title: mex67-5 xpo1-1 cytoplasm rep3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.17.1.14.
STAR version 2.5.2a was used to align the reads to the sacCer3 genome using 2 mismatches within 50 bases.
featureCounts version 1.5.0-p1 was used to quantify reversely-stranded reads (-s 2) for genes in sacCer3 version 68.
Genome_build: sacCer3 version 68
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include gene counts.
Supplementary_files_format_and_content: *.gtf: The annotation of the aligned files was performed using a custom GTF.

source_name: Cytoplasmic fraction of cells

extract_protocol:
NucleoSpin® RNA; Macherey-Nagel.
Non-stranded mRNA Seq TruSeq standard according to the Illumina protocol.

treatment_protocol: Shifted to 37°C for 1h.

value: Shifted to 37C for 1h

tag: cell fraction

value: Cytoplasmic


title: Tax-CTL,  long PR2909_02_a

status: Public on Apr 30 2024

type: SRA

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

country: Japan

institute: Jichi Medical University Saitama Medical Center

description:
Tax-CTL,  long
977cells

library_source: transcriptomic

data_processing:
NovaSeq Control Software 1.7.5
Real Time Analysis (RTA) 3.4.4
bcl2fastq2 2.20
DRAGEN Bio-IT Platform 3.7.5
Assembly: GRCh38.primary_assembly.genome.fa.gz
Assembly: gencode.v39.primary_assembly.annotation.gtf.gz
Assembly: GENCODE
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio, Inc.)  with modified direct lysis protocol
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio, Inc.)  with modified thermal cylces, and standarad Illumina kit

tag: tissue

value: peripheral blood

tag: cell type

value: sorted CTL

tag: disease type

value: acute ATL

tag: clinical outcomes

value: long-term survivor


title: mex67-5 xpo1-1 cytoplasm rep2

country: Germany

organism: Saccharomyces cerevisiae

tag: strain

tag: genotype

tag: condition


title: Tax-CTL,  long PR2909_01_a

description:
Tax-CTL,  long
1000 cells


title: HAOEC M(con) 4

type: RNA

city: Gaithersburg

first: Atsushi

last: Sakamoto

state: MD

address: 19 Firstfield Road

country: USA

institute: CVPath Institute

hyb_protocol: All reactions and hybridizations were carried out according to the manufacturer's protocol (Affymetrix; Thermo Fisher Scientific). Affymetrix GeneChip Human Clariom S array (Thermo Fisher Scientific) were washed using the GeneChipTM Fluidics Station 450 (Thermo Fischer Scientific).

scan_protocol: Affymetrix GeneChip Human Clariom S arrays were scanned with the GeneChip Scanner 7000 (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fischer Scientific) using default analysis setting. GO enrichment analysis of unbiased differentially expressed genes (DEGs) were conducted by Metascape online bioinformatics resources.

label: biotin

source_name: HAOEC, M(con), 6h.

label_protocol: GeneChipTM WT Plus Reagent Kit were used for generating biotinylated ss-cDNA for hybridization.

growth_protocol: HAOEC (Cell applications) were cultured using MesoEndo Cell Growth medium (Cell applications) in humidified air (5% of CO2) at 37 °C.

extract_protocol: Total RNA was extracted using Rneasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Human Peripheral blood mononuclear cells (PBMC) collected from healthy volunteers (Astarte Biologics) were seeded into culture plates (3-4 x 106 cell/well). After 6 hours incubation, non-attached cells were removed, and culture media was replaced. Remaining monocyte/macrophage fraction were differentiated over 6 days into macrophages with RPMI 1640 medium supplemented with 10% human serum and penicillin-streptomycin in humidified air (5% of CO2) at 37 °C. Prior to use, human hemoglobin and haptoglobin were reconstituted in RPMI 1640 medium, which were added to cultured monocytes at 6 hours after plating (hemoglobin:haptoglobin complexes [HH], final concentration of 0.1 mg/ml,). After differentiation of human monocytes over 6-days with or without HH, supernatant from control macrophages [M(con)] and HH-differentiated [M(Hb)] macrophages were used in further experiments. HAOECs were cultivated for 6 hours in M(con) or M(Hb) macrophage supernatant.

tag: agent

value: M(con) supernatant

tag: time pont

value: 6 hours

value: HAOEC


title: 7d_FHdonor2

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC.
TrimGalore was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA after which the resulting reads were aligned to the reference genome fasta (genome.fa) using the STAR aligner.
Followup QC on the mapped (bam) files was done using Sambamba, RSeQC and PreSeq.
Read counts were then generated using the Subread FeatureCounts module with the Homo_sapiens.GRCh37.74.gtf file as annotation
Assembly: Genome Reference Consortium Human Build 37
Supplementary files format and content: CSV files containing DESeq2 normalized transcript counts

source_name: human fetal liver tissue

extract_protocol:
total RNA was isolated using TRIzol Reagent (Thermo Fisher)
RNA libraries were prepared using TruSeq Stranded mRNA polyA kit (Illumina)

value: human fetal liver tissue

value: wild type

tag: treatment


title: WTE075-20 t(8;21)

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: WTE075-20 t(8;21)

hyb_protocol: Hybridization of the microarrays was performed in a GeneChip® Hybridization Oven 645 (Affymetrix/Thermo Fisher Scientific). GeneChips were washed and stained

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy)

data_processing: Primary data analysis was performed with Transcriptome Analysis Console software version 4.0 (TAC 4.0.2.15). Differentially expressed RNA were estimated by fold-change filtering combined with Student’s t-test. Transcripts with fold change in expression ≥ ±2.0 and FDR<0.05 were considered significantly differentially expressed. Hierarchical clustering was performed to show the distinguishing genes expression pattern among samples

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy) was used to generates amplified and biotinylated sense-strand DNA targets from total RNA; it uses a reverse transcription priming method that primes the entire length of RNA. Amplified cDNA was quantified, fragmented, marked, and prepared for hybridization from the GeneChip® Clariom S Human Array (Thermo Fisher Scientific) for expression level measurement

extract_protocol: RNA was extracted from bone marrow or peripheral blood samples using a QIAamp RNA Blood Mini Kit (Qiagen) at a QIAcube automated station

value: Unsorted Bone Marrow Cells


title: mex67-5 xpo1-1 cytoplasm rep1


title: WTE033-21 WT

description: WTE033-21 WT

source_name: WT CTL#13


title: 24h_FHdonor2


title: 14h_FHdonor2


title: mex67-5 xpo1-1 total rep2

source_name: Total cell lysate

value: Total


title: WTE072-20 t(8;21)

description: WTE072-20 t(8;21)


title: MDM, Donor3, 89.6 Vpr-null, rep2

city: Ann Arbor

first: Kathleen

middle: Loretta

last: Collins

state: MI

address: 1150 W. Medical Center Drive

institute: University of Michigan

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw gene expression sequencing data were mapped and preprocessed using CellRanger Version 3.0.0
Assembly: GRCh38
Supplementary files format and content: RNA count data from CellRanger in zipped Matrix Market format

source_name: Blood

growth_protocol: Cell cultures were maintained at 37degC in a 5% CO2 humidified atmosphere. Leukocytes isolated from anonymous donors by apheresis. Peripheral blood mononuclear cells (PBMCs) were purified by Ficoll density gradient. CD14+ monocytes were positively selected using a CD14 sorting kit (cat# 17858, StemCell Technologies, Vancouver, Canada) following the manufacturer’s instructions. Monocyte derived macrophages (MDM) were obtained by culturing monocytes in R10 [RPMI-1640 with 10% certified endotoxin-low fetal bovine serum (Invitrogen, ThermoFisher), penicillin (100 Units/mL), streptomycin (100 mg/mL), L-glutamine (292 mg/mL), carrier-free M-CSF (50 ng/mL, R and D Systems, Minneapolis, Minnesota) and GM-CSF (50 ng/mL, R and D Systems)] for seven days.

extract_protocol:
At 10 days post-infection, uninfected, 89.6 WT, and 89.6 vpr-null infected MDMs were lifted using enzyme free cell dissociation buffer (ThermoFisher), counted, and prepared according to manufacturer instructions for 10X Chromium Next GEM Single Cell 3’ capture sequencing (10X Genomics).
Single Cell Gene Expression libraries were prepared according to the 10X Chromium Next GEM Single Cell 3' v3 Gene Expression user guide for standard Illumina paired-end sequencing.

treatment_protocol: Prior to infection, half the medium was removed from each well of MDMs and saved to make diluted conditioned media post-infection. MDM were infected with no virus, WT 89.6, or Vpr-null 89.6 virus in diluted in R10 for 6 hr at 37degC. After the 6 hr infection, media was removed and replaced with conditioned media diluted 1:2 with fresh R10.

value: Blood

tag: cell line

value: Primary Cells

value: Monocyte Derived Macrophages (MDM)

value: HIV-1 89.6 Vpr-null


title: MDM, Donor3, Mock, rep1

description: 10X Genomics


title: MDM, Donor2, 89.6 Vpr-null, rep1

description: 10X Genomics


title: cells_FHdonor2


title: WTE032-21 WT

description: WTE032-21 WT

source_name: WT CTL#2


title: Wild type cytoplasm rep3

value: Wild type

value: Shifted to 37C for 1h


title: tissue_FHdonor2


title: 72h_FHdonor2


title: mex67-5 xpo1-1 total rep1


title: WTE029-21 AML-NK

description: WTE029-21 AML-NK


title: 48h_FHdonor2


title: WTE036-21 t(8;21)

description: WTE036-21 t(8;21)


title: ps+1d_FHdonor1


title: mex67-5 xpo1-1 total rep3


title: Wild type cytoplasm rep2

value: Cytoplasmic


title: MDM, Donor2, Mock, rep1

description: 10X Genomics


title: MDM, Donor3, 89.6 Vpr-null, rep1

description: 10X Genomics


title: MDM, Donor2, 89.6 WT, rep1

description: 10X Genomics


title: WTE031-21 WT

description: WTE031-21 WT

source_name: WT CTL#1


title: WTE027-21 AML-NK

description: WTE027-21 AML-NK


title: Wild type cytoplasm rep1


title: WTE028-21 AML-NK

description: WTE028-21 AML-NK


title: MDM, Donor1, 89.6 Vpr-null, rep1

description: 10X Genomics


title: 72h_FHdonor1


title: MDM, Donor1, 89.6 WT, rep1

description: 10X Genomics


title: WTE030-21 AML-NK

description: WTE030-21 AML-NK


title: Wild type total rep3


title: 48h_FHdonor1


title: Wild type total rep2


title: WTE018-21 t(X;21)

description: WTE018-21 t(X;21)


title: MDM, Donor1, Mock, rep1

description: 10X Genomics


title: Wild type total rep1


title: 24h_FHdonor1


title: WTE022-21 AML-NK

description: WTE022-21 AML-NK


title: WTE020-21 t(X;21)

description: WTE020-21 t(X;21)


title: 14h_FHdonor1


title: MPS II Pt4-1,biol rep 1

city: Taipei

first: Tzu-Yu

last: Chen

address: No.1 Jen Ai road section 1 Taipei 100 Taiwan R.O.C.

country: Taiwan

institute: National Taiwan University College of Medicine

data_processing:
benchworkTrimmomatic (v0.38)
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed edgeR (v3.28.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.26.0) with biological duplicate.
Supplementary files format and content: GRCh38
Supplementary files format and content: excel files include normalisedReadCounts for each Sample

source_name: MPS II Pt4-1

growth_protocol: Induced pluripotent stem cell- derived neurons were maintained in 1:1 DMEM/F12 neuronbasal medium supplemented with N2, B27 and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using GENEzol TriRNA Pure Kit (Geneaid). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using KAPA mRNA HyperPrep Kit following manufacturer's protocols.

value: MPS II Pt4-1

value: induced pluripotent stem cells

value: MPS II

value: Neuronal differentiation

tag: time

value: 15 weeks


title: P.troglodytes iPSC medium polysomal fraction biol rep 2

city: Santa Cruz

first: Jeremy

last: Sanford

state: CA

address: 1156 High St

institute: University of California, Santa Cruz

description:
cips_polm_jd950
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

data_processing:
mapping to hg38/panTro6/ponAbe3 with STAR (v 2.7)
repeatmasking with bowtie2
identification of unannotated transcripts with Stringtie
identification and quantification of pairwise alternative splicing events with in house python scripts (junctionCounts)
Assembly: hg38, panTro6, ponAbe3
Supplementary files format and content: *_splice_lib_events.gtf - tab delimited file in GTF format containing all identified splice events for each cell line
Supplementary files format and content: all_species_junctioncounts_restricted.tsv - tab delimited file containing pairwise splicing events (between all combinations of cell lines), the number of reads supporting the isoforms and the percent spliced in (PSI) value
Supplementary files format and content: all_distances.tsv - tab delimited file containing multiple distance metrics computed between pair wise splicing events
Supplementary files format and content: all_dpsi.tsv - tab delimited file containing delta PSI values for all events contained in all_species_junctioncounts_restricted.tsv
Supplementary files format and content: all_ddpsi.tsv - tab delimited file containing delta delta PSI values for all events contained in all_species_junctioncounts_restricted.tsv

molecule: polyA RNA

organism: Pan troglodytes

growth_protocol: C305 cells were cultured on matrigel in mTeSR, Eip-8919-1A and Jos-C31 were cultured on vitronectin in Essential 8 media

extract_protocol:
Frac-seq experiments were performed as previously published (Sterne-Weiler et al. 2013) using human, chimpanzee, and orangutan iPSC lines, with modification to the number of fractions collected. Cytosolic extracts from cell lines/tissues are fractionated by sucrose gradient centrifugation. We collected the total cytosolic lysate, the monoribosomal fraction (80s), as well as light (P2-4), medium (P5-8), and heavy (P9+) polyribosomal fractions.
polyA+ selected RNA from each fraction and individually barcoded libraries using the Bioo NEXTflex Directional RNASeq kit.

treatment_protocol: not applicable

value: iPSC

tag: fraction

value: medium polysomal fraction


title: 7d_FHdonor1

value: human fetal liver tissue

value: wild type


title: MPS II Pt3-2,biol rep 2

source_name: MPS II Pt3-2

value: MPS II Pt3-2


title: cells_FHdonor1


title: WTE021-21 t(X;21)

description: WTE021-21 t(X;21)

value: Unsorted Bone Marrow Cells


title: Larval body wall muscles, madRNAi1

city: New York

first: Mary

last: Baylies

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files were mapped to Drosophila genome using Rsubread in R
Count matrix was generated using the GenomicAlignments package
Assembly: dm6
Supplementary files format and content: comma-separated .csv table including normalized counts for each sample

organism: Drosophila melanogaster

source_name: Larval body wall musculature

growth_protocol: Larvae grown to wandering third instar stage

extract_protocol:
Trizol extraction
RNA libraries were prepared using Poly A enrichment following oligo-dT-mediated purification
PE50 run

treatment_protocol: Tissue-specific knockdown under Dmef2 promotor

value: Larval body wall musculature

value: Muscle enriched

value: Mad knockdown


title: Larval body wall muscles, madRNAi2


title: MPS II Pt4-2,biol rep 2

source_name: MPS II Pt4-2

value: MPS II Pt4-2


title: Larval body wall muscles, mCherryRNAi3

value: control knockdown


title: P.troglodytes iPSC medium polysomal fraction biol rep 1

description:
cips_polm_jd944
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: WTE019-21 t(X;21)

description: WTE019-21 t(X;21)


title: MPS II Pt3-1,biol rep 1

source_name: MPS II Pt3-1

value: MPS II Pt3-1


title: P.troglodytes iPSC heavy polysomal fraction biol rep 1

description:
cips_polh_jd945
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: heavy polysomal fraction


title: P.troglodytes iPSC light polysomal fraction biol rep 2

description:
cips_poll_jd949
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: light polysomal fraction


title: shSmad4.Bmp4_26

city: Heidelberg

first: Lap Hing

last: Chi

state: Victoria

address: 145 Studley Road

department: Translational Breast Cancer Program

country: Australia

institute: Olivia Newton-John Cancer Research Institute

data_processing:
The quality of the sequencing output was checked with the FastQC quality control tool.
Sequence alignment and feature counting were completed in R using the Rsubread package and the genome reference consortium human build 38 (hg38) assembly available at http://asia.ensembl.org/info/data/ftp/index.html.
Lowly expressed genes with counts per million (CPM) values lower than 0.5 (equivalent to approximately less than 10 counts) in more than 12 samples were removed to avoid interference with downstream statistical analysis.
Gene expression was then normalised and analysed using the edgeR and limma packages. Interactive volcano and MD plots were generated using the Glimma package. Additional plots were generated using gplots, ggplot2, ggrepel and ggpubr packages.
Gene set testing was completed using the camera function in limma and curated molecular signature databases available at http://bioinf.wehi.edu.au/software/MSigDB/.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: TurboGFP-tagged MDA-MB-231-HM cells (one million in 1:1 Cultrex:PBS) with modified expression of BMP4 and/or SMAD4 were injected into the fourth mammary fat pad of NSG mice. Tumours were resected when they reached 400 mm3 in volume.

extract_protocol:
Total RNA from TurboGFP-positive MDA-MB-231-HM cells (recovered by FACS) was extracted using the RNeasy micro kit with on-column DNase treatment. Samples from four different tumours with an RNA integrity number (RIN) above 9.9 and the highest RNA concentration, as determined by the Tapestation RNA ScreenTape, were included for each tumour type in downstream analysis.
cDNA library from purified mRNA was synthesised according to the Illumina TruSeq RNA sample preparation workflow. The pooled library containing 16 indexed samples was sequenced in four lanes using the NextSeq 500/550 high output kit (75 cycles) at the La Trobe Genomics Platform (Bundoora, Victoria, Australia).

value: Enforced

value: Low


title: Larval body wall muscles, mCherryRNAi2


title: tissue_FHdonor1


title: shSmad4.Bmp4_24


title: MPS II Pt2-2,biol rep 2

source_name: MPS II Pt2-2

value: MPS II Pt2-2

value: induced pluripotent stem cells

value: MPS II

value: Neuronal differentiation

value: 15 weeks


title: P.troglodytes iPSC light polysomal fraction biol rep 1

description:
cips_poll_jd943
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: iPSC


title: MPS II Pt2-1,biol rep 1

source_name: MPS II Pt2-1

value: MPS II Pt2-1


title: shSmad4.Bmp4_23


title: P.troglodytes iPSC mono-ribosomal fraction biol rep 2

description:
cips_mono_jd948
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: mono-ribosomal fraction


title: MPS II Pt1-3,biol rep 3

source_name: MPS II Pt1-3

value: MPS II Pt1-3


title: P.troglodytes iPSC heavy polysomal fraction biol rep 2

description:
cips_polh_jd951
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: P.troglodytes iPSC mono-ribosomal fraction biol rep 1

description:
cips_mono_jd942
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: MPS II Pt1-2,biol rep 2

source_name: MPS II Pt1-2

value: MPS II Pt1-2


title: P.troglodytes iPSC total cytosolic lysate biol rep 2

description:
cips_cyto_jd946
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: total cytosolic lysate


title: shSmad4.Vc_16

value: High


title: MPS II Pt1-1,biol rep 1

source_name: MPS II Pt1-1

value: MPS II Pt1-1


title: shSmad4.Vc_14


title: P.abelii iPSC heavy polysomal fraction biol rep 2

description:
oips_polh_jd939
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

organism: Pongo abelii

value: heavy polysomal fraction


title: healthy control-3

value: WT


title: P.troglodytes iPSC total cytosolic lysate biol rep 1

description:
cips_cyto_jd940
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: shSmad4.Vc_11


title: P.abelii iPSC medium polysomal fraction biol rep 2

description:
oips_polm_jd938
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: medium polysomal fraction


title: healthy control-2


title: NonSil.Bmp4_25

value: Expressing

value: Enforced

value: Low


title: NonSil.Bmp4_26


title: P.abelii iPSC medium polysomal fraction biol rep 1

description:
oips_polm_jd932
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: siF3

city: Xi’an

first: Xiaohong

last: Zheng

state: Shaanxi

address: 127 Changle West Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Fourth Military Medical University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
RNA sequencing libraries were generated with an insert size ranging from 370 to 420 bp, and sequenced using the Illumina NovaSeq 6000 platform (Novogene-Tianjin, China). Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.5) software. Quantification of gene expression level featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for all Samples

source_name: Umbilical cord

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSCs were transfected with NC-siRNA  or FSTL1 siRNA for 24 h

value: Mesenchymal stem cells

value: Follistatin like 1(FSTL1) silencing


title: Larval body wall muscles, mCherryRNAi1

value: Larval body wall musculature

value: Muscle enriched

value: control knockdown


title: siF2


title: NC3

value: control


title: NonSil.Bmp4_24


title: P.abelii iPSC light polysomal fraction biol rep 2

description:
oips_poll_jd937
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: iPSC

value: light polysomal fraction


title: P.abelii iPSC light polysomal fraction biol rep 1

description:
oips_poll_jd931
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: shSmad4.Bmp4_22


title: NC2


title: NonSil.Vc_15


title: NC1


title: P.abelii iPSC heavy polysomal fraction biol rep 1

description:
oips_polh_jd933
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: healthy control-1

value: induced pluripotent stem cells

value: Neuronal differentiation

value: 15 weeks


title: P.abelii iPSC mono-ribosomal fraction biol rep 2

description:
oips_mono_jd936
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: mono-ribosomal fraction


title: shSmad4.Vc_12

value: High


title: P.abelii iPSC mono-ribosomal fraction biol rep 1

description:
oips_mono_jd930
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: NonSil.Vc_13


title: NonSil.Vc_11


title: P.abelii iPSC total cytosolic fraction biol rep 2

description:
oips_cyto_jd934
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: total cytosolic fraction


title: NonSil.Vc_12

value: Expressing


title: siF1


title: NonSil.Bmp4_21

value: Enforced


title: C.unvax.SA.d34.2

status: Public on Apr 29 2024

city: Seattle

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

institute: Seattle Children's Research Institute

description:
SI-TT-F11
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.

data_processing:
The Seurat R package was used for initial QC filtering and integration. First. a filtering step was applied across all samples. requiring all passing cells to have UMIs mapped to at least 500 distinct genes. and fewer than 5% of UMIs mapped to mitochondrial genes. Genes detected in fewer than 3 cells per mouse were excluded from further analysis. The Seurat integration pipeline56 was then applied to correct for batch effects and align cells across conditions including all combinations of mouse strain. Mtb strain. time post challenge. and CoMtb status.
Initial cell type assignment was performed using the CellTypist python package.57 As CellTypist does not have an available cell type model suitable for mouse lung or mouse immune cells. we created a de novo mouse lung immune cell type model using two published mouse cell atlases. namely the Tabula Muris58 and scMCA59 resources. Cell type labels were harmonized between both sources (e.g. macrophage -> Macrophage) and both datasets were filtered to retain immune and lung-associated cell types. excluding cells specific to other organs. The CellTypist python package was then used to train a mouse lung cell type model based on this combined resource. This model was then used to assign cell types to count-normalized log transformed data on a per-cell level from mouse lung scRNAseq samples. using the python scanpy60 package to normalize total counts per cell to 10.000 and log transform as required by CellTypist.
Assembly: mm10-2020-A (10X Genomics)
Supplementary files format and content: R Seurat object containing raw and normalized counts, per-sample and per-cell metadata, cell type label assignments, calculated UMAP and PCA co-ordinates.

organism: Mus musculus

source_name: Lung

extract_protocol:
After one round of washing with ice-cold DPBS. cells were resuspended to 1000 cells/ml in DPBS. and 8000 cells were inputted into the 10X Genomics pipeline following the manufacturer’s recommendations.
Per 10x protocol

treatment_protocol: We performed single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected animals with and without CoMtb (10^4 CFU of Mtb injected i.d. 8 weeks prior to aerosol Mtb infection) immediately pre-infection and at 10. 17 and 34 days after CD infection. Single cell suspensions were generated from lung samples prior to Mtb infection and at days 10. 17 and 34 post-Mtb infection. Cells were resuspended in 200 ul MACS buffer (PBS containing 2.5% FBS plus 1 mM EDTA). filtered through a 70 um filter. and run on a FACS AriaII (BD) sorter. To collect parenchymal cells for single-cell RNA sequencing. alveolar macrophages (AM. SiglecF+CD11c+) were sorted separately into one collection tube to account for autofluorescence in the IV label channel. and all other IV-negative cells were sorted into another collection tube. After sorting. the two populations were combined and counted on a hemocytometer.

value: Lung

tag: mtb strain

tag: timepoint


title: C.unvax.none.d0.2

description:
SI-TT-G9
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.SA.d34.4

description:
SI-TT-H11
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.SA.d34.3

description:
SI-TT-G11
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.SA.d34.1

description:
SI-TT-E11
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.none.d0.4

description:
SI-TT_H9
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.none.d0.3

description:
SI-TT-A1
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.none.d0.1

description:
SI-TT-F9
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.SA.d17.3

description:
SI-TT-E7
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.SA.d17.2

description:
SI-TT-E6
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: WT_pCV2_SB6_2

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description:
Biological replicate 2
WT_pCV2_SB6_forw.wig
WT_pCV2_SB6_reve.wig

data_processing:
Raw sequencing reads were adapter and quality trimmed using TrimGalore v.0.6.10, and subsequently aligned against the Rhodobacter capsulatus genome (NC_014034.1 and NC_014035.1) version ASM2186v1 using READemption v.1.0.5 and stored as binary alignment maps (BAM).
DESeq2 v.1.32 was used for the normalization of the reads and the identification of transcriptional changes.
Coverage tracks for each file were generated using the coverage function of the READemption pipeline and stored as .wig files. Merged .wig files were generated within R v.1.32.
5’ end mapping was performed by identification of the first base of each BAM file using bedtools’ genome cov function (DOI: 10.1093/bioinformatics/btq033).
Assembly: NCBI Reference Sequence: NC_014034.1 and NC_014035.1 (Version ASM2186v1)
Supplementary files format and content: wiggle format containing the total read coverage merged from the biological triplicates

organism: Rhodobacter capsulatus SB 1003

source_name: bacterial cells

growth_protocol: Independent biological triplicates of each strain were grown in malate minimal medium under microaerobic growth conditions (~25 µM dissolved oxygen).

extract_protocol:
Total RNA was isolated as published (Grützner et al., 2021, Nucelic Acids Res. 49(6), doi: 10.1093/nar/gkab146)
RNA was processed as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146); NEBnext Multiplex Small RNA Library Prep Set

treatment_protocol: Expression of cas13a was repressed during growth in 0.1 µM crystal violet (CV) or induced by further addition of 0.5 mM IPTG. Cells were harvested during exponential growh phase.

value: wild type carrying plasmid pCV2_SB6

value: bacterial cells

value: Induced by CV + IPTG


title: WT_pCV2_SB6_1

description:
Biological replicate 1
WT_pCV2_SB6_forw.wig
WT_pCV2_SB6_reve.wig


title: WT_pCV2_SB6_3

description:
Biological replicate 3
WT_pCV2_SB6_forw.wig
WT_pCV2_SB6_reve.wig


title: C.unvax.SA.d17.1

description:
SI-TT-E5
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: WT_3

description:
Biological replicate 3
WT_forw.wig
WT_reve.wig

value: wild type


title: C.unvax.SA.d10.4

description:
unvax_C3H_4
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: P.abelii iPSC total cytosolic fraction biol rep 1

description:
oips_cyto_jd928
orangutan_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: HCC1937_p53-R282W

city: Shanghai

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

data_processing:
Raw sequence reads were initially processed using FastQC (Babraham Institute, Cambridge, UK) for quality control, then adapter sequences and poor-quality reads were removed using Cutadapt.
Quality-filtered reads were then mapped to the human genome using STAR software, and only uniquely mapped reads were kept. Read counts were calculated by using htseq count.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes FPKM value of each sample

source_name: Breast caner cell line

growth_protocol: HCC1937 and THP-1 cells were cultured at 37 ℃ in medium suggested in the repository, supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
Total RNA was isolated using a Total RNA Purification Kit (B518651, Sangon Biotech)
Sequencing libraries was constructed from 1 μg of purified mRNA using an Illumina TruSeq RNA Sample Prep Kit (cat# FC-122-1001)

treatment_protocol: HCC1937 cells infected with  p53-R282W were treated with 0.3 μM DAC for 5 days. THP-1 cells infected with  p53-R282W were treated with 5 μM DAC for 2 days.

value: HCC1937 (p53-/-) cells  infected with p53-R282W

tag: dac treatment

value: no


title: WT_2

description:
Biological replicate 2
WT_forw.wig
WT_reve.wig


title: HCC1937_p53-R282W+DAC

value: yes


title: WT_1

description:
Biological replicate 1
WT_forw.wig
WT_reve.wig


title: C.unvax.Rv.d34.4

description:
SI-TT-G8
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: promoterless_Cas13a_pCV2_SB6_2

description:
Biological replicate 2
promoterless_Cas13a_pCV2_SB6_forw.wig
promoterless_Cas13a_pCV2_SB6_reve.wig

value: promoterless Cas13a strain carrying plasmid pCV2_SB6


title: C.unvax.SA.d10.1

description:
unvax_C3H_1
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: promoterless_Cas13a_pCV2_SB6_3

description:
Biological replicate 3
promoterless_Cas13a_pCV2_SB6_forw.wig
promoterless_Cas13a_pCV2_SB6_reve.wig


title: C.unvax.Rv.d34.3

description:
SI-TT-G7
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: promoterless_Cas13a_pCV2_SB6_1

description:
Biological replicate 1
promoterless_Cas13a_pCV2_SB6_forw.wig
promoterless_Cas13a_pCV2_SB6_reve.wig


title: C.unvax.Rv.d34.2

description:
SI-TT-G6
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: promoterless_Cas13a_2

description:
Biological replicate 2
promoterless_Cas13a_forw.wig
promoterless_Cas13a_reve.wig

value: promoterless Cas13a strain


title: C.unvax.Rv.d17.3

description:
SI-TT-D7
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.Rv.d34.1

description:
SI-TT-G5
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.Rv.d17.4

description:
SI-TT-D8
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: inducible_Cas13a_IPTG_pCV2_SB6_3

description:
Biological replicate 3
inducible_Cas13a_IPTG_pCV2_SB6_forw.wig
inducible_Cas13a_IPTG_pCV2_SB6_reve.wig

value: inducible Cas13a strain carrying plasmid pCV2_SB6


title: C.unvax.Rv.d17.2

description:
SI-TT-D6
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: promoterless_Cas13a_1

description:
Biological replicate 1
promoterless_Cas13a_forw.wig
promoterless_Cas13a_reve.wig


title: inducible_Cas13a_IPTG_pCV2_SB6_2

description:
Biological replicate 2
inducible_Cas13a_IPTG_pCV2_SB6_forw.wig
inducible_Cas13a_IPTG_pCV2_SB6_reve.wig


title: inducible_Cas13a_IPTG_pCV2_SB6_1

description:
Biological replicate 1
inducible_Cas13a_IPTG_pCV2_SB6_forw.wig
inducible_Cas13a_IPTG_pCV2_SB6_reve.wig


title: C.unvax.Rv.d17.1

description:
SI-TT-D5
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: inducible_Cas13a_IPTG_3

description:
Biological replicate 3
inducible_Cas13a_IPTG_forw.wig
inducible_Cas13a_IPTG_reve.wig

value: inducible Cas13a strain


title: C.cotb.none.d0.3

description:
SI-TT-G10
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.

value: CoMtb


title: C.cotb.none.d0.4

description:
SI-TT-H10
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.unvax.SA.d10.3

description:
unvax_C3H_3
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: inducible_Cas13a_IPTG_2

description:
Biological replicate 2
inducible_Cas13a_IPTG_forw.wig
inducible_Cas13a_IPTG_reve.wig


title: inducible_Cas13a_IPTG_1

description:
Biological replicate 1
inducible_Cas13a_IPTG_forw.wig
inducible_Cas13a_IPTG_reve.wig


title: C.cotb.none.d0.2

description:
SI-TT-A2
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.SA.d34.3

description:
SI-TT-G12
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: Larval body wall muscles, madRNAi3

value: Larval body wall musculature

value: Muscle enriched

value: Mad knockdown


title: C.cotb.none.d0.1

description:
SI-TT-F10
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: inducible_Cas13a_CV_pCV2_SB6_2

description:
Biological replicate 2
inducible_Cas13a_CV_pCV2_SB6_forw.wig
inducible_Cas13a_CV_pCV2_SB6_reve.wig

value: Repressed by CV


title: C.cotb.SA.d34.4

description:
SI-TT-H12
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.

value: Lung


title: inducible_Cas13a_CV_pCV2_SB6_3

description:
Biological replicate 3
inducible_Cas13a_CV_pCV2_SB6_forw.wig
inducible_Cas13a_CV_pCV2_SB6_reve.wig


title: C.cotb.SA.d34.2

description:
SI-TT-F12
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, Intetumumab-5ug/ml 4h, rep3

city: Vienna

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer-Ingelheim

data_processing:
Libraries were pooled and were sequenced at NextSeq2000 Illumina platform with SR75 setup.
Primary and differential analysis of SLAM-seq data were performed using the SLAM DUNK pipeline  to quantify de-novo transcribed sequences (Neumann et al. 2019).
Assembly: GRCh38 (version 86)
Supplementary files format and content: tab-delimited text file containing raw de-novo counts quantified from the SLAM-seq samples
Library strategy: SLAM-seq

growth_protocol: SNU-761 cells are cultured in culture medium (RPMI-1640 medium ATCC-modification + 10% FBS) at 37°C 5% CO2 until a confluency of 75-90% is reached.

extract_protocol:
RNA extraction was performed with Maxwell RSC 48 with simplyRNA Cells Kit (Cat No: AS1390, Promega). Iodoacetamide (Cat No: I6125-10G, Sigma Aldrich) was dissolved in absolute ethanol with 6mM final concentration.
500ng RNAs were used for library preparation. Libraries were prepared with Lexogen’s QuantSeq 3′ mRNA-Seq V2 FWD with UDI for Illumina (Cat. No: 193.384, Lexogen) using 500ng of input RNA for all samples with 12 cycles. All steps were performed according to the manufacturer’s protocol.

treatment_protocol: After overnight incubation, VT107 treatment was added at 0.1 uM and 2.15 uM concentrations and the respective amount of DMSO for samples to compare against. Similarly, Intetumumab Biosimilar – Anti-ITGAV_ITGB3 mAb (Prote Genix PX-TA1230) was added at 1.5 µg/ml and 5 µg/ml concentrations. We used  Isotype IgG1, Kappa from human myeloma plasma (Sigma -Aldrich I5154) as a control. Treated cells were incubated again at 37°C 5% CO2 for a defined time. After 4h of treatment, cells were collected and samples were prepared for the SLAM-seq protocol (Muhar et al., 2018). Thiouridine (Cat. No: T4509-25MG, Sigma Aldrich) freshly dissolved in nuclease free water (Cat. No: AM9938, Ambion) to 100mM stock concentration.

value: liver carcinoma

value: WT

value: Intetumumab, 5ug/ml


title: C.cotb.SA.d17.4

description:
SI-TT-F8
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.SA.d34.1

description:
SI-TT_E12
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, Intetumumab-5ug/ml 4h, rep2


title: promoterless_Cas13a_3

description:
Biological replicate 3
promoterless_Cas13a_forw.wig
promoterless_Cas13a_reve.wig

value: bacterial cells


title: SNU761, Intetumumab-5ug/ml 4h, rep1


title: SNU761, Intetumumab-1.5ug/ml 4h, rep1

value: Intetumumab, 1.5ug/ml


title: SNU761, Intetumumab-1.5ug/ml 4h, rep2


title: C.cotb.SA.d17.1

description:
SI-TT-F5
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.SA.d17.2

description:
SI-TT-F6
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.SA.d10.4

description:
coMtb_C3H_4
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, IgG-Ctrl 4h, rep3

value: Isotype IgG1


title: C.cotb.SA.d10.2

description:
coMtb_C3H_2
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.SA.d10.3

description:
coMtb_C3H_3
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: inducible_Cas13a_CV_pCV2_SB6_1

description:
Biological replicate 1
inducible_Cas13a_CV_pCV2_SB6_forw.wig
inducible_Cas13a_CV_pCV2_SB6_reve.wig


title: C.cotb.SA.d10.1

description:
coMtb_C3H_1
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, IgG-Ctrl 4h, rep2


title: SNU761, IgG-Ctrl 4h, rep1


title: C.cotb.Rv.d34.3

description:
SI-TT-H7
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, Unlabelled, Intetumumab-experiment

value: No


title: SNU761, VT107 2.15uM 4h, rep1


title: SNU761, VT107 2.15uM 4h, rep2


title: C.cotb.Rv.d34.2

description:
SI-TT-H6
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, VT107 0.1uM 4h, rep1


title: C.cotb.Rv.d34.4

description:
SI-TT-H8
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.Rv.d34.1

description:
SI-TT-H5
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, VT107 0.1uM 4h, rep2


title: C.cotb.Rv.d17.2

description:
SI-TT-C6
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.SA.d17.3

description:
SI-TT-F7
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: C.cotb.Rv.d17.4

description:
SI-TT-C8
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, Intetumumab-1.5ug/ml 4h, rep3


title: C.cotb.Rv.d17.3

description:
SI-TT-C7
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, Unlabelled, VT107-experiment


title: C.cotb.Rv.d17.1

description:
SI-TT-C5
Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.


title: SNU761, DMSO 4h, rep2

value: DMSO


title: SNU761, DMSO 4h, rep1


title: HD1,scRNAseq

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

description: 10x Genomics

data_processing:
Raw sequencing reads from single cells were aligned against the human reference (GRCh38) and processed using count module of Cell Ranger. Gene-barcodes matrices containing only barcodes with UMI counts passing threshold were imported to Seurat for further analysis. Genes detected in less than 3 cells were excluded; cells with less than 200 genes detected or greater than 10% mitochondrial UMIs were also filtered out. Doublets were detected using Scrublet, DoubletFinder, scDblFinder, and doubletCells implemented in scran, assuming 0.08% doublet rate for every 1,000 sequenced cells. Cells identified as doublets by at least two algorithms were removed from further analysis. Raw UMI counts were log normalized and the top 5000 variable genes were identified using “vst” method implemented in the FindVaribleFeatures function in Seurat. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring function.
To further remove batch effects, individual samples were integrated using FindIntegrationAnchors and IntegrateData functions. Briefly, dimension reduction was performed on each sample using diagonalized CCA and L2-normalization was applied to the canonical correlation vectors to project all samples into a shared space. The mutual nearest neighbors (MNS) across cells from different datasets were used as “anchors” to encode the cellular relationship between samples. Samples were integrated based on correction vectors for sample calculated form anchors.
Integrated data were further scaled using ScaleData function by regressing against total reads count, % of mitochondrial UMIs, and cell cycle phase scores (S and G2/M). A shared nearest neighbor (SNN) based graph was constructed using top 40 principal components, and clusters were identified using the Louvain algorithm using FindCluster function at resolution=1 (33 clusters). Uniform Manifold Approximation and Projection (UMAP) were generated by RunUMAP function and used for visualization.
Assembly: GRCh38

source_name: Bone marrow

extract_protocol:
RNA was isolated using NucleoSpin RNA II kit.
Library was performed using Chromium Single Cell 3’ Reagent Kits (v2) per user guideline (CG00052, Rev D). Sequencing was performed on a Nextseq 2000 platform (Illumina).

value: Bone marrow

value: Human primary bone marrow cells

value: Normal cells

value: No treatment


title: RC_LPS_2

city: Bethesda

first: Mark

middle: R

last: Cookson

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

data_processing:
fastq files were created using Illumina bcl2fastq2 v2.20
cellranger v3.1.0 was applied to process the generate single cell feature counts (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count)
Assembly: mm10
Supplementary files format and content: Filtered feature matrix folders containing files for features, barcodes, and expression matrix, in .tar.gz format

source_name: Brain

extract_protocol:
Mice were euthanized with CO2 and brains quickly removed. Single cells were dissociated using Miltenyli Adult Brain Dissociation Kit, and Myelin Removal Beads. Libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 per manufacturer's instructions, and targeting 5,000 cells.
10xGenomics Libraries: (protocol - Chromium Next GEM Single Cell 3', reagent Kit v3.1), Ribo-Zero GOLD kit

treatment_protocol: Animals were injected with LPS or PBS intrastriatally, and sacrificed 48 hours post injection.

value: Brain

value: Lrrk2 R1441C

value: LPS


title: GS_LPS_2

value: Lrrk2 G2019S


title: RC_LPS_3


title: WT,scRNAseq

description: 10x Genomics

data_processing:
A customized reference genome was built by adding MYC sequences to GRCm38 mouse transcriptome using mkref module of Cell Ranger (v6.0, 10X Genomics). Raw sequencing reads from single cells were aligned against the customized mouse reference and processed using count module of Cell Ranger. Gene-barcodes matrices containing only barcodes with UMI counts passing threshold were imported to Seurat 115 for further analysis. Genes detected in less than 3 cells were excluded; cells with less than 200 genes detected or greater than 10% mitochondrial UMIs were also filtered out. Doublets were detected using Scrublet 116, DoubletFinder 117, scDblFinder 118, and doubletCells implemented in scran 119, assuming 0.08% doublet rate for every 1,000 sequenced cells. Cells identified as doublets by at least two algorithms were removed from further analysis. Raw UMI counts were log normalized and the top 5000 variable genes were identified using “vst” method implemented in the FindVaribleFeatures function in Seurat. T cell receptor and immunoglobulin genes were removed from the variable genes to prevent clustering based on V(D)J transcripts. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring function.
To further remove batch effects, individual samples were integrated using FindIntegrationAnchors and IntegrateData functions 120 with 8000 anchor genes and 40 dimensions of canonical correlation analysis (CCA). Briefly, dimension reduction was performed on each sample using diagonalized CCA and L2-normalization was applied to the canonical correlation vectors to project all samples into a shared space. The mutual nearest neighbors (MNS) across cells from different datasets were used as “anchors” to encode the cellular relationship between samples. Samples were integrated based on correction vectors for sample calculated form anchors.
Integrated data were further scaled using ScaleData function by regressing against total reads count, % of mitochondrial UMIs, and cell cycle phase scores (S and G2/M). A shared nearest neighbor (SNN) based graph was constructed using top 40 principal components, and clusters were identified using the Louvain algorithm using FindCluster function at resolution=1 (33 clusters). Uniform Manifold Approximation and Projection (UMAP) were generated by RunUMAP function and used for visualization.
Assembly: mm10

extract_protocol:
RNA was isolated using NucleoSpin RNA II kit.
Library was performed using Chromium Single Cell 3’ Reagent Kits (v2) per user guideline (CG00052, Rev D). Sequencing was performed on a Nextseq 2000 platform (Illumina) aiming for a minimum of 50,000 reads/cells.

value: Primary bone marrow cells

value: Hematopoietic cells


title: GS_LPS_1

description: This sample was excluded from downstream analysis due to poor mouse condition and lack of a classical inflammatory response.


title: HD3,scRNAseq

description: 10x Genomics


title: MYC,scRNAseq

description: 10x Genomics


title: WT_LPS_2

value: Wild-type


title: HD2,scRNAseq

description: 10x Genomics


title: microglia MGcCI 3m rep2

city: Seville

first: Juan Jose

last: Perez-Moreno

address: Instituto de Biomedicina de Sevilla (IBiS), Campus Hospital Universitario Virgen del Rocío, Avda. Manuel Siurot

department: Cell Biology

country: Spain

institute: University of Seville

description: Gene expression data from microglia isolated from 3-months-old MGcCI mouse brain cortex

hyb_protocol: cDNA synthesis, hybridization and stain were performed using the Clariom S Pico Assay, mouse (Applied Biosystems).

scan_protocol: Array scanning was performed using the Expression Console Software and the Scanner 3000 (Affymetrix).

data_processing:
Raw data from  were exported to the R enviroment using LIMMA/Bioconductor packages.
logFC: log2-fold change; AveExpr: average log2-expression level for that gene across all the arrays and channels in the experiment; t: the moderated t-statistic; P.Value: associated p-value; adj.P.Value: p-value adjusted for multiple testing.

label: Biotin

source_name: FACS-isolated microglia MGcCI 3m

label_protocol: Affymetrix standard protocol

growth_protocol: Mice were housed under controlled temperature (22ºC) and humidity conditions in a 12 h light/12 h dark cycle with ad libitum access to food and water.

extract_protocol:
Brain cortex was dissected in HBSS (no calcium, no magnesium), and homogenized and disaggregated by physical and papain treatments. Percoll gradient centrifugation was used to separate cells from the rest of the tissue.
Cells were stained with the antibodies CD11b-BV711, CD45-PE and ACSA2-APC. Microglia cells (immunoreactive for both CD11b-BV711,CD45-PE) and astrocytes (immunoreactive for ACSA2-APC) were isolated by FACS.
RNA was extracted using TRIzol reagent.

treatment_protocol: Mice were anesthetized and transcardially perfused with PBS.

value: Brain cortex

tag: animal age

tag: gender

value: Male


title: microglia MGcCI 3m rep6

tag: tissue

value: Female


title: microglia MGcCI 3m rep5


title: microglia MGcCI 3m rep3


title: microglia MGcCI 3m rep4


title: ATAC_JMURTK2_Mock_CP2_24h

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

institute: National Cancer Center Research Institute

library_source: genomic

data_processing:
Raw sequencing data were trimmed using fastp version 0.12.4 35 and mapped to the human reference genome (hg38) using Bowtie2 version 2.4.5, with parameters –k 1
Prior to all downstream analyses, duplicate reads were removed using the MarkDuplicates command in picard-tools version 2.26.11 (Li et al., 2009).
CPM values in the genome tracks were calculated by subtracting those in the input tracks as the background value of each cell.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using the bamCoverage command from deepTools version 3.5.1 include CPM counts for each sample.

molecule: genomic DNA

extract_protocol:
Cells were lysed and the transposition reaction was performed with the Tn5 Transposase (Illumina, FC121-1030) at 37°C for 30 min. The reaction liquid was purified using the MinElute PCR Purification Kit (Qiagen, 28004).
Five cycles of PCR were conducted using custom Nextera PCR primers 34 and NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB, M0543S). The number of additional PCR cycles was determined by qPCR of the partly amplified products. The PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), using double size selection (left ratio: 1.4x; right ratio: 0.5x) according to the manufacturer’s protocol. The samples were sequenced using the MGI Tech DNBSEQ-G400R sequencer, with 150 bp paired end reads.


title: ATAC_JMURTK2_Mock_NT2_24h


title: ATAC_JMURTK2_SMARCB1_NT_24h

data_processing:
Raw sequencing data from ChIP-seq, CUT&RUN-seq, and ATAC-seq were trimmed using fastp version 0.12.4 35 and mapped to the human reference genome (hg38) using Bowtie2 version 2.4.5, with parameters –k 1
Prior to all downstream analyses, duplicate reads were removed using the MarkDuplicates command in picard-tools version 2.26.11 (Li et al., 2009).
In ChIP-seq and CUT&RUN data, CPM values in the genome tracks were calculated by subtracting those in the input tracks as the background value of each cell.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using the bamCoverage command from deepTools version 3.5.1 include CPM counts for each sample.


title: microglia MGcCI 3m rep1


title: GS_LPS_3


title: microglia control 3m rep5

description: Gene expression data from microglia isolated from 3-months-old Control mouse brain cortex

source_name: FACS-isolated microglia control 3m


title: microglia control 3m rep6


title: GS_PBS_3

value: PBS


title: RC_LPS_1


title: microglia control 3m rep4


title: microglia control 3m rep3


title: WT_LPS_3


title: microglia control 3m rep2


title: ATAC_JMURTK2_siCBPsip300_48h


title: WT_LPS_1


title: ATAC_JMURTK2_Mock_NT_24h


title: microglia MGcCI 1m rep4

description: Gene expression data from microglia isolated from 1-month-old MGcCI mouse brain cortex

source_name: FACS-isolated microglia control 1m


title: RC_PBS_3


title: GS_PBS_1


title: ATAC_JMURTK2_siNT_48h


title: microglia MGcCI 1m rep3


title: microglia MGcCI 1m rep2


title: ATAC_JMURTK2_Mock_A2_24h


title: microglia MGcCI 1m rep1


title: microglia control 1m rep5

description: Gene expression data from microglia isolated from 1-month-old Control mouse brain cortex


title: RC_PBS_2


title: microglia control 1m rep4


title: PDX,scRNAseq

description: 10x Genomics

tag: cell type

value: Myelofibrosis

value: Trisomy 8+, JAK2/MPL/CALR mutations negative


title: N2_emb_RNA_rep3

city: New York City

first: Sevinc

last: Ercan

state: NY

address: 31 Washington Place

department: Biology

institute: New York University

data_processing:
Basecalls were performed using CASAVA version 1.8.
RNA-seq:We aligned reads to the WS220 genome version using HISAT2 version 2.2.1 (Kim et al., 2019) using the parameter --rna-strandness R. Count data was calculated using HTSeq version 0.13.5 (Anders et al., 2015). The raw counts were normalized FPKM using cufflinks version 2.2.1 (Roberts et al., 2011), and then FPKM was converted to TPM. The raw counts were used for the R package DESeq2 version 1.30.0 (Love et al., 2014).
Assembly: WS220
Supplementary files format and content: RNA-seq: normalized counts (TPM and FPKM) for individual replicates. Log2fold change values generated using DEseq2

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C.

extract_protocol:
RNA-seq: Total RNA was purified following Trizol manufacturer’s instructions after freeze-cracking samples five times. RNA was cleaned up using Qiagen RNeasy MinElute Cleanup kit. mRNAs were purified using Sera-Mag Oligo (dT) beads (Thermo Scientific) from 10 µg of total RNA. cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212, cDNA synthesis was performed in the presence of dUTP in order to prepare stranded mRNA-seq libraries.
RNA-seq: cDNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Auxin treatment: synchronized L2/L3s were washed three times with M9 and split into two aliquots. Half of the worms were transferred to NGM plates containing 1mM of indole-3-acetic-acid (Fisher 87-51-4) prepared as in (Zhang et al., 2015). The other half were placed in normal NGM plates (no-auxin control) for the indicated time. Worms were then washed one time with M9 and processed accordingly to future application. For ChIP and Hi-C, L2/L3 worms were incubated in 2% formaldehyde for 30 minutes, followed by quenching with glycine, one wash with M9 and two washes with PBS, PMSF and protease inhibitors. For RNA-seq, worms were stored in Trizol.

value: whole worms

value: embryo

value: WT


title: N2_emb_RNA_rep2


title: WT_PBS_3


title: N2_emb_RNA_rep1


title: microglia control 1m rep1


title: GS_PBS_2


title: microglia control 1m rep3


title: microglia control 1m rep2


title: microglia control 3m rep1


title: astrocytes MGcCI 3m rep4

description: Gene expression data from astrocytes isolated from 3-months-old MGcCI mouse brain cortex

source_name: FACS-isolated astrocytes control 3m


title: WT_PBS_2


title: astrocytes MGcCI 3m rep3


title: astrocytes MGcCI 3m rep1


title: SEA06_emb_RNA_rep3

value: SEA06 (EM08 - rex-1 deletion ; 3X Backcross)

value: rex-1 depletion


title: SEA06_emb_RNA_rep2


title: astrocytes MGcCI 3m rep2


title: astrocytes control 3m rep2

description: Gene expression data from astrocytes isolated from 3-months-old Control mouse brain cortex


title: astrocytes control 3m rep4


title: astrocytes control 3m rep3


title: WT_PBS_1

value: Brain


title: SEA06_emb_RNA_rep1


title: astrocytes control 3m rep1


title: RNA-seq after pulldown of GFPbio in primary cortical neurons

city: Amsterdam

first: Max

last: Koppers

address: de Boelelaan 1085

department: CNCR

institute: Vrije Universiteit Amsterdam

data_processing:
Read 1 was used to identify the Illumina library index and CEL-seq2 sample barcodes. Read 2 was aligned to the Rattus norvegicus mRatBN7 reference genome using STARSolo 2.7.10a.77 Sample data was demultiplexed by using je-suite-2.0.78 Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables were done using the STARSolo 2.7.10a aligner.
Assembly: mRatBN7
Supplementary files format and content: Excel file contained raw read counts per gene for each sample/replicate

organism: Rattus norvegicus

source_name: primary cortical neurons

growth_protocol: Neurons were maintained in neurobasal medium (NB; Gibco) supplemented with 1x B27 (Gibco), 0.5 mM glutamine (Gibco), 15.6 μM glutamate (Sigma), and 1% penicillin/streptomycin (Gibco) and incubated under controlled temperature and CO2 conditions (37°C, 5% CO2)

extract_protocol:
For RNA-immunoprecipitation, the same procedure was followed with a few adaptations. SUPERase-in RNase Inhibitor (Thermo Fisher) was added to lysis and wash buffers. After bead incubation and 4 washes, RLT buffer (QIAGEN) + β-mercaptoethanol was added to the beads and incubated with vortexing for 2 minutes. The sample was then separated from the beads on a magnetic rack and transferred to a RNeasy column for RNA isolation (QIAGEN) according to protocol. RNA was stored at -80°C until processing for RNA-sequencing.
Isolated RNA as described above was used for library preparation and sequencing. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol CEL-Seq2.75,76 In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight in vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. The DNA library was paired-end sequenced on an Illumina Nextseq 500, high output, with a 1x75bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles).

value: primary cortical neurons


title: RNA-seq after pulldown of P180GFPbio in primary cortical neurons


title: Memory_SF_ATAC_rep1

city: Mexico City

first: Marti

last: Wilson-Verdugo

state: Mexico City

address: Ciudad Universitaria

country: Mexico

institute: Instituto de Fisiologia Celular

data_processing:
Data quality was assessed using FastQC.
Alignments of paired-end samples were generated Bowtie2 with the flag “-X 1000"
Mitochondrial and PCR duplicate reads were discarded using Samtools and PicardTools, respectively. ENCODE blacklist-mapped reads were filtered via Bedtools.
Peaks were called using MACS2 with flags “--broad --broad-cutoff 0.05 --keep-dup all”.
Assembly: hg38
Supplementary files format and content: Tab-delimited files include peaks called by MACS2 in bed format

source_name: Vascular endothelium

growth_protocol: Pooled-donor human umbilical vein endothelial cells (HUVEC) from Lonza (C2519A) were cultured in endothelial basal medium EBM (CC-3121) supplemented with SingleQuots (CC-4133) at 37°C, 5% CO2, and 8% O2

extract_protocol:
50,000 HUVEC were harvested, resuspended in ice-cold DPBS, and centrifuged (1 min at 1300 x g, 4°C). Pelleted cells were resuspended in 50 μL of cold lysis buffer and centrifuged (10 min at 1200 x g, 4°C). After discarding supernatant, 50 μL of transposase mix with 2.5 uL of Tn5 transposase (Illumina) were added and incubated for 30 min at 37°C. The reaction was stopped by purification with MinElute PCR purification kit (Qiagen) following manufacturer’s instructions.
Library amplification by PCR was done after determining number of cycles needed. Products were size-selected with Agencourt AMPureXP beads (Beckman Coulter) and sequenced on a Nextseq 500 System (Illumina, 75 bp paired-end reads).

treatment_protocol: HUVECs were cultured in three different treatments: control (8 days in 5.5 mM glucose), high glucose (8 days in 30 mM glucose), or memory (4 days in 30 mM glucose followed by 4 days in 5.5 mM glucose)

value: Vascular endothelium

value: HUVEC

value: 30 mM glucose for 4 days; then 5.5 mM glucose + 1 uM sulforaphane for 4 days


title: HG_SF_rep1

data_processing:
Data quality was assessed using FastQC.
Alignments of paired-end samples were generated using STAR v2.7.3a with default parameters
Raw gene count matrices were generated using FeatureCounts with flags “-p -s 2”.
VST normalized counts were generated using DESeq2
Assembly: hg38
Supplementary files format and content: Tab-delimited file includes VST normalized counts for all samples

source_name: HUVEC

extract_protocol:
Total RNA was isolated using the QuickRNA Microprep kit (Zymo Research) following the manufacturer’s instructions
Libraries were prepared from 1 μg of total RNA using the TruSeq Stranded mRNA library prep kit (Illumina) following the reference guide

treatment_protocol: HUVECs were cultured in 7 different treatments: control (8 days in 5.5 mM glucose), high glucose (8 days in 30 mM glucose),  memory (4 days in 30 mM glucose followed by 4 days in 5.5 mM glucose), high glucose + NRF2 overexpression, memory + NRF2 overexpression, high glucose + sulforaphane, and memory + sulforaphane

value: 30 mM glucose 8 days + 1 uM sulforaphane


title: HG_SF_rep2


title: Memory_SF_rep2

value: 30 mM glucose 4 days; 5.5 mM glucose 4 days + 1 uM sulforaphane


title: Memory_NRF2-OE_rep3

value: NRF2 overexpression

value: 30 mM glucose 4 days; 5.5 mM glucose 4 days + NRF2 overexpression


title: Memory_SF_rep1


title: HG_SF_rep3


title: HG_NRF2-OE_rep3

value: 30 mM glucose 8 days + NRF2 overexpression


title: HG_NRF2-OE_rep1


title: Memory_rep3

value: 30 mM glucose 4 days; 5.5 mM glucose 4 days


title: Memory_NRF2-OE_rep2


title: Memory_NRF2-OE_rep1


title: Memory_rep1


title: HG_NRF2-OE_rep2


title: High_glucose_rep3

value: 30 mM glucose 8 days


title: RC_PBS_1

value: Lrrk2 R1441C

value: PBS


title: High_glucose_rep2

value: WT


title: Memory_rep2


title: Amniotic fluid cells from Homo sapiens Case No. 20

type: genomic

city: Changchun

first: Hongguo

last: Zhang

state: Jilin

address: 1 Xinmin Street, Changchun, Jilin 130021, P.R. China

department: Center for Reproductive Medicine and Center for Prenatal Diagnosis

institute: First Hospital, Jilin University, Changchun, China

description:
Amniotic fluid cells from Homo sapiens
Risk of fetal trisomy 21: 1/15

hyb_protocol: DNA was restriction digested, 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 GeneChip System 3000Dx v.2.

data_processing:
ChAS console from Affymetrix was used to assess genome wide copy number frequencies. Log2 Ratio copy number values with associated chromosome positions are available on the series record.
Per marker Log2 Ratio of normalized intensity with respect to a reference, with further correction for sample specific variation.

source_name: amniotic fluid fetal cells

label_protocol: Labelling and hybridizations were performed according to the manufacturer’s protocol.

growth_protocol: not applicable

extract_protocol: Genomic DNA of amniotic fluid cells or peripheral blood sampling of the parents was extracted with using the QIAamp DNA Blood Mini Kit (Qiagen, Inc., Hilden, Germany) according to the manufacturer’s protocol.

tag: tag

value: cell type:amniotic fluid fetal cells  diagnosis:microduplication of 16p11.2


title: Memory_SF_ATAC_rep2


title: MZB,KO,rep1

city: Pohang-Si

first: Jongseok

last: Park

address: Cheongam-Ro, 77

department: Department of Life Science

country: South Korea

institute: POSTECH

data_processing:
Reads for each sample were mapped to the reference genome (mm10) by Tophat (v2.0.13).
The aligned were added to Cuffdiff (v2.2.0) to report differentially expressed genes.
For library normalization and dispersion estimation, geometric and pooled methods were applied.
The TPM (Transcripts Per Kilobase of transcript per Million Mapped reads) value is used as a normalization value.
Assembly: mm10
Supplementary files format and content: List of differentially expressed genes (DEGs) between Cd19-Cre and Cicf/f;Cd19-Cre MZB cells are presented in DEGs of Cic-null MZB cells.xslx file. Cic KO versus Control fold change, p-value are shown in DEGs of Cic-null MZB cells.xslx file.
Supplementary files format and content: TPM value are shown in total_tpm_info.xslx file.

source_name: Spleen

extract_protocol:
MZB cells (CD19+CD93-CD21+CD23-) from the spleen of Cd19-Cre and Cicf/f;Cd19-Cre mice were sorted by a MoFlo Astrios (Beckman Coulter). Total RNA was extracted with TRIzol (GeneAll) according to the manufacturer's instruction.
The library for RNA sequencing was generated using the Truseq Stranded mRNA/Total Library Prep Kit (Illumina)

value: Spleen


title: MZB,Control,rep1


title: MZB,Control,rep2


title: MZB,KO,rep2


title: Control_rep3

value: 5.5 mM glucose 8 days


title: Control_rep1


title: Memory_ATAC_rep2


title: Memory_SF_rep3


title: Memory_ATAC_rep1


title: Amniotic fluid cells from Homo sapiens Case No. 18

description:
Amniotic fluid cells from Homo sapiens
Advanced maternal age, recurrent miscarriage


title: Patch cell Sample 719, Pomc+, High fat diet

city: BORDEAUX

first: Carmelo

last: QUARTA

address: 146 rue Léo Saignat

country: France

institute: Inserm U1215

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.10 and Fastp v0.20.0 tools.
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR aligner v2.7.5a (parameters --outFilterType Normal --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNoverReadLmax 0.04 --outFilterMatchNmin 0 --outFilterMismatchNmax 10 --alignIntronMin 20 --alignIntronMax 0 --alignMatesGapMax 0 --quantMode GeneCounts --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample/Cell
Supplementary files format and content: tab-delimited text file includes normalized DESeq2 counts for each Sample/Cell

source_name: hypothalamus

extract_protocol:
At the end of the recording, each cell in the pipette was aspirated for 3 min. The pipette was then broken into an RNAse-free 200 µL Eppendorf tube containing the reaction mix from the SMART-Seq® Single Cell Kit (Takara, 634472).
cDNA synthesis was performed according to SMART-Seq® Single Cell Kit (Takara, 634472) and the manufacturer instructions, and libraries have been prepared with the Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).
scRNA-seq PATCH-seq

value: hypothalamus

value: Pomc+

tag: diet

value: High fat diet


title: Control_rep2

value: HUVEC

value: Vascular endothelium

tag: genotype


title: Patch cell Sample 718, Pomc+, High fat diet


title: Control_ATAC_rep2


title: High_glucose_rep1


title: Amniotic fluid cells from Homo sapiens Case No. 19

description:
Amniotic fluid cells from Homo sapiens
Advanced maternal age


title: High_glucose_ATAC_rep2


title: Patch cell Sample 720, Ghost, High fat diet

value: Ghost


title: High_glucose_ATAC_rep1


title: Control_ATAC_rep1


title: Amniotic fluid cells from Homo sapiens Case No. 16

description:
Amniotic fluid cells from Homo sapiens
Voluntary request


title: Patch cell Sample 715, Ghost, High fat diet


title: Patch cell Sample 717, Pomc+, High fat diet


title: OCIAML3, M3, H3K27ac, Abcam

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

institute: UMCG

data_processing:
Sequenced reads were trimmed for adapter sequences.
Data analysis was done as described in Orlando et al. 2014.
In short, metagenomes were generated for human hg38 and mm10 or hg38 and dm6. Paired-end reads were aligned to the reference metagenome using BWA with default settings.
Generated SAM files were split into a file containing the reads aligning to human chromosomes and a file containing the reads aligning to mouse or dm6 chromosomes.
Bigwig files were generated using BEDTools and BedGrapToBigWig from UCSC
Peaks were called using MACS2 with the estimated fragment size using broad settings
Assembly: hg38+mm10
Assembly: hg38+dm6
Supplementary files format and content: BigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes, followed by quenching and cell lysis. Next, cells were sonicated using a Bioruptor (Diagenode) and samples were spiked with mouse chromatin or drosophila chromatin for OCI AML3.
ChIP-seq libraries were generated using the KAPA Hyper Prep Kit (Roche Sequencing and Life Sciences) according to manufacturer's protocol and sequenced on an Illumina NextSeq500 using default parameters

value: Acute myeloid leukemia (AML)

tag: chip antibody

value: H3K27ac (Diagenode; C15410196)


title: Amniotic fluid cells from Homo sapiens Case No. 15

description:
Amniotic fluid cells from Homo sapiens
Ventricular septal defect, tricuspid atresia, right ventricular dysplasia,  absence of nasal bone

value: cell type:amniotic fluid fetal cells  diagnosis:microdeletion of 16p11.2


title: Patch cell Sample 714, Pomc+, High fat diet


title: OCIAML3, DMSO, H3K27ac, Abcam

value: DMSO


title: OCIAML3, M3, H3K4me3, Abcam

value: H3K4me3 (Diagenode; C15410003)


title: Patch cell Sample 716, Pomc+, High fat diet


title: OCIAML3, DMSO, H3K27me3, Abcam

value: H3K27me3 (Diagenode; C15410195


title: OCIAML3, DMSO, H3K4me3, Abcam


title: Patch cell Sample 713, Ghost, High fat diet


title: AML22, M3, H3K27me3, Abcam

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells


title: OCIAML3, M3, H3K27me3, Abcam


title: Amniotic fluid cells from Homo sapiens Case No. 12

description:
Amniotic fluid cells from Homo sapiens
Aberrant right subclavian artery


title: AML22, M3, H3K4me3, Abcam


title: Amniotic fluid cells from Homo sapiens Case No. 17

description:
Amniotic fluid cells from Homo sapiens
Advanced maternal age, abnormal karyotype of the husband 46,XY,inv(2)(p11.2q13)


title: AML5, M3, H3K27me3, Abcam


title: AML22, DMSO, H3K27me3, Abcam


title: Amniotic fluid cells from Homo sapiens Case No. 13

description:
Amniotic fluid cells from Homo sapiens
Hemivertebrae deformity


title: AML22, M3, H3K27ac, Abcam


title: AML5, DMSO, H3K27me3, Abcam


title: Amniotic fluid cells from Homo sapiens Case No. 11

description:
Amniotic fluid cells from Homo sapiens
Increased nuchal translucency (2.83mm)


title: Patch cell Sample 709, Ghost, Chow diet

value: Chow diet


title: Amniotic fluid cells from Homo sapiens Case No. 7

description:
Amniotic fluid cells from Homo sapiens
Fetal growth restriction, short HL, polyhydramnios, nasal bone dysplasia


title: Patch cell Sample 712, Ghost, Chow diet


title: AML22, DMSO, H3K27ac, Abcam


title: Patch cell Sample 711, Ghost, Chow diet


title: Amniotic fluid cells from Homo sapiens Case No. 10

description:
Amniotic fluid cells from Homo sapiens
Non-invasive prenatal testing infers high risk of chromosome 16


title: AML2, M3, H3K4me3, Abcam


title: Patch cell Sample 710, Pomc+, Chow diet


title: Amniotic fluid cells from Homo sapiens Case No. 6

description:
Amniotic fluid cells from Homo sapiens
Ventricular septal defect


title: AML22, DMSO, H3K4me3, Abcam


title: Amniotic fluid cells from Homo sapiens Case No. 14

description:
Amniotic fluid cells from Homo sapiens
Abnormal childbearing history: an eight year-old cerebral palsy child  who can not creep or sit before  one year old died at the age of 11


title: Amniotic fluid cells from Homo sapiens Case No. 5

description:
Amniotic fluid cells from Homo sapiens
Advanced maternal age, aberrant right subclavian artery, abnormal childbearing history: child with cerebral palsy


title: AML5, M3, H3K27ac, Abcam


title: Amniotic fluid cells from Homo sapiens Case No. 9

description:
Amniotic fluid cells from Homo sapiens
Renal agenesis, echogenic bowel


title: AML5, DMSO, H3K27ac, Abcam


title: Patch cell Sample 707, Pomc+, Chow diet


title: AML2, M3, H3K27me3, Abcam


title: AML2, DMSO, H3K4me3, Abcam


title: AML2, M3, H3K27ac, Abcam


title: AML5, DMSO, H3K4me3, Abcam


title: AML5, M3, H3K4me3, Abcam


title: Amniotic fluid cells from Homo sapiens Case No. 3

description:
Amniotic fluid cells from Homo sapiens
The mother’s karyotype:47,XXX


title: p300_JMURTK2_SMARCB1_2

extract_protocol:
Cells were fixed for 15 min at 25°C with 1% formaldehyde. Fixation was stopped by the addition of 125 mM glycine. The fixed cells were washed twice with PBS and chromatin was isolated by addition of lysis buffer, followed by disruption using a Dounce homogenizer.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs using the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500, with 75 bp single end reads.


title: Patch cell Sample 701, Pomc+, Chow diet


title: AML2, DMSO, H3K27me3, Abcam


title: Patch cell Sample 704, Pomc+, Chow diet


title: AML2, DMSO, H3K27ac, Abcam


title: Patch cell Sample 705, Ghost, Chow diet


title: Amniotic fluid cells from Homo sapiens Case No. 8

description:
Amniotic fluid cells from Homo sapiens
Cleft lip and palate, echogenic bowel


title: Amniotic fluid cells from Homo sapiens Case No. 4

description:
Amniotic fluid cells from Homo sapiens
Increased nuchal translucency (9.9 mm)


title: Amniotic fluid cells from Homo sapiens Case No. 1

description:
Amniotic fluid cells from Homo sapiens
Non-invasive prenatal testing infers high risk of chromosome 5


title: p300_JMURTK2_Mock_1


title: Patch cell Sample 703, Pomc+, Chow diet


title: WERI-RB1 cells, ATAC-Seq, cancer cell

first: He

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

data_processing:
We aligned the ATAC-seq data to the hg19 reference genome by bowtie2 with default parameter, followed by removing the multiple aligned reads, PCR duplications with samtools.
To eliminate the impact of human genomic problematic regions, we downloaded the ENCODE blacklist, and discarded the reads aligned this region through bedtools.
Specially, for ATAC-seq data, we additionally removed reads aligned to chromosome mitochondria.
Finally, we used macs2 to calling peaks with control, using a q value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: bigWig and narrowPeak files for each sample

source_name: retina

growth_protocol: WERI-RB1 cells were cultured in RPMI-1640 medium (GIBCO). ARPE19 cells were cultured in DMEM (GIBCO). All media were supplemented with 10% FBS (GIBCO), 1% penicillin/streptomycin (GIBCO). All cells were incubated at 37℃ and 5% CO2.

extract_protocol:
Here we used Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling. 50,000 cells were lysed in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) for 3 min, and then centrifuged at 500 r.c.f. for 5 min at 4°C. Cell pellets were resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin, and then incubated on ice for 3 min.
After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added and mixed well. Nuclei were then centrifuged at 500 r.c.f. for 10 min at 4 °C. Nuclei were resuspended in 50 μl of transposition mix containing 25 μl of 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20% Dimethyl Formamide), 2.5 μl of transposase (100 nM final), 16.5 μl of PBS, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween-20, and 5 μl of sterile H2O. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Transposed DNA was purified with MinElute PCR Purification Kit (Qiagen) and eluted in 10 μl of EB buffer. End repair, A adding, adaptor adding reaction and PCR amplification were performed sequentially. The libraries were sequenced by the Illumina PE150 paired-end sequencing platform.

value: retina

value: grape-like clusters of round cells that were isolated from the retina of a female 1-year-old, with Retinoblastoma

value: WT


title: Patch cell Sample 698, Ghost, High fat diet

value: hypothalamus


title: Patch cell Sample 697, Ghost, High fat diet


title: Patch cell Sample 706, Pomc+, Chow diet

value: Pomc+


title: WERI-RB1 cells, RNA-Seq, cancer cell

data_processing:
For read alignment and expression quantification, we first removed low quality reads, and trimmed the adaptor sequence with Trim Galore.
Then we mapped the remaining pair-end reads to the hg19 reference genome using STAR.
Using HTSeq-count, we counted the uniquely mapped reads, and normalized the read count by trimmed mean of M values (TMM), and transformed to reads per kilobases per million reads (RPKM) by edgeR.
With an expression cutoff of RPKM 1 in at least one cell line sample, we removed low abundant genes, and detected the differentially expressed genes using edgeR.
Genes were considered differentially expressed when the overall false discovery rate (FDR) < 0.05 and fold change is above 2.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM and FKPM values for each Sample

extract_protocol:
RNA was extracted from ARPE19 and WERI-RB1 cells using the TRIzol reagent (Invitrogen). RNA purity and concentration were confirmed on a 2100 Bioanalyzer (Agilent Technologies) and a Qubit 2.0 fluorometer with the Qubit RNA Assay Kit (Life Technologies).
2 μg total RNA per sample was used as input material for the RNA sample preparation. Library preparation was completed using the VAHTS Total RNA-seq Library Prep Kit for Illumina (Vazyme) following the manufacturer’s recommendations. The libraries were sequenced by the Illumina PE150 paired-end sequencing platform.


title: Amniotic fluid cells from Homo sapiens Case No. 2

description:
Amniotic fluid cells from Homo sapiens
Non-invasive prenatal testing  infers high risk of chromosome 7


title: Patch cell Sample 695, Ghost, High fat diet

value: High fat diet


title: Mouse_ID_87_78 wks drinking water

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description:
Sample_ID_87
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user. The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Excessive deviation of gene expression ranking in individual samples from the average was assessed by Spearman rank regression. Any sample that exhibited an R^2 value of less than 0.7 was excluded from further analysis (10 of 78 samples)
Count data was loaded into Partek Flow 10.0.22.0524 (build version 0, St. Louis, MO)
Raw gene counts were offset by 1.0, then normalized by media ratio. Genes with very low expression were eliminated from further analysis (those <3.4 (20%) geometric mean counts across all samples) as the final filter.
Differentially expressed genes from age-matched controls using DESeq2 (significance based on false discovery rate (FDR) ≤0.05)
Assembly: mm10
Supplementary files format and content: Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv; aligned reads
Supplementary files format and content: Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv; media ratio normalized counts, low quality samples removed
Supplementary files format and content: Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv; filtered genes (20% of lowest expressed genes by geometric mean across samples)

source_name: liver

growth_protocol: All procedures involving animal care were approved by an EPA Institutional Animal Care and Use Committee. Briefly, mice were received at age 21 days to the EPA AAALAC International accredited facility from Charles River Laboratories in Morrisville, NC, and acclimated for 7 days prior to treatment initiation. The animals were housed in polycarbonate cages in a laminar flow room and maintained under standard conditions (20 ± 2 C°; 40–60% relative humidity; 12 h light/dark cycle) and fed ad libitum Purina 5001 laboratory rodent diet (Purina Test Diets, St. Louis, MO). The study animals

extract_protocol:
Measurements were taken from direct lysates of archived mouse liver sections derived from FFPE blocks. Two to three sections of 15 µM from each sample block were closely trimmed to remove excess paraffin and placed into -20°C storage until shipment overnight on dry ice to the vendor (BioSpyder, Inc., Carlsbad, CA) for processing. There, liver was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos (DOs), with each pair of DOs targeting a single transcript within the mouse genome.
Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 2,205 Mus musculus target genes (TempO-Seq Mouse S1500+ surrogate attenuation panel, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads.

treatment_protocol: The target dose of 3.5 g/L (429 mg/kg-day) dichloroacetic acid (DCA; CAS 79-43-6, Aldrich, Milwaukee, WI) was based on the earlier carcinogenicity results observed in male mice, and is equivalent to 65 mg/kg-day in humans. The actual dose was estimated based on intake, body weight and water DCA concentrations, and the daily water concentration (ml/kg-day) by cage was measured every 4-5 weeks beginning with week 4. Drinking water stocks were prepared every 12-14 days and checked by ultraviolet absorption at 231nm to confirm DCA concentration (Beckman DU Series 600 spectrophotometer, Beckman Coulter, Brea, CA). The stock water pH was adjusted to 6.8-7.2 with NaOH, stored at 4-6°C and changed every 5-7 days, based on studies showing DCA to be stable over 1-2 weeks. As previously detailed, water consumption was initially 5-22% lower in the DCA drinking water groups, although by 52 weeks, water consumption was equivalent in all groups. The removal of DCA quickly returned water consumption to control levels, regardless of exposure length.

tag: strain

tag: Sex

value: male

tag: age

value: 4 wks

value: liver

value: 78 wks

tag: dose

value: CTL

value: 78 wks drinking water


title: Mouse_ID_86_78 wks drinking water

description:
Sample_ID_86
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

tag: time

tag: treatment


title: ARPE19 cells, RNA-Seq, normal control

source_name: retinal pigment epithelia

value: retinal pigment epithelia

tag: cell line

value: a spontaneously arising retinal pigment epithelia (RPE) cell line derived from the normal eyes of a 19-year-old male who died from head trauma in a motor vehicle accident


title: Patch cell Sample 700, Pomc+, Chow diet


title: WERI-RB1 cells, Hi-C, cancer cell

data_processing:
To call the valid Hi-C interactions, we aligned them to hg19 reference genome by HiC-Pro. Using HiC-Pro, we removed the duplicate reads, assigned the reads to HindIII restriction fragments, and filter the invalid interactions.
Then we binned the interaction to 100k resolution for compartmentation, and 40 k for TAD identification.
To perform compartment analysis, we first smoothed 100k matrix by smoothMat implemented in HiCRep in bin level.
Then we calculated the dominant eigenvector of the smoothed contact matrices using matrix2compartment.pl from (https://github.com/dekkerlab/cworld-dekker) and smoothed the compartmentation in TAD level.
We assigned TADs to either the A- or the B- compartments, by calculating the average dominant eigenvector of each TAD.
Assembly: hg19
Supplementary files format and content: bed files for 40 kb TAD of each sample

extract_protocol:
2×107 cells were fixed in 1% formaldehyde for 10 min at room temperature and quenched with glycine. Fixed cells were permeabilized in 1 ml lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% NP-40 and protease inhibitor cocktail (Sigma)) on ice for 15 min and spun down at 2,500 g for 5 min at 4℃.
The pellet was resuspended in 345 μl of 1×NEBuffer r2.1 (NEB), and incubated with 38 μl of 1% SDS at 65℃ for 10 min. Next, 43 μl of 10% Triton X-100 was added to quench the SDS at 37℃ for 15 min. Then 12 μl of 10×NEBuffer r2.1 and 400 U HindIII (NEB) were added per aliquot, and mixed gently to digest the chromatin overnight at 37℃ on a rocking platform. On the next day, the HindIII restriction enzyme was inactivated at 65℃ for 25 min. Then, biotin-14-dATP (Life Technologies), dCTP, dGTP, dTTP and DNA polymerase I Klenow were added (NEB), and incubated at 37℃ for 2 h. The digested chromatin was diluted and re-ligated by T4 DNA ligase (NEB), incubated at 16℃ for 4 h, and shaken manually for three times. The chromatin products were de-cross-linked overnight by adding 50 μl of 10 mg ml-1 proteinase K (Sigma), and incubated at 65℃ overnight. DNA was extracted by phenol-chloroform extraction protocol. RNA was digested by adding 1 μl of RNase A (Sigma) and incubating at 37℃ for 30 min. Then T4 DNA polymerase (NEB) was used to remove biotin from un-ligation ends for 4 h at 20℃, and the enzymes were inactivated for 20 min at 75℃. DNA was purified and sheared to a size of 350 bp (Covaris M220). DNA size selection was conducted using AMPure XP beads (Beckman Coulter). Biotin-marked ligation products was isolated with MyOne Streptavidin C1 beads (Life Technologies). End repair, A adding, adaptor adding reaction, PCR amplification and DNA products size selection were performed sequentially. The libraries were sequenced by the Illumina PE150 paired-end sequencing platform.


title: ARPE19 cells, Hi-C, normal control


title: Patch cell Sample 699, Pomc+, Chow diet


title: Patch cell Sample 693, Pomc+, High fat diet


title: Mouse_ID_84_57 wks drinking water

description:
Sample_ID_84
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks

value: 57 wks drinking water


title: ARPE19 cells, ATAC-Seq, normal control


title: Mouse_ID_88_78 wks drinking water

description:
Sample_ID_88
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_90_78 wks drinking water

description:
Sample_ID_90
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Input_JMURTK2_MockSMARCB1Mix_3

extract_protocol:
Cells were suspended in 1 x Wash Buffer and attached to concanavalin A beads, permeabilized with 100 μL of Antibody Binding Buffer containing digitonin.
Libraries were created by Takara Bio using the ThruPLEX DNA-Seq Kit (Takara, R400674) and amplified for 16 cycles under the following conditions: denaturation at 98°C for 20 s, followed by annealing and extension at 72°C for 50 s. The samples were sequenced by Takara Bio using the NovaSeq 6000 platform (Illumina), with 150 bp paired end reads.


title: Patch cell Sample 692, Pomc+, Chow diet

value: Chow diet


title: Mouse_ID_89_78 wks drinking water

description:
Sample_ID_89
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_85_78 wks drinking water

description:
Sample_ID_85
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_83_57 wks drinking water

description:
Sample_ID_83
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_82_57 wks drinking water

description:
Sample_ID_82
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 694, Ghost, High fat diet

value: Ghost


title: Mouse_ID_80_57 wks drinking water

description:
Sample_ID_80
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_78_32 wks drinking water

description:
Sample_ID_78
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 32 wks

value: 32 wks drinking water


title: Mouse_ID_79_57 wks drinking water

description:
Sample_ID_79
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 691, Ghost, Chow diet

value: hypothalamus


title: Mouse_ID_77_32 wks drinking water

description:
Sample_ID_77
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv