title: GA H4K20me3 Rep2 (expt2)

description:
Corresponding replicate: ADPH-92
GA_H4K20me3.bw
GA_H4K20me3_c35.0_C20.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: Tri-Methyl-Histone H4 (Lys20) (D84D2) Rabbit mAb, CST, 5737S, Lot No 1


title: RI rep2 [ATAC-seq]

status: Public on Nov 05 2020

type: SRA

city: London

first: Anastasios

last: Karadimitris

address: Hammersmith Campus, Du Cane Road

department: Department of Immunology and Inflammation

country: United Kingdom

institute: Imperial College London

library_source: genomic

data_processing:
Quality check using FastQC.
Reads trimming using cutadapt, reads aligned by bowtie2, duplicate marking using sambamba, bam cleaning/filtering using Picard.
Filter blacklist genes using bedtools, filter reads using samtools, convert to BED files using bedtools, Tn5 shifting to obtain awk files.
Tn5 tagAlign using BEDPE.
Peak calling using MACS2.
Subsampling.
Genome_build: mm10
Supplementary_files_format_and_content: *_peaks.narrowPeak: Peak files.

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
50,000 cells were collected and washed at 500g at 40C for 5 min. The cells were resuspended in lysis buffer and immediately spun at 500g at 40C for 10 min. The nuclei were subjected to transposase reaction for 30 min at 37oC; termination of the reaction and DNA purification were performed using a MinElute Kit (Qiagen).
The purified DNA was amplified as described before with NEBNext High-Fidelity 2x PCR Master Mix (NEB). The PCR amplified product was cleaned with AMPure beads (Beckman).
The quality of the libraries was assessed with the Bioanalyser High Sensitivity DNA kit (Agilent). Libraries were quantified using the Universal Library Quantification Kit for Illumina (Kapa Biosystems) on a StepOne Plus Real-Time PCR (Applied Biosystems). The libraries were sequenced at the Genomics Facility at MRC/LIMS of ICL using the Illumina HiSeq 2500 platform to obtain paired-end 100bp reads.

treatment_protocol: Replicates were treated with RANKL, RANKL/I-BET, or I-BET for 4 hours.

tag: cell line

tag: cell type

value: Monocyte-derived cell line

tag: treatment

value: RANKL+Ibet

tag: time point

value: 4 hours


title: GA H4K20me3 Rep1 (expt2)

city: Roscoff

first: J. Mark

last: Cock

address: Place Georges Teissier

country: France

institute: Station Biologique de Roscoff

description:
Corresponding replicate: ADPH-93
GA_H4K20me3.bw
GA_H4K20me3_c35.0_C20.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

data_processing:
Illumina base calling
Sequence quality was evaluated with FASTQC and poor quality sequence removed with Flexcat (Dodt M, Roehr JT, Ahmed R, Dieterich C. 2012. FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology 1: 895–905). For the RNA-seq, reads that were shorter than 50 nucleotides after trimming were removed. For ChIP-seq, reads that were shorter than 22 nucleotides after trimming were removed.
ChIP-seq Illumina reads were mapped onto the Ectocarpus genome using Bowtie (v2.2.5; Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013).
Peaks corresponding to regions enriched in PTMs were identified using the MACS2 (version 2.1.1) callpeak module (minimum FDR of 0.01) and refined with the MACS2 bdgpeakcall and bdgbroadcall modules (Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biology 9: R137). Colocalised peaks corresponding to regions enriched in several PTMs were detected using MACS2 outputs in BedTools multiinter (Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, Oxford, England 26: 841–842).
Trimmed RNA-seq reads were mapped to the Ectocarpus reference genome using Tophat2 (Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36).
Mapped RNA-seq data was processed using featureCounts (Liao Y, Smyth GK, Shi W, 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics (Oxford, England) 30: 923–930) to obtain counts of numbers of reads mapped to exons. Expression values were represented as TPM.
Differential expression was detected using the DESeq2 package (Bioconductor; Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550) using an adjusted p‐value cut‐off of 0.05 and a minimal fold‐change of 2.
Genome_build: Ectocarpus sp. Ec32 genome v2 2018 (https://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtracted from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or GAPPEDPEAK (bed12+3) format.

organism: Ectocarpus sp. Ec32

source_name: gametophyte

growth_protocol: Cultures were grown in 140 mm round Petri dishes in natural sea water with 0.01% Provasoli enrichment at 13°C with a 12h/12h day/night cycle and 20 (µmol photons).m-2.s-1 irradiance.

extract_protocol: For ChIP-seq, Ectocarpus tissue was fixed for five minutes in seawater containing 2% formaldehyde and the formaldehyde eliminated by rapid filtering followed by incubation in PBS containing 400 mM glycine. Nuclei were isolated by grinding in liquid nitrogen and in a Tenbroeck Potter in nuclei isolation buffer (0.1% triton X-100, 125 mM sorbitol, 20 mM ptassium citrate, 30 mM MgCl2, 5 mM EDTA, 5 mM β-mercaptoethanol 55 mM HEPES at pH 7.5 with complete ultra protease inhibitors), filtering through Miracloth and then washing the precipitated nuclei in nuclei isolation buffer with and then without triton X-100. Chromatin was fragmented by sonicating the purified nuclei in nuclei lysis buffer (10 mM EDTA, 1% SDS, 50 mM Tris-HCl at pH 8 with complete ultra protease inhibitors) in a Covaris M220 Focused-ultrasonicator (duty 25%, peak power 75, cycles/burst 200, duration 900 sec at 6°C). The chromatin was incubated with an anti-histone PTM antibody overnight at 4°C and the immunoprecipitation carried out using Dynabeads protein A and Dynabeads protein G. Following immunoprecipitation and washing, a reverse cross-linking step was carried out by incubating for at least six hours at 65°C in 5 M Na Cl and the samples were then digested with Proteinase K and RNAse A. The purified DNA was then prepared for Illumina sequencing. For MNase digestion, nuclei were prepared using the same procedure as that used for ChIP samples except that the isolation buffer did not contain EDTA. Each sample of nuclei was digested with 400 agarose gel units of MNase for 10 min at 37°C in MNase reaction buffer (5 mM CaCl2, 60 mM KCl, 0.5 mM DTT, 15 mM NaCl, 125 mM sorbitol, 50 mM Tris-HCl pH 7.5). Following lysis of the nuclei, reverse cross-linking and digestion with Proteinase K and RNAse A, 120-210 bp fragments were excised from a 2% agarose gel and sequenced on a HiSeq 4000 platform. using the same procedure as that used for ChIP samples except that the isolation buffer did not contain EDTA. Each sample of nuclei was digested with 400 agarose gel units of MNase for 10 min at 37°C in MNase reaction buffer (5 mM CaCl2, 60 mM KCl, 0.5 mM DTT, 15 mM NaCl, 125 mM sorbitol, 50 mM Tris-HCl pH 7.5). Following lysis of the nuclei, reverse cross-linking and digestion with Proteinase K and RNAse A, 120-210 bp fragments were excised from a 2% agarose gel and sequenced on a HiSeq 4000 platform. For RNA-seq, RNA was extracted from the same duplicate sporophyte and gametophyte cultures as were used for the ChIP-seq analysis using the Qiagen RNeasy plant mini kit with an on-column Deoxyribonuclease I treatment. RNA quality and concentration was then analysed on 1.5% agarose gel stained with ethidium bromide and a NanoDrop ND-1000 spectrophotometer (NanoDrop products, Wilmington, DE, USA).

treatment_protocol: No treatment

tag: Sex

value: male

tag: tissue

value: whole organism

tag: Stage

value: mature, 4 weeks old

tag: phenotype

value: wild type

tag: generation

value: gametophyte

tag: chip antibody

tag: sample code


title: MYC RI [ChIP-seq_MYC_MAX]

data_processing:
Quality check using FastQC.
Reads alignment using bowtie2 (2.3.4.1 64bit).
Subsampling based on the same INPUT file for MYC and MAX samples.
Peak calling using MACS2 (VERSION 2.1.1.20160309) for subsamples.
MSPC used for filtering peaks, and then the peaks/tracks files were merged from subsamples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pileup track files (bigwig format) for merged subsamples.
Supplementary_files_format_and_content: Peak files (bed format) for merged subsamples.

growth_protocol: Treated and untreated cells were cultured using DMEM medium. 10e7 cells per ChIP were cross-linked with 1% formaldehyde for 15min. The ChIP protocol was the same as for ChIP-qPCR until the elution.

extract_protocol:
The ChIP DNA was purified with AMPure beads (Beckman).
ChIP and input DNA libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) following manufacturer’s protocols. The quantity was determined using the Qubit High Sensitivity DNA kit (Life Technologies) and library size was determined using the Bioanalyser High Sensitivity DNA kit (Agilent). Libraries were quantified using the Universal Library Quantification Kit for Illumina (Kapa Biosystems) and run on AB StepOne Plus Real-Time PCR (Applied Biosystems). Libraries were diluted to 2nM and sequenced at the MRC Imperial facility using the Illumina HiSeq 2500 platform to obtain single-end 50bp reads.

value: Myc


title: GA H2AZ Rep2 (expt2)

description:
Corresponding replicate: ADPH-106
GA_H2AZ.bw

value: Anti-Histone H2A.Z antibody - ChIP Grade, Abcam, ab97966, received 09/04/18


title: PP1

city: Beijing

first: Yanan

last: Wang

state: China

address: No. 1 Shuai Fu Yuan Street

country: China

institute: Peking Union Medical College Hospital

library_source: transcriptomic

data_processing:
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC HG19)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Genome_build: hg19
Supplementary_files_format_and_content: peak

molecule: total RNA

organism: Homo sapiens

source_name: skin tissue

extract_protocol:
RNA extraction protocol
Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library  Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
MeRIP-seq

value: epidermis and dermis

tag: condition

value: involved psoriatic skin


title: Genomic DNA from umbilical cord blood buffycoat 181

type: genomic

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

institute: University of Oxford

description:
U198
Umbilical cord blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
R v3.4.2
Beta_for_GEO.txt includes Beta-mixture Quantile (BMIQ) normalized Beta Values.

label: Cy5 and Cy3

source_name: umbilical cord blood buffy coat 181

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from cord blood samples using QIAamp Blood DNA mini kit according to standard instructions.

tag: gender

value: Female

value: Umbilical cord blood buffy coat

tag: maternal gdm status

value: No GDM


title: IBET rep2 [ATAC-seq]

value: Ibet only


title: Genomic DNA from umbilical cord blood buffycoat 180

description:
U197
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 180


title: GA H3K79me2 Rep2 (expt2)

description:
Corresponding replicate: ADPH-89
GA_H3K79me2.bw
GA_H3K79me2_c40.0_C35.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: Di-Methyl-Histone H3 (Lys79) (D15E8) XP Rabbit mAb, CST, 5427S, Lot No 4


title: GA H3K79me2 Rep1 (expt2)

description:
Corresponding replicate: ADPH-90
GA_H3K79me2.bw
GA_H3K79me2_c40.0_C35.00_l200_g50_G800_broad.bed12.GAPPEDPEAK


title: PN3

value: uninvolved psoriatic skin


title: RANKL rep2 [ATAC-seq]

value: Monocyte-derived cell line

value: RANKL


title: PN4


title: GA H3K27me3 Rep2 (expt2)

description:
Corresponding replicate: ADPH-84
GA_H3K27me3.bw

value: male

value: Tri-Methyl-Histone H3 (K27) (C36B11) Rabbit mAb, CST, 9733S, Lot No 14


title: Raw rep2 [ATAC-seq]

value: Untreated


title: PN2


title: GA H3K36me3 Rep2 (expt2)

description:
Corresponding replicate: ADPH-86
GA_H3K36me3.bw
GA_H3K36me3_c75.0_C74.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: whole organism

value: mature, 4 weeks old

value: wild type

value: Tri-Methyl-Histone H3 (Lys36) (D5A7) XP Rabbit mAb, CST, 4909S, Lot No 2


title: GA H3K27me3 Rep1 (expt2)

description:
Corresponding replicate: ADPH-85
GA_H3K27me3.bw

value: gametophyte


title: RI rep1 [ATAC-seq]

value: RANKL+Ibet

value: 4 hours


title: GA H3K36me3 Rep1 (expt2)

description:
Corresponding replicate: ADPH-88
GA_H3K36me3.bw
GA_H3K36me3_c75.0_C74.00_l200_g50_G800_broad.bed12.GAPPEDPEAK


title: PN1

value: epidermis and dermis


title: Genomic DNA from umbilical cord blood buffycoat 177

description:
U194
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 177

value: Female

value: Umbilical cord blood buffy coat

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 178

description:
U195
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 178

value: GDM


title: Genomic DNA from umbilical cord blood buffycoat 179

description:
U196
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 179

value: Male


title: Genomic DNA from umbilical cord blood buffycoat 176

description:
U193
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 176


title: GA H3K14ac Rep2 (expt2)

description:
Corresponding replicate: ADPH-95
GA_H3K14ac.bw
GA_H3K14ac_c20.0_l200_g50_peaks.narrowPeak

value: Acetyl-Histone H3 (Lys14) (D4B9) Rabbit mAb, CST, 7627S, Lot No 0001


title: GA H3K14ac Rep1 (expt2)

description:
Corresponding replicate: ADPH-99
GA_H3K14ac.bw
GA_H3K14ac_c20.0_l200_g50_peaks.narrowPeak

value: male


title: RANKL rep1 [ATAC-seq]

value: Monocyte-derived cell line

value: RANKL


title: Raw rep1 [ATAC-seq]

value: Untreated


title: Genomic DNA from umbilical cord blood buffycoat 175

description:
U192
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 175


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW-pob3-E154K, 30C, 2

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

country: USA

institute: Harvard Medical School

description:
full genotype name:
MATα (V5)x3-SPN1 spt6-YW pob3-E154K ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.

data_processing:
Reads were demultiplexed using fastq-multx (Aronesty, 2013), allowing one mismatch to the index sequence and A-tail. Cutadapt (Martin, 2011) was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2 (Langmead and Salzberg, 2012), and alignments with a mapping quality of at least 5 were selected using SAMtools (Li et al., 2009). The median fragment size estimated by MACS2 (Zhang et al., 2008b) cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. The quality of raw, cleaned, non-aligning, and uniquely aligning reads was assessed using FastQC (Andrews, 2014).
Genome_build: S. cerevisiae R64-2-1, S. pombe ASM294v2
Supplementary_files_format_and_content: BigWigs of spike-in normalized estimated factor protection, estimated fragment midpoints, and the log2 ratio of IP over input.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures were grown in YPD at 30ºC or were shifted to growth at 37ºC for 80 minutes before further processing or collection of the cells, as described previously (Cheung et al., 2008)

extract_protocol:
The cultures were processed for cross-linking and collecting as previously described (Doris et al., 2018). Chromatin was prepared using standard methods (Gopalakrishnan et al., 2019). Each chromatin sample was mixed with S. pombe chromatin (strain FWP570) at 10% level by protein mass for spike-in normalization and split into aliquots of 500 µg of chromatin for immunoprecipitation. Chromatin precipitations were performed overnight at 4°C using either 50 µl of anti-FLAG M2 affinity gel (Sigma) for Spt6, 30 µl of anti-Myc antibodies (9E10, Santa Cruz Biotechnology), 8 µl of 8WG16 antibodies (Millipore Sigma) for Rpb1, or 5 µl of anti-V5 antibodies (Invitrogen) per 500 µg of chromatin.
DNA isolated from each sample before precipitation (inputs) and after precipitation (IP) was used for library generation as previously described (Gopalakrishnan et al., 2019).

tag: strain

tag: genotype

value: V5-Spn1 background spt6-YW-pob3-E154K

tag: rna population


title: RI h24 rep2 [RNA-seq]

data_processing:
Quality Check (FastQC).
Sequence reads aligned to the GRCm38 by STAR (version 2.5.3a) --alignTranscriptsPerReadNmax 100000 --limitGenomeGenerateRAM 20000000000, and chimeric outputs were allowed.
Raw counts of each library were obtained using the Rsubread (version 1.24.2) R/Bioconductor package.
The DESeq2 (version 1.16.1) R/Bioconductor package was used for normalizing the counts and implementing the DE analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: allsamples_RPKM_withmm10.csv: Normalized counts (RPKM) file for all samples; comma-separated text file.
Supplementary_files_format_and_content: brd_allrawcounts.csv: Raw counts for all samples; comma-separated text file.

extract_protocol:
RNA extraction: Nucleospin RNA kit (Macherey-Nagel).
Libraries preparation: NEBNext poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra RNA Library Prep kit; Sequenced: Illumina HiSeq 2500 paired-end 100bp reads. Two replicates per time point and treatment were made.

treatment_protocol: Total RNA was isolated from RAW264.7 cells at 0, 4, 14 and 24h after RANKL, RANKL/I-BET, or I-BET treatment.

tag: cell line

value: RI

value: hour 24


title: RI h24 rep1 [RNA-seq]

tag: cell type


title: Genomic DNA from umbilical cord blood buffycoat 173

description:
U190
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 173


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 pob3-E154K ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes.

value: V5-Spn1 background pob3-E154K


title: GA H3K4me2 Rep2 (expt2)

description:
Corresponding replicate: ADPH-87
GA_H3K4me2.bw
GA_H3K4me2_c23.0_l200_g50_peaks.narrowPeak

value: whole organism

value: mature, 4 weeks old

value: wild type

value: gametophyte

value: Di-Methyl-Histone H3 (Lys4) (C64G9) Rabbit mAb, CST, 9725S, Lot No 9


title: IBET h24 rep2 [RNA-seq]

tag: treatment

value: IBET


title: Genomic DNA from umbilical cord blood buffycoat 174

description:
U191
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 174

value: Female

value: Umbilical cord blood buffy coat

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 172

description:
U189
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 172


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 1

source_name: V5-Spn1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: IBET h24 rep1 [RNA-seq]

tag: time point


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW-pob3-E154K, 30C, 1

source_name: V5-Spn1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: RANKL h24 rep2 [RNA-seq]


title: Genomic DNA from umbilical cord blood buffycoat 171

description:
U188
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 171

value: Male


title: RANKL h24 rep1 [RNA-seq]

value: Monocyte-derived cell line


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 spt6-YW ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq IP library from an spt6-YW strain shifted to 30°C for 80 minutes.

value: V5-Spn1 background spt6-YW


title: Genomic DNA from umbilical cord blood buffycoat 170

description:
U187_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 170


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes.

value: V5-Spn1 background wild type


title: GA Input Rep1 (expt2)

description: Corresponding replicate: ADPH-110

tag: Sex

value: male


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 1

source_name: V5-Spn1 ChIP-seq IP library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: GA H3K4me2 Rep1 (expt2)

description:
Corresponding replicate: ADPH-91
GA_H3K4me2.bw
GA_H3K4me2_c23.0_l200_g50_peaks.narrowPeak

source_name: gametophyte

tag: tissue


title: pSP RNA Rep 1 (expt1)

description:
Corresponding replicate: GPO-165
featureCounts_output_rmdup_batch1.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx
GPO-164

data_processing:
Illumina base calling
Sequence quality was evaluated with FASTQC and poor quality sequence removed with Flexcat (Dodt M, Roehr JT, Ahmed R, Dieterich C. 2012. FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology 1: 895–905). For the RNA-seq, reads that were shorter than 50 nucleotides after trimming were removed. For ChIP-seq, reads that were shorter than 22 nucleotides after trimming were removed.
Fastq files that end with 50bp_R1 were derived from the corresponding R1 file by trimming to 50 bp.
ChIP-seq Illumina reads were mapped onto the Ectocarpus genome using Bowtie (v2.2.5; Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013)
Peaks corresponding to regions enriched in PTMs were identified using the MACS2 (version 2.1.1) callpeak module (minimum FDR of 0.01) and refined with the MACS2 bdgpeakcall and bdgbroadcall modules (Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biology 9: R137). Colocalised peaks corresponding to regions enriched in several PTMs were detected using MACS2 outputs in BedTools multiinter (Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, Oxford, England 26: 841–842).
Trimmed RNA-seq reads were mapped to the Ectocarpus reference genome using Tophat2 (Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36).
Mapped RNA-seq data was processed with featureCounts (Liao Y, Smyth GK, Shi W, 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics (Oxford, England) 30: 923–930) to obtain counts of numbers of reads mapped to exons. Expression values were represented as TPM.
Differential expression was detected using the DESeq2 package (Bioconductor; Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550) using an adjusted p‐value cut‐off of 0.05 and a minimal fold‐change of 2.
Genome_build: Ectocarpus sp. Ec32 genome v2 2018 (https://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtract from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or GAPPEDPEAK (bed12+3) format.

source_name: partheno-sporophyte

extract_protocol: For ChIP-seq, Ectocarpus tissue was fixed for five minutes in seawater containing 2% formaldehyde and the formaldehyde eliminated by rapid filtering followed by incubation in PBS containing 400 mM glycine. Nuclei were isolated by grinding in liquid nitrogen and in a Tenbroeck Potter in nuclei isolation buffer (0.1% triton X-100, 125 mM sorbitol, 20 mM ptassium citrate, 30 mM MgCl2, 5 mM EDTA, 5 mM β-mercaptoethanol 55 mM HEPES at pH 7.5 with complete ultra protease inhibitors), filtering through Miracloth and then washing the precipitated nuclei in nuclei isolation buffer with and then without triton X-100. Chromatin was fragmented by sonicating the purified nuclei in nuclei lysis buffer (10 mM EDTA, 1% SDS, 50 mM Tris-HCl at pH 8 with complete ultra protease inhibitors) in a Covaris M220 Focused-ultrasonicator (duty 25%, peak power 75, cycles/burst 200, duration 900 sec at 6°C). The chromatin was incubated with an anti-histone PTM antibody overnight at 4°C and the immunoprecipitation carried out using Dynabeads protein A and Dynabeads protein G. Following immunoprecipitation and washing, a reverse cross-linking step was carried out by incubating for at least six hours at 65°C in 5 M Na Cl and the samples were then digested with Proteinase K and RNAse A. The purified DNA was then prepared for Illumina sequencing. For RNA-seq, RNA was extracted from the same duplicate sporophyte and gametophyte cultures as were used for the ChIP-seq analysis using the Qiagen RNeasy plant mini kit with an on-column Deoxyribonuclease I treatment. RNA quality and concentration was then analysed on 1.5% agarose gel stained with ethidium bromide and a NanoDrop ND-1000 spectrophotometer (NanoDrop products, Wilmington, DE, USA).

tag: Stage

value: partheno-sporophyte


title: pSP RNA Rep 2 (expt1)

description:
Corresponding replicate: GPO-164
featureCounts_output_rmdup_batch1.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx
GPO-165

tag: phenotype


title: Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 1

source_name: V5-Spn1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes.


title: SP_FAIRE_2 (expt1)

description:
Corresponding replicate: JGP-3
JGP-4.RPKM.rmdup.bw

tag: generation


title: RI h14 rep2 [RNA-seq]

source_name: Bone marrow

value: RI

value: hour 14


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 168

description:
U185
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 168


title: GA Input Rep2 (expt2)

description: Corresponding replicate: ADPH-105

value: whole organism

tag: chip antibody


title: RI h14 rep1 [RNA-seq]


title: Genomic DNA from umbilical cord blood buffycoat 167

description:
U184
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 167

value: GDM


title: IBET h14 rep2 [RNA-seq]


title: SP_K27me2_2 (expt1)

description:
Corresponding replicate: GPO-132
SP_H3K27me2.bw

value: mature, 4 weeks old

value: wild type

value: Anti-dimethyl-Histone H3 (Lys27), Millipore, 07-452, Lot No 2593892

tag: sample code


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 30C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: SP_K27me2_1 (expt1)

description:
Corresponding replicate: GPO-138
SP_H3K27me2.bw


title: Genomic DNA from umbilical cord blood buffycoat 166

description:
U183
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 166


title: IBET h14 rep1 [RNA-seq]

value: IBET


title: Genomic DNA from umbilical cord blood buffycoat 165

description:
U182
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 165

value: Female


title: Genomic DNA from umbilical cord blood buffycoat 169

description:
U186
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 169

value: Umbilical cord blood buffy coat


title: Genomic DNA from umbilical cord blood buffycoat 164

description:
U181
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 164

value: No GDM


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 30C, 1

source_name: Spt16-myc ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: RANKL h14 rep2 [RNA-seq]

value: RANKL


title: SP_K9me3_1 (expt1)

description:
Corresponding replicate: GPO-136
SP_H3K9me3.bw

value: Histone H3K9me3 antibody (pAb), ActiveMotif, 39161, Lot No 13509002


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT16-Myc pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes.

value: Spt16-myc background pob3-E154K


title: SP_K9me3_2 (expt1)

description:
Corresponding replicate: GPO-130
SP_H3K9me3.bw


title: RANKL h14 rep1 [RNA-seq]

value: Monocyte-derived cell line


title: Genomic DNA from umbilical cord blood buffycoat 162

description:
U179
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 162


title: Genomic DNA from umbilical cord blood buffycoat 163

description:
U180
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 163

value: Male


title: RI h4 rep1 [RNA-seq]

value: hour 4


title: SP_FAIRE_1 (expt1)

description:
Corresponding replicate: JGP-4
JGP-3.RPKM.rmdup.bw

value: male

value: partheno-sporophyte


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 1

source_name: Spt16-myc ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes.


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 2

description:
full genotype name:
MATα SPT16-Myc pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: RI h4 rep2 [RNA-seq]

value: RI


title: Genomic DNA from umbilical cord blood buffycoat 161

description:
U178
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 161


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 1

source_name: Spt16-myc ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: IBET h4 rep2 [RNA-seq]


title: SP_K27ac_2 (expt1)

description:
Corresponding replicate: GPO-131
SP_H3K27ac.bw
SP_H3K27ac_c15.0_l200_g50_peaks.narrowPeak

value: whole organism

value: Anti-acetyl-Histone H3 (Lys27) (rabbit antiserum), Millipore, 07-360, Lot No 2987402


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 37C, 1

source_name: Spt16-myc ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 37C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from an spt6-YW strain shifted to 37°C for 80 minutes.

value: Spt16-myc background Spt16-YW


title: Genomic DNA from umbilical cord blood buffycoat 160

description:
U177
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 160


title: Genomic DNA from umbilical cord blood buffycoat 159

description:
U176
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 159

value: GDM


title: IBET h4 rep1 [RNA-seq]

value: IBET


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 37C, 1

source_name: Spt16-myc ChIP-seq IP library from an spt6-YW strain shifted to 37°C for 80 minutes.


title: SP_K9me2_2 (expt1)

description:
No replicate
SP_H3K9me2.bw

source_name: partheno-sporophyte

value: mature, 4 weeks old

value: wild type

value: ChIPAb+ Dimethyl Histone H3 (Lys9), Millipore, 17-681, Lot No 2909708


title: RANKL h4 rep2 [RNA-seq]

source_name: Bone marrow

value: RANKL


title: Genomic DNA from umbilical cord blood buffycoat 158

description:
U175
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 158

value: Umbilical cord blood buffy coat

value: No GDM


title: SP_K9ac_1 (expt1)

description:
Corresponding replicate: GPO-134
SP_H3K9ac.bw
SP_H3K9ac_c30.0_l200_g50_peaks.narrowPeak

value: Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb, CST, 9649S, Lot No 0011


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 30C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 157

description:
U174
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 157

value: Male


title: RANKL h4 rep1 [RNA-seq]

value: Monocyte-derived cell line

value: hour 4


title: SP_K4me3_2 (expt1)

description:
Corresponding replicate: GPO-127
SP_H3K4me3.bw
SP_H3K4me3_c25.0_l200_g50_peaks.narrowPeak

value: male

value: partheno-sporophyte

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb, CST, 9751S, Lot No 0009


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 2

description:
full genotype name:
MATα SPT16-Myc leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes.

value: Spt16-myc background wild type


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 30C, 1

source_name: Spt16-myc ChIP-seq IP library from an spt6-YW strain shifted to 30°C for 80 minutes.

value: Spt16-myc background Spt16-YW


title: SP_K4me3_1 (expt1)

description:
Corresponding replicate: GPO-133
SP_H3K4me3.bw
SP_H3K4me3_c25.0_l200_g50_peaks.narrowPeak

value: whole organism


title: Genomic DNA from umbilical cord blood buffycoat 155

description:
U170
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 155

value: Female


title: SP_K27ac_1 (expt1)

description:
Corresponding replicate: GPO-137
SP_H3K27ac.bw
SP_H3K27ac_c15.0_l200_g50_peaks.narrowPeak

value: mature, 4 weeks old

value: Anti-acetyl-Histone H3 (Lys27) (rabbit antiserum), Millipore, 07-360, Lot No 2987402


title: Genomic DNA from umbilical cord blood buffycoat 156

description:
U171
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 156


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 2

description:
full genotype name:
MATα SPT16-Myc leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 154

description:
U169
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 154


title: SP_H3_1 (expt1)

description:
Corresponding replicate: GPO-141
SP_H3Cterm.bw

value: wild type

value: Histone H3 (D2B12) XP Rabbit mAb (ChIP Formulated), CST, 4620S, Lot No 12


title: SP_H3_2 (expt1)

description:
Corresponding replicate: GPO-112
SP_H3Cterm.bw


title: AIF5_F

city: Parkville

first: Kathryn

last: Gurner

state: VIC

address: Royal Parade

country: Australia

institute: University of Melbourne

description:
DESeq2_result_file_on_data_IVC_v_Con_liver.txt
DESeq2_result_file_on_data_IVC_v_GF_liver.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of  raw FASTQ data files was assessed with FastQCgroomer
Trim Galore! was used to trim the 13 bp of Illumina standard adapters from the ends of reads.
Reads were aligned to the UCSC GRCm38.98/mm10 reference genome with RNA STAR
featureCounts was used to measure gene expression as counted reads
DESeq2 was used to identify differentially expressed genes (DEGs) and their fold changes from count data.
Genome_build: UCSC GRCm38.98/mm10
Supplementary_files_format_and_content: DESeq2 txt/tabular files contain Ensembl Gene IDs (ENSG), mean normalised counts, log2(fold change), standard error of the log2(fold change), Wald statistic, p-value, and p-value adjusted with the Benjamini-Hochberg procedure which controls false discovery rate (FDR), for each gene

source_name: Murine 14.5 Liver

growth_protocol: Embryos were collected from superovulated female mice and cultured individually in 2uL drops under 5% Oxygen. D4 blastocysts were transferred to the uteri of pseudopregnant female mice and allowed to grow for 10 days. Fetuses and placentas were collect on E14.5 and tissues harvested for RNA extraction

extract_protocol:
Livers and placentas were removed, flash frozen in Liquid nitrogen. Tissues were lysed and total RNA was harvested using Qiagen RNAeasy Minikit. RNA was analysed on the Illumina HiSeq 2500 system at the Australian Genome Research Facility (AGRF)  with 1 ug of total RNA as input for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Embryos (and resultant fetal tissues) designated treatment were cultured in G series media supplemenented with a combination of growth factors and cytokines (VEGF, IGF1, IGF2, PDGF, GCSF) for the duration of the culture period. Control embryos were cultured in G series media containing no growth factors or cytokines.

value: Liver

tag: developmental stage

value: C57BI/6 x CBA F1

value: In vivo developed


title: Control(h0) rep1 [RNA-seq]

value: Control

value: hour 0


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 1

source_name: Spt16-myc ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes.


title: AIF6_F


title: SP_K9ac_2 (expt1)

description:
Corresponding replicate: GPO-128
SP_H3K9ac.bw
SP_H3K9ac_c30.0_l200_g50_peaks.narrowPeak

value: Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb, CST, 9649S, Lot No 0011


title: AIF4_F


title: Genomic DNA from umbilical cord blood buffycoat 153

description:
U168
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 153

tag: gender

value: Umbilical cord blood buffy coat

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 152

description:
U167
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 152

value: Male

tag: maternal gdm status


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 37C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.

tag: strain

value: Spt6-FLAG background spt6-YW-pob3-E154K


title: Control(h0) rep2 [RNA-seq]

value: Monocyte-derived cell line


title: Genomic DNA from umbilical cord blood buffycoat 150

description:
U164
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 150


title: GA RNA Rep 2 (expt1)

description:
Corresponding replicate: GPO-162
featureCounts_output_rmdup_batch1.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx
GPO-163

source_name: gametophyte

value: male

value: whole organism

value: gametophyte


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 37C, 1

source_name: Spt6-FLAG ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.

tag: genotype


title: AIF3_M


title: AIF1_M


title: GA RNA Rep 1 (expt1)

description:
Corresponding replicate: GPO-163
featureCounts_output_rmdup_batch1.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx
GPO-162

value: mature, 4 weeks old


title: SP_Input_2 (expt1)

description: Corresponding replicate: GPO-111

value: wild type

value: partheno-sporophyte


title: Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 1

source_name: Spt16-myc ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes.

value: Spt16-myc background wild type

tag: rna population


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 30C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: AIF2_M

value: Liver

value: C57BI/6 x CBA F1


title: GTF6_F

description:
DESeq2_result_file_on_data_Con_v_GF_liver.txt
DESeq2_result_file_on_data_IVC_v_GF_liver.txt

value: C57BI/6 x CBA F2

value: Female

value: In vitro treated


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 30C, 1

source_name: Spt6-FLAG ChIP-seq IP library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: Ga_FAIRE_2 (expt1)

description:
Corresponding replicate: JGP-1
JGP-2.RPKM.rmdup.bw


title: Genomic DNA from umbilical cord blood buffycoat 149

description:
U163
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 149

value: Umbilical cord blood buffy coat


title: Ga_FAIRE_1 (expt1)

description:
Corresponding replicate: JGP-2
JGP-1.RPKM.rmdup.bw


title: Genomic DNA from umbilical cord blood buffycoat 148

description:
U162
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 148

value: GDM


title: SP_Input_1 (expt1)

description: Corresponding replicate: GPO-113

source_name: partheno-sporophyte


title: Genomic DNA from umbilical cord blood buffycoat 147

description:
U161
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 147

value: Male

value: No GDM


title: Ga_K27me2_2 (expt1)

description:
Corresponding replicate: GPO-120
GA_H3K27me2.bw

value: Anti-dimethyl-Histone H3 (Lys27), Millipore, 07-452, Lot No 2593892


title: GCF6_F

description:
DESeq2_result_file_on_data_IVC_v_Con_liver.txt
DESeq2_result_file_on_data_Con_v_GF_liver.txt

value: In vitro control


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background pob3-E154K


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 1

source_name: Spt6-FLAG ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes.


title: GIF6_F

value: In vivo developed


title: Ga_K27me2_1 (expt1)

description:
Corresponding replicate: GPO-126
GA_H3K27me2.bw

value: male

value: whole organism

value: mature, 4 weeks old

value: gametophyte


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 146

description:
U160
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 146


title: Genomic DNA from umbilical cord blood buffycoat 151

description:
U165
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 151


title: GTF5_F

value: Liver


title: Ga_K9me3_2 (expt1)

description:
Corresponding replicate: GPO-118
GA_H3K9me3.bw

value: wild type

value: Histone H3K9me3 antibody (pAb), ActiveMotif, 39161, Lot No 13509002


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 1

source_name: Spt6-FLAG ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 145

description:
U159
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 145


title: Ga_K9me3_1 (expt1)

description:
Corresponding replicate: GPO-124
GA_H3K9me3.bw


title: GFC5_F

source_name: Murine 14.5 Liver

value: C57BI/6 x CBA F1

value: Female


title: Genomic DNA from umbilical cord blood buffycoat 144

description:
U158
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 144

value: Umbilical cord blood buffy coat


title: GIF5_F


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from an spt6-YW strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background spt6-YW


title: GTF4_F

value: In vitro treated


title: Ga_K9me2_2 (expt1)

description:
Corresponding replicate: GPO-117
GA_H3K9me2.bw

value: ChIPAb+ Dimethyl Histone H3 (Lys9), Millipore, 17-681, Lot No 2909708


title: GCF4_F


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 1

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: Ga_K9me2_1 (expt1)

description:
Corresponding replicate: GPO-123
GA_H3K9me2.bw


title: Ga_K27ac_2 (expt1)

description:
Corresponding replicate: GPO-119
GA_H3K27ac.bw
GA_H3K27ac_c15.0_l200_g50_peaks.narrowPeak

value: Anti-acetyl-Histone H3 (Lys27) (rabbit antiserum), Millipore, 07-360, Lot No 2987402


title: GIF4_F

description:
DESeq2_result_file_on_data_IVC_v_Con_liver.txt
DESeq2_result_file_on_data_IVC_v_GF_liver.txt


title: Ga_K9ac_2 (expt1)

description:
Corresponding replicate: GPO-116
GA_H3K9ac.bw
GA_H3K9ac_c18.0_l200_g50_peaks.narrowPeak

value: Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb, CST, 9649S, Lot No 0011


title: Ga_K27ac_1 (expt1)

description:
Corresponding replicate: GPO-125
GA_H3K27ac.bw
GA_H3K27ac_c15.0_l200_g50_peaks.narrowPeak


title: MYC RANKL [ChIP-seq_MYC_MAX]

source_name: Bone marrow

tag: cell line

value: Monocyte-derived cell line

value: RANKL

value: 4 hours

value: Myc


title: Genomic DNA from umbilical cord blood buffycoat 140

description:
U154
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 140

value: Male

value: GDM


title: Genomic DNA from umbilical cord blood buffycoat 141

description:
U155
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 141


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 1

description:
full genotype name:
MATα SPT6-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background wild type


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 2

source_name: Spt6-FLAG ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes.


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 2

source_name: Spt6-FLAG ChIP-seq IP library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes.


title: GTF3_M

description:
DESeq2_result_file_on_data_Con_v_GF_liver.txt
DESeq2_result_file_on_data_IVC_v_GF_liver.txt

value: Liver


title: GIF3_M

value: In vivo developed


title: Genomic DNA from umbilical cord blood buffycoat 142

description:
U156
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 142


title: Genomic DNA from umbilical cord blood buffycoat 139

description:
U153
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 139

value: No GDM


title: GCF3_M

description:
DESeq2_result_file_on_data_IVC_v_Con_liver.txt
DESeq2_result_file_on_data_Con_v_GF_liver.txt

value: C57BI/6 x CBA F1

value: In vitro control


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 1

source_name: Spt6-FLAG ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes.


title: Ga_K9ac_1 (expt1)

description:
Corresponding replicate: GPO-122
GA_H3K9ac.bw
GA_H3K9ac_c18.0_l200_g50_peaks.narrowPeak

source_name: gametophyte

value: male

value: whole organism

value: mature, 4 weeks old

value: wild type

value: gametophyte


title: Genomic DNA from umbilical cord blood buffycoat 138

description:
U152
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 138

value: Female

value: Umbilical cord blood buffy coat


title: Genomic DNA from umbilical cord blood buffycoat 143

description:
U157
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 143


title: Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 1

source_name: Spt6-FLAG ChIP-seq IP library from an spt6-YW strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background spt6-YW


title: Genomic DNA from umbilical cord blood buffycoat 135

description:
U149
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 135


title: Ga_K4me3_2 (expt1)

description:
Corresponding replicate: GPO-115
GA_H3K4me3.bw
GA_H3K4me3_c15.0_l200_g50_peaks.narrowPeak

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb, CST, 9751S, Lot No 0009


title: GIF2_M

value: Male


title: Ga_K4me3_1 (expt1)

description:
Corresponding replicate: GPO-121
GA_H3K4me3.bw
GA_H3K4me3_c15.0_l200_g50_peaks.narrowPeak


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 1

description:
full genotype name:
MATα (V5)x3-SPN1 spt6-YW pob3-E154K ura3-52 lys2-128δ leu2Δ1 his3Δ200
Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).

value: V5-Spn1 background spt6-YW pob3-E154K


title: GTF2_M

value: In vitro treated


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 2

source_name: Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: Genomic DNA from umbilical cord blood buffycoat 134

description:
U148
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 134


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 pob3-E154K ura3-52 lys2-128δ leu2Δ1 his3Δ200
Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).

value: V5-Spn1 background pob3-E154K


title: Genomic DNA from umbilical cord blood buffycoat 133

description:
U147
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 133


title: Genomic DNA from umbilical cord blood buffycoat 136

description:
U150
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 136


title: GCF2_M

source_name: Murine 14.5 Liver

value: Liver


title: Ga_H3_2 (expt1)

description:
Corresponding replicate: GPO-108
GA_H3Cterm.bw

value: Histone H3 (D2B12) XP Rabbit mAb (ChIP Formulated), CST, 4620S, Lot No 12


title: Ga_Input_1 (expt1)

description: Corresponding replicate: GPO-109


title: Genomic DNA from umbilical cord blood buffycoat 132

description:
U146
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 132

value: No GDM


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 1

source_name: Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: GIF1_M

value: C57BI/6 x CBA F1

value: In vivo developed


title: Ga_H3_1 (expt1)

description:
Corresponding replicate: GPO-110
GA_H3Cterm.bw

value: male

value: whole organism


title: Ga_Input_2 (expt1)

description: Corresponding replicate: GPO-107

value: mature, 4 weeks old

value: wild type


title: Genomic DNA from umbilical cord blood buffycoat 137

description:
U151
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 137

value: Female


title: GCF1_M

value: In vitro control


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 spt6-YW ura3-52 lys2-128δ leu2Δ1 his3Δ200
Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 30°C for 80 minutes (Spt16-myc background).

value: V5-Spn1 background spt6-YW


title: AIP6_F

description:
DESeq2_result_file_on_data_IVC_v_Con_placenta.txt
DESeq2_result_file_on_data_IVC_v_GF_placenta.txt

source_name: Murine 14.5 Placenta

value: Placenta


title: Genomic DNA from umbilical cord blood buffycoat 131

description:
U145
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 131

value: Male

value: Umbilical cord blood buffy coat


title: Rv1720c.mutant_Glycerol_3

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description:
RBB308
gene_read_counts_mux4168.txt.gz

data_processing:
Raw reads (FASTQ files) were mapped to the M. tuberculosis H37Rv (GenBank accession AL123456) using bowtie2 using default parameters.
The read counts of genes were then counted using featureCounts v1.6.3 using the genome annotations provided in the GenBank file.
Computations were done using the R statistical language version 3.3.1.
Genome_build: M. tuberculosis H37Rv (GenBank accession AL123456)
Supplementary_files_format_and_content: Tab delimited text file with read counts for genes

organism: Mycobacterium tuberculosis

growth_protocol: The logphase culture of Mtb strains was washed with PBST twice and grown in “minimal media” (pH6.5; 0.5 g/L asparagine, 1 g/L KH2PO4, 2.5 g/L Na2HPO4, 50mg/L ferric ammonium citrate, 0.5g/L MgSO4*7H2O, 0.5mg/L CaCl2, 0.1 mg/L ZnSO4) containing either 0.1% glycerol (v/v) or 0.01% cholesterol (w/v). To assess the effect of rifampicin (RIF) on the generation of persisters, in some conditions RIF was added. RNA was isolated from the cultures at day4 using Qiagen RNaeasy Minikit according to manufacturer’s protocols (Qiagen 74104). The RNA was DNase treated using Turbo DNA free kit using manufacturer’s protocol (Thermo Fischer scientific) to remove any genomic DNA contamination. All Mycobacterial total RNAs were analyzed using an Agilent Bioanalyser (Agilent, Santa Clara, CA, USA) for quality assessment with RNA Integrity Number (RIN) range of 5.6 to 9.7 and a median of 7.5. Ribosomal RNA (rRNA) were depleted from 500ng of bacterial RNA using RiboMinus™ Bacteria transcriptome isolation kit (Invitrogen Thermo Fisher Scientific Waltham, MA, USA), according to manufacturer's protocol.

extract_protocol:
cDNA libraries were prepared from the resultant rRNA depleted RNA and 1 ul of a 1:500 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific, Waltham, MA, USA) using Lexogen SENSE Total RNA-Seq Library Prep Kit (Lexogen GmnH, Vienna, Austria) according to manufacturer's protocol except with 21 PCR cycles. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA).
All samples were subjected to an indexed paired-end sequencing run of 2x51 cycles on an Illumina HiSeq 2000 system (Illumina, San Diego, CA, USA) (16 samples/lane).

value: Rv1720c mutant

value: mutant Mtb

tag: media

value: Glycerol

tag: agent

value: No drug


title: Rv1720c.mutant_Glycerol_4

description:
RBB309
gene_read_counts_mux4168.txt.gz

tag: time point


title: Genomic DNA from umbilical cord blood buffycoat 130

description:
U144
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 130

value: No GDM


title: Rv1720c.mutant_Glycerol_2

description:
RBB307
gene_read_counts_mux4168.txt.gz


title: GTF1_M

value: Liver

value: C57BI/6 x CBA F1

tag: Sex

tag: treatment

value: In vitro treated


title: AIP5_F

tag: tissue

value: In vivo developed


title: AIP4_F


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 1

description:
full genotype name:
MATα (V5)x3-SPN1 ura3-52 lys2-128δ leu2Δ1 his3Δ200
Rpb1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes (Spt16-myc background).

value: V5-Spn1 background wild type


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 1

source_name: Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 2

source_name: Rpb1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes (Spt16-myc background).

value: Spt16-myc background spt6-YW pob3-E154K


title: Rv1720c.mutant_Glycerol_1

description:
RBB306
gene_read_counts_mux4168.txt.gz


title: Genomic DNA from umbilical cord blood buffycoat 128

description:
U142
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 128

value: Female


title: Rv1720c.mutant_Cholesterol_4

description:
RBB313
gene_read_counts_mux4168.txt.gz

value: Cholesterol


title: AIP3_M


title: Genomic DNA from umbilical cord blood buffycoat 127

description:
U141
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 127


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 1

source_name: Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes (Spt16-myc background).


title: AIP2_M


title: Rv1720c.mutant_Cholesterol_3

description:
RBB312
gene_read_counts_mux4168.txt.gz


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: Genomic DNA from umbilical cord blood buffycoat 126

description:
U140
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 126

value: GDM


title: Rv1720c.mutant_Cholesterol_1

description:
RBB310
gene_read_counts_mux4168.txt.gz


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT16-Myc pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes (Spt16-myc background).

value: Spt16-myc background pob3-E154K


title: Genomic DNA from umbilical cord blood buffycoat 125

description:
U139
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 125

value: Male


title: Genomic DNA from umbilical cord blood buffycoat 124

description:
U138
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 124

value: Umbilical cord blood buffy coat


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 1

source_name: Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: Genomic DNA from umbilical cord blood buffycoat 129

description:
U143
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 129


title: GCP6_F

description:
DESeq2_result_file_on_data_IVC_v_Con_placenta.txt
DESeq2_result_file_on_data_Con_v_GF_placenta.txt

value: Placenta

value: In vitro control


title: Genomic DNA from umbilical cord blood buffycoat 123

description:
U137
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 123


title: Genomic DNA from umbilical cord blood buffycoat 122

description:
U136
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 122


title: H37Rv_Glycerol_4

description:
RBB301
gene_read_counts_mux4168.txt.gz

value: Wild type

value: Glycerol


title: H37Rv_Glycerol_3

description:
RBB300
gene_read_counts_mux4168.txt.gz

value: No drug


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 1

source_name: Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes (Spt16-myc background).


title: GIP6_F


title: Genomic DNA from umbilical cord blood buffycoat 121

description:
U135
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 121


title: H37Rv_Glycerol_2

description:
RBB299
gene_read_counts_mux4168.txt.gz


title: GTP5_F

description:
DESeq2_result_file_on_data_Con_v_GF_placenta.txt
DESeq2_result_file_on_data_IVC_v_GF_placenta.txt

source_name: Murine 14.5 Placenta


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 1

description:
full genotype name:
MATα SPT16-Myc pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: GCP5_F


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 2

source_name: Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: GTP6_F


title: H37Rv_Glycerol_1

description:
RBB298
gene_read_counts_mux4168.txt.gz


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 37C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 37°C for 80 minutes (Spt16-myc background).

value: Spt16-myc background spt6-YW


title: H37Rv_Cholesterol_4

description:
RBB305
gene_read_counts_mux4168.txt.gz


title: Rv1720c.mutant_Cholesterol_2

description:
RBB311
gene_read_counts_mux4168.txt.gz

value: Rv1720c mutant

value: mutant Mtb


title: Genomic DNA from umbilical cord blood buffycoat 119

description:
U133
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 119

value: No GDM


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 37C, 1

source_name: Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 37°C for 80 minutes (Spt16-myc background).


title: GIP5_F

value: C57BI/6 x CBA F1

value: In vivo developed


title: Genomic DNA from umbilical cord blood buffycoat 120

description:
U134
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 120


title: H37Rv_Cholesterol_3

description:
RBB304
gene_read_counts_mux4168.txt.gz


title: Genomic DNA from umbilical cord blood buffycoat 118

description:
U132
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 118

value: Female


title: H37Rv_Cholesterol_2

description:
RBB303
gene_read_counts_mux4168.txt.gz

value: Cholesterol


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 30C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 30C, 1

source_name: Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: GCP4_F


title: Genomic DNA from umbilical cord blood buffycoat 117

description:
U131
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 117


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 2

description:
full genotype name:
MATα SPT16-Myc leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes (Spt16-myc background).

value: Spt16-myc background wild type


title: GIP4_F


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 1

source_name: Rpb1 ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes (Spt16-myc background).


title: GCP3_M


title: Genomic DNA from umbilical cord blood buffycoat 116

description:
U130
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 116


title: Genomic DNA from umbilical cord blood buffycoat 114

description:
U128
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 114


title: GTP2_M

value: In vitro treated


title: Genomic DNA from umbilical cord blood buffycoat 115

description:
U129
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 115

value: Male

value: GDM


title: GTP3_M

value: Placenta


title: Day_15_WT_489_6

city: Rehovot

first: Ruth

last: Scherz-Shouval

address: Hertzel 234

department: Biomolecular sciences

country: Israel

institute: Weizmann institute of science

data_processing:
Illumina NovaSeq 6000
Reads were trimmed using FastX toolkit,  fastx_trimmer -f 7 -Q33 -i ${sample} -o ${sample}_trimmed (https://www.lexogen.com/sense-data-analysis/)
Low quality tails were removed by fastq_quality_trimmer -t 10 -l 20 -Q33 -v -i ${sample} -o ${sample}_clean (https://www.lexogen.com/sense-data-analysis/)
Reads were mapped to genome /shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Counting was done using STAR. Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Pipeline was constructed using Snakemake (DOI: 10.1093/bioinformatics/bts480).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Distal colon from HSF1 WT mouse

growth_protocol: 8 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions

extract_protocol:
Colons were dissociated by Bead ruptor elite (OMNI international) with metal beads in Micro-tube (Sarstedt #72.694.006). RNA isolation was performed by RNeasy fibrous tissue mini kit (Qiagen #74704) according to manufacturer’s instructions.
Libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen USA) according to the instructions of the manufacturer.

treatment_protocol: HSF1 WT or HSF1 null male mice were injected at the age of 8 weeks 10 mg/kg azoxymethane IP, At day 7 post-injection, mice were given 1.5% dextran sulfate sodium in their drinking water for 5 days, after which mice were sacrficed along with control counterparts (non-treated) and colons were exscied, cleaned and flas-frozen for RNA extraction.

value: HSF1 WT BALB/c x 129SvEV, by McMillan, D. R. et al. 1998

value: IP injection of AOM at week 8, and treatment with 1.5% DSS in drinking water at week 9 for 5 days

value: colon

value: HSF1 WT

tag: mouse age

value: 10 weeks


title: Day_15_KO_511_10

source_name: Distal colon from HSF1 null mouse

value: HSF1 null BALB/c x 129SvEV, by McMillan, D. R. et al. 1998

value: HSF1 NULL


title: Day_15_KO_496_8


title: H37Rv_Cholesterol_1

description:
RBB302
gene_read_counts_mux4168.txt.gz

value: Wild type

value: No drug


title: GIP3_M

value: C57BI/6 x CBA F1

value: In vivo developed


title: Genomic DNA from umbilical cord blood buffycoat 111

description:
U125
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 111

value: Umbilical cord blood buffy coat

value: No GDM


title: Day_0_KO_445_3

value: Control age matched without treatment


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 1

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes (Spt6-FLAG background).

value: Spt6-FLAG background spt6-YW pob3-E154K


title: Genomic DNA from umbilical cord blood buffycoat 113

description:
U127
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 113

value: Male

value: GDM


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 2

description:
full genotype name:
MATα SPT16-Myc leu2Δ1 ura3-52 lys2-128δ
Rpb1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes (Spt16-myc background).

value: Spt16-myc background wild type


title: Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 1

source_name: Rpb1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes (Spt16-myc background).


title: GTP4_F

source_name: Murine 14.5 Placenta

value: Placenta

value: Female

value: In vitro treated


title: AIP1_M


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 1

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes (Spt6-FLAG background).


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes (Spt6-FLAG background).

value: Spt6-FLAG background pob3-E154K


title: Day_15_WT_488_5

value: HSF1 WT BALB/c x 129SvEV, by McMillan, D. R. et al. 1998

value: IP injection of AOM at week 8, and treatment with 1.5% DSS in drinking water at week 9 for 5 days

value: colon

value: HSF1 WT

value: 10 weeks


title: Day_0_WT_434_1


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 1

source_name: Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 37°C for 80 minutes (Spt6-FLAG background).


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 2

source_name: Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes (Spt6-FLAG background).


title: Genomic DNA from umbilical cord blood buffycoat 109

description:
U123
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 109


title: Genomic DNA from umbilical cord blood buffycoat 112

description:
U126
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 112


title: GCP2_M

value: C57BI/6 x CBA F1

value: In vitro control


title: Day_0_KO_446_4

value: HSF1 null BALB/c x 129SvEV, by McMillan, D. R. et al. 1998

value: HSF1 NULL


title: Genomic DNA from umbilical cord blood buffycoat 110

description:
U124
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 110

value: Umbilical cord blood buffy coat

value: No GDM


title: GIP2_M

value: Male

value: In vivo developed


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes (Spt6-FLAG background).


title: Genomic DNA from umbilical cord blood buffycoat 108

description:
U122
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 108


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 1

source_name: Rpb1 ChIP-seq IP library from a pob3-E154K strain shifted to 30°C for 80 minutes (Spt6-FLAG background).


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 2

source_name: Rpb1 ChIP-seq IP library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes (Spt6-FLAG background).

value: Spt6-FLAG background spt6-YW pob3-E154K


title: Native young Rep1

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

country: Germany

institute: Saarland University

description:
single-nuclei RNA
Native_counttable.txt.gz

data_processing:
Raw sequence reads for each sample and dataset were downsampled to 2x200 million PE reads in a PE read-sensitive manner using the seqtk toolkit (v1.3, parameters: sample -s100 <fwd_reads.fq.gz> 200000000) before mapping reads using the mapping software zUMIs (Parekh et al., 2018) (v2.5, relevant parameters: sequence_files: file1: base_definition: -BC(1-16) -UMI(17-27) file2: base_definition: -cDNA(1-91); filter_cutoffs: numb_bases:1 phred: 20 UMI_filter: num_baes: 1 phred: 20; barcodes: barcode_num: 40000 barcode_file: null automatic: yes BarcodeBinning: 1 nReadsperCell: 100 counting_opts: introns:yes downsampling: 0 strand: 0 Ham_Dist: 0 write_ham: no primaryHit: yes twoPass: yes read_layout: SE). We supplied the current version of the mm10 reference genome and gencode annotation (vM22) for the mapping. We targeted for each sample and dataset the top 40,000 cell barcodes, and counted reads in introns and exons, given the considerable amount of intronic reads in nuclear transcripts (following the official 10X guidelines). Cells/nuclei were called using the defaultDrops function (parameters: expected=7000, upper.quant:0.98, lower.prop=0.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: The processed files contain for each library type the concatenated UMI count matrices obtained from the intron+exon matrices of the zUMIs pipeline.

source_name: Hippocampus

growth_protocol: Animals  Aged C57BL/6J male wild-type mice (18 months old) were obtained from the National Institute on Aging, and young C57BL/6J males (2 months of age) were purchased from The Jackson Laboratory. Mice were housed under a 12-h light–dark cycle in pathogen-free conditions in accordance with the Guide for Care and Use of Laboratory Animals of the National Institutes of Health.    All animal procedures were approved by the VA Palo Alto Committee on Animal Research and the institutional administrative panel of laboratory animal care at Stanford University. Male mice were used for all experiments.

extract_protocol:
Nuclei were isolated as described previously in (Habib et al., 2017). Per replicate, we isolated nuclei from the flash-frozen, whole hippocampus of the right hemisphere. All reagents were placed on ice. A lab dish was placed on ice and frozen tissue was placed on the dish before being covered with 1 ml lysis buffer from the Nuclei EZ Prep Kit (Sigma-Aldrich, St. Louis, USA). Tissue was cut into 2 mm-small pieces and the tissue-buffer mix was transferred on a 2 ml tissue grinder placed on ice. 1 ml of fresh lysis buffer was used to rinse the lab dish and then loaded on the tissue grinder as well (2 ml total volume). Tissues were homogenized with 25 strokes with pastel A followed by 15 strokes with pastel B. Tissue homogenate was transferred to a fresh tube on ice, and the tissue grinder was rinsed with 2 ml of fresh lysis buffer, which were subsequently added to said tube (4 ml total volume), followed by 5 min incubation on ice. Nuclei were pelleted with 5 min centrifugation at 500g, before resuspending the pellet with 4 ml fresh lysis buffer. Following further 5 min centrifugation at 500g, lysis buffer was removed and the pellet washed with 4 ml PBS. Nuclei were pelleted and resuspended in 500 μl PBS containing 2 U/ml Protector RNase Inhibitor (Sigma-Aldrich, St. Louis, USA). Nuclei solution was parsed through a 40 μm mesh. Nuclei were counted and concentrations adjusted to ~1 mio nuclei/ml.
Reagents of the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics, Pleasanton, USA) were thawed and prepared according to the manufacturer's protocol. Nuclei/master mix solution was adjusted to target 7,500 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, Pleasanton, USA), according to the manufacturer’s protocol. All reaction and quality control steps, including library construction (using Chromium Single Cell 3′ Library Construction Kit v3) were conducted according to the manufacturer’s protocol and with recommended reagents, consumables and instruments. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent, Santa Clara USA) at the Stanford Protein and Nucleic Acid Facility (http://pan.stanford.edu/index.html).    Native libraries: Illumina sequencing of 10X snRNA-seq libraries was performed by Novogene Co. Inc. (Sacramento, US; https://en.novogene.com/). Multiplexed libraries were sequenced with 2x150-bp paired-end (PE) reads in a single S4 lane on a Illumina Novaseq S4 (Illumina, San Diego, USA), targeting 215 million reads per library. Base calling, demultiplexing and generation of FastQ files was conducted by Novogene.    Converted libraries: Libraries generated using the Chromium 10X Single Cell 3’ (version 3) kit require a conversion step using the MGIEasy Universal Library Conversion kit (Part Number: 1000004155, MGI Tech Co., Ltd, Shenzhen, China) before DNA nanoballs (DNBs) can be generated. For each library, 50 ng of final 10X library product was further amplified using 5 cycles of PCR to incorporate a 5’ phosphorylation on the forward strand only. Purified PCR product was then denatured and mixed with a “splint” oligonucleotide that is homologous to both P5 and P7 adapter regions of the library to generate a circle. A ligase reaction was then performed to create a complete ssDNA circle of the forward strand. Then an exonuclease digest was performed to remove single stranded non-circularized DNA molecules and splint oligonucleotide. DNBs were then prepared using the MGI CoolMPS PE100 beta sets now available as commercial products (Part Number 1000016935, MGI Tech Co., Ltd, Shenzhen, China). Rolling circle replication time for DNB preparation was set to 25 min. DNBs were loaded onto DNBSEQ-G400 4-lane flowcell provided with the PE100 sequencing set by manual pipetting of DNBs mixed with loading buffer into flowcell lanes using the MGIDL-200H DNB loader as described in the CoolMPS High-throughput Sequencing Set User Manual provided with the kit. Sequencing primers in the MGI CoolMPS PE100 kit were replaced with the primers provided in the High-Throughput Pair-End Sequencing Primer Kit (App-A) (Part Number 1000004156, MGI Tech Co., Ltd, Shenzhen, China) according to the instructions described in the Primer Kit manual. Sequencing was performed with a customized program with 28 sequencing cycles (cell barcode) for the 1st strand and 98 cycles of cDNA followed by 8 cycles of the sample barcode reading for the 2nd strand.  Base calling and generation of FastQ files on the DNBSEQ-G400 was performed using the software release for CoolMPS (BasecallLite version_1.0.7.84).

tag: group

value: Native

tag: age

value: 2 months (young)


title: Native old Rep2

value: 18 months (old)


title: KO#3_GTCCGC

city: Stanford

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

data_processing:
bcl2fastq was used for demultiplexing and fastq file generation from bcl files
fastq files were trimmed with trimmomatic
fastq files were aligned to mm10 using HISAT2
transcripts were annotated using stringtie
differential gene analysis was done using ballgown
Genome_build: mm10
Supplementary_files_format_and_content: fold change file was created using ballgown; counts file was created using stringtie, Gene IDs are ucsc gene ids.

source_name: E17.5 growth plate

extract_protocol:
embryonic growth plates were manually disected and snap frozen. RNA was extracted using trizol and RNA columns
libraries were prepared according to llumina's instructions accompanying the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat

value: growth plate

value: C57BL/6 x 129S4/SvJae


title: Day_0_WT_435_2

value: HSF1 WT BALB/c x 129SvEV, by McMillan, D. R. et al. 1998

value: Control age matched without treatment

value: colon


title: Native young Rep2


title: Genomic DNA from umbilical cord blood buffycoat 106

description:
U120_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 106


title: WT#3_ATGTCA


title: KO#1_CCGTCC


title: Genomic DNA from umbilical cord blood buffycoat 105

description:
U119
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 105

value: Female


title: KO#2_GTGAAA


title: GTP1_M

value: Placenta

value: C57BI/6 x CBA F1

value: In vitro treated


title: GIP1_M

description:
DESeq2_result_file_on_data_IVC_v_Con_placenta.txt
DESeq2_result_file_on_data_IVC_v_GF_placenta.txt


title: GCP1_M

value: In vitro control


title: CITE-seq Aged_Ctrl v ABX ADT

city: Dallas

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

data_processing:
Library strategy: CITE-seq
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V3.0.2 was used for alignment, filtering, barcoding counting, cDNA UMI counting and antibody counting
Nextera primers and HTO1-6 were used for sample level demultiplexing and group assignment. Primer combination; SI-GA-A2, UDI01 and UDP01 were from the young control and young ABX libraries. Reads with this primer combination divided into separate samples by the following HTO assignments: HTO1: young control brain, replicate 1; HTO2: young control brain, replicate 2; HTO3: young control brain, replicate 3; HTO4: young ABX brain, replicate 1; HTO5: young ABX brain, replicate 2; HTO6: young ABX brain, replicate 3. Primer combination; SI-GA-B2, UDI02 and UDP04 were from the aged control and aged ABX libraries. Reads with this primer combination divided into separate samples by the following HTO assignments: HTO1: aged control brain, replicate 1; HTO2: aged control brain, replicate 2; HTO3: aged control brain, replicate 3; HTO4: aged ABX brain, replicate 1; HTO5: aged ABX brain, replicate 2; HTO6: aged ABX brain, replicate 3.
After generating the digital gene expression data matrices, the Seurat v3.0.1 R pacckage was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10-3.0.0 (10x genomics)
Supplementary_files_format_and_content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts
Supplementary_files_format_and_content: SCT.normalized.RNA.counts.csv: RNA counts
Supplementary_files_format_and_content: ADT.counts.csv: ADT counts
Supplementary_files_format_and_content: metadata.csv: Metadata
Supplementary_files_format_and_content: TotalA_Ref.csv: CITE-seq antibody list

source_name: brain cells

extract_protocol:
Mice were perfused with PBS and brains extracted. Brains digested with papain-based multi-tissue dissocation kit (Miltenyi). Mononuclear cells enriched by 70%/37%/30% percoll gradient centrifugation.
For RNA expression (cDNA), we followed 10x genomics single cell 3’ v3 assay standard protocol. For ADT and HTO, we followed CITE-seq and Cell hashing protocol as provided here:https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf
10x genomics single cell 3’ v3.1 assay

tag: mouse strain

value: female

value: whole brain

tag: molecule subtype

value: ADT (cell surface)


title: WT#2_AGTTCC


title: Genomic DNA from umbilical cord blood buffycoat 102

description:
U116
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 102

tag: gender

value: Male

value: Umbilical cord blood buffy coat

value: GDM


title: Genomic DNA from umbilical cord blood buffycoat 104

description:
U118
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 104

tag: maternal gdm status


title: Genomic DNA from umbilical cord blood buffycoat 107

description:
U121
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 107

value: No GDM


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 1

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 30°C for 80 minutes (Spt6-FLAG background).

tag: strain

value: Spt6-FLAG background spt6-YW


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 37°C for 80 minutes (Spt6-FLAG background).

tag: genotype


title: CITE-seq Aged_Ctrl v ABX HTO

value: HTO1-HTO6 (hashing marker)


title: Native old Rep1

value: Native

value: 18 months (old)


title: Genomic DNA from umbilical cord blood buffycoat 103

description:
U117
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 103


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 1

source_name: Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 37°C for 80 minutes (Spt6-FLAG background).

tag: rna population


title: K562 Drosha KD-2

city: San Francisco

first: Giorgio

last: Lagna

state: CA

address: 555 Mission Bay Blvd South

department: CVRI

institute: UCSF

data_processing:
Reads were mapped to a collection of rRNAs, snoRNAs, tRNAs and miRNAs using bowtie2 (2.3.4.1).
Unmapped reads were mapped to the human genome (hg38) using STAR (2.6.0a)
supplied with the GENCODE v25 .gtf file
Counts on exonic regions were obtained using GenomicAlignments (1.20.1)
Differential analysis was performed with DESeq2 (1.24.0)

growth_protocol: 10%FBS in RPMI1640 media (Corning 10-040-CV) supplemented with 200μM L-glutamine, 100 μM sodium pyruvate and 1% penicillin/streptomycin at 37˙C, 5% CO2

extract_protocol:
Whole cell lysate was prepared by mechanical trituration in lysis buffer (20mM Tris pH 7.4, 150mM NaCl, 5mM MgCl2, 1mM DTT, 1% Triton X-100, 25U/ml TURBO Dnase) followed by RNA extraction using Zymo Research DIRECT-ZOL RNA Kit.
Libraries were contructed using the TruSeq Stranded Total RNA kit from Illumina

treatment_protocol: infected with crispr lentivirus and then selected with 2.5 ng/μl puromycin

tag: cell line

tag: crispr

value: DROSHA

tag: passages


title: Genomic DNA from umbilical cord blood buffycoat 101

description:
U114
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 101


title: CITE-seq Aged_Ctrl v ABX mRNA/cDNA

value: mRNA/cDNA (transcriptome)


title: CITE-seq Young_Ctrl v ABX HTO


title: WT#1_AGTCAA

value: growth plate

value: C57BL/6 x 129S4/SvJae


title: K562 Ctrl-2

value: non-pecific


title: Genomic DNA from umbilical cord blood buffycoat 100

description:
U113
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 100


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes (Spt6-FLAG background).

value: Spt6-FLAG background wild type


title: Genomic DNA from umbilical cord blood buffycoat 98

description:
U111
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 98


title: CITE-seq Young_Ctrl v ABX mRNA/cDNA

description: Zhang_Golomb_Young-Ctrl-ABX_SI-GA-A2_Lib

value: female


title: K562 Ctrl-1

value: non-specific


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 1

source_name: Rpb1 ChIP-seq IP library from a wild-type strain shifted to 37°C for 80 minutes (Spt6-FLAG background).


title: Genomic DNA from umbilical cord blood buffycoat 99

description:
U112
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 99


title: CITE-seq Young_Ctrl v ABX ADT

value: whole brain

value: ADT (cell surface)


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 2

source_name: Rpb1 ChIP-seq IP library from a spt6-YW strain shifted to 30°C for 80 minutes (Spt6-FLAG background).


title: Genomic DNA from umbilical cord blood buffycoat 97

description:
U110
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 97

value: Male

value: Umbilical cord blood buffy coat


title: SREBP

city: dallas

first: Philipp

last: Scherer

address: 5323 harry hines

institute: UTsouthwestern

data_processing:
RNA sequencing via Illumina platforms, based on mechanism of SBS (sequencing by synthesis), has a large range of benefits on high throughput and high accuracy out of low sample requirements. This technical method can be a powerful tool for researching RNA transcriptional activity.
RNA sequencing projects are carried out as follows:
RNA=>library prep=>sequencing=>bioinfomatic analysis
Analysis Software Version Parameter
Mapping STAR v2.6.1 mismatch = 2
Quantification HTSeq v0.6.1
Differential Analysis DESeq2 v2_1.6.3 padj<0.05
EdgeR v3.16.5 padj<0.005 and |log2(FoldChange)| > 1 For sample without bio-replicate
Enrichment Analysis ClusterProfiler v2.4.3 padj < 0.05
Protein-Protein Interaction Analysis NCBI BLAST v2.2.28 e-value = 1e-10
Alternative splicing rMATS v3.2.5 Default
Fusion gene Star-fusion v1.5.0 Default
SNP/InDel Analysis GATK v4.1 MQ < 40.0 and QD < 2.0
ANNOVAR v2.4 Default SNP/InDel Annotation
Novel Gene prediction StringTie v1.3.3b Default
CuffCompare v2.1.1 Default Compare transcriptomes
Genome_build: mm10
Supplementary_files_format_and_content: fpkm, XLS

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent with columm.
RNA libraries were prepared Novogen (https://en.novogene.com/)

value: FVB

value: liver

value: 12 months

value: hSREBP transgenic


title: SREBP-ETP

value: hSREBP/Endotrophin transgenic


title: K562 Drosha KD-1

value: DROSHA


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Rpb1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes (Spt6-FLAG background).


title: ChIP-seq input DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 spt6-YW pob3-E154K ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq input library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.

data_processing:
Reads were demultiplexed using fastq-multx (Aronesty, 2013), allowing one mismatch to the index sequence and A-tail. Cutadapt (Martin, 2011) was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2 (Langmead and Salzberg, 2012), and alignments with a mapping quality of at least 5 were selected using SAMtools (Li et al., 2009). The median fragment size estimated by MACS2 (Zhang et al., 2008b) cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. The quality of raw, cleaned, non-aligning, and uniquely aligning reads was assessed using FastQC (Andrews, 2014).
Genome_build: S. cerevisiae R64-2-1, S. pombe ASM294v2
Supplementary_files_format_and_content: BigWigs of spike-in normalized estimated factor protection and estimated fragment midpoints.

value: V5-Spn1 background spt6-YW pob3-E154K


title: Genomic DNA from umbilical cord blood buffycoat 96

description:
U109
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 96

value: GDM


title: H37Rv_Glycerol_Rifampicin_8

description:
RBB466
gene_read_counts_mux5708.txt.gz

value: Wild type

tag: time point

tag: media

value: Glycerol

tag: agent

value: Rifampicin


title: ChIP-seq input DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 1

source_name: V5-Spn1 ChIP-seq input library from a spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: Kasumi-1, siRR treated replicate 3

city: Newcastle Upon Tyne

first: Olaf

last: Heidenreich

address: Brewery Lane

department: Wolfson Childhood Cancer Research Centre

institute: Newcastle University

description: nascent RNA

data_processing:
Sequenced reads were aligned using the function subjunc from the R/Bioconductor library Rsubread v.1.22.3 with default parameters. Only uniquely mapped reads with the maximum of 3 mismatched bases in the alignment were collected.
The function featureCounts from the R/Bioconductor library Rsubread was used to assign the mapped RNA-Seq reads to the genomic features in case of exonic and/or intronic bins or to the meta-features (genes) in case of exon clusters. Each read pair was counted in unstranded mode with the minimum 1 base overlapping an exonic bin or exon cluster and minimum 5 bases overlapping an intronic bin.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every sample
Supplementary_files_format_and_content: tab-delimited text file with raw exon-exon junction counts for every sample

source_name: Kasumi1 cells after RUNX1/RUNX1T1 knockdown

growth_protocol: Kasumi-1 (DSMZ no. ACC 220) cells were obtained from the DSMZ (LGC Standards GmbH, Wesel, Germany) and cultivated according to the standard approaches.

extract_protocol:
Kasumi-1 cells were lysed using TRI Reagent® (Sigma-Aldrich, St Louis, USA) and RNA was purified according to the manufacturer’s instruction. Next, 4-thiouridine-incorporated RNA was biotinylated by labelling with 1 mg/ml Biotin-HPDP (Abcam, Cambridge, UK) for 90 minutes at room temperature. Following chloroform extraction, labelled RNA was separated using magnetic streptavidin beads, beads were washed and RNA was eluted in two rounds of elution with 100 μl 100 mM DTT. Finally, RNA was purified using RNeasy MinElute Cleanup Kit (QIAGEN GmbH, Hilden, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Kasumi-1 cells were treated with 500 μM 4-thiouridine for 1 hour.

tag: treatment

value: transfection with  RUNX1/RUNX1T1 siRNA


title: Kasumi-1, siRR treated replicate 1

description: nascent RNA


title: ChIP-seq input DNA: V5-Spn1 background: pob3-E154K, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 pob3-E154K ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq input library from a pob3-E154K strain shifted to 30°C for 80 minutes.

value: V5-Spn1 background pob3-E154K


title: H37Rv_Glycerol_Rifampicin_7

description:
RBB465
gene_read_counts_mux5708.txt.gz


title: Genomic DNA from umbilical cord blood buffycoat 94

description:
U107
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 94

value: Female

tag: tissue


title: Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 1

source_name: Rpb1 ChIP-seq IP library from a wild-type strain shifted to 30°C for 80 minutes (Spt6-FLAG background).

value: Spt6-FLAG background wild type


title: Kasumi-1, siMM treated replicate 3

description: nascent RNA

source_name: Kasumi1 cells transfected with mismatch siRNA

value: transfection with mismatch siRNA


title: H37Rv_Glycerol_Rifampicin_6

description:
RBB461
gene_read_counts_mux5708.txt.gz


title: Genomic DNA from umbilical cord blood buffycoat 95

description:
U108
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 95

value: Male

value: Umbilical cord blood buffy coat

value: No GDM


title: H37Rv_Glycerol_Rifampicin_5

description:
RBB460
gene_read_counts_mux5708.txt.gz


title: Genomic DNA from umbilical cord blood buffycoat 92

description:
U105
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 92


title: Kasumi-1, siMM treated replicate 2

description: nascent RNA


title: Kasumi-1, siMM treated replicate 1

description: nascent RNA


title: ChIP-seq input DNA: V5-Spn1 background: pob3-E154K, 30C, 1

source_name: V5-Spn1 ChIP-seq input library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: Kasumi-1, siRR treated replicate 2

description: nascent RNA


title: ChIP-seq input DNA: V5-Spn1 background: spt6-YW, 30C, 1

description:
full genotype name:
MATα (V5)x3-SPN1 spt6-YW ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq input library from an spt6-YW strain shifted to 30°C for 80 minutes.

value: V5-Spn1 background spt6-YW


title: ChIP-seq input DNA: V5-Spn1 background: spt6-YW, 30C, 2

source_name: V5-Spn1 ChIP-seq input library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: H37Rv_Glycerol_7

description:
RBB463
gene_read_counts_mux5708.txt.gz

value: No drug


title: H37Rv_Glycerol_8

description:
RBB464
gene_read_counts_mux5708.txt.gz


title: Genomic DNA from umbilical cord blood buffycoat 91

description:
U104
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 91


title: ChIP-seq input DNA: V5-Spn1 background: wild type, 30C, 2

description:
full genotype name:
MATα (V5)x3-SPN1 ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq input library from a wild-type strain shifted to 30°C for 80 minutes.

value: V5-Spn1 background wild type


title: H37Rv_Glycerol_6

description:
RBB459
gene_read_counts_mux5708.txt.gz