title: Primary human samples, RNA; patient 2 EOC14

city: San Francisco

first: Catherine

last: Smith

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description: Library name: VenGilt34_CITEseq5GEX

data_processing:
FASTQ files from single-cell DAb-seq samples were processed via an open-source pipeline as described previously by Abate et al. FASTQ files from CITEseq samples were processed with CellRanger v 4.0.0.
Pooled DAbseq runs were demultiplexed into individual patient samples using the SNACS algorithm by Kennedy et al. CITEseq runs were demultiplexed using HTOdemux.
Assembly: hg38
Supplementary files format and content: Pipline (Abate et al) output files: sample.hdf5. Variant calls, ADT data, and HTO data are compressed into a single hdf5 file.
Library strategy: CITE-seq

source_name: mononuclear cells

extract_protocol:
For DAB-seq, Cryopreserved cells were thawed and normalized to 10,000 cells/μL in 180 μL PBS (Corning). Samples with more than one million viable cells recovered were additionally incubated with Human TruStain FcX (Biolegend) and salmon sperm DNA (Invitrogen) for 15 minutes at 4C. A pool of 9 oligo-conjugated antibodies (CD3, CD4, CD11b, CD13, CD19, CD33, CD34, CD117, CD45)  was added, and cells were incubated for an additional 30 minutes. In addition, individual samples were also incubated with unique hashtags (BioLegend) to provide sample-level identifiers, and groups of 3 individual patients were pooled together in multiplexed runs. Samples were resuspended in Cell Buffer (MissionBio), diluted to 4-7e6 cells/mL, and loaded onto a microfluidics cartridge, where individual cells were encapsulated, lysed, and barcoded using the Tapestri instrument. DNA from barcoded cells was amplified via PCR using a custom targeted panel that included 288 amplicons across 66 genes associated with acute leukemia generally and known clinical mutations in these samples specifically. For CITEseq, 1-2 million cells were blocked with Human TruStain FcX (BioLegend) and stained with a panel of TotalSeq-C antibodies from the Human Universal Cocktail (1 μg/each, BioLegend) in Cell Buffer (BioLegend) for 20 minutes at 4C. After staining, cells were washed in Staining Buffer, resuspended at 1,000 cells/μL, and immediately processed with the 10x Genomics controller and the Single Cell 5’ reagent kit with feature barcoding technology for cell-surface proteins.
For DABseq, DNA PCR products were isolated, purified with AmpureXP beads (Beckman Coulter), used as a PCR template for library generation, and then repurified with AmpureXP beads. Protein PCR products (when applicable) were isolated from the supernatant from AmpureXP bead purification via incubation with a 5’ Biotin Oligo (ITD). Protein PCR products were then purified using Streptavidin C1 beads (Thermo Fisher Scientific), used as a PCR template for library generation, and then repurified using AmpureXP beads. Both DNA and protein libraries were quantified and assessed for quality via a Qubit fluorometer (Life Technologies) and Bioanalyzer (Agilent Technologies) prior to pooling for sequencing on an Illumina Novaseq. For CITEseeq, 5’ gene expression and feature barcoding libraries were constructed using a 10x Genomics library preparation kit. Library quality was assessed using Agilent High Sensitivity DNA kit and Bioanalyzer 2100, and libraries were quantified using dsDNA High-Sensitivity (HS) assay kit (Invitrogen) on Qubit fluorometer before being sequenced on an Illumina Novaseq.

value: mononuclear cells

value: mixed mononuclear cells

value: Patient 2 EOC14


title: Primary human samples, cell surface proteins for immunophenotype; patient 1 EOC13

status: Public on Apr 01 2026

type: SRA

state: California

country: USA

description: Library name: VenGilt32_CITEseqFB

library_source: other

molecule: protein

organism: Homo sapiens

tag: tissue

tag: cell type

tag: treatment

value: Patient 1 EOC13


title: Western Diet 2

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description:
Library name: M8
auranofin effect on atherosclerosis progression

library_source: transcriptomic

data_processing:
Trimmed reads were mapped using STAR v2.6.1d
Alignments mapping to genes were counted using FeatureCounts from the subread package v1.6.3
Assembly: GRCm39 GENCODE M32
Supplementary files format and content: gene counts per sample

molecule: total RNA

organism: Mus musculus

source_name: whole aorta

growth_protocol: 6-weeks old ApoE-/- mice were fed western diet (WD) -/+ auranofin or atorvastatin for 16 weeks to follow effect of the drug on atherosclerosis progression.

extract_protocol:
Isolated mouse atherosclerotic aortas were stored in RNA later (Cat.# AM7021, Invitrogen) for 24 hours, then tissue was stored at -80 C until processed for RNA extraction using the gentleMACSTM Octo Dissociator (Miltenyi Biotec) homogenization protocol for total RNA isolation, the QIAzol Lysis Reagent (Qiagen, Cat.# 79306) and RNA clean-up using the RNAeasy Mini kit (Qiagen).
Sample quality and quantity was determined with Agilent 2100 bioanalyzer, using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Cat.# 5067-1511). For RNA-sequencing, 250ng of RNA were used as input for poly-A library construction.
Transcriptome Library - non-stranded mRNA sequencing on DNBseq platform

treatment_protocol:
Mice were randomized into 4 groups and fed Western diet (WD, % by kcal: protein, 17.3%, carbohydrate, 43%, fat, 40%; catalog no. D12079B, Research Diet, Inc.), alone or in combination with either 10 mg/kg/day atorvastatin, (catalog no. D16102901, Research Diet, Inc.),
3 mg/kg/day auranofin, (catalog no. D16102902, Research Diet, Inc.) or auranofin plus atorvastatin (catalog no. D16102903, Research Diet, Inc.) for 16 weeks.

value: whole aorta

tag: genotype

value: ApoE-/-

value: Western Diet

tag: time

value: Week 16


title: Primary human samples, cell surface proteins for immunophenotype; patients 1 pre-treatment

description: Library name: VenGilt31_CITEseqFB

value: Patient 1 pre-treatment


title: Western Diet 1

description:
Library name: M1
auranofin effect on atherosclerosis progression


title: Western Diet 3

description:
Library name: M11
auranofin effect on atherosclerosis progression


title: Primary human samples, RNA; patient 1 EOC13

description: Library name: VenGilt32_CITEseq5GEX


title: Primary human samples, cell surface proteins for immunophenotype; patient 2 pre-treatment

description: Library name: VenGilt33_CITEseqFB

value: Patient 2 pre-treatment


title: Primary human samples, RNA; patient 2 pre-treatment

description: Library name: VenGilt33_CITEseq5GEX


title: Primary human samples, cell surface proteins for immunophenotype; patient 2 EOC14

description: Library name: VenGilt34_CITEseqFB


title: Primary human samples, RNA; Patient 13 EOC3, Patient 14 EOC2

description: Library name: VenGilt30_CITEseq5GEX

value: Mixed sample (Patient 13 pre-treatment, Patient 14 pre-treatment)


title: Primary human samples, RNA; patient 1 pre-treatment

description: Library name: VenGilt31_CITEseq5GEX


title: 4D NMP, rep 3

city: Los Angeles

first: Samantha

last: Butler

address: 610 Charles E Young Drive East

department: Neurobiology

institute: University of California, Los Angleles

description: Library name: Sample 6

data_processing:
Reads were obtained as raw FASTQ files, assessed for quality with FASTQC, and aligned to the human reference genome (GRCh38, GENCODE v29 annotation) using STAR. Gene-level counts were obtained with featureCounts (exon-level, paired-end read counting).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file generated using featureCounts containing gene-level read counts for each sample.

growth_protocol: H9 hESCs are thawed and mantained for two passages post-thaw in mTeSR+ media.

extract_protocol:
NMP cultures subjected to bulk-RNA sequencing were first washed with 1X DPBS to remove the media. Cells were then lysed by directly adding 600μL of RLT buffer in the culture wells, and the lysate is then collected and flash frozen with liquid nitrogen to be stored at -80ºC. The total RNA was then purified using Qiagen’s RNeasy kit, and eluted in 50μL of RNAse-free water. Using a microvolume spectrophotometer, RNA concentrations were determined and diluted to 1μg/μL.
RNA samples were further subjected to quality control assessment using Agilent Technologies 2100 Bioanalyzer and only samples with a RIN score >8.0 were used for library construction using Universal plus mRNA sequencing kit (NuGEN).

treatment_protocol: NMPs are induced by the addition of FGF (10ng/mL) for 1 day and FGF + CHIR-99021 (3µM) for 1 day/3 days/9 days to generate 2/4/10-day NMPs respectively. GDF11 was added on the 6th day for 4 days as a separate condition to generate 10-day NMPs + GDF11.

tag: cell line

value: 4D NMP


title: Mono 7 ANTI

type: RNA

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

country: France

institute: Université Claude Bernard Lyon 1

hyb_protocol: cDNA was then hybridized to GeneChip® HumanGene1.0ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: chips were washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.

data_processing: Data were normalized using RMA with Partek Genomics Suite.

label: biotin

source_name: Anti-inflammatory Macrophages (IL-10+dex treated)

label_protocol: not provided

growth_protocol: Primary cells were differentiated and cultured in FBS supplemented medium as in Saclier et al (PMID: 23169615).

extract_protocol: Total RNAs were extracted Trizol

treatment_protocol: Macrophages were treated or not with IL-4, LPS, IL-10+dexamethasone for 3 days as described in Saclier et al 2013 (PMID: 23169615)

value: Macrophages


title: S12 EtOH

city: Columbus

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

description: Library name: Sample12

data_processing:
Alignment and mapping using Rsubread and featureCounts
Assembly: GRCm39
Supplementary files format and content: Raw counts matrix (counts_matrix.csv)

source_name: subcutaneous WAT

extract_protocol:
RNA was isolated from WAT using a Takara NucleoSpin RNA kit according to the manufacturer’s instructions, and 300ng total RNA was sequenced
QIAseq Fast Select rRNA HMR; QIAseq Low Input RNA Library Kit (primers N6-T RT and ODT-RT)

value: subcutaneous WAT

value: EtOH

tag: batch


title: Primary human samples, cell surface proteins for immunophenotype and multiplexing; Patient 13 EOC3, Patient 14 EOC2

description: Library name: VenGilt30_CITEseqFB


title: Mono 7 NT

source_name: Untreated Macrophages


title: S11 EtOH

description: Library name: Sample11


title: Primary human samples, cell surface proteins for multiplexing; Patient 13 EOC3, Patient 14 EOC2

description:
Library name: VenGilt28_hashprotein
VenGilt28.hdf5

data_processing:
FASTQ files from single-cell DAb-seq samples were processed via an open-source pipeline as described previously by Abate et al. FASTQ files from CITEseq samples were processed with CellRanger v 4.0.0.
Pooled DAbseq runs were demultiplexed into individual patient samples using the SNACS algorithm by Kennedy et al. CITEseq runs were demultiplexed using HTOdemux.
Assembly: hg38
Supplementary files format and content: Pipline (Abate et al) output files: sample.hdf5. Variant calls, ADT data, and HTO data are compressed into a single hdf5 file.

value: Mixed sample (Patient 13 EOC3, Patient 14 EOC2)


title: Primary human samples, cell surface proteins for immunophenotype and multiplexing, Patient 13, 14 pre-treatment

description: Library name: VenGilt29_CITEseqFB


title: S10 EtOH

description: Library name: Sample10


title: Primary human samples, cell surface proteins for immunophenotype; Patient 13 EOC3, Patient 14 EOC2

description:
Library name: VenGilt28_Protein
VenGilt28.hdf5


title: S8 EtOH

description: Library name: Sample8


title: Primary human samples, DNA; Patient 13 pre-treatment, Patient 14 pre-treatment

description:
Library name: VenGilt27_DNA
VenGilt27.hdf5

library_source: genomic

molecule: genomic DNA


title: Primary human samples, RNA, Patient 13 pre-treatment and Patient 14 pre-treatment

description: Library name: VenGilt29_CITEseq5GEX


title: Primary human samples, cell surface proteins for multiplexing; Patient 13 pre-treatment, Patient 14 pre-treatment

description:
Library name: VenGilt27_hashprotein
VenGilt27.hdf5


title: Mono 7 PRO

source_name: Pro-inflammatory Macrophages (LPS treated)


title: Primary human samples, DNA; Patient 13 EOC3, Patient 14 EOC2

description:
Library name: VenGilt28_DNA
VenGilt28.hdf5


title: S9 EtOH

description: Library name: Sample9


title: Primary human samples, cell surface proteins for immunophenotype; Patient 13 pre-treatment, Patient 14 pre-treatment

description:
Library name: VenGilt27_Protein
VenGilt27.hdf5


title: Mono 6 PRO


title: S7 EtOH

description: Library name: Sample7


title: Mono 6 NT


title: Primary human samples, DNA; Patient 10 EOC1

description:
Library name: VenGilt26_DNA
VenGilt26.hdf5

value: atient 10 EOC1


title: Mono 7 ALTER

source_name: Macrophages alternatively activated (IL-4 treated)


title: Primary human samples, DNA; Patient 9 EOC1

description:
Library name: VenGilt24_DNA
VenGilt24.hdf5

value: mononuclear cells

value: Patient 9 EOC1


title: Primary human samples, DNA; Patient 10 pre-treatment

description:
Library name: VenGilt25_DNA
VenGilt25.hdf5

value: mixed mononuclear cells

value: Patient 10 pre-treatment


title: Primary human samples, DNA; Patient 8 EOC1

description:
Library name: VenGilt23_DNA
VenGilt23.hdf5

value: Patient 8 EOC1


title: S6 ctrl

description: Library name: Sample6

value: Vehicle


title: Mono 6 ALTER


title: Mono 2 PRO


title: Primary human samples, cell surface proteins for immunophenotype; Patient 6 pre-treatment

description:
Library name: VenGilt21_Protein
VenGilt21.hdf5

value: Patient 6 pre-treatment


title: Primary human samples, cell surface proteins for multiplexing; Patient 4 EOC6

description:
Library name: VenGilt18_hashprotein
VenGilt18.hdf5

value: Patient 4 EOC6


title: Mono 2 NT


title: Primary human samples, DNA; Patient 6 EOC1

description:
Library name: VenGilt22_DNA
VenGilt22.hdf5

value: Patient 6 EOC1


title: Primary human samples, DNA; Patient 5 EOC1

description:
Library name: VenGilt19_DNA
VenGilt19.hdf5

value: Patient 5 EOC1


title: S5 ctrl

description: Library name: Sample5


title: S2 ctrl

description: Library name: Sample2


title: Mono 6 ANTI


title: Primary human samples, DNA; Patient 6 pre-treatment

description:
Library name: VenGilt21_DNA
VenGilt21.hdf5


title: S4 ctrl

description: Library name: Sample4


title: Primary human samples, DNA; Patient 4 EOC4

description:
Library name: VenGilt17_DNA
VenGilt17.hdf5

value: Patient 4 EOC4


title: Primary human samples, DNA; Patient 4 EOC1

description:
Library name: VenGilt16_DNA
VenGilt16.hdf5

value: Patient 4 EOC1


title: Primary human samples, DNA; Patient 4 EOC6

description:
Library name: VenGilt18_DNA
VenGilt18.hdf5


title: Primary human samples, cell surface proteins for immunophenotype; Patient 4 EOC6

description:
Library name: VenGilt18_Protein
VenGilt18.hdf5


title: G_WT_vehicle_HNF4_4h

city: Hiroshima

first: Yoshihiro

last: Tsuchiya

state: Hiroshima

address: 4-13-1 Ushita Higashi Higashi-ku

department: Department of Nutrition and Health Promotion

country: Japan

institute: Hiroshima Jogakuin University

description:
Library name: G_lib
6-week-old male mouse liver; ChIP HNF4alpha; control WT Input (A); anti-HNF4alpha (Abcam)

data_processing:
Reads were aligned to the mouse reference genome (mm10) using Bowtie. Peaks were called using MACS2 v2.0.10.20120913 with matched input controls.
Align reads to mm10; retain uniquely mapped reads.
Handle PCR duplicates using standard duplicate marking/removal.
Call peaks with MACS2 using matched input controls.
If provided, genome browser signal tracks (coverage) may be included as bigWig (.bw) files for ChIP and input samples.
Assembly: mm10
Supplementary files format and content: Processed data files include MACS2 peak output tables (.xls) and peak coordinate files (.bed) for each ChIP condition versus matched input.
Supplementary files format and content: Peak coordinate BED files contain chrom, start, end, peak name/ID, and score. Optional bigWig files provide genome-wide signal tracks for visualization.

source_name: liver

growth_protocol: Mouse livers were harvested from 6-week-old male mice (WT or TG) maintained under standard SPF conditions with ad libitum access to food and water.

extract_protocol:
Liver tissue was crosslinked with 1% formaldehyde for 10 min at 37 C with gentle shaking and quenched with 0.125 M glycine. Chromatin was isolated and sonicated to ~200-500 bp.
Chromatin was immunoprecipitated with 2 ug control IgG (Santa Cruz Biotechnology), anti-RNA polymerase II (Active Motif), or anti-HNF4alpha (Abcam). Immunoprecipitated DNA was purified by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. ChIP-seq libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina) and sequenced on Illumina HiSeq 2000 (single-end).

treatment_protocol: Mice received a single intravenous injection of mouse TNFalpha (BioLegend) at 7.5 ug/kg (or vehicle control) and were euthanized 4 h after injection.

value: liver

value: WT

value: vehicle, intravenous; collected 4 h

tag: strain

value: mouse (strain not recorded)

tag: Sex

value: male

tag: age

value: 6 weeks

tag: antibody

value: anti-HNF4alpha (Abcam)

tag: time point

value: 4 h

tag: input control

value: A (WT input)


title: S3 ctrl

description: Library name: Sample3

value: subcutaneous WAT


title: Primary human samples, DNA; Patient 5 EOC4

description:
Library name: VenGilt20_DNA
VenGilt20.hdf5

value: mononuclear cells

value: mixed mononuclear cells

value: Patient 5 EOC4


title: H_WT_TNF_HNF4_4h

description:
Library name: H_lib
6-week-old male mouse liver; ChIP HNF4alpha; control WT+TNFalpha Input (B); anti-HNF4alpha (Abcam)

value: mouse TNFalpha (BioLegend) 7.5 ug/kg, intravenous; collected 4 h

value: B (WT+TNF input)


title: Primary human samples, cell surface proteins for multiplexing; Patient 4, 5, 12  pre-treatment

description:
Library name: VenGilt15_hashprotein
VenGilt15.hdf5

value: Mixed sample (Patient 4 pre-treatment, Patient 5 pre-treatment, Patient 12 pre-treatment)


title: Mono 2 ALTER

value: Macrophages


title: I_TG_vehicle_HNF4_4h

description:
Library name: I_lib
6-week-old male mouse liver; ChIP HNF4alpha; control TG Input (C); anti-HNF4alpha (Abcam)

value: liver

value: TG

value: C (TG input)


title: Mono 2 ANTI


title: F_TG_vehicle_Pol2_4h

description:
Library name: F_lib
6-week-old male mouse liver; ChIP RNA polymerase II; control TG Input (C); anti-RNA polymerase II (Active Motif)

value: vehicle, intravenous; collected 4 h

value: mouse (strain not recorded)

value: anti-RNA polymerase II (Active Motif)


title: S1 ctrl

description: Library name: Sample1

value: Vehicle


title: Primary human samples,cell surface proteins for immunophenotype; Patient 3 EOC4, Patient 3 EOC7

description:
Library name: VenGilt14_Protein
VenGilt14.hdf5

value: Mixed sample (Patient 3 EOC4, Patient 3 EOC7)


title: A_WT_vehicle_Input_4h

description:
Library name: A_lib
6-week-old male mouse liver; Input DNA

value: WT

value: male

value: 6 weeks

value: Input

value: 4 h

value: none (input)


title: Primary human samples, DNA; Patient 7 EOC1

description:
Library name: VenGilt11_DNA
VenGilt11.hdf5

value: mononuclear cells

value: mixed mononuclear cells

value: Patient 7 EOC1


title: Primary human samples, DNA; Patient 3 pre-treatment, Patient 8 pre-treatment, Patient 9 pre-treatment

description:
Library name: VenGilt13_DNA
VenGilt13.hdf5

value: Mixed sample (Patient 3 pre-treatment, Patient 8 pre-treatment, Patient 9 pre-treatment)


title: Primary human samples,cell surface proteins for multiplexing; Patient 3 EOC4, Patient 3 EOC7

description:
Library name: VenGilt14_hashprotein
VenGilt14.hdf5


title: Primary human samples, DNA; Patient 4 pre-treatment, Patient 5 pre-treatment, Patient 12 pre-treatment

description:
Library name: VenGilt15_DNA
VenGilt15.hdf5

value: Mixed sample (Patient 4 pre-treatment, Patient 5 pre-treatment, Patient 12 pre-treatment)


title: E_WT_TNF_Pol2_4h

description:
Library name: E_lib
6-week-old male mouse liver; ChIP RNA polymerase II; control WT+TNFalpha Input (B); anti-RNA polymerase II (Active Motif)

value: liver

value: mouse TNFalpha (BioLegend) 7.5 ug/kg, intravenous; collected 4 h

value: B (WT+TNF input)


title: B_WT_TNF_Input_4h

description:
Library name: B_lib
6-week-old male mouse liver; Input DNA

value: mouse (strain not recorded)


title: Primary human samples, cell surface proteins for multiplexing; Patient 3, 8, 9 pre-treatment

description:
Library name: VenGilt13_hashprotein
VenGilt13.hdf5


title: Lin- cells, PF9363 treatment, rep1

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description:
Library name: PF9363_1
Column name in raw counts 260115_RNA-raw-counts.txt: PF9363_1

data_processing:
Paired-end reads were trimmed using Fastp with adapter detection and poly-G trimming.
Trimmed reads were aligned to the mouse genome (GRCm38/mm10) using STAR.
For each experiment, a raw gene-level counts matrix was generated from STAR-aligned reads. DESeq2 was used for read count normalization and differential expression analysis.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text files contains raw counts for each sample.

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: For mouse bone marrow lineage-negative cells: IMDM medium with 15% FBS, 2mM glutamine, 1x penicillin/streptomycin in the presence of SCF, IL6, and IL3.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen, 74106). 500ng of total RNA (or 100ng of total RNA for MYST inhibitor experiment) was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Watchmaker mRNA Library Prep Kit (7K0105-024) following manufacturer's protocols. For MYST inhibitor profiling, 100 ng of total RNA was submitted to Novogene for library preparation and sequencing.

treatment_protocol: Lentivirus were generated by co-transfecting psPAX2 (Addgene: 12260), pMD2.G (Addgene: 12259), and pSMAL_Luciferase (control) or pSMAL_SETBP1D868N into LentiX cells (Takara) with Fugene 6 (Promega E2691), according to the manufacturer's instructions. Mouse lineage-negative (Lin-) bone marrow primary cells were lentivirally transduced with either a control (luciferase) or SETBP1D868N mutant. To assess transcriptional changes following MYST inhibitor treatment, RNA-seq analysis was also conducted in mouse bone marrow lineage-negative (Lin⁻) primary cells lentivirally transduced with the SETBP1D868N mutant, followed by treatment with DMSO or PF-9363 (2.5uM) for 4 days.

value: Bone marrow

value: lineage-negative bone marrow primary cells

value: wild-type

value: lentiviral transduction with SETBP1D868N mutant followed by PF-9363 treatment


title: Primary human samples, DNA; Patient 3 EOC4, Patient 3 EOC7

description:
Library name: VenGilt14_DNA
VenGilt14.hdf5

value: Mixed sample (Patient 3 EOC4, Patient 3 EOC7)


title: Primary human samples, cell surface proteins for immunophenotype; Patient 3, 8, 9 pre-treatment

description:
Library name: VenGilt13_Protein
VenGilt13.hdf5


title: Primary human samples, cell surface proteins for multiplexing; Patient 11 pre-treatment and patient 11 EOC1

description:
Library name: VenGilt10_hashprotein
VenGilt10.hdf5

value: Mixed sample (Patient 11 pre-treatment and patient 11 EOC1)


title: Lin- cells, PF9363 treatment, rep3

description:
Library name: PF9363_3
Column name in raw counts 260115_RNA-raw-counts.txt: PF9363_3


title: Lin- cells, PF9363 treatment, rep4

description:
Library name: PF9363_4
Column name in raw counts 260115_RNA-raw-counts.txt: PF9363_4


title: Lin- cells, DMSO control, rep3

description:
Library name: DMSO_3
Column name in raw counts 260115_RNA-raw-counts.txt: DMSO_3

value: lentiviral transduction with SETBP1D868N mutant followed by DMSO treatment


title: Lin- cells, DMSO control, rep4

description:
Library name: DMSO_4
Column name in raw counts 260115_RNA-raw-counts.txt: DMSO_4


title: Primary human samples, cell surface proteins for immunophenotype; Patient 4, 5, 12  pre-treatment

description:
Library name: VenGilt15_Protein
VenGilt15.hdf5


title: Lin- cells, PF9363 treatment, rep2

description:
Library name: PF9363_2
Column name in raw counts 260115_RNA-raw-counts.txt: PF9363_2


title: Primary human samples, DNA; Patient 7 EOC3

description:
Library name: VenGilt12_DNA
VenGilt12.hdf5

value: Patient 7 EOC3


title: Primary human samples, cell surface proteins for immunophenotype; Patient 11 pre-treatment and patient 11 EOC1

description:
Library name: VenGilt10_Protein
VenGilt10.hdf5

value: mononuclear cells


title: Primary human samples, DNA; Patient 11 pre-treatment and patient 11 EOC1

description:
Library name: VenGilt10_DNA
VenGilt10.hdf5

value: mixed mononuclear cells


title: Lin- cells, DMSO control, rep2

description:
Library name: DMSO_2
Column name in raw counts 260115_RNA-raw-counts.txt: DMSO_2


title: D_WT_vehicle_Pol2_4h

description:
Library name: D_lib
6-week-old male mouse liver; ChIP RNA polymerase II; control WT Input (A); anti-RNA polymerase II (Active Motif)

value: WT

value: vehicle, intravenous; collected 4 h

value: male

value: 6 weeks

value: anti-RNA polymerase II (Active Motif)

value: 4 h

value: A (WT input)


title: NeuID knockdown 6

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

description: Library name: Sample 12

data_processing:
bcl2fastq
sequencing reads were mapped with STAR to GrCM38/mm10 genome
sequencing reads were counted using FeaturesCount
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: primary hippocampal neurons

growth_protocol: primary hippocampal neurons were maintained in Neurobasal medium supplemented with 1% B27 and antibiotics in a humidified chamber at 37°C

extract_protocol:
RNA was isolated using the Zymo RNA clean & Concentrator-5 Kit.
RNA-seq libraries were prepared using  SMARTer® Stranded Total RNA-Seq Kit v2 -Pico Input kit (Takara).

treatment_protocol: Primary hippocampal neurons were treated with either control gapmers or NeuID targeting gapmers at DIV7 and RNA was isolated on DIV10

value: primary hippocampal neurons

value: NeuID targeting gapmers


title: C_TG_vehicle_Input_4h

description:
Library name: C_lib
6-week-old male mouse liver; Input DNA

value: liver

value: TG

value: mouse (strain not recorded)

value: Input

value: none (input)


title: Lin- cells, DMSO control, rep1

description:
Library name: DMSO_1
Column name in raw counts 260115_RNA-raw-counts.txt: DMSO_1

value: Bone marrow

value: lineage-negative bone marrow primary cells

value: wild-type

value: lentiviral transduction with SETBP1D868N mutant followed by DMSO treatment


title: NeuID knockdown 5

description: Library name: Sample 11

value: WT


title: Primary human samples, DNA; Patient 1 EOC9

description:
Library name: VenGilt9_DNA
VenGilt9.hdf5

value: mononuclear cells

value: mixed mononuclear cells

value: Patient 1 EOC9


title: Primary human samples, DNA; Patient 1 EOC1

description:
Library name: VenGilt7_DNA
VenGilt7.hdf5

value: Patient 1 EOC1


title: Primary human samples, cell surface proteins for immunophenotype; patient 1 pre-treatment

description:
Library name: VenGilt6_Protein
VenGilt6.hdf5

value: Patient 1 pre-treatment


title: NeuID knockdown 4

description: Library name: Sample 10

value: primary hippocampal neurons


title: NeuID knockdown 3

description: Library name: Sample 9

value: NeuID targeting gapmers


title: Primary human samples, DNA; patient 1 pre-treatment

description:
Library name: VenGilt6_DNA
VenGilt6.hdf5


title: Primary human samples, cell surface proteins for multiplexing; Patient 2 EOC 14, Patient 1 EOC 14, Patient 12 EOC1

description:
Library name: VenGilt5_hashprotein
VenGilt5.hdf5

value: mixed sample (Patient 2 EOC 14, Patient 1 EOC 14, Patient 12 EOC1)


title: Primary human samples, DNA; Patient 2 EOC 14, Patient 1 EOC 14, Patient 12 EOC1

description:
Library name: VenGilt5_DNA
VenGilt5.hdf5


title: Primary islets treated with prolactin replicate 3

city: Baltimore

first: Nelmari

last: Ruiz Otero

email: nelmari634@gmail.com, nruizot1@jhu.edu

state: MD

address: 5501 Hopkins Bayview Circle Allergy & Immunology Center Bayview Campus Lab 2A10

institute: Johns Hopkins University

description: Library name: P3

data_processing:
We performed the genome alignment using histat2 v2.2 and the output sam file was converted, sorted and indexed using samtools v1.21.
A matrix of the raw counts was created using featureCounts (subread-2.1.0).
To determine differentially expressed genes we used the DESeq2 package for R v. 1.46.0.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files contain the raw counts of each individual sample.
Supplementary files format and content: CSV file contains the relative PRL vs control values of differentially expressed genes

source_name: Pancreatic islets

extract_protocol:
RNA was isolated using the TRIzol (TFS, #15596026).
A total RNA of 500 ng was used for library construction with the NEBNext Ultra II RNA Library Prep Kit for Illumina (BioLabs, #E7775), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (BioLabs, #E7490) and the NEBNext Multiplex Oligos for Illumina (Dual Index Primer Set I, Biolabs # E7600). All preparations were performed according to the manufacturer’s instructions. The quality of the constructed library was assessed, and sequencing was performed in the Illumina Novaseq X Plus Lane system by the Genetic Resources Core Facility (GRCF, Johns Hopkins University, School of Medicine, Baltimore, MD).

treatment_protocol: Isolated islets were cultured in RPMI-1640 (Thermo Fisher Scientific, # 22400089) supplemented with 10% FBS and 2% penicillin-streptomycin overnight at 37C in a humid chamber to allow for recovery. Islets were treated with DMSO (control) or 500ng/mL of recombinant mouse prolactin (Bio-Techne, # 1445-PL-050) for 24 hours.

value: Pancreatic islets

value: Mixed

value: Wild Type (C57B6)

value: Prolactin (500ng/mL-24hours)


title: Primary human samples, cell surface proteins for immunophenotype; Patient 2 EOC 14, Patient 1 EOC 14, Patient 12 EOC1

description:
Library name: VenGilt5_Protein
VenGilt5.hdf5


title: Primary islets treated with prolactin replicate 2

description: Library name: P2


title: Primary islets treated with prolactin replicate 1

description: Library name: P1


title: NeuID knockdown 1

description: Library name: Sample 7


title: Primary islets control replicate 3

description: Library name: C3

value: DMSO


title: Primary human samples, DNA; Patient 1 EOC4

description:
Library name: VenGilt8_DNA
VenGilt8.hdf5

value: Patient 1 EOC4


title: Primary human samples, DNA; Patient 2 EOC 7

description:
Library name: VenGilt4_DNA
VenGilt4.hdf5

value: Patient 2 EOC 7


title: NeuID knockdown 2

description: Library name: Sample 8


title: Primary human samples, cell surface proteins for multiplexing; patient 1 pre-treatment

description:
Library name: VenGilt6_hashprotein
VenGilt6.hdf5


title: Control 6

description: Library name: Sample 6

value: control gapmers


title: Primary human samples, DNA; Patient 2 EOC 4

description:
Library name: VenGilt3_DNA
VenGilt3.hdf5

value: Patient 2 EOC 4


title: Primary human samples, DNA; Patient 2 end of cycle (EOC) 1

description:
Library name: VenGilt2_DNA
VenGilt2.hdf5

value: mononuclear cells

value: Patient 2 EOC1


title: Prrimary human samples, cell surface proteins for multiplexing; Patients 2 pre-treatment and 7 pre-treatment

description:
Library name: VenGilt1_hashprotein
VenGilt1.hdf5

value: mixed mononuclear cells

value: mixed sample (patient 2 pre-treatment, patient 7 pre-treatment)


title: Control 5

description: Library name: Sample 5

value: WT


title: Primary human samples, DNA; Patients 2 pre-treatment and 7 pre-treatment

description:
Library name: VenGilt1_DNA
VenGilt1.hdf5


title: CNT_rep1

city: Baton Rouge

first: Manas

middle: Ranjan

last: Gartia

state: LA

address: 3261 Patrick F Taylor Hall

department: Mechanical and Industrial Engineering

institute: Louisiana State University

description:
Library name: CNT_2
column name in 01.rawdata : CNT_2

data_processing:
FASTQ formatted RNA sequencing files were decompressed and sequencing reads were quality-checked via the RseQC (version 5.0.3 ), adapter trimmed using Cutadapt , mapped to the mouse reference genome (GRCm39) via STAR (version 2.7.11b) , and converted to raw counts with featurecounts from the RSubreads (version 2.20.0) .
Raw counts were normalized via the TMM-normalization method in the edgeR package (v. 3.38.4) ,
Differential gene expression analysis was performed via the limma package using the trend function (version 3.56.1) ,
Assembly: Mouse reference genome GRCm39
Supplementary files format and content: tab limited text containing raw counts

source_name: Brain-cortex

extract_protocol:
Total RNA was extracted from flash frozen cortical tissue of FAD5x and C57BL/6 mice using TRIzol reagent (Invitrogen, USA) and the Qiagen RNeasy Mini Kit (Qiagen, catalog no. 217004)
NEED TO FILL BY WHOEVER CREATED THE LIBRARIES

value: Brain-cortex

value: Control


title: Primary human samples, cell surface proteins for immunophenotype; Patients 2 pre-treatment and 7 pre-tretment

description:
Library name: VenGilt1_Protein
VenGilt1.hdf5


title: HepG2,CTNNB1,OE,rep2,WGBS

city: hangzhou

first: HONGJIAN

last: QI

state: zhejiang

address: Dunyu road No.600

country: China

institute: westlake university

description: Library name: HepG2 CTNNB1 OE rep2 WGBS

data_processing:
Whole-genome bisulfite sequencing (WGBS) reads were quality- and adapter-trimmed using TrimGalore (v0.6.10) in paired-end mode with the parameters --length 20 --gzip --clip_R2 10.
Trimmed reads were aligned to the bisulfite-converted hg38 reference genome using Bismark (v0.24.1) in conjunction with Bowtie2 (v2.4.1), employing the options --un --ambiguous -q -L 20 -D 20 -R 3 --score_min L,0,-0.4.
PCR duplicates were removed using deduplicate_bismark, and methylation calling was performed with bismark_methylation_extractor.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Genomic DNA was extracted from approximately 100,000 cells.
Purified genomic DNA was fragmented to an average size of 300–500 bp using a Covaris S220 sonicator. Fragments were purified with 1.6× SPRI Select beads. Libraries were constructed following standard Illumina protocols, including end repair and adenylation, and EM-seq™ methylated adapters were ligated. Bisulfite conversion was performed according to the EZ DNA Methylation-Gold Kit protocol (Zymo Research, USA). The resulting single-stranded DNA fragments were PCR-amplified using the KAPA HiFi HotStart Uracil+ ReadyMix (Roche Diagnostics) and purified.

treatment_protocol: For ARID1A knockout samples, NUGC4 cells were transfected with CRISPR-Cas9 constructs targeting ARID1A and single-cell clones were isolated and validated. Wild-type parental cells served as controls. For β-catenin pathway activation, an EF1α-driven FLAG-CTNNB1(ΔEx3)-GFP expression cassette was constructed into a lentiviral vector using Gibson assembly (E2611, NEB). The sequence-validated CTNNB1(ΔEx3) plasmid was co-transfected with psPAX2 (Addgene #12260) and pMD2.G (Addgene #12259) into HEK293T cells for lentivirus packaging. Lentivirus was collected 36 hours post-transfection and used to infect HepG2 cells at MOI less than 0.3.

value: hepatocellular carcinoma cell

value: CTNNB1 overexpression


title: Primary islets control replicate 1

description: Library name: C1

value: Pancreatic islets

value: Mixed


title: Primary islets control replicate 2

description: Library name: C2

value: Wild Type (C57B6)


title: Control 2

description: Library name: Sample 2

value: primary hippocampal neurons


title: Control 3

description: Library name: Sample 3


title: NUGC4,ARID1AKO,rep1,WGBS

description: Library name: NUGC4 ARID1AKO rep1 WGBS

value: gastric cancer cell

value: ARID1A knockout


title: Control 4

description: Library name: Sample 4

value: control gapmers


title: HepG2,CTNNB1,OE,rep1,WGBS

description: Library name: HepG2 CTNNB1 OE rep1 WGBS


title: HepG2,CTNNB1,Vec2,WGBS

description: Library name: HepG2 CTNNB1 Vec2 WGBS

value: Empty vector


title: CNT_rep2

description:
Library name: CNT_3
column name in 01.rawdata : CNT_3


title: HepG2,CTNNB1,Vec1,WGBS

description: Library name: HepG2 CTNNB1 Vec1 WGBS


title: CNT_rep3

description:
Library name: CNT_4
column name in 01.rawdata : CNT_4


title: NUGC4,ARID1AKO,rep2,WGBS

description: Library name: NUGC4 ARID1AKO rep2 WGBS


title: Control 1

description: Library name: Sample 1


title: NUGC4,WT,rep2,WGBS

description: Library name: NUGC4 WT rep2 WGBS

value: wild type


title: Tumor Infiltrating Lymphocyte, Day13, rep6

city: Xiamen

first: Hongjiao

last: Wang

address: xiangannanlu

institute: xiamen university

data_processing:
HTSeq (v0.6.1)
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Supplementary files format and content: tab-delimited excel files include raw counts for each sample
Supplementary files format and content: tab-delimited excel files include FPKM values for each sample

source_name: B16 Tumor

extract_protocol:
1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads.

value: B16 Tumor

value: Dentridic cells

value: Dyrk1a knock out


title: AD_rep3

description:
Library name: AD_3
column name in 01.rawdata : AD_3


title: NUGC4,H3K27me3,KO,rep2

description: Library name: NUGC4 H3K27me3 KO 2

data_processing:
reads were processed using trim_galore (version 1.11.5) in paired-end mode for quality control and adapter trimming. Trimming enforced a minimum read length of 20 and stringent trimming (stringency 3).
Bowtie2 (version 2.7.9) was employed for alignment to the human genome assembly hg38 with parameters '-p 8 --no-mixed --no-discordant -X 2000', filtering reads longer than 2000 base pairs, and retaining only mapped reads.
PCR duplicates were initially marked and removed using sambamba markdup (version 0.7.1). Subsequently, Picard's MarkDuplicates (version 2.23.1) was employed with settings to retain all duplicate reads for downstream analysis.
Reads were converted from BAM files to normalized coverage files in BigWig format using bamCoverage with RPKM normalization and a bin size of 50 base pairs.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: NUGC4 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were trypsinized and permeabilized in ONMI buffer (10 mM Tris-HCl pH 7.5, 0.1% Tween20, 0.1% NP40, 0.01% digitonin, 3 mM MgCl2, 10 mM NaCl) for 5 min at 4°C. Approximately 100,000 permeabilized cells were resuspended in 50 µl buffer Med1 (2 mM EDTA, 2% BSA, 300 mM NaCl, 20 mM HEPES pH 7.5, 0.01% Digitonin, 0.5 mM spermidine, 0.01% NP40, 1x Protease Inhibitor Cocktail) containing 1 µl H3K27me3 antibody (Abcam, ab192985) and 1 µl pA-Tn5 transposase, and incubated with gentle rotation at 4°C overnight. Excess antibody and pA-Tn5 were removed by three washes with buffer Med2 (2% BSA, 300 mM NaCl, 20 mM HEPES pH 7.5, 0.01% Digitonin, 0.5 mM spermidine, 0.01% NP40, 1x Protease Inhibitor). Tagmentation was initiated by addition of 10 mM MgCl2 to Med2, followed by incubation at 37°C for 1 h. Fragmented DNA was purified using QIAquick PCR Purification Kit (Qiagen, #28106).
Purified tagmented DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541L). Libraries were purified, quality-checked, and size-selected. Paired-end 150 bp sequencing was performed on an Illumina NovaSeq X Plus platform.

treatment_protocol: For ARID1A knockout samples, NUGC4 cells were transfected with CRISPR-Cas9 constructs targeting ARID1A and single-cell clones were isolated and validated. Wild-type parental cells served as controls.

value: anti-H3K27me3; Abcam; ab192985


title: NUGC4,WT,rep1,WGBS

description: Library name: NUGC4 WT rep1 WGBS


title: AD_rep2

description:
Library name: AD_2_B
column name in 01.rawdata : AD_2_B

value: Brain-cortex


title: NUGC4,H3K27me3,KO,rep1

description: Library name: NUGC4 H3K27me3 KO 1


title: AD_rep1

description:
Library name: AD_2
column name in 01.rawdata : AD_2


title: HepG2,CTNNB1,OE,rep1

description: Library name: HepG2 CTNNB1 OE rep1

data_processing:
RNA-seq reads were aligned to the human genome assembly hg38 using STAR (v2.7.10a) with parameters --winAnchorMultimapNmax 200 and --outFilterMultimapNmax 100 to allow for robust mapping of repetitive sequences.
Quantification of reads mapped to both transposable elements (TEs) and genes was performed using TElocal (v1.1.1).
For TE quantification, only reads mapping to intergenic loci were retained, and expression values were aggregated at the TE subfamily level.
Assembly: hg38
Supplementary files format and content: counts txt

extract_protocol:
Total RNA was extracted using TRIzol reagent (15596018, Thermo Fisher Scientific) and dissolved in RNase-free water (10977023, Thermo Fisher Scientific).
mRNA was captured using Poly(A) mRNA Capture Module (RK20340, Abclonal). RNA-seq libraries were constructed using Fast RNA-seq Lib Prep Kit V2 (RK20306, Abclonal).


title: HepG2,CTNNB1,vec,rep1

description: Library name: HepG2 CTNNB1 vec rep1

value: empty vector control


title: NUGC4,ATAC,KO,rep1

description: Library name: NUGC4 ATAC KO 1

data_processing:
reads were processed using trim_galore (version 1.11.5) in paired-end mode for quality control and adapter trimming. Trimming enforced a minimum read length of 20 and stringent trimming (stringency 3).
Bowtie2 (version 2.7.9) was employed for alignment to the human genome assembly hg38 with parameters '-p 8 --no-mixed --no-discordant -X 2000', filtering reads longer than 2000 base pairs, and retaining only mapped reads.
PCR duplicates were initially marked and removed using sambamba markdup (version 0.7.1). Subsequently, Picard's MarkDuplicates (version 2.23.1) was employed with settings to retain all duplicate reads for downstream analysis.
Reads were converted from BAM files to normalized coverage files in BigWig format using bamCoverage with RPKM normalization and a bin size of 50 base pairs.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Approximately 100,000 cells were isolated and permeabilized. The permeabilized nuclei were resuspended in 50 µl tagmentation buffer (33 mM Tris-Ac, 66 mM K-Ac, 11 mM Mg-Ac, 16% DMF, pH 7.8) with 1 µl Tn5 transposase and incubated at 37°C for 30 min. Fragmented DNA was purified using QIAquick PCR Purification Kit (Qiagen, #28106).
Purified tagmented DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541L). Libraries were purified, quality-checked, and size-selected. Paired-end 150 bp sequencing was performed on an Illumina NovaSeq X Plus platform.


title: Tumor Infiltrating Lymphocyte, Day13, rep2

value: WT


title: Tumor Infiltrating Lymphocyte, Day13, rep5


title: NUGC4,H3K27me3,WT

description: Library name: NUGC4 H3K27me3 WT


title: NUGC4,ARID1A,CRISPRi,sgRNA1,rep2

description: Library name: NUGC4 ARID1A CRISPRi sgRNA1 rep2

value: ARID1A CRISPRi knockdown (sgRNA1)


title: Tumor Infiltrating Lymphocyte, Day13, rep3


title: Tumor Infiltrating Lymphocyte, Day13, rep4


title: NUGC4,ATAC,WT

description: Library name: NUGC4 ATAC WT


title: HepG2,CTNNB1,vec,rep2

description: Library name: HepG2 CTNNB1 vec rep2

value: hepatocellular carcinoma cell


title: Tumor Infiltrating Lymphocyte, Day13, rep1


title: NUGC4,ARID1A,CRISPRi,sgRNA1,rep1

description: Library name: NUGC4 ARID1A CRISPRi sgRNA1 rep1


title: NUGC4,ATAC,KO,rep2

description: Library name: NUGC4 ATAC KO 2


title: HepG2,CTNNB1,OE,rep2

description: Library name: HepG2 CTNNB1 OE rep2

value: CTNNB1 overexpression


title: 941

first: Jennifer

middle: C

last: Chan

address: 1470 Madison Ave 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 28
Illumina Stranded mRNA Prep

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples

source_name: Brain

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 and Illumina Stranded mRNA Prep

value: Brain

tag: region

value: dHF

tag: group

value: Control RE

tag: virus

tag: ruvs k_value


title: 945

description:
Library name: Sample 29
Illumina Stranded mRNA Prep

tag: tissue

value: ELS


title: 946

description:
Library name: Sample 30
Illumina Stranded mRNA Prep


title: 939

description:
Library name: Sample 27
Illumina Stranded mRNA Prep


title: NUGC4,ARID1A,CRISPRi,vector,rep2

description: Library name: NUGC4 ARID1A CRISPRi vector rep2

value: gastric cancer cell

value: CRISPRi vector control


title: 937

description:
Library name: Sample 26
Illumina Stranded mRNA Prep


title: NUGC4,ARID1A,CRISPRi,vector,rep1

description: Library name: NUGC4 ARID1A CRISPRi vector rep1


title: RNA-seq of Gr34 Aedes aegypti brain, Rep 3 Library 1

city: Riverside

first: Anupama

last: Dahanukar

state: CA

address: 900 University Aveenue

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

description:
Library name: Gr34_BR3_Lib
25152_STAR

data_processing:
Quality of reads was first checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). You can download reports for individual libraries at the link below: https://caltech.box.com/s/2511n73ec7rj5142v9d2i4f8561nccb4  The reads were then mapped to the AaegL5.0 version of Aedes genome (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_002204515.2/) using RNA-specific aligner STAR (https://github.com/alexdobin/STAR) and gene expression was quantified with featureCounts, which is a part of the Subread package (https://subread.sourceforge.net/featureCounts.html). Raw counts were converted to TPM values using a custom Perl script.
Differential gene expression analysis was performed for each tissue comparing Gr34 and WT using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Genes with adjusted p-value (padj) <0.05 were considered significantly differentially expressed.
Assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002204515.2/
Supplementary files format and content: "combined_count_tpm.annotations_ncbi.go.xlsx" includes normalized data (TPM), in addition to NCBI and AAEL IDs, gene names, descriptions, and GO terms where available. This processed file contains TPM counts for all 12 samples across both tissues and both genotypes. Please refer to description values to link column in processed file to sample type.
Supplementary files format and content: "deseq2_brain.annotations_ncbi.go.xlsx" is a dataset of differential analysis of genes in the brain across WT and AaegGr34 mutants.
Supplementary files format and content: "deseq2_brain.annotations_ncbi.go.xlsx" is a dataset of differential analysis of genes in the brain across WT and AaegGr34 mutants.

organism: Aedes aegypti

source_name: brain

growth_protocol: Aedes aegypti wild-type (Liverpool) and mutant strains were maintained and reared at 25-28ºC, 70-80% relative humidity, and under a 12-12 hr light-dark cycle. These mosquitoes had constant access to a 10% sucrose solution on cotton balls or filter paper. Blood-feeding was carried out using a membrane feeder with bovine or horse blood warmed to 39-40°C using a water bath. Eggs laid on wet filter papers were transferred to water trays. Larvae were fed TetraMin (Tetra) fish food.

extract_protocol:
Total RNA was extracted from the tissues using Qiagen RNeasy mini kit (#74104). gDNA was removed through the manufacturer’s gDNA eliminator column
RNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, # E7770). mRNA was fragmented to ~200nt by a 15 min incubation period at 94ºC. cDNA was synthesized using random primers and ProtoScript II Reverse Transcriptase, followed by second-strand synthesis with the NEB Second Strand Synthesis Enzyme Mix. The resulting DNA fragments underwent end repair, dA tailing, and ligation to NEBNext hairpin adaptors (NEB, #E7335). After ligation, the adaptors were converted into a "Y" shape through treatment with USER enzyme. DNA fragments were then size-selected using Agencourt AMPure XP beads (Beckman Coulter, #A63880) to obtain fragments ranging from 250 to 350 bp. The adaptor-ligated DNA was PCR-amplified and subsequently purified with AMPure XP beads.

value: brain


title: NUGC4,WT,rep4

description: Library name: NUGC4 WT rep4

value: wild type


title: RNA-seq of Gr34 Aedes aegypti brain, Rep 2 Library 1

description:
Library name: Gr34_BR2_Lib
25151_STAR


title: NUGC4,WT,rep3

description: Library name: NUGC4 WT rep3


title: 927

description:
Library name: Sample 23
Illumina Stranded mRNA Prep


title: RNA-seq of WT Aedes aegypti brain, Rep 3 Library 1

description:
Library name: WT_BR3_Lib
25149_STAR


title: NUGC4,ARID1AKO,rep2

description: Library name: NUGC4 ARID1AKO rep2

value: ARID1A knockout


title: RNA-seq of WT Aedes aegypti brain, Rep 2 Library 1

description:
Library name: WT_BR2_Lib
25148_STAR


title: 930

description:
Library name: Sample 24
Illumina Stranded mRNA Prep


title: NUGC4,WT,rep2

description: Library name: NUGC4 WT rep2


title: NUGC4,WT,rep1

description: Library name: NUGC4 WT rep1


title: 932

description:
Library name: Sample 25
Illumina Stranded mRNA Prep


title: RNA-seq of Gr34 Aedes aegypti brain, Rep 1 Library 1

description:
Library name: Gr34_BR1_Lib
25150_STAR


title: 925

description:
Library name: Sample 22
Illumina Stranded mRNA Prep


title: NUGC4,ARID1AKO,rep1

description: Library name: NUGC4 ARID1AKO rep1


title: GFPc18_96h_rep2_RNAseq

city: Boulder

first: Mingfeng

last: Liu

state: CO

address: 709 Mohawk Dr

institute: University of Colorado

description: Library name: GFPc18_96_2

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/rnaseq v3.14.0 (Ewels et al. 2020).
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome and quantified using GENCODE v38 annotations.
Supplementary files format and content: .csv, raw gene counts and tpm

source_name: hiPSCs

extract_protocol:
RNA was harvested using Directzol RNA Miniprep kit (ZymoResearch). RNA integrity and quantity were assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Ribosomal RNA was depleted from total RNA using a commercial rRNA depletion kit. Strand-specific sequencing libraries were constructed following standard Illumina-compatible protocols. Library quality was assessed, and paired-end sequencing was performed on an Illumina platform. All library construction and sequencing steps were conducted by Novogene Co., Ltd.

value: hiPSCs


title: GFPc18_96h_rep3_RNAseq

description: Library name: GFPc18_96_3


title: 923

description:
Library name: Sample 21
Illumina Stranded mRNA Prep


title: GFPc18_96h_rep1_RNAseq

description: Library name: GFPc18_96_1


title: GFPc18_48h_rep3_RNAseq

description: Library name: GFPc18_48_3


title: GFPc18_48h_rep2_RNAseq

description: Library name: GFPc18_48_2


title: RNA-seq of WT Aedes aegypti brain, Rep 1 Library 1

description:
Library name: WT_BR1_Lib
25147_STAR


title: RNA-seq of Gr34 Aedes aegypti fat body, Rep 2 Library 1

description:
Library name: Gr34_FB2_Lib
25145_STAR

source_name: fat body

value: fat body


title: RNA-seq of Gr34 Aedes aegypti fat body, Rep 3 Library 1

description:
Library name: Gr34_FB3_Lib
25146_STAR


title: GFPc18_48h_rep1_RNAseq

description: Library name: GFPc18_48_1


title: GFPc18_24h_rep3_RNAseq

description: Library name: GFPc18_24_3


title: 921

description:
Library name: Sample 19
Illumina Stranded mRNA Prep


title: GFPc18_24h_rep2_RNAseq

description: Library name: GFPc18_24_2


title: 922

description:
Library name: Sample 20
Illumina Stranded mRNA Prep


title: GFPc18_16h_rep3_RNAseq

description: Library name: GFPc18_16_3


title: 914

description:
Library name: Sample 17
Illumina Stranded mRNA Prep


title: RNA-seq of WT Aedes aegypti fat body, Rep 3 Library 1

description:
Library name: WT_FB3_Lib
25143_STAR


title: 904

description:
Library name: Sample 16
Illumina Stranded mRNA Prep


title: RNA-seq of Gr34 Aedes aegypti fat body, Rep 1 Library 1

description:
Library name: Gr34_FB1_Lib
25144_STAR


title: GFPc18_24h_rep1_RNAseq

description: Library name: GFPc18_24_1


title: GFPc18_16h_rep2_RNAseq

description: Library name: GFPc18_16_2


title: GFPc18_8h_rep2_RNAseq

description: Library name: GFPc18_8_2


title: RNA-seq of WT Aedes aegypti fat body, Rep 1 Library 1

description:
Library name: WT_FB1_Lib
25141_STAR


title: 915

description:
Library name: Sample 18
Illumina Stranded mRNA Prep


title: GFPc18_8h_rep3_RNAseq

description: Library name: GFPc18_8_3


title: RNA-seq of WT Aedes aegypti fat body, Rep 2 Library 1

description:
Library name: WT_FB2_Lib
25142_STAR


title: GFPc18_4h_rep3_RNAseq

description: Library name: GFPc18_4_3


title: 962

description:
Library name: Sample 15
Illumina Stranded mRNA Prep

value: NP


title: GFPc18_8h_rep1_RNAseq

description: Library name: GFPc18_8_1


title: GFPc18_16h_rep1_RNAseq

description: Library name: GFPc18_16_1


title: Spleen-CFA

city: Chongqing

first: Rui

last: Fan

state: Chongqing

address: 1st Youyi Road, Yuzhong District, Chongqing 400016, China

department: Neurology

institute: The First Affiliated Hospital of Chongqing Medical University

description:
Library name: Sample10
Spl-Ctrl

library_source: transcriptomic single cell

data_processing:
The secondary analysis performed on the feature-barcode matrix of single-cell RNA sequencing was processed via the Seurat v2.0 package (Butler et al., 2018). The genes expressed in less than 3 cells, cells with less than 200 expressed genes and mitochondria gene counts more than 5% were discarded. The filtered seurat object was normalized by “NormalizeData” function using “LogNormalize” method and scaled to 5,000 transcripts per cell. The most variable genes were detected using FindVariableGenes function (nfeature=5,000), and the matrix were regressed out using the ScaleData method. Dimension reduction of the matrix was performed by principal component analysis (PCA). RunHarmony function was used to preform data integration and corrected batch effects between samples. The clusters were identified used FindNeighbors and FindClusters functions by K-nearest neighbor (KNN) graph method (resolution: 0.5) on Harmony-corrected PC embeddings (PCA Dims: 1-20 ). UMAP dimensionality reduction was carried out using RunUMAP and UMAPPlotplot function. Identifying top differentially expressed genes for each cluster was performed using the FindAllMarkers function. The immune cells were identified by key markers including T cells (Cd3d,  Cd4, Cd8a), NK cells (Nkg7), B cells (Cd19), Plasma cells (Jchain), Neutrophils (S100a9, S100a8), Mo&Mac (Cd68), DCs (Siglech, Irf8), Clycling cells (Top2a, Mki67), Megakaryocytes (Itga2b, Pf4), Red blood cells (Hbb). Single-cell pseudotime trajectory was constructed using Monocle 2 using Mo&Mac cells from the Spleen scRNA-seq data. The DDRTree dimension reduction method were used to generate the plot and pseudotime trajectory. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed by “clusterProfiler” package (http://dx.doi.org/10.1089/omi.2011.0118), the annotation package was “org.Rn.eg.db” (version 3.19.1), and visualized by “ggplot2”  (version 3.5.1), “GOplot” (version 1.0.2), “enrichplot” packages( https://yulab-smu.github.io/clusterProfiler-book/ ).
Assembly: GRCr8
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

organism: Rattus norvegicus

source_name: Spleen

extract_protocol:
Lennon score in the EAMG group were assessed, and 3 rats with a clinical score ≥ 2, along with corresponding control rats in 28 days after second immunization, were selected for the experiment. The rats were anesthetized and placed in a biosafety cabinet, where blood was collected from the eyeball into EDTA-anticoagulated tubes. The spleen, thymus, lymph nodes, and tibias were dissected out and immediately placed in 5 mL of RPMI 1640 medium. The spleen, thymus, and lymph node tissues were thoroughly homogenized, then centrifuged at 300g for 5 minutes at room temperature. The supernatant was discarded, and after washing, the cell pellet was resuspended in PBS (HyClone, Marlborough, MA, USA) to form a single-cell suspension. GEXSCOPE red blood cell lysis buffer (Singleron Biotechnologies, Nanjing, China) was added to the cell suspension to remove red blood cells. The mixture was then centrifuged and resuspended in PBS. Trypan blue exclusion test was used to assess cell viability. We counted the cells using a TC20 automated cell counter (Bio-Rad, Hercules, CA, USA) and prepared a cell suspension with a final concentration of 1 × 10^5 cells/mL. The single-cell suspension was loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. The scRNA-seq library was constructed using the GEXSCOPE® Single Cell RNA Library Kit (Singleron Biotechnologies, Nanjing, China) and the Singleron Matrix® Automated Single Cell Processing System (Singleron Biotechnologies, Köln, Germany) based on the Singleron GEXSCOPE® protocol. After dilution to 4 nM, individual libraries were pooled for sequencing. The libraries were then sequenced on an Illumina HiSeq X with 150 bp paired-end reads (Illumina, San Diego, CA, USA).
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 (Martin,M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17, 10–12.) to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a (Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner[J]. Bioinformatics, Volume 29, Issue 1, 1 January 2013, Pages 15–21.) to map reads to the reference genome GRCr8. UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).) software, and used to generate expression matrix files for subsequent analysis.

value: Spleen

value: Primary cells

tag: cell type

value: Immune cells

value: Wild-type

value: untreated


title: GFPc18_4h_rep2_RNAseq

description: Library name: GFPc18_4_2


title: 961

description:
Library name: Sample 14
Illumina Stranded mRNA Prep

value: Brain


title: GFPc18_4h_rep1_RNAseq

description: Library name: GFPc18_4_1


title: Spleen-EAMG

description:
Library name: Sample9
Spl-EA

tag: treatment

value: T-AChR


title: GFPc18_2h_rep3_RNAseq

description: Library name: GFPc18_2_3


title: 959

description:
Library name: Sample 13
Illumina Stranded mRNA Prep

value: dHF


title: 958

description:
Library name: Sample 12
Illumina Stranded mRNA Prep


title: GFPc18_2h_rep1_RNAseq

description: Library name: GFPc18_2_1


title: GFPc18_2h_rep2_RNAseq

description: Library name: GFPc18_2_2


title: Lymph-EAMG

description:
Library name: Sample7
Lym-EAMG

source_name: Lymph

value: Lymph

tag: genotype


title: GFPc18_0h_rep1_RNAseq

description: Library name: GFPc18_0_1


title: GFPc18_0h_rep2_RNAseq

description: Library name: GFPc18_0_2


title: TUG1217_96h_rep1_RNAseq

description: Library name: TUG1217_96_1


title: Bone-EAMG

description:
Library name: Sample5
Bone-EA

value: Bone marrow


title: TUG1217_96h_rep2_RNAseq

description: Library name: TUG1217_96_2


title: 950

description:
Library name: Sample 11
Illumina Stranded mRNA Prep

value: Control RE


title: TUG1217_96h_rep3_RNAseq

description: Library name: TUG1217_96_3


title: Bone-CFA

description:
Library name: Sample6
Bone-Ctrl


title: Thymus-EAMG

description:
Library name: Sample3
Thy-EA

source_name: Thymus

value: Thymus


title: 947

description:
Library name: Sample 9
Illumina Stranded mRNA Prep


title: GFPc18_0h_rep3_RNAseq

description: Library name: GFPc18_0_3


title: TUG1217_48h_rep2_RNAseq

description: Library name: TUG1217_48_2


title: Lymph-CFA

description:
Library name: Sample8
Lym-Ctrl


title: 943

description:
Library name: Sample 8
Illumina Stranded mRNA Prep

value: Early Stress RE


title: 949

description:
Library name: Sample 10
Illumina Stranded mRNA Prep


title: TUG1217_48h_rep3_RNAseq

description: Library name: TUG1217_48_3


title: TUG1217_24h_rep3_RNAseq

description: Library name: TUG1217_24_3


title: Thymus-CFA

description:
Library name: Sample4
Thy-Ctrl


title: TUG1217_48h_rep1_RNAseq

description: Library name: TUG1217_48_1


title: 928

description:
Library name: Sample 7
Illumina Stranded mRNA Prep


title: Blood-CFA

description:
Library name: Sample2
Blood-Ctrl

source_name: Whole Blood

value: Whole Blood


title: TUG1217_24h_rep2_RNAseq

description: Library name: TUG1217_24_2

value: hiPSCs


title: 924

description:
Library name: Sample 6
Illumina Stranded mRNA Prep


title: TUG1217_16h_rep2_RNAseq

description: Library name: TUG1217_16_2


title: 918

description:
Library name: Sample 5
Illumina Stranded mRNA Prep


title: TUG1217_4h_rep3_RNAseq

description: Library name: TUG1217_4_3


title: 903

description:
Library name: Sample 2
Illumina Stranded mRNA Prep


title: TUG1217_16h_rep1_RNAseq

description: Library name: TUG1217_16_1


title: TUG1217_8h_rep2_RNAseq

description: Library name: TUG1217_8_2


title: TUG1217_8h_rep1_RNAseq

description: Library name: TUG1217_8_1


title: Blank control 5, normal diet, saline administration (5 mL/kg/d) for 7 days

city: Guangzhou 510275

first: Weiyang

address: School of Life Sciences, Sun Yat-sen University, No. 135 Xingang West Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

description:
Library name: Ctl-Exo-5
Column name in Processed data.txt: Ctl-Exo-5

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Rnor_6.0
Supplementary files format and content: count and TPM  for each Sample

source_name: serum

growth_protocol: Twenty male Sprague-Dawley (SD) rats, aged 6-8 weeks and weighing 180 ~ 220 g

extract_protocol:
At the end of the experiment, blood was drawn from the abdominal aorta of SD rats to sterile centrifuge tubes. The 10 mL blood was extracted from each SD rat and was centrifuged at 8,000 g for 30 minutes at 4°C. The sediment was discarded, and the serum was further purified by centrifuging at 10,000 g for 30 minutes using a Thermo Multifuge X1R centrifuge at 4°C (Thermo Scientific, USA). A total of 110 mL serum was ultra-centrifuged at 4°C using the SW28 rotors of an OptimaL-100XP centrifuge at 140,000 g for 90 minutes (Beckman, USA), and the circulating exosomes were dissolved in PBS. Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: SD rats were randomly divided into two groups (10/group) and received oral gavage treatment for 7 days: 1. Blank control group, normal diet, saline administration (5 mL/kg/d); 2. NXT group, normal diet, NXT administration (1000 mg/kg/d).

value: serum

value: Sprague-Dawley (SD)

value: circulating exosomes

value: male

value: normal diet, saline administration (5 mL/kg/d) for 11 days


title: TUG1217_4h_rep1_RNAseq

description: Library name: TUG1217_4_1


title: NXT 3, normal diet, NXT administration (1000 mg/kg/d) for 7 days

description:
Library name: NXT-Exo-3
Column name in Processed data.txt: NXT-Exo-3

value: normal diet, Naoxintong Capsule(NXT) administration (1000 mg/kg/d) for 9 days


title: TUG1217_24h_rep1_RNAseq

description: Library name: TUG1217_24_1


title: NXT 4, normal diet, NXT administration (1000 mg/kg/d) for 7 days

description:
Library name: NXT-Exo-4
Column name in Processed data.txt: NXT-Exo-4

value: normal diet, Naoxintong Capsule(NXT) administration (1000 mg/kg/d) for 10 days


title: Blood-EAMG

description:
Library name: Sample1
Blood-EA

value: Primary cells

value: Immune cells

value: Wild-type


title: TUG1217_16h_rep3_RNAseq

description: Library name: TUG1217_16_3


title: TUG1217_8h_rep3_RNAseq

description: Library name: TUG1217_8_3


title: NXT 5, normal diet, NXT administration (1000 mg/kg/d) for 7 days

description:
Library name: NXT-Exo-5
Column name in Processed data.txt: NXT-Exo-5

value: normal diet, Naoxintong Capsule(NXT) administration (1000 mg/kg/d) for 11 days


title: TUG1217_4h_rep2_RNAseq

description: Library name: TUG1217_4_2


title: 907

description:
Library name: Sample 3
Illumina Stranded mRNA Prep

value: Brain

value: dHF


title: 917

description:
Library name: Sample 4
Illumina Stranded mRNA Prep


title: TUG1217_2h_rep3_RNAseq

description: Library name: TUG1217_2_3


title: Hashtag expression library from mouse sarcomas treated with vehicle or abemaciclib; GEM reaction 2

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description:
Library name: reaction2-HTO
hashtags 1-4 vehicle; hashtags 5-8 abemaciclib

data_processing:
In order to generate gene expression and hashtag count matrices, fastq files were processed with the 10x Genomics Cell Ranger software using the "count" pipeline, with hashtag oligonucleotide sequences specified in the feature_reference_TotalB_Antibody.csv file.
Cell quality metrics were computed and then used to filter cells using Seurat v5. R packages SoupX and scDblFinder were used to remove ambient RNA signal and to predict doublets, respectively. Hashtag demultiplexing, SCTransform, principal component analysis, clustering, and cell-type annotation were performed in Seurat.
Raw expression counts, SoupX-corrected counts, and transformed (SCT) counts were saved in assay slots "uncorrected," "RNA," and "SCT," respectively. Doublet detection results from scDblFinder were saved in metadata columns named "sDFx_call" and "sDFx_score" where x referred to 3 different doublet detection modes: (1) findDoubletClusters, (2) computeDoubletDensity, and (3) scDblFinder in cluster-based mode. Hashtag demultiplexing results were stored in metadata column "hash_idents."
Assembly: mm10
Supplementary files format and content: *.tar.gz archives: outputs of Cell Ranger Count pipeline
Supplementary files format and content: seurat_obj.rds: Analysis-ready Seurat object generated as desribed above. Raw expression counts, SoupX-corrected counts, and transformed (SCT) counts were saved in assay slots "uncorrected," "RNA," and "SCT," respectively. Doublet detection results from scDblFinder were saved in metadata columns named "sDFx_call" and "sDFx_score" where x referred to 3 different doublet detection modes: (1) findDoubletClusters, (2) computeDoubletDensity, and (3) scDblFinder in cluster-based mode. Hashtag demultiplexing results were stored in metadata column "hash_idents."
Library strategy: CITE-seq

source_name: Mouse sarcoma tumors

growth_protocol: p53-/- Ccne1 o.e. mouse UPS cells (either knocked-down or wild-type for Lpar4) were transplanted into C57/Bl6 recipient mice (150,000 cells seeded on a polymer scaffold, DSM Biomedical CS1-0502). Tumors grew until the average volume of the untreated group reached 1000 mm³.

extract_protocol:
Tumors harvested when the average volume of the untreated group reached 1000 mm³, then were enzymatically and mechanically dissociated using the Mouse Tumor Dissociation Kit (130-096-730, Miltenyi Biotec) on the gentleMAC Octo Dissociator with Heaters (Miltenyi Biotec). Resulting cell suspensions were filtered through 70-µM strainers, and red blood cells were removed using ACK lysis buffer. Samples were hashtagged using antibody-conjugated oligo barcodes (TotalSeq-B hashtag reagents #1-8, Biolegend). Cells were stained with the viability dye Ghost Dye 710 (Cytek), and live cells were isolated by FACS. The resulting sample was concentrated to 1000 cells/uL and loaded into two reaction wells of the Next GEM 3' v3.1 scRNA-seq Chip G (10x Genomics) and captured on the Chromium X.
Preparation of gene expression and hashtag libraries was executed according to manufacturer protocols for the Next GEM 3' v3.1 scRNA-seq kit (10x Genomics) and TotalSeq-B hashtags (Biolegend).

treatment_protocol: When tumors reached an average volume of approximately 100 mm³, mice were randomized into treatment groups and administered saline or abemaciclib methanesulfonate (HY-16297, MedChemExpress, dissolved in PBS at 20 mg/ml) at 75 mg/kg daily by oral gavage.

value: Mouse sarcoma tumors

value: p53-/- Ccne1 o.e. UPS cells

value: live-enriched tumor and immune cells

value: Vehicle or abemaciclib


title: TUG1210c3_96h_rep2_RNAseq

description: Library name: TUG1210c3_96_2

value: hiPSCs


title: TUG1210c3_96h_rep3_RNAseq

description: Library name: TUG1210c3_96_3


title: 963

description:
Library name: Sample 1
Illumina Stranded mRNA Prep

value: NP


title: TUG1217_0h_rep3_RNAseq

description: Library name: TUG1217_0_3


title: TUG1217_0h_rep2_RNAseq

description: Library name: TUG1217_0_2


title: TUG1217_2h_rep1_RNAseq

description: Library name: TUG1217_2_1


title: Hashtag expression library from mouse sarcomas treated with vehicle or abemaciclib; GEM reaction 1

description:
Library name: reaction1-HTO
hashtags 1-4 vehicle; hashtags 5-8 abemaciclib


title: NXT 1, normal diet, NXT administration (1000 mg/kg/d) for 7 days

description:
Library name: NXT-Exo-1
Column name in Processed data.txt: NXT-Exo-1

value: serum

value: Sprague-Dawley (SD)

value: circulating exosomes

value: normal diet, Naoxintong Capsule(NXT) administration (1000 mg/kg/d) for 7 days


title: TUG1217_2h_rep2_RNAseq

description: Library name: TUG1217_2_2


title: NXT 2, normal diet, NXT administration (1000 mg/kg/d) for 7 days

description:
Library name: NXT-Exo-2
Column name in Processed data.txt: NXT-Exo-2

value: male

value: normal diet, Naoxintong Capsule(NXT) administration (1000 mg/kg/d) for 8 days


title: TUG1210c3_96h_rep1_RNAseq

description: Library name: TUG1210c3_96_1


title: hos_mut_1_R1_001

city: Ulm

first: Deung-Dae

last: Park

address: Albert-Einstein-Allee 23

department: Internal Medicine II

institute: University Ulm

data_processing:
Processing of raw FASTQ files and alignment to Ensembl GRCz10 was done by the Genomics Core Facility at University Ulm. After creating the count matrix for Ensembl IDs and samples, low count reads (< ten counts per million in less than 3 samples) were removed.
Counts were TMM normalized using the R/Bioconductor package edgeR (Robinson et al., 2010). The count data were further processed using the voom transformation, lmfit and eBayes functions included in the R/Bioconductor package limma (Ritchie et al., 2015).
The calculated DEGs were annotated using the R/Bioconductor package AnnotationDbi (Pagès H, 2021).
To test for over-representation of gene ontology (GO) terms the goana function of the limma package was used.
Assembly: GRCz10
Supplementary files format and content: Tab-separated values files and matrix files (DEGs, GO terms)

organism: Danio rerio

source_name: heart of stone, zebrafish embryonic RNA-seq_heart, mutant

extract_protocol:
For heart-specific RNA-seq, three independent RNA samples for hos mutants and siblings (5 hearts/sample), were isolated and the RNA was extracted using the NucleoSpin RNA XS Kit (Machery-Nagel) according to manufacture’s instructions.
The libraries for RNA-seq were generated and sequenced on the Illumina HiSeq 2000 by the Genomics Core Facility at University Ulm (Single-end, 50 bp, 10 million reads per sample).

value: Heart

value: cardiomyocytes

value: mut

tag: times

value: 96 hours post fertilization


title: Gene expression library from mouse sarcomas treated with vehicle or abemaciclib; GEM reaction 2

description:
Library name: reaction2-GEX
hashtags 1-4 vehicle; hashtags 5-8 abemaciclib

data_processing:
In order to generate gene expression and hashtag count matrices, fastq files were processed with the 10x Genomics Cell Ranger software using the "count" pipeline, with hashtag oligonucleotide sequences specified in the feature_reference_TotalB_Antibody.csv file.
Cell quality metrics were computed and then used to filter cells using Seurat v5. R packages SoupX and scDblFinder were used to remove ambient RNA signal and to predict doublets, respectively. Hashtag demultiplexing, SCTransform, principal component analysis, clustering, and cell-type annotation were performed in Seurat.
Raw expression counts, SoupX-corrected counts, and transformed (SCT) counts were saved in assay slots "uncorrected," "RNA," and "SCT," respectively. Doublet detection results from scDblFinder were saved in metadata columns named "sDFx_call" and "sDFx_score" where x referred to 3 different doublet detection modes: (1) findDoubletClusters, (2) computeDoubletDensity, and (3) scDblFinder in cluster-based mode. Hashtag demultiplexing results were stored in metadata column "hash_idents."
Assembly: mm10
Supplementary files format and content: *.tar.gz archives: outputs of Cell Ranger Count pipeline
Supplementary files format and content: seurat_obj.rds: Analysis-ready Seurat object generated as desribed above. Raw expression counts, SoupX-corrected counts, and transformed (SCT) counts were saved in assay slots "uncorrected," "RNA," and "SCT," respectively. Doublet detection results from scDblFinder were saved in metadata columns named "sDFx_call" and "sDFx_score" where x referred to 3 different doublet detection modes: (1) findDoubletClusters, (2) computeDoubletDensity, and (3) scDblFinder in cluster-based mode. Hashtag demultiplexing results were stored in metadata column "hash_idents."

tag: cell line


title: hos_mut_2_R1_001


title: TUG1210c3_48h_rep3_RNAseq

description: Library name: TUG1210c3_48_3


title: TUG1217_0h_rep1_RNAseq

description: Library name: TUG1217_0_1


title: hos_mut_3_R1_001


title: TUG1210c3_48h_rep2_RNAseq

description: Library name: TUG1210c3_48_2


title: Sarcoma, shLpar4, abemaciclib, rep 3

description: Library name: shLpar4-Abe_rep3

data_processing:
Reads containing adapters, greater than 10% undetermined bases, or greater than 50% low quality bases were removed.
fastq files were quantified using salmon v1.10.2 with default settings.
salmon quantifications were summarized to gene level and annotated using R packages tximport and tximeta.
Assembly: Gencode vM37 transcripts and GRCm39 genome assembly
Supplementary files format and content: quants_GSE.rds file (SummarizedExperiment object readable in R) containing all samples, their metadata, and gene expression data.

source_name: Cultured mouse sarcoma cells

growth_protocol: p53-/- Ccne1 o.e. mouse UPS cells were maintained in high-glucose DMEM supplemented with 10% heat-inactivated FBS and 1% penicillin-streptomycin in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
RNA was extracted from cells using TRIzol. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis; then end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cells were treated with 125 nM abemaciclib (LY2835219 methanesulfonate, 1231930-82-7, Cayman Chemical, dissolved in PBS with 30% DMSO) for 72 hours prior to collection.

value: Cultured mouse sarcoma cells

value: undifferentiated sarcoma

value: p53 k.o. Ccne1 o.e. shLpar4

value: abemaciclib 125 nM, 72h


title: Gene expression library from mouse sarcomas treated with vehicle or abemaciclib; GEM reaction 1

description:
Library name: reaction1-GEX
hashtags 1-4 vehicle; hashtags 5-8 abemaciclib

value: Mouse sarcoma tumors

value: p53-/- Ccne1 o.e. UPS cells

value: live-enriched tumor and immune cells

value: Vehicle or abemaciclib

tag: batch


title: TUG1210c3_48h_rep1_RNAseq

description: Library name: TUG1210c3_48_1

value: hiPSCs


title: hos_sib_3_R1_001

source_name: heart of stone, zebrafish embryonic RNA-seq_heart, sibling

value: wt


title: TUG1210c3_24h_rep3_RNAseq

description: Library name: TUG1210c3_24_3


title: Sarcoma, shLpar4, abemaciclib, rep 2

description: Library name: shLpar4-Abe_rep2


title: Sarcoma, shLpar4, abemaciclib, rep 1

description: Library name: shLpar4-Abe_rep1


title: TUG1210c3_24h_rep2_RNAseq

description: Library name: TUG1210c3_24_2


title: hos_sib_2_R1_001


title: TUG1210c3_16h_rep2_RNAseq

description: Library name: TUG1210c3_16_2


title: TUG1210c3_16h_rep3_RNAseq

description: Library name: TUG1210c3_16_3


title: hos_sib_1_R1_001


title: Sarcoma, shLpar4, not treated, rep 3

description: Library name: shLpar4-NT_rep3


title: Sarcoma, shLpar4, not treated, rep 2

description: Library name: shLpar4-NT_rep2


title: TUG1210c3_8h_rep3_RNAseq

description: Library name: TUG1210c3_8_3


title: TUG1210c3_8h_rep2_RNAseq

description: Library name: TUG1210c3_8_2


title: TUG1210c3_4h_rep3_RNAseq

description: Library name: TUG1210c3_4_3


title: TUG1210c3_24h_rep1_RNAseq

description: Library name: TUG1210c3_24_1


title: Sarcoma, shLpar4, not treated, rep 1

description: Library name: shLpar4-NT_rep1


title: TUG1210c3_4h_rep2_RNAseq

description: Library name: TUG1210c3_4_2


title: TUG1210c3_8h_rep1_RNAseq

description: Library name: TUG1210c3_8_1


title: TUG1210c3_4h_rep1_RNAseq

description: Library name: TUG1210c3_4_1


title: Sarcoma, shSCR, abemaciclib, rep 3

description: Library name: SCR-Abe_rep3

value: p53 k.o. Ccne1 o.e. shSCR


title: TUG1210c3_16h_rep1_RNAseq

description: Library name: TUG1210c3_16_1


title: TUG1210c3_2h_rep3_RNAseq

description: Library name: TUG1210c3_2_3


title: Sarcoma, shSCR, abemaciclib, rep 2

description: Library name: SCR-Abe_rep2


title: TUG1210c3_2h_rep1_RNAseq

description: Library name: TUG1210c3_2_1


title: TUG1210c3_2h_rep2_RNAseq

description: Library name: TUG1210c3_2_2


title: E42_B Beta

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 220
Illumina

data_processing:
The analysis pipeline described in Li et al., 2019 was used to obtain bulk TCR CDR3 sequences found in blood samples (Li et al., Nat. Protoc. 2019)
Assembly: Human GRCh38
Supplementary files format and content: csv files
Library strategy: TCR-Seq

source_name: PBMCs

extract_protocol:
Matched peripheral blood was collected prior to initiation of treatment and at serial timepoints aligned with tumor samples as described in the protocol.
Concentration, 260/280 and 260/230nm ratios were measured with ND1000 spectrophotometer (Nanodrop Technologies, Thermo-Fisher Scientific) and then DNA/RNA was quantified using a Qubit fluorometer (Life Technologies).

value: PBMCs


title: Sarcoma, shSCR, abemaciclib, rep 1

description: Library name: SCR-Abe_rep1


title: TUG1210c3_0h_rep1_RNAseq

description: Library name: TUG1210c3_0_1


title: E42_EOT Alpha

description:
Library name: Sample 221
Illumina


title: TUG1210c3_0h_rep3_RNAseq

description: Library name: TUG1210c3_0_3


title: TUG1210c3_0h_rep2_RNAseq

description: Library name: TUG1210c3_0_2


title: TUG1210c9_96h_rep2_RNAseq

description: Library name: TUG1210c9_96_2


title: Sarcoma, shSCR, not treated, rep 2

description: Library name: SCR-NT_rep2


title: TUG1210c9_96h_rep3_RNAseq

description: Library name: TUG1210c9_96_3


title: E42_B Alpha

description:
Library name: Sample 219
Illumina


title: Sarcoma, shSCR, not treated, rep 3

description: Library name: SCR-NT_rep3


title: E41_FU2 Beta

description:
Library name: Sample 218
Illumina


title: TUG1210c9_48h_rep3_RNAseq

description: Library name: TUG1210c9_48_3


title: TUG1210c9_96h_rep1_RNAseq

description: Library name: TUG1210c9_96_1


title: TUG1210c9_48h_rep1_RNAseq

description: Library name: TUG1210c9_48_1


title: TUG1210c9_48h_rep2_RNAseq

description: Library name: TUG1210c9_48_2


title: E41_FU1 Alpha

description:
Library name: Sample 215
Illumina


title: eCRS_Exo1

city: Shanghai

first: Boyu

last: Cai

state: Shanghai

address: 1279 Sanmen Road, Hongkou District

department: Department of ORL-HNS

institute: Shanghai Fourth People's Hospital Affiliated to Tongji University

description: Library name: Sample7

data_processing:
fastp v0.19.4
Raw paired-end fastq reads were filtered by Fastp discard the adapters and low quality bases.
The clean reads obtained were then aligned to the mm10 mouse genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie.
Assembly: mm10
Supplementary files format and content: Text file, normalized counts (FPKM) of sequencing reads for the features.

source_name: nasal mucosal tissue

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN, Cat.No.DP424), which yielded > 2 μg of total RNA per sample.
The poly(A) RNA was subsequently fragmented and reverse-transcribed to generate cDNA. Enhance cDNA for the creation of the complementary DNA strand. Purify cDNA products via the AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: Mice were administered 20μg of papain (Sigma-Aldrich) intranasally in 20μl of PBS on days 0–2 and days 7–11.  The mice received intranasal injection of MSC-Exos or PBS from days 7 to 11 and were killed on day 12.

value: nasal mucosal tissue

value: WT

value: papain+MSC-Exos


title: eCRS_Exo2

description: Library name: Sample8


title: TUG1210c9_24h_rep2_RNAseq

description: Library name: TUG1210c9_24_2


title: TUG1210c9_24h_rep3_RNAseq

description: Library name: TUG1210c9_24_3


title: TUG1210c9_16h_rep2_RNAseq

description: Library name: TUG1210c9_16_2


title: eCRS_Exo3

description: Library name: Sample9


title: TUG1210c9_16h_rep3_RNAseq

description: Library name: TUG1210c9_16_3


title: eCRS3

description: Library name: Sample6

value: papain


title: TUG1210c9_24h_rep1_RNAseq

description: Library name: TUG1210c9_24_1


title: E41_FU2 Alpha

description:
Library name: Sample 217
Illumina


title: E41_EOT Beta

description:
Library name: Sample 214
Illumina


title: TUG1210c9_16h_rep1_RNAseq

description: Library name: TUG1210c9_16_1


title: TUG1210c9_8h_rep3_RNAseq

description: Library name: TUG1210c9_8_3


title: eCRS2

description: Library name: Sample5


title: TUG1210c9_8h_rep1_RNAseq

description: Library name: TUG1210c9_8_1


title: eCRS1

description: Library name: Sample4


title: TUG1210c9_8h_rep2_RNAseq

description: Library name: TUG1210c9_8_2


title: TUG1210c9_4h_rep2_RNAseq

description: Library name: TUG1210c9_4_2


title: E41_B Beta

description:
Library name: Sample 212
Illumina


title: E41_B Alpha

description:
Library name: Sample 211
Illumina


title: TUG1210c9_4h_rep3_RNAseq

description: Library name: TUG1210c9_4_3


title: TUG1210c9_4h_rep1_RNAseq

description: Library name: TUG1210c9_4_1


title: control3

description: Library name: Sample3


title: TUG1210c9_2h_rep3_RNAseq

description: Library name: TUG1210c9_2_3


title: control2

description: Library name: Sample2


title: E40_FU2 Beta

description:
Library name: Sample 210
Illumina


title: TUG1210c9_2h_rep2_RNAseq

description: Library name: TUG1210c9_2_2


title: TUG1210c9_2h_rep1_RNAseq

description: Library name: TUG1210c9_2_1


title: control1

description: Library name: Sample1


title: TUG1210c9_0h_rep3_RNAseq

description: Library name: TUG1210c9_0_3


title: E40_FU2 Alpha

description:
Library name: Sample 209
Illumina


title: TUG1210c9_0h_rep2_RNAseq

description: Library name: TUG1210c9_0_2


title: E40_FU1 Beta

description:
Library name: Sample 208
Illumina


title: SPFIBD

city: New Haven

first: Yang

state: CT

address: 300 George St., Room 8300C 8th floor

department: Pathology

institute: Yale University

description:
Library name: SPFIBD
Freshe Frozen spatial transcriptomics

data_processing:
For sequence alignment and generation of the gene expression matrix, RNA data mapping followed our previous report.Briefly, Read 1 was processed using the ST pipeline v.1.8.1, mapping against combined mouse genome (GRCm38) and genome for individual bacteria species, while Read 2 was processed for extraction of unique molecular identifiers (UMIs) and spatial Barcode A and Barcode B. Spatial barcodes corresponding to microfluidic channels were demultiplexed, and the ENSEMBL ID matrix was converted to a gene names matrix for downstream analysis. The identification of pixel locations on tissues was performed using customized matlab scripts using MATLAB 2023B (https://github.com/edicliuyang/Hiplex_proteome).
Assembly: GRCm38
Supplementary files format and content: stdata.tsv  gene expression matrix
Supplementary files format and content: .png .jpg  tissue images
Library strategy: Spatial Transcriptomics

source_name: colon

extract_protocol: Library preparation was conducted using the Nextera XT Library Prep Kit. Purified cDNA (1 ng) was diluted in RNase-free water to a total volume of 5 µL. Then, 10 µL of Tagment DNA buffer and 5 µL of Amplicon Tagment mix were added, and the mixture was incubated at 55°C for 5 minutes. Afterward, 5 µL of NT buffer was added and incubated at room temperature for 5 minutes. PCR master solution (15 µL of PCR master mix, 1 µL of 10 µM P5 primer, 1 µL of 10 µM indexed P7 primer, and 8 µL of RNase-free water) was added, and the PCR reaction was performed with the following program: 95°C for 30 seconds, followed by 12 cycles of 95°C for 10 seconds, 55°C for 30 seconds, 72°C for 30 seconds, and a final extension at 72°C for 5 minutes. The PCR product was purified using 0.6× Ampure XP beads to obtain the library.

value: colon

value: No treatment


title: Sarcoma, shSCR, not treated, rep 1

description: Library name: SCR-NT_rep1

value: Cultured mouse sarcoma cells

value: undifferentiated sarcoma


title: TUG1210c9_0h_rep1_RNAseq

description: Library name: TUG1210c9_0_1


title: RP11_96h_rep3_RNAseq

description: Library name: RP11_96_3


title: E40_FU1 Alpha

description:
Library name: Sample 207
Illumina


title: RP11_96h_rep2_RNAseq

description: Library name: RP11_96_2


title: RP11_48h_rep3_RNAseq

description: Library name: RP11_48_3


title: Intmix

description:
Library name: Intmix
Freshe Frozen spatial transcriptomics

source_name: intestine

value: intestine


title: RP11_48h_rep2_RNAseq

description: Library name: RP11_48_2


title: RP11_96h_rep1_RNAseq

description: Library name: RP11_96_1


title: IntGF

description:
Library name: IntGF
Freshe Frozen spatial transcriptomics


title: SPF

description:
Library name: SPF
Freshe Frozen spatial transcriptomics


title: E40_EOT Alpha

description:
Library name: Sample 205
Illumina


title: RP11_24h_rep2_RNAseq

description: Library name: RP11_24_2


title: RP11_24h_rep3_RNAseq

description: Library name: RP11_24_3


title: E40_EOT Beta

description:
Library name: Sample 206
Illumina


title: RP11_48h_rep1_RNAseq

description: Library name: RP11_48_1


title: Colonmix

description:
Library name: Colonmix
Freshe Frozen spatial transcriptomics


title: E41_EOT Alpha

description:
Library name: Sample 213
Illumina


title: E40_B Beta

description:
Library name: Sample 204
Illumina


title: Proband_PB_AML

type: genomic

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

description: CytoScan HD Array GeneChip

hyb_protocol: DNA was restriction digested, ligated, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 4.3 (ChAS) software with filters set at 200 Kb for Copy Number Alterations (CNAs) and 50 Mb for copy neutral Loss Of Heterozygosity (cnLOH). Our data refer to NetAffx Build 20211122 (hg19) database
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Peripheral Blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis

value: FXN trinucleotide-GAA repeat expansion (1000±50); RUNX1 c.681dup, p.L228Tfs*33; MPO c.2031-2A>C; RTEL1 c.3437C>T

value: Peripheral Blood


title: RP11_24h_rep1_RNAseq

description: Library name: RP11_24_1


title: E40_B Alpha

description:
Library name: Sample 203
Illumina


title: RP11_16h_rep3_RNAseq

description: Library name: RP11_16_3


title: RP11_16h_rep1_RNAseq

description: Library name: RP11_16_1


title: CMS

description:
Library name: CMS
Freshe Frozen spatial transcriptomics


title: E39_FU2 Beta

description:
Library name: Sample 202
Illumina


title: ColonGF

description:
Library name: ColonGF
Freshe Frozen spatial transcriptomics


title: RP11_8h_rep3_RNAseq

description: Library name: RP11_8_3


title: E39_FU2 Alpha

description:
Library name: Sample 201
Illumina


title: RP11_16h_rep2_RNAseq

description: Library name: RP11_16_2


title: CMM

description:
Library name: CMM
Freshe Frozen spatial transcriptomics


title: R_E18_5_CKO_3

city: zhejiang

first: Siyu

last: Chen

address: zhejiang

institute: zhejiang university

description: Library name: R_E18_5_CKO_3

data_processing:
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm10) with STAR v2.7.11a and ERCC spike-in sequences using Hisat2 v2.2.1. Only uniquely mapped reads were assembled into transcripts using feature Counts v2.0.6. The expression level of each transcript was quantified to the normalized TPM and normalized to the ERCC spike-in. Only transcripts with TPM > 1 in at least one sample were considered in all analyses.
Assembly: mm10
Supplementary files format and content: TPM

source_name: ovary

extract_protocol:
Single cells are obtained by lysing of ovaries from mice in Lysis Buffer (DMEM, 13 WU/ml Liberase™ DH, Dnase I).
Library construction was performed based on the well-established protocol using the Fast RNA-seq Lib Prep Kit V2 (ABclonal).

value: ovary

tag: strain

value: oocyte

value: Hnrnpl-null


title: R_E18_5_CKO_2

description: Library name: R_E18_5_CKO_2


title: RP11_8h_rep1_RNAseq

description: Library name: RP11_8_1

source_name: hiPSCs

value: hiPSCs


title: RP11_4h_rep3_RNAseq

description: Library name: RP11_4_3


title: RP11_4h_rep1_RNAseq

description: Library name: RP11_4_1


title: RP11_8h_rep2_RNAseq

description: Library name: RP11_8_2


title: E39_FU1 Beta

description:
Library name: Sample 200
Illumina


title: RP11_4h_rep2_RNAseq

description: Library name: RP11_4_2


title: E39_FU1 Alpha

description:
Library name: Sample 199
Illumina


title: RP11_2h_rep3_RNAseq

description: Library name: RP11_2_3


title: R_E18_5_CKO_1

description: Library name: R_E18_5_CKO_1


title: E41_FU1 Beta

description:
Library name: Sample 216
Illumina


title: RP11_2h_rep2_RNAseq

description: Library name: RP11_2_2


title: R_E18_5_WT_3

description: Library name: R_E18_5_WT_3


title: E39_EOT Beta

description:
Library name: Sample 198
Illumina


title: E39_B Beta

description:
Library name: Sample 196
Illumina


title: R_E18_5_WT_2

description: Library name: R_E18_5_WT_2


title: RP11_2h_rep1_RNAseq

description: Library name: RP11_2_1


title: E39_EOT Alpha

description:
Library name: Sample 197
Illumina


title: E38_FU2 Beta

description:
Library name: Sample 194
Illumina


title: RP11_0h_rep1_RNAseq

description: Library name: RP11_0_1


title: E39_B Alpha

description:
Library name: Sample 195
Illumina


title: PNKY_48h_rep3_RNAseq

description: Library name: PNKY_48_3


title: PNKY_96h_rep3_RNAseq

description: Library name: PNKY_96_3


title: RP11_0h_rep2_RNAseq

description: Library name: RP11_0_2


title: PNKY_96h_rep2_RNAseq

description: Library name: PNKY_96_2