title: 10_C3D1

value: YES

tag: epithelioid


title: Bulk RNA-seq, line C4.1, HepaCAM+, d200

status: Public on Oct 31 2024

type: SRA

city: Atlanta

first: Steven

last: Sloan

state: Georgia

address: 615 Michael Street, Room 375

country: USA

institute: Emory University

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d200_RNA

library_source: transcriptomic

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38). We used FeatureCounts to assemble transcripts and generate raw count matrices.
Assembly: hg38
Supplementary files format and content: xlsx count matrix

molecule: total RNA

organism: Homo sapiens

source_name: human cortical organoid

growth_protocol: Human cortical organoids: Following 3D formation, spheroids were treated daily in neural induction media (DMEM/F12, KSR, NEAA, Glutamax, Pen/Strep, Beta-mercaptoethanol) supplemented with Dorsomorphin (Sigma, Cat. 142 P5499-25MG, 5 μM) and SB-431542 (Selleck Chemicals, Cat. S1067, 10 μM) for 6 days.  Following this treatment, organoids were treated daily with neural media supplemented with EGF (R&D Systems, Cat. 236-EG-01M, 20 ng/mL) and FGF2 (R&D Systems, Cat. 233-FB-01M, 20 ng/mL) for 10 days, and every other day for days 16-24. At day 25, organoids were treated every other day with neural media supplemented with BDNF (PeproTech, Cat. 450-02- 1mg, 20 ng/mL) and NT-3 (R&D Systems, Cat. 267-N3-005/CF, 20 ng/mL) to promote differentiation of progenitors. From day 43 onwards, organoids were fed every 3 days with neural media only.

extract_protocol:
RNA was harvested using miRneasy kit (Qiagen).
Libraries were prepared with Takara Bio SMART-Seq v4 Ultra Low Input RNA Kit and NEBNext Ultra II kit.

treatment_protocol: Addition of D2HG or DMSO for several primary human fetal astrocyte samples

tag: tissue

value: human cortical organoid

tag: cell line

tag: cell type

value: HepaCAM+ cells

tag: Sex

value: female


title: WT, N, sample1

city: South San Francisco

first: Jackson

last: Liang

state: CA

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

data_processing:
HTSeqGenie pipeline
Assembly: GRCm38
Supplementary files format and content: TAB (Raw counts and rpkm per gene)

organism: Mus musculus

source_name: Mammary mature luminal cells

growth_protocol: Animals were raised under standard husbandry methods until 6 months of age.

extract_protocol:
Mammary glands were dissected from treated animals; mature luminal cells were isolated from tissues by FACS. RNA was isolated from mature luminal cells via Qiagen Rneasy Micro Plus kit.
Libraries were prepared from cDNA using the Nextera XT DNA Sample Preparation kit.

treatment_protocol: Animals were implanted with hormone pellets (E2 & P4), then dosed daily with giredestrant (30 mg/kg, p.o.) for four days

tag: er mutation

value: WT

tag: treatment

value: E2/P4 + giredestrant

value: Mammary gland

value: Novel


title: 7_C3D1

city: Nedlands

first: Nicola

last: Principe

state: WA

address: 6 Verdun St

country: Australia

institute: University of Western Australia

data_processing:
Alignment of 5’ VDJ sequencing data was performed with cell ranger. Sequences spanning the third complementary determining region (CDR3) of TRA, TRB, TRD and TRG genes from individual cells were derived. We focused on conventional TCRαβ T cells with productive rearrangements of the TRA, TRB CDR3 region. We used TraCeR56, a computational method to identify clonally related cells. We removed individual cells that produced >= 2 unique TRB CDR3 sequences, and cells that produced > 2 unique TRA CDR3 sequences. We called clones as individual T cells with identical combination of TRA/TRB CDR3 amino acid sequences, or cells with an identical TRB, or TRA CDR3 sequence.
Assembly: Cellranger v7.1.0
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Supplementary files format and content: Processed data files are output from CellRanger for each sample.
Library strategy: scTCR-Seq

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were thawed by immersing the cryotube in a 37°C water bath until a small ice shard remained. The cryotube contents were then mixed using a 1 mL pipette and transferred to a 50 mL centrifuge tube. Additionally, 1 mL of media was mixed with the cryovial and then transferred to the same 50 mL tube. Four sequential dilutions were performed by incrementally adding media to the centrifuge tube while gently agitating the mixture. Specifically, 2 mL, 4 mL, 8 mL, and 16 mL were added in succession, with a 30-second interval between each step. The PBMCs were subsequently centrifuged at 400g for 5 minutes. The supernatant was removed, leaving approximately 1 mL, in which the cells were resuspended. An additional 9 mL of media was added, followed by another 5-minute centrifugation at 400g. The supernatant was once again removed and discarded. The cells were finally resuspended in 1xDPBS+0.04% BSA. Cell count and viability were assessed using a Cellometer K2 and Acridine Orange/Propidium Iodide (AO/PI) staining.
Single cell libraries were constructed using the 10x Genomics chromium 5′ v2 workflow according to the manufacturer’s protocol. All experiments and conditions aimed for a capture of approximately 6000 cells. Libraries were quantified with Qubit and checked for fragment size using the TapeStation D1000 kit (Agilent). Libraries were pooled in equimolar concentration for a total pooled concentration of 1.8 nM. The libraries were sequenced using S4 (200 cycle) sequencing kits on the Illumina NovaSeq 6000 with a read one length of 100 cycles, and a read two length of 100 cycles. TCR libraries were constructed from the cDNA generated for each sample during the 5’ v2 workflow according to the manufacturers protocol (CG000331 REV A). The TCR libraries were then quantified using the QUBIT DNA HS kit (cat# Q32854) and fragment size determined using the TapeStation D1000 kit (Agilent). The libraries were then pooled in equimolar concentration for a total pooled concentration of 2nM. The libraries were sequenced using SP (100 cycle) sequencing kits on the Illumina NovaSeq 6000 with a read one length of 26 cycles, and a read two length of 90 cycles.

value: peripheral blood mononuclear cells

tag: patient

tag: timepoint

tag: pfs 6m_response

tag: gender

value: Female


title: Bulk RNA-seq, line C4.1, HepaCAM+, d150

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d150_Hepa_RNA


title: Y541S, N, sample3


title: 44_C2D1

value: Male


title: T Cells, ACUTE exhaustion, H3K27me3, rep R2

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

library_source: genomic

data_processing:
Alignment: reads were aligned to the mm10 reference genome using Bowtie (v2.4.1).
Filtering: only uniquely mapped reads were kept and duplicates were removed using Picard (v1.141) MarkDuplicates.
Peak Calling: peaks were called using MACS2 (v2.1.2) with parameters -p 1e-8 --min-length 500 --max-gap 800 --broad for H3K27me3 and -q 0.05 --broad for H3K27ac. For both marks, peaks that only occurred in one replicate were removed. Peaks were then merged across replicates per condition and mark using bedtools merge (v2.26.0) then annotated using HOMER annotatePeaks (v4.11.1).
Track Creation: bigWig files were generated using deepTools2 bamCoverage (v3.5.4) and average bigWigs across replicates were generated using deepTools2 bigwigAverage then displayed using the UCSC Genome Browser.
Assembly: mm10 / GRCm38
Supplementary files format and content: Supplemental bigWigs represent single samples or else replicates averaged using bigWigAverage (*avg.bw).
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV

growth_protocol: Mice were housed at the University of Pennsylvania in a specific pathogen–free facility and experiments and procedures were performed in accordance with Institutional Animal Care and Use Committee. For the in vitro model, P14 transgenic mice expressing a TCR specific for the LCMV peptide DbGP33–41 were backcrossed to C57BL/6 mice (Charles River), transferred from the lab of John Wherry, and bred in house. Mice were between 8 and 24 weeks old, randomly assigned to experimental groups, and sexes were alternated between experiments.

extract_protocol:
The CUT&RUN assay was performed as previously described with some modifications. In brief, after sorting for live CD8 positive T cells from the in vitro model, 20,000 cells per antibody were washed twice with cell wash buffer, bound to 40 ul of concanavalin A-coated magnetic beads, and then split to incubate overnight rotating at 4 °C in 250 ul of antibody buffer with either H3K27me3 (Cell Signaling, #9733) or H3K27ac (Active Motif, #39133) antibodies. Cells were then washed and resuspended in 0.1% digitonin buffer with pA-MN fusion protein at 700 ng/ml and incubated rotating at 4 °C for 1 hour. Cells were then washed, resuspended in the digitonin buffer, brought down to 0 °C, and CaCl2 was added to a final concentration of 2mM for digestion at 0 °C for 30 minutes. 2X stop buffer was then added to the reaction and incubated at 37°C for 10 minutes to release the fragments followed by centrifugation. SDS (0.1%) and proteinase K (0.2 mg/ml) were then added to the supernatant, incubated at 70°C for 10 minutes, and followed by phenol-chloroform DNA extraction.
Library preparation was performed according to manufacturer’s guidelines using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645L). The NEBNext® Library Quant Kit for Illumina® (E7630L) and bioanalyzer were used to assess library quality and concentration. Libraries were sequenced using the Illumina® NextSeq 500.

treatment_protocol: Complete RPMI (cRPMI) in this protocol is RPMI 1640 (Corning Cellgro) supplemented with 10% fetal bovine serum, 50 μM β-mercaptoethanol, 2 mM glutamine (Gibco), penicillin (100 U/ml; Sigma-Aldrich), streptomycin (100 μg/ml; Sigma-Aldrich), 100 μM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), and 20 mM Hepes buffer (Invitrogen). CD8 T cells were isolated from spleens of naïve P14 transgenic mice by homogenizing against a 70-μm cell strainer, washing with cRPMI, passing through a 70-μm cell strainer again, and then isolation via a negative selection kit (STEMCELL Technologies) per the manufacturer’s instructions. DCs were isolated from spleens of naïve C57BL/6 mice by cutting samples into small pieces, incubating at 37°C for 30-45 min with deoxyribonuclease I (1 U/ml; Roche) and collagenase D (10 U/ml; Roche) in cRPMI, then homogenization against a 70-μm cell strainer. Red blood cells were lysed with ammonium-chloride-potassium (ACK) lysis buffer (Gibco) for 5 min, the cell suspension was quenched and washed with phosphate-buffered saline (PBS) and then passed through a 70-μm cell strainer again. DCs were isolated with CD11c+ Microbeads (Miltenyi) per the manufacturer’s instructions and then pulsed with DbGP33–41 peptide (0.1 μM, GenScript) in cRPMI for 30 min-1 hour at 37°C. CD8 P14 cells and DCs were then cocultured in cRPMI at a 1:1 ratio (105 DCs + 105 P14 cells per well) in a flat-bottom 96-well plate. At day 2, 4, and 6 of coculture, P14 cells were counted via BD Accuri and normalized to a concentration of 0.5 × 106 P14 cells/ml (105 P14 cells per well) to be replated into in vitro culture. Chronically stimulated P14 cells received DbGP33–41 peptide (1 nM) at day 2, 4, and 6 and both in vitro conditions (chronic and acute) received recombinant human IL-2 (10 U/ml; PeproTech) at day 2, 4, and 6. For EED inhibition experiments, EED226 (#22031) was bought from Cayman Chemical, resuspended in DMSO to make a stock concentration of 10mM and added to in vitro cell culture media at a concentration of 4uM. Control conditions were given an equivalent amount of DMSO.

tag: strain

tag: group

value: ACUTE exhaustion

tag: genotype

value: Armstrong strain of the LCMV

tag: antibody

tag: antibody catalog

value: Cell Signaling, #9733

tag: replicate


title: Bulk RNA-seq, line C3.1, HepaCAM+, d200

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d200_RNA

value: male


title: Bulk RNA-seq, line C4.1, cd49+, d150

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d150_cd49_RNA

value: cd49f+ cells


title: T Cells, ACUTE exhaustion, H3K27me3, rep R1

value: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV


title: 36_C3D1

value: NO

tag: epithelioid

value: YES


title: Y541S, N, sample2

tag: tissue


title: Bulk RNA-seq, line C3.1, cd49+, d150

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d150_RNA

value: human cortical organoid

tag: cell line


title: Y541S, N, sample1

tag: cell type


title: T Cells, ACUTE exhaustion, H3K27ac, rep R4

value: Active Motif, #39133


title: Y541S, ML, sample3

value: ML


title: Bulk RNA-seq, line C4.1, cd49+, d100

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d100_RNA

tag: Sex

value: female


title: T Cells, ACUTE exhaustion, H3K27ac, rep R3


title: T Cells, ACUTE exhaustion, H3K27me3, rep R3


title: 28_C3D1


title: Bulk RNA-seq, line C3.1, cd49+, d100

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d100_RNA


title: Y541S, ML, sample2

tag: er mutation

value: E2/P4 + giredestrant

value: Mammary gland


title: T Cells, ACUTE exhaustion, H3K27ac, rep R2


title: 28_C2D1

value: peripheral blood mononuclear cells


title: Bulk RNA-seq, line C4.1, cd49+, d80

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d80_RNA


title: T Cells, ACUTE exhaustion, H3K27ac, rep R1


title: Bulk RNA-seq, line C3.1, cd49+, d80

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d80_RNA


title: Y541S, ML, sample1

tag: treatment


title: 18_C2D1

tag: patient


title: 13_BL

tag: timepoint

value: BL

value: Female


title: T Cells,CHRONIC exhaustion, EED226-treated, 04122023 sequenced, rep 2

data_processing:
Alignment: reads were aligned to the mm10 reference genome using STAR (v2.7.1a)
Normalization: aligned files were normalized using PORT gene-based normalization (https://github.com/itmat/Normalization) with default parameters.
Differential gene expression: performed using DESeq2 (v1.38.3) where genes expressing less than 10 reads across all samples were removed.
Assembly: mm10 / GRCm38
Supplementary files format and content: Supplemental table has gene counts per sample after re-sampling with PORT, and should be treated as normalized for use with DESeq2

molecule: polyA RNA

extract_protocol:
RNA was extracted using TRIzol reagent according to the manufacturer’s instructions.
RNA-seq libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760L). The NEBNext® Library Quant Kit for Illumina® (E7630L) and bioanalyzer were used to assess library quality and concentration then libraries were sequenced using the Illumina® NextSeq 500 and NextSeq 1000.

value: Clone 13 strain of the LCMV

tag: date sequenced

tag: exhaustion

value: CHRONIC


title: 2_C3D1

tag: pfs 6m_response

tag: gender

value: Male


title: T Cells,CHRONIC exhaustion, EED226-treated, 04122023 sequenced, rep 1

tag: genotype

tag: strain


title: D542G, N, sample2

value: Novel


title: T Cells,CHRONIC exhaustion, DMSO-treated, 04122023 sequenced, rep 2

value: DMSO


title: 54_C2D1


title: 33_BL


title: MeDIP-seq, GBM33, tumor

description: 30 million PE reads

data_processing:
Fastq files were first mapped using Bowtie 2 (2.4.4) 127 with “--no-mixed --no-discordant” parameters. To identify differential 5mC and 5hmC signal between IDH1mt and IDHwt samples, the human genome sequence was binned to 500 bp bins and reads of each sample were counted in each bin.
Assembly: hg38
Supplementary files format and content: tdf files

source_name: human glioblastoma

extract_protocol:
GBM tissue was digested in a lysis buffer (10 mM Tris pH 8.0, 5 mM EDTA, 200 mM NaCl, 0.2% SDS) with 30 l proteinase K (20 mg/ml) and incubated at 55C overnight. After the overnight digestion, the lysates were brought to room temperature and incubated with 5 L of RNase A solution (20 mg/ml) for 1 hour at 37 C. This was followed by adding equal volume of buffered phenol:chloroform:isoamyl alcohol (25:24:1 ratio) and centrifuged at 14,000 RPM at room temperature for 20 minutes. Supernatant was transferred to clean tubes and 5 l of 5 M NaCl, 2 l Glycogen, and equal volume of 100% ethanol were added. After overnight incubation at -20C, samples were centrifuged at 10,000 g for 10 minutes at 4C, and the DNA pellet was washed in 70% ethanol twice. After all ethanol was removed, the DNA pellet was dissolved in nuclease-free water and incubated overnight at 4C, before being quantified by Nanodrop.
3 µg of genomic DNA was fragmented to 300-400 base pairs using a Covaris focused-ultrasonicator Me220. DNA fragments were then subjected to end repair, A-tailing, adaptor ligation, and USER digestion using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs, Cat. E7645S), according to the manufacturer’s protocol. Following USER digestion and purification, DNA was denatured for 10 minutes at 95C and immunoprecipitated overnight at 4C with 4 L of either 5mC antibody (Active Motif, Cat. 39649) or IgG antibody (Sigma, Cat. 12-371) in IP buffer (500 mM Tris-HCl, pH 7.4, 750 mM NaCl and 0.25% TritonX). The mixture was then incubated with Protein G coated Dynabeads (ThermoFisher, Cat. 10004D) for at least 2 hours at 4C, washed with ice cold IP buffer, and finally washed in ice cold high salt IP buffer (IP buffer plus extra 300 mM NaCl). After the final washing, the beads were treated with 200 L of digestion buffer (1X TE Buffer, pH 7.4, 0.25% SDS, 0.25% Proteinase K (2.5 mg/mL)) and shaken at 1000 rpm for 2 hours at 55C. The methylated DNA was recovered by phenol:chloform:isoamyl alcohol (25:24:1) extraction, followed by precipitation in 3X volume of 100% ethanol, supplemented with 3 L glycogen (5mg/mL) and 15 L NaAC (pH 5.2), and then incubated overnight at -20C. The next day, DNA was pelleted and washed with 75% ethanol and dissolved in nuclease-free water.

value: human glioblastoma

value: male, IDH1mt


title: D542G, ML, sample3


title: MeDIP-seq, GBM40, tumor

description: 30 million PE reads


title: MeDIP-seq, GBM43, tumor

description: 30 million PE reads

value: female, IDH1mt


title: 51_BL

value: YES


title: MeDIP-seq, GBM34, tumor

description: 30 million PE reads

value: male, IDHwt


title: D542G, ML, sample2

value: ML


title: T Cells,ACUTE exhaustion, EED226-treated, 04122023 sequenced, rep 2

value: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV

value: Armstrong strain of the LCMV

value: ACUTE


title: 41_BL

value: peripheral blood mononuclear cells


title: MeDIP-seq, GBM25, tumor

description: 30 million PE reads

value: female, IDHwt


title: D542G, ML, sample1

value: E2/P4 + giredestrant

value: Mammary gland


title: 33_C2D1

value: NO


title: D542G, N, sample3


title: MeDIP-seq, GBM20, tumor

description: 30 million PE reads


title: WT, ML, sample2

value: WT


title: WT, ML, sample3


title: 29_C3D1

value: Male


title: T Cells,ACUTE exhaustion, DMSO-treated, 04122023 sequenced, rep 1

value: DMSO


title: D542G, N, sample1

value: Novel


title: T Cells,CHRONIC exhaustion, DMSO-treated, 01192023 sequenced, rep 3

value: Clone 13 strain of the LCMV

value: CHRONIC


title: 13_C3D1

value: YES

value: Female


title: hMe-Seal-seq, GBM43, tumor

description: 30 million PE reads

data_processing:
Fastq files were first mapped using Bowtie 2 (2.4.4) 127 with “--no-mixed --no-discordant” parameters. To identify differential 5mC and 5hmC signal between IDH1mt and IDHwt samples, the human genome sequence was binned to 500 bp bins and reads of each sample were counted in each bin.
Assembly: hg38
Supplementary files format and content: tdf files
Library strategy: hMe-Seal-seq

extract_protocol:
GBM tissue was digested in a lysis buffer (10 mM Tris pH 8.0, 5 mM EDTA, 200 mM NaCl, 0.2% SDS) with 30 l proteinase K (20 mg/ml) and incubated at 55C overnight. After the overnight digestion, the lysates were brought to room temperature and incubated with 5 L of RNase A solution (20 mg/ml) for 1 hour at 37 C. This was followed by adding equal volume of buffered phenol:chloroform:isoamyl alcohol (25:24:1 ratio) and centrifuged at 14,000 RPM at room temperature for 20 minutes. Supernatant was transferred to clean tubes and 5 l of 5 M NaCl, 2 l Glycogen, and equal volume of 100% ethanol were added. After overnight incubation at -20C, samples were centrifuged at 10,000 g for 10 minutes at 4C, and the DNA pellet was washed in 70% ethanol twice. After all ethanol was removed, the DNA pellet was dissolved in nuclease-free water and incubated overnight at 4C, before being quantified by Nanodrop.
5hmC capture was performed according to the methods described in Kuehner et al, 2021. 5 µg of genomic DNA was fragmented to 300-400 base pairs through sonication and 5hmCs were glycosylated by T4 phage ß-glucosyltransferase enzyme and UDP-6-N3-glucose. The glycosylated fragments were purified with Ampure XP beads (BeckmanCoulter; Cat. A63881), biotinylated by click reaction with disulfide biotin, and pulled down with Dynabeads MyOne Streptavidin C1 beads (ThermoFisher; Cat. 65001). The 5hmC fragments were released from the beads using dithiothreitol and purified with Ampure XP beads for a final time. DNA fragments were eluted in nuclease-free water and quantified by Qubit.

value: human glioblastoma

value: female, IDH1mt


title: T Cells,CHRONIC exhaustion, DMSO-treated, 01192023 sequenced, rep 2

value: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV


title: WT, ML, sample1

value: ML


title: T Cells,CHRONIC exhaustion, DMSO-treated, 04122023 sequenced, rep 1


title: 5_BL

value: peripheral blood mononuclear cells

value: BL


title: hMe-Seal-seq, GBM33, tumor

description: 30 million PE reads

value: male, IDH1mt


title: hMe-Seal-seq, GBM40, tumor

description: 30 million PE reads


title: 2_C2D1


title: T Cells,ACUTE exhaustion, DMSO-treated, 01192023 sequenced, rep 3

value: Armstrong strain of the LCMV

value: ACUTE


title: hMe-Seal-seq, GBM34, tumor

description: 30 million PE reads

value: male, IDHwt


title: T Cells,ACUTE exhaustion, DMSO-treated, 01192023 sequenced, rep 2


title: 49_C3D1

value: NO

value: Male


title: Y541S, EP, SERD, N, sample3 (RNA-seq)

extract_protocol:
Mammary glands were dissected from treated animals; cell populations (mature luminal, ML, luminal progenitor, LP, basal, and 'novel') were isolated from tissues by FACS. RNA was isolated from mature luminal cells via Qiagen Rneasy Micro Plus kit.
Libraries were prepared from cDNA using the Nextera XT DNA Sample Preparation kit.

treatment_protocol: Animals were implanted with hormone pellets (E2 & P4), then dosed daily with vehicle (MCT) or giredestrant (30 mg/kg, p.o.) for four days

value: E2/P4 + giredestrant

value: mammary gland

value: Novel


title: Y541S, EP, SERD, B, sample3 (RNA-seq)

value: Basal


title: hMe-Seal-seq, GBM25, tumor

description: 30 million PE reads

value: female, IDHwt


title: WT, EP, SERD, B, sample2 (ATAC-seq)

data_processing:
MACS2 peak calling (ENCODE ATAC pipeline)
Assembly: GRCm38
Supplementary files format and content: narrowPeak

extract_protocol:
Mammary glands were dissected from treated animals; mature luminal cells were isolated from tissues by FACS. RNA was isolated from mature luminal cells via Qiagen Rneasy Micro Plus kit.
Performed as described in Corces, et al. 'Omni-ATAC-seq: Improved ATAC-seq'. (2017)

value: WT

value: Mammary gland


title: Y541S, EP, SERD, LP, sample3 (RNA-seq)

value: LP


title: T Cells,ACUTE exhaustion, EED226-treated, 04122023 sequenced, rep 1

value: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV


title: hMe-Seal-seq, GBM20, tumor

description: 30 million PE reads

value: human glioblastoma


title: WT, EP, SERD, LP, sample2 (ATAC-seq)


title: Y541S, EP, SERD, ML, sample3 (RNA-seq)

value: ML


title: 42_BL

value: peripheral blood mononuclear cells

value: BL

value: YES


title: Y541S, EP, SERD, N, sample2 (RNA-seq)


title: Bulk ATAC-seq, GBM40, tumor

description: 60 million PE reads

data_processing:
Fastq file processing included the following steps: (1) Nextera adapters were trimmed using TrimGalore 109, (2) reads were mapped to the hg19 reference genome using Bowtie2 110, (3) mitochondrial and non-unique alignment reads were removed using Samtools 111, (4) PCR duplicates were removed with Picard tools 112, (5) black-listed reads were removed using Bedtools 113, and (6) peaks were called using MACS2 114 with the following parameters: shift -75 –extsize 150 –nomodel –call-summits –nolambda -p 0.01 -B –SPMR
Assembly: hg19
Supplementary files format and content: bigWig files

extract_protocol:
10,000-50,000 cells were washed with cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water), and permeabilized with ATAC-seq lysis buffer (RSB supplemented with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin).
For the transposition step, nuclei were resuspended in 50 µl of transposition mix (25 µl 2× TD buffer, 2.5 µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, and 5 µl water) and incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. The DNA fragments were cleaned up with the Qiagen MinElute PCR Purification kit (Qiagen, Cat. 28004) and PCR amplified for 5 cycles with Illumina Nextera adaptors using NEBNext High Fidelity 2x Master Mix (New England Biolabs, Cat. M0541S). Next, a qPCR reaction was performed using 10% of the pre-amplified PCR product. We looked for the Ct value at ¼ maximum fluorescence to determine the number of additional cycles to amplify the ATAC-seq libraries. After a second round of PCR amplification (all together, a total of 8-10 cycles), we performed a second cleanup with 1.8x Ampure XP beads (Aline biosciences, Cat. C-1003-50).

value: HepaCAM+ cells


title: WT, EP, SERD, ML, sample2 (ATAC-seq)


title: 33_C3D1

value: NO


title: Bulk ATAC-seq, GBM40, margin

description: 60 million PE reads


title: Y541S, EP, SERD, B, sample2 (RNA-seq)


title: Bulk ATAC-seq, GBM38, tumor

description: 60 million PE reads

value: male, IDHwt


title: 28_BL

value: Male


title: Y541S, EP, SERD, LP, sample2 (RNA-seq)

value: E2/P4 + giredestrant

value: mammary gland


title: 27_BL


title: WT, EP, SERD, LP, sample1 (ATAC-seq)


title: Y541S, EP, SERD, ML, sample2 (RNA-seq)


title: Bulk ATAC-seq, GBM38, margin

description: 60 million PE reads

value: male


title: WT, EP, SERD, ML, sample1 (ATAC-seq)


title: 24_C2D1


title: Bulk ATAC-seq, GBM37, tumor

description: 60 million PE reads

value: IDHwt


title: Y541S, EP, SERD, N, sample1 (RNA-seq)

value: Novel


title: Bulk ATAC-seq, GBM37, margin

description: 60 million PE reads


title: 54_C3D1


title: Y541S, EP, SERD, B, sample1 (RNA-seq)

value: Basal


title: 4_C2D1


title: Y541S, EP, B, sample3 (ATAC-seq)

value: E2/P4 + vehicle

value: Mammary gland


title: 45_C2D1


title: 27_C3D1


title: Y541S, EP, B, sample2 (ATAC-seq)


title: WT, EP, SERD, B, sample1 (ATAC-seq)

value: WT


title: Bulk ATAC-seq, GBM33, tumor

description: 60 million PE reads

value: human glioblastoma

value: male, IDH1mt


title: Bulk ATAC-seq, GBM32, tumor

description: 60 million PE reads

value: female, IDHwt


title: Y541S, EP, ML, sample2 (ATAC-seq)

value: ML


title: Y541S, EP, SERD, LP, sample1 (RNA-seq)

value: LP


title: Bulk ATAC-seq, GBM32, margin

description: 60 million PE reads

value: HepaCAM+ cells

value: female


title: 46_C2D1

value: peripheral blood mononuclear cells

value: YES

value: Female


title: D542G, EP, SERD, N, sample3 (RNA-seq)

value: E2/P4 + giredestrant

value: mammary gland


title: Y541S, EP, B, sample1 (ATAC-seq)


title: Y541S, EP, SERD, ML, sample1 (RNA-seq)


title: 26_BL

value: BL

value: Male


title: Bulk ATAC-seq, GBM31, tumor

description: 60 million PE reads


title: 9_C3D1


title: Bulk ATAC-seq, GBM31, margin

description: 60 million PE reads

value: male


title: Y541S, EP, ML, sample3 (ATAC-seq)

value: E2/P4 + vehicle

value: Mammary gland


title: 9_C2D1


title: D542G, EP, B, sample3 (ATAC-seq)

value: Basal


title: Bulk ATAC-seq, GBM30, tumor

description: 60 million PE reads

value: human glioblastoma

value: male, IDHwt


title: D542G, EP, SERD, B, sample3 (RNA-seq)


title: D542G, EP, ML, sample3 (ATAC-seq)

value: ML


title: 2_BL


title: D542G, EP, SERD, ML, sample3 (RNA-seq)


title: D542G, EP, B, sample2 (ATAC-seq)


title: D542G, EP, SERD, N, sample2 (RNA-seq)

value: Novel


title: Bulk ATAC-seq, GBM28, tumor

description: 60 million PE reads

value: HepaCAM+ cells

value: IDHwt


title: 15_BL

value: peripheral blood mononuclear cells

value: NO


title: Bulk ATAC-seq, GBM25, tumor

description: 60 million PE reads

value: female, IDHwt


title: D542G, EP, SERD, B, sample2 (RNA-seq)

value: E2/P4 + giredestrant


title: Bulk ATAC-seq, GBM24, margin

description: 60 million PE reads

value: female


title: D542G, EP, SERD, LP, sample2 (RNA-seq)

value: mammary gland

value: LP


title: 55_C2D1

value: YES

value: Male


title: Bulk ATAC-seq, GBM24, tumor

description: 60 million PE reads

value: female, IDH1mt


title: 6_C3D1


title: D542G, EP, ML, sample2 (ATAC-seq)

value: E2/P4 + vehicle

value: Mammary gland


title: Y541S, EP, ML, sample1 (ATAC-seq)


title: D542G, EP, SERD, N, sample1 (RNA-seq)


title: D542G, EP, B, sample1 (ATAC-seq)

value: Basal


title: 6_C2D1


title: D542G, EP, SERD, ML, sample2 (RNA-seq)

value: ML


title: D542G, EP, ML, sample1 (ATAC-seq)


title: WT, EP, B, sample3 (ATAC-seq)

value: WT


title: 32_BL

value: BL

value: Female


title: D542G, EP, SERD, LP, sample3 (RNA-seq)


title: Bulk ATAC-seq, GBM22, margin

description: 60 million PE reads

value: human glioblastoma

value: HepaCAM+ cells

value: male


title: WT, EP, ML, sample3 (ATAC-seq)


title: D542G, EP, SERD, B, sample1 (RNA-seq)

value: E2/P4 + giredestrant


title: 34_C3D1

value: peripheral blood mononuclear cells

value: NO


title: Bulk ATAC-seq, GBM21, tumor

description: 60 million PE reads


title: D542G, EP, SERD, LP, sample1 (RNA-seq)

value: mammary gland

value: LP


title: 15_C2D1

value: YES


title: D542G, EP, SERD, ML, sample1 (RNA-seq)


title: Bulk ATAC-seq, GBM21, margin

description: 60 million PE reads

value: female


title: 44_BL

value: Male


title: WT, EP, B, sample2 (ATAC-seq)

value: E2/P4 + vehicle

value: Mammary gland


title: WT, EP, ML, sample2 (ATAC-seq)

value: ML


title: Bulk ATAC-seq, GBM22, tumor

description: 60 million PE reads

value: male, IDH1mt


title: WT, EP, SERD, B, sample3 (RNA-seq)

value: WT

value: Basal


title: WT, EP, B, sample1 (ATAC-seq)


title: Bulk ATAC-seq, GBM18, tumor

description: 60 million PE reads

value: human glioblastoma

value: male, IDHwt


title: WT, EP, ML, sample1 (ATAC-seq)


title: HUVEC shSHP2 Estradiol rep3

city: Nanjing

first: Jie

last: Pan

address: xianlin street 1800

department: School of Life sciences

country: China

institute: Nanjing University

description: shSHP2 Estradiol_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/ , version:cutadapt-1.9).
The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value <20) bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ , 0.11.9), including the Q20, Q30 and GC-content of the clean data.
We aligned reads of all samples to the Homo sapiens reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/ , version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: Tab-delimited text file includes raw counts and FPKM values for each Sample.

source_name: HUVEC

growth_protocol: HUVECs were cultured in ECM supplemented with ECGS, 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA libraries were 300±50 bp.

treatment_protocol: HUVECs treated with estradiol (E2) with or without SHP099 for 6 h, and SHP2-knockdown HUVECs treated with estradiol for 6 h, were collected and subjected to RNA-Seq.

value: HUVEC

value: Human umbilical vein endothelial cells

value: SHP2 knockdown

value: Estradiol


title: WT, EP, SERD, ML, sample3 (RNA-seq)

value: E2/P4 + giredestrant

value: mammary gland


title: D542G, EP, SERD, N, sample3 (ATAC-seq)

value: Novel


title: HUVEC shSHP2 Estradiol rep2

description: shSHP2 Estradiol_2


title: WT, EP, SERD, LP, sample3 (RNA-seq)

value: LP


title: Bulk ATAC-seq, GBM17, tumor

description: 60 million PE reads

value: HepaCAM+ cells


title: Bulk ATAC-seq, GBM16, margin

description: 60 million PE reads

value: male


title: D542G, EP, SERD, B, sample3 (ATAC-seq)

value: Mammary gland


title: Bulk ATAC-seq, GBM15, tumor

description: 60 million PE reads


title: WT, EP, SERD, LP, sample2 (RNA-seq)


title: WT, EP, SERD, B, sample2 (RNA-seq)


title: WT, EP, SERD, ML, sample2 (RNA-seq)

value: ML


title: Bulk ATAC-seq, GBM12, tumor

description: 60 million PE reads


title: HUVEC shSHP2 Estradiol rep1

description: shSHP2 Estradiol_1


title: D542G, EP, SERD, ML, sample3 (ATAC-seq)


title: Bulk ATAC-seq, GBM20, tumor

description: 60 million PE reads


title: HUVEC Estradiol+SHP099 rep2

value: Estradiol and SHP099


title: HUVEC Estradiol+SHP099 rep3

value: WT


title: WT, EP, SERD, B, sample1 (RNA-seq)

value: Basal


title: D542G, EP, SERD, N, sample2 (ATAC-seq)


title: Bulk ATAC-seq, GBM12, margin

description: 60 million PE reads

value: human glioblastoma


title: 49_BL

value: peripheral blood mononuclear cells

value: BL

value: NO

value: Male


title: HUVEC Estradiol+SHP099 rep1

value: HUVEC

value: Human umbilical vein endothelial cells


title: WT, EP, SERD, LP, sample1 (RNA-seq)

value: E2/P4 + giredestrant

value: mammary gland


title: Bulk ATAC-seq, GBM11, tumor

description: 60 million PE reads

value: male, IDHwt


title: D542G, EP, SERD, B, sample2 (ATAC-seq)


title: WT, EP, SERD, ML, sample1 (RNA-seq)


title: HUVEC Estradiol rep3

value: Estradiol


title: D542G, EP, SERD, LP, sample2 (ATAC-seq)

value: LP


title: HUVEC Estradiol rep2


title: HUVEC Estradiol rep1


title: D542G, EP, SERD, LP, sample3 (ATAC-seq)

value: Mammary gland


title: Y541S, EP, ML, sample3 (RNA-seq)

value: E2/P4 + vehicle

value: ML


title: Bulk ATAC-seq, line C4.1, HepaCAM+, d550

description: 60 million PE reads

value: human cortical organoid

value: HepaCAM+ cells

value: female


title: HUVEC DMSO rep3

value: WT

value: DMSO


title: D542G, EP, SERD, N, sample1 (ATAC-seq)

value: Novel


title: Bulk ATAC-seq, line C4.1, HepaCAM+, d450

description: 60 million PE reads


title: Y541S, EP, B, sample2 (RNA-seq)

value: Basal


title: Bulk ATAC-seq, line C3.1, HepaCAM+, d550

description: 60 million PE reads

value: male


title: HUVEC DMSO rep2

value: HUVEC

value: Human umbilical vein endothelial cells


title: D542G, EP, SERD, LP, sample1 (ATAC-seq)

value: E2/P4 + giredestrant


title: Y541S, EP, ML, sample2 (RNA-seq)

value: mammary gland


title: Y541S, EP, B, sample1 (RNA-seq)


title: Bulk ATAC-seq, line C3.1, HepaCAM+, d450

description: 60 million PE reads


title: D542G, EP, SERD, ML, sample1 (ATAC-seq)


title: Bulk ATAC-seq, line C4.1, HepaCAM+, d400

description: 60 million PE reads


title: Bulk ATAC-seq, GBM10, tumor

description: 60 million PE reads

value: human glioblastoma

value: male, IDHwt


title: Y541S, EP, ML, sample1 (RNA-seq)


title: WT, EP, SERD, B, sample3 (ATAC-seq)

value: Mammary gland


title: DUS2L 5-ClUrd 1

city: Princeton

first: Nathan

last: Yu

state: New Jersey

address: Frick Chemistry Laboratory

department: Chemistry

institute: Princeton University

data_processing:
Discard duplicate reads and trim adaptor/barcode sequences using iCount Primary Analysis pipeline
Mapped trimmed reads to tRNA/rRNA with STAR (v.2.7.0f)
Unique mapped reads from iCount were used for peak calling analysis by Paraclu
Parameters of Paraclu: minimal sum of 10, maximal cluster size of 5, minimal density increase of 2
Only analyzed peaks that overlapped with, or were 1 nt adjacent to U residues.
Assembly: hg38
Supplementary files format and content: .bed files
Supplementary files format and content: Each .bed file contains data containing tRNA isotype, residue number, cDNA count, and strand direction

source_name: kidney

growth_protocol: Human Flp-In T-Rex 293 cells expressing 3xFLAG-DUS1L or 3xFLAG-DUS2L cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2 in 10-cm plates.

extract_protocol:
Cells were washed twice with cold PBS and lysed with 500 µL of lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NaCl, 1% NP-40, 0.1% SDS and 0.5% sodium deoxycholate), from previous literature precedent
iCLIP workflow

treatment_protocol: Cells were induced with 1 µg/mL tetracycline at 60% confluency. After 12 h, medium was exchanged with fresh medium containing 1 µg/mL tetracycline or 1 µg/mL tetracycline with 100 µM 5-ClUrd for 12 h.

value: kidney

value: Flp-In T-Rex 293

value: human embryonic kidney cells

value: Flp-In modified to express 3xFLAG-DUS2L

value: 1 µg/mL tetracycline, 12 h; 1 µg/mL tetracycline, 12 h, 100 µM 5-ClUrd 12 h


title: DUS2L 5-ClUrd 2


title: Bulk ATAC-seq, GBM10, margin

description: 60 million PE reads

value: HepaCAM+ cells


title: Y541S, EP, B, sample3 (RNA-seq)

value: E2/P4 + vehicle


title: D542G, EP, SERD, ML, sample2 (ATAC-seq)

value: ML


title: D542G, EP, B, sample3 (RNA-seq)

value: Basal


title: Bulk ATAC-seq, line C3.1, HepaCAM+, d400

description: 60 million PE reads

value: human cortical organoid

value: male


title: WT, EP, SERD, LP, sample3 (ATAC-seq)

value: WT

value: LP


title: Bulk ATAC-seq, line C3.1, HepaCAM+, d350

description: 60 million PE reads


title: DUS2L ctrl 2

value: 1 µg/mL tetracycline, 12 h; 1 µg/mL tetracycline


title: D542G, EP, ML, sample3 (RNA-seq)

value: mammary gland


title: WT, EP, SERD, ML, sample3 (ATAC-seq)

value: E2/P4 + giredestrant


title: DUS2L ctrl 1


title: Bulk ATAC-seq, line C4.1, HepaCAM+, d300

description: 60 million PE reads

value: female


title: D542G, EP, B, sample2 (RNA-seq)


title: HUVEC DMSO rep1

value: HUVEC

value: Human umbilical vein endothelial cells

value: DMSO


title: Bulk ATAC-seq, line C3.1, HepaCAM+, d300

description: 60 million PE reads


title: D542G, EP, SERD, B, sample1 (ATAC-seq)

value: Mammary gland


title: DUS1L 5-ClUrd 1

value: kidney

value: Flp-In T-Rex 293

value: human embryonic kidney cells

value: Flp-In modified to express 3xFLAG-DUS1L

value: 1 µg/mL tetracycline, 12 h; 1 µg/mL tetracycline, 12 h, 100 µM 5-ClUrd 12 h


title: Bulk ATAC-seq, line C4.1, HepaCAM+, d250

description: 60 million PE reads

value: human cortical organoid

value: HepaCAM+ cells


title: Y541S, EP, SERD, N, sample3 (ATAC-seq)

value: Novel


title: Y541S, EP, SERD, LP, sample3 (ATAC-seq)

value: LP


title: D542G, EP, ML, sample1 (RNA-seq)

value: E2/P4 + vehicle

value: ML


title: Bulk ATAC-seq, line C3.1, HepaCAM+, d250

description: 60 million PE reads

value: male


title: WT, EP, B, sample3 (RNA-seq)

value: WT

value: mammary gland

value: Basal


title: DUS1L ctrl 1

value: 1 µg/mL tetracycline, 12 h; 1 µg/mL tetracycline


title: Bulk ATAC-seq, line C4.1, HepaCAM+, d200

description: 60 million PE reads

value: female


title: Y541S, EP, SERD, N, sample2 (ATAC-seq)

value: E2/P4 + giredestrant

value: Mammary gland


title: HeLa WT NaBH4_rep 1

data_processing:
Forward and reverse reads were paired.
Adaptor trimming and low quality reads removal was performed by fastp.
Filtered reads were aligned to a human mature tRNA reference by RNA STAR.
Reads from biological replicates of the same samples were merged by MergeSamFiles.
Mutational analysis was performed by VarScan somatic.
Assembly: hg38 tRNA
Supplementary files format and content: tRNA NaBH4 Seq 103023.xlsx
Supplementary files format and content: Spreadsheet containing all mutational events at tRNA positions, corresponding to sequenced samples

source_name: cervical cancer

growth_protocol: Human HEK293T and HeLa cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2 in 10-cm plates.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent following the manufacturer's protocol. Transfer RNA was isolated from total RNA by gel extraction.
RNA-seq libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina® (NEB #E7330S) following the manufacturer's protocols.

treatment_protocol: Cells were collected at 80% confluency without any drug treatment.

value: cervical cancer

value: HeLa

value: human cervical cancer

value: wild type

value: Sodium borohydride treatment followed by tRNA isolation


title: WT, EP, ML, sample3 (RNA-seq)


title: Y541S, EP, SERD, LP, sample2 (ATAC-seq)


title: Y541S, EP, SERD, B, sample2 (ATAC-seq)


title: DUS1L 5-ClUrd 2

value: kidney

value: Flp-In T-Rex 293

value: human embryonic kidney cells

value: Flp-In modified to express 3xFLAG-DUS1L

value: 1 µg/mL tetracycline, 12 h; 1 µg/mL tetracycline, 12 h, 100 µM 5-ClUrd 12 h


title: D542G, EP, ML, sample2 (RNA-seq)

value: E2/P4 + vehicle

value: ML


title: Bulk ATAC-seq, line C4.1, HepaCAM+, d150

description: 60 million PE reads

value: human cortical organoid

value: HepaCAM+ cells


title: HeLa WT no treatment control_rep 2

value: tRNA isolation


title: Bulk ATAC-seq, line C4.1, cd49+, d150

description: 60 million PE reads

value: cd49f+ cells

value: female


title: WT, EP, ML, sample2 (RNA-seq)

value: WT

value: mammary gland


title: Y541S, EP, SERD, ML, sample2 (ATAC-seq)

value: E2/P4 + giredestrant

value: Mammary gland


title: Y541S, EP, SERD, B, sample3 (ATAC-seq)

value: Basal


title: WT, EP, B, sample2 (RNA-seq)


title: HeLa WT no treatment control_rep 1

value: cervical cancer

value: HeLa

value: human cervical cancer

value: wild type


title: HeLa WT NaBH4_rep 2

value: Sodium borohydride treatment followed by tRNA isolation


title: Bulk ATAC-seq, line C3.1, cd49+, d150

description: 60 million PE reads

value: male


title: WT, EP, B, sample1 (RNA-seq)

value: E2/P4 + vehicle


title: Y541S, EP, SERD, N, sample1 (ATAC-seq)

value: Novel


title: DUS1L ctrl 2

value: kidney

value: Flp-In T-Rex 293

value: human embryonic kidney cells

value: Flp-In modified to express 3xFLAG-DUS1L

value: 1 µg/mL tetracycline, 12 h; 1 µg/mL tetracycline


title: Y541S, EP, SERD, ML, sample3 (ATAC-seq)

value: ML


title: D542G, EP, B, sample1 (RNA-seq)

value: mammary gland


title: Bulk ATAC-seq, line C4.1, cd49+, d100

description: 60 million PE reads

value: human cortical organoid

value: cd49f+ cells

value: female


title: HEK393T WT NaBH4_rep 3

value: human embryonic kidney


title: Bulk ATAC-seq, line C3.1, cd49+, d100

description: 60 million PE reads


title: Bulk ATAC-seq, line C3.1, HepaCAM+, d200

description: 60 million PE reads

value: HepaCAM+ cells


title: WT, EP, ML, sample1 (RNA-seq)

value: WT


title: Y541S, EP, SERD, LP, sample1 (ATAC-seq)

value: E2/P4 + giredestrant

value: Mammary gland

value: LP


title: Y541S, EP, SERD, B, sample1 (ATAC-seq)

value: Basal


title: non-T1D_PBMC_pool10_VDJ

city: Boston

first: MD ZOHORUL

last: ISLAM

state: MA

address: 1 Joslin Pl Rm 4503, Kostic Lab

department: Section on Pathophysiology and Molecular Pharmacology

institute: Joslin Diabetes Center

description: S4, 10X configuration, lane

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v 6.0.2
Assembly: mm10-2020-A and GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Single T cell cells were siolated from blood and islets using CD3 magnetic beads. CD3+ T cells were isolated using the Miltenyi MACS CD3 microbead kit (Miltenyi catalog#130-094-973) following the manufacturer and 10x genomics recommended guidelines (10x Protocol CG000123 Rev B).
Single-cell 5’ gene expression (GEX) and V(D)J sequencing libraries of T cells were generated using the Chromium Next GEM Single Cell 5' Dual Index Reagent Kits v2 (10x Genomics, Pleasanton, CA, USA) following the manufacturer guidelines (10X protocol CG000331 Rev A).

value: Blood

value: Primary cells

value: T cell

value: NOD-ShiLtJ

tag: disease state

value: non-diabetic


title: HEK393T DUS3L KO no treatment control_rep 3

value: kidney

value: DUS3L KO

value: tRNA isolation


title: HEK393T WT no treatemnt control_rep 3

value: wild type


title: Bulk ATAC-seq, line C4.1, cd49+, d80

description: 60 million PE reads

value: human cortical organoid

value: cd49f+ cells

value: female


title: non-T1D_PBMC_pool9_VDJ

description: S4, 10X configuration, lane


title: Y541S, EP, SERD, ML, sample1 (ATAC-seq)

value: ML


title: Bulk ATAC-seq, line C3.1, cd49+, d80

description: 60 million PE reads

value: male


title: HEK293T DUS3L KO NaBH4_rep 2

value: human embryonic kidney

value: Sodium borohydride treatment followed by tRNA isolation


title: non-T1D_PBMC_pool7_VDJ

description: S4, 10X configuration, lane


title: HEK293T WT NaBH4_rep 2


title: HEK393T DUS3L KO NaBH4_rep 3


title: T1D_PBMC_pool6_VDJ

description: S4, 10X configuration, lane

value: Diabetic


title: 4B

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Count table per cell were generated using umi-tools following the manual with small modifications (details in File_S1.pdf). The low quality reads and adaptor sequences were removed using TrimmomaticSE. Then, reads were mapped to the mouse genome (GRCm38) using STAR (v. 2.7.1a). Reads were then assigned to the genes using featureCounts (v. 1.6.0) using the annotation genecode.vM8.gtf. The BAM files were sorted and indexed using samtools and the final table with information about counts of UMI per gene per cell were generated using umi_tools count.
The raw count tables from all samples were first loaded into a Single Cell Experiment object. Genes that were not detected across all samples, were removed. R package DropletUtils was used to identify empty drops in the dataset, and only “cells” with more than 200, less than 5000 UMIs and FDR ≤ 0.05 were processed in the next step. The Scater package was used to calculate the Quality control matrix, and features which were not detected in at least two cells were removed from the dataset. The data was then changed into a Seurat object and normalized. UMAP clustering with PCA reduction were used to identify cell clusters. Two clusters, which were identified as cell debris were removed from analysis and the new subset of cells were reclustered again. In total 654 cells were identified. The markers of cell clusters were identified using the function “FindConservedMarkers” and clusters of similar cell type were merged into one.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include matrix of non-normalized counts of reads "per cell", normalized count of reads and table with the name of the cells with assigned cell type.

source_name: cell suspension after dissociation of 4T1 tumour

extract_protocol:
A pool of 6 pieces of the tumour from different mice were used for each condition. Pieces of tumour were transferred into gentleMACS C tubes (Miltenyi Biotec) containing dissociation solution composed of: 5 ml of RPMI media, Protease from Bacillus licheniformis (5 mg/ml), CaCl2 (10 mM) and according to the given condition, Actinomycin D (2nM). Tubes were mixed for 1 hour using the gentleMACS dissociator either at 4°C or gentleMACS OctoDissociater with heaters set to 37°C. Immediately after dissociation, all tubes were kept on ice while all solutions were pre-chilled in the ice. Cell suspension was filtered through a 30 µm strainer. Cells were spun down (5 min, 800 g). The medium was discarded and the cells were dissociated in 15 mL of ice cold ACK solution (0.15 M NH4Cl; 10 mM KHCO3; 0.1 mM EDTA; pH 7.3) to remove erythrocytes. The cells suspension were immediately spun (5 min, 800 g). The debris were removed using debris removal solution (Miltenyi Biotec) according to the manufacturer's protocol. Next, the Dead Cells Removal Kit (Miltenyi Biotec) was used to remove dead cells. The collected effluent was spun (5 min, 800 g), supernatant removed and the cells were resuspended to final concentration of 2500 cell/μl in PBS-/-.
ScRNA-Seq libraries were prepared using the SureCell WTA 3' Library Prep Kit for the ddSEQ System (Illumina/Bio-Rad) according to the manufacturer´s protocol.

tag: temperature

tag: inhibitor

value: yes

tag: replicate

value: B


title: 3B

value: no


title: 2B


title: HEK293T DUS3L KO no treatment control_rep 2

tag: tissue

tag: cell line


title: T1D_PBMC_pool5_VDJ

description: S4, 10X configuration, lane

value: Blood

value: Primary cells

tag: cell type

value: T cell

value: NOD-ShiLtJ


title: 1B


title: HEK293T WT no treatemnt control_rep 2

value: kidney

value: tRNA isolation


title: Pa01c-shMAP3K8#2 rep1

city: ST LOUIS

first: KIAN

middle: HUAT

last: LIM

state: MO

address: 660 S. Euclid Avenue  Campus Box 8069, St. Louis

department: internal Medicine

institute: WashU

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: Pancreatic cancer

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic cancer

value: Pa01c cells espressing shMAP3K8#2 replicate 1


title: Pa01c-scram rep3

value: Pa01c cells expressing empty vector replicate 3


title: Pa01c-shMAP3K8#2 rep3

value: Pa01c cells espressing shMAP3K8#2 replicate 3


title: T1D_PBMC_pool4_VDJ

description: S4, 10X configuration, lane


title: 4A

value: A


title: Pa01c-scram rep2

value: Pa01c cells expressing empty vector replicate 2


title: HEK293T DUS3L KO  NaBH4_rep 1

value: human embryonic kidney

value: DUS3L KO

value: Sodium borohydride treatment followed by tRNA isolation


title: HEK293T WT NaBH4_rep 1

value: wild type


title: 3A

value: no


title: T1D_PBMC_pool3_VDJ

description: S4, 10X configuration, lane

value: Blood

value: Diabetic


title: non-T1D_PBMC_pool8_VDJ

description: S4, 10X configuration, lane

value: Primary cells

value: T cell

value: non-diabetic


title: Pa01c-shMAP3K8#2 rep2

value: Pa01c cells espressing shMAP3K8#2 replicate 2


title: Pa01c-scram rep1

value: Pancreatic cancer

value: Pa01c cells expressing empty vector replicate 1


title: T1D_PBMC_pool1_VDJ

description: S4, 10X configuration, lane

value: NOD-ShiLtJ


title: 1A


title: T1D_Islets_pool6_VDJ

description: S4, 10X configuration, lane

source_name: Islets

value: Islets


title: 2A

value: yes

value: A


title: T1D_PBMC_pool2_VDJ

description: S4, 10X configuration, lane


title: T1D_Islets_pool5_VDJ

description: S4, 10X configuration, lane


title: HEK293T DUS3L KO 2-8 tRNA library_replicate 1

data_processing:
Forward and reverse reads were paired.
Adaptor trimming and low quality reads removal was performed by fastp.
Filtered reads were aligned to a human mature tRNA reference containing the 3 spike-in E. coli tRNA sequences by RNA STAR.
featureCounts was performed to measure gene expression from the BAM files.
DESeq2 analysis was performed to evaluate the differential expression of tRNAs on the idsodecoder and anticodon levels.
Assembly: hg38 tRNA
Supplementary files format and content: tRNA_DESeq2_102723.xlsx
Supplementary files format and content: Spreadsheet containing abundance data of tRNAs corresponding to samples

growth_protocol: Human HEK293T WT and DUS1L/2L/3L-KO cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2 in 10-cm plates.

value: kidney

value: human embryonic kidney

value: tRNA isolation


title: HEK293T DUS3L KO 2-8 tRNA library_replicate 2

value: DUS3L KO


title: T1D_Islets_pool4_VDJ

description: S4, 10X configuration, lane


title: HEK293T DUS3L KO 2-8 tRNA library_replicate 3


title: HEK293T DUS3L KO 1-5 tRNA library_replicate 3


title: HEK293T DUS3L KO no treatment control_rep 1


title: T1D_Islets_pool2_VDJ

description: S4, 10X configuration, lane


title: HEK293T DUS3L KO 1-5 tRNA library_replicate 2


title: HEK293T WT no treatemnt control_rep 1

value: wild type


title: T1D_Islets_pool1_VDJ

description: S4, 10X configuration, lane


title: non-T1D_PBMC_pool10_GEX

description: S4, 10X configuration, lane

value: Blood


title: HEK293T WT 2 tRNA library_replicate 3


title: T1D_Islets_pool3_VDJ

description: S4, 10X configuration, lane

value: Diabetic


title: HEK293T DUS3L KO 1-5 tRNA library_replicate 1


title: non-T1D_PBMC_pool9_GEX

description: S4, 10X configuration, lane

value: Primary cells


title: HEK293T WT 2 tRNA library_replicate 2


title: H3K27ac_HiChIP.Old.Rep2.Batch3

data_processing:
Alignment: data were aligned using bowtie2 through the HiC-Pro pipeline (default parameters, mm10 assembly)
Filtering: unpaired mates and multi-mappers were filtered out through the HiC-Pro pipeline (default parameters)
Mate classification: aligned mate-pairs were classified into unique, valid, and cis- interactions using the HiC-Pro pipeline (default parameters)
Loop identification: contact maps were constructed at default resolution and genomic binning, and maps were ICE adjusted through HiC-Pro (default parameters).
Enhancer clique identification: in-house R scripts were used to identify connected graphs of cis-looped anchor points and to assign genes to these cliques by loops at their promoters.
Assembly: GRCm38/mm10
Supplementary files format and content: BED files show the mm10 coordinates of each looped anchor point, or "node," identified in either young or old animals.
Supplementary files format and content: Tab-separated values files (*clique.mm10.tsv) show enhancer cliques, with (i) the clique ID, (ii) the # anchors, (iii) the gene targets, separated by semicolons, and (iv) the anchor points/nodes, separated by semicolons, in columns 1-4 respectively. If a clique targets no genes, the gene column has "nonpromoter."
Library strategy: Hi-ChIP

source_name: liver

growth_protocol: Male, 3-month-old C57BL/6 mice purchased from Charles River Laboratories (Wilmington, MA) and 23-month-old male mice from the US National Institute on Aging stock located in Charles River Laboratories were used in this experiment. Mice were maintained at Sanford Burnham Prebys vivarium for 2 months prior to experiment to allow mice to acclimate. Mice were maintained under a specific pathogen-free environment and kept under standard conditions with a 12-h light/dark cycle and fed ad libitum on a regular diet. All animal experiments were carried out under procedural guidelines of Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Mice were anesthetized, and the livers were perfused with perfusion media (HBSS without calcium and magnesium, 500 μM EGTA) through the portal vein and then digested with digestion media with collagenase I. Digested tissue was suspended with DMEM media, and the suspension was passed through a 100 μm nylon mesh filter (BD Falcon). Suspended tissue was centrifuged at 50 g for 3 min to pellet hepatocytes. Red blood cells were removed. Cells were washed with PBS, and then used for downstream experiments.
Libraries were sequenced in paired-end mode on a NextSeq 550 instrument.

treatment_protocol: Mice were procured at different ages; see growth protocol.

value: liver

value: hepatocytes

tag: age (months)

tag: antibody

value: Abcam ab4729

tag: Sex

value: male


title: H3K27ac_HiChIP.Old.Rep2.Batch2


title: non-T1D_PBMC_pool8_GEX

description: S4, 10X configuration, lane

value: T cell

value: non-diabetic


title: HEK293T WT 2 tRNA library_replicate 1

tag: treatment


title: non-T1D_PBMC_pool7_GEX

description: S4, 10X configuration, lane

value: NOD-ShiLtJ


title: H3K27ac_HiChIP.Old.Rep2.Batch1


title: HEK293T DUS2L KO 2-1 tRNA library_replicate 3

value: DUS2L KO


title: HEK293T DUS2L KO 2-1 tRNA library_replicate 2


title: T1D_PBMC_pool6_GEX

description: S4, 10X configuration, lane


title: T1D_PBMC_pool5_GEX

description: S4, 10X configuration, lane


title: H3K27ac_HiChIP.Old.Rep1.Batch2


title: T1D_PBMC_pool4_GEX

description: S4, 10X configuration, lane


title: HEK293T DUS2L KO 1-8 tRNA library_replicate 3


title: H3K27ac_HiChIP.Old.Rep1.Batch1


title: T1D_PBMC_pool3_GEX

description: S4, 10X configuration, lane


title: Leaf-Water-rep2-21deg_comp3_cy3

type: RNA

city: Angers

first: Alexandre

last: Degrave

address: André Lenôtre

country: France

institute: Agrocampus Ouest

hyb_protocol: The hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 3 μm resolution with an Innoscan-710 scanner and data files were extracted from the scanned images using Mapix v8.2.5 associated software (Innopsys, Carbonne, France).

data_processing: We used the dye switch approach for statistical analysis as described in Depuydt et al. (2009). Analyses were performed using the R language (R Development Core Team, 2009); data were normalized with the lowess method, and differential expression analyses were performed using the lmFit function and the Bayes moderated t test using the package LIMMA (Smyth, Michaud, and Scott 2005).

organism: Malus domestica

source_name: Apple seedling leaf tissue, sampled 3 days after water treatment, 21°C

label_protocol: Complemantary DNA (cDNA) were synthesized starting with 200 ng of total RNA and further hybridized with the Low Input Quick Amp Labeling Kit, two-color (Agilent, Foster City, CA, USA).

growth_protocol: Plants were grown under greenhouse conditions (natural photoperiod supplemented with artificial light if needed during a 16 h photophase, 23–25°C day, 17°C night).

extract_protocol: Each sample corresponds to a pool of 10 leaf discs (diam 9mm) punched out from the parenchyma of the youngest expanded leaf from 5 replicate plants per condition. Samples were snap-frozen in liquid nitrogen and further ground to a fine powder in liquid nitrogen using a tissue lyser (Retsch, Haan, Germany) and total RNA were extracted using the Nucleospin® RNA Plant Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s procedure, and by adding 2% PVP-40 in the extraction buffer. The quality of total RNAs was verified in 1.2% agarose gel before amplification steps. Samples purity and concentration were assayed with the Agilent 2100 bioanalyzer system and the RNA 6000 Nano LabChip kit (Agilent Technologies, Waldbroon, Germany).

treatment_protocol: To assess ASM action, plants were sprayed to runoff (with a pressurized hand sprayer) with the commercial product Bion 50WG (Syngenta, Basel, Switzerland; 50% of ASM) prepared in reverse osmosis water at a final concentration of 0.4 g/L. The same water was used as control.

value: Water

tag: comparison

value: Comparison 3


title: Leaf-ASM-rep1-21deg_comp3_cy3

source_name: Apple seedling leaf tissue, sampled 3 days after ASM treatment, 21°C

value: ASM


title: Leaf-ASM-rep2-35deg_comp4_cy3

source_name: Apple seedling leaf tissue, sampled 3 days after ASM treatment, 35°C

value: Comparison 4


title: Leaf-Water-rep1-21deg_comp3_cy5


title: T1D_PBMC_pool2_GEX

description: S4, 10X configuration, lane


title: H3K27ac_HiChIP.Young.Rep2.Batch3


title: Leaf-ASM-rep1-35deg_comp4_cy3


title: HEK293T DUS2L KO 1-8 tRNA library_replicate 2

value: kidney

value: human embryonic kidney

value: tRNA isolation


title: Leaf-Water-rep2-35deg_comp1_cy5

source_name: Apple seedling leaf tissue, sampled 3 days after water treatment, 35°C

value: Comparison 1


title: Leaf-Water-rep2-35deg_comp4_cy5


title: H3K27ac_HiChIP.Old.Rep1.Batch3


title: Leaf-ASM-rep2-21deg_comp2_cy3

value: Comparison 2


title: Leaf-Water-rep1-35deg_comp4_cy5


title: HEK293T DUS2L KO 2-1 tRNA library_replicate 1


title: H3K27ac_HiChIP.Young.Rep2.Batch2

value: liver


title: Leaf-ASM-rep1-35deg_comp2_cy3


title: Leaf-ASM-rep1-21deg_comp2_cy5


title: Leaf-ASM-rep2-21deg_comp3_cy5


title: HEK293T DUS2L KO 1-8 tRNA library_replicate 1


title: HEK293T DUS1L KO 2-4 tRNA library_replicate 2

value: DUS1L KO


title: H3K27ac_HiChIP.Young.Rep2.Batch1

value: hepatocytes

value: Abcam ab4729


title: Leaf-ASM-rep2-35deg_comp2_cy5


title: Leaf-Water-rep1-35deg_comp1_cy3


title: HEK293T DUS1L KO 2-4 tRNA library_replicate 3


title: H3K27ac_HiChIP.Young.Rep1.Batch3

value: male


title: T1D_Islets_pool5_GEX

description: S4, 10X configuration, lane

value: Islets

value: Primary cells

value: T cell

value: Diabetic


title: H3K27ac_HiChIP.Young.Rep1.Batch2


title: HEK293T DUS1L KO 1-9 tRNA library_replicate 3


title: T1D_PBMC_pool1_GEX

description: S4, 10X configuration, lane

value: Blood

value: NOD-ShiLtJ


title: H3K27ac_HiChIP.Young.Rep1.Batch1


title: Liver-36

first: Alan

middle: C.

last: Mullen

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Assembly: GRCh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Frozen samples were dissociated on a GentleMACS in 1mL of TST buffer (https://www.nature.com/articles/s41591-020-0844-1). Nuclei were counted and resuspended in PBS+BSA+RNAse inhibitor before loading on a 10x 3' v3.1 channel.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, after nuclei loading and gel bead-in-emulsion (GEM) formation, the poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Samples were placed in cryo-tubes after removal of liquid by gently wiping it samples on the side of the container. Tubes were then covered in dry ice and transferred to −80 °C for long-term storage.

tag: age

value: M

value: Normal

value: Liver


title: T1D_Islets_pool3_GEX

description: S4, 10X configuration, lane


title: HEK293T DUS1L KO 2-4 tRNA library_replicate 1

value: kidney

value: human embryonic kidney

value: tRNA isolation


title: Liver-35

value: F


title: Leaf-Water-rep1-21deg_comp1_cy5

value: Water

value: Comparison 1


title: Leaf-Water-rep2-21deg_comp1_cy3


title: HEK293T DUS1L KO 1-9 tRNA library_replicate 2

value: DUS1L KO


title: RNA.ventral striatum.ACSS2 KO.female.NQ6

description:
NQ6VS_S30
Counts.Females.txt

data_processing:
Alignment: sequencing data were aligned to mouse genome assembly GRCm38/mm10 using STAR v2.5.2a with command-line parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesCommand zcat --outFilterMismatchNoverReadLmax 0.04. The STAR index was constructed GENCODE M25 annotation (ENSEMBL 100 assembly).
Filtering: aligned data were filtered for poor mapping tags using samtools v1.1 subcommand view -bS -q 255.
Pooling: filtered data from two flowcells (*FC1.*, *FC2.*, i.e., technical repeat samples from two flowcells) were combined using samtools merge and aligned tags were sorted by chromosome position and indexed using samtools sort and index, respectively.
Quantitation: HTseq v0.6.1 was used to quantify tag counts over exons with command-line parameters -f bam -r pos -s reverse -t exon -i gene_id --additional-attr=gene_name.
Analysis: differentially expressed genes (DEGs) between ACSS2 KO and WT samples were detected separately in each tissue and each sex using DESeq2 in R v4.0.2 with the FDR controlled at 0.1. Sexes were analyzed separately and so the uploaded gene counts tables are also separated by sex.
Assembly: GRCm38 / mm10
Supplementary files format and content: Counts.Males.txt and Counts.Females.txt contain the results of HTSeq run on all male or female samples, respectively.

source_name: ventral striatum

growth_protocol: We used CRISPR/Cas9 technology to generate constitutive ACSS2 KO mice as previously described (Alexander et al, PNAS 2022, PMID: 35921439). Pairs of single-guide RNAs (sgRNA) targeting intronic regions of the Acss2 locus upstream of exon 3 and downstream of exon 7 were designed with the CRISPOR online tool (crispor.org) using the mm10 genome assembly as template. The resulting guides (5'[exon 3]) were selected to maximize specificity while retaining high on-target efficiency. sgRNAs were synthesized by in vitro transcrip- tion (T7 High Yield RNA Synthesis Kit; NEB, E2040S). Cas9 mRNA (100 ng/μL; Trilink, L-6125) and both sgRNAs (100 ng/μL each) were diluted in injection buffer (10 mM Tris, pH 7.5; 0.1 mM EDTA). This mix was injected into the cyto- plasm of single-cell C57Bl6/J mouse embryos. Resulting founder mice were screened for the desired deletion using primer pairs amplified across each cut site. Sanger sequencing confirmed sites of nonhomologous end joining. To reduce off-target effects, founder mice were backcrossed to C57Bl6/J mice (Jackson Laboratories) for three generations.

extract_protocol:
Briefly, total RNA was extracted using Trizol-chloroform. Total RNA quality was assessed on the Bioanalyzer platform using the RNA 6000 Nano assay (Agilent). mRNA was isolated from 300 ng total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L).
Libraries were prepared using the NEBNext® UltraTM II RNA Library Prep Kit for Illumina® (E7770).

treatment_protocol: Single-housed adult mice of both sexes were allowed to voluntarily consume ethanol in the drinking-in-the-dark (DID) paradigm, an extensively used rodent model of binge-like drinking. During the habituation period, mice were acclimated to having two bottles (2BC) in the housing cage. Following the 1-week habituation period, ethanol intake was evaluated in the DID-2BC paradigm. For this, mice had access to 15% (v/v) ethanol and water for 2 h on days 1-3 and 4 h on day 4. The position of the bottles was alternated daily to avoid side preference. On the second week of DID, mice had access to 15% ethanol in a similar schedule, but water was not available during the drinking session (DID-1B). All drinking sessions started 1.0-1.5 h into the dark phase of the light cycle. Bottles were weighed to the nearest hundredth at the beginning and end of each DID session to determine fluid consumption. Mice were weighed at the beginning of each DID session to determine ethanol dose (g/kg). Ethanol consumption was calculated using r15_ethanol=0.97897 g/mL and r100_ethanol=0.789 g/mL. Ethanol preference was calculated as the ratio of ethanol to total fluid intake (mL ethanol solution/mL total fluid).

value: ventral striatum

value: female

value: ACSS2 KO

value: DiD 2BC + 1B

tag: mouse id


title: HEK293T DUS1L KO 1-9 tRNA library_replicate 1


title: T1D_Islets_pool2_GEX

description: S4, 10X configuration, lane

value: Islets

value: Primary cells

value: T cell

value: Diabetic


title: RNA.ventral hippocampus.ACSS2 KO.female.NQ6

description:
NQ6vHPC_S6
Counts.Females.txt

source_name: ventral hippocampus

value: ventral hippocampus


title: HEK293T WT tRNA library_replicate 3

value: wild type


title: Liver-31

value: Normal

value: Liver


title: T1D_Islets_pool1_GEX

description: S4, 10X configuration, lane

value: NOD-ShiLtJ


title: scRNA-seq

city: Guangzhou

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description: gene expression

data_processing:
For scRNA-seq and scTCR-seq, the BD Genomics Rhapsody Targeted Analysis pipeline was used to demultiplex cellular barcodes, map reads to the reference genome. For bulk RNA-seq, STAR-2.5.2b software was used to map reads to the reference genome.
Assembly: mm10
Supplementary files format and content: Matrix table with raw UMI counts for every gene and every cell
Supplementary files format and content: tab-delimited text files include FPKM values for bulk RNA-seq Samples

source_name: murine liver tissue

extract_protocol:
For bulk RNA sequencing, total RNA was extracted utilizing RNA iso Plus (TaKaRa, 9109) from liver tissues or 5×10^5 CD8+ T cells that were isolated using a FACS Aria II cell sorter
For single cell RNA-seq and BCR-seq, CD45+ cells from dnTGFβRII, Aire-/-, dnTGFβRII Aire+/- and dnTGFβRII Aire -/- mice (each sample mixed with hepatic cells from 2-3 mice) were sorted using the FACS Aria II cell sorter and dispensed into individual microwell plates following the manufacturer’s instruction of BD Rhapsody system,The transcriptome  was split to construct the TCR library and the targeted mRNA library; For bulk RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols or BGI protocols.

value: 2-4 weeks

value: TG, Aire-/-, TG Aire+/- and TG Aire-/-

value: CD45+ cells from 4 groups


title: RNA.prefrontal cortex.ACSS2 KO.female.NQ6

description:
NQ6PFC_S30
Counts.Females.txt

source_name: prefrontal cortex

value: prefrontal cortex


title: scTCR-seq

description: vdj-t


title: HEK293T WT tRNA library_replicate 2

value: kidney

value: human embryonic kidney

value: tRNA isolation


title: Liver-30

value: F


title: HEK293T WT tRNA library_replicate 1


title: RNA.dorsal striatum.ACSS2 KO.female.NQ6

description:
NQ6DS_S18
Counts.Females.txt

source_name: dorsal striatum

value: dorsal striatum

value: female

value: ACSS2 KO

value: DiD 2BC + 1B


title: T1D_Islets_pool4_GEX

description: S4, 10X configuration, lane

value: Islets

value: Primary cells

value: T cell

value: Diabetic


title: RNA.dorsal hippocampus.ACSS2 KO.female.NQ6

description:
NQ6dHPC_S6
Counts.Females.txt

source_name: dorsal hippocampus

value: dorsal hippocampus


title: Liver-28

value: Normal

value: Liver


title: mice sample tag

description: sample tag

data_processing:
Library strategy: TCR-Seq
For scRNA-seq and scTCR-seq, the BD Genomics Rhapsody Targeted Analysis pipeline was used to demultiplex cellular barcodes, map reads to the reference genome. For bulk RNA-seq, STAR-2.5.2b software was used to map reads to the reference genome.
Assembly: mm10
Supplementary files format and content: Matrix table with raw UMI counts for every gene and every cell
Supplementary files format and content: tab-delimited text files include FPKM values for bulk RNA-seq Samples

value: 2-4 weeks

value: TG, Aire-/-, TG Aire+/- and TG Aire-/-

value: CD45+ cells from 4 groups


title: Liver-29


title: RNA.amygdala.ACSS2 KO.female.NQ6

description:
NQ6Amygdala_S42
Counts.Females.txt

source_name: amygdala

value: amygdala


title: siRCC2-3

city: Beijing

first: Bao

last: Zhang

address: No.15, Yuquan Road

institute: Aerospace Center Hospital

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: GRCh38
Supplementary files format and content: Matrix table with FPKM and TPM values for each gene and each sample.

source_name: Cell line

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: Cell line

value: human prostatic cancer cell

value: RCC2 knockdown


title: TA+/- liver tissue

description:
gene expression
liver_tissue_rpkm.txt

value: TG Aire+/-

value: liver total cells


title: T1D_Islets_pool6_GEX

description: S4, 10X configuration, lane

value: NOD-ShiLtJ


title: RNA.cortex.ACSS2 KO.female.NQ6

description:
NQ6ctx_S18
Counts.Females.txt

source_name: cortex

value: cortex

value: female

value: ACSS2 KO

value: DiD 2BC + 1B


title: A-/- liver tissue

description:
gene expression
liver_tissue_rpkm.txt

value: Aire-/-


title: siRCC2-2


title: Liver-27

value: M

value: Normal


title: RNA.ventral hippocampus.ACSS2 KO.female.NQ5

description:
NQ5vHPC_S5
Counts.Females.txt

value: ventral hippocampus


title: A+/+ liver tissue

description:
gene expression
liver_tissue_rpkm.txt

value: 2-4 weeks

value: Aire+/+


title: Pcif1-KO+siPcf11 HEK293T, T4P

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

data_processing:
Basecalls performed using FASTQ Generation v1.0.0. for Nextseq output.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 --nextseq-trim -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using bowtie2 2.2.5 -N 1 --no-mixed --no-discordant.
Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates using custom Python scripts.
bigWig files were generated using bamCoverage --effectiveGenomeSize 2913022398 --normalizeUsing CPM -e.ChIP-seq heatmaps and metagene profiles were generated using Metagene2 with group_coverages normalization mode "log2_ratio", with only genes not within 2kb of other genes, were included for analysis.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37°C, and in DMEM supplemented with 10% FBS. Cells within passage 3–25 were used for experiments. HEK293T cells were regularly subjected to MycoAlert Plus Mycoplasma kit (Lonza LT07) to verify that they were mycoplasma-free.

extract_protocol:
Cells were seeded in 150mm dishes and grown till 70-80% confluency. Media was aspirated and cells were washed with PBS and fixed with 10ml 1% formaldehyde (ThermoFisher 28906) in PBS at room temperature for 5min, with agitation every 2min. The fixing reaction was then quenched by adding 562ul of 2.5M glycine (Thermo J16407.A1) and incubated at room temperature for 5min, with agitation every 2min. The quenched solution was removed and fixed cells were washed twice with 10ml cold PBS. Cells were scraped in 10ml cold PBS+1%BSA and transferred to 50ml tubes pre-blocked with PBS+1%BSA. 5ml cold PBS+1%BSA was used to harvest and residual cells from plates. Cells were pelleted at 300rcf 4degC for 5min and resuspended in 1ml cold PBS+1%BSA. 2e7 cells were counted and transferred to a new cold LoBind tube before being washed twice by resuspending in 1ml cold PBS and centrifuging at 300rcf 4degC for 5min. Cells were resuspended in 0.9ml IP lysis buffer (50mM Tris pH 8, 100mM NaCl, 1.0% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA 1x Complete protease inhibitor) and lysed on ice for 15min. Lysate was split into 3x300ul aliquots in pre-chilled LoBind tubes and sonicated at high setting for 15min (30s ON 30s OFF) using the Bioruptor Plus (Diagenode B01020001). SOnicated lysate was recombind and clarified via centrifuging at 13krpm 4degC for 10min. Meanwhile, 100ul Dynabead-Protein A (ThermoFisher 10001D) was washed twice in 1ml IP lysis buffer. Beads were resuspended in 200ul IP lysis buffer and split into 2 portions. 1 portion (“pre-clear beads”) was incubated with the clarified lysate at 4degC for 1hr to pre-clear the lysate. To the other portion, 10ug of anti-PCF11 antibody (Abcam ab134391) was added and mixed by tumbling at room temperature for 1hr (“IP beads”). IP beads were washed twice with 500ul IP lysis buffer. Both pre-clear beads and IP beads were magnetized and the pre-cleared lysate supernatant from the pre-clear beads was transferred to the decanted IP beads to be tumbled at 4degC overnight. 20ul of this mixture was set aside as “INPUT” and mixed with 80ul H2O and 100ul 2x elution buffer(). The remainder IP beads was washed once with 1ml low-salt buffer (50mM Tris pH 8, 100mM NaCl, 1% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA), twice with 1ml mid-salt buffer (50mM Tris pH 8, 250mM NaCl, 1% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA), twice with 1ml high-salt buffer (50mM Tris pH 8, 500mM NaCl, 1% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA) and once again with 1ml low-salt buffer with a tube-change. Decanted beads were then eluted with 100ul 1x elution buffer (), shaking at 1krpm 30degC for 15min, before deads were magnetized and the elution supernatant was collected. A second elution was performed and the elutions were combined for a total of 200ul. 8ul 5M NaCl and 4ul 10mg/ml Rnase A (ThermoFisher EN0531) was added to both INPUT and IP elutions before shaking at 1krpm 65degC overnight. 4ul 20mg/ml proteinase K was added and the reactions shaken at 1krpm 60degC for 1hr before allowing them to cool to room temperature. DNA was purified with MinElute PCR cleanup kit (Qiagen 28004) and quantified with Qubit.
Illumina sequencing libraries were constructed using KAPA hyper-prep kit (Roche 07962347001), including a dual size selection step according to the manufacturer’s protocol. Libraries were quantified using KAPA library quantification (Roche KK4824), pooled and sequenced on Illumina Nextseq PE75.

value: Human embryonic kidney

tag: chip antibody

value: Active motif 61361


title: siCtrl-2

value: Cell line

value: human prostatic cancer cell

tag: genotype

value: RCC2 wild type


title: siRCC2-1

value: RCC2 knockdown


title: RNA.prefrontal cortex.ACSS2 KO.female.NQ5

description:
NQ5PFC_S29
Counts.Females.txt

value: prefrontal cortex

tag: strain


title: Liver-26

value: F

tag: disease state

value: Liver


title: RNA.ventral striatum.ACSS2 KO.female.NQ5

description:
NQ5VS_S29
Counts.Females.txt

value: ventral striatum

value: female

value: ACSS2 KO


title: siCtrl-1


title: WT+siPcf11 HEK293T, T4P

value: WT


title: siCtrl-3


title: Tumor, scRNAseq

first: Li

last: Zhou

address: Room 701, Block B, Building 3, Yard 8,Haiying Road, Fengtai District

institute: ERT

data_processing:
The Cell Ranger software pipline(version 7.0.1)provided by 10xGenomics was used to demutiplex cellula barcode,map reads to the genome and transcriptome  using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Supplementary files format and content: hg38
Supplementary files format and content: Matrix table with raw gene count for every gene and every cell

source_name: Lung

extract_protocol:
A single-cell suspension of kidney cells was prepared using Multi Tissue Dissociation Kit 2 (#130-110-203, Miltenyi Biotec) according to the manufacturer’s instructions. Kidneys were harvested from anesthetized mice, cut into quarters, and transferred into the gentleMACS C Tube containing the enzyme mix. After digesting the tissues using gentleMACS Dissociator, they were passed through a 70-μm and 40-μm cell strainer, sequentially, and washed with ice-cold PBS to obtain the single-cell suspension. Red blood cells were lysed using 10×RBC lysis buffer (#00-4300, eBioscience).Single cells isolated from the IRI kidneys at indicated time points were stained with Zombie NIR viability dye (BioLegend); CD45- and CD 45+ live cells were sorted using BD FACS AriaTM cell sorter. FACS-sorted cells were resuspended to a ﬁnal cell concentration of 700–1200 cells/μL with > 80% viability as determined by LUNA-FL™ Automated Fluorescence Cell Counter (Logos Biosystems).
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Lung


title: TA-/- liver tissue

description:
gene expression
liver_tissue_rpkm.txt

value: TG Aire-/-

value: liver total cells


title: TA-/- PD-1-CD8+ T

description:
gene expression
liver_PD-1CD8T_rpkm.txt

value: 2-4 weeks

value: PD-1-CD8+ T cells


title: Pcif1-KO+siPcf11 HEK293T, Input

value: Human embryonic kidney


title: TA-/- PD-1+CD8+ T

description:
gene expression
liver_PD-1CD8T_rpkm.txt

value: PD-1+CD8+ T cells


title: RNA.dorsal striatum.ACSS2 KO.female.NQ5

description:
NQ5DS_S17
Counts.Females.txt

value: dorsal striatum

value: DiD 2BC + 1B


title: WT+siScram HEK293T, T4P

value: Active motif 61361


title: TA+/- PD-1-CD8+ T

description:
gene expression
liver_PD-1CD8T_rpkm.txt

value: TG Aire+/-


title: Pcif1-KO+siScram HEK293T, T4P


title: RNA.cortex.ACSS2 KO.female.NQ5

description:
NQ5ctx_S17
Counts.Females.txt

value: cortex


title: RNA.ventral striatum.ACSS2 KO.female.NQ4

description:
NQ4VS_S28
Counts.Females.txt


title: A-/- PD-1-CD8+ T

description:
gene expression
liver_PD-1CD8T_rpkm.txt

value: Aire-/-


title: Pcif1-KO+siScram HEK293T, Input


title: Liver-25

value: F

value: Normal

value: Liver


title: Blood, scRNAseq

source_name: Blood

value: Blood


title: Tree Shrew Primary Neurons, meth-2, 24h, rep4

city: Kunming City

first: shu wei

last: zhang

state: Yunnan Province

address: Chenggong District

department: School of Forensic Medicine

institute: Kunming Medical University

data_processing:
After constructing the library, a preliminary quantification was performed using Qubit 2.0, and the library was diluted to 2 ng/µL. The insert size of the library was then assessed with the Agilent 2100 Bioanalyzer. Once the insert size met the expected criteria, the effective concentration of the library was accurately quantified using qPCR (quantitative PCR). Ensuring that the effective concentration of the library is above 2 nM guarantees the quality of the library.
After the library passes quality control, different libraries should be pooled according to their effective concentrations and the desired sequencing data output. The pooled libraries are then subjected to sequencing using the Illumina HiSeq or MiSeq platforms.
The raw image data files generated from high-throughput sequencing platforms, such as the Illumina HiSeq 2500, are converted into sequencing reads through a process known as Base Calling. These sequencing reads are referred to as Raw Data or Raw Reads. The results are stored in the FASTQ (fq) file format, which includes both the sequence information of the reads and their corresponding quality scores.
The raw reads obtained from sequencing contain adapters and low-quality reads. To ensure the quality of downstream data analysis, it is essential to process the raw reads to obtain clean reads.
Assembly: ASM18137v1
Supplementary files format and content: Readcount_TPM txt files inlude readcount values for each sample

organism: Tupaia belangeri

source_name: brain

growth_protocol: Place the culture plates in a CO2 incubator set to 5% CO2, 37°C, and 95% humidity, and cultivate the cells using a complete neuronal medium. The composition of the complete medium includes Neurobasal-A, 15% fetal bovine serum, 2% penicillin/streptomycin, 2% B-27 supplement, and 2% L-glutamine.

extract_protocol:
Agarose gel electrophoresis was used to assess the degree of RNA degradation and potential contamination. The purity of the RNA (OD260/280 ratio) was measured using Nanodrop, while the RNA concentration was precisely quantified with Qubit. The integrity of the RNA was accurately evaluated using the Agilent 2100 Bioanalyzer.
Using the Smal RNA Sample Prep Kit, a library was constructed by leveraging the unique structures of the 3' and 5' ends of small RNA (with a complete phosphate group at the 5' end and a hydroxyl group at the 3' end). Starting with B RNA as the initial sample, adapters were directly added to both ends of the small RNA, followed by reverse transcription to synthesize DNA. The resulting DNA was then amplified by PCR, and the target DNA fragments were separated by PAGE gel electrophoresis. The desired cDNA library was obtained by excising and recovering the gel fragments.

treatment_protocol: When the primary neurons of the tree shrew reach 80% confluency, aspirate the culture medium from the flasks and rinse the cells 1-2 times with PBS. For the control group, add 1ml of complete neuronal medium per well. For the METH group, add 995μl of complete neuronal medium and 5μl of 100mmol METH per well. After 24 hours, collect the cells for further use.

value: brain

value: primary cell

value: primary neuron

value: meth


title: RNA.ventral hippocampus.ACSS2 KO.female.NQ4

description:
NQ4vHPC_S4
Counts.Females.txt

value: ventral hippocampus

value: female

value: ACSS2 KO


title: Tree Shrew Primary Neurons, meth-4, 24h, rep4


title: RNA.amygdala.ACSS2 KO.female.NQ5

description:
NQ5Amygdala_S41
Counts.Females.txt

value: amygdala


title: MOLM13 Monocytes, SGF29 knockout, rep 1

city: La Jolla

first: Karina

middle: Ofelia

last: Barbosa Guerra

address: 10901 North Torrey Pines Rd, Deshpande Lab RM6210B

department: Tumor Initiation & Maintenance Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
MOLM13_SGF29_KO_Rep1
MOLM13_SGF29_TPM.txt.gz

data_processing:
Raw reads were preprocessed by trimming Illumina Truseq adapters, polyA, and polyT sequences using cutadapt v2.3 with parameters “cutadapt -j 4 -m 20 --interleaved -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Fastq1 Fastq2 | cutadapt --interleaved -j 4 -m 20 -a "A{100}" -A "A{100}" - | cutadapt -j 4 -m 20 -a "T{100}" -A "T{100}" -”.
Trimmed reads were subsequently aligned to human genome version hg38 using STAR aligner  v2.7.0d_0221 with parameters according to ENCODE long RNA-seq pipeline.
Gene expression levels were quantified using RSEM v1.3.1. Ensembl v84 gene annotations were used for the alignment and quantification steps. RNA-seq sequence, alignment, and quantification qualities were assessed using FastQC v0.11.5 and MultiQC v1.8. Lowly expressed genes were filtered out by retaining genes with estimated counts (from RSEM) ≥ number of samples times 5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen) and 900ng of total RNA per sample were used for library preparation.
RNA library prep was performed with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) follownig the manufacturer's instructions.

treatment_protocol: Cells were transduced with CRISPR sgRNA lentivirus targeting SGF29 or non-targeting control. Puromycin (1ug/ul) was added 2 days after to select for transduced cells and removed from the culture upon selection completion. Cells were harvested by centrifugation 7 days after puromycin removal and washed with 1X PBS and protease inhibitors.

value: Monocytes

value: SGF29 knockout

value: CRISPR sgRNA lentiviral transduction


title: WT+siPcf11 HEK293T, Input

value: Human embryonic kidney

value: WT


title: Pcif1-KO HEK293T, S2P

value: Abcam ab5095


title: RNA.prefrontal cortex.ACSS2 KO.female.NQ4

description:
NQ4PFC_S28
Counts.Females.txt

value: prefrontal cortex

value: DiD 2BC + 1B


title: RNA.dorsal striatum.ACSS2 KO.female.NQ4

description:
NQ4DS_S16
Counts.Females.txt

value: dorsal striatum


title: Normal, scRNAseq

value: Lung


title: Tree Shrew Primary Neurons, meth-3, 24h, rep4

value: brain

value: primary cell


title: MOLM13 Monocytes, SGF29 knockout, rep 2

description:
MOLM13_SGF29_KO_Rep2
MOLM13_SGF29_TPM.txt.gz


title: MOLM13 Monocytes, SGF29 knockout, rep 3

description:
MOLM13_SGF29_KO_Rep3
MOLM13_SGF29_TPM.txt.gz


title: WT+siScram HEK293T, Input


title: Tree Shrew Primary Neurons, PBS-3, 24h, rep4

value: primary neuron

value: PBS


title: RNA.dorsal hippocampus.ACSS2 KO.female.NQ5

description:
NQ5dHPC_S5
Counts.Females.txt

value: dorsal hippocampus

value: female


title: Tree Shrew Primary Neurons, meth-1, 24h, rep4

value: meth


title: RNA.cortex.ACSS2 KO.female.NQ4

description:
NQ4ctx_S16
Counts.Females.txt

value: cortex

value: ACSS2 KO


title: Tree Shrew Primary Neurons, PBS-2, 24h, rep4


title: MOLM13 Monocytes, non-targeting control, rep 3

description:
MOLM13_NTC_Rep3
MOLM13_SGF29_TPM.txt.gz

value: Monocytes

value: Non-targeting control

value: CRISPR sgRNA lentiviral transduction


title: Muscle biopsy, 32-0030L

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description:
bilat_gene_counts.csv
bilat_dds.rda

data_processing:
trimming the Illumina universal adapters by Trimmomatic
alignment against genome built GRCh38(p13) by Rsubread
gene features were collected from GENCODE, version 35 and the gene counts were profiled by using the GenomicAlignment::summarizedOverlap() function with “IntersectionStrict” mode
Assembly: GRCh38.p13
Supplementary files format and content: bilat_dds.rda: DESeqDataSet instance containing gene counts, TPM gene annotation, and gene ranges
Supplementary files format and content: bilat_gene_counts.csv

source_name: tibialis anterior muscle biopsy

growth_protocol: needle muscle biopsy of both tibialis anterior muscles from 34 FSHD subjects

extract_protocol:
RNA was extracted from frozen crushed muscle biopsy material using TRIzol and single end 100 nt Illumina sequencing
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).

value: tibialis anterior muscle biopsy

tag: condition

value: FSHD

tag: location

value: L


title: RNA.amygdala.ACSS2 KO.female.NQ4

description:
NQ4Amygdala_S40
Counts.Females.txt

value: amygdala

value: DiD 2BC + 1B


title: Brain, glioblastoma, rep4

city: Debrecen

first: Zsuzsanna

last: Birkó

address: Egyetem tér 1.

department: Humangenetics

country: Hungary

institute: University of Debrecen

data_processing:
Fastq data were generated by BaseSpace (Illumina)
Raw sequencing data (fastq) was aligned to human reference genome version GRCh38 using Novoalign algorithm and BAM files were generated
Downstream analysis was performed using StrandNGS software (Deseq) where the FPKM values were generated
Assembly: GRCh38 human reference genome
Supplementary files format and content: FPKM values of each samples
Supplementary files format and content: tab-delimited matrix text file that include the FPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA including small RNAs was isolated by the miRNeasy Mini Kit (Qiagen) according to the protocol provided by the manufacturer.
Library preparation was performed by the NEBNext Multiplex Small RNA Perp Set for Illumina (1-48) 96 rxn kit (New England BioLabs) according to the protocol provided by the manufacturer.

value: Brain

value: glioblastoma


title: RNA.ventral striatum.WT.male.NQ3

description:
NQ3VS_S27
Counts.Males.txt

value: ventral striatum

value: male

value: WT


title: WT HEK293T, S2P

value: Human embryonic kidney

value: Abcam ab5095


title: Brain, glioblastoma, rep6


title: Muscle biopsy, 32-0030R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: R


title: RNA.dorsal hippocampus.ACSS2 KO.female.NQ4

description:
NQ4dHPC_S4
Counts.Females.txt

value: dorsal hippocampus

value: female

value: ACSS2 KO


title: MOLM13 Monocytes, non-targeting control, rep 2

description:
MOLM13_NTC_Rep2
MOLM13_SGF29_TPM.txt.gz

value: Monocytes

value: Non-targeting control

value: CRISPR sgRNA lentiviral transduction


title: MOLM13 Monocytes, non-targeting control, rep 1

description:
MOLM13_NTC_Rep1
MOLM13_SGF29_TPM.txt.gz