title: 2 Day-Cort-3

city: Manchester

first: Jonathan

last: Wray

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description:
2019_Wray_2day _raw_counts.txt
2019_Wray_2day_normalised_outliers_excluded.txt

data_processing:
Basecalls performed using CASAVA 1.7
Reads were mapped to the Mus Musculus GRCm38 reference assembly (Ensembl) in RStudio using Rsubread
Counts were determined in Rstudio using featureCounts
Differential expression analysis was performed in Rstudio using the DESeq2 package
Genome_build: Mus Musculus GRCm38
Supplementary_files_format_and_content: counts

source_name: Hypothalamic arcuate nucleus

extract_protocol:
Brains were coronally cryosectioned onto RNAse free slides. Sections were fixed and rehydrated in ethanol, stained with cresyl violet, and dehydrated in a graded ethanol series. The entire hypothalamic arcuate nucleus was dissected from each sample using laser capture microdissection. RNA was extracted using an RNeasy Micro Plus Kit (Qiagen) according to manufacturer’s instructions and analyzed for RNA integrity on an Agilent 2100 Bioanalyzer using an RNA 6000 Pico Kit. All RNA that was subsequently used had RNA integrity (RIN) scores >6.5.
RNA was converted to cDNA using the Ovation RNA-seq System V2 (NuGEN). The resultant cDNA was then fragmented to an average size of ~200bp using Bioruptor Pico (Diagenode) before end repair and adaptor ligation was performed using the Ovation Rapid DR Multiplex System 9-16 (NuGEN) to allow multiplex sequencing. Prepared libraries were quantified using KAPA Library Quantification Kit (KAPA Biosystems) before sequencing in a single lane on a HiSeq4000 (Illumina; 2 day samples) or HiSeq2500 (Illumina; 4 week samples).

treatment_protocol: 2 day samples - 10 week old C57BL6/J mice were administered either corticosterone (Cort; 75µg/ml dissolved in 1% ethanol) or vehicle (1% ethanol) in the drinking water for 2 days. Mice were culled by rising CO2. Brains were immediately dissected and snap frozen on dry ice.   4 week samples - 10 week old C57BL6/J mice were administered either corticosterone (Cort; 75µg/ml dissolved in 1% ethanol) or vehicle (1% ethanol) in the drinking water for 4 weeks. After 4 weeks mice were fasted for 16 hours (6pm-10am), and refed for 24hrs. Mice were maintained on Cort or vehicle treatment throughout fast/refeed period. Mice were then culled by rising CO2. Brains were immediately dissected and snap frozen on dry ice.

tag: strain

value: Hypothalamic arcuate nucleus

value: Corticosterone (75µg/ml) in 1% ethanol

tag: treatment length

value: 2 days


title: 2 Day-Cort-4

status: Public on Apr 01 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment


title: 2 Day-Cort-1


title: 2 Day-Cort-2


title: 2 Day-Cort-5


title: 2 Day-Veh-5

value: Vehicle (1% Ethanol)


title: 2 Day-Veh-3


title: 2 Day-Veh-4


title: 2 Day-Veh-2


title: 047_GS1169_11_MHCI_IFNgamma_pos_TEM_56

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Research Center

description: X047_GS1169_11_MHCI_IFNgamma_pos_TEM_56_N707S517

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts of sequencing reads of genes for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human PBMCs were rested overnight at 37 °C and subsequently stimulated with DENV CD8 T cell peptide pool (1 μg/ml for individual peptides) for 3 h (Weiskopf et al., 2015b). IFN-gamma-producing cells were labeled using IFN-γ Secretion Assay – Detection Kit (catalog# 130-054-202, Miltenyi Biotech) according to the manufacturer’s instructions. Subsequently, PBMCs were stained with anti-human CD3, CD4, CD8, CD14, CD19, CD45RA, and CCR7 (see Supplementary Table 2 for antibody details). CD8 IFN-gamma- and IFN-gamma+ naïve (CD14-CD19-CD3+CD4-CD8+CD45RA+CCR7+), TCM (CD14-CD19-CD3+CD4-CD8+CD45RA-CCR7+), TEM (CD14-CD19-CD3+CD4-CD8+CD45RA-CCR7-), and TEMRA (CD14-CD19-CD3+CD4-CD8+CD45RA+CCR7-) cells were sorted into 8 μL of lysis buffer consisting of Triton X-100 (Sigma-Aldrich), recombinant ribonuclease inhibitor (Takara), and dNTP mix (Thermo Fisher Scientific).

extract_protocol:
For each condition, 200 cells were collected at 4 ˚C in 8 μL of lysis buffer composed by 0.2% Triton X-100, 2 U/ul of recombinant RNase inhibitor (Clontech/Takara), 5 mM dNTP mix (Life Technologies) in 0.2 ml PCR tube (Maxymum recovery, Axygen). Right after sort, tubes were vortexed at medium speed, spun for 5 minutes at >2000 g and stored at -80˚C until the completion of the whole set of samples. Purified total RNA (≈5 ng) was amplified following the Smart-seq2 protocol (Picelli et al., 2014; Rosales et al., 2018). Briefly, mRNA was captured using poly-dT oligos and directly reverse-transcribed into full-length cDNA using the described template-switching oligo (Picelli et al., 2014; Rosales et al., 2018). cDNA was amplified by PCR for 18 cycles and purified using AMPure XP magnetic bead (0.9:1 (vol:vol) ratio, Beckman Coulter).
For each sample, 1 ng of cDNA was used to prepare a standard NextEra XT sequencing library (NextEra XT DNA library prep kit and index kits; Illumina). Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR preamplification cycles, and fragment library size. Samples that failed quality controls were eliminated from downstream steps. Library that passed strict quality controls were pooled at equimolar concentration, loaded and sequenced on the Illumina Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina) mapping uniquely to mRNA reference, generating a total of about 204.3 million mapped reads (median of about 8.6 million filtered mapped reads per sample).
RNA-Seq (Microscaled (SmartSeq2) cDNA amplification; HISeq 2500 illumina, Single-end 50bp)

tag: disease group

value: Sri Lanka secondary

tag: donor id

tag: cell subset


title: 2 Day-Veh-1


title: 063_GS1178_3_Bulk_TEM_72

source_name: Cryopreserved PBMC_Bulk_TEM


title: 015_GS1149_11_MHCI_IFNgamma_pos_TEM_16

description: X015_GS1149_11_MHCI_IFNgamma_pos_TEM_16_N702S517


title: PN7I5

city: Sainte Anne de Bellevue

first: Manjurul

last: Haque

state: Quebec

address: Institute of Parasitology, Mac campus

department: Institute of Parasitology

country: Canada

institute: McGill University

data_processing:
BAM files obtained from Genome Quebec, McGill University, Canada
used SAM tools to sort the paired end BAM files by name
Htseq was used for counting of expressed transcripts
Count table was used in http://www.networkanalyst.ca for differential expression and further downstream analysis
Genome_build: mm9
Supplementary_files_format_and_content: txt format with raw counts

source_name: Postnatal day7_Infection

growth_protocol: Pregnant mice were purchased on gestation day 4 and kept in indivudual cages in 12 h dark and 12h light cycles

extract_protocol:
Commercial kit (NucleoSpin® RNA) was used to extract the total RNA
libraries were constructed by Genome Quebec, McGill University, Canada

treatment_protocol: On gestation day 5 mice were randomly assigned to two  groups  (control and infection). Infection were given on gestation day 7, 12 and 17 and post natal day 3

value: CD1 outbred

value: whole brain

tag: age

value: Postnatal day7


title: PN7I4


title: PN7I2


title: PN7I3


title: PN7C5

source_name: Postnatal day7_control


title: PN7I1


title: PN2I3

source_name: Postnatal day2_Infection

value: Postnatal day2


description: X071_GS1178_12_MHCI_IFNgamma_pos_TEMRA_80_N710S517


title: PN7C1


title: PN2I2


title: PN2C4

source_name: Postnatal day2_control


title: PN2I1


title: PN2C3


title: OE2_3891_L: 35S:KLU2, rep3

city: Potsdam

first: Alisdair

last: Fernie

address: Am Mühlenberg 1

department: Department Willmitzer

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

data_processing:
RNA-seq reads were mapped to A.thaliana reference genome (TAIR10) using STAR (version 020201).
Expression levels (in terms of FPKM, fragments per kilobase of transcript per million mapped reads) of all annotated protein-coding genes were estimated by RSEM (version 1.2.22).
Differentially expressed genes across the four developmental stages were identified by analysis of variance (ANOVA) based on FPKM values. Resulting p-values were adjusted for multiple comparisons by false discovery rate (FDR) (Benjamini and Hochberg 1995).
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown in a climatized greenhouse under short day conditions(8 h light, 16 h dark).

extract_protocol:
RNAs were isolated by the Total RNA was extracted using by Zymo-Spin™ IIC RNA column (Zymo Research Europe GmbH) according to manufacturer.
500 ng was used as input for polyA enrichment followed by fragmentation and library preparation as recommended by the vendor (NEBNext® Ultra™ II Directional RNA Library Prep Kit Illumina).

tag: ecotype

tag: genotype/variation

value: klu overexpression line2

value: leaf

tag: time

value: 35 days


title: OE2_3891_J: 35S:KLU2, rep1


title: OE2_3891_K: 35S:KLU2, rep2


title: PN2C1


title: OE1_3891_I: 35S:KLU1, rep3

value: klu overexpression line1


title: PN2C2


title: IRE1 KO NK at day 7 replicate 3

city: New York

first: Yichi

last: Xu

state: NY

address: 1275 York Avenue

institute: MSKCC

description: Replicates are paired as WT and KO

data_processing:
Sequence data from Illumina's HiSeq4000 sequencer were 'de-multiplexed' to generate FASTQ files for each sample with Illumina's CASAVA pipeline (version 1.8.2).
The reads that passed Illumina's quality and purity filter (> 90%) were aligned to the mouse genome (mm9 build) with tophat2 with default parameters.
The resulting SAM alignment files were then converted to the BAM file format, then were sorted and indexed with SAMtools (version 0.1.14).
The HTSeq was used for summarization of the aligned sequence reads into counts.
Differential gene expression was analyzed with the DESeq2. Transcripts with adjusted P value < 0.01 were considered differentially expressed between genotypes (wild-type and IRE1 KO) and infection times (day 0, 1.5, 7).
Genome_build: mm9
Supplementary_files_format_and_content: Gene count number was generated for each sample by HTseq2 as supplementary files.

source_name: NK cells

growth_protocol: Mice were bred at Dana-Farber Cancer Institute and Weill Cornell Medical Center in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC).Host C57BL/6 × B6.SJL animals (CD45.1+CD45.2+) were lethally irradiated with 900 grays of radiation and reconstituted with a 1:1 mixture of bone marrow cells from B6.SJL WT (CD45.1+) and knockout or transgenic donor (CD45.2+) mice, co-injected with anti-NK1.1 (clone PK136) to deplete any residual donor or host mature NK cells. CD45.1+CD45.2+ host NK cells were excluded from all analyses.

extract_protocol:
Total RNA from sorting-purified Ly49H+ WT or IRE1NK NK cells was extracted with the RNeasy RNA purification micro kit (Qiagen) according to the manufacturer’s instructions.
poly(A)+ RNA-seq libraries (pair-end 75) were prepared with an Illumina TruSeq RNA Sample Preparation Kit V2 according to the manufacturer's instructions (Illumina).

treatment_protocol: Mice were infected with 7.5 × 103  PFU of MCMV by i.p. injection and spleens were harvested at day0, 1.5 and 7 after infection.

tag: genotype

value: IRE1 KO

tag: sample time

value: day 7

tag: virus

value: yes


title: IRE1 KO NK at day 7 replicate 2

description: Replicates are paired as WT and KO


title: IRE1 KO NK at day 1.5 replicate 3

description: Replicates are paired as WT and KO

value: day 1.5


title: OE1_3891_H: 35S:KLU1, rep2


title: OE1_3891_G: 35S:KLU1, rep1


title: IRE1 KO NK at day 7 replicate 1

description: Replicates are paired as WT and KO


title: MT_3891_F: klu, rep3

value: klu mutant


title: PN7C3


title: Col0_3891_B: Col-0, rep2

value: wild-type


title: Col0_3891_C: Col-0, rep3


title: IRE1 KO NK at day 1.5 replicate 1

description: Replicates are paired as WT and KO


title: IRE1 KO NK at day 1.5 replicate 2

description: Replicates are paired as WT and KO


title: IRE1 KO NK at day 0 replicate 3

description: Replicates are paired as WT and KO

value: day 0

value: no


title: MT_3891_D: klu, rep1


title: PN7C4


title: MT_3891_E: klu, rep2


title: IRE1 KO NK at day 0 replicate 1

description: Replicates are paired as WT and KO


title: WT NK at day 7 replicate 3

description: Replicates are paired as WT and KO


title: PN7C2


title: Col0_3891_A: Col-0, rep1


title: WT NK at day 7 replicate 1

description: Replicates are paired as WT and KO


title: IRE1 KO NK at day 0 replicate 2

description: Replicates are paired as WT and KO


title: WT NK at day 1.5 replicate 3

description: Replicates are paired as WT and KO


title: WT NK at day 1.5 replicate 1

description: Replicates are paired as WT and KO


title: WT NK at day 0 replicate 3

description: Replicates are paired as WT and KO


title: WT NK at day 0 replicate 1

description: Replicates are paired as WT and KO


title: WT NK at day 0 replicate 2

description: Replicates are paired as WT and KO


title: FedSSS-GFPp-ATAC.rep1.R1

city: San Francisco

first: Walter

last: Eckalbar

state: CA

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

library_source: genomic

data_processing:
Fastq files were generated with Casava 1.8
RNA-seq reads were aligned with STAR (version 2.5.2b), ChIP-seq reads aligned with Bowtie (version 1.2) and ATAC-seq reads aligned with bowtie2 (v2.2.6)
Duplicate reads were removed using Picardtools MarkDuplicates
ChIP-seq and ATAC-seq peak calling: Peaks were called for each replicate and for the merged repicates using Macs2 (ChIP-seq parameters:  -f BAM -g mm --keep-dup 1 --bw 500 -n $MACSOUT --nomodel --extsize 300 --slocal 2000 --llocal 20000 -p 0.001 --broad. ATAC-seq parameters:  -f BAMPE -g mm --keep-dup 1 --bw 1000 -m 2 100 -n $MACSOUT.pe.bt2.p0.01.forIDR -p 1e-2) . Reporducible peaks were then identified with the ENCODE IDR pipeline (version 2.0.2, parameters :  --samples $rep1.broadPeak $rep2.broadPeak --peak-list $pooled.broadPeak --plot  --idr-threshold 0.1 --input-file-type broadPeak --output-file $out.broadPeak). Peaks where then merged across all treatments but then paritioned. ChIP-seq was partitioned by each each condition, while ATAC-seq was partitioned by the merged set of GFP positive or GFP negative peaks. For both sets, partitioned peaks <200bp long were removed.
RNA-seq: expression measures for each gene were counted over intronic and exonic reads using HT-seq (version 0.6.0). ChIP-seq and ATAC-seq: Read counts were obtained for each merged peak using HT-seq (merging and partitioning were done with BedOps version 2.4.20).
All differential expression (RNA-seq) or enrichment (ChIP and ATAC-seq) tests were carried out using DESeq2 (version 1.16.1).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files for ChIP-seq and ATAC-seq peaks are described above. Genomic coverage graph files were produced by first deduplicating the bam files, creating genomic coverage bedGraph files over100bp windows of the mm9 genome, then transforming the coverage by setting the median genomic coverage to 0, and the 99.9 percentile coverage to 1 (Ie coverage value = [x-median]/[99.9th percentile - median]).
Processed data file for RNA-Seq samples: All_genes.Leptin_RNA.xlsx

molecule: genomic DNA

source_name: Mus Musculus hypothalamus

extract_protocol:
Hypothalami were pooled and homogenized by douncing 30 times in 1 mL lysis buffer (15 mM Tris-HCL (pH 7.5), 0.1 mM EGTA, 15 mM NaCl, 60 mM KCl, 5 mM MgCl2, 300 mM sucrose, 1 mM DTT, 0.1 mM PMSF, 0.15 mM spermine, 0.5 mM spermidine, Complete protease inhibitor (Roche) and 20mM Na-butyrate (Sigma), RiboLock RNase inhibitor) using a tissue grinder type B (Kimble Chase). The cell lysate was centrifuged at 500 g for 5 minutes at 4ºC. Pellet was re-suspended in 1 mL lysis buffer, and equal volume of nuclei isolation buffer (lysis buffer supplemented with NP40 at 0.4%) was added. The lysate was incubated on ice for 5 minutes, followed by centrifugation at 7000 g for 5 minutes at 4ºC. Cell nuclei pellet was re-suspended in 250 uL FACS buffer (0.15 mM spermine, 0.5 mM spermidine, Complete protease inhibitor (Roche) and 20mM Na-butyrate (Sigma), RiboLock RNase inhibitor in PBS). FACS was performed with FACS Aria II (BD Biosciences) equipped with 70 um nozzle.  RNA-seq: 50,000-70,000 GFP positive and negative nuclei were sorted directly into buffer RLT supplemented with beta-mercaptoethanol. RNA was extracted using RNeasy mini kit (Qiagen) following the manufacture’s protocol. ChIP-seq: 300,000-540,000 GFP positive and negative nuclei were sorted into PBS. After FACS, FACS buffer was added for a final volume of 10 mL. 50 uL of 1M CaCl2 and 30 uL of 1M MgAc2 was added and incubated on ice for 5 minutes, followed by centrifugation at 1800 g for 15 minutes at 4ºC. The supernatant was removed and FACS buffer supplemented with 1% formaldehyde was gently added onto the pellet to crosslink chromatin. The crosslinked pellet was then washed with FACS buffer supplemented with 125 mM glycine without disturbing the pellet. The crosslinked chromatin was lysed in 130 uL of Buffer B (LowCell# ChIP kit, diagenode) supplemented with Complete protease inhibitor (Roche) and 20mM Na-butyrate (Sigma). The lysed chromatin was sheared using a Covaris S2 sonicator to obtain on average 250bp size fragments. 870 uL of Buffer A (LowCell# ChIP kit, diagenode) supplemented with complete protease inhibitor (Roche) and 20mM Na-butyrate (Sigma) was added. 20 uL of the chromatin solution was saved as an input control. A mixture of 40 uL of Dynabeads protein A and 40 uL of Dynabeads protein G was washed twice with Buffer A (LowCell# ChIP kit, diagenode) and resuspended in 800 uL of Buffer A. 10 ug of H3K27ac antibody (ab4729, Abcam) was added to the beads, and gently agitated at 4ºC for 2 hours. The beads-antibody complex was precipitated with a magnet, and the supernatant was removed. 800 uL of shared chromatin was added to the beads-antibody complex and rotated at 4ºC overnight. The immobilized chromatin was then washed with Buffer A three times and Buffer C once, and eluted in 100 uL of IPure elution buffer (IPure kit, diagenode). In addition, 80 uL of IPure elution buffer was added to 20 uL input. DNA was purified using the IPure kit according to manufacture’s protocol. ATAC-seq: After FACS, 49 uL of sorted nuclei (11,200-18,000 nuclei) were mixed with 50 uL Tagment DNA buffer (Nextera DNA sample preparation kit, Illumina) and 1 uL of Tagment DNA enzyme (Nextera DNA sample preparation kit, Illumina), followed by incubation at 37ºC for 30 minutes. Tagmented DNA was purified with MinElute reaction cleanup kit (Qiagen).
RNA-seq: RNA was quantified with Qubit RNA HS assay kit. cDNA was amplified using Ovation V2 kit (NuGEN) and sequencing libraries were generated using NexteraXT kit (Illumina). ChIP-seq: Sequencing libraries were generated using Accel-NGS 2S Plus DNA library kit (Swift Biosciences). DNA was quantified with Qubit DNA HS assay kit and Bioanalyzer (Agilent) using the DNA High Sensitivity kit. ATAC-seq: After FACS, 49 uL of sorted nuclei (11,200-18,000 nuclei) were mixed with 50 uL Tagment DNA buffer (Nextera DNA sample preparation kit, Illumina) and 1 uL of Tagment DNA enzyme (Nextera DNA sample preparation kit, Illumina), followed by incubation at 37ºC for 30 minutes. Tagmented DNA was purified with MinElute reaction cleanup kit (Qiagen). The DNA was size-selected using SPRIselect (Beckman Coulter) according to manufacture’s double size selection protocol. DNA:SPRIselect ratio was 5:3 for right side, and 2:3 for left side selection.

treatment_protocol: Mice were fed ad libitum Picolab mouse diet 20, 5058 containing 20% protein, 9% fat, 4% fiber for whole study. Calories provided by: protein 23.210%, fat (ether extract) 21.559% and carbohydrates 55.231% and were grown for at least two months. LepRcre/+; SUN1-sfGFP/+ mice were then randomly chosen (see Supplementary Table 5 for number of mice and genders used) for the following treatments: 1) Fed ad libitum for 36 hours; 2) Fasted for 36 hours and injected with saline three times (12, 24, and 34 hours after the beginning of fasting); 3) Fasted for 36 hours and injected with leptin (5 mg/kg body weight) three times (12, 24, and 34 hours after the beginning of fasting); 4) Fasted for 36 hours and injected with leptin (5 mg/kg body weight) (Los Angeles Biomedical Research Institute) at 34 hours. The mice were euthanized and the hypothalami were dissected. All animal work was approved by the UCSF Institutional Animal Care and Use Committee.

tag: sort

value: LepRb -  possitive

value: hypothalamus

value: Fed - Saline


title: FedSSS-GFPp-ATAC.rep2.R1


title: WT NK at day 1.5 replicate 2

description: Replicates are paired as WT and KO


title: FedSSS-GFPn-ATAC-inp.rep1.R1

value: LepRb -  negative


title: FasSSS-GFPp-ATAC-inp.rep1.R1

value: Fasted - Saline


title: FedSSS-GFPn-ATAC.rep1.R1


title: WT NK at day 7 replicate 2

description: Replicates are paired as WT and KO


title: FasSSS-GFPn-ATAC-inp.rep1.R1


title: FasSSS-GFPp-ATAC.rep2.R1


title: FedSSS-GFPn-ATAC.rep2.R1


title: FasSSS-GFPp-ATAC.rep1.R1


title: FasSSS-GFPn-ATAC.rep1.R1


title: FasSSS-GFPn-ATAC.rep2.R1


title: 4 Week-Cort-5

description:
2019_Wray_4week _raw_counts.txt
2019_Wray_4week_normalised_outliers_excluded.txt

value: Hypothalamic arcuate nucleus

value: Corticosterone (75µg/ml) in 1% ethanol

value: 4 Weeks


title: 4 Week-Cort-4


title: 4 Week-Cort-3


title: FasSSL-GFPn-ATAC.rep2.R1

value: Fasted - 2 hours Leptin


title: FedSSS-GFPp-ATAC-inp.rep1.R1


title: FasSSL-GFPn-ATAC.rep1.R1


title: FasSSL-GFPp-ATAC.rep1.R1


title: 4 Week-Cort-2


title: 4 Week-Veh-5

value: Vehicle (1% Ethanol)


title: 4 Week-Cort-1


title: 4 Week-Veh-4


title: FasLLL-GFPp-ATAC.rep2.R1

value: Fasted - 24 hours Leptin


title: FasSSL-GFPp-ATAC.rep2.R1


title: FasLLL-GFPn-ATAC.rep2.R1


title: FasLLL-GFPp-ATAC.rep1.R1


title: 4 Week-Veh-3


title: FedSSS.GFPp.ChIP.K27ac.rep2

tag: chip antibody


title: 4 Week-Veh-1


title: 4 Week-Veh-2


title: FasLLL-GFPn-ATAC.rep1.R1


title: FedSSS.GFPn.ChIP.K27ac.rep2


title: FedSSS.GFPp.ChIP.Inp.rep1


title: FedSSS.GFPp.ChIP.Inp.rep2


title: Lung adenocarcinoma Omomyc biological replica 2

type: RNA

city: Barcelona

first: Marie-Eve

last: Beaulieu

state: Catalunya

address: Natzaret 115-117

country: Spain

institute: Peptomyc

hyb_protocol: Total RNA was linearly amplified using WT Plus (Affymetrix). The resulting ssDNA was used to hybridize Affimetrix microarrays. Hybridization data was acquired using the Affimetrix GeneChip/GeneTitan platforms. Transcriptomes were determined on a genome wide Mouse Gene 2.0 ST Array (Affimetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Partek Genomic Suite followed by GSEA 3.0 software from Broad Institute.

label: Biotin

source_name: Lung adenocarcinoma from KRasLSL-G12D/+ mice treated with Omomyc

label_protocol: Labeling of samples was carried out according to the manufacturer’s standard protocol

growth_protocol: KRasLSL-G12D/+ mice were infected with Adeno-Cre to induce Kras-driven lung adenocarcinomas.

extract_protocol: 50-100 mg of tumor tissue was homogenized with a pestle in TRIzol. Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: KRasLSL-G12D/+ mice were treated with Omomyc by intranasal administration sixteen weeks after Adeno-Cre infection. Mice (n=2 for vehicle treated and n=3 for Omomyc treated group) were euthanized three days post-treatment and lung tumors were excised and flash frozen at -80ºC until processing.

value: Lung adenocarcinoma

value: Omomyc

tag: strain/genotype


title: Lung adenocarcinoma Omomyc biological replica 1


title: Lung adenocarcinoma Omomyc biological replica 3


title: Lung adenocarcinoma Vehicle biological replica 2

source_name: Lung adenocarcinoma from KRasLSL-G12D/+ mice treated with Vehicle

value: vehicle


title: Lung adenocarcinoma Vehicle biological replica 1


title: Active Phase_Sedentary_ZT12_rep6

city: College Station

first: Shogo

last: Sato

state: Texas

address: 3258 TAMU, Biological Science Building West (BSBW) 309

department: Biology

institute: Texas A&M University

description: Gene expression data from mouse seletal muscle at indicated ZT

data_processing:
FastQC (v0.11.5) was applied for quality control.
RNA-seq reads were subjected to trimming of adapters and low quality flanking ends using Trim_Galore (v0.4.3 using Cutadapt v1.16).
Pre-processed reads were mapped to mm10 using STAR aligner (v2.5.3a) and gene coverages were computed with featureCounts (v1.5.2) and the Gencode annotation (GRCm38).
The list of RNAs was filtered for those with a read coverage larger than 2 CPM (counts per million) in at least 34 samples, and 11461 of the total 52636 annotated RNAs survived this inclusion criterion.
edgeR (v3.2.23) was used for examinning differential expression of replicated count data.
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene counts in units of count per million (CPM)

source_name: Gastrocnemius muscle

growth_protocol: Mice were reared at 22±1oC with 12 hr light/dark cycle (light on at 6AM (ZT0) and light off at  6PM (ZT12)) and fed a standard rodent laboratory diet (#1310, Altromin, Germany) ad libitum.

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, #80224). RNA was checked for quality using the Bioanalyzer instrument (Agilent Technologies, Santa Clara,  CA) and subject to the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol  (Illumina, San Diego, CA).
Libraries were subjected to 100-bp paired end sequencing on HiSeq 2500 (Illumina) at the Beijing Genomics Institute (BGI, Hong Kong).

treatment_protocol: At 10-11 weeks of age, the mice were divided into two different groups of exercise or sham-exercise  treatment either during the early rest phase group (ZT3) or the early active phase  group (ZT15). Exercised mice in the early rest phase group were subjected to a single-bout of  acute exercise for 1 hour at ZT3, whereas exercised mice in the early active phase group were  subjected to the exercise for 1 hour at ZT15. Sedentary control mice for corresponding  exercised mice at the different daily times were placed on a stationary treadmill for 1 hour  (sham-exercise). Mice were returned into their home cages and allowed free feeding and  drinking after the exercise and sham-exercise treatment. At 0, 4, 8, 12,16 and 20 hours  following exercise or sham-exercise treatment at each early rest and active phase, mice were  sacrificed under isoflurane anesthesia and the gastrocnemius muscles were isolated. The tissues were immediately snap frozen in liquid nitrogen and stored at -  80oC for subsequent use.

tag: strain

value: Gastrocnemius muscle

tag: gender

value: Male

value: Sedentary

tag: phase

value: Active phase (ZT15)

tag: zt


title: FedSSS.GFPn.ChIP.Inp.rep1

tag: tissue

value: hypothalamus

tag: treatment


title: Active Phase_Exercise_ZT12_rep6

value: Exercise


title: Active Phase_Sedentary_ZT12_rep5


title: FedSSS.GFPn.ChIP.Inp.rep2

value: LepRb -  negative

value: Fed - Saline


title: FedSSS.GFPn.ChIP.K27ac.rep1


title: Active Phase_Sedentary_ZT8_rep6


title: Active Phase_Sedentary_ZT8_rep5


title: Active Phase_Exercise_ZT8_rep5


title: FasSSS.GFPp.ChIP.K27ac.rep2

value: LepRb -  possitive

value: Fasted - Saline


title: FedSSS.GFPp.ChIP.K27ac.rep1


title: FasSSS.GFPp.ChIP.Inp.rep2


title: FasSSS.GFPp.ChIP.Inp.rep1


title: FasSSS.GFPp.ChIP.K27ac.rep1


title: Active Phase_Sedentary_ZT4_rep6


title: Active Phase_Sedentary_ZT4_rep5


title: FasSSS.GFPn.ChIP.K27ac.rep1


title: Active Phase_Exercise_ZT4_rep5


title: FasSSS.GFPn.ChIP.K27ac.rep2


title: Active Phase_Exercise_ZT12_rep5


title: FasSSS.GFPn.ChIP.Inp.rep1


title: FasSSS.GFPn.ChIP.Inp.rep2


title: FasSSL.GFPp.ChIP.K27ac.rep2


title: FasSSL.GFPp.ChIP.K27ac.rep1


title: Active Phase_Exercise_ZT0_rep6


title: Active Phase_Sedentary_ZT0_rep5


title: Active Phase_Sedentary_ZT0_rep6


title: FasSSL.GFPp.ChIP.Inp.rep2


title: FasSSL.GFPp.ChIP.Inp.rep1


title: FasSSL.GFPn.ChIP.K27ac.rep2


title: FasSSL.GFPn.ChIP.K27ac.rep1


title: Active Phase_Exercise_ZT4_rep6


title: Active Phase_Exercise_ZT20_rep5


title: FasSSL.GFPn.ChIP.Inp.rep2


title: Active Phase_Exercise_ZT20_rep6


title: Active Phase_Sedentary_ZT20_rep5


title: Active Phase_Sedentary_ZT20_rep6


title: Active Phase_Exercise_ZT16_rep6


title: Active Phase_Sedentary_ZT16_rep6


title: FasLLL.GFPp.ChIP.K27ac.rep1


title: FasLLL.GFPp.ChIP.K27ac.rep2


title: Active Phase_Sedentary_ZT16_rep5


title: FasSSL.GFPn.ChIP.Inp.rep1


title: Active Phase_Exercise_ZT0_rep5


title: FasLLL.GFPp.ChIP.Inp.rep2


title: Rest Phase_Sedentary_ZT0_rep6

value: Rest phase (ZT3)


title: Rest Phase_Exercise_ZT0_rep6


title: FasLLL.GFPn.ChIP.K27ac.rep2


title: Rest Phase_Sedentary_ZT0_rep5


title: FasLLL.GFPp.ChIP.Inp.rep1


title: Rest Phase_Exercise_ZT0_rep5


title: FasLLL.GFPn.ChIP.K27ac.rep1


title: Rest Phase_Sedentary_ZT20_rep6


title: FasLLL.GFPn.ChIP.Inp.rep2


title: FasLLL.GFPn.ChIP.Inp.rep1


title: Rest Phase_Exercise_ZT20_rep6


title: FedSSSGFPp_RNA_rep3


title: FedSSSGFPp_RNA_rep2


title: Rest Phase_Sedentary_ZT20_rep5


title: FedSSSGFPp_RNA_rep1


title: Rest Phase_Exercise_ZT20_rep5


title: FedSSSGFPn_RNA_rep2


title: Rest Phase_Sedentary_ZT16_rep6


title: Rest Phase_Exercise_ZT16_rep6


title: FedSSSGFPn_RNA_rep3


title: FedSSSGFPn_RNA_rep1


title: Rest Phase_Sedentary_ZT16_rep5


title: Rest Phase_Sedentary_ZT12_rep6


title: FasSSSGFPp_RNA_rep2


title: FasSSSGFPp_RNA_rep3


title: Rest Phase_Exercise_ZT12_rep6


title: Active Phase_Exercise_ZT16_rep5


title: FasSSSGFPp_RNA_rep1


title: Rest Phase_Sedentary_ZT12_rep5


title: Rest Phase_Exercise_ZT12_rep5


title: FasSSSGFPn_RNA_rep2


title: FasSSSGFPn_RNA_rep3


title: FasSSLGFPp_RNA_rep3

value: Fasted - 2 hours Leptin


title: FasSSSGFPn_RNA_rep1


title: FasSSLGFPp_RNA_rep2


title: Rest Phase_Sedentary_ZT8_rep5


title: Rest Phase_Sedentary_ZT8_rep6


title: Rest Phase_Exercise_ZT8_rep5


title: FasSSLGFPp_RNA_rep1


title: FasSSLGFPn_RNA_rep3


title: Rest Phase_Exercise_ZT4_rep6


title: Rest Phase_Sedentary_ZT4_rep5


title: FasSSLGFPn_RNA_rep2


title: FasSSLGFPn_RNA_rep1


title: Rest Phase_Exercise_ZT16_rep5


title: FasLLLGFPp_RNA_rep4


title: FasLLLGFPp_RNA_rep3


title: Active Phase_Sedentary_ZT12_rep4


title: Active Phase_Sedentary_ZT12_rep3


title: FasLLLGFPp_RNA_rep2


title: FasLLLGFPn_RNA_rep4


title: Active Phase_Exercise_ZT12_rep3


title: Active Phase_Exercise_ZT12_rep4


title: FasLLLGFPn_RNA_rep2


title: Active Phase_Exercise_ZT8_rep4


title: Rest Phase_Exercise_ZT8_rep6


title: Active Phase_Sedentary_ZT8_rep3


title: Endometrial cells_Clinical_2683

city: Dunsany

first: Kieran

middle: Gerard

last: Meade

state: Co. Meath

address: Grange

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

data_processing:
Data was quality and adapter trimmed using the BBDuk java package to trim Illumina adapter sequences and any low quality bases (Phred score <20) from the 3’ end of sequence read pairs. Reads were aligned to the bovine genome UMD3.1 using the Spliced Transcripts Alignment to a Reference (STAR) aligner
Read counts overlapping all protein coding genes in the UMD3.1 Ensembl (v.86) annotation were estimated using featureCounts
Remaining gene counts were normalized  and differential gene expression was determined using the R (version 3.3.2) Bioconductor package EdgeR (version 3.18.0)
Genome_build: UMD3.1
Supplementary_files_format_and_content: Excel Spreadsheet of gene expression

organism: Bos taurus

source_name: Endometrial cells

extract_protocol:
RNA was extracted from endometrial cytobrushes acquired at 7 days postpartum
Libraries were prepared according to Illumina's instructions acccompanying the Illumina TruSeq Stranded mRNA Library Prep Kit

tag: health status

value: Clinical

tag: cell type

value: Endometrial cells


title: Endometrial cells_Clinical_2672


title: Active Phase_Exercise_ZT8_rep3

tag: age


title: Active Phase_Sedentary_ZT4_rep4


title: Endometrial cells_Healthy_2570

value: Healthy


title: Endometrial cells_Clinical_2622


title: Endometrial cells_Clinical_2520


title: Active Phase_Exercise_ZT4_rep4


title: Rest Phase_Sedentary_ZT4_rep6


title: Active Phase_Sedentary_ZT4_rep3


title: Rest Phase_Exercise_ZT4_rep5


title: Endometrial cells_Sub-clinical_2421

value: Sub-clinical


title: Active Phase_Exercise_ZT4_rep3


title: Endometrial cells_Sub-clinical_2382


title: Active Phase_Sedentary_ZT0_rep4


title: Endometrial cells_Healthy_2392


title: Active Phase_Exercise_ZT0_rep4


title: Endometrial cells_Healthy_2224


title: Endometrial cells_Clinical_2202


title: Endometrial cells_Clinical_2188


title: Active Phase_Exercise_ZT20_rep4


title: Active Phase_Sedentary_ZT0_rep3


title: Endometrial cells_Sub-clinical_2178


title: Endometrial cells_Sub-clinical_2167


title: Endometrial cells_Sub-clinical_2184


title: Active Phase_Sedentary_ZT20_rep4


title: Active Phase_Sedentary_ZT16_rep4


title: Active Phase_Sedentary_ZT16_rep3


title: Endometrial cells_Sub-clinical_2064


title: Endometrial cells_Healthy_2053


title: Endometrial cells_Sub-clinical_2039


title: Active Phase_Exercise_ZT16_rep3


title: Endometrial cells_Healthy_2006


title: Endometrial cells_Sub-clinical_1944


title: Rest Phase_Sedentary_ZT0_rep3


title: Rest Phase_Exercise_ZT0_rep4


title: Rest Phase_Exercise_ZT0_rep3


title: Rest Phase_Sedentary_ZT20_rep4


title: Rest Phase_Exercise_ZT20_rep4


title: Endometrial cells_Clinical_1829


title: Endometrial cells_Healthy_1831


title: Active Phase_Sedentary_ZT20_rep3


title: Endometrial cells_Sub-clinical_1378


title: Endometrial cells_Healthy_1340


title: Rest Phase_Exercise_ZT16_rep4


title: Endometrial cells_Clinical_2161


title: Active Phase_Exercise_ZT16_rep4


title: Rest Phase_Sedentary_ZT16_rep4


title: Rest Phase_Exercise_ZT20_rep3


title: Rest Phase_Sedentary_ZT0_rep4


title: Endometrial cells_Clinical_1194


title: Endometrial cells_Sub-clinical_1183


title: Endometrial cells_Clinical_1239


title: Rest Phase_Exercise_ZT16_rep3


title: Rest Phase_Sedentary_ZT12_rep4


title: Rest Phase_Sedentary_ZT16_rep3


title: Endometrial cells_Healthy_1890


title: RTG3_del_mut_Myriocin_Rep2

city: Würzburg

first: Valentina

last: del Olmo Toledo

state: Bayern

address: Josef-Schneider-Str. 2/D15

institute: Institute of Molecular Infection Biology

description: processed data file:  rtg3_vs_WT_in_myriocin_genes.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. albicans Build 21 transcriptome using STAR v2.5.3a with parameters --runThreadN 3 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Raw read counts per reference feature were calculated using HTSeq v0.7.2
Raw read counts were normalized and analysed for differentially expressed genes using DESeq2 v1.14.1
Genome_build: Candida albicans Build 21
Supplementary_files_format_and_content: Tab-delimeted (.count) text files include raw read counts for each sample. Tab-delimited (.txt) text files contain the mean of normalized counts, log2 fold change, p-value and -log10(p-value) for each replicate pair after differential gene expression analysis sample

organism: Candida albicans

source_name: yeast cell

growth_protocol: Wild-type and rtg3 deletion mutant strains were grown in YPD medium at 37°C for 2 hours in the presence or absence of either caffeine (15mM) or myriocin (3µg/ml)

extract_protocol:
Total RNA was extracted using RiboPure(TM) RNA purification kit for yeast (Ambion, Life Technologies)
Library construction was carried out by GATC Biotech (Konstanz, Germany). Briefly, the protocol included poly(A)+ RNA selection, mRNA  fragmentation, random primer cDNA synthesis, adaptor ligation and Illumina(HiSeq2500) sequencing

value: rtg3 deletion mutant

tag: drug addition

value: Myriocin


title: Rest Phase_Exercise_ZT12_rep4

value: Gastrocnemius muscle

value: Male


title: Rest Phase_Exercise_ZT12_rep3


title: RTG3_del_mut_Myriocin_Rep1


title: Rest Phase_Sedentary_ZT8_rep4

value: Sedentary


title: RTG3_del_mut_Caffeine_Rep2

description: processed data file: rtg3_vs_WT_in_caffeine_genes.txt

value: Caffeine


title: Active Phase_Exercise_ZT8_rep6

value: Exercise

value: Active phase (ZT15)


title: Rest Phase_Sedentary_ZT20_rep3


title: Endometrial cells_Healthy_1570


title: RTG3_del_mut_Caffeine_Rep1


title: Rest Phase_Sedentary_ZT8_rep3


title: RTG3_del_mut_YPD_Rep2

description: processed data file:  rtg3_vs_WT_in_YPD_genes.txt


title: Rest Phase_Exercise_ZT8_rep3


title: RTG3_del_mut_YPD_Rep1


title: WT_Myriocin_Rep2

description: processed data file:  WT_myriocin_genes.txt

value: wildtype


title: WT_Myriocin_Rep1


title: Endometrial cells_Healthy_1066


title: WT_Caffeine_Rep2

description: processed data file:  WT_caffeine_genes.txt


title: Rest Phase_Exercise_ZT4_rep3


title: Rest Phase_Exercise_ZT4_rep4


title: Active Phase_Sedentary_ZT12_rep2


title: Rest Phase_Sedentary_ZT4_rep4


title: WT_Caffeine_Rep1


title: Active Phase_Exercise_ZT12_rep2


title: WT_YPD_Rep2


title: WT_YPD_Rep1


title: Active Phase_Exercise_ZT12_rep1


title: Rest Phase_Exercise_ZT8_rep4


title: Strain McFY [GLN4 tet-off] sample C, untreated by doxycycline

city: Aberdeen

first: Ian

last: Stansfield

address: Foresterhill

department: Institute of Medical Sciences

institute: University of Aberdeen

data_processing:
Base calling software RTA v 2.4.11
Concatenate: component fastq files were concatenated in Galaxy using the Concatenate function (tool = cat (GNU coreutils) 8.22) using database key sacCer3
Fastq Groomer was used with 'Sanger & Illumina 1.8+' as input settings, and 'Sanger' as output format
The Galaxy Trim tool was used to clip sequences by removing  nucleotides 1-12, and all nucleotides beyond nt 70, after which read quality began to degrade for some samples
Tophat was used with settings TopHat v1.4.0 / tophat -p 6  -a 8 -m 0 -i 70 -I 5000 -g 40 --library-type fr-unstranded --no-novel-indels --coverage search --min-coverage-intron 50 --max-coverage-intron 5000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --segment
Cufflinks within Galaxy was used with the following switch settings; max intron length =5000, Min Isoform Fraction = 0.05, Pre MRNA Fraction  =0.05, Perform quartile normalization=no, Perform Bias Correction=No, Use multi-read correct = Yes, Use effective length correction=Yes
Cuffdiff within Galaxy was used with the following settings; Library normalization method = geometric; Dispersion estimation method = pooled; a alse Discovery Rate of 0.05; a Min Alignment Count of 10; multiread correct = false; no bias correction; no length correction;
Genome_build: R64, synonym Saccer3, https://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/
Supplementary_files_format_and_content: transcript_FPKM, transcript_differential_expression

organism: Saccharomyces cerevisiae

source_name: baker's yeast liquid culture

growth_protocol: Cultures were grown at 30 degrees C, 200 rpm in liquid culture in 100 ml volumes in 250 ml conical flasks in YEPD complete medium

extract_protocol:
Total RNA was extracted from the cultures using a Nucleospin RNA kit (Macherey-Nagel)
Libraries were prepared with Illumina TruSeq stranded mRNA using 1ug total RNA input and TruSeq RNA dual indexes according to the manufacturer’s instructions (kit type RSS-122-2103)

treatment_protocol: Cultures were treated with either 1 µg/ml doxycycline, or left untreated as indicated in Sample data

value: MAT{alpha} his3D1 leu2D0 lys2D0 ura3D0 PGLN4::KanMX4-tTA-tetO7

value: 0 µg/ml doxycycline


title: Strain McFY [GLN4 tet-off] sample C, treated by doxycycline, 1 µg/ml

value: 1 µg/ml doxycycline


title: Strain McFY [GLN4 tet-off] sample A, treated by doxycycline, 1 µg/ml


title: Strain McFY [GLN4 tet-off] sample B, treated by doxycycline, 1 µg/ml


title: Active Phase_Sedentary_ZT8_rep2


title: Active Phase_Exercise_ZT8_rep1


title: Rest Phase_Sedentary_ZT4_rep3

value: Rest phase (ZT3)


title: Strain BY4742 wild-type reference sample C, treated by doxycycline, 1 µg/ml

value: MAT{alpha} his3D1 leu2D0 lys2D0 ura3D0


title: Active Phase_Sedentary_ZT4_rep2


title: Strain McFY [GLN4 tet-off] sample A, untreated by doxycycline


title: Strain McFY [GLN4 tet-off] sample B, untreated by doxycycline


title: Strain BY4742 wild-type reference sample B, treated by doxycycline, 1 µg/ml


title: Active Phase_Sedentary_ZT4_rep1


title: Active Phase_Exercise_ZT4_rep2


title: Strain BY4742 wild-type reference sample A, treated by doxycycline, 1 µg/ml


title: Strain BY4742 wild-type reference sample B, untreated by doxycycline


title: Strain BY4742 wild-type reference sample C, untreated by doxycycline


title: Active Phase_Sedentary_ZT12_rep1


title: Strain BY4742 wild-type reference sample A, untreated by doxycycline


title: Active Phase_Exercise_ZT4_rep1


title: Active Phase_Sedentary_ZT0_rep2


title: Active Phase_Exercise_ZT0_rep2


title: Active Phase_Exercise_ZT0_rep1


title: WT_Diazaborine_45min_repA

city: Boston

first: Blake

middle: W.

last: Tye

state: MA

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

description:
rRNA-depleted total cellular RNA
WT_DMSO_Diazaborine_45min_DESeq.txt

data_processing:
Adapter sequence removed by Cutadapt, minimum length 18
Quality filtered with PRINSEQ, minimum quality 20
Alignment with TopHat v2.1.0, segment length 25, mismatches 2
Merge the BAM files from each of the four sequencing lanes with samtools merge
Number of reads per transcript with HTSeq count using ENSEMBL release 91 of S. cerevisiae for gtf
Quantification using DESeq2 for auxin experiments (two untreated versus two treated replicates) or by calculating RPKM for +/- diamide experiment
Genome_build: Saccharomyces cerevisiae assembly R64 (UCSC: sacCer3)
Supplementary_files_format_and_content: Quanitified data are presented as csv or txt files containing the output of DESeq2 or RPKM measurements used for log2 fold change measurements

source_name: Whole yeast cells

growth_protocol: Each strain was grown to mid-log in YPD. Replicates were grown on separate days.

extract_protocol:
TruSeq RNA (stranded)
RNA was extracted from frozen cell pellets by hot acidic phenol and alcohol precipitated.
For all samples, rRNA was depleted by Yeast Ribo-Zero Gold. For all auxin and diazaborine experiments (including vehicle/untreated controls), libraries were prepared by TruSeq directional RNA kit by manufacturer's instructions. For diamide experiment, libraries were prepared by custom in-house protocol. RNA fragmented in alkaline buffer, size selected, treated with T4 PNK, 3' adapter ligated (with random hexamer), reverse transcribed with SuperScript III, circularized with CircLigase, PCR amplified with Phusion

treatment_protocol: For rRNA processing factor depletions, each culture was mock or auxin (100 uM indole-3-acetic acid) treated for 20 min . For oxidative stress, WT (BY4741 derivative) cells were treated with diamide (1.5 mM) for 0 or 15 min. For ribosomal protein assembly inhibition, WT cells were treated with vehicle (0.1% DMSO) or diazaborine (15 ug/ml) for 15 or 45 min).

tag: cell treatment

value: diazaborine, 15 ug/ml, 45 mn


title: WT_Diazaborine_45min_repB


title: Active Phase_Sedentary_ZT8_rep1


title: Active Phase_Exercise_ZT8_rep2


title: WT_DMSO_45min_repB


title: WT_DMSO_45min_repA


title: Active Phase_Sedentary_ZT20_rep1


title: Active Phase_Exercise_ZT20_rep2


title: Active Phase_Exercise_ZT20_rep1


title: Active Phase_Sedentary_ZT20_rep2


title: WT_Diazaborine_15min_repA

description:
rRNA-depleted total cellular RNA
WT_DMSO_Diazaborine_15min_DESeq.txt

value: diazaborine, 15 ug/ml, 15 mn


title: WT_DMSO_15min_repB


title: WT_DMSO_15min_repA


title: Active Phase_Exercise_ZT16_rep2


title: Active Phase_Sedentary_ZT16_rep2


title: Active Phase_Sedentary_ZT16_rep1


title: WT_Diamide_15min

description:
rRNA-depleted total cellular RNA
150520-WT-DiaT15-RNA-RPKM-Both.txt

extract_protocol:
Custom in-house protocol. RNA fragmented in alkaline buffer, size selected, treated with T4 PNK, 3' adapter ligated (with random hexamer), reverse transcribed with SuperScript III, circularized with CircLigase, PCR amplified with Phusion
RNA was extracted from frozen cell pellets by hot acidic phenol and alcohol precipitated.
For all samples, rRNA was depleted by Yeast Ribo-Zero Gold. For all auxin and diazaborine experiments (including vehicle/untreated controls), libraries were prepared by TruSeq directional RNA kit by manufacturer's instructions. For diamide experiment, libraries were prepared by custom in-house protocol. RNA fragmented in alkaline buffer, size selected, treated with T4 PNK, 3' adapter ligated (with random hexamer), reverse transcribed with SuperScript III, circularized with CircLigase, PCR amplified with Phusion

value: YSC001 (BY4741 with RPB3-3xFLAG::natMX6)

value: diamide, 1.5 mM, 15 min


title: Active Phase_Exercise_ZT16_rep1


title: WT_Diamide_0min

description:
rRNA-depleted total cellular RNA
150520-WT-DiaT00-RNA-RPKM-Both.txt


title: Rrp17AID_Aux_repB

description:
rRNA-depleted total cellular RNA
Rrp17AID_Unt_Aux_DESeq.txt

value: YBT171 (BY4741 with leu{delta}::GPD1pr-osTIR1 RPB3-3xFLAG (URA pop-out) RRP17-3xV5-IAA7::KanMX6)

value: auxin (indole-3-acetic acid), 100 uM, 20 min


title: Active Phase_Sedentary_ZT0_rep1

value: Gastrocnemius muscle

value: Male


title: Rest Phase_Sedentary_ZT0_rep2

value: Sedentary


title: Rest Phase_Sedentary_ZT0_rep1


title: Rest Phase_Exercise_ZT0_rep2

value: Exercise


title: Rest Phase_Exercise_ZT0_rep1


title: Rrp17AID_Aux_repA


title: Rrp17AID_Unt_repB


title: Rest Phase_Sedentary_ZT20_rep2


title: Las1AID_Aux_repA

description:
rRNA-depleted total cellular RNA
Las1AID_Unt_Aux_DESeq.txt

value: YBT178 (BY4741 with leu{delta}::GPD1pr-osTIR1 RPB3-3xFLAG (URA pop-out) LAS1-3xV5-IAA7::KanMX6)


title: Rest Phase_Sedentary_ZT20_rep1


title: WT_Diazaborine_15min_repB


title: Las1AID_Aux_repB


title: Las1AID_Unt_repB


title: Rest Phase_Sedentary_ZT16_rep2


title: Rest Phase_Exercise_ZT20_rep2


title: Rrp44AID_Aux_repA

description:
rRNA-depleted total cellular RNA
Rrp44AID_Unt_Aux_DESeq.txt

value: YBT174 (BY4741 with leu{delta}::GPD1pr-osTIR1 RPB3-3xFLAG (URA pop-out) RRP44-3xV5-IAA7::KanMX6)


title: Rest Phase_Exercise_ZT16_rep2


title: Rest Phase_Sedentary_ZT16_rep1


title: Rrp44AID_Aux_repB


title: Rest Phase_Exercise_ZT20_rep1


title: Rest Phase_Exercise_ZT16_rep1


title: Rest Phase_Sedentary_ZT12_rep2


title: Rrp44AID_Unt_repA


title: Rat1AID_Aux_repA

description:
rRNA-depleted total cellular RNA
Rat1AID_Unt_Aux_DESeq.txt

value: YBT100 (BY4741 with leu{delta}::GPD1pr-osTIR1 RPB3-3xFLAG (URA pop-out) RAT1-3xV5-IAA7::KanMX6)


title: Rest Phase_Exercise_ZT12_rep2


title: Rat1AID_Aux_repB


title: Rest Phase_Sedentary_ZT12_rep1


title: Rat1AID_Unt_repB


title: Rest Phase_Exercise_ZT12_rep1


title: Rrp17AID_Unt_repA


title: WTAID_Aux_repB

description:
rRNA-depleted total cellular RNA
WTAID_Unt_Aux_DESeq.txt

value: YBT155 (BY4741 with leu{delta}::GPD1pr-osTIR1 RPB3-3xFLAG (URA pop-out))


title: Rest Phase_Sedentary_ZT8_rep2


title: WTAID_Aux_repA


title: Rest Phase_Sedentary_ZT8_rep1


title: Las1AID_Unt_repA


title: Rest Phase_Exercise_ZT8_rep2


title: WTAID_Unt_repB


title: Rest Phase_Exercise_ZT8_rep1


title: WTAID_Unt_repA


title: Rest Phase_Exercise_ZT4_rep2


title: Rrp44AID_Unt_repB


title: Rest Phase_Exercise_ZT4_rep1


title: Rat1AID_Unt_repA


title: Cyp2bnull_HFD_2_male

city: Clemson

first: William

middle: S

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

data_processing:
Illumina HiSeq 2500 Control Software/Real-Time Analysis (RTA) was used for base-calling.
Samples were sequenced to an average sequencing depth of 20,000,000 read pairs with a 2 x 125 paired-end module.
Quality metrics were checked using FastQC on all samples sequenced, and Trimmomatic was used to trim low quality bases.
Trimmed reads were aligned to the Mus musculus reference genome (GCF_000001635.25_GRCm38.p5) using GSNAP.  Subread feature counts software finds reads that aligned with known genes.
Raw read counts and EdgeR were used to determine differential gene expression.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-deliminated text file includes raw counts for each sample.

source_name: liver

extract_protocol:
Livers were removed and stored at -80 degrees C. RNA was extracted from each treatment group (n=3) using RNeasy Plus Universal kit (Qiagen).
Libraries were prepared using TruSeq Total RNA Library Prep kit.

treatment_protocol: WT and Cyp2b-null mice were fed either a normal chow diet (ND) or high fat diet (HFD, 60 % fat) for 10 weeks.

tag: genotype

value: Cyp2b9/10/13-null (Cyp2bnull)

tag: Sex

value: male

value: liver


title: Cyp2bnull_HFD_3_male


title: Denr overexpressing, rep3

city: Lausanne

first: David

last: Gatfield

address: Genopode

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Alignment: bowtie2 (mm10) allowing 2 mismatches
Post-alignment filtering: Sequences  with  the  same  UMI  and  starting  at  the  same position - likely representing PCR duplicates - were excluded
Peak calling: high confidence crosslink sites were calculated with the iCount function “peaks” with options “RegionsAsOne” and  15 nt flank
Genome_build: Genome Reference Consortium GRCm38.84 (mm10)
Supplementary_files_format_and_content: peak files were generated with iCount (http://icount.biolab.si)
Supplementary_files_format_and_content: bed file containing significant peaks (FDR0.05)

source_name: Fibroblasts

growth_protocol: DMEM, 10% FBS, 1% penicillin/streptomycin; 5% CO2

extract_protocol:
cell lysis (50 mM Tris-HCl, pH 7.4; 100 mM NaCl, 1\% Igepal, 0.1\% SDS, 0.5\% sodium deoxycholate, EDTA-free protease inhibitors). RNA was partially digested with 0.2 U RNAse I
iCLIP protocol

treatment_protocol: UV-C (254 nm) at 150 mJ/cm2

tag: experimental condition

value: Denr overexpressing


title: Non-transfected cells, rep1

value: Non-transfected


title: IgG-IP, rep2

value: IP control


title: Denr overexpressing, rep2


title: Cyp2bnull_HFD_1_male


title: Non-transfected cells, rep2


title: Dam-TRF2S-Rep1

first: Alexandre

last: Neves

address: 1100 Fairview Av N

department: Basic Sciences Division

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4.
Sequencing data was processed via damidseq_pipeline (https://owenjm.github.io/damidseq_pipeline/).
This pipeline includes steps of sequence alignment, read extension, binned counts, normalization, pseudocount addition and final ratio file generation. Raw reads were mapped to the Drosophila melanogaster genome r6.14
The find peaks software (https://github.com/owenjm/find_peaks) was used to call significant peaks present in the dataset. The output log2 ratio files was converted to TDF for viewing in IGV using igvtools. The annotation and further analysis of significant peaks were done using HOMER (http://homer.ucsd.edu/homer/index.html, version v4.9).
Genome_build: dm6
Supplementary_files_format_and_content: peak file

organism: Drosophila melanogaster

source_name: whole central nervous systems

growth_protocol: The UAS-Dam, UAS-Dam-TBP, UAS-Dam-TRF2S and UASDam-TAF5 transgenes were induced for 72h at 30° using a worniuGAL4, UAS-GFP, tubGAL80ts driver.

extract_protocol:
Genomic DNA from 100 nervous systems each was extracted in duplicate, processed and amplified essentially as described in except that removal of DamID adaptors was performed before DNA shearing on a Covaris S2.
KAPA hyper

value: wandering 3rd instar larvae

value: whole central nervous systems


title: Denr overexpressing, rep1


title: Dam-TBP-Rep1


title: IgG-IP, rep1


title: Dam-TRF2S-Rep2


title: Dam-TBP-Rep2


title: Rest Phase_Sedentary_ZT4_rep2

value: Rest phase (ZT3)


title: Dam-Rep2


title: WT_HFD_3_male

value: wild type (WT)


title: Dam-TAF5-Rep1


title: WT_HFD_2_male


title: Dam-TAF5-Rep2


title: WT_HFD_1_male


title: Dam-Rep1


title: TRF2 replicate 3

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4.
RNA-seq reads were aligned to the Drosophila melanogaster genome using TopHat v2.1.0
Gene counts were generated using the Python package HTSeq v0.6.0 with the “intersection-strict” overlap mode
Differentially expressed genes, defined as |log2 (ratio)| ≥1 with the FDR set at 5%, were identified using the Bioconductor package edgeR, v3.16.5 after removing lowly expressed genes.
Genome_build: dm6
Supplementary_files_format_and_content: tab delimited files with counts for each gene

source_name: Neural stem and progenitor cells

growth_protocol: Virgin female flies expressing  asense-Gal4, UAS-Stinger::GFP were crossed to male flies expressing the control (mCherry) or experimental RNAi transgenes (TBP, TRF2, TAF5 or TAF9). The progeny was raised at  29C by and larval brains from wandering larvae were dissected and prepared for FAC-sorting.

extract_protocol:
Neural stem and progenitor cells were sorted directly into  TRIzol, homogenized with a pestle and then RNA was extracted according to the manufacturer’s instructions, using Glycoblue 500mg/ml (Ambion, AM9516) as a co-precipitant
We used SMART-seq v4 ultra-low input kit (Clontech, 634889) to generate double-stranded cDNA for each replicate, using 1ng of total RNA as input. 1ng of the resulting cDNA, amplified with 11 cycles of PCR in the cDNA amplification step, was used to prepare sequencing libraries with the Nextera XT kit (Illumina).


title: Rest Phase_Sedentary_ZT4_rep1

value: Gastrocnemius muscle

value: Male


title: Cyp2bnull_ND_3_male


title: TRF2 replicate 2


title: Cyp2bnull_ND_1_male


title: TRF2 replicate 1


title: Cyp2bnull_ND_2_male


title: WT_ND_3_male


title: TBP replicate 3


title: TBP replicate 2


title: WT_ND_1_male


title: TAF9 replicate 3


title: mCherry replicate 3


title: TBP replicate 1


title: TAF9 replicate 2


title: mCherry replicate 1


title: mCherry replicate 2


title: TR_scrsh_1; RNA-seq; scramble shRNA, rep1

data_processing:
Base-calling: Casava 1.82
Adapter trimming: Adapter sequences were removed using cutadapt utility with following options: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --match-read-wildcards -m 6
Insert size filtering: Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA
Alignment: Trimmed and filtered insert sequences were mapped sequentially to following databases: mouse rRNA, mouse tRNA, mouse cDNA (Ensembl.v.84) and mouse genome (GRCm38.p2). All but last one were mapped using bowtie2 (version 2.2.1) using following parameters: -p 2 -L 15 -k 20 –no-unal. Mapping against genomic sequence was performed using tophat (v2.0.11) with following parameters: --transcriptome-index=Mmusculus.GRCm38.84.dna.ensembl_data -p 2. After each alignment, only reads that were not aligned were used in the following mapping. For further analysis (processed data files), only alignments against mouse cDNA were used. Separately from this alignment strategy, each query set was also directly aligned against mouse genome using tophat with similar parameters (“global tophat”).
Post-alignment filtering: For each query sequence, only alignments with maximum score were kept. The output of “global tophat” alignment was used to estimate expressed transcript models using cufflinks (v2.2.1) . Transcript FPKM estimates from all samples were merged using cuffcompare. Resulting FPKM tracking information was parsed with an in-house Python script to filter out transcripts which were not found to have an FPKM > 0.1, a LOW95 > 0.05 and a FMI > 2.0 in at least 3 samples. A database of expressed transcripts was used in further analysis.
Abundance measurement: mRNA and RPF (ribosome protected fragment) levels were estimated per locus. An in-house Python script was used to count uniquely (by gene) mapped reads within each annotation feature (5'UTR, CDS, 3'UTR). For multi-isoform loci, preference order used was CDS, 5'UTR, 3'UTR.
Normalization: Read counts of total RNA and RPF were normalized with upper quantile method of R package edgeR. Prior to normalization, transcripts which did not have at least 10 counts in at least one fourth of the samples were removed from the datasets.
Normalization: RPKM values were calculated as the number of counted reads per 1000 mappable and countable bases per geometric mean of normalized read counts per million.
Genome_build: Genome Reference Consortium GRCm38.84 (mm10)
Supplementary_files_format_and_content: rpkm files were generated with R; txt file containing ENSEMBL gene IDs – RPKM in CDS – RPKM in 5'UTR

extract_protocol:
Cells were lyzed in 1 ml lysis buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, 100 μg ml-1 cycloheximide, 1% Triton X-100, 0.5% Sodium deoxycholate, complete EDTA-free protease inhibitors (Roche) ). Lysates were incubated for 10 min on ice and cleared by centrifugation at 1000 x g, 4°C for 3 min in a tabletop centrifuge. Supernatants were flash-frozen and stored in liquid nitrogen.  Total RNA-seq libraries were generated from the lysate pool. For ribosome profiling libraries, lysate pools were digested with 5 U ART-Seq nuclease per OD for 45 min at room temperature and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
ART-Seq (Illumina)

treatment_protocol: Cycloheximide 100ug/ml; 2 min; 37C

value: control

tag: cell line

value: Fibroblasts


title: WT_ND_2_male


title: TR_gfpsh_1; RNA-seq; Gfp shRNA, rep1


title: TR_gfpsh_2; RNA-seq; Gfp shRNA, rep2


title: TAF9 replicate 1


title: TR_denr1_2; RNA-seq; Denr shRNA1, rep2

value: Denr knockdown


title: TR_denr2_1; RNA-seq; Denr shRNA2, rep1


title: TR_denr1_3; RNA-seq; Denr shRNA1, rep3


title: TR_scrsh_3; RNA-seq; scramble shRNA, rep3


title: TR_denr2_2; RNA-seq; Denr shRNA2, rep2


title: RP_scrsh_3; RPF-seq; scramble shRNA, rep3

description: ribosome protected RNA


title: TR_scrsh_2; RNA-seq; scramble shRNA, rep2


title: RP_scrsh_2; RPF-seq; scramble shRNA, rep2

description: ribosome protected RNA


title: TR_denr2_3; RNA-seq; Denr shRNA2, rep3


title: RP_gfpsh_2; RPF-seq; Gfp shRNA, rep2

description: ribosome protected RNA


title: RP_scrsh_1; RPF-seq; scramble shRNA, rep1

description: ribosome protected RNA


title: RP_denr2_2; RPF-seq; Denr shRNA2, rep2

description: ribosome protected RNA


title: RP_denr2_1; RPF-seq; Denr shRNA2, rep1

description: ribosome protected RNA


title: 24 hours at 250 mM NaCl_replicate 3

city: London

first: larrouy-maumus

last: gerald

address: exhibition road

department: life sciences

institute: Imperial college london

description: Biological replicate 3 out of 6 24hrs 250 mM NaCl

hyb_protocol: Mycobacterium tuberculosis whole genome microarray slides (prepared at St. George's, University of London) were initially prehybridized in 3.5× SSC, 0.1% SDS and 10 mg/mL BSA for 20 min at 65 °C and then washed with deionized water and isopropanol. Labelled samples were heated for 2 min at 95 °C in 4xSSC and 0.3% SDS and hybridized on microarray slides under Lifter Slips (Thermo Scientific) for 16–20 h at 65 °C in a dark hybridization chamber. Hybridized slides were washed once with 1XSSC, 0.05% SDS at 65 °C and then twice with 0.06xSSC at room temperature.

scan_protocol: Scan on Agilent Technologies Scanner G2505C Grids were fitted to the raw microarray images, and background normalization and spot quantitation was performed using Bluefuse software (BlueGnome Ltd., Cambridge, United Kingdom) and normalized readings were plotted using GeneSpring 10 software (Silicon Genetics).

data_processing: Data were obtained for six slides, including dye swaps, from three bacterial cultures. Data were initially filtered on expression and the lower 20th percentile was eliminated from the analysis. Genes that showed >2-fold change in absolute expression with a p-value <0.05 (Student's t-test) were considered to be altered.

organism: Mycobacterium tuberculosis

label_protocol: Fluorescently labeled cDNA was generated from total RNA (1 μg) by direct incorporation of Cy3- or Cy5-dCTP (GE Healthcare) using Superscript II Reverse Transcriptase (Invitrogen Life Technologies) in the presence of random hexamers (3 μg), dNTPs (185 μM dCTP and 463 μM each of dATP, dGTP and dTTP) and Cy3-dCTP or Cy5-dCTP (1.7 nmoles). RNA and random hexamers were initially mixed, made up to a volume of 11 μl and heated to 95 °C for 5 min. The mixture was then chilled on ice for 2 min. Remaining components of the reverse transcriptase reaction were added and the mixture was incubated for 10 min at 25 °C, followed by 42 °C for 90 min. Samples to be compared were mixed and the labelled cDNA was purified using MinElute PCR purification columns (Qiagen).

growth_protocol: M. tuberculosis was grown in 7H9 liquid medium in roller bottles at 37 °C containing 10mM NaCl.

extract_protocol: Total RNA was extracted using a Fast RNA Pro Blue kit (MP Biomedicals). RNA was treated with RNase-free DNase (Promega) and purified using RNAeasy columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Bacteria were stressed by addition of NaCl to a concentration of 250 mM or 1000 mM NaCl for 2, 8 and 24h at mid-log phase (light transmittance at 600 nm ∼ 0.6).

value: bacteria 10 mM NaCl

source_name: Mtb_treated by 250 mM NaCl

value: bacteria 250 mM NaCl 24hours


title: RP_denr2_3; RPF-seq; Denr shRNA2, rep3

description: ribosome protected RNA


title: 24 hours at 250 mM NaCl_replicate 5

description: Biological replicate 5 out of 6 24hrs 250 mM NaCl


title: 24 hours at 250 mM NaCl_replicate 1

description: Biological replicate 1 out of 6 24hrs 250 mM NaCl


title: 8 hours at 250 mM NaCl_replicate 2

description: Biological replicate 2 out of 6 8hrs 250 mM NaCl

value: bacteria 250 mM NaCl 8hours


title: 24 hours at 250 mM NaCl_replicate 2

description: Biological replicate 2 out of 6 24hrs 250 mM NaCl


title: 24 hours at 250 mM NaCl_replicate 4

description: Biological replicate 4 out of 6 24hrs 250 mM NaCl


title: 8 hours at 250 mM NaCl_replicate 6

description: Biological replicate 6 out of 6 8hrs 250 mM NaCl


title: RP_gfpsh_1; RPF-seq; Gfp shRNA, rep1

description: ribosome protected RNA


title: 24 hours at 250 mM NaCl_replicate 6

description: Biological replicate 6 out of 6 24hrs 250 mM NaCl


title: Utx_sperm_Mnase_seq_rep2

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description:
Utx_sperm_H3K27me3_rep2_peaks.bed
Utx_control_H3K27me3_ChIP_2kbtiles.txt

data_processing:
ChIP-seq reads were filtered using fastq_quality_filter from FASTX Toolkit version 0.0.14 with parameters –q 20 –p80, and aligned to the mm10 mouse genome using bowtie version 1.2 with parameters –m 1 –k 1 –n 1  -l 40. Peaks were called using MACS version 2.1.0 with parameters –broad –broad-cutoff 0.01 –keep-dup 1 –nomodel. ChIP-seq signal was quantitated in 2 kilobase tiles across the genome using methods from Hisano et al., 2013. ChIP and input (MNase-only) data were scaled to get reads per million, input was substracted from ChIP signal for each tile and any negative values set to zero.  Each dataset was then re-scaled using the inverse of the reads-per-million scaling parameter originally used for the ChIP sample.
ChIP-seq reads were filtered using fastq_quality_filter from FASTX Toolkit version 0.0.14 with parameters –q 20 –p80, and aligned to the mm10 mouse genome using bowtie version 1.2 with parameters –m 1 –k 1 –n 1  -l 40. Peaks were called using MACS version 2.1.0 with parameters –broad –broad-cutoff 0.01 –keep-dup 1 –nomodel. ChIP-seq signal was quantitated in 2 kilobase tiles across the genome using methods from Hisano et al., 2013. ChIP and input (MNase-only) data were scaled to get reads per million, input was substracted from ChIP signal for each tile and any negative values set to zero.  Each dataset was then re-scaled using the inverse of the reads-per-million scaling parameter originally used for the ChIP sample.
Genome_build: mm10
Supplementary_files_format_and_content: .bed files with peak coordinates; single tab-delimited .txt file containing K27me3 ChIP signal scaled to reads per million, with input signal subtracted, in 2 kilobase tiles across the genome

source_name: sperm

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: GTGGCC.
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane).

tag: chip antibody

tag: condition

value: Utx cKO


title: 2 hours at 250 mM NaCl_replicate 5

description: Biological replicate 5 out of 6 2hrs 250 mM NaCl

tag: strain

value: bacteria 250 mM NaCl 2hours


title: TR_denr1_1; RNA-seq; Denr shRNA1, rep1


title: 2 hours at 250 mM NaCl_replicate 4

description: Biological replicate 4 out of 6 2hrs 250 mM NaCl


title: 8 hours at 250 mM NaCl_replicate 4

description: Biological replicate 4 out of 6 8hrs 250 mM NaCl


title: 2 hours at 250 mM NaCl_replicate 6

description: Biological replicate 6 out of 6 2hrs 250 mM NaCl


title: 2 hours at 250 mM NaCl_replicate 2

description: Biological replicate 2 out of 6 2hrs 250 mM NaCl


title: 2 hours at 250 mM NaCl_replicate 3

description: Biological replicate 3 out of 6 2hrs 250 mM NaCl


title: 8 hours at 250 mM NaCl_replicate 5

description: Biological replicate 5 out of 6 8hrs 250 mM NaCl


title: RP_denr1_3; RPF-seq; Denr shRNA1, rep3

description: ribosome protected RNA


title: control_sperm_Mnase_seq_rep2

description:
control_sperm_H3K27me3_rep2_peaks.bed
Utx_control_H3K27me3_ChIP_2kbtiles.txt

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: GAGTGG.
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane).


title: 8 hours at 250 mM NaCl_replicate 1

description: Biological replicate 1 out of 6 8hrs 250 mM NaCl


title: RP_denr1_2; RPF-seq; Denr shRNA1, rep2

description: ribosome protected RNA


title: Utx_sperm_H3K27me3_ChIPseq_rep2

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: GTTTCG.
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane).

value: H3K27me3 (Abcam, ab6002)


title: control_sperm_H3K27me3_ChIPseq_rep2

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: ACTGAT.
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane).


title: RP_denr1_1; RPF-seq; Denr shRNA1, rep1

description: ribosome protected RNA


title: 24 hours at 1000 mM NaCl_replicate 6

description: Biological replicate 6 out of 6 24hrs 1000 mM NaCl

source_name: Mtb_treated by 1000 mM NaCl

value: bacteria 1000 mM NaCl 24hours


title: 2 hours at 250 mM NaCl_replicate 1

description: Biological replicate 1 out of 6 2hrs 250 mM NaCl


title: 8 hours at 250 mM NaCl_replicate 3

description: Biological replicate 3 out of 6 8hrs 250 mM NaCl


title: 24 hours at 1000 mM NaCl_replicate 5

description: Biological replicate 5 out of 6 24hrs 1000 mM NaCl


title: UtxF1_LT_RRBS_rep1

description:
bisulfite-converted genomic DNA
one raw file/SRA run (SRR)contains reads, one contains the 6bp UMI

data_processing:
trim_galore version 0.4.2 was used to remove adapter sequences from RRBS reads, and a script provided with the NuGen Ovation RRBS kit was used to trim diversity sequences.  Reads were aligned to the genome using Bismark version 0.16.3 and bowtie2.  PCR duplicates were removed using the unique molecular identifiers (UMIs) added during library prep.  Percent methylation in 100 bp tiles across the genome was called using the methylKit package in R, and only tiles covered by at least 10 reads were considered in further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt files with percent methylation (percentage of reads with C vs T after bisulfite conversion) at each CpG covered by at least 10 reads.

source_name: liver tumor

extract_protocol:
Tumors were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: GGAGAA.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.

value: liver tumor

value: Utx F1


title: controlF1_LT_RRBS_rep2

description: bisulfite-converted genomic DNA

value: control F1


title: controlF1_LT_RRBS_rep1


title: UtxF1_BM_spleen_rep3

description: bisulfite-converted genomic DNA

source_name: spleen

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: GGAGAA.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.

value: spleen

value: healthy Utx F1


title: 24 hours at 1000 mM NaCl_replicate 4

description: Biological replicate 4 out of 6 24hrs 1000 mM NaCl


title: UtxF1_BM_spleen_rep2

description: bisulfite-converted genomic DNA

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: TCAGAG.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: UtxF1_LT_RRBS_rep2

description: bisulfite-converted genomic DNA


title: controlF1_spleen_RRBS_rep5

description: bisulfite-converted genomic DNA

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: CGTAGA.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: 24 hours at 1000 mM NaCl_replicate 3

description: Biological replicate 3 out of 6 24hrs 1000 mM NaCl


title: controlF1_spleen_RRBS_rep3

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). "Index" fastq file contains 6bp UMI. Barcode: AGCATG.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: UtxF1_BM_spleen_rep1

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  "Index" fastq file contains 6bp UMI.  Barcode: GAGTCA.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: controlF1_spleen_RRBS_rep4

description: bisulfite-converted genomic DNA

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: ACCTCA.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: 24 hours at 1000 mM NaCl_replicate 1

description: Biological replicate 1 out of 6 24hrs 1000 mM NaCl


title: 8 hours at 1000 mM NaCl_replicate 6

description: Biological replicate 6 out of 6 8hrs 1000 mM NaCl

value: bacteria 1000 mM NaCl 8hours


title: controlF1_spleen_RRBS_rep2

description: bisulfite-converted genomic DNA

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: AACCAG.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: 8 hours at 1000 mM NaCl_replicate 5

description: Biological replicate 5 out of 6 8hrs 1000 mM NaCl


title: controlF1_spleen_RRBS_rep1

description: bisulfite-converted genomic DNA

extract_protocol:
Spleens were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.
Tissues were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: 24 hours at 1000 mM NaCl_replicate 2

description: Biological replicate 2 out of 6 24hrs 1000 mM NaCl


title: 8 hours at 1000 mM NaCl_replicate 2

description: Biological replicate 2 out of 6 8hrs 1000 mM NaCl


title: 2 hours at 1000 mM NaCl_replicate 6

description: Biological replicate 6 out of 6 2hrs 1000 mM NaCl

value: bacteria 1000 mM NaCl 2hours


title: 8 hours at 1000 mM NaCl_replicate 4

description: Biological replicate 4 out of 6 8hrs 1000 mM NaCl


title: 2 hours at 1000 mM NaCl_replicate 5

description: Biological replicate 5 out of 6 2hrs 1000 mM NaCl


title: Patient 331

first: SAUMYA

last: Das

address: 185 Cambridge Street

institute: MGH

description:
Test
SAMPLE 331

data_processing: The study does not have the normalized Ct values. This is because raw CT values after applying a threshold (Ct<=22) was used.

label: FAM

source_name: Plasma extracelular RNA

label_protocol: According to BioMark System protocol.

extract_protocol: RNA was extracted from plasma (331 patients, OMEGA-REMODEL trial) using miRCURY RNA Isolation Kit – Biofluids (Exiqon) and reverse transcribed using miScript II RT Kit (Qiagen, Fredrick, MD, USA). cDNA samples were pre-amplified with miScript Microfluidics PreAMP Kit (Qiagen, Fredrick, MD, USA) and RT-qPCR miRNA profiling analyses performed on the BioMark System (Fluidigm Corp. South San Francisco, CA) using miScript miRNA Assays (Qiagen, Fredrick, MD, USA) and Dynamic Array 96.96 (Fluidigm Corp. South San Francisco, CA). A Ct value of 23 was set as the cut-off point for detectable miRNA species.

tag: individual

value: patient who underwent a myocardial infarction

value: plasma

tag: gender

value: Female

tag: race

value: Caucasian

tag: diabetes

tag: omega-3 fatty acid therapy


title: 24 hours at 2000 mM sucrose_replicate 2

description: Biological replicate 2 out of 6 24hrs 2000 mM sucrose

tag: treatment

value: bacteria 10 mM NaCl

source_name: Mtb_treated by 2000 mM sucrose

value: bacteria 2000 mM sucrose 24hours


title: 24 hours at 2000 mM sucrose_replicate 4

description: Biological replicate 4 out of 6 24hrs 2000 mM sucrose


title: 24 hours at 2000 mM sucrose_replicate 3

description: Biological replicate 3 out of 6 24hrs 2000 mM sucrose


title: 24 hours at 2000 mM sucrose_replicate 1

description: Biological replicate 1 out of 6 24hrs 2000 mM sucrose


title: 8 hours at 1000 mM NaCl_replicate 1

description: Biological replicate 1 out of 6 8hrs 1000 mM NaCl


title: 24 hours at 2000 mM sucrose_replicate 5

description: Biological replicate 5 out of 6 24hrs 2000 mM sucrose


title: Patient 330

description:
Test
SAMPLE 330

tag: tissue

value: Male


title: 2 hours at 1000 mM NaCl_replicate 2

description: Biological replicate 2 out of 6 2hrs 1000 mM NaCl


title: 8 hours at 2000 mM sucrose_replicate 6

description: Biological replicate 6 out of 6 8hrs 2000 mM sucrose

value: bacteria 2000 mM sucrose 8hours


title: 8 hours at 2000 mM sucrose_replicate 3

description: Biological replicate 3 out of 6 8hrs 2000 mM sucrose


title: 2 hours at 1000 mM NaCl_replicate 4

description: Biological replicate 4 out of 6 2hrs 1000 mM NaCl


title: 2 hours at 2000 mM sucrose_replicate 1

description: Biological replicate 1 out of 6 2hrs 2000 mM sucrose

value: bacteria 2000 mM sucrose 2hours


title: 8 hours at 2000 mM sucrose_replicate 2

description: Biological replicate 2 out of 6 8hrs 2000 mM sucrose


title: 2 hours at 2000 mM sucrose_replicate 6

description: Biological replicate 6 out of 6 2hrs 2000 mM sucrose


title: 24 hours at 2000 mM sucrose_replicate 6

description: Biological replicate 6 out of 6 24hrs 2000 mM sucrose


title: 2 hours at 1000 mM NaCl_replicate 3

description: Biological replicate 3 out of 6 2hrs 1000 mM NaCl


title: Patient 326

description:
Test
SAMPLE 326

tag: age


title: 2 hours at 1000 mM NaCl_replicate 1

description: Biological replicate 1 out of 6 2hrs 1000 mM NaCl


title: Patient 327

description:
Test
SAMPLE 327

value: Other


title: Patient 329

description:
Test
SAMPLE 329


title: 2 hours at 2000 mM sucrose_replicate 4

description: Biological replicate 4 out of 6 2hrs 2000 mM sucrose


title: 8 hours at 2000 mM sucrose_replicate 4

description: Biological replicate 4 out of 6 8hrs 2000 mM sucrose


title: 8 hours at 2000 mM sucrose_replicate 1

description: Biological replicate 1 out of 6 8hrs 2000 mM sucrose


title: 2 hours at 2000 mM sucrose_replicate 5

description: Biological replicate 5 out of 6 2hrs 2000 mM sucrose


title: 2 hours at 2000 mM sucrose_replicate 3

description: Biological replicate 3 out of 6 2hrs 2000 mM sucrose


title: 8 hours at 2000 mM sucrose_replicate 5

description: Biological replicate 5 out of 6 8hrs 2000 mM sucrose


title: 2 hours at 2000 mM sucrose_replicate 2

description: Biological replicate 2 out of 6 2hrs 2000 mM sucrose


title: Patient 328

description:
Test
SAMPLE 328


title: 8 hours at 1000 mM NaCl_replicate 3

description: Biological replicate 3 out of 6 8hrs 1000 mM NaCl


title: Patient 325

description:
Test
SAMPLE 325


title: Patient 324

description:
Test
SAMPLE 324

value: Hispanic


title: Patient 323

description:
Test
SAMPLE 323


title: Patient 322

description:
Test
SAMPLE 322


title: Patient 321

description:
Test
SAMPLE 321

value: African American


title: Patient 318

description:
Test
SAMPLE 318


title: Patient 319

description:
Test
SAMPLE 319


title: Patient 320

description:
Test
SAMPLE 320


title: Patient 315

description:
Test
SAMPLE 315


title: Patient 316

description:
Test
SAMPLE 316


title: Patient 314

description:
Test
SAMPLE 314


title: Patient 313

description:
Test
SAMPLE 313


title: Patient 312

description:
Test
SAMPLE 312


title: Patient 310

description:
Test
SAMPLE 310


title: Patient 311

description:
Test
SAMPLE 311


title: Patient 307

description:
Test
SAMPLE 307


title: Patient 305

description:
Test
SAMPLE 305


title: Patient 304

description:
Test
SAMPLE 304


title: Patient 309

description:
Test
SAMPLE 309


title: Patient 308

description:
Test
SAMPLE 308


title: MDA-MB-231 siAxl2

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the GRCh37 genome with TopHat v2.0.10
Raw alignment counts were calculated with Htseq-count v0.5.3.
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt file with raw counts and differential expression

source_name: MDA-MB-231 siAxl

extract_protocol:
Total RNA was extracted using RNeasy columns (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TNBC cell line MDA-MB-231

value: siAxl


title: Patient 303

description:
Test
SAMPLE 303


title: MDA-MB-231 siAxl1


title: Patient 306

description:
Test
SAMPLE 306


title: MLS402_BRD4

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: MLS402 BRD4 ChIP-seq

data_processing:
Raw fastq files were aligned to human gneome using bowtie and duplicates were removed using picard. Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01. Alignment and peak calling pipelines with hard-coded parameters are available at https://github.com/PoisonAlien/chiptk.
ChIP signals (Bedgraph) were simultaneously generated and input signal was subtracted with MACS2 bdgmp function. Bedgraphs were later converted to bigwig files with UCSC bedGraphTobigWig utility.
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million.

growth_protocol: LPS cells were  cultured in Roswell Park Memorial Institute medium 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
ChIP was performed by following a standard protocol. Briefly, cells were fixed with 1% formaldehyde for 10 min at room temperature, followed with 3 washes by cold PBS. Nuclei were extracted and re-suspended in SDS lysis buffer for 10 min on ice before sonication by Bioruptor (Diagenode). Optimal condition of sonication yielded genomic fragments around 200 to 500 bp. After sonication, cell debris was removed by centrifugation (13,000 rpm, 10 min). Supernatant was then pre-cleared and incubated with magnetic beads (Invitrogen Dynabeads) conjugated with specific antibodies (Supplementary Table 5).  After overnight incubation, magnetic beads were washed stepwise with cold low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer. Bound DNA was eluted, reverse-crosslinked, and purified by QIAquick PCR purification kit (Qiagen).
Standard Illumina library preparation protocol

tag: cell type

value: liposarcoma cells

value: BRD4 (Bethyl, #A301-985A, lot4)


title: Patient 301

description:
Test
SAMPLE 301


title: Patient 317

description:
Test
SAMPLE 317


title: Patient 300

description:
Test
SAMPLE 300


title: MDA-MB-231 siCt2

source_name: MDA-MB-231 siCt

value: siCt


title: MDA-MB-231 siCt1


title: Patient 299

description:
Test
SAMPLE 299

value: patient who underwent a myocardial infarction


title: Patient 298

description:
Test
SAMPLE 298

value: plasma


title: Patient 297

description:
Test
SAMPLE 297

value: Female


title: ActD treated cells rep2

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description:
ActD treatment 24hours rep2
Processed data file: 24hr_allValidPairs.txt

data_processing:
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.8.1. The sequenced reads were mapped to the hg19 human reference genome, and corrected for biases, including read depth2. There was a high correlation among all the Hi-C biological replicates (Fig. 1c, Supplementary Fig. 1a), indicating the high quality and reproducibility of the datasets.
Genome_build: hg19
Supplementary_files_format_and_content: HiC-Pro all valid read pairs file

source_name: ActD treated cells

growth_protocol: K562 cells were obtained from (ATCC #CCL-243) and cultured in RPMI 1640 (Thermo Fisher #22400-105), 10% Fetal Bovine Serum (Thermo Fisher #26140-079), 1% L-Glutamine (Thermo Fisher #25030-164) and 1% Penicillin/Streptomycin (Thermo Fisher #15140-163) in a 37°C incubator.  The media was changed every 2 days, and when the cells’ density reached ~8x10^5 cells/mL, the culture was split to ~3x10^5 cells/mL with fresh, warm media. Transcription inhibition was achieved by treating the cells with actinomycin D (5micrograms/mL) for 24 hours.

extract_protocol: Hi-C libraries were generated with the in-situ ligation using the HindIII restriction enzyme (PMID: 28435001), Briefly, after crosslinking the cells with 1% formaldehyde for 10 minutes at room temperature, the nuclei were extracted by dounce homogenization. Next, the chromatin was digested with HindIII either in the presence of 500μg RNase A (Qiagen #19101), or 30U of RNase Inhibitor (NEB, #M0314L).  These samples that are treated after formaldehyde crosslinking (aXL) are referred as “aXL RNase A” and “aXL CTRL”, respectively. The bXL samples were processed according to the original protocol(PMID: 28435001). The digested chromatin was then end-labelled with biotin-14-dCTP (Thermo Fisher 19519016), and in-situ ligation was performed. Extraction of the DNA was performed by phenol-chloroform extraction, and the biotin was removed from unligated ends, followed by shearing of the DNA by using a Covaris S220 instrument to 100-500bp size range. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument. Hi-C libraries for each condition were generated in two biological replicates.

treatment_protocol: For the RNase A treatment before crosslinking (bXL) condition, ~10 x 10^6 K562 cells were aliquoted and spun down at 1000xg for 10 minutes at 4°C.  The supernatant was removed and the cell pellet was re-suspended with 1mL of cold PBS + 0.02% Tween-20 followed by incubation on ice for 10 minutes. Next, Either of 500μg RNase A (Qiagen #19101), or 30U of RNase Inhibitor (NEB, #M0314L) was added to the suspension, and incubated at 37°C for 30 mins in a thermomixer at 950rpm.  Next, the cells were spun down at 1000xg for 10 minutes at 4°C, washed once with 1mL cold PBS with protease inhibitor cocktail (Roche, #04693159001), and then re-suspended in 10mL 1X PBS at room temperature with protease inhibitor cocktail, followed by crosslinking of the cells with formaldehyde at 1% final concentration and quenching the formaldehyde with glycine. Then, the RNase A and RNase inhibitor treated samples were processed for downstream Hi-C experiments.

value: ActD treated cells


title: Old2

city: Kyoto

first: Yukino

last: Hatazawa

address: 1-5 Hangi-cho, Shimogamo, Sakyo-ku

country: Japan

institute: Kyoto Prefectural University

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Feature Number version) was used.

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner to detect Cy3 fluorescence.

data_processing: The scanned images were analyzed using Feature Extraction Software 9.5 (Agilent) with default parameters (protocol: GE1_1100_Jul11 and Grid: 028005_D_F_20150604 to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction Software as Non-uniform outliers were excluded.

label_protocol: Cy3-labeled cRNA (1.65 μg) was mixed and fragmented according to the Agilent Technologies protocol.

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of young mice and old mice. RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany).

value: 25 months

value: male

value: skeletal muscle


title: Patient 302

description:
Test
SAMPLE 302

value: Male

value: Caucasian


title: control sample for ActD treatment rep2

description:
ActD treatment control rep2
Processed data file: 0hr_allValidPairs.txt

source_name: control sample for ActD treatment

value: control sample for ActD treatment


title: Young1

value: 13 weeks


title: Young3


title: Old3


title: ActD treated cells rep1

description:
ActD treatment 24hours rep1
Processed data file: 24hr_allValidPairs.txt


title: Young2


title: Patient 295

description:
Test
SAMPLE 295


title: Patient 292

description:
Test
SAMPLE 292


title: Patient 293

description:
Test
SAMPLE 293

value: African American


title: Old1


title: MLPS_T2_Input

description: MLPS_T2_Input_FCHNY2LBBXX_L3_wHAPPI076352-63_1

value: MLPS primary tissue


title: MLPS_T1_Input

description: MLPS_T1_Input_FCHTL3HBBXX_L8_CHKPEI85218040353_1


title: MLPS_T1_H3K27ac

description: MLPS_T1_H3K27ac_FCHTL3HBBXX_L8_CHKPEI85218040354_1

value: H3K27ac (Abcam, #ab4729)


title: DDLPS_T2_Input

description: DDLPS_T2_Input_FCHNY2LBBXX_L3_wHAPPI076356-61_1

value: DDLPS primary tissue


title: Patient 291

description:
Test
SAMPLE 291

value: Other


title: control sample for ActD treatment rep1

description:
ActD treatment control rep1
Processed data file: 0hr_allValidPairs.txt


title: Patient 287

description:
Test
SAMPLE 287


title: Patient 286

description:
Test
SAMPLE 286


title: DDLPS_T1_Input

description: DDLPS_T1_Input_FCHNY2LBBXX_L2_wHAPPI076365-54_1


title: Patient 285

description:
Test
SAMPLE 285


title: Patient 294

description:
Test
SAMPLE 294