraph.gz;
esc1.MACC_WholeChromatin.ReplicateSet_bin500.bedGraph.gz

value: J1  ESC


title: ESC1 whole chromatin rep2 1U MNase


title: ESC1 whole chromatin rep1 16U MNase


title: NPC1 whole chromatin rep1 4U MNase


title: ESC1 whole chromatin rep1 4U MNase


title: ESC1 whole chromatin rep2 16U MNase


title: ESC1 whole chromatin rep1 1U MNase


title: Single_cell_RNA-seq_NKT2_64

city: La Jolla

first: Pandurangan

last: Vijayanand

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

data_processing:
Single-cell RNA-Seq data was mapped against the mouse mm10 reference genome using tophat (v1.4.1., --library-type fr-secondstrand) and the RefSeq gene annotation downloaded from the UCSC genome Bioinformatics Site.
Genome_build: mm10.
Supplementary_files_format_and_content: abundance measurements

growth_protocol: NKT cells subtypes were isolated from Thymuses and directly sorted by Flow cytometry into a 96-well plate wells with lysis buffer with RNAase inhibitor (Takara) - Described in Picelli et al. Nat Protoc. 2014, PMID:24385147. No particular cell growth procedure was required.

extract_protocol:
For RNA isolation from thymic iNKT cell subsets, thymus cell suspensions were enriched for iNKT cells by negative selection of cells expressing CD8b.2, CD19 or TER-119 via magnetic selection utilizing reagents and equipment from Stem Cell Technologies. The remaining cells were then stained using an 11-parameter panel of reagents that included tetramers of CD1d loaded with either aGalcer or PBS57 combined with streptavidin-brilliant violet (BV)421 (produced in-house or obtained from the NIH Tetramer Core Facility), anti-CD44-V500 (BD Biosciences #56780), live/dead yellow (ThermoFisher Scientific #L34959), anti-CD4-Qdot 605 (ThermoFisher Scientific #Q10092), anti-CD103-FITC (Affymetrix #11-1031), anti-CD24-PerCPCy5.5 (Affymetrix #45-0242), anti-CD27-APC (Affymetrix #E07114), anti-CD8a-AF700 (Biolegend 100730), anti-TCRb-APC-eF780 (Affymetrix #47-5961), anti-CCR6-PE (Biolegend #129803), and anti-NK1.1-PE-Cy7 (BD Biosciences #552878).  iNKT subsets were sorted using a FACSaria III (BD Biosciences).
Single cell RNAseq was perfromed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. We performed 22 cycles of amplification.
Single cell RNAseq was perfromed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. Barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014); Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (TruSeq® Rapid Kit, Illumina).

tag: gender

value: female

value: 5 weeks

value: Thymus

tag: cell type surface markers

value: ICOShigh, NK1.1−, CD27high, and CD4high

tag: vα14 inkt thymocyte subset


title: Single_cell_RNA-seq_NKT2_68


title: Single_cell_RNA-seq_NKT2_65


title: Single_cell_RNA-seq_NKT2_67


title: Single_cell_RNA-seq_NKT2_63


title: Single_cell_RNA-seq_NKT2_66


title: Single_cell_RNA-seq_NKT2_58


title: Single_cell_RNA-seq_NKT2_57


title: Single_cell_RNA-seq_NKT2_59


title: ESC2 whole chromatin rep1 1U MNase


title: Single_cell_RNA-seq_NKT2_55


title: Single_cell_RNA-seq_NKT2_54


title: ESC1 whole chromatin rep2 4U MNase


title: Single_cell_RNA-seq_NKT2_52


title: Single_cell_RNA-seq_NKT2_51


title: Single_cell_RNA-seq_NKT2_49


title: ESC1 whole chromatin rep2 64U MNase


title: Single_cell_RNA-seq_NKT2_50


title: Single_cell_RNA-seq_NKT2_53


title: Single_cell_RNA-seq_NKT2_48


title: Single_cell_RNA-seq_NKT2_45


title: Single_cell_RNA-seq_NKT2_61


title: Single_cell_RNA-seq_NKT2_46


title: Single_cell_RNA-seq_NKT2_44


title: Single_cell_RNA-seq_NKT2_62


title: Single_cell_RNA-seq_NKT2_60


title: Single_cell_RNA-seq_NKT2_42


title: Single_cell_RNA-seq_NKT2_36


title: Single_cell_RNA-seq_NKT2_37


title: Single_cell_RNA-seq_NKT2_41


title: Single_cell_RNA-seq_NKT2_38


title: Single_cell_RNA-seq_NKT2_39


title: Single_cell_RNA-seq_NKT2_56


title: Single_cell_RNA-seq_NKT2_40


title: Single_cell_RNA-seq_NKT2_33


title: Single_cell_RNA-seq_NKT2_35


title: Single_cell_RNA-seq_NKT2_32


title: Single_cell_RNA-seq_NKT2_30


title: Single_cell_RNA-seq_NKT2_29


title: Single_cell_RNA-seq_NKT2_31


title: Single_cell_RNA-seq_NKT2_28


title: Single_cell_RNA-seq_NKT2_47


title: Single_cell_RNA-seq_NKT2_43


title: Single_cell_RNA-seq_NKT2_25


title: Single_cell_RNA-seq_NKT2_27


title: Single_cell_RNA-seq_NKT2_20


title: Single_cell_RNA-seq_NKT2_23


title: Single_cell_RNA-seq_NKT2_21


title: Single_cell_RNA-seq_NKT2_17


title: Single_cell_RNA-seq_NKT2_19


title: Single_cell_RNA-seq_NKT2_16


title: Single_cell_RNA-seq_NKT2_11


title: Single_cell_RNA-seq_NKT2_12


title: Single_cell_RNA-seq_NKT2_14


title: Single_cell_RNA-seq_NKT2_13


title: Single_cell_RNA-seq_NKT2_8


title: Single_cell_RNA-seq_NKT2_34


title: Single_cell_RNA-seq_NKT2_26


title: Single_cell_RNA-seq_NKT2_18


title: Single_cell_RNA-seq_NKT2_24


title: Single_cell_RNA-seq_NKT2_6


title: Single_cell_RNA-seq_NKT2_5


title: Single_cell_RNA-seq_NKT2_3


title: Single_cell_RNA-seq_NKT2_22


title: Single_cell_RNA-seq_NKT2_4


title: Single_cell_RNA-seq_NKT2_2


title: Single_cell_RNA-seq_NKT2_7


title: Single_cell_RNA-seq_NKT17_44

value: CD24low, CD27low, CD4–, CCR6+, CD103high


title: Single_cell_RNA-seq_NKT17_42


title: Single_cell_RNA-seq_NKT17_43


title: Single_cell_RNA-seq_NKT17_41


title: Single_cell_RNA-seq_NKT17_40


title: Single_cell_RNA-seq_NKT17_38


title: Single_cell_RNA-seq_NKT17_39


title: Single_cell_RNA-seq_NKT17_37


title: Single_cell_RNA-seq_NKT17_36


title: Single_cell_RNA-seq_NKT17_28


title: Single_cell_RNA-seq_NKT17_35


title: Single_cell_RNA-seq_NKT17_29


title: Single_cell_RNA-seq_NKT17_32


title: Single_cell_RNA-seq_NKT2_10


title: Single_cell_RNA-seq_NKT17_34


title: Single_cell_RNA-seq_NKT17_26


title: Single_cell_RNA-seq_NKT17_31


title: Single_cell_RNA-seq_NKT17_33


title: Single_cell_RNA-seq_NKT17_30


title: Single_cell_RNA-seq_NKT17_25


title: Single_cell_RNA-seq_NKT17_24


title: S2 H4 ChIP rep2 6.25U MNase

description:
processed_data file:
s2.Pooled_H4.ReplicateSet_bin300.bedGraph.gz;
s2.MACC_H4.ReplicateSet_bin300.bedGraph.gz

data_processing:
Mnase-seq and ChIP-seq:  The sequenced paired-end reads were mapped to dm3, hg19, and mm9 genomes in the cases of D. melanogaster, H. sapiens and M. musculus data respectively using Bowtie aligner v. 0.12.939. Only uniquely mapped reads with no more than two mismatches were retained.  The reads with the insert sizes less than 50 bp or larger than 500 bp were filtered out. Genomic positions with the numbers of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded. Read frequencies were computed in 300-bp non-overlapping bins in the case of fly data and in 500-bp bins in the case of human data for each titration point independently. The read frequencies were normalized by the corresponding library sizes to represent values per one million of mapped reads. To facilitate the comparison of the results between different genomes, the frequencies were additionally scaled by the factors representing ratios between the corresponding genome size and 100 Mb, similarly to the approach described in Kasinathan et al. (Nat Methods 2014).
RNA-seq:  Tags were aligned using Tophat software package with default parameters. RNA-Seq tag frequencies were normalized for GC-content using bioconductor package EDASeq and then the expression estimates for each gene were obtained using bioconductor package DESeq.
Genome_build: dm3, mm9 and hg19
Supplementary_files_format_and_content: bedGraph files representing either tag occupancy profiles normalized to library sizes or MNase accessibility (MACC) profiles

organism: Drosophila melanogaster

source_name: S2 H4 ChIP 6.25U MNase

tag: cell line

value: S2 cells


title: S2 H4 ChIP rep2 25U MNase

source_name: S2 H4 ChIP 25U MNase


title: S2 H4 ChIP rep2 1.5U MNase

source_name: S2 H4 ChIP 1.5U MNase


title: S2 H4 ChIP rep1 25U MNase


title: Single_cell_RNA-seq_NKT17_21


title: Single_cell_RNA-seq_NKT2_1


title: Single_cell_RNA-seq_NKT17_22


title: S2 H4 ChIP rep1 1.5U MNase


title: S2 H4 ChIP rep1 6.25U MNase


title: Single_cell_RNA-seq_NKT17_20


title: Single_cell_RNA-seq_NKT17_27


title: Single_cell_RNA-seq_NKT17_19


title: S2 H4 ChIP rep1 100U MNase

source_name: S2 H4 ChIP 100U MNase


title: Single_cell_RNA-seq_NKT17_23


title: Single_cell_RNA-seq_NKT17_17


title: S2 H4 ChIP rep2 100U MNase


title: Single_cell_RNA-seq_NKT17_14


title: Single_cell_RNA-seq_NKT17_16


title: Single_cell_RNA-seq_NKT17_15


title: S2 whole chromatin rep2 100U MNase additional set

source_name: S2 cells


title: S2 whole chromatin rep2 25U MNase additional set


title: S2 whole chromatin rep2 1.5U MNase additional set


title: S2 rep1 RNA expression


title: S2 whole chromatin rep2 6.25U MNase additional set


title: Single_cell_RNA-seq_NKT17_12


title: Single_cell_RNA-seq_NKT17_13


title: S2 rep2 RNA expression


title: S2 whole chromatin rep1 100U MNase additional profile


title: Tvd-ID133761-A

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

description: rRNA-depleted RNA (ribozero)

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Read alignment with tophat 2.0.8: tophat -p 8 -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded R1.fastq R2.fastq
Read alignment with tophat 2.0.8: tophat -p 8 -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded R1.fastq R2.fastq
Genome_build: mm9
Supplementary_files_format_and_content: text file with eRPKMs

source_name: tet-Myc V394D liver tumor

growth_protocol: primary mouse samples

extract_protocol:
Total RNA from liver or tumor tissue was purified as described elsewhere (5). Briefly, tissue was homogenized in Trizol (Invitrogen) and chloroform was added. After centrifugation, RNA was purified using RNeasy Mini columns (Qiagen) according to the manufacturers protocol, including the on-column DNase I digestion step. 1µg total RNA was retro-transcribed into cDNA using the reverse transcriptase ImPromII (Promega) and oligodT and random primers. 10ng of cDNA were used for each quantitative reverse transcriptase PCR (qRT-PCR) analysis. Amplification was performed with the FAST SYBR Green Master Mix and quantified using the 7500 Fast Real-Time PCR machine (both Applied Biosystems).   For RNA sequencing, 5µg of total RNA of good quality (RNA integrity number ≥ 7.5) were treated according to the Ribozero rRNA removal kit (Epicentre) and purified on RNeasy MinElute columns (Qiagen). RNA integrity and successful removal of ribosomal RNA were assessed with the Agilent 2100 Bioanalyser (Agilent Technologies) or the LabChip® GX II Gel Electrophoresis (PerkinElmer).
RNA-seq libraries were prepared with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s protocol starting from the RNA fragmentation step.

treatment_protocol: Where indicated, exogenous tet-Myc (wt or V394D) expression was induced in utero using the liver-specific LaptTA. Tet-Myc expression was switched off by providing doxycycline-containing food for 16h.

value: FVB

value: liver tumor

tag: genotype/variation

value: tet-MycVD/LAPtTA (tet-Myc expression on)


title: Single_cell_RNA-seq_NKT17_11


title: S2 whole chromatin rep1 25U MNase additional profile

tag: cell type


title: Tvd-ID134664-A

description: rRNA-depleted RNA (ribozero)


title: Tvd-ID134668-A

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT2_9


title: Single_cell_RNA-seq_NKT17_10


title: Single_cell_RNA-seq_NKT17_18


title: S2 whole chromatin rep1 6.25U MNase additional profile


title: Tvd-ID133765-A

description: rRNA-depleted RNA (ribozero)


title: S2 whole chromatin rep1 1.5U MNase additional profile


title: Single_cell_RNA-seq_NKT17_9


title: Single_cell_RNA-seq_NKT17_8


title: Tvd-ID133764-A

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT17_7


title: S2 H3 ChIP rep2 1.5U MNase

description:
processed data file:
s2.Pooled_H3.ReplicateSet_bin300.bedGraph.gz;
s2.MACC_H3.ReplicateSet_bin300.bedGraph.gz

tag: chip antibody

value: H3 (Abcam, ab1791)


title: Single_cell_RNA-seq_NKT17_6


title: Single_cell_RNA-seq_NKT17_5


title: S2 H3 ChIP rep2 6.25U MNase


title: Single_cell_RNA-seq_NKT17_4


title: S2 H3 ChIP rep2 100U MNase


title: Tvd-ID134660-A

description: rRNA-depleted RNA (ribozero)


title: Tvd-ID133762-A

description: rRNA-depleted RNA (ribozero)


title: S2 H3 ChIP rep1 1.5U MNase


title: S2 H3 ChIP rep2 25U MNase


title: Single_cell_RNA-seq_NKT17_3


title: Tvd-ID133765-B

description: rRNA-depleted RNA (ribozero)


title: Tvd-ID133079-A

description: rRNA-depleted RNA (ribozero)


title: Tvd-ID133074-A

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT17_1


title: S2 H3 ChIP rep1 6.25U MNase


title: S2 H3 ChIP rep1 25U MNase


title: Single_cell_RNA-seq_NKT1_46

value: CD24low, TCRßlow, NK1.1high, CD27high, CCR6−


title: Single_cell_RNA-seq_NKT2_15


title: S2 H3 ChIP rep1 100U MNase


title: Single_cell_RNA-seq_NKT1_45


title: Single_cell_RNA-seq_NKT17_2


title: S2 whole chromatin rep2 1.5U MNase

description:
processed data file:
s2.Pooled_WholeChromatin.ReplicateSet_bin300.bedGraph.gz;
s2.MACC_WholeChromatin.ReplicateSet_bin300.bedGraph.gz


title: Tvd-ID133763-A

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_44


title: S2 whole chromatin rep2 6.25U MNase


title: S2 whole chromatin rep2 25U MNase


title: Single_cell_RNA-seq_NKT1_43


title: Toff-ID150584-C

description: rRNA-depleted RNA (ribozero)

source_name: tet-Myc liver tumor (tet-Myc inactivated for 16h)

value: tet-Myc/LAPtTA (tet-Myc expression off)


title: Toff-ID153344-B

description: rRNA-depleted RNA (ribozero)


title: Toff-ID153344-A

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_42


title: Toff-ID151964-A

description: rRNA-depleted RNA (ribozero)


title: Toff-ID150584-B

description: rRNA-depleted RNA (ribozero)


title: Toff-ID151964-B

description: rRNA-depleted RNA (ribozero)


title: S2 whole chromatin rep1 6.25U MNase


title: Single_cell_RNA-seq_NKT1_41


title: Toff-ID153344-C

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_40


title: Twt-ID126948-C

description: rRNA-depleted RNA (ribozero)

source_name: tet-Myc liver tumor

value: tet-Myc/LAPtTA (tet-Myc expression on)


title: S2 whole chromatin rep1 25U MNase


title: Single_cell_RNA-seq_NKT1_39


title: Single_cell_RNA-seq_NKT1_38


title: S2 whole chromatin rep1 100U MNase


title: Twt-ID126948-A

description: rRNA-depleted RNA (ribozero)


title: Twt-ID128285-B

description: rRNA-depleted RNA (ribozero)


title: Twt-ID128285-A

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_37


title: Single_cell_RNA-seq_NKT1_36


title: Bulk_RNA-seq_NKT17_2

data_processing:
Bulk RNA-Seq data was mapped against the mouse mm9 reference genome using tophat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome Bioinformatics Site. Sequencing read coverage per gene was counted using HTSeqcount (-m union -s yes -t exon -i gene_id, http://www-huber.embl.de/users/anders/HTSeq/)
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

molecule: polyA RNA

growth_protocol: NKT cells subtypes were isolated from Thymuses and directly sorted by Flow cytometry into lysis buffer (Trizol LS). No particular cell growth procedure was required.

extract_protocol:
Bulk RNA-seq was performed as described in PMID:24997565 and PMID:25092889. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Bulk RNA-seq was performed as described in PMID:24997565 and PMID:25092889. Briefly, 10-15 ng of purified total RNA was used for poly-A mRNA selection (Poly(A) Purist Mag kit, Life Technologies). Poly(A)-selected mRNA was amplified with a whole transcriptome amplification sequencing technology kit (SEQR, Sigma-Aldrich) as per the manufacturer’s recommendations. One microgram of this amplified cDNA was treated with the restriction enzyme (SEQR, Sigma-Aldrich) to remove the primer sequences and then purified using AMPure XP beads (Beckman Coulter). The efficiency of removal of SEQR primer sequences was assessed by quantitative PCR. 250 ng of purified amplifed cDNA was sonicated with a Covartis E220 multiplex sonicator to generate 100-250-bp DNA fragments. 250 ng DNA was used for preparing a standard SOLiD sequencing library (5500 SOLiD fragment 48 library core kit andfragment library barcode adaptors 1–96).
Whole Transcriptome Amplification (MDA); cDNA amplified RNA-Seq: Following emulsion PCR (SOLiD EZ Bead E120 system kits) samples were sequenced on the 5500 SOLiD sequencer to obtain 35-bp single end reads.

treatment_protocol: For RNA isolation from thymic iNKT cell subsets, thymus cell suspensions were enriched for iNKT cells by negative selection of cells expressing CD8b.2, CD19 or TER-119 via magnetic selection utilizing reagents and equipment from Stem Cell Technologies. The remaining cells were then stained using an 11-parameter panel of reagents that included tetramers of CD1d loaded with either aGalcer or PBS57 combined with streptavidin-brilliant violet (BV)421 (produced in-house or obtained from the NIH Tetramer Core Facility), anti-CD44-V500 (BD Biosciences #56780), live/dead yellow (ThermoFisher Scientific #L34959), anti-CD4-Qdot 605 (ThermoFisher Scientific #Q10092), anti-CD103-FITC (Affymetrix #11-1031), anti-CD24-PerCPCy5.5 (Affymetrix #45-0242), anti-CD27-APC (Affymetrix #E07114), anti-CD8a-AF700 (Biolegend 100730), anti-TCRb-APC-eF780 (Affymetrix #47-5961), anti-CCR6-PE (Biolegend #129803), and anti-NK1.1-PE-Cy7 (BD Biosciences #552878).  iNKT subsets were sorted using a FACSaria III (BD Biosciences). For Bulk RNA seq cells were lysed in Trizol LS (Life Technologies).


title: Bulk_RNA-seq_NKT17_3


title: Bulk_RNA-seq_NKT17_1


title: Twt-ID130395-A

description: rRNA-depleted RNA (ribozero)


title: S2 whole chromatin rep2 100U MNase


title: Single_cell_RNA-seq_NKT1_35


title: Toff-ID150584-A

description: rRNA-depleted RNA (ribozero)


title: S2 whole chromatin rep1 1.5U MNase


title: Bulk_RNA-seq_NKT2_3

value: CD24low, TCRbhigh, NK1.1−, CD27high, CD4high


title: Twt-ID125324-D

description: rRNA-depleted RNA (ribozero)


title: Bulk_RNA-seq_NKT2_1


title: Twt-ID125324-B

description: rRNA-depleted RNA (ribozero)


title: Bulk_RNA-seq_NKT2_2


title: Twt-ID125324-C

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_33


title: Single_cell_RNA-seq_NKT1_32


title: Single_cell_RNA-seq_NKT1_31


title: Single_cell_RNA-seq_NKT1_30


title: Twt-ID125324-A

description: rRNA-depleted RNA (ribozero)


title: Bulk_RNA-seq_NKT1_3

value: CD24low, TCRblow, NK1.1high, CD27high, CCR6−


title: Twt-ID126947-A

description: rRNA-depleted RNA (ribozero)


title: Bulk_RNA-seq_NKT1_2


title: Single_cell_RNA-seq_NKT1_29


title: Bulk_RNA-seq_NKT1_1


title: Twt-ID128992-B

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_28


title: Single_cell_RNA-seq_NKT1_27


title: Single_cell_RNA-seq_NKT1_34


title: Twt-ID125320-B

description: rRNA-depleted RNA (ribozero)


title: Twt-ID125320-D

description: rRNA-depleted RNA (ribozero)


title: Twt-ID125320-A

description: rRNA-depleted RNA (ribozero)


title: Twt-ID125320-C

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_25


title: Twt-ID128992-A

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_24


title: C-ID142608

description: rRNA-depleted RNA (ribozero)

source_name: normal liver

value: liver

value: control liver


title: C-ID142606

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_23

value: female


title: Single_cell_RNA-seq_NKT1_22

value: 5 weeks


title: C-ID141048

description: rRNA-depleted RNA (ribozero)


title: C-ID141041

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_21

value: Thymus


title: Single_cell_RNA-seq_NKT1_19


title: Single_cell_RNA-seq_NKT1_26


title: C-ID132859

description: rRNA-depleted RNA (ribozero)


title: K562 whole chromatin rep1 79.2U MNase

description:
processed data file:
k562.Pooled_WholeChromatin_bin500.bedGraph.gz;
k562.MACC_WholeChromatin_bin500.bedGraph.gz

source_name: K562 cells

value: K562 cells


title: C-ID128994

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_17


title: K562 whole chromatin rep1 20.6U MNase


title: K562 whole chromatin rep1 5.4U MNase


title: C-ID125322

description: rRNA-depleted RNA (ribozero)


title: C-ID128993

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_16


title: C-ID128990

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_20


title: Single_cell_RNA-seq_NKT1_15


title: Single_cell_RNA-seq_NKT1_14


title: C-ID128988

description: rRNA-depleted RNA (ribozero)


title: Single_cell_RNA-seq_NKT1_13


title: w1118_8dpi

city: Stanford

first: Alexander

last: Louie

address: 299 Campus Dr

department: Microbiology and Immunology

institute: Stanford University

data_processing:
Allignment: STAR default parameters
Counts: Rsubread default parameters supplied with genes.gtf from UCSC dm3
Normalization: edgeR. Generalized linear model ~Genotype+Time, method = "bin.spline"
Genome_build: UCSC dm3
Supplementary_files_format_and_content: .csv samples are arranged in columns and rows correspond to genes, gene expression level is represented in counts per million mapped reads

source_name: Whole fly

growth_protocol: Flies were maintained on standard dextrose media at 25°C with 65% humidity and 12 hour light/dark cycles. Shortly after eclosion, adult flies were collected into bottles containing dextrose fly media. At least 24hours post eclosion adult flies were anesthetized with carbon dioxide, males were sorted into groups of 20 and placed into vials containing standard dextrose fly media. Experiments were performed on male flies 5-7 days post eclosion.

extract_protocol:
For each sample 20 male flies were anesthetized with carbon dioxide, collected into TRIzol, homogenized and stored at -80°C. RNA preparation was preformed using a standard TRIzol RNA protocol. Messenger RNA was enriched by poly-T selection.
Barcoded TruSeq cDNA librararies were prepared by following Illumina's standard protocol

treatment_protocol: At 5 to 7 days post eclosion male flies were anesthetized with carbon dioxide and were injected with 50nl of Listeria (OD600 = 0.001, or approximately 100CFUs) or left manipulated. Following injection, flies were placed in vials containing dextrose fly media and incubated at 29°C. Samples were separated into three groups: Moribund, recovering and uninfected control. Moribund flies were infected and samples were collected on the following days post infection (dpi): 0.25, 1, 2, 2.25, 3, 4, 5 and 6. Recovering flies were infected and flipped onto dextrose fly media containing 1 mg/ml ampicillin 2 days post infection. Recovering samples were collected on the following dpi: 2.25, 3, 4, 5, 6, 7, 9, and 16. Uninfected control flies were not infected but were flipped onto dextrose fly media containing 1mg/ml ampicillin 2 dpi. Uninfected control samples were collected on the following dpi: 2.25, 3, and 9.

tag: Sex

value: male

tag: developmental stage

value: adult

tag: days post infection

tag: infection

value: Listeria monocytogenes

tag: agent

value: Ampicillin


title: w1118_6dpi

tag: strain


title: K562 whole chromatin rep1 304U MNase

tag: mnase concentration (u)


title: C-ID125319

description: rRNA-depleted RNA (ribozero)

value: FVB

tag: tissue


title: w1118_4dpi


title: input

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Significant peaks call using the Model-based Analysis of ChIP-Seq (MACS) 2.0.9, pvalue cutoff 1e-5;
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

extract_protocol:
Tumor nodules or control liver tissue were washed in PBS, cut into pieces ≤ 2mm diameter and fixed for 15 min in 1% of formaldehyde (Sigma) in PBS. Tissue was washed in PBS and stored at -80°C until further processing. Upon thawing, tissue was incubated in 125 mM glycin (5 min, room temperature), washed in PBS and nuclei were prepared on ice using a dounce homogenizer. All following steps were performed on ice, if not specified otherwise. Nuclei were washed in PBS, resuspended in ChIP buffer (4 ml of buffer per 0.5 ml of tissue; 100mM NaCl, 133mM Tris pH 8.0, 5 mM EDTA, 0.2% NaN3, 0.67% SDS, 1.67% Triton X-100) supplemented with protease inhibitors (cOmplete Protease Inhibitor Cocktail Tablets, Roche) and phosphatase inhibitors (50 mM NaF, 1 mM β-GP, 1 mM NaV). Chromatin was sonicated to an average length of 300 bp, pre-cleared once with proteinA-sepharose and once with proteinG-sepharose beads, both blocked with 0.5% E. coli tRNA (Sigma) and 0.5% BSA. In this study, the following antibodies were used: Myc N262 (Santa Cruz, sc-764X), RNA Pol II N20 (Santa Cruz, sc-899X), H3K4me1 (Abcam, ab8895), H3K4me3 (Active Motif, 39159), and H3K27ac (Abcam, ab4729). Normal rabbit IgG (Santa Cruz, sc-2027) was used as background control.  For Myc and RNA Pol II, 10 µg of antibodies were incubated overnight with 500µl of chromatin (+ 500µl of ChIP buffer to each a volume of 1ml per reaction). Blocked protein G-sepharose beads were added, incubated for 2-3h and washed as follows: 3x with mixed micelle buffer (150 mM NaCl, 20 mM Tris pH 8.1, 5 mM EDTA, pH 8.0, 5.2% sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), 2x with buffer 500 (50 mM HEPES pH 7.5, 0.1% sodium deoxycholate, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.2% NaN3), 2x with LiCl/detergent buffer (10 mM Tris pH 8.0, 0.5% sodium deoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.2% NaN3) and once with TE. DNA was de-crosslinked overnight (2% SDS in TE, 65°C), purified using QiaQuick columns (Qiagen) and quantified using PicoGreen (Invitrogen). For histone marks, 5 µg of antibody were pre-bound overnight to proteinG-coupled paramagnetic beads (Dynabeads, Invitrogen) in PBS/BSA 0.5%. Beads were washed and added to the chromatin (50-100 µl in a total volume of 1ml of ChIP buffer) and after overnight incubation washed 7x in RIPA-like buffer (50mM HEPES pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% sodium deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted from the beads in TE-2% SDS (15 min, 65°C), de-crosslinked overnight (65°C), purified and quantified using PicoGreen (Invitrogen).
Blecher-Gonen R1, Barnett-Itzhaki Z, Jaitin D, Amann-Zalcenstein D, Lara-Astiaso D, Amit I., High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc. 2013 Mar;8(3):539-54

value: tet-Myc (transgene off)


title: Single_cell_RNA-seq_NKT1_12

tag: age

value: CD24low, TCRßlow, NK1.1high, CD27high, CCR6−


title: w1118_2dpi

value: Untreated


title: w1118_3dpi


title: Single_cell_RNA-seq_NKT1_11


title: Single_cell_RNA-seq_NKT1_18


title: H3K27ac.Toff3

value: liver tumor

value: tet-Myc/LAPtTA (tet-Myc expression off)

value: H3K27ac (abcam ab4729)


title: Single_cell_RNA-seq_NKT1_10


title: w1118_18dpi


title: H3K27ac.Toff2


title: H3K27ac.Toff1


title: w1118_16dpi


title: H3K27ac.T4

value: tet-Myc/LAPtTA (tet-Myc expression on)


title: w1118_14dpi


title: w1118_12dpi


title: Single_cell_RNA-seq_NKT1_8


title: H3K27ac.T3


title: Single_cell_RNA-seq_NKT1_9


title: w1118_0dpi_rep2


title: H3K27ac.T2


title: Single_cell_RNA-seq_NKT1_6


title: H3K27ac.T1


title: w1118_0dpi_rep1


title: H3K27ac.C4

value: liver

value: wildtype


title: uninfected_w1118_4dpi

value: Uninfected


title: uninfected_w1118_6dpi


title: H3K27ac.C3


title: uninfected_w1118_8dpi


title: Single_cell_RNA-seq_NKT1_4

value: female

value: 5 weeks

value: Thymus


title: Single_cell_RNA-seq_NKT1_5


title: Single_cell_RNA-seq_NKT1_3


title: H3K27ac.C2

value: LAPtTA


title: Single_cell_RNA-seq_NKT1_2


title: Single_cell_RNA-seq_NKT1_1


title: uninfected_w1118_2dpi

value: male

value: adult


title: H3K27ac.C1

value: FVB

value: tet-Myc (tet-Myc expression off)


title: uninfected_w1118_3dpi

value: Ampicillin


title: H3K4me3.Toff3

value: H3K4me3 (Active Motif #39159)


title: Single_cell_RNA-seq_NKT0_45

value: CD8α-, CD1d-αGalcer tetramer-binding, TCRßmedium, CD24high, CD44low, NK1.1-


title: Single_cell_RNA-seq_NKT1_7

value: CD24low, TCRßlow, NK1.1high, CD27high, CCR6−


title: uninfected_w1118_18dpi


title: H3K4me3.Toff2

value: liver tumor

value: tet-Myc/LAPtTA (tet-Myc expression off)


title: Single_cell_RNA-seq_NKT0_44


title: uninfected_w1118_16dpi


title: H3K4me3.T4

value: tet-Myc/LAPtTA (tet-Myc expression on)


title: Single_cell_RNA-seq_NKT0_43


title: Single_cell_RNA-seq_NKT0_42


title: H3K4me3.Toff1


title: H3K4me3.T3


title: Single_cell_RNA-seq_NKT0_41


title: uninfected_w1118_10dpi


title: H3K4me3.T2


title: uninfected_w1118_12dpi


title: uninfected_w1118_1dpi

value: Untreated


title: Single_cell_RNA-seq_NKT0_40


title: Single_cell_RNA-seq_NKT0_39


title: H3K4me3.C4

value: liver

value: wildtype


title: H3K4me3.T1


title: uninfected_w1118_0dpi_rep2

value: Uninfected


title: Single_cell_RNA-seq_NKT0_37

value: female

value: 5 weeks

value: Thymus


title: H3K4me3.C3


title: H3K4me3.C2

value: LAPtTA


title: Ral359_6dpi

value: male

value: adult

value: Listeria monocytogenes


title: uninfected_w1118_14dpi

value: Ampicillin


title: Single_cell_RNA-seq_NKT0_35

value: CD8α-, CD1d-αGalcer tetramer-binding, TCRßmedium, CD24high, CD44low, NK1.1-


title: Ral359_4dpi


title: Single_cell_RNA-seq_NKT0_36


title: H3K4me3.C1

value: FVB

value: tet-Myc (tet-Myc expression off)

value: H3K4me3 (Active Motif #39159)


title: Ral359_8dpi


title: Ral359_3dpi


title: Single_cell_RNA-seq_NKT0_34


title: RNAPII.Toff3

value: liver tumor

value: tet-Myc/LAPtTA (tet-Myc expression off)

value: RNAPII (Santa Cruz sc899-X)


title: RNAPII.Toff2


title: RNAPII.Toff1


title: Single_cell_RNA-seq_NKT0_32


title: Ral359_18dpi


title: Ral359_2dpi

value: Untreated


title: Single_cell_RNA-seq_NKT0_38


title: uninfected_w1118_0dpi_rep1

value: Uninfected


title: RNAPII.T4

value: tet-Myc/LAPtTA (tet-Myc expression on)


title: Ral359_16dpi


title: RNAPII.T3


title: Ral359_14dpi


title: Ral359_12dpi


title: Single_cell_RNA-seq_NKT0_30

value: female

value: 5 weeks


title: Single_cell_RNA-seq_NKT0_28

value: Thymus


title: Single_cell_RNA-seq_NKT0_27


title: RNAPII.T2


title: Single_cell_RNA-seq_NKT0_26


title: RNAPII.T1


title: Ral359_1dpi

value: male


title: Ral359_10dpi

value: adult


title: Single_cell_RNA-seq_NKT0_33


title: Ral359_0dpi_rep2

value: Listeria monocytogenes


title: RNAPII.C2

value: liver

value: LAPtTA


title: RNAPII.C1

value: FVB


title: Single_cell_RNA-seq_NKT0_24

value: CD8α-, CD1d-αGalcer tetramer-binding, TCRßmedium, CD24high, CD44low, NK1.1-


title: Single_cell_RNA-seq_NKT0_23


title: Single_cell_RNA-seq_NKT0_25


title: Ral359_0dpi_rep1


title: pcmt_8dpi

value: Ampicillin


title: Single_cell_RNA-seq_NKT0_31


title: Myc.Toff2

value: liver tumor

value: c-Myc N262 (Santa Cruz sc764-X)


title: Single_cell_RNA-seq_NKT0_22


title: pcmt_6dpi


title: Single_cell_RNA-seq_NKT0_29


title: RNAPII.C3

value: wildtype

value: RNAPII (Santa Cruz sc899-X)


title: Myc.Toff3

value: tet-Myc/LAPtTA (tet-Myc expression off)


title: Myc.Toff1


title: pcmt_3dpi


title: Myc.T6

value: tet-Myc/LAPtTA (tet-Myc expression on)


title: Single_cell_RNA-seq_NKT0_20

value: female


title: RNAPII.C4


title: pcmt_2dpi

value: Untreated


title: Single_cell_RNA-seq_NKT0_19

value: 5 weeks

value: Thymus


title: pcmt_18dpi

value: male

value: adult


title: Single_cell_RNA-seq_NKT0_18


title: pcmt_16dpi

value: Listeria monocytogenes


title: Myc.T5


title: Myc.T3


title: Myc.T2


title: Single_cell_RNA-seq_NKT0_17


title: Single_cell_RNA-seq_NKT0_16


title: pcmt_14dpi


title: pcmt_4dpi


title: pcmt_12dpi


title: Myc.T1


title: Single_cell_RNA-seq_NKT0_21


title: Myc.C4

value: liver


title: Single_cell_RNA-seq_NKT0_14


title: pcmt_0dpi_rep2


title: pcmt_1dpi


title: pcmt_0dpi_rep1


title: Myc.C2

value: FVB

value: LAPtTA


title: Single_cell_RNA-seq_NKT0_11

value: CD8α-, CD1d-αGalcer tetramer-binding, TCRßmedium, CD24high, CD44low, NK1.1-


title: CG2247_8dpi

value: Ampicillin


title: Single_cell_RNA-seq_NKT0_13


title: Myc.C1

value: tet-Myc (tet-Myc expression off)

value: c-Myc N262 (Santa Cruz sc764-X)


title: Myc.T4

value: liver tumor


title: Single_cell_RNA-seq_NKT0_10


title: Myc.C3

value: wildtype


title: Tc0 liver Bio-CAP rep1

source_name: liver


title: Single_cell_RNA-seq_NKT0_15


title: Tc0 liver Bio-CAP rep2


title: CG2247_6dpi


title: CG2247_4dpi


title: Tc0 liver Bio-CAP INPUT rep1 INPUT


title: Single_cell_RNA-seq_NKT0_12


title: CG2247_3dpi


title: Single_cell_RNA-seq_NKT0_7


title: Tc0 testis Bio-CAP rep2

source_name: testis


title: Single_cell_RNA-seq_NKT0_9


title: pcmt_10dpi


title: CG2247_2dpi


title: Tc0 testis Bio-CAP rep1


title: CG2247_18dpi


title: Single_cell_RNA-seq_NKT0_5


title: Tc0 testis Bio-CAP INPUT rep1 INPUT


title: Tc1 testis BioCAP INPUT 41208 rep1 INPUT

tag: animal


title: Single_cell_RNA-seq_NKT0_4

tag: gender


title: Single_cell_RNA-seq_NKT0_3

tag: cell type surface markers


title: Tc1 testis BioCAP INPUT 44166 rep1 INPUT


title: Tc1 testis Bio-CAP 41208 rep2


title: CG2247_12dpi


title: Single_cell_RNA-seq_NKT0_2

tag: vα14 inkt thymocyte subset


title: Tc1 liver Bio-CAP 41208 rep2


title: Single_cell_RNA-seq_NKT0_8


title: Single_cell_RNA-seq_NKT0_1


title: CG2247_1dpi


title: Tc1 testis Bio-CAP 44166 rep1


title: Single_cell_RNA-seq_NKT0_6


title: CG2247_0dpi_rep2


title: ChIP-seq_H3K27Ac_NKT17_2

data_processing:
H3K27ac ChIP-Seq data was mapped against the mouse mm9 reference genome using bowtie v.0.12.7 (-n 2 -m 1). The obtained sam files were converted and merged into separated bam files using samtools v.0.1.18.
Genome_build: mm9
Supplementary_files_format_and_content: bed

growth_protocol: NKT cells subtypes were isolated from Thymuses and directly sorted by Flow cytometry into a collection buffer (50% PBS, 50% FCS). No particular cell growth procedure was required.

extract_protocol:
ChIP-seq was performed as described in  Seumois et al., Nat Immunol. 2014, PMID:24997565. Briefly: frozen cells were lysed in 120 μl of lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, 1 mM phenyl methane sulfonylfluoride, 20 mg/ml sodium butyrate, proteinase inhibitor cocktail; Sigma), and chromatin was sheared by sonication, using BioRuptorTM (Diagenode), to generate 100–500 bp DNA fragments. Chromatin was diluted in 1 ml of radioimmunoprecipitation assay (RIPA) buffer and immunoprecipitation was done overnight at 4 °C by incubating 1 μl of H3K27ac antibody (rabbit polyclonal IgG, lot# Gr167929-1, Abcam) pre-coated on 10 μl protein A coated magnetic beads (Invitrogen). Immunocomplexes were captured, washed, and ChIP DNA eluted as described previously. One ng of ChIP DNA was PCR amplified for 18 to 22 cycles using whole genome amplification (WGA) primers (WGA-SEQX, Sigma) following the manufacturer’s instructions.
Approximately 100 ng amplified DNA was used for preparing a standard Illumina sequencing library (TruSeq® Nano DNA HT Sample Preparation Kit, Illumina).
Whole Genome Amplification (MDA); Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (TruSeq® Rapid Kit, Illumina).

treatment_protocol: Once th esort is completed, cell were centrigufed 400G for 5 minutes, resuspended with Tcell medium at a concentration of 1-2million cells/ ml and fixed with 1% Formaldehyde for 10 minutes. Fixation was stopped by adding Glycine 250mM. Cells were washed thrice with Ice-cold PBS and finally Snap fozen as a pellet in Liquid nitrogen and stored at -80˚C.

value: thymus

value: CD24low, CD27low, CD4–, CCR6+, CD103high

value: rabbit polyclonal Anti-Histone H3K27ac antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: Tc1 liver Bio-CAP 44166 rep1


title: NSP 4

city: Tokyo

first: Sumako

last: Kameishi

address: 2-2, Wakamatsucho, Shinjukuku

department: Advanced Science and Engineering

country: Japan

institute: Graduate School of Waseda University

data_processing:
Fastq files were prepared using Torrent Suite
Reads were mapped on CLC Genomics Workbench 7.0.4
Supplementary_files_format_and_content: Total reads per gene

organism: Oryctolagus cuniculus

source_name: limbal epithelial cells

extract_protocol:
Limbal epithelial SP and NSP cells were isolated with Hoechst 33342 staining
The library was prepared using an Ion Proton Sequencer

value: New Zealand white rabbit

tag: weight


title: CG2247_0dpi_rep1

tag: Sex

value: male

value: Untreated


title: ChIP-seq_H3K27Ac_NKT17_1

value: female

value: 5 weeks

tag: chip antibody


title: CG2247_16dpi

tag: developmental stage

value: adult

tag: days post infection

value: Listeria monocytogenes


title: ChIP-seq_H3K27Ac_NKT2_4

value: ICOShigh, NK1.1−, CD27high, and CD4high


title: ChIP-seq_H3K27Ac_NKT2_3


title: NSP 3


title: SP 4


title: ChIP-seq_H3K27Ac_NKT2_2


title: CG2247_10dpi

tag: infection

tag: agent

value: Ampicillin


title: SP 3

tag: strain


title: CG2247_14dpi


title: ChIP-seq_H3K27Ac_NKT1_4

tag: tissue

value: NK1.1high, ICOSlow , CD27high, CCR6−


title: NSP 2


title: NSP 1


title: ChIP-seq_H3K27Ac_NKT1_3

tag: age


title: ChIP-seq_H3K27Ac_NKT17_3


title: ChIP-seq_H3K27Ac_NKT2_1


title: ChIP-seq_H3K27Ac_NKT1_1


title: ChIP-seq_H3K27Ac_NKT1_2


title: SP 1


title: SP 2


title: WT_212

status: Public on Apr 16 2016

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina software was used for instrument control (HSCS version 2.0.12.0), basecalling and quality control (RTA version 1.17.21.3) and fastq file generation and de-multiplexing (CASAVA version 1.8.2).
Short reads were mapped using the subread alignment algorithm from the Rsubread package (version 1.18.0, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.18.0) using the in-built mm10 annotation.
Reads per kilobase per million (RPKM) values were calculated using the edgeR package (version 3.11.5, Robinson et al. Bioinformatics 2010).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Wild-type platelets

extract_protocol:
RNA was isolated from freshly purifed platelets using a Norgen RNA purification Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq RNA v2 sample preparation kit, TruSeq PE Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3).

value: BALB/c

value: Blood

value: 20 week-old male

tag: genotype

value: Nxf1 wild type

tag: batch


title: WT_208


title: WT_204


title: S_cerevisiae_spt4Δ_mRNAseq

city: Ithaca

first: Gregory

middle: Thomas

last: Booth

state: New York

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

description: messenger RNA

data_processing:
mRNA-seq: Adaptor sequences were clipped from reads.  Using STAR (version 2.3.0) reads were aligned to a combined genome of S. cerevisiae and S. pombe. Only uniquely alinging reads with fewer than 2 mismatches were used for downstream analysis. Unique reads were parsed based on their species of origin. Bedgraph files were created by recording only the most 3' base of each read (this facilitates counting/normalization for downstream applications).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
Chromosome nomenclature used (e.g. the first column of bedgraph):  for S. cerevisiae:  'chrI'; for S. pombe: 'chr01'.  Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).

organism: Saccharomyces cerevisiae

source_name: background: w303 α

growth_protocol: S. cerevisiae cultures were grown in YPD media from a starting OD600 of 0.2 to a final OD600 = 0.5.  S. pombe cultures were grown in YES media with the same starting and ending OD600 as used for budding yeast.

extract_protocol:
Immediately prior to harvesting cultures, a fixed amount of spike-in culture (i.e. S.pombe into S. cerevisaie samples) was added to each sample culture for PRO-seq and RNA-seq experiments.  For PRO-seq and PRO-cap assays, cultures were then spun down and washed once in ice-cold water.  Samples were then spun again and resuspended in ice-cold permeabilization buffer (0.05% sarkosyl) and left on ice for 20 minutes.  Permeabilized cells were then spun down at 400XG for 5 minutes.  Permeabilized cell pellets were resuspeneded in 120 uL 2.5X transcription buffer (50 mM Tris-HCl, pH 7.7, 500 mM KCl, 12.5 mM MgCl2).  To the reaction buffer we then added 3.75 uL of each biotin-11-NTP (epicentre), 6 uL .1M DTT, 3 uL SUPERase Inhibitor (invitrogen) and 141 uL DEPC treated water.  The run-on was then performed by adding 15 uL 10% sarkosyl and placing samples at 30°C for 5 minutes.  After the run-on, samples were spun and the reaction buffer was removed.  RNA was then isolated using the hot acid phenol extraction protocol, followed by ethanol precipitation.
PRO-seq and PRO-cap Libraries were prepared according to Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. Science (2013).  mRNA-seq libraries were prepared using Illumina's TruSeq Stranded mRNA Sample Preparation LS protocol.

tag: background

value: w303 alpha

tag: assay

value: mRNA-seq


title: S_cerevisiae_WT_mRNAseq

description: messenger RNA

data_processing:
mRNA-seq: Adaptor sequences were clipped from reads.  Using STAR (version 2.3.0) reads were aligned to a combined genome of S. cerevisiae and S. pombe. Only uniquely alinging reads with fewer than 2 mismatches were used for downstream analysis.  Unique reads were parsed based on their species of origin. Bedgraph files were created by recording only the most 3' base of each read (this facilitates counting/normalization for downstream applications).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
Chromosome nomenclature used (e.g. the first column of bedgraph):  for S. cerevisiae:  'chrI'; for S. pombe: 'chr01'.  Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).

source_name: background: w303 a


title: S_cerevisiae_WT_PROseq

description: Nascent RNA

data_processing:
Adaptor sequences were clipped from reads.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment.
Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).

extract_protocol:
Immediately prior to harvesting cultures, a fixed amount of spike-in culture (i.e. S.pombe into S. cerevisaie samples) was added to each sample culture for PRO-seq and RNA-seq experiments.  Cultures were then spun down and washed once in ice-cold water.  Samples were then spun again and resuspended in ice-cold permeabilization buffer (0.05% sarkosyl) and left on ice for 20 minutes.  Permeabilized cells were then spun down at 400XG for 5 minutes.  Permeabilized cell pellets were resuspeneded in 120 uL 2.5X transcription buffer (50 mM Tris-HCl, pH 7.7, 500 mM KCl, 12.5 mM MgCl2).  To the reaction buffer we then added 3.75 uL of each biotin-11-NTP (epicentre), 6 uL .1M DTT, 3 uL SUPERase Inhibitor (invitrogen) and 141 uL DEPC treated water.  The run-on was then performed by adding 15 uL 10% sarkosyl and placing samples at 30°C for 5 minutes.  After the run-on, samples were spun and the reaction buffer was removed.  RNA was then isolated using the hot acid phenol extraction protocol followed by ethanol precipitation.
PRO-seq and PRO-cap Libraries were prepared according to Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. Science (2013).  mRNA-seq libraries were prepared using Illumina's TruSeq Stranded mRNA Sample Preparation LS protocol.
Other (PRO-seq), Other (PRO-cap) or RNA-seq

value: PRO-seq


title: S_cerevisiae_WT_PROcap

description: Nascent RNA

data_processing:
PRO-cap: Adaptor sequences were clipped from reads.  Sequences were trimmed to a maximum length of 36 (minimum = 15). Using Bowtie (version 1.0) Reads were first aligned to the ribosomal DNA genome.  Any reads that failed to align to ribosomal DNA were then aligned to the genome of interest. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.  Begraph files were created by recording only the position of the most 5' nucleotide for each read.  Counts at each genome position were then normalized by the total number of mapple reads (RPM). Normalized bedgraphs were then converted to bigwig formatted files.
Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).

extract_protocol:
Immediately prior to harvesting cultures, a fixed amount of spike-in culture (i.e. S.pombe into S. cerevisaie samples) was added to each sample culture for PRO-seq and RNA-seq experiments.  For PRO-seq and PRO-cap assays, cultures were then spun down and washed once in ice-cold water.  Samples were then spun again and resuspended in ice-cold permeabilization buffer (0.05% sarkosyl) and left on ice for 20 minutes.  Permeabilized cells were then spun down at 400XG for 5 minutes.  Permeabilized cell pellets were resuspeneded in 120 uL 2.5X transcription buffer (50 mM Tris-HCl, pH 7.7, 500 mM KCl, 12.5 mM MgCl2).  To the reaction buffer we then added 3.75 uL of each biotin-11-NTP (epicentre), 6 uL .1M DTT, 3 uL SUPERase Inhibitor (invitrogen) and 141 uL DEPC treated water.  The run-on was then performed by adding 15 uL 10% sarkosyl and placing samples at 30°C for 5 minutes.  After the run-on, samples were spun and the reaction buffer was removed.  RNA was then isolated using the hot acid phenol extraction protocol followed by ethanol precipitation.
PRO-seq and PRO-cap Libraries were prepared according to Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. Science (2013).  mRNA-seq libraries were prepared using Illumina's TruSeq Stranded mRNA Sample Preparation LS protocol.

value: PRO-cap


title: S_cerevisiae_spt4Δ_PROseq

description: Nascent RNA

data_processing:
PRO-seq: Adaptor sequences were clipped from reads.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment.  Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).

extract_protocol: Immediately prior to harvesting cultures, a fixed amount of spike-in culture (i.e. S.pombe into S. cerevisaie samples) was added to each sample culture for PRO-seq and RNA-seq experiments.  For PRO-seq and PRO-cap assays, cultures were then spun down and washed once in ice-cold water.  Samples were then spun again and resuspended in ice-cold permeabilization buffer (0.05% sarkosyl) and left on ice for 20 minutes.  Permeabilized cells were then spun down at 400XG for 5 minutes.  Permeabilized cell pellets were resuspeneded in 120 uL 2.5X transcription buffer (50 mM Tris-HCl, pH 7.7, 500 mM KCl, 12.5 mM MgCl2).  To the reaction buffer we then added 3.75 uL of each biotin-11-NTP (epicentre), 6 uL .1M DTT, 3 uL SUPERase Inhibitor (invitrogen) and 141 uL DEPC treated water.  The run-on was then performed by adding 15 uL 10% sarkosyl and placing samples at 30°C for 5 minutes.  After the run-on, samples were spun and the reaction buffer was removed.  RNA was then isolated using the hot acid phenol extraction protocol, followed by ethanol precipitation.  Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files. PRO-seq and PRO-cap Libraries were prepared according to Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. Science (2013).  mRNA-seq libraries were prepared using Illumina's TruSeq Stranded mRNA Sample Preparation LS protocol.


title: S_pombe_WT_mRNAseq

description: messenger RNA

organism: Schizosaccharomyces pombe

source_name: background: 972 h-


title: S_pombe_WT_PROcap

description: Nascent RNA

data_processing:
PRO-cap: Using Bowtie (version 1.0) Reads were first aligned to the ribosomal DNA genome.  Any reads that failed to align to ribosomal DNA were then aligned to the genome of interest. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.  Begraph files were created by recording only the position of the most 5' nucleotide for each read.  Counts at each genome position were then normalized by the total number of mapple reads (RPM). Normalized bedgraphs were then converted to bigwig formatted files.
Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).


title: S_pombe_WT_PROseq

description: Nascent RNA

data_processing:
PRO-seq: Adaptor sequences were clipped from reads.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment. Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.  Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).


title: Senescent IMR90 JQ1_1

status: Public on Apr 15 2016

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al 2014). RNA-seq reads were then aligned to GRCh37.75(hg19) with STAR (Dobin et. al 2012) and genome-wide transcript counting was performed by HTSeq (Anders et al. 2015)  to generate a matrix of fragments per kilobase of exon per million fragments mapped (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing normalized count tables from each experiment

source_name: IMR90 human fibrobasts

growth_protocol: IMR90 human fibroblasts were co-transduced with either pWZL- Hygro (empty vector control) or a pWZL- HRASV12- Hygro and indicated LMP vectors encoding validated GFP-linked shRNAs targeting BRD4 (Zuber et al., 2011), p65 (Chien et al., 2011), p53 (Lujambio et al., 2013), p53/Rb, or p21/p16 (Chicas et al., 2010). The infected population was selected using 2 μg/mL puromycin (Sigma) and 75 μg/mL hygromycin B (Roche) and cultured in DMEM 10% FBS. Quiescence was induced in cells transduced with PWZL-Hygro (empty vector) and LMP vectors by culturing for 4 days in 0.1% FBS.  For all samples RNA was extracted at Day 12 post-infection.RNA from independent triplicates was extracted.

extract_protocol:
Cells were lysed by adding RLT buffer directly to the culture dish. RNA was extracted using Rneasy Qiagen Kit.
RNA samples were used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).

treatment_protocol: For JQ1 treatments, cells were treated with 100 nM of JQ1 or DMSO as vehicle for 48 hours (hr) prior to harvest. A working solution of JQ1 at 1 mM was prepared to use a final concentration of vehicle (DMSO) no higher than 1/10000

tag: cell type

value: fetal lung fibroblasts

tag: cell line

tag: cell condition

value: senescent

tag: viral transduction

value: cotransduced with pWZL HRASV12 and shRen

tag: treatment


title: S_pombe_spt4Δ_PROseq

description: Nascent RNA

data_processing:
PRO-seq: Adaptor sequences were clipped from reads.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment.
PRO-seq: Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
PRO-seq:  Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
PRO-cap: Adaptor sequences were clipped from reads.  Sequences were trimmed to a maximum length of 36 (minimum = 15).
PRO-cap: Using Bowtie (version 1.0) Reads were first aligned to the ribosomal DNA genome.  Any reads that failed to align to ribosomal DNA were then aligned to the genome of interest. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
PRO-cap: Begraph files were created by recording only the position of the most 5' nucleotide for each read.  Counts at each genome position were then normalized by the total number of mapple reads (RPM). Normalized bedgraphs were then converted to bigwig formatted files.
mRNA-seq: Adaptor sequences were clipped from reads.
mRNA-seq:  Using STAR (version 2.3.0) reads were aligned to a combined genome of S. cerevisiae and S. pombe. Only uniquely alinging reads with fewer than 2 mismatches were used for downstream analysis.
mRNA-seq: Unique reads were parsed based on their species of origin. Bedgraph files were created by recording only the most 3' base of each read (this facilitates counting/normalization for downstream applications).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
Chromosome nomenclature used (e.g. the first column of bedgraph):  for S. cerevisiae:  'chrI'; for S. pombe: 'chr01'
Genome_build: S. pombe: ASM294v2;  S. cerevisiae: sacCer3
Supplementary_files_format_and_content: processed files are in bigwig format. Each bigwig file contains normalized counts of either read 3'-ends (PRO-seq & mRNA seq), or read 5'-ends (PRO-cap).


title: Senescent IMR90 JQ1_2


title: Quiescent IMR90 JQ1_2

value: quiescent

value: cotransduced with pWZL-Hygro and shRen


title: Senescent IMR90 JQ1_3


title: Quiescent IMR90 JQ1_1


title: Quiescent IMR90 JQ1_3


title: Senescent IMR90 DMSO_3

value: DMSO 48h


title: Quiescent IMR90 DMSO_3


title: Proliferating IMR90 JQ1_1

value: proliferating


title: Proliferating IMR90 JQ1_3


title: Senescent IMR90 DMSO_2


title: Quiescent IMR90 DMSO_1


title: Proliferating IMR90 DMSO_3


title: Senescent IMR90 DMSO_1


title: Proliferating IMR90 DMSO_2


title: Proliferating IMR90 DMSO_1


title: Senescent IMR90 shp53/Rb_3

value: cotransduced with pWZL HRASV12 and shp53/Rb

value: no treatment


title: Senescent IMR90 shp53/Rb_2


title: S_pombe_spt4Δ_mRNAseq

description: messenger RNA


title: Quiescent IMR90 shp53/Rb_3

value: cotransduced with pWZL-Hygro and shp53/Rb


title: Senescent IMR90 shp53/Rb_1


title: Quiescent IMR90 shp53/Rb_1


title: Proliferating IMR90 shp53/Rb_3


title: Quiescent IMR90 shp53/Rb_2


title: Proliferating IMR90 JQ1_2


title: Senescent IMR90 shp16/p21_2

value: cotransduced with pWZL HRASV12 and shp16/p21


title: Proliferating IMR90 shp53/Rb_2


title: Senescent IMR90 shp16/p21_3


title: Proliferating IMR90 shp53/Rb_1


title: HS90002_CM

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Reads were mapped to the Ensembl GRCh37 human genome and transcriptome annotation (obtained from Illumina iGenomes) using Tophat 2 and uniquely mapped reads associated with each gene were counted using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited table of raw counts of uniquely mapped reads for each gene

source_name: Donor HS90002 Central Memory T cells

extract_protocol:
T cell subsets were sorted by fluorescence activated cell sorting (FACS) and total RNA was extracted using Trizol and isopropanol precipitation. Poly(A)+ mRNA was then isolated from each total RNA sample using streptavidin-coated superparamagnetic beads (Dynabeads, Life Technologies) coated in biotinylated LNA-oligo(dT) (Exiqon).
Purified poly(A)+ mRNA from each sample was reverse transcribed and Illumina sequencing libraries were enriched usign the SMARTer Stranded RNA-Seq kit (Clontech). The resulting libraries were sequenced on an Illumina NextSeq 500 with single-end 75-base reads.

tag: donor id

value: Central memory T cells


title: HS60223_CM

source_name: Donor HS60223 Central Memory T cells


title: LH097_CM

source_name: Donor LH097 Central Memory T cells


title: Senescent IMR90 shp16/p21_1


title: Quiescent IMR90 DMSO_2


title: Quiescent IMR90 shp16/p21_3

value: cotransduced with pWZL-Hygro and shp16/p21


title: Quiescent IMR90 shp16/p21_2


title: Proliferating IMR90 shp16/p21_3


title: LH068_TMNP

source_name: Donor LH068 TMNP cells

value: TMNP


title: LH097_TMNP

source_name: Donor LH097 TMNP cells


title: Proliferating IMR90 shp16/p21_2


title: LH068_N

source_name: Donor HS90002 Naïve T cells

value: naive T cells


title: HS60223_TMNP

source_name: Donor HS60223 TMNP cells


title: LH083_N

source_name: Donor LH083 Naïve T cells


title: Proliferating IMR90 shp16/p21_1


title: LH068_CM

source_name: Donor LH068 Central Memory T cells


title: LH097_N

source_name: Donor LH097 Naïve T cells


title: Senescent IMR90 shBrd4_3

value: cotransduced with pWZL HRASV12 and shBrd4


title: LH083_CM

source_name: Donor LH083 Central Memory T cells


title: Quiescent IMR90 shp16/p21_1


title: Senescent IMR90 shBrd4_1


title: HS90002_EM

source_name: Donor HS90002 Effector Memory T cells

value: Effector Memory T cells


title: HS60223_N

source_name: Donor HS60223 Naïve T cells


title: LH068_EM

source_name: Donor LH068 Effector Memory T cells


title: Quiescent IMR90 shBrd4_3

value: fetal lung fibroblasts

value: cotransduced with pWZL-Hygro and shBrd4


title: LH083_EM

source_name: Donor LH083 Effector Memory T cells


title: LH068_TEMRA

source_name: Donor LH068 TEMRA cells

value: TEMRA


title: Proliferating IMR90 shBrd4_3

source_name: IMR90 human fibrobasts


title: Quiescent IMR90 shBrd4_1

value: quiescent


title: LH083_TEMRA

source_name: Donor LH083 TEMRA cells


title: Senescent IMR90 shp65_3

value: senescent

value: cotransduced with pWZL HRASV12 and shp65


title: Quiescent IMR90 shBrd4_2


title: Quiescent  IMR90 shp65_3

value: cotransduced with pWZL-Hygro and shp65


title: LH097_EM

source_name: Donor LH097 Effector Memory T cells


title: HS60223_EM

source_name: Donor HS60223 Effector Memory T cells


title: Quiescent  IMR90 shp65_2


title: Senescent IMR90 shp65_2


title: Proliferating IMR90 shBrd4_1

value: proliferating


title: Proliferating IMR90 shp65_3

value: no treatment


title: Proliferating IMR90 shBrd4_2


title: Proliferating IMR90 shp65_2


title: LH097_TEMRA

source_name: Donor LH097 TEMRA cells


title: Senescent IMR90 shp65_1


title: Quiescent IMR90 shp65_1


title: HS60223_TEMRA

source_name: Donor HS60223 TEMRA cells


title: TAA-2

first: Jae-Sang

last: Hong

state: Seoul

address: building life science and biotech west building L204

institute: Korea University

data_processing:
3’ adaptor and low-quality sequences from raw sequencing reads, the reads length over 16 nt were retrieved to produce ‘clean reads’ in Galaxy.
The small RNA length distribution was performed and then aligned to the mouse genome (mm10) using the BOWTIE program with the options of -m 10 -p 8 --best –strata (version 0.12.7), allowing up to two mismatches.
Genome aligned sequences were screened against the miRNA public database (miRBase, release 21)  for miRNA and Ensenbl (release 83) for other RNA species using htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: TXT files include read count of mouse mature miRNAs

source_name: Liver

growth_protocol: 12 hour light-dark cycle and a humidity and temperature controlled environment with free access to food and water.

extract_protocol:
Total RNA was isolated from each liver tissue using an miRNeasy mini Kit (Qiagen), according to the manufacturer’s instructions.
We used small RNAs as an input to construct a cDNA library using a TruSeq Small RNA Sample Preparation kit (Illumina) following the manufacturer’s protocol.

treatment_protocol: Intraperitoneal (IP) injection of 200 mg/kg TAA three times a week for 10 weeks.

value: Liver

value: 15 week


title: Senescent IMR90 shBrd4_2


title: Proliferating IMR90 shp65_1


title: Senescent IMR90 shp53_3

value: cotransduced with pWZL HRASV12 and shp53


title: TAA-1

value: 200 mg/kg TAA three times a week for 10 weeks


title: Control-2

value: control


title: Control-1


title: Senescent IMR90 shp53_1


title: Senescent IMR90 shp53_2


title: nm_ux_tn_F6_141204

first: Fred

middle: H

last: Gage

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

description:
sn_ne_counts.txt
sn_ne_tpm.txt

data_processing:
sequencing reads were trimmed for low base-quality and aligned to mm10 using rsem-calculate-expression running bowtie version 1.0.0
expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: sn_hc_counts.txt: tab-delimited file of counts (abundance measurements) from nuclei dissociated from a homecage mouse
Supplementary_files_format_and_content: sn_hc_tpm.txt: tab-delimited file of TPM values (normalized abundance) from nuclei dissociated from a homecage mouse
Supplementary_files_format_and_content: sn_ne_counts.txt: tab-delimited file of counts (abundance measurements) from FOS positive and FOS negative nuclei dissociated from a mouse exposed to a novel environment
Supplementary_files_format_and_content: sn_ne_tpm.txt:  tab-delimited file of TPM values (normalized abundance) from FOS positive and FOS negative nuclei dissociated from a mouse exposed to a novel environment
Supplementary_files_format_and_content: wc_counts.txt: tab-delimited file of counts (abundance measurements) from PTZ- and saline-treated whole cells
Supplementary_files_format_and_content: wc_tpm.txt: tab-delimited file of TPM values (normalized abundance) from PTZ- and saline-treated whole cells

source_name: DGC_novel environment_single-nuclei

growth_protocol: All animal procedures were performed in accordance with the animal guidelines at the Salk Institute for Biological Studies.

extract_protocol:
dissociation protocol: Dounce
Smart-seq2
TSO concentration: 10uM
ERCC dilution: 1:2000

tag: sequencing method

value: single-nuclei RNA-seq

value: novel environment

tag: facs sort

value: dentate granule cell


title: Quiescent IMR90 shp53_3

value: fetal lung fibroblasts

value: cotransduced with pWZL-Hygro and shp53


title: Quiescent IMR90 shp53_2


title: nm_ux_tn_F5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_tn_F2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_tn_F4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_tn_F3_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_tn_F1_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Proliferating IMR90 shp53_3


title: nm_ux_tn_E6_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt