title: DND41_DMSO_H3K27ac_ChIPseq_rep1

value: GSI naive


title: DND41_DMSO_H3K27ac_ChIPseq_rep2

status: Public on Aug 07 2023

type: SRA

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Reads from H3K27ac ChIP-seq experiments were trimmed with Trim Galore (version 606 0.4.1) with parameters -q 15 --phred33 --gzip --stringency 5 -e 0.1 --length 20. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (H. Li and Durbin 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6 and paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) from ChIP-seq were generated with bedtools genomecov. Genome-wide uploadable bigWig files were generated with UCSC tools (version 329) (Kent et al. 2010) bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

molecule: genomic DNA

organism: Homo sapiens

source_name: DND-41 cell line

growth_protocol: DND-41 cells (DSMZ, cat# ACC525) were purchased from the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Lines. Cells were cultured in RPMI 1,640 (Corning, 538 cat# 10-040-CM) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, cat# 539 SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg mL−1 peni-540 cillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 541 11140-050), 1 mM sodium pyruvate (Gibco, cat# 11360-070) and 0.1 mM of 2-mercaptoethanol (Sigma, cat# M6250). All cells were grown at 37 °C and 5% CO2 with media refreshed every 3-4 days.

extract_protocol:
We performed H3K27ac ChIP-seq as previously described (Petrovic et al. 2019). Briefly, we sonicated and cleared chromatin samples prepared from 107 fixed cells with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated these cells with antibodies recognizing H3K27ac (Active Motif, cat# 39133). We captured Antibody-chromatin complexes with recombinant protein G–conjugated Agarose beads, washed them with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted them. After reversal of cross-linking, we performed RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment and purified DNA with QIAquick PCR Purification Kit (Qiagen, cat# 28106).
We then prepared libraries using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). We validated indexed libraries for quality and size distribution using a TapeStation 2200  (Agilent). We performed paired-end sequencing (38 bp+38 bp) on a NextSeq 550.

treatment_protocol: To generate GSI-resistant cells, DND-41 treatment-naïve cells were cultured in the presence of 125 nM GSI for at least six weeks. The establishment of GSI-resistance was determined with IC50 assay as described above. GSI-resistant DND-41 cells can tolerate 10 μM GSI with less than 20% cell death. Short-term DMSO treatment was performed on treatment-naïve DND-41 cells with 125 nM DMSO for 24 hours.

tag: cell line

tag: cell type

value: T Acute Lymphoblastic Leukemia

tag: chip antibody

tag: drug response


title: OVCAR3 p300 TAZ2 sg1 rep2 [ATAC-seq]

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Danpos2 (v2.2.2).
Genome_build: hg38

growth_protocol: OVCAR3 is cultured in DMEM/F-12 with 10% FBS.

extract_protocol:
DNA were extracted by ATAC-Seq Kit (Active Motif, Cat. 53150).
Libraries were constructed using Illumina standard protocols.

tag: genotype/treatment

value: p300 TAZ2 sg1


title: ATAC-Seq mESCs mCherry rep 2

city: Salt Lake City

first: Brad

last: Cairns

state: Utah

address: 2000 Cicle of Hope

department: Oncological Sciences

institute: University of Utah

description: mESCs mCherry rep 2

data_processing:
Sequence reads were trimmed using TrimGalore0.5.0 (-q --phred33 --fastqc --paired)
Trimmed reads were aligned using BowTie2 version 2.4.2
Duplicates were removed using Picard version 2.26.2
Biological replicate samples were merged and indexed using samtools version 1.15
Samples were normalized to mCherry only sample using bamCompare for a log2ratio normalization
Deeptools was used to compute a Matrix at DUX binding sites and create heatmaps or profile plots
Assembly: mm10
Supplementary files format and content: Big wig files with merged biological replicates that were normalized to mCherry only constructs

organism: Mus musculus

source_name: mESCs Dux-/-

growth_protocol: mESCs were maintained in 2iLIF and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Nuclei were pelleted and resuspended in transposase buffer and transposition reaction took place for 30 minutes
ATAC-seq libraries were creating using pre-loaded Mosiac En A/B adaptor and NEBnext High-Fidelity 2X PCR Master Mix followed by a PCR clean-up.

treatment_protocol:
After a 24 hour recovery after plating 1million cells, cells were treated with 0.25ug/mL doxycyline (Clonetech) for 12 hours
Cells were washed 1X with PBS, pelleted, resuspended, and lysed in cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630).

value: mESCs Dux-/-

value: mouse embryonic stem cells

tag: genotype

value: mCherry

tag: treatment

value: 0.25 ug/mL doxycycline

tag: time


title: CF71326_post_15, bulk TCR-seq

city: Amsterdam

first: Joleen

last: Traets

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Count data of TCRb clone IDs in PBMCs, including a column containing the clone ID that matches the scTCRseq data (of the matching patient)

data_processing:
Preprocessing of raw data, including filtering and V/J segment identification was performed using Adaptive's immunoSEQ Analyzer pipeline (Adaptive Biotechnologies, Seattle, WA). Clone IDs were assigned to the unique TCR β chain sequences.
Supplementary files format and content: Table containing the number of templates from each clone IDs detected in the PBMC sample. Overlapping clone IDs based on the TCR β chain detected in the corresponding tumor sample (single cell TCRseq) are indicated in the column “overlapping_clone_ID_tumor”.
Assembly: hg38
Library strategy: bulk TCR-seq

source_name: PBMCs

extract_protocol:
DNA from the PBMCs was extracted in line with the standard protocol for the ImmunoSEQ assay (Adaptive Biotechnologies, Seattle, WA)
Libraries were prepared according to Illumina protocol (by Adaptive Biotechnologies, Seattle, WA.)

tag: tissue

value: PBMCs

tag: patient

tag: response

value: RE

tag: timepoint

value: post


title: OVCAR3 p300 TAZ2 sg1 rep1 [ATAC-seq]


title: phoB::Kn mutant, biological replicate 5, 1 mM K2HPO4 (Pi)

city: Hershey

first: Mauricio

middle: Henriques

last: Pontes

state: PA

address: 500 University Drive

institute: Penn State University

description: total RNA, ribosomal RNA-depleted

library_source: transcriptomic

data_processing:
Untrimmed reads were mapped to the Salmonella enterica serovar Typhimurium 14028s reference genome (plasmid NC_016855.1 and chromosome NC_016856.1) using default settings in the SeqMan NGen (DNASTAR v17.0.2.1) software.
Assembly files were analyzed in Geneious Prime v11 software. RPKM, FPKM, and TPM read counts were calculated using Geneious prior to differential expression analysis using the DeSeq2 Geneious plugin with a false discovery rate of 0.1.
Genes with log 2-fold changes above and adjusted p-values less than 0.01 were considered significantly different.
Assembly: ASM824478v1
Supplementary files format and content: tsv files containing annotated genes, their corresponding locus tags, differential expression values and associated statistic tests and p-values for differentail expressions. Four comparisons were performed: assembled reads from phoB mutant grown in medium lacking phosphorus (P) vs. phoB mutant grown in medium containing phosphate 1 mM K2HPO4 (Pi) for the plasmids and chromosome (phoB_no P vs Pi_NC_016855.tsv and phoB_no P vs Pi_NC_016856.tsv files, respectively), and assembled reads from wild-type  grown in medium lacking P vs. wild-type grown in medium containing Pi for the plasmids and chromosome (WT_no P vs Pi_NC_016855.tsv and WT_no P vs Pi_NC_016856.tsv files, respectively).

molecule: total RNA

organism: Salmonella enterica

growth_protocol: Four independent biological replicates of wild-type and phoB strains were grown in MOPS medium supplemented with 1 mM K2HPO4 to an OD600 of 0.4-0.45. Bacterial cultures were subsequently split into two equal fractions of approximately 10 OD600 units, and were labeled either as “-P” or “+Pi”. -P-treatment cells were washed twice (6,000 X g, 5 min) with MOPS medium lacking K2HPO4 (or any other P source). Conversely, +Pi-treatment cells were washed in MOPS medium supplemented with 1 mM K2HPO4. Bacterial cultures were then grown for 35 min to induce the Pi-starvation response. Cultures were then treated with RNAprotect (Qiagen) for 5 min at RT to stabilize mRNA, and then collected by centrifugation (6,000 X g, 5 min).

extract_protocol:
Cultures were then treated with RNAprotect (Qiagen) for 5 min at RT to stabilize mRNA, and then collected by centrifugation (6,000 X g, 5 min). Total RNA was isolated by hot-phenol extraction, and further purified using the RNeasy Kit (Qiagen) with on-column DNase I treatment. The eluates were treated with Turbo DNase (Invitrogen) for 30 min before a second round of purification using the RNeasy Kit.  rRNA was depleted using the NEBNext® rRNA Depletion kit (Bacteria) and purified from the enzymatic reactions using RNAClean XP magnetic beads (Beckman Coulter) following manufacturer’s instructions. RNA quality and ribosomal depletion was assessed using BioAnalyzer (Agilent).
RNA-seq libraries were made and sequenced by the Genomics Core Facility at Penn State University.

treatment_protocol:
35 minutes in MOPS medium lacking a phosphorus source.
35 minutes in MOPS medium containing 1 mM K2HPO4.

value: Planktonic

value: phoB deletional insertion (deltaphoB::Kn)

value: 1 mM K2HPO4

value: 35 minutes


title: ATAC-Seq mESCs mCherry rep 1

description: mESCs mCherry rep 1


title: ATAC-Seq mESCs deltC12345+14 rep 2

description: mESCs deltC12345+14 rep 2

value: mCherry-deltC12345+14 Dux


title: DND41_GSI_Resistant_scATAC

description: GSI-resistant cells

data_processing:
FASTQ file generation and alignment to hg19 were performed using Cell Ranger ATAC v1.2.0 with default arguments.
Genome_build: hg19
Supplementary_files_format_and_content: Sequencing fragment files

growth_protocol: Cells were cultured in RPMI 1,640 supplemented with 10% fetal bovine serum , 2mM Lglutamine, 100U/mL and 100 μgmL−1 penicillin/streptomycin, 100mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol. All cells were grown at 37 degree C and 5% CO2 with media refreshed every 3-4 days. Cells were regularly tested for mycoplasma contamination.

extract_protocol:
Cells were washed with PBS + 0.04% BSA. After counting, single-cell ATAC-seq was performed using 10X Genomics Chromium Single Cell ATAC Library and Gel Bead Kit and Chromium Chip E Single Cell ATAC Kit following the manufacturer’s instruction.
Cells were loaded onto independent channels of a Chromium Controller for targeted recovery of 4,000 cells per condition. Libraries were assessed with Agilent TapeStation using High sensitivity D1000 chip and quantified using KAPA Library Quantification Kits for Illumina platform (KAPA Biosystems, Roche, cat # KK4824). Paired-end sequencing were performed on NextSeq 550 using 150 cycles High Output kit.

treatment_protocol: To generate GSI-resistant cells, DND41 treatment-naïve cells were cultured in the presence of 125 nM GSI for at least six weeks. Short-term DMSO treatment was performed on treatment-naïve DND41 cells with 125 nM DMSO for 24 hours.

value: T-cell acute lymphoblastic leukemia

tag: drug treatment

value: Gamma Secretase Inhibitor


title: OVCAR3 GFP sg1 rep3 [ATAC-seq]

value: GFP sg1


title: DND41_DMSO_scATAC

description: DMSO treated cells

value: DMSO


title: phoB::Kn mutant, biological replicate 5, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted

value: No phosphorus


title: OVCAR3 GFP sg1 rep2 [ATAC-seq]


title: OVCAR3 p300 TAZ2 sg2 rep1 [ATAC-seq]

value: p300 TAZ2 sg2


title: phoB::Kn mutant, biological replicate 4, 1 mM K2HPO4 (Pi)

description: total RNA, ribosomal RNA-depleted


title: phoB::Kn mutant, biological replicate 4, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted


title: OVCAR3 GFP sg1 rep1 [ATAC-seq]


title: ATAC-Seq mESCs deltC12345+14 rep 1

description: mESCs deltC12345+14 rep 1

value: mESCs Dux-/-

value: mouse embryonic stem cells


title: ATAC-Seq mESCs C3delt14 rep 2

description: mESCs C3delt14 rep 2

value: mCherry-C3delt14 Dux

value: 0.25 ug/mL doxycycline


title: DLD-1 input [ChIP-seq]

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Danpos2 (v2.2.2).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

growth_protocol: OVCAR3 is cultured in DMEM/F-12 with 10% FBS, DLD-1 is cultured in RPMI1640 with 10% FBS.

extract_protocol:
Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).
Libraries were constructed using Illumina standard protocols.

value: input


title: ATAC-Seq mESCs C3delt14 rep 1

description: mESCs C3delt14 rep 1


title: Sperm_HiC_DNaseDTT

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

data_processing:
Hi-C data was analyzed using the Open Chromosome Collective suite (https://github.com/open2c). Briefly, 50bp paired-end fastq files were mapped to mm10 mouse reference genome using the distiller-nf (https://github.com/mirnylab/distiller-nf), invoking bwa mem to map fastq pairs in a single-side regime (-SP). Aligned reads were allowed a 1bp flexibility for removal of optical and PCR duplicates using pairtools (https://github.com/mirnylab/pairtools).
After removal of identical positions and strand orientations, remaining valid pairs were binned into contact matrices of various  resolutions using cooler (Abdennur and Mirny 2020). An iterative balancing procedure (Imakaev et al. 2012) was applied to all matrices, ignoring the first 2 diagonals to avoid short-range ligation artifacts at a given resolution, and bins with low coverage were removed using MADmax filter with default parameters.
Resultant “.cool” contact matrices were used in downstream analyses using cooltools (https://github.com/mirnylab/cooltools) and uploaded to a HiGlass server (Kerpedjiev et al. 2018) via the Reservoir Genome Browser (https://resgen.io/).
Assembly: mm10
Supplementary files format and content: mcool

source_name: Sperm

extract_protocol:
Cells were fixed in 1% formaldehyde and after washing in PBS, left for 1 hour in 50 mM DTT. After quenching with 100mM NEM (N-ethylmaleimide) and washing in PBS, cells were incubated with DpnII overnight at 37°C. After restriction digestion, cells were incubated for 4 hours at 23°C with the Klenow DNA polymerase I to fill in the 5’ overhang and incorporate biotin-14-dATP followed by chromatin ligation for 4 hours at 16°C with T4 DNA ligase (Invitrogen). Then cells were left overnight in 400 ng/ml proteinase K and 0.5% SDS at 60°C overnight to reverse cross-linking.
After DNA purification and precipitation, DNA was sonicated to 200-300 bp fragments and an additional size selection was done with Ampure beads. To repair DNA ends after sonication, T4 DNA polymerase (NEB) and Klenow DNA polymerase (NEB) were used together with T4 polynucleotide kinase (NEB). Biotinylated ligation products were pulled down using streptavidin beads (Invitrogen) followed by A-tailing and adaptor ligation for library construction

value: DNaseDTT

value: Sperm

value: WT


title: Sperm_HiC_DTT

value: DTT


title: phoB::Kn mutant, biological replicate 3, 1 mM K2HPO4 (Pi)

description: total RNA, ribosomal RNA-depleted

value: Planktonic

value: phoB deletional insertion (deltaphoB::Kn)

value: 1 mM K2HPO4

value: 35 minutes


title: HNP SCZ MPRA DNA

city: Chapel Hill

first: Hyejung

last: Won

address: 116 Manning Drive, CB# 7250

institute: University of North Carolina at Chapel Hill

description: Barcoded DNA

library_source: other

data_processing:
Using the barcode-variant relationship decoded from the barcode mapping step, RNA and DNA barcodes from RNA- and DNA-sequencing were mapped back to their corresponding variants. We counted the number of barcodes mapped to each variant and found that each variant was mapped to ~1000 barcodes on average. Next, we aggregated the RNA and DNA barcode counts for each variant. Because different combinations of barcodes could be introduced to different biological replicates, using the same DNA counts measured from the AAV-MPRA library for all biological replicates could lead to incorrect normalization. To mitigate this, if a given RNA barcode was missing in one biological replicate, that barcode was not counted in aggregating DNA counts for that replicate. This way, even when the DNA from the AAV-MPRA library was used, each biological replicate could have different DNA barcode counts guided by RNA barcodes. For example, if barcodes 1, 2, and 3 were mapped to the variant1, and barcode 2 was missing from the RNA barcode count, we would simply sum up the counts for barcodes 1 and 3 for both DNA and RNA. In contrast, if none of the barcodes were measured, that corresponding variant will have NA count. After merging both DNA and RNA counts by those criteria, we discarded any variants that had more than eight NAs across ten replicates.
Assembly: hg19
Supplementary files format and content: Sequenced barcodes from each replicates.

molecule: other

organism: Adeno-associated virus

source_name: AAV DNA input

growth_protocol: Human neural progenitors (HNPs) from Donor number 54 was used for all experiments. 6-well plates were coated with PBS with Poly-L-Ornithine (10 μg/ml; Sigma-Aldrich, cat#P3655-100MG) and PBS with fibronectin (5 μg/ml; Sigma-Aldrich, cat#F1141-5MG). HNPs were plated at 400K cells/well. The cells were plated in Neurobasal A media (Thermo Fisher, cat#10888022) supplemented with primocin (100 μg/ml; Invitrogen, cat#ant-pm-2), BIT 9500 (10%; STEMCELL, cat#09500), glutamax 100X (1%; Fisher Scientific, cat#5112367), Heparin (1 μg/ml; Sigma-Aldrich, cat#H3393-100KU), and growth factors: EGF (20 μg/ml; PeproTech, cat#AF-100-15), FGF (20 μg/ml; PeproTech, cat#AF-100-15), PDGF (20 ng/ml; PeproTech, cat#100-00AB), and LIF (2 ng/ml; PeproTech, cat# 300-05).

extract_protocol:
RNA was extracted from each well using Qiagen RNeasy kit (Qiagen, cat#74004), using 10 uL of Mercaptoethanol (Sigma-Aldrich, cat#60-24-2) per 1 mL of Qiagen RLT buffer. The columns were treated with DNase (Qiagen, cat#79256). To acquire an initial input of DNA put into the cells, DNA was extracted from the AAV which contained the AAV-MPRA library using a NucleoSpin virus kit (Macherey-Nagel, cat#740983.50).
The variant and barcode region of the AAV-variant-barcode library was PCR amplified using NEBNext 2X Q5 Hifi HS Mastermix with primers that contain Illumina P5 and P7 adapters (Bcmap_P5_AAV_R and Bcmap_P7_AAV_F). The PCR product was cleaned up using Zymo PCR clean and concentrator-5. The resulting library was sequenced using custom sequencing primers (BCmap_R1Seq_AAV_R and BCmap_R2Seq_AAV_F) via Novaseq 6000 SP (2x250bp) by the UNC High-Throughput Sequencing Facility (HTSF).

treatment_protocol: Each well was transduced with the AAV-MPRA library at 7,000 multiplicity of infection (MOI). One well per plate was a no-virus control to monitor general cell health. After the AAV-MPRA library was added to the cells, the plates were spun in a centrifuge for 5 minutes at 37°C at 1000 rcf. Cells were half-fed with 2X growth factors every other day for two weeks after transduction.

tag: disease state

value: AAV DNA input


title: ATAC-Seq mESCs C3+14 rep 2

description: mESCs C3+14 rep 2

value: mCherry-C3+14 Dux


title: DLD-1 CBP HAT sg1 H3K27ac [ChIP-seq]

value: p300 HAT sg1

value: Anti-H3K27ac antibody [EP16602] - ChIP Grade (Abcam, ab177178, GR262881-6)


title: Sperm_CUTandTag_panH3_DNaseDTT

data_processing:
Paired-end reads were trimmed using Trim Galore (version 0.4.5), followed by reads alignment to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 700 no-mixed no-discordant.
PCR duplicates were removed using “MarkDuplicates” from Picard Tools (version 2.8.0) (https://broadinstitute.github.io/picard/). Only non-PCR duplicates and uniquely aligned reads (alignment records without “XS” tag) were used for downstream analyses.
The RPKM values for each 100-bp bin were calculated following the formula “read counts/((bin_length/1000) × (total_reads/106))
Peak calling for H3K4me3 and H3K27me3 datasets were done by MACS2 with parameters: --nolambda --nomodel, and --broad-cutoff 0.1 ---nolambda --nomodel, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
After CUT&Tag experiment, total DNA was extracted using PCI/ethanol precipitation
Library preparation was carried out by direct PCR using indexed primers

tag: antibody

value: Histone H3:Abcam, ab1791


title: Sperm_CUTandTag_polIIS2P_DNaseDTT

value: Serine 2 Phospho-Rpb1 CTD:Cell Signal 13499S


title: phoB::Kn mutant, biological replicate 3, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted

value: No phosphorus


title: phoB::Kn mutant, biological replicate 2, 1 mM K2HPO4 (Pi)

description: total RNA, ribosomal RNA-depleted


title: DLD-1 CBP TAZ2 sg2 H3K27ac [ChIP-seq]

value: p300 TAZ2 sg2


title: phoB::Kn mutant, biological replicate 2, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted


title: ATAC-Seq mESCs C12345delt14 rep 2

description: mESCs C12345delt14 rep 2

value: mESCs Dux-/-

value: mouse embryonic stem cells

value: mCherry-C12345delt14aa Dux

value: 0.25 ug/mL doxycycline


title: ATAC-Seq mESCs C3+14 rep 1

description: mESCs C3+14 rep 1


title: DLD-1 CBP TAZ2 sg1 H3K27ac [ChIP-seq]

value: p300 TAZ2 sg1


title: Sperm_CUTandTag_H3K4me3_Untreated

value: Untreated

value: Sperm

value: WT

value: H3K4me3:Abcam, ab8580


title: Sperm_CUTandTag_H3K4me3_DNaseDTT

value: DNaseDTT


title: wild-type, biological replicate 5, 1 mM K2HPO4 (Pi)

description: total RNA, ribosomal RNA-depleted

value: Planktonic

value: wild-type

value: 1 mM K2HPO4

value: 35 minutes


title: DLD-1 p300 HAT sg1 H3K27ac [ChIP-seq]

value: p300 HAT sg1

value: Anti-H3K27ac antibody [EP16602] - ChIP Grade (Abcam, ab177178, GR262881-6)


title: Sperm_CUTandTag_H3K36me3_Untreated

value: H3K36me3:Abcam, ab9050


title: ATAC-Seq mESCs C12345delt14 rep1

description: mESCs C12345delt14 rep1

value: mESCs Dux-/-


title: DLD-1 p300 TAZ2 sg2 H3K27ac [ChIP-seq]

value: p300 TAZ2 sg2


title: wild-type, biological replicate 5, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted

value: No phosphorus


title: ATAC-Seq mESCs FL Dux rep 1

description: mESCs FL Dux rep 1

value: mouse embryonic stem cells

value: mCherry-FL Dux

value: 0.25 ug/mL doxycycline


title: wild-type, biological replicate 4, 1 mM K2HPO4 (Pi)

description: total RNA, ribosomal RNA-depleted


title: Sperm_CUTandTag_H3K27me3_Untreated

value: Untreated

value: Sperm

value: H3K27me3:ThermoFisher, MA5-11198


title: DLD-1 p300 TAZ2 sg1 H3K27ac [ChIP-seq]

value: p300 TAZ2 sg1


title: Sperm_CUTandTag_H3K27me3_DNaseDTT

value: DNaseDTT

value: WT


title: wild-type, biological replicate 4, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted

value: Planktonic

value: wild-type


title: CUT&Tag mESCs mCherry rep 1 SMARCC1

description: mESCs mCherry rep 1 SMARCC1

extract_protocol:
Nuclei were extracted using nuclear extraction buffer (20 mM HEPES-KOH [7.9], 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine, 1X protease inhibitors) and 50,000 nuclei were added to ConA-streptavidin beads paired with the antibody of interest)
CUT&Tag libraries were prepared by paired a secondary guinea pig anti-rabbit (primary antibodies were rabbit), washed, libraries created using pre-loaded Mosiac En A/B adaptor and NEBnext High-Fidelity 2X PCR Master Mix and eluted using AMPure

treatment_protocol: After a 24 hour recovery after plating 1million cells, cells were treated with 0.25ug/mL doxycyline (Clonetech) for 12 hours


title: mESC, vitamin C, rep 4

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

description:
VC35C.vitC
mESC_vitC-35C

data_processing:
Adaptors and low-quality base calls were trimmed using Trim Galore with default parameters.
Trimmed reads were mapped using HiSat2 with --no-softclip and --no-unal. Reads with MAPQ<2 were removed.
Raw read counts for each gene were extracted using Seqmonk's RNA-seq quantitation pipeline.
Gene expression values for each sample were generated using the variance-stabilizing transformation in DESeq2.
Transposable element subfamily counts were generated using SQuIRE
Assembly: mm10, hg38
Supplementary files format and content: Matrix containing normalised (variance-stabilizing transformation) gene expression values
Supplementary files format and content: SQuIRE output containing raw and normalised counts for transposable element subfamilies

growth_protocol: Mouse ESCs were grown in 2i medium comprising 50% DMEM/F-12 and 50% neurobasal media, supplemented with N2, B27, beta-mercaptoethanol, 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 1 mM sodium pyruvate, 1000 U/mL ESGRO LIF, 1 µM PD-035901 and 3 µM CHIR-99021. Human ESCs were maintained in conventional medium (KSR/FGF) comprised of DMEM/F-12 with 20% KSR and 10 ng/ml bFGF, supplemented with 2mM l-glutamine, 100 μM 2-mercaptoethanol, 1% MEM non-essential amino acids, and 50 mg/ml Penicillin-Streptomycin.

extract_protocol:
RNA was extracted with Quick-DNA/RNA Miniprep Kit (Zymo Research) and DNAse treated with the TURBO DNA-free Kit (Ambion)
Total RNA samples were processed with the NEBNext rRNA Depletion Kit or mRNA Isolation Kit. Libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated with 100 µg/ml of vitamin C for 24 hours, and compared to untreated controls.

value: Embryonic stem cells

value: Vitamin C


title: DLD-1 GFP sg1 H3K27ac [ChIP-seq]

value: GFP sg1

value: Anti-H3K27ac antibody [EP16602] - ChIP Grade (Abcam, ab177178, GR262881-6)


title: CUT&Tag mESCs deltC12345+14 rep 2 SMARCC1

description: mESCs deltC12345+14 rep 2 SMARCC1

value: mESCs Dux-/-


title: mESC, control, rep 4

description:
VC35C.ctrl
mESC_ctrl-35C

value: Control


title: wild-type, biological replicate 3, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted

value: No phosphorus

value: 35 minutes


title: OVCAR3 input [ChIP-seq]

value: input


title: OVCAR3 p300 HAT sg1 rep3 H3K27ac [ChIP-seq]

value: p300 HAT sg1


title: CUT&Tag mESCs deltC12345+14 rep 1 SMARCC1

description: mESCs deltC12345+14 rep 1 SMARCC1

value: mouse embryonic stem cells


title: mESC, vitamin C, rep 3

description:
VC35B.vitC
mESC_vitC-35B


title: OVCAR3 p300 HAT sg1 rep2 H3K27ac [ChIP-seq]


title: CUT&Tag mESCs C3delt14 rep 2 SMARCC1

description: mESCs C3delt14 rep 2 SMARCC1


title: wild-type, biological replicate 2, 1 mM K2HPO4 (Pi)

description: total RNA, ribosomal RNA-depleted

value: 1 mM K2HPO4


title: OVCAR3 p300 HAT sg1 rep1 H3K27ac [ChIP-seq]


title: CUT&Tag mESCs C3delt14 rep 1 SMARCC1

description: mESCs C3delt14 rep 1 SMARCC1


title: wild-type, biological replicate 2, no phosphorus (P)

description: total RNA, ribosomal RNA-depleted


title: mESC, control, rep 3

description:
VC35B.ctrl
mESC_ctrl-35B


title: OVCAR3 p300 TAZ2 sg2 rep3 H3K27ac [ChIP-seq]

value: p300 TAZ2 sg2


title: mESC, vitamin C, rep 2

description:
VC11.vitC
mESC_vitC-11


title: mESC, control, rep 2

description:
VC11.ctrl
mESC_ctrl-11


title: CUT&Tag mESCs C3+14 rep 2 SMARCC1

description: mESCs C3+14 rep 2 SMARCC1


title: CUT&Tag mESCs mCherry rep 2 SMARCC1

description: mESCs mCherry rep 2 SMARCC1


title: CUT&Tag mESCs C3+14 rep 1 SMARCC1

description: mESCs C3+14 rep 1 SMARCC1


title: OVCAR3 p300 TAZ2 sg2 rep2 H3K27ac [ChIP-seq]


title: CUT&Tag mESCs C12345delt14 rep 2 SMARCC1

description: mESCs C12345delt14 rep 2 SMARCC1


title: OVCAR3 p300 TAZ2 sg2 rep1 H3K27ac [ChIP-seq]


title: mESC, vitamin C, rep 1

description:
VC10.vitC
mESC_vitC-10


title: wild-type, biological replicate 3, 1 mM K2HPO4 (Pi)

description: total RNA, ribosomal RNA-depleted


title: mESC, control, rep 1

description:
VC10.ctrl
mESC_ctrl-10


title: OVCAR3 p300 TAZ2 sg1 rep3 H3K27ac [ChIP-seq]

value: p300 TAZ2 sg1


title: CUT&Tag mESCs C12345delt14 rep1 SMARCC1

description: mESCs C12345delt14 rep1 SMARCC1


title: OVCAR3 p300 TAZ2 sg1 rep1 H3K27ac [ChIP-seq]


title: astrocytes, p65, SLF, inflamm, ChIP, biol rep 2

city: Kyoto

first: Andres

last: Canela

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Kyoto University

department: The Hakubi Center for Advanced Research / Radiation Biology Center

country: Japan

institute: Kyoto University

data_processing:
Basecalls performed using Illumina's bcl2fastq 2.20.0.422.
Reads were aligned to the mouse genome (GRCm38p2/mm10) using Bowtie 2.3.5 using default parameters.
Aligned-read bam files were first converted to bedgraph files using bedtools genomeCoverageBed (scaled per million aligned reads) followed by bedGraphToBigWig to obtain a bigwig file.
Assembly: GRCm38p2/mm10
Supplementary files format and content: Bigwig

source_name: cerebral cortex

growth_protocol: To obtain primary astrocytes cultures, mixed glial cells were isolated from cortices of murine pups (postnatal day 1–3) and maintained in vented capped T75 or T175 flasks (Corning, NY, USA) in high glucose Dulbecco’s modified Eagle’s medium  (Nacalai Tesque) supplemented with 10% fetal bovine serum (Nichirei Biosciences, Tokyo, Japan), 100 U/mL penicillin, 100 mg/mL streptomycin, and 0.5 mM L-glutamine (all purchased from Nacalai Tesque). The medium was changed every 3–4 d, and after the cultures reached full confluence, the microglia were removed either by shaking vigorously or by Cd11b-positive selection (Miltenyi Biotec, Bergisch Gladbach, Germany); the remaining cells were passaged once or twice then replated for different assays.

extract_protocol:
3–4 million astrocytes were fixed in 1% formaldehyde (F1635, Sigma). Fixation was quenched by the addition of glycine-PBS (Nacalai Tesque) at a final concentration of 0.125 M, followed by nuclear membrane extraction using Farnham lysis buffer (5 mM PIPES, pH 8.0; 85 mM KCl; 0.5% NP-40) supplemented with a protease inhibitor cocktail (Nacalai Tesque).  Pellets of extracted membrane were resuspended in RIPA buffer (10 mM Tris-HCl, pH 7.4; 1 mM EDTA, pH 8.0; 0.1% SDS; 0.1% sodium deoxycholate; 1% Triton X-100). Sonication was performed using the Branson Sonifier (SFX-550) at 35% amplitude, using 12 cycles of 20 s sonication and 30 s of pause at 4°C. Chromatin was clarified using centrifugation at maximum speed and pre-cleared with 40 μL of washed Dynabeads protein A (ThermoFisher) for 30 min at 4°C, followed by immunoprecipitation using 40 μL of washed Dynabeads protein A and 5 μL of control IgG, anti-p65 p65 (CST, #8242), or anti-Nrf2 antibodies NRF2 (CST, #12721). After overnight incubation at 4°C, the beads were washed twice with cold RIPA buffer, twice with RIPA buffer containing 0.3 M NaCl, twice with LiCl buffer (0.25 M LiCl; 0.5% Igepal-630; 0.5% sodium deoxycholate), once with TE (10 mM Tris, pH 8.0; 1 mM EDTA) and 0.2% Triton X-100, and once with TE. Cross linking was reversed by incubating the beads at 65°C for 4 h and incubated at 37°C for 30 min with 0.5 μg of RNaseA (ThermoFisher), then at 50°C for 1 h in the presence of 0.3% SDS and 1 mg/mL Proteinase K (Nacalai Tesque). DNA was purified using Zymo ChIP DNA clean and Concentrator kit (Zymo Research).
Total ChIP DNA was used to prepare Illumina sequencing libraries. End-repair was performed in 75 μL of T4 ligase reaction buffer, 0.4 mM dNTPs, 4 U of T4 DNA polymerase (NEB), 13.5 U of T4 Polynucleotide Kinase (NEB), and 1.5 U of Klenow fragment (NEB) at 24°C for 30 min in a ThermoMixer C (Eppendorf, Hamburg, Germany) at 400 rpm. End-repair reaction was cleaned using 2x Agencourt AMPure XP beads (Beckman Coulter, CA, USA) and eluted in 15 μL of EB. The eluate was used for the A-tailing reaction in 30 μL of NEBNext dA-Tailing reaction buffer (NEB) with 7.5 U of Klenow fragment exo- (NEB) at 37°C for 30 min. Thirty microlitres of the A-tailing reaction mixture was mixed with Quick Ligase Buffer 2X (NEB), 3,000 U of Quick ligase, and 5 nM annealed adaptor (Illumina truncated adaptor), and the total volume was made up to 75 μL; the mixture was incubated at 25°C for 20 min. Adaptor was prepared by annealing the following HPLC-purified oligos: 5′-phosphate/GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCT CTTCCGATC∗T-3′ (∗phosphorothioate bond). Ligation was stopped by adding 50 mM EDTA and cleaned with 1.8x Agencourt AM- Pure XP beads and eluted in 15 μL of EB. The eluate was used for PCR amplification in a 50 μL reaction mixture with 1 μM primers (TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC∗T; TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T; NNNNNNNN represents barcode and ∗ represents a phosphothiorate bond), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosystems, MA, USA). The PCR conditions were as follows: 45 s at 98°C followed by 15 cycles of 15 s at 98°C, 30 s at 63°C, and 30 s at 72°C, and a final 5-min extension at 72°C. PCR products were cleaned with Agencourt AMPure XP beads (Beckman Coulter), run on a 2% agarose gel, and a smear of gel corresponding to 200–500 bp DNA in size was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined using KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on Illumina Nextseq500 (75-bp single-end reads).

treatment_protocol: The astrocytes were treated with DMSO or 5 µM Sulforaphane (SLF) for 1 h, then stimulated (inflamm) or not (NT) with the cytokine cocktail containing 3 ng/mL IL-1α (Peprotech, NJ, USA, 211-11A, 30 ng/mL TNF α (Peprotech, 315-01A), and 400 ng/mL C1q (Prospec, Rehovot, Israel, PRO-554) for 4 h.

value: cerebral cortex

value: primary cells in culture

value: astrocytes

value: wildtype

value: The astrocytes were treated with DMSO or 5 µM Sulforaphane ("SLF")  for 1 h, and then stimulated ("inflamm") or not ("NT") with a cytokine cocktail containing 3 ng/mL IL-1α, 30 ng/mL TNFα, and 400 ng/mL C1q.


title: CUT&Tag mESCs FL Dux rep 1 SMARCC1

description: mESCs FL Dux rep 1 SMARCC1


title: CUT&Tag mESCs FL Dux rep 2 SMARCC1

description: mESCs FL Dux rep 2 SMARCC1


title: astrocytes, p65, DMSO, inflamm, ChIP, biol rep 2


title: astrocytes, p65, SLF, NT, ChIP, biol rep 2


title: CUT&Tag mESCs deltC12345+14 rep 2 H3K9ac

description: mESCs deltC12345+14 rep 2 H3K9ac


title: CUT&Tag mESCs deltC12345+14 rep 1 H3K9ac

description: mESCs deltC12345+14 rep 1 H3K9ac


title: OVCAR3 GFP sg1 rep3 H3K27ac [ChIP-seq]

value: GFP sg1


title: CUT&Tag mESCs C3delt14 rep 2 H3K9ac

description: mESCs C3delt14 rep 2 H3K9ac


title: astrocytes, NRF2, SLF, inflamm, ChIP, biol rep 2


title: OVCAR3 GFP sg1 rep1 H3K27ac [ChIP-seq]

value: Anti-H3K27ac antibody [EP16602] - ChIP Grade (Abcam, ab177178, GR262881-6)


title: A549 p300 TAZ2 sg2 SAHA rep3 [RNA-seq]

description:
processed data file:
A549_htseq_count.txt

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Read counts were generated by HTSeq (v0.11.3).
Genome_build: hg38
Supplementary_files_format_and_content: htseq_count.txt

growth_protocol: OVCAR3 is cultured in DMEM/F-12 with 10% FBS, DLD-1 is cultured in RPMI1640 with 10% FBS, A549 is cultured in DMEM with 10% FBS.

extract_protocol:
Total RNA were extracted by RNeasy Plus Mini Kit (QIAGEN, Cat. 74136).
Libraries were constructed using Illumina standard protocols.

treatment_protocol: DMSO or SAHA were added 24 h before harvest cells.

value: p300 TAZ2 sg2 SAHA

value: 0.5 mM SAHA


title: astrocytes, NRF2, SLF, NT, ChIP, biol rep 2


title: astrocytes, NRF2, DMSO, inflamm, ChIP, biol rep 2


title: CUT&Tag mESCs C3+14 rep 2 H3K9ac

description: mESCs C3+14 rep 2 H3K9ac

value: mESCs Dux-/-


title: astrocytes, NRF2, DMSO, NT, ChIP, biol rep 2


title: CUT&Tag mESCs C3delt14 rep 1 H3K9ac

description: mESCs C3delt14 rep 1 H3K9ac


title: A549 p300 TAZ2 sg2 SAHA rep1 [RNA-seq]


title: A549 p300 TAZ2 sg2 DMSO rep3 [RNA-seq]

value: p300 TAZ2 sg2 DMSO


title: OVCAR3 p300 TAZ2 sg1 rep2 H3K27ac [ChIP-seq]


title: A549 p300 TAZ2 sg2 DMSO rep2 [RNA-seq]


title: CUT&Tag mESCs C12345delt14 rep 2 H3K9ac

description: mESCs C12345delt14 rep 2 H3K9ac


title: astrocytes, p65, SLF, inflamm, ChIP, biol rep 1


title: astrocytes, p65, DMSO, NT, ChIP, biol rep 2


title: OVCAR3 GFP sg1 rep2 H3K27ac [ChIP-seq]


title: A549 p300 TAZ2 sg2 DMSO rep1 [RNA-seq]


title: CUT&Tag mESCs FL Dux rep 1 H3K9ac

description: mESCs FL Dux rep 1 H3K9ac


title: CUT&Tag mESCs FL Dux rep 2 H3K9ac

description: mESCs FL Dux rep 2 H3K9ac


title: astrocytes, p65, DMSO, NT, ChIP, biol rep 1


title: A549 p300 TAZ2 sg1 SAHA rep2 [RNA-seq]

value: p300 TAZ2 sg1 SAHA


title: astrocytes, p65, SLF, NT, ChIP, biol rep 1


title: astrocytes, p65, DMSO, inflamm, ChIP, biol rep 1


title: A549 p300 TAZ2 sg2 SAHA rep2 [RNA-seq]


title: astrocytes, NRF2, SLF, inflamm, ChIP, biol rep 1


title: astrocytes, NRF2, DMSO, inflamm, ChIP, biol rep 1


title: CUT&Tag mESCs C3+14 rep 1 H3K9ac

description: mESCs C3+14 rep 1 H3K9ac


title: CUT&Tag mESCs mCherry rep 2 mCherry

description: mESCs mCherry rep 2 mCherry

value: mCherry (ab167453)


title: astrocytes, NT, DMSO, ChIP


title: A549 p300 TAZ2 sg1 DMSO rep2 [RNA-seq]

value: p300 TAZ2 sg1 DMSO


title: astrocytes, NRF2, SLF, NT, ChIP, biol rep 1


title: CUT&Tag mESCs mCherry rep 1 mCherry

description: mESCs mCherry rep 1 mCherry

value: mouse embryonic stem cells


title: CUT&Tag mESCs rep 2 H3K9ac

description: mESCs rep 2 H3K9ac


title: CUT&Tag mESCs deltC12345+14 rep 2 mCherry

description: mESCs deltC12345+14 rep 2 mCherry


title: A549 p300 TAZ2 sg1 SAHA rep1 [RNA-seq]


title: A549 p300 TAZ2 sg1 DMSO rep1 [RNA-seq]


title: CUT&Tag mESCs C12345delt14 rep1 H3K9ac

description: mESCs C12345delt14 rep1 H3K9ac


title: A549 GFP sg1 SAHA rep3 [RNA-seq]

value: GFP sg1 SAHA


title: astrocytes, NRF2, DMSO, NT, ChIP, biol rep 1


title: astrocytes, SLF, inflamm, nascentRNA, biol rep 2

extract_protocol:
Total RNA was extracted using Direct-zol RNA kit (Zymo Research, CA, USA) and rRNA depleted using the NEBNext rRNA depletion kit (human/mouse/rat) (NEB)
rRNA-depleted RNA was used for biotinylation via the Click-IT reaction (Click-iT Nascent RNA Capture Kit, ThermoFisher C10365) as per the manufacturer’s instructions. First-strand cDNA was synthesised using the captured nascent RNA using the SuperScript VILO cDNA synthesis kit (Invitrogen), followed by purification with 1.8x volume of AMPure XP beads and elution in 20 μL. The second-strand was synthesised using 0.6 mM dATP, 0.6 mM dCTP, 0.6 mM dGTP, and 1.2 mM dUTP in the presence of 2 U of RNase H (Invitrogen) and 20 U of E. coli DNA polymerase I (Invitrogen) in a total volume of 30 μL for 2.5 h at 16°C. cDNA was purified using 1.8x volume AMPure XP beads and eluted in 20 μL of EB. Next, the sequencing libraries were prepared. End-repair was performed in 50 μL of T4 ligase reaction buffer (1×), dNTPs (0.4 nM), T4 DNA polymerase (NEB, 3 U), T4 Polynucleotide Kinase (NEB, 9 U), and Klenow fragment (NEB, 1 U) at 24°C for 30 min in a ThermoMixer at 400 rpm. End-repair reaction was cleaned using 1.8x volume AMPure XP beads and eluted in 15 μL of EB. A-tailing reaction was performed using NEBNext dA-Tailing reaction buffer (NEB, 1×) with Klenow fragment exo- (NEB, 7.5 U) at 37°C for 30 min. A-tailing reaction mixture was mixed with Quick Ligase Buffer (NEB), Quick ligase (NEB, 3,000 U), and 5 nM annealed adaptor (Illumina truncated adaptor) in a volume of 75 μL and incubated at 25°C for 20 min. The adaptor was prepared by annealing the following HPLC-purified oligos: 5′-phosphate/GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ (∗phosphoro-thioate bond). Ligation reaction was stopped by adding 50 mM EDTA, then the DNA was purified with 1.8x volume AMPure XP beads and eluted in 15 μL of EB. Next, 0.5 U of Uracil-DNA glycosylase (ThermoFisher) was added and the mixture was incubated for 15 min at 37°C. PCR was performed in 50 μL reaction mixture with 1 μM primers (TruSeq barcoded primer p5; AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC∗T; TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T; NNNNNNNN represents barcode and ∗ a phosphothiorate bond), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The PCR program was as follows: 98°C for 45 s; 15 cycles of 98°C for 15 s, 63°C for 30 s, and 72°C for 30 s, and a final extension at 72°C for 5 min. PCR products were cleaned with AMPure XP beads, and 200–500 bp fragments were extracted after running on 2% agarose gel. Libraries were purified using QIA-quick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed using Illumina Nextseq 500 (75 bp single-end reads).
nascent RNA-seq

treatment_protocol: The astrocytes were treated with DMSO or 5 µM Sulforaphane (SLF) for 1 h, then stimulated (inflamm) or not (NT) with the cytokine cocktail containing 3 ng/mL IL-1α (Peprotech, NJ, USA, 211-11A, 30 ng/mL TNF α (Peprotech, 315-01A), and 400 ng/mL C1q (Prospec, Rehovot, Israel, PRO-554) for 4 h and labelled with 0.5 mM 5-ethynyl uridine (EU) during last 30 min of stimulation.


title: cy1045_02_postART

city: Madison

first: Shelby

last: O'Connor

state: WI

address: 555 Science Drive

institute: University of Wisconsin-Madison

description: salmon.merged.gene_counts.xlsx:  column cy1045_02

data_processing:
BCL to FASTQ conversion was performed. FASTQ files were then used as input into the NextFlow v22.04.5 pipeline nf-core/rnaseq pipelinee v3.8.1 using Macaca fascicularis genome version 6.0.107 (MacFas6) for alignment and annotation.
Salmon gene count matrix was performed with removal of genes where the total count across samples was less than 10, as well as redundant gene_name rows (Y_RNA) and all poorly annotated ENSMFAG# format genes.
EBSeq was used to determine statistical significance and was run for 2 conditiioin comparison on median normalzied counts data for a total of 5 iiterations.
Assembly: MacFas6
Supplementary files format and content: tab-deliminated files corresponding to feature counts of each sample
Supplementary files format and content: compiled matrix of STAR salmon-called gene counts with each column corresponding to a given sample and each row corresponding to a gene.

organism: Macaca fascicularis

source_name: CD8+ T cell

extract_protocol:
RNA was isolated from enriched CD8 + T cells using a TRIzol/phenol chloroform extraction with DNAse treatement.
RNA libraries were prepared by the University of Wisconsin-Madison Biotechnology Center. Briefly, cDNA was synthesized via reverse transcription and amplified by long-distance PCR using the Takara SMARTer v4 kiit.

value: CD8+ T cell

tag: animal group

value: Post-treatment controller

value: post-ART


title: A549 p300 TAZ2 sg1 SAHA rep3 [RNA-seq]


title: CUT&Tag mESCs deltC12345+14 rep 1 mCherry

description: mESCs deltC12345+14 rep 1 mCherry


title: A549 GFP sg1 SAHA rep2 [RNA-seq]


title: astrocytes, DMSO, inflamm, nascentRNA, biol rep 2

value: cerebral cortex

value: primary cells in culture

value: astrocytes


title: astrocytes, SLF, NT, nascentRNA, biol rep 2

value: wildtype

value: The astrocytes were treated with DMSO or 5 µM Sulforaphane ("SLF")  for 1 h, and then stimulated ("inflamm") or not ("NT") with a cytokine cocktail containing 3 ng/mL IL-1α, 30 ng/mL TNFα, and 400 ng/mL C1q.


title: A549 GFP sg1 SAHA rep1 [RNA-seq]


title: CUT&Tag mESCs rep 1 H3K9ac

description: mESCs rep 1 H3K9ac


title: CUT&Tag mESCs C3delt14 rep 1 mCherry

description: mESCs C3delt14 rep 1 mCherry


title: cy1044_02_postART

description: salmon.merged.gene_counts.xlsx:  column cy1044_02


title: CUT&Tag mESCs C3delt14 rep 2 mCherry

description: mESCs C3delt14 rep 2 mCherry


title: astrocytes, DMSO, NT, nascentRNA, biol rep 2


title: A549 p300 TAZ2 sg1 DMSO rep3 [RNA-seq]


title: cy1045_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy1045_01

value: on ART


title: CUT&Tag mESCs C3+14 rep 2 mCherry

description: mESCs C3+14 rep 2 mCherry


title: cy1043_02_postART

description: salmon.merged.gene_counts.xlsx:  column cy1043_02

value: Rebounder


title: astrocytes, SLF, inflamm, nascentRNA, biol rep 1


title: A549 GFP sg1 DMSO rep2 [RNA-seq]

value: GFP sg1 DMSO


title: astrocytes, DMSO, inflamm, nascentRNA, biol rep 1


title: CUT&Tag mESCs C3+14 rep 1 mCherry

description: mESCs C3+14 rep 1 mCherry

value: mESCs Dux-/-


title: A549 GFP sg1 DMSO rep1 [RNA-seq]


title: cy1044_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy1044_01


title: astrocytes, SLF, NT, nascentRNA, biol rep 1


title: CUT&Tag mESCs C12345delt14 rep 2 mCherry

description: mESCs C12345delt14 rep 2 mCherry


title: cy1039_02_postART

description: salmon.merged.gene_counts.xlsx:  column cy1039_02


title: DLD-1 CBP HAT sg1 rep2 [RNA-seq]

description:
processed data file:
DLD1_htseq_count.txt

value: CBP HAT sg1


title: CUT&Tag mESCs C12345delt14 rep1 mCherry

description: mESCs C12345delt14 rep1 mCherry

value: mCherry (ab167453)


title: cy1039_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy1039_01


title: cy1043_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy1043_01


title: CUT&Tag mESCs FL Dux rep 2 mCherry

description: mESCs FL Dux rep 2 mCherry


title: DLD-1 CBP TAZ2 sg2 rep2 [RNA-seq]

value: CBP TAZ2 sg2


title: cy1036_02_postART

description: salmon.merged.gene_counts.xlsx:  column cy1036_02


title: CUT&Tag mESCs FL Dux rep 1 mCherry

description: mESCs FL Dux rep 1 mCherry

value: mouse embryonic stem cells


title: A549 GFP sg1 DMSO rep3 [RNA-seq]


title: DLD-1 CBP TAZ2 sg2 rep1 [RNA-seq]


title: Region capture Hi-C, CASTxB6, rep1

city: Cambridge

first: Daniel

last: Loftus

state: Massachusetts

address: 16 Divinity Ave, Rm 4004

department: MCB

institute: Harvard University

description:
CB_maternal_all.header.medium.sorted.txt
CB_paternal_all.header.medium.sorted.txt

data_processing:
The mm10 reference genome was N-masked using SNPsplit_genome_preparation from SNPsplit. The N-masked reference genome was then digested in silico according to the Arima restriction enzymes using HiCUP. Bowtie2 was then used to map fastq files to the digested N-masked reference genome using the HiCUP wrapper. Resulting SAM files were split into maternal and paternal reads using SNPsplit. Allelic SAM files were converted to the Juicer medium format.
Assembly: mm10
Supplementary files format and content: Medium format. Whitespace separated file that contains the following on each line: <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>

source_name: Cortex

extract_protocol:
Hi-C libraries were generated using the Arima Hi-C kit using 3 ug of chromatin from ESCs or day 6 iNs.
End repair and adapter ligation was performed using the Accel-NGS 2S DNA Library Kit (Swift Biosciences). Agilent SureSelect probes against the Peg13-Kcnk9 locus were designed against mm10 chr15:71850001-73350000. Probes overlapping musculus/castaneous SNPs were designed to perfectly match both genotypes (i.e. two probes per SNP). End repaired and adapter ligated Hi-C libraries were then enriched using Agilent SureSelectXT HS Target Enrichment System.

value: Cortex


title: Region capture Hi-C, CASTxB6, rep2


title: Region capture Hi-C, B6xCAST, rep2

description:
BC_maternal_all.header.medium.sorted.txt
BC_paternal_all.header.medium.sorted.txt


title: RNA-Seq mESCs mCherry rep 2

description: mESCs mCherry rep 2

data_processing:
Sequence reads were trimmed using TrimGalore version 0.5.0 (-q --phred33 --fastqc --paired)
Trimmed sequence reads were mapped to mm10 using STAR2.7.2c
Read count extraction and normalization were performed using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include matrixes for median of ratios normalization method. Chi file includes FL, C3+14, C1C3a, C1C3b, C1C3c, C1+14, and mCherry. The HD_TE (homedomin) file include: FL, C12345delt14, deltC12345+14, deltC12345delt14

molecule: polyA RNA

extract_protocol:
RNA was harvested using using a TRIZOL extraction. 500ng  of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ilumina TruSeq Stranded mRNA Library Prep with UDI

value: mCherry

value: 0.25 ug/mL doxycycline


title: cy0726_02_postART

description: salmon.merged.gene_counts.xlsx:  column cy0726_02

value: CD8+ T cell

value: post-ART


title: cy1036_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy1036_01

value: Post-treatment controller


title: DLD-1 CBP TAZ2 sg1 rep2 [RNA-seq]

value: CBP TAZ2 sg1


title: RNA-Seq mESCs mCherry rep 1

description: mESCs mCherry rep 1


title: cy0726_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy0726_01


title: DLD-1 CBP TAZ2 sg1 rep1 [RNA-seq]


title: RNA-Seq mESCs C1C3c rep 2

description: mESCs C1C3c rep 2

value: mCherry-C1C3c Dux


title: Region capture Hi-C, B6xCAST, rep1


title: Yng_D3.5_C

city: Ithaca

first: Lauren

middle: D

last: Walter

state: NY

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

library_source: transcriptomic single cell

data_processing:
Sequences were aligned to mm10 using cellranger v5.0.0 pipeline
Ambient RNA content was removed using SoupX v1.4.5
Gene expression data was processed with Seurat v3.2.3
Filtering by the number genes expressed in included cells (minimum 200), number of UMIs in included cells (minimum 750), percent mitochondiral genes in included cells (maximum 25%)
Log-normalization of expression data
Assembly: mm10
Supplementary files format and content: zipped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices

source_name: Tibialis anterior muscle

extract_protocol:
Single-cell RNA-sequencing (scRNA-seq) libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer.
scRNA-seq libraries were prepared for sequencing using standard Illumina protocols

value: Tibialis anterior muscle

tag: age

value: 4.7 months

tag: Sex

value: F

tag: injury

value: Notexin injury (Day 3.5)


title: Yng_D3.5_D


title: DLD-1 p300 HAT sg1 rep2 [RNA-seq]

tag: cell line

value: p300 HAT sg1


title: DLD-1 p300 HAT sg1 rep1 [RNA-seq]


title: DLD-1 CBP HAT sg1 rep1 [RNA-seq]

value: CBP HAT sg1


title: cy0724_02_postART

description: salmon.merged.gene_counts.xlsx:  column cy0724_02

tag: cell type

value: Rebounder


title: Yng_D3.5_B


title: RNA-Seq mESCs C1C3b rep 2

description: mESCs C1C3b rep 2

value: mESCs Dux-/-

value: mCherry-C1C3b Dux


title: cy0724_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy0724_01

value: on ART


title: RNA-Seq mESCs C1C3c rep 1

description: mESCs C1C3c rep 1

value: mouse embryonic stem cells


title: cy0721_02_postART

description: salmon.merged.gene_counts.xlsx:  column cy0721_02


title: astrocytes, DMSO, NT, nascentRNA, biol rep 1

value: cerebral cortex

value: primary cells in culture

value: astrocytes

value: wildtype

value: The astrocytes were treated with DMSO or 5 µM Sulforaphane ("SLF")  for 1 h, and then stimulated ("inflamm") or not ("NT") with a cytokine cocktail containing 3 ng/mL IL-1α, 30 ng/mL TNFα, and 400 ng/mL C1q.


title: DLD-1 p300 TAZ2 sg2 rep2 [RNA-seq]

tag: genotype/treatment

value: p300 TAZ2 sg2


title: RNA-Seq mESCs C1C3b rerp 1

description: mESCs C1C3b rerp 1

tag: genotype

value: 0.25 ug/mL doxycycline


title: DLD-1 p300 TAZ2 sg2 rep1 [RNA-seq]


title: Yng_D3.5_A

value: Tibialis anterior muscle

value: 4.7 months


title: Yng_D1_D

value: F

value: Notexin injury (Day 1)


title: DLD-1 p300 TAZ2 sg1 rep2 [RNA-seq]

value: p300 TAZ2 sg1


title: cy0721_01_onART

description: salmon.merged.gene_counts.xlsx:  column cy0721_01

value: CD8+ T cell

value: Rebounder


title: Yng_D1_C


title: RNA-Seq mESCs C1C3a rep 2

description: mESCs C1C3a rep 2

value: mESCs Dux-/-

value: mCherry-C1C3a Dux

tag: treatment


title: RNA-Seq mESCs C1C3a rep 1

description: mESCs C1C3a rep 1

value: mouse embryonic stem cells

tag: time


title: DLD-1 GFP sg1 rep2 [RNA-seq]

value: GFP sg1


title: Yng_D1_B

tag: tissue


title: DLD-1 p300 TAZ2 sg1 rep1 [RNA-seq]


title: RNA-Seq mESCs C1+14 rep 1

description: mESCs C1+14 rep 1

value: mCherry-C1+14 Dux


title: RNA-Seq mESCs C1+14 rep 2

description: mESCs C1+14 rep 2


title: Yng_D1_A


title: DLD-1 GFP sg1 rep1 [RNA-seq]


title: OVCAR3 p300 HAT sg1 rep3 [RNA-seq]

description:
processed data file:
OVCAR3_htseq_count.txt

value: p300 HAT sg1


title: RNA-Seq mESCs deltC12345delt14 rep 1

description: mESCs deltC12345delt14 rep 1

value: mCherry-deltC12345delt14 Dux


title: RNA-Seq mESCs deltC12345delt14 rep 2

description: mESCs deltC12345delt14 rep 2


title: OVCAR3 p300 HAT sg1 rep2 [RNA-seq]


title: Ger_D7_D

tag: strain

value: 26 months

value: Notexin injury (Day 7)


title: Ger_D7_C


title: RNA-Seq mESCs deltC12345+14 rep 2

description: mESCs deltC12345+14 rep 2

value: mCherry-deltC12345+14 Dux

value: 0.25 ug/mL doxycycline


title: OVCAR3 p300 HAT sg1 rep1 [RNA-seq]


title: Ger_D7_B

value: Tibialis anterior muscle


title: Sample143.Prairie vole.204549720004_R05C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Brain species=Prairie vole

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Microtus ochrogaster

source_name: Brain

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

value: Brain

tag: confidenceinageestimate

value: Male

value: Pair bonded

tag: animalid


title: OVCAR3 p300 TAZ2 sg2 rep3 [RNA-seq]

value: p300 TAZ2 sg2


title: Sample144.Prairie vole.204549720004_R06C02

value: Female

value: Sex naïve


title: RNA-Seq mESCs C3delt14 rep 2

description: mESCs C3delt14 rep 2

value: mESCs Dux-/-

value: mCherry-C3delt14 Dux


title: OVCAR3 p300 TAZ2 sg2 rep2 [RNA-seq]


title: Sample141.Prairie vole.204549720004_R03C02


title: Sample142.Prairie vole.204549720004_R04C02


title: Ger_D5_D

value: F

value: Notexin injury (Day 5)


title: Ger_D7_A


title: Sample140.Prairie vole.204549720004_R02C02


title: RNA-Seq mESCs C3delt14 rep 1

description: mESCs C3delt14 rep 1

value: mouse embryonic stem cells


title: RNA-Seq mESCs C3+14 rep 2

description: mESCs C3+14 rep 2

value: mCherry-C3+14 Dux


title: Ger_D5_C

value: 26 months


title: OVCAR3 p300 TAZ2 sg1 rep3 [RNA-seq]

value: p300 TAZ2 sg1


title: Ger_D5_B


title: Sample139.Prairie vole.204549720004_R01C02


title: RNA-Seq mESCs C3+14 rep 1

description: mESCs C3+14 rep 1


title: OVCAR3 p300 TAZ2 sg1 rep2 [RNA-seq]


title: RNA-Seq mESCs deltC12345+14 rep 1

description: mESCs deltC12345+14 rep 1

value: mCherry-deltC12345+14 Dux


title: Sample138.Prairie vole.204549720004_R06C01


title: Sample137.Prairie vole.204549720004_R05C01


title: Ger_D5_A


title: OVCAR3 p300 TAZ2 sg1 rep1 [RNA-seq]


title: RNA-Seq mESCs C12345delt14 rep 2

description: mESCs C12345delt14 rep 2

value: mCherry-C12345delt14aa Dux

value: 0.25 ug/mL doxycycline


title: Sample136.Prairie vole.204549720004_R04C01

value: Brain


title: OVCAR3 p300 TAZ2 sg2 rep1 [RNA-seq]


title: RNA-Seq mESCs FL Dux rep 2

description: mESCs FL Dux rep 2

value: mCherry-FL Dux


title: OVCAR3 GFP sg1 rep3 [RNA-seq]

value: GFP sg1


title: Sample133.Prairie vole.204549720004_R01C01

value: Male


title: OVCAR3 GFP sg1 rep2 [RNA-seq]


title: Ger_D3.5_D

value: Tibialis anterior muscle

value: Notexin injury (Day 3.5)


title: Ger_D3.5_C


title: Sample135.Prairie vole.204549720004_R03C01

value: Sex naïve


title: Sample134.Prairie vole.204549720004_R02C01

value: Female

value: Pair bonded


title: RNA-Seq mESCs FL Dux rep 1

description: mESCs FL Dux rep 1

value: mESCs Dux-/-


title: Ger_D3.5_A

value: F


title: OVCAR3 GFP sg1 rep1 [RNA-seq]


title: 2x BNT162b2 + BNT162b2:BNT162b4, B cells, CITE [G12-B-CITE]

first: Huitian

last: Diao

address: 40 Erie Street, Suite 110

institute: BioNTech US Inc.

description: Antibody-derived oligonucleotide library and cell hasing library

data_processing:
library strategy: Single cell 5' RNA, VDJ and CITE seq
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger 6.0.1
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Spleen

extract_protocol:
Splenocytes from immunized animals were thawed and incubated with fluorescently-labelled S protein or S pMHC tetramers. Antigen-positive cells were sorted using the BD FACSAria Cell Sorter, and up to 8000 cells per animal were collected.
Cells were pooled by treatment group, and each group was loaded into a channel on the 10X Chromium Connect using Chromium Next Automated GEM 5’ v2 kit. Gene expression libraries were generated using the automated library construction kit, CITEseq libraries were generated using the Chromium Automated 5’ Feature Barcode kit and VDJ libraries were generated using Chromium Automated Mouse BCR/TCR Amplification and Library Construction kit. Sequencing was carried out on the Illumina NovaSeq 6000 platform with an S1 flow cell.

value: B cells

value: Spleen

value: 4-10 weeks

tag: molecule

value: protein


title: airway scar rep 7

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
10x Genomics Cell Ranger 5.0.0 was used to build reference genome index
Reads were mapped to reference genome and then quantified
Cells labeled with sample-specific hashtags (feature barcoding antibodies) were demultiplexed
scRNABatchQC was used for quality control
Cells were removed if they had unique features counts of less than 200 or larger than 8000, had fewer than 500 read counts and/or had greater than 40% mitochondrial read counts
Seurat was used for sctransform-based normalization, dimension reduction, and clustering
Cell type of each cluster was initially classified based on cell activity database PanglaoDB and then manually refined based on cell type specific marker gene expression.
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: rds file that contains metadata of filtered and analyzed single cells; csv file that contains final cell type for clusters

source_name: Subglottis

extract_protocol:
Samples were placed in an enzymatic cocktail [collagenase I/dispase II (1 μg/ml) tissue for 60 minutes followed by mechanical disruption. Tissue lysates were serially filtered 100- and 40-μm sterile filters (Fischer) and used as input for generation of scRNA-seq libraries.
scRNA-seq libraries were generated using the 10x Chromium platform 3′ v2 or 5′ library preparation kits (10x Genomics) following the manufacturer’s recommendations and targeting 5000 to 10,000 cells per sample.
scRNA-seq with 10X Genomics Chromium platform

value: subglottic mucosa

tag: phenotype

value: airway scar


title: 2x BNT162b2 + BNT162b2:BNT162b4, B cells, Immune receptor [G12-B-TCR]

description: 5' mRNA library of immune receptor

value: mRNA, Immune Receptor


title: Ger_D2_D

value: 26 months

value: Notexin injury (Day 2)


title: airway scar rep 6


title: Sample132.Prairie vole.204549720011_R06C02

value: Brain


title: Ger_D2_C

value: Tibialis anterior muscle


title: Sample131.Prairie vole.204549720011_R05C02


title: RNA-Seq mESCs C12345delt14 rep1

description: mESCs C12345delt14 rep1

value: mouse embryonic stem cells

value: mCherry-C12345delt14aa Dux

value: 0.25 ug/mL doxycycline


title: 2x BNT162b2 + BNT162b2:BNT162b4, B cells, Gene expression [G12-B-GEX]

description: 5' mRNA library

value: mRNA


title: airway scar rep 5


title: Ger_D3.5_B

value: Notexin injury (Day 3.5)


title: Ger_D2_B

value: F


title: 3x BNT162b2, B cells, CITE [G9-B-CITE]

value: B cells


title: airway scar rep 4


title: airway scar rep 3


title: Sample130.Prairie vole.204549720011_R04C02

value: Female

value: Pair bonded


title: Ger_D1_C

value: Notexin injury (Day 1)


title: 3x BNT162b2, B cells, Immune receptor [G9-B-TCR]

description: 5' mRNA library of immune receptor

value: Spleen

value: 4-10 weeks


title: 3x BNT162b2, B cells, Gene expression [G9-B-GEX]

description: 5' mRNA library


title: Ger_D1_D


title: airway scar rep 1

value: subglottic mucosa

value: airway scar


title: Sample127.Prairie vole.204549720011_R01C02

value: Sex naïve


title: healthy subglottis rep 3

value: healthy mucosa (matched to sample 8)


title: airway scar rep 2


title: healthy subglottis rep 2

value: healthy mucosa (matched to sample 9)


title: Sample126.Prairie vole.204549720011_R06C01

value: Brain

value: Male


title: Vehicle, B cells, Gene expression [G7-B-GEX]

description: 5' mRNA library


title: Sample125.Prairie vole.204549720011_R05C01


title: Sample128.Prairie vole.204549720011_R02C02


title: Sample129.Prairie vole.204549720011_R03C02


title: 2x BNT162b2 + BNT162b2:BNT162b4, T cells, CITE [G12-T-CITE]

value: T cells

value: protein


title: Ger_D1_B

value: Tibialis anterior muscle

value: 26 months


title: Ger_D0_C

value: F

value: Uninjured


title: Sample124.Prairie vole.204549720011_R04C01


title: 2x BNT162b2 + BNT162b2:BNT162b4, T cells, Immune receptor [G12-T-TCR]

description: 5' mRNA library of immune receptor

value: mRNA, Immune Receptor


title: Ger_D2_A

value: Notexin injury (Day 2)


title: Sample122.Prairie vole.204549720011_R02C01

value: Female

value: Pair bonded


title: Vehicle, B cells, CITE [G7-B-CITE]

value: B cells

value: Spleen

value: 4-10 weeks


title: Sample123.Prairie vole.204549720011_R03C01


title: Ger_D0_B


title: Vehicle, B cells, Immune receptor [G7-B-TCR]

description: 5' mRNA library of immune receptor


title: Ger_D1_A

value: Notexin injury (Day 1)


title: 2x BNT162b2 + BNT162b2:BNT162b4, T cells, Gene expression [G12-T-GEX]

description: 5' mRNA library

value: mRNA


title: Patient 9 Group: Exercise (Baseline) L001

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FASTQC toolkit was performed for quality control of FASTQ files
The fastp tool was performed to trim adapters and low-quality reads
Cleaned reads of total RNA sequencing were aligned to the reference genome using the STAR RNA sequencing aligner.
Feature counts were calculated by subread v2.0.02 from the bam files generated from STAR
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: rectosigmoid colon

extract_protocol:
Total RNA was extracted using direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA) ac-cording to manufacturer’s instructions
Sample preparation, library construction, and RNA sequencing were performed at MDACC Ad-vanced Technology Genomics Core Facility using the NovaSeq6000 S1-200 (100nt PE format).

value: colorectal mucosa

tag: patient id

tag: race

value: White or Caucasian

tag: ethinicity

value: Not Hispanic or Latino

tag: gene mutated

tag: group

value: Exercise

tag: visit

value: Baseline


title: Ger_D0_D

value: Tibialis anterior muscle

tag: age

value: 26 months

tag: Sex

tag: injury


title: 3x BNT162b2, T cells, CITE [G9-T-CITE]

tag: cell type

value: T cells

value: protein


title: Sample120.Prairie vole.204549720006_R06C02

value: Brain

value: Sex naïve


title: Sample121.Prairie vole.204549720011_R01C01

value: Female


title: mouse testis small RNA, IP with antibody against pseudouridine, replicate 3

city: Cold Spring Harbor

last: Martienssen

email: martiens@cshl.edu, aschorn@cshl.edu

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: total RNA, size selected (17-40nt)

data_processing:
reads that align to tRNAs were processed separately and analyzed according to PMID28666125
bowtie2 -N 1 -L 10 --gbar 20 -f -R10 --no-unal -x mm10_bowtie2index
aligned reads were intersected with the specified annotations using bedtools intersect (-f 1.00)
rmsk repeat annotation: ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmskOutCurrent.txt.gz
piRNA cluster annotation, June 2020: https://www.smallrnagroup.uni-mainz.de/piCdb/
Assembly: mm10
Supplementary files format and content: raw read counts; reads that overlap rmsk (not structural repeats) and piRNA cluster

source_name: testis

extract_protocol:
tissue ground in liquid nitrogen, Trizol total RNA extraction, 15% urea PAGE fractionation, 17-40nt cut and eluted ON
NEBNext small RNA sequencing kit (CMC samples); Perkin Elmer Nextflex v3 (IP samples)

treatment_protocol: N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC); pseudouridine antibody (D347-3, MBL)

value: male

value: testis

value: 8 weeks

tag: treatment

value: IP with pseudouridine antibody


title: Patient 9 Group: Exercise (Baseline) L002

tag: tissue


title: 3x BNT162b2, T cells, Immune receptor [G9-T-TCR]

description: 5' mRNA library of immune receptor

value: Spleen

tag: strain

value: 4-10 weeks

value: mRNA, Immune Receptor


title: Sample119.Prairie vole.204549720006_R05C02

tag: confidenceinageestimate


title: Ger_D0_A

value: F

value: Uninjured


title: mouse testis small RNA, IP with antibody against pseudouridine, replicate 2

description: total RNA, size selected (17-40nt)


title: Patient 8 Group: Exercise (Baseline) L001

value: colorectal mucosa

value: Asian

value: Not Hispanic or Latino

value: Exercise

value: Baseline


title: Sample118.Prairie vole.204549720006_R04C02

value: Brain

tag: animalid


title: healthy subglottis rep 1

value: subglottic mucosa

value: healthy mucosa (matched to sample 10)


title: Sample117.Prairie vole.204549720006_R03C02

value: Male

value: Sex naïve


title: Patient 7 Group: Exercise (Baseline) L002

value: White or Caucasian


title: mouse testis small RNA, IP with antibody against pseudouridine, replicate 1

description: total RNA, size selected (17-40nt)

value: male

value: testis

value: 8 weeks

value: IP with pseudouridine antibody


title: 3x BNT162b2, T cells, Gene expression [G9-T-GEX]

description: 5' mRNA library

value: T cells

value: Spleen

value: 4-10 weeks

tag: molecule

value: mRNA


title: mouse testis small RNA, input of IP, replicate 3

description: total RNA, size selected (17-40nt)

value: input (IP)


title: Vehicle, T cells, CITE [G7-T-CITE]

value: protein


title: Sample116.Prairie vole.204549720006_R02C02

value: Pair bonded


title: Sample115.Prairie vole.204549720006_R01C02

value: Brain


title: Patient 7 Group: Exercise (Baseline) L001

value: colorectal mucosa

value: Not Hispanic or Latino

value: Exercise

value: Baseline


title: Patient 5 Group: Exercise (Baseline) L002

value: White or Caucasian


title: Vehicle, T cells, Immune receptor [G7-T-TCR]

description: 5' mRNA library of immune receptor

value: mRNA, Immune Receptor


title: mouse testis small RNA, input of IP, replicate 1

description: total RNA, size selected (17-40nt)

value: male

value: testis


title: Patient 5 Group: Exercise (Baseline) L001


title: Vehicle, T cells, Gene expression [G7-T-GEX]

description: 5' mRNA library


title: mouse testis small RNA, input of IP, replicate 2

description: total RNA, size selected (17-40nt)

value: 8 weeks


title: Patient 8 Group: Exercise (Baseline) L002

value: Asian


title: Patient 21 Group: Usual care (End-of-Study) L002

value: Usual care

value: End-of-Study


title: Patient 21 Group: Usual care (End-of-Study) L001


title: mouse testis small RNA, flow-through of IP, replicate 3

description: total RNA, size selected (17-40nt)

value: flow-through (IP)


title: awake microglia

city: Hangzhou

first: Kelei

last: Cao

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description: 10x Genomics

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou, China) at a minimum depth of 20,000 reads per cell.
Raw sequencing data demultiplexing and converting were carried out by Illumina bcl2fastq software.
Sample demultiplexing, barcode processing and single-cell 3’ gene counting were included in the preprocessing steps of Cell Ranger pipeline (version 3.1.0).
Data were aligned to Ensembl genome GRCm38 reference genome.
Assembly: GRCm38
Supplementary files format and content: Expression matrices output by Cellranger are provided as mtx files. The gene and cell barcode name files that accompany the mtx files are provided as tsv files (.tsv) for each sample.

source_name: brain

growth_protocol: C57BL/6J mice were purchased from Shanghai SLAC Laboratory Animal Corporation (China). All animals were housed under a 12-h light/dark cycle with food and water available.

extract_protocol:
Awake and anesthesia mouse brains were rapidly dissected and transferred to a pre-chilled dish with cold PBS on ice. The brains were minced and dissociated in DMEM medium (Fischer Scientific) containing 0.5 mg/ml collagenase IV (Sigma) and 10 U/ml DNase I (Roche). Myelin and tissue debris were removed by centrifuging through a 37-70% (v/v) Percoll gradient (GE Healthcare BioSciences) density. Mononuclear cells were collected and incubated with different antibodies as indicated, and microglia were purified as a CD11b+CD45low populations on a BD FACSAria II using the 80 μm micron nozzle.
Single-cells were captured and libraries were prepared following the manufacturer’s instructions of 10x Chromium Next GEM Single Cell 3' GEM and Library & Gel Bead Kit v3.

treatment_protocol: Mice injected with normal saline (3 mice, control group) or 100 mg/kg sodium pentobarbital (3 mice, anesthetic group).

value: brain

tag: developmental stage

value: adult

value: microglia

tag: genotype

value: awake


title: Sample114.Prairie vole.204549720006_R06C01

value: Brain

value: Female

value: Pair bonded


title: mouse testis small RNA, flow-through of IP, replicate 1

first: Robert

description: total RNA, size selected (17-40nt)


title: mouse testis small RNA, flow-through of IP, replicate 2

description: total RNA, size selected (17-40nt)


title: anesthesia microglia

description: 10x Genomics

value: anesthesia


title: Sample112.Prairie vole.204549720006_R04C01

value: Male


title: mouse testis small RNA, CMC-treated, replicate 3

description: total RNA, size selected (17-40nt)

value: CMC-treated


title: SW6

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FastQC (Version 0.72) was performed on the concatenated replicate raw sequencing paired-end reads from each library to ensure minimal PCR duplication and sequencing quality.
Reads were aligned to the mouse mm10 genome using HISAT2 (Version 2.1.0) and annotated against Ensembl v90.
After removal of multiple-aligned reads, remaining reads were counted using featurecounts (Version 2.0.1) with default parameters, and filtered to remove genes with low counts (<10 reads across samples).
For male 48-hr CSDS RNA-seq, RUVg was performed to normalize read counts based on empirically determined control genes that do not vary between control and susceptible groups (i.e. genes with p-val > 0.5 based on a first-pass differential expression analysis performed prior to RUVg normalization). For female RNA-seq experiments and the serotonylation manipulation experiments with the Q5A virus, RUVr was performed to normalized read counts based on the residuals from a first-pass GLM regression of the unnormalized counts on the covariates of interest.
DESEQ2 (Version 2.11.40.6) was used to perform pairwise differential expression analyses between indicated comparisons.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing raw counts

source_name: adult (6-wk) dorsal raphe nucleus tissue

extract_protocol:
RNA-seq, RNA was harvested using Rneasy Micro kit (Qiagen). 300 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Truseq RNA Library Prep Kit V2 following manufacturer's protocols.

value: stress

tag: condition

value: sw

tag: virus

value: wt


title: Patient 19 Group: Usual care (End-of-Study) L002

value: colorectal mucosa

tag: patient id

tag: race

value: White or Caucasian

tag: ethinicity

value: Not Hispanic or Latino

tag: gene mutated


title: Patient 19 Group: Usual care (End-of-Study) L001

tag: age

tag: group

value: Usual care

tag: visit

value: End-of-Study


title: SW5

value: adult (6-wk) dorsal raphe nucleus tissue


title: Patient 4 Group: Exercise (Baseline) L002

value: Exercise

value: Baseline


title: Sample111.Prairie vole.204549720006_R03C01

value: Brain

tag: Sex

value: Sex naïve


title: mouse testis small RNA, CMC-treated, replicate 2

description: total RNA, size selected (17-40nt)

value: male

tag: tissue

value: testis

value: 8 weeks

tag: treatment


title: Sample110.Prairie vole.204549720006_R02C01

tag: confidenceinageestimate

value: Male


title: SW11

value: stress


title: mouse testis small RNA, CMC-treated, replicate 1

description: total RNA, size selected (17-40nt)

tag: strain

value: CMC-treated


title: Sample108.Prairie vole.204549720010_R06C02

value: Female

tag: animalid


title: Sample113.Prairie vole.204549720006_R05C01


title: Sample109.Prairie vole.204549720006_R01C01

value: Pair bonded


title: Patient 4 Group: Exercise (Baseline) L001

value: colorectal mucosa

value: White or Caucasian


title: SW9

value: sw

value: wt


title: SQ8

value: adult (6-wk) dorsal raphe nucleus tissue

value: sq


title: Sample107.Prairie vole.204549720010_R05C02


title: Patient 17 Group: Usual care (End-of-Study) L002

value: Not Hispanic or Latino

value: Usual care

value: End-of-Study


title: mouse testis small RNA, untreated, replicate 3

description: total RNA, size selected (17-40nt)

value: male

value: mock treated


title: Sample106.Prairie vole.204549720010_R04C02

value: Brain


title: SG7

value: sg

value: gfp


title: SQ7

value: stress


title: Patient 17 Group: Usual care (End-of-Study) L001


title: Patient 16 Group: Usual care (End-of-Study) L002


title: mouse testis small RNA, untreated, replicate 2

description: total RNA, size selected (17-40nt)

value: testis

value: 8 weeks


title: SG9


title: SG6


title: Mux24_HTO

city: Philadelphia

first: Patrick

last: Seale

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

data_processing:
In order to adjust for downstream effects of ambient RNA expression within mouse nuclei, we used the "remove-background" module from CellBender (version 0.2.0) to remove counts due to ambient RNA molecules from the count matrices and to estimate the true cells.
Genes were subsequently filtered such that only genes detected in two or more cells and with at least 6 total counts (across all cells) were retained. Sample demultiplexing via hashtag oligonucleotide sequences (HTOs) was performed with the Cumulus sc/snRNA-Seq processing pipeline[ref.5]. Specifically, HTO quantification was performed with the Cumulus Tool on Feature Barcoding, which provided a cell-by-HTO count matrix. This HTO count matrix, along with the gene count matrices generated via Cell Ranger (above) were used to assign each cell to their respective sample(s) with the demuxEM program. Only cells that were identified as singlets were retained (i.e. no cells identified as a multiplet or unassigable) in the per-sample CellBender-ed gene count matrices.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files containing feature names and cell barcodes and matrix files containing feature counts

source_name: Inguinal White Adipose

extract_protocol:
Nuclei were isolated from frozen mouse inguinal white adipose tissue samples for 10X snRNA-seq as previously described, with the following modifications to integrate hash multiplexing and FANS-assisted nuclear quality thresholding and sample pooling. Briefly, 300 mg of flash-frozen adipose samples were held on dry ice until immediately before nuclei isolation, and all sample handling steps were performed on ice. Each sample was placed into a gentleMACS C tube (Miltenyi Biotec) with 2 mL freshly prepared TST buffer (0.03% Tween 20 (Bio-Rad), 0.01% Molecular Grade BSA (New England Biolabs), 146 mM NaCl (ThermoFisher Scientific), 1 mM CaCl2 (VWR International), 21 mM MgCl2 (Sigma Aldrich), and 10 mM Tris-Hcl pH 7.5 (ThermoFisher Scientific) in Ultrapure water (ThermoFisher Scientific)) with 0.2 U/μL of Protector RNase Inhibitor (Sigma Aldrich). gentleMACS C tubes were then placed on the gentleMACS Dissociator (Miltenyi Biotec) and tissue was dissociated by running the program "mr_adipose_01" three times, and then incubated on ice for 10 minutes. Lysate was passed through a 40 μm nylon filter (CellTreat) and collected into a 50 mL conical tube (Corning). Filter was rinsed with 3 mL of freshly prepared ST buffer (146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2; 10 mM Tris-Hcl pH 7.5) with 0.2 U/μL RNase Inhibitor, and collected into the same tube. Flow-through was passed through a 20 μm pre-separation filter (Miltenyi Biotec) set on top of a 5 mL FACS tube (Corning) and collected into the same tube. Suspension was centrifuged in a swinging-bucket centrifuge (Eppendorf) at 500 × g for 5 minutes at 4°C with brake set to low. Following centrifugation, supernatant was removed and 5 mL of PBS pH 7.4 (ThermoFisher Scientific) with 0.02% BSA and 0.2 U/μL RNase Inhibitor was added without resuspending the nuclear pellet. Sample was centrifuged again at 500 × g for 5 minutes at 4°C with brake set to low. Following centrifugation, supernatant was removed, and the nuclear pellet was resuspended in 1 mL PBS-0.02% BSA with 0.2 U/μL RNase Inhibitor. Each sample was split into two 500 μL aliquots and transferred to new 5 mL FACS tubes for subsequent hashing. Each aliquot of resuspended nuclei was stained with NucBlue (Thermofisher Scientific), labeled with 1 μg of a unique TotalSeq anti-Nuclear Pore Complex Proteins Hashtag Antibody (Biolegend), and then incubated on ice for 30 minutes. Suspension was centrifuged at 500 × g for 5 minutes at 4°C with brake set to low. Following centrifugation, 450 μL of supernatant was removed and the nuclear pellet was resuspended in 450 μL PBS-0.02% BSA with 0.2 U/μL RNase Inhibitor. For nuclear quality thresholding, fluorescence-activated nuclear sorting (FANS) was implemented to collect 4,000-4,300 nuclei from hashtagged aliquots directly into a shared well of a 96-well PCR plate (Thermo Scientific) containing 24.6 μL of 10X RT Reagent B with 1U/uL RNase Inhibitor on a Beckman Coulter MoFlo AstriosEQ fitted with a 70 μm nozzle. High-quality nuclei were selected by initial gating at 360 nm with laser filter 405-448/59 followed by SSC-H and FSC-H to remove doublets and unlysed cells.
Once all sample aliquots were FANS-sorted, the pool of 43,000 nuclei was loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer's protocol. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). Libraries of hashtag oligo fractions were generated according to the manufacturer’s instructions (Biolegend). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent). cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (ThermoFisher Scientific). Gene expression libraries were multiplexed and sequenced on the Nextseq 500 (Illumina) using a 75-cycle kit and the following read structure: Read 1: 28 cycles, Read 2: 55 cycles, Index Read 1: 8 cycles. Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0). Digital expression matrices were generated from the FASTQ files using Cell Ranger (version 6.1.2) with the option to include intronic reads (--include-introns). Reads were aligned against the GRCm38 mouse genome assembly and gene counts were obtained, per-droplet, by summarizing exonic and intronic UMIs that overlapped with the GENCODE mouse annotation (release 24) for each gene symbol.

value: Inguinal White Adipose

tag: batch

value: multiplexed sample

tag: time


title: Patient 14 Group: Usual care (End-of-Study) L002

value: colorectal mucosa

value: White or Caucasian


title: Sample105.Prairie vole.204549720010_R03C02

value: Male

value: Sex naïve


title: SG5

value: adult (6-wk) dorsal raphe nucleus tissue

tag: condition


title: Sample104.Prairie vole.204549720010_R02C02


title: Mux19_HTO

tag: genotype


title: Sample103.Prairie vole.204549720010_R01C02

value: Female

value: Pair bonded


title: Sample102.Prairie vole.204549720010_R06C01


title: Patient 14 Group: Usual care (End-of-Study) L001

tag: patient id

value: Not Hispanic or Latino

value: Usual care

value: End-of-Study


title: CQ7

value: con

value: cq

tag: virus


title: Patient 13 Group: Usual care (End-of-Study) L002

tag: race

tag: ethinicity


title: CQ6


title: 2610035D17rik Pull-down Antisense probe 3

city: Jupiter

first: Sathya

last: Puthanveettil

state: Florida

address: 120 Scripps way

institute: UF Scripps Biomedical Research

description: Sample 6 (394_6)

data_processing:
The adaptor trimming was performed  with Trim Galore (v0.6.5), read quality assessment with MultiQC (v1.8), transcript alignment and counting with Salmon.
Assembly: M. musculus-UCSC-mm10
Supplementary files format and content: raw counts
Library strategy: RNA pulldown

source_name: Brain Hippocampus

extract_protocol:
RNA from complexes was isolated using Trizol-Chloroform protocol.
The adaptor trimming was performed  with Trim Galore (v0.6.5), read quality assessment with MultiQC (v1.8), transcript alignment and counting with Salmon.

value: Brain Hippocampus

value: male

value: Antisense probe


title: Mux24_GEX

molecule: nuclear RNA

value: Inguinal White Adipose

tag: age


title: mouse testis small RNA, untreated, replicate 1

description: total RNA, size selected (17-40nt)

value: testis

value: 8 weeks

value: mock treated


title: Sample101.Prairie vole.204549720010_R05C01

value: Brain

value: Male


title: Patient 13 Group: Usual care (End-of-Study) L001

value: colorectal mucosa

value: White or Caucasian

tag: gene mutated

tag: group


title: Patient 16 Group: Usual care (End-of-Study) L001

tag: visit


title: CQ5

tag: tissue

value: adult (6-wk) dorsal raphe nucleus tissue


title: 2610035D17rik Pull-down Antisense probe 2

description: Sample 5 (394_5)

tag: Sex

tag: treatment


title: Patient 11 Group: Exercise (End-of-Study) L002

value: Not Hispanic or Latino

value: Exercise


title: Mux19_GEX

value: multiplexed sample


title: CQ4

value: con


title: 2610035D17rik Pull-down Antisense probe 1

description: Sample 4 (394_4)


title: Sample100.Prairie vole.204549720010_R04C01

tag: confidenceinageestimate

value: Female

value: Pair bonded


title: Sample99.Prairie vole.204549720010_R03C01

tag: animalid


title: Patient 11 Group: Exercise (End-of-Study) L001

value: End-of-Study


title: Sample97.Prairie vole.204549720010_R01C01


title: Sample98.Prairie vole.204549720010_R02C01


title: Sample96.Prairie vole.204529320014_R06C02

description: genomic DNA methylation from tissue=Liver species=Prairie vole

source_name: Liver

value: Liver

value: Sex naïve


title: 2610035D17rik Pull-down Sense probe 3

description: Sample 3 (394_3)

value: Brain Hippocampus

value: male

value: Sense probe


title: Patient 9 Group: Exercise (End-of-Study) L002


title: Sample95.Prairie vole.204529320014_R05C02


title: 2610035D17rik Pull-down Sense probe 2

description: Sample 2 (394_2)


title: CG6

value: cg

value: gfp


title: CG5


title: Patient 9 Group: Exercise (End-of-Study) L001

value: colorectal mucosa


title: 2610035D17rik Pull-down Sense probe 1

description: Sample 1 (394_1)


title: Patient 3 Group: Exercise (Baseline) L002

value: White or Caucasian

value: Baseline


title: SW4

value: adult (6-wk) dorsal raphe nucleus tissue

value: stress

value: sw

value: wt


title: CA1 Hippocampus mice CFC (2/2) Shock

description: Sample 6 (192_629)

data_processing:
The reads were mapped to the mouse genome (mouse-UCSC : M.musculus-UCSC-mm10 : downloaded March 22, 2016) using the star version 2.5.2a aligner and gene abundance was estimated with python version 2.7.11, and htseq version 0.8.0.
Assembly: mm10
Supplementary files format and content: counts

source_name: Brain Hippocampus CA1

extract_protocol:
RNA was isolated using Trizol-Chloroform protocol.
NEBNext rRNA Depletetion and NEBNext Ultra II directional RNA library prep kit for Illumina

value: Brain Hippocampus CA1

value: Shock


title: Patient 8 Group: Exercise (End-of-Study) L002

value: Asian

value: Not Hispanic or Latino

value: Exercise

value: End-of-Study


title: CA1 Hippocampus mice CFC (1/2) Shock

description: Sample 5 (192_528)


title: Patient 3 Group: Exercise (Baseline) L001


title: Patient 8 Group: Exercise (End-of-Study) L001


title: CG7

value: con


title: CA1 Hippocampus mice CFC (1/2) Context

description: Sample 3 (192_326)

value: Context


title: Sample93.Prairie vole.204529320014_R03C02

description: genomic DNA methylation from tissue=Ear species=Prairie vole

source_name: Ear

value: Ear

value: Male

value: Pair bonded


title: SW1


title: SW2


title: Sample90.Prairie vole.204529320014_R06C01

value: Female

value: Sex naïve


title: Sample91.Prairie vole.204529320014_R01C02


title: CA1 Hippocampus mice CFC (2/2) Context

description: Sample 4 (192_8)


title: Sample92.Prairie vole.204529320014_R02C02

value: Liver


title: SW3

value: adult (6-wk) dorsal raphe nucleus tissue

value: stress


title: Patient 7 Group: Exercise (End-of-Study) L001

value: colorectal mucosa

value: White or Caucasian


title: Patient 5 Group: Exercise (End-of-Study) L002


title: Patient 4 Group: Exercise (End-of-Study) L001


title: SG4

value: sg

value: gfp


title: SG3


title: Sample94.Prairie vole.204529320014_R04C02


title: Region capture Hi-C, ESC, rep2

source_name: ESC

tag: cell type

value: ESC

value: musc x cast


title: Region capture Hi-C, ESC, rep1


title: CA1 Hippocampus mice CFC (2/2) Context + Shock

description: Sample 2 (192_12)

value: Brain Hippocampus CA1

value: Context + Shock


title: Patient 5 Group: Exercise (End-of-Study) L001

value: Not Hispanic or Latino

value: Exercise

value: End-of-Study


title: SQ1b

value: sq


title: Patient 4 Group: Exercise (End-of-Study) L002


title: Sample84.Prairie vole.204529320079_R06C02

value: Female


title: Patient 3 Group: Exercise (End-of-Study) L002


title: Sample89.Prairie vole.204529320014_R05C01

value: Male

value: Sex naïve


title: SG11

value: adult (6-wk) dorsal raphe nucleus tissue


title: HCT15-COPS7B-RPF-1

city: Harbin

first: Jing

last: Tang

state: Heilongjiang

address: No. 157 Baojian Road, Nangang District

institute: Harbin medical university

data_processing:
The generated reads were processed using Cutadapt (v3.5) to remove adaptors and perform quality-based trimming.
The ribosome-protected fraction (RPF) and input reads were mapped to the GRCh38 reference genome using STAR (v2.7.9).
Reads with lengths of 25-50 nts and 50-150 nts were used for RPF and input mapping, respectively. HTseq (v2.0.2) was employed to analyze the Ribo-seq and RNA-seq data.
The Xtail R package was applied to analyze changes in translation efficiency (TE) of genes across different cells
Assembly: GRCh38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Library strategy: Ribo-seq

source_name: colon

growth_protocol: DMEM for 293TN and HCT15, L15 for SW620, RPMI-1640 for HCT116, and EMEM for 841-CON. The culture media were supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin. Cell cultures were maintained at 37°C in a 5% CO2 chamber, except for SW620, which was cultured in an air incubator.

extract_protocol:
The samples were then subjected to ultracentrifugation (38,000 rpm, 3 hours, 4℃), and the ribosome-protected RNA fragments were isolated using the RNA Clean and Concentrator-25 kit (Zymo Research, USA).
Subsequent steps involved rRNA removal and construction of cDNA libraries using the Next Multiple Small RNA library preparation Set for Illumina (New England Biolabs, USA) as described previously, The constructed cDNA libraries were sequenced using the Illumina HiSeqTM ×10 platform

treatment_protocol: The cells were treated with  Cycloheximide (CHX) (100μg/mL) at 37℃ for 10 minutes.  The collected cells were lysed using a lysis buffer (20mM Tris-HCl, pH 7.4, 5mM Mgcl2, 150mM NaCl, 1% Triton X-100, RNase inhibitor, 1× protein inhibitor, 100μg/mL CHX and 1mM DTT). A 10%-50% sucrose gradient was prepared, and the cell lysate was centrifuged at 15,000 rpm for 15 minutes. The supernatant was loaded onto the prepared sucrose gradient solution and centrifuged at 4℃, 38,000 rpm for 3 hours using a Beckman rotor SW41Ti.

value: colon

tag: cell line

value: colon cancer cell

value: COPS7B overexpression


title: Sample85.Prairie vole.204529320014_R01C01

value: Liver

value: Pair bonded


title: Sample88.Prairie vole.204529320014_R04C01

value: Ear


title: HCT15-COPS7B-RPF-2


title: Patient 2 Group: Exercise (End-of-Study) L002

value: colorectal mucosa

value: White or Caucasian


title: SQ2

value: stress

tag: condition


title: Sample83.Prairie vole.204529320079_R05C02


title: Sample81.Prairie vole.204529320079_R03C02


title: Patient 3 Group: Exercise (End-of-Study) L001

value: Not Hispanic or Latino


title: HCT15-COPS7B-INPUT-1

tag: genotype


title: Patient 1 Group: Exercise (End-of-Study) L002

tag: patient id

value: Exercise


title: Patient 2 Group: Exercise (End-of-Study) L001

value: End-of-Study


title: CW2

value: con

value: cw

tag: virus

value: wt


title: CQ3

value: cq


title: Patient 21 Group: Usual care (Baseline) L002

tag: race

value: Usual care

value: Baseline


title: Sample82.Prairie vole.204529320079_R04C02

value: Female

value: Sex naïve


title: CQ2

value: adult (6-wk) dorsal raphe nucleus tissue


title: CW1


title: Sample80.Prairie vole.204529320079_R02C02

value: Pair bonded


title: Patient 7 Group: Exercise (End-of-Study) L002

tag: ethinicity


title: SQ3

value: sq


title: Patient 21 Group: Usual care (Baseline) L001

value: colorectal mucosa

tag: age


title: SG1

value: sg

value: gfp


title: Sample79.Prairie vole.204529320079_R01C02

value: Ear


title: Sample76.Prairie vole.204529320079_R04C01

value: Male


title: CA1 Hippocampus mice CFC (1/2) Context + Shock

description: Sample 1 (192_9)

value: Brain Hippocampus CA1

value: Context + Shock


title: Sample87.Prairie vole.204529320014_R03C01

value: Liver


title: HCT15-COPS7B-INPUT-2

value: colon

value: colon cancer cell

value: COPS7B overexpression


title: HCT15-PLVX-RPF-2

value: WT


title: Patient 1 Group: Exercise (End-of-Study) L001

value: White or Caucasian

value: Not Hispanic or Latino

tag: gene mutated

value: Exercise

value: End-of-Study


title: Patient 2 Group: Exercise (Baseline) L002

tag: group

value: Baseline


title: CQ1

value: adult (6-wk) dorsal raphe nucleus tissue

value: con

value: cq


title: CG3

value: cg

value: gfp


title: Sample78.Prairie vole.204529320079_R06C01

value: Male

value: Pair bonded


title: HCT15-PLVX-RPF-1


title: HCT15-PLVX-INPUT-2


title: CG2


title: CG4


title: HCT15-PLVX-INPUT-1


title: Patient 19 Group: Usual care (Baseline) L002

value: colorectal mucosa

value: Usual care

tag: visit


title: SQ11

tag: tissue

value: stress

value: sq


title: Sample77.Prairie vole.204529320079_R05C01

value: Ear

tag: Sex

value: Sex naïve


title: Patient 2 Group: Exercise (Baseline) L001

value: White or Caucasian

value: Not Hispanic or Latino


title: SW620_RPF-2

value: colon

value: colon cancer cell

value: WT


title: SW620_INPUT-2


title: Patient 19 Group: Usual care (Baseline) L001

value: Baseline


title: SW620_RPF-1


title: CG1

value: adult (6-wk) dorsal raphe nucleus tissue

value: con


title: Sample75.Prairie vole.204529320079_R03C01

value: Liver

value: Female


title: Patient 17 Group: Usual care (Baseline) L002


title: D5_2847_S9

value: Defeat


title: D4_2852_S7


title: Patient 17 Group: Usual care (Baseline) L001

value: colorectal mucosa


title: HCT15_RPF-2


title: SW620_INPUT-1


title: D6_2850_S11


title: Sample74.Prairie vole.204529320079_R02C01

value: Male

value: Pair bonded


title: HCT15_INPUT-2


title: HCT15_RPF-1


title: Sample73.Prairie vole.204529320079_R01C01


title: Patient 16 Group: Usual care (Baseline) L002

value: Usual care


title: Patient 16 Group: Usual care (Baseline) L001


title: Sample72.Prairie vole.204529320081_R06C02


title: Sample70.Prairie vole.204529320081_R04C02

value: Ear


title: HCT15_INPUT-1


title: Sample71.Prairie vole.204529320081_R05C02


title: Patient 14 Group: Usual care (Baseline) L002


title: Sample69.Prairie vole.204529320081_R03C02


title: D2_2849_S3


title: Region capture Hi-C, iN, rep2

source_name: iN

value: iN

value: musc x cast


title: HCT116_RPF-2


title: D1_2840_S1


title: C6_2843_S12

value: Control


title: HCT116_RPF-1

value: colon


title: C5_2842_S10


title: Region capture Hi-C, iN, rep1


title: D3_2851_S5


title: Sample67.Prairie vole.204529320081_R01C02


title: Patient 14 Group: Usual care (Baseline) L001

value: White or Caucasian

value: Not Hispanic or Latino


title: C4_2845_S8


title: HCT116_INPUT-2

value: colon cancer cell

value: WT


title: HCT116_INPUT-1


title: Patient 13 Group: Usual care (Baseline) L001

value: Baseline


title: Patient 13 Group: Usual care (Baseline) L002


title: Sample66.Prairie vole.204529320081_R06C01

value: Liver

value: Sex naïve


title: Sample65.Prairie vole.204529320081_R05C01

value: Female


title: Sample86.Prairie vole.204529320014_R02C01


title: Sample68.Prairie vole.204529320081_R02C02


title: Patient 11 Group: Exercise (Baseline) L002

value: colorectal mucosa

value: Exercise


title: Sample63.Prairie vole.204529320081_R03C01


title: 841CON_RPF-1

value: normal colon epithelium cell


title: 841CON_RPF-2


title: C3_2841_S6

value: adult (6-wk) dorsal raphe nucleus tissue


title: Patient 11 Group: Exercise (Baseline) L001


title: C1_2844_S2


title: S24

value: SUS


title: Patient 1 Group: Exercise (Baseline) L002


title: Sample62.Prairie vole.204529320081_R02C01

value: Ear


title: S23


title: 40_SessileSerratedAdenoma/Polyp_5

city: Seoul

first: Jaeseung

last: Song

department: Life Science

country: South Korea

institute: Dongguk University

data_processing:
Base-calling were performed using real time analysis.
Raw data were cleaned with BBduk (ver 38.8.1).
Cleaned FASTQ files were aligned to reference genome using STAR aligner (ver. 2.7.3a) with default setting.
Aligned files were then converted into BAM files using Samtools (ver 1.10).
HTSeq (ver. 0.11.4) were used for extracting read counts.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Table in txt file format having Ensemble gene identifiers as rownames and Samples in column. Each values were normalized and transformed into log2(cpm +1).

source_name: SSA/P

extract_protocol:
Dissected samples were treated with Trizol and stored at -80℃ in a deep freezer.
Library was constructed using SureSelectXT RNA Direct Reagent Kit (Agilent, Santa Clara, CA, USA) following manufacturer's protocol.

tag: patient id no.

value: F

tag: date

tag: diagnosis

value: Sessile serrated adenoma/polyp

tag: location

value: Ascending colon

tag: other diseases

value: HTN, dyslipidemia, bronchial asthma, osteoporosis


title: CCB080031

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Hisat2 mapping to genome
FeatureCount summarization to gene read count
addition of 3 reads to all values
quantile normalization
Assembly: CanFam3.1
Supplementary files format and content: tab delimited txt file of normalized counts

organism: Canis lupus familiaris

source_name: osteosarcoma tumor tisue

growth_protocol: fresh frozen tumor tissue

extract_protocol:
Ambion miRvana kit.
Illumina paired end RNA-Seq standard

value: osteosarcoma tumor tisue

tag: breed

value: Great Dane

tag: tumor location

value: Femur


title: Sample60.Prairie vole.204529320068_R06C02

tag: confidenceinageestimate

value: Pair bonded

tag: animalid