title: lambda, st14, rep3

value: whole embryo, st14

value: lambda

value: nhomie replaced by lambdaDNA


title: nh_inverted, st14, rep1

status: Public on Apr 04 2024

type: SRA

city: Princeton

first: Wenfan

last: Ke

state: New Jersey

address: 119 Lewis Thomas Laboratory

department: Department of Molecular Biology

country: USA

institute: Princeton University

library_source: genomic

data_processing:
MicroC data for D. melanogaster were aligned to custom genomes edited from the Berkeley Drosophila Genome Project (BDGP) Release 6 reference assembly (dos Santos et al., 2015) with BWA-MEM (Li and Durbin, 2009) using parameters -S -P -5 -M.  Briefly, the custom genomes are simply insertions of the transgenic sequence into the –142kb integration site, as predicted from perfect integration.  These events were confirmed using PCR post-integration.  The resultant BAM files were parsed, sorted, de-duplicated, filtered, and split with Pairtools (https://github.com/mirnylab/pairtools).  We removed pairs where only half of the pair could be mapped, or where the MAPQ score was less than three.  The resultant files were indexed with Pairix (https://github.com/4dn-dcic/pairix).  The files from replicates were merged with Pairtools before generating 100bp contact matrices using Cooler (Abdennur and Mirny, 2020).  Finally, balancing and Mcool file generation was performed with Cooler’s Zoomify tool.
Assembly: dm6
Supplementary files format and content: mcool files generated by cooler for visualizing 3D genome organization
Library strategy: Micro-C

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: whole embryo, st14

growth_protocol: Embryos were collected on yeasted apple juice plates in population cages for 4 hours, incubated for 12 hours at 25℃, then subjected to fixation

extract_protocol:
Embryos were dechorionated for 2 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass vials containing 5 mL PBST (0.1% Triton-X100 in PBS), 7.5 mL n-heptane, and 1.5mL fresh 16% formaldehyde.  Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 3.7 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction.  Embryos were washed twice with 15 mL PBST and subjected to secondary crosslinking.  Secondary crosslinking was done in 10mL of freshly prepared 3mM final DSG and ESG in PBST for 45 mins at room temperature with passive mixing.  The reaction was quenched by addition of 3.7mL 2M Tris-HCl pH7.5 for 5 mins, washed twice with PBST, snap-frozen, and stored at -80℃ until library construction.
Micro-C libraries were prepared as previously described (Batut et al., 2022) with the following modifications: 50uL of 12-16hr embryos were used for each biological replicate.  60U of MNase was used for each reaction to digest chromatin to a mononucleosome:dinucleosome ratio of 4.
Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100 nt Flowcell (read length 50 bases per mate, 6-base index read)

tag: tissue

tag: genotype

tag: genetic modification

value: nhomie replaced by nhomie reversed


title: SNU-668 Erastin resistant-1

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

country: China

institute: Fudan university shanghai cancer center

description: raw counts

library_source: transcriptomic

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp  software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean  reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference
genome (hg38). featureCounts software (v2.0) was used to get the raw gene level mRNA read counts  as the mRNA expression profile.
Assembly: hg38
Supplementary files format and content: raw counts within excel file

molecule: total RNA

organism: Homo sapiens

source_name: gastric cancer cell line SNU-668

growth_protocol: SNU-668 Erastin-resistant cells and SUN-484 RSL3-resistant cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). rRNA was removed from total RNA. Then enriched with oligo dT.
KAPA Stranded RNA-Seq library Prep Kit (Roche) was used for library constructioin. Then Agilent 2100 Bioanalyzer was used to examine the library quality. And then library was sequenced on a DNBSEQ-T7 platerform.

treatment_protocol: SNU-484 or SNU-668 cells (2 × 10^6) were inoculated in a 10-cm cell culture dish and exposed to low concentration of RSL3 (0.5 μM) or Erastin (2 μM) for 28 days, then these cells were exposed to high concentration of RSL3 (1 μM) or Erastin (5 μM) for another 28 days. The culture medium was routinely changed every other day, and the concentrations of the compounds were maintained at the indicated levels. The surviving clones were trypsinized, collected and expanded. A cell viability assay was utilized to assess the sensitivity of the surviving cells to Erastin or RSL3. The acquired ferroptosis-resistance was validated.

tag: cell line

value: gastric cancer cell line SNU-668

tag: cell type

value: gastric cancer cells

value: WT

tag: treatment

value: Erastin resistant


title: nh_inverted, st14, rep2


title: lambda, st14, rep2


title: colorectal cancer tissue sample AUS2_778_T3

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene expression estimates as RMA values on log2-scale.

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene level expression values were estimated according to the robust multi-array average (RMA) approach implemented with the justRMA function in the R package affy and using custom CDF files from Brainarray. A batch effect from different lot numbers of the GeneChip™ WT Plus Reagent Kit was corrected with ComBat in the R package sva using default parameters (the batch of each sample is indicated as analysis batch.

label: biotin

source_name: Colorectal cancer patient

label_protocol: 100 ng total RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer tissue sample

value: no


title: colorectal cancer tissue sample AUS2_776_INV

value: INV


title: CD14+ monocytes patient B pre-upadacitinib

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

data_processing:
BGISEQ platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads.Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: peripheral blood

growth_protocol: Blood was obtained in K2-EDTA tubes. Human Peripheral Blood Mononuclear Cells (PBMC) were isolated over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells) and total RNA was isolated.

extract_protocol:
Total RNA was extracted using the Rneasy Micro kit (QIAgen). RNA integrity was validated by LabChip RNA Analysis (Perkin Elmer).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Three patients with rheumatoid arthritis (RA) and inadequate response to disease modifying anti-rheumatic drugs (DMARD) receiving upadacitinib as indicated by the treating rheumatologist were invited to participated in this study. Informed consent was obtained from these participants and the study was conducted in accordance with the Declaration of Helsinki, and approved by the Ethical Committee of Hospital General Universitario Gregorio Marañón (protocol code: JAKi-2022-v1). The three patients with seropositive RA were female with a mean (SD) age of 45 (15) years and moderate disease activity before initiating upadacitinib treatment (rinvoq 15 mg daily) with a mean (SD) CRP basedDisease Activity Score 28- joint counts (DAS28-CRP) of 4.1 (0.7). The three patients showed improvementatthree months follow-up with a mean (SD) DAS28-CRP of1.1 (0.2).

value: peripheral blood

value: monocytes

value: Peripheral blood monocytes

tag: subject status

value: rheumatoid arthritis patient

value: Pre-treatment


title: colorectal cancer tissue sample AUS2_774_T2


title: colorectal cancer tissue sample AUS2_780_T

value: T


title: CD14+ monocytes patient C pre-upadacitinib

institute: Hospital General Universitario Gregorio Marañón


title: colorectal cancer tissue sample AUS2_774_T3


title: Upadacitinib-100-GM-MØ macrophage donor4 rep4

source_name: Monocyte-derived GM-CSF macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from four healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10^6 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages (GM-MØ).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). RNA integrity was validated by LabChip RNA Analysis (Perkin Elmer).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FBS containing GM-CSF  (at day 0, 2 and 5) and daily exposure to 10 nanomolar of the JAK inhibitor Baricitinib (BARI), 10 nanomolar of the JAK inhibitor Upadacitinib (UPA) or 100 nanomolar of the JAK inhibitor Upadacitinib (UPA). Upadacitinib and Baricitinib were dissolved in DMSO, and control experiments were done by exposing macrophages to the same amount of DMSO.

value: macrophages

value: 100nM Upadacitinib-treated


title: lambda, st14, rep1

value: whole embryo, st14

value: lambda

value: nhomie replaced by lambdaDNA


title: LhomieG, st14, rep1+2

description: LhomieGmerged.mcool

value: LhomieG


title: colorectal cancer tissue sample AUS2_774_T


title: CD14+ monocytes patient B 3 month post-upadacitinib treatment

value: 3 month-Upadacitinib treatment


title: Upadacitinib-100-GM-MØ macrophage donor1 rep1


title: h, st14, rep2

value: h

value: nhomie replaced by homie


title: Upadacitinib-100-GM-MØ macrophage donor2 rep2


title: h, st14, rep3


title: Upadacitinib-100-GM-MØ macrophage donor3 rep3


title: colorectal cancer tissue sample AUS2_778_T

value: colorectal cancer tissue sample

value: no


title: Upadacitinib-10-GM-MØ macrophage donor3 rep3

value: 10nM Upadacitinib-treated


title: h, st14, rep1


title: Upadacitinib-10-GM-MØ macrophage donor2 rep2


title: colorectal cancer tissue sample AUS2_773_T2

value: splenic flexure


title: colorectal cancer tissue sample AUS2_773_T


title: LeimohG, st14, rep2

description:
LeimohG2.mcool
LeimohGmerged.mcool

value: LeimohG


title: colorectal cancer tissue sample AUS2_773_T3

value: sigmoid colon


title: LeimohG, st14, rep1

description:
LeimohG1.mcool
LeimohGmerged.mcool


title: Upadacitinib-10-GM-MØ macrophage donor4 rep4


title: colorectal cancer tissue sample AUS2_773_INV1


title: GlambdaL, st14, rep1

description:
GlambdaL1.mcool
GlambdaLmerged.mcool

value: GlambdaL


title: Upadacitinib-10-GM-MØ macrophage donor1 rep1


title: colorectal cancer tissue sample AUS2_771_T2


title: colorectal cancer tissue sample AUS2_771_T

value: T


title: Baricitinib-GM-MØ macrophage donor4 rep4

value: macrophages

value: 10nM Baricitinib-treated


title: colorectal cancer tissue sample AUS2_770_T2


title: GhomieL, st14, rep2

description:
GhomieL2.mcool
GhomieLmerged.mcool

value: whole embryo, st14

value: GhomieL


title: colorectal cancer tissue sample AUS2_770_T3


title: colorectal cancer tissue sample AUS2_773_INV2


title: GeimohL, st14, rep3

description: GeimohLmerged.mcool

value: GeimohL


title: GhomieL, st14, rep1

description:
GhomieL1.mcool
GhomieLmerged.mcool


title: Baricitinib-GM-MØ macrophage donor3 rep3


title: GlambdaL, st14, rep2

description:
GlambdaL2.mcool
GlambdaLmerged.mcool


title: Baricitinib-GM-MØ macrophage donor2 rep2


title: GeimohL, st14, rep1

description:
GeimohL1.mcool
GeimohLmerged.mcool


title: Untreated-GM-MØ macrophage donor3 rep3

value: untreated


title: Untreated-GM-MØ macrophage donor4 rep4


title: Baricitinib-GM-MØ macrophage donor1 rep1


title: Untreated-GM-MØ macrophage donor2 rep2


title: GeimohL, st14, rep2

description: GeimohLmerged.mcool


title: Untreated-GM-MØ macrophage donor1 rep1


title: colorectal cancer tissue sample AUS2_770_T


title: CMP-1 5 days growth, rep3

city: Paterna (Valencia)

first: Carolina

last: Ropero-Pérez

state: Comunidad Valenciana

address: Carrer del Catedràtic Agustín Escardino Benlloch, 7

department: Biotechnology

institute: Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC)

data_processing:
Analysis was performed using software packages included in OmicsBox software (Version 2.0.36). Quality of reads was checked with FastQC version 0.11.8. Adapters were removed and reads were trimmed (3’ end trimming when Q < 20) and filtered (average Q < 20, read length < 25 bp) using Trimmomatic 0.38
Filtered reads were mapped onto P. expansum CECT20906 (CMP-1 strain) genome (NCBI, GenBank assembly accession GCA_000769755.1) with STAR (v.2.7.8a)
Gene count analysis and DEGs identification was carried out with the OmicsBox suite  (OmicsBox 2.0.36). The number of reads that overlap with exon features for each gene were counted based on HT-Seq 0.9.0.
Genes for which Count Per Millions (CPM) < 0.5 in a minimum of three samples were removed and library sizes were normalized using the Trimmed Mean of M-values (TMM) method. Pairwise differential expression analysis was performed with edgeR. Differentially expressed genes (DEGs) were identified using |log2(Fold change)| > 1 and false discovery rate (FDR) < 0.05.
Assembly: GCA_000769755.1
Supplementary files format and content: tab-delimited text file include raw counts of sequencing reads correspondant to exon features of each gene (htseq-count output). Each row is a gene and each column is a sample

organism: Penicillium expansum

source_name: mycelia

growth_protocol: Erlenmeyer flasks of 100 mL volume containing 25 mL of PcMM were inoculated with 1 x 106 conidia/mL of each strain. Samples were cultured for 3 or 5 days at 25 ºC and 150 rpm.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, United States) following manufacturer’s instruction
Complementary DNA (cDNA) libraries were prepared with the TruSeq mRNA stranded kit (Illumina)

value: mycelia

value: Growth in PcMM


title: CMP-1 5 days growth, rep2


title: CMP-1 5 days growth, rep1


title: CMP-1 3 days growth, rep3


title: colorectal cancer tissue sample AUS2_769_T3


title: PEME0055 (ΔafpA disruption mutant), 5 days growth, rep3


title: CMP-1 3 days growth, rep2


title: PEME0055 (ΔafpA disruption mutant), 5 days growth, rep2


title: CMP-1 3 days growth, rep1


title: colorectal cancer tissue sample AUS2_769_T


title: colorectal cancer tissue sample AUS2_767_T


title: colorectal cancer tissue sample AUS2_767_T2


title: PEME0055 (ΔafpA disruption mutant), 5 days growth, rep1


title: colorectal cancer tissue sample AUS2_769_T2


title: colorectal cancer tissue sample AUS2_767_T3


title: mos11_cyt_FC2_rep5

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

description: UMIs in header

data_processing:
Reads were mapped to the TAIR10 genome (Lamesch et al., 2012) and ERCC sequences using STAR (v2.7.8a, ‘--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000  --outFilterMismatchNoverReadLmax 0.04 --outSAMmultNmax 1 –outMultimapperOrder Random’).
After tagging duplicated sequences using Picard MarkDuplicates (v2.21.8) (https://broadinstitute.github.io/picard/) the UMIs were used to remove technical duplicates using umi_tools dedup (v1.0.1).
For the differential gene expression analysis, the resulting reads from the pipeline outlined above were used to create a count table using the featureCounts function of the rsubread package (v1.6.3) (Liao et al., 2019)
Code is available at GitHub (uschwartz/mos11)
Assembly: TAIR10
Supplementary files format and content: tab delimited text file includes raw counts for each sample after merging samples on different flow cells

organism: Arabidopsis thaliana

source_name: rosette

growth_protocol: Seeds of Arabidopsis thaliana (Col-0) were stratified in darkness for 48 h at 4°C and plants were grown and propagated at 21°C on soil in a phytochamber or on MS medium in plant incubators (PolyKlima) under long-day conditions (16h light at 21°C and 8h darkness at 18°C).

extract_protocol:
Nuclear and cytoplasmic fractions were prepared from rosettes of 14-d plants adapting a previously described protocol based on differential centrifugation (Park et al., 2005). RNA was isolated from nuclear and cytoplasmic fractions using the RNeasy Plant Mini Kit (Qiagen). Additionally, the ERCC RNA Spike-In Mix (ambion) was added
RNA-seq libraries were prepared using NuGEN Universal Plus RNA-Seq with NuQuant User Guide v3 (Tecan Genomics) in combination with Arabidopsis rRNA AnyDeplete module

value: rosette

tag: age

tag: sequencing run

tag: compartment

value: cytoplasm


title: colorectal cancer tissue sample AUS2_766_T3

value: colorectal cancer tissue sample

value: no


title: colorectal cancer tissue sample AUS2_766_T2


title: PEME0055 (ΔafpA disruption mutant), 3 days growth, rep3


title: colorectal cancer tissue sample AUS2_763_T


title: colorectal cancer tissue sample AUS2_762_T3


title: colorectal cancer tissue sample AUS2_763_T2


title: mos11_cyt_FC1_rep5

description: UMIs in header


title: colorectal cancer tissue sample AUS2_762_T2


title: colorectal cancer tissue sample AUS2_762_T


title: DNA-meIP-HAP1-M-IFN-lib4-922-2021_S2_L004

city: Bethesda

first: Gary

last: Felsenfeld

address: 9000 Rockville Pike

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2. Peaks were called using MACS2. Bigwig files were generated with Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: MEDIP-seq

growth_protocol: HAP1 control cells and MAZ KO cells are cultured in IMDM with 10% FBS and 1% Pen/Strep. K562 control cells and MAZ knocking down cells were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 10 mM HEPES (pH 7.3), and 1% penicillin-streptomycin.

extract_protocol:
DNA was extracted using the Quick-DNA MicroPrep kit following manufacturer's instructions.
MEDIP-seq was performed using the MagMeDIP-seq Package from Diagenode in HAP1 control and HAP1 MAZ knockout  cells following manufacturer's instructions.

tag: chip antibody

value: C02010041 Diagenode

value: IFNγ

tag: treatment time_(hr)


title: BPA_female_P3W_Cx_rep3

city: Kyoto

first: Takeshi

last: Yaoi

address: Kawaramachi-Hirokoji

country: Japan

institute: Kyoto Prefectural University of Medicine

description: Bisphenol A (BPA) was exposed maternally and via lactation

hyb_protocol: For each hybridization, 1.65 μg of Cy3 labeled cDNA were hybridized at 65 ℃ for 17 hours to an Agilent Mouse GE 8x60K Microarray (Design ID: 028005).

scan_protocol: Microarrays were scanned using an Agilent Technologies Scanner G2505C.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features which were flagged as no errors (present flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated and population outliers (marginal and absent flags). Normalization was performed using Agilent GeneSpring GX version 11.0.2. (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples).

organism: Mus musculus

source_name: BPA, female, P3W, Cerebral cortex, replicate 3

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions. Briefly, 100ng of total RNA was reversed transcribed to double-strand cDNA using a poly dT-T7 promoter primer. Primer, template RNA and quality-control transcripts of known concentration and quality were first denatured at 65 ℃ for 10 min and incubated for 2 hours at 40 ℃ with 5X first strand Buffer, 0.1 M DTT, 10 mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was inactivated at 70 ℃ for 15 min. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3 labeled-CTP and incubated at 40 ℃ for 2 hours. Labeled cRNAs were purified using QIAGEN’s RNeasy mini spin columns and eluted in 30 μl of nuclease-free water. After amplification and labeling, cRNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

extract_protocol: RNA was prepared from each fresh frozen tissue using NucleoSpin RNA II kit (TaKaRa-Bio, Japan) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Cerebral cortex

tag: gender

value: female


title: PEME0055 (ΔafpA disruption mutant), 3 days growth, rep1


title: Control_female_P3W_Cx_rep2

description: Vehicle (ethanol) was exposed maternally and via lactation

source_name: Control, female, P3W, Cerebral cortex, replicate 2


title: DNA-meIP-HAP1-M-lib3-922-2021_S7_L004


title: Control_female_P3W_Cx_rep3

source_name: Control, female, P3W, Cerebral cortex, replicate 3


title: colorectal cancer tissue sample AUS2_759_T2


title: PEME0055 (ΔafpA disruption mutant), 3 days growth, rep2


title: DNA-meIP-HAP1-p-IFN-lib2-922-2021_S4_L004


title: BPA_female_P3W_Cx_rep2

source_name: BPA, female, P3W, Cerebral cortex, replicate 2


title: BPA_male_P3W_Cx_rep2

source_name: BPA, male, P3W, Cerebral cortex, replicate 2

value: male


title: Control_male_P3W_Cx_rep3

source_name: Control, male, P3W, Cerebral cortex, replicate 3


title: BPA_female_P3W_Cx_rep1

source_name: BPA, female, P3W, Cerebral cortex, replicate 1


title: mos11_cyt_FC2_rep4

description: UMIs in header


title: BPA_male_P3W_Cx_rep3

source_name: BPA, male, P3W, Cerebral cortex, replicate 3


title: mos11_cyt_FC1_rep4

description: UMIs in header


title: DNA-meIP-HAP1-p-lib1-922-2021_S1_L004


title: BPA_male_P3W_Cx_rep1

source_name: BPA, male, P3W, Cerebral cortex, replicate 1


title: mos11_cyt_FC2_rep3

description: UMIs in header


title: Control_female_P3W_Cx_rep1

source_name: Control, female, P3W, Cerebral cortex, replicate 1


title: Control_male_P3W_Cx_rep1

source_name: Control, male, P3W, Cerebral cortex, replicate 1


title: colorectal cancer tissue sample AUS2_759_T

value: T


title: Control_male_P3W_Cx_rep2

source_name: Control, male, P3W, Cerebral cortex, replicate 2


title: colorectal cancer tissue sample AUS2_766_T

source_name: Colorectal cancer patient


title: RNAseq-K562-siMAZ-Lib7-rep-2-Nov2-2021

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bbtools-BBMap (v.38.76). The number of reads on each gene were counted with Subread (v.2.0.3).  Read count data were analyzed with the R package DESeq2 (v.1.32.0).
Assembly: hg19

extract_protocol:
Total RNA was extracted using an RNeasy mini Kit (Qiagen, 74104)
1 μg of the treated total RNA was used to prepare libraries with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, catalog no. E7490) and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, catalog no.7760s) following the manufacturer’s instructions.


title: 4374

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

description: treated with 30 mpk OCA dissolved in 40% DMSO and& 60% polyethylene glycol (PEG) orally every day

data_processing:
Fastqc was used to exclude poor quality samples.
STAR was used to align reads to transcriptome using a GRCh38.p14 genome build.
Salmon quantification in alignment-based mode was used to obtain transcript-level abundance.
Transcript-level abundance was imported into gene-level abundance with the R package tximport.
Genes with low expression were identified and filtered out from further analysis if total read counts for a given gene across all samples was less than ten.
Regularized log transformation (rlog) was performed using the DESeq2 R package.
Differential gene expression analysis was also conducted using DESeq2.
Gene Set Enrichment Analysis (GSEA) software version 4.3.3 were used for pathway analysis.
RLOG normalized and transformed expression values were used for heirarchical clustering and plotting of heatmaps.
Assembly: GRCh38.p14
Supplementary files format and content: Salmon quant.sf files contain transcirpt level abundances.

source_name: Human TNBC Tumor

growth_protocol: The UTHSC Animal Care and Use Committee (IACUC) approved all protocols and methods following protocol #23-0432. All animals in the study were kept on a 12 hr light/dark cycle and fed a standard breeder’s chow diet. MDA-MB-231 cells were harvested in serum-free DMEM media and suspended into equal volumes of Matrigel (Product No. 354234, Corning®, Tewksbury, MA) for orthotopic mammary injection in N = 30 female NSG mice (12–13 weeks old). Five x 10^5 cells were injected in 100 µL into the 4th right mammary gland at a final Matrigel concentration of 4.5 mg/mL. The injected mice were palpated three times weekly until the tumor grew to a palpable size of 80–150 mm3 in volume using a digital caliper.

extract_protocol:
Total RNA was isolated from tumors using the RNeasy Mini Kit (#74104, Qiagen) according to the manufacturer’s instructions for the vehicle controls (n = 7) and the OCA-treated (n = 6) fresh-frozen samples. The integrity of the RNA was assessed using Agilent TapeStation, and samples with RIN > 6.0 were used.
Library prep was conducted at Azenta.
mRNA-seq libraries for the Illumina platform were generated and sequenced at Azenta using the Illumina HiSeq 2 × 150 bp configuration following the manufacturer’s protocol. ~350M raw paired-end reads per lane.

treatment_protocol: Mice with equivalent tumor size were randomly separated into 3 groups and that included vehicle (40% DMSO and 60% polyethylene glycol (PEG), n = 8), OCA (30 mg/kg, n = 7), or chemotherapy paclitaxel (“Ptax”, 10 mg/kg, n = 6) as a positive control. Ptax did not undergo RNAseq. The animals treated with vehicle or OCA were gavaged daily, and Ptax was administered thrice a week intraperitoneally until the endpoint. Tumor size was calculated using the formula (width2 × length/2). Body weights were recorded every other day. Mice were sacrificed at endpoint. Tumors were excised for ex vivo measurement of tumor volume and weight, photographed, and snap-frozen in liquid nitrogen.

value: Human TNBC Tumor

value: Triple negative breast cancer cells

value: NSG Immunocompetent Mouse

value: OCA


title: colorectal cancer tissue sample AUS2_756_T


title: mos11_cyt_FC1_rep3

description: UMIs in header


title: 4349


title: 4351


title: 4371


title: RNAseq-K562-siMAZ-Lib7-Nov2-2021_R1


title: colorectal cancer tissue sample AUS2_755_T3


title: mos11_cyt_FC1_rep2

description: UMIs in header


title: mos11_cyt_FC2_rep2

description: UMIs in header


title: RNAseq-K562-SiMAZ-IFNLib8-rep-2-Nov2-2021


title: colorectal cancer tissue sample AUS2_756_T2


title: mos11_cyt_FC2_rep1

description: UMIs in header


title: 4340


title: RNAseq-K562-Ctr-Lib5-rep-2-Nov2-2021


title: RNAseq-K562-Ctr-Lib5-Nov2-2021


title: 4347

description: treated with 40% DMSO and& 60% polyethylene glycol (PEG) orally every day

value: Vehicle


title: mos11_nuc_FC1_rep5

description: UMIs in header

value: nucleus


title: RNAseq-K562-Ctr-IFN-Lib6-rep-2-Nov2-2021


title: mos11_cyt_FC1_rep1

description: UMIs in header


title: RNAseq-K562-SiMAZ-IFNLib8-Nov2-2021


title: mos11_nuc_FC1_rep4

description: UMIs in header


title: RNAseq-K562-Ctr-IFN-Lib6-Nov2-2021


title: colorectal cancer tissue sample AUS2_755_T


title: Tx-mRNA-seq-HAP1-p-lib1-962021


title: colorectal cancer tissue sample AUS2_755_T2


title: 4345


title: mos11_nuc_FC1_rep3

description: UMIs in header


title: Tx-mRNA-seq-HAP1-p-IFN-lib2-962021


title: 4346


title: colorectal cancer tissue sample AUS2_754_T3


title: 4385


title: 4381


title: colorectal cancer tissue sample AUS2_754_T2


title: mos11_nuc_FC1_rep2

description: UMIs in header


title: 4348


title: colorectal cancer tissue sample AUS2_756_T3


title: Tx-mRNA-seq-HAP1-MZ-lib3-962021


title: colorectal cancer tissue sample AUS2_753_T


title: 4384


title: colorectal cancer tissue sample AUS2_753_T3


title: mos11_nuc_FC1_rep1

description: UMIs in header


title: 4379


title: Tx-mRAN-seq-HAP1-p-lib1-2-962021


title: Col-0_cyt_FC2_rep4

description: UMIs in header


title: colorectal cancer tissue sample AUS2_754_T


title: mos11_nuc_FC2_rep2

description: UMIs in header


title: Tx-mRNA-seq-HAP1-MZ-IFN-lib4-962021


title: colorectal cancer tissue sample AUS2_752_T2


title: colorectal cancer tissue sample AUS2_753_T2


title: E. coli O104:H4 rpoS ATG>ATA_transition_Rep3

city: Münster

first: Petya

last: Berger

address: Robert-Koch Straße 41

department: Institute of Hygiene

institute: University of Münster

description:
75 bp read length
rpoSATA_T3

data_processing:
quality trimming and adapter removal using cutadapt 2.10
poly A-tail removal using READemption 1.0.5
mapping of reads to E. coli O104:H4 using READemption 1.0.5 and segemehl 0.3.4
gene wise quantification (quantification of the number of reads overlapping with the locations of the annotation entries) using READemption 1.0.5
differential gene expression analysis based on the gene wise qunatification for  E. coli O104:H4 annotation using READemption 1.0.5 and DESeq2 1.39.0
Assembly: GCF_000299455.1
Supplementary files format and content: csv, gene_wise_quantifications_combined

organism: Escherichia coli

source_name: transition to stationary phase (OD600 = 3.0-3.4)

growth_protocol: Overnight cultures were diluted till OD600 of 0.005 in LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm to log growth phase (OD600 of 0.4 - 0.5) and transition to stationary phase (OD600 of 3 - 3.4) .

extract_protocol:
Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The concentration of the samples was determined with Qubit; efficiency of the gDNA removal was determined by qPCR and the RNA integrity was once more verified using the Agilent 2200 TapeStation.
Strand specific cDNA libraries were constructed by Vertis Biotechnologie AG (Freising, Germany). rRNA were depleted and RNA was fragmented using ultra sound. 3' sequencing adapter was ligated to 3'OH ends of fragmented RNA and M-MLV reverse transcriptase and the 3’ adapter as primer were used in the first strand cDNA synthesis step. After purification of the first strand cDNA, 5’ sequencing adapter was ligated to the 3’ end of anti-sense first-strand cDNA. cDNA was PCR amplified using proofreading enzyme, gel fractionated and the size fraction optimally suited for Illumina sequencing was selected.

treatment_protocol: After treatment with stop solution (5 % phenol/95 % ethanol), cells pellets were immediately lysed with cell lysis buffer (85 mg/mL lysozyme in TE buffer, pH 8). Trizol reagent was added and samples were stored at -20oC till the RNA isolation protocol was resumed.

tag: serotype

value: serotype O104:H4

tag: strain

value: strain LB226692

value: rpoS ATG>ATA


title: Tx-mRAN-seq-HAP1-MZ-lib3-2-962021


title: Col-0_cyt_FC2_rep3

description: UMIs in header

value: rosette

value: cytoplasm


title: Col-0_cyt_FC1_rep4

description: UMIs in header


title: Col-0_cyt_FC1_rep3

description: UMIs in header


title: Tx-mRAN-seq-HAP1-MZ-IFN-lib4-2-962021


title: Tx-mRAN-seq-HAP1-p-IFN-lib2-2-962021


title: E. coli O104:H4 rpoS ATG>ATA_transition_Rep2

description:
75 bp read length
rpoSATA_T2

value: transition to stationary phase (OD600 = 3.0-3.4)


title: E. coli O104:H4 _transition_Rep3

description:
75 bp read length
rpoSATA_L3

value: wild type


title: colorectal cancer tissue sample AUS2_752_T3

value: colorectal cancer tissue sample

value: no


title: colorectal cancer tissue sample AUS2_751_T3


title: colorectal cancer tissue sample AUS2_751_T


title: colorectal cancer tissue sample AUS2_752_T


title: E. coli O104:H4 _transition_Rep2

description:
75 bp read length
rpoSATA_L2


title: colorectal cancer tissue sample AUS2_751_T2


title: E. coli O104:H4 rpoS ATG>ATA_transition_Rep1

description:
75 bp read length
rpoSATA_T1


title: Col-0_cyt_FC2_rep2

description: UMIs in header


title: colorectal cancer tissue sample AUS2_750_T


title: Col-0_cyt_FC2_rep1

description: UMIs in header


title: BAT and Artery

city: Munich

first: Sabine

last: Steffens

address: Pettenkoferstrasse 9b

department: Clinical Pathobiochemistry

institute: Institute for Cardiovascular Prevention-LMU Klinikum

data_processing:
The reads were demultiplexed using deML and then filtered.
The reads were mapped to the mouse genome (mm10, GRCm38), and counted using zUMIs (version 2.5.5) with STAR.
Differential gene expression analysis was performed using DESeq2.
The characterization of enriched the molecular functions or pathways of differentially expressed genes (DEGs) was performed by using Gene Ontology in clusterProfiler.
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: BAT and Artery

extract_protocol:
The aortas (i.e., aortic arch to the iliac bifurcation) were isolated after perfusion with PBS and incubated with 10 mg/mL collagenase IV (Worthington) and 20 U/mL DNase I at 37°C for 40 min digestion, The interscapular brown adipose tissue (BAT) were collected, cut into small pieces and incubated with the digestion cocktail at 37°C for 30 min. The digested tissues were filtered through a 30-μm cell strainer and centrifuged to obtain single-cell suspensions. The single-cell suspensions were sorted using a BD FACSAria III Cell Sorter gated live CD45lowCD31highCD107ahigh cells as aortic endothelial cells, and live CD45-CD31+ as BAT endothelial cells. The sorted cells were deep-frozen in 2× TCL buffer (Qiagen) plus 1% beta-mercaptoethanol kept at -80°C until subsequent RNA extraction and library preparation.
Libraries were then constructed with the NEB Next Ultra II FS kit (E6177S, NEB) using the prime-seq specifications

value: BAT and Artery

value: endothelial

value: ApoE-/-


title: GD, pre-EX, subject 2

city: Tucson

first: Forrest

middle: Lee

last: Baker

state: Arizona

address: 1501 N. Cmapbell Ave CRC Building Room 5340

department: School of Nutritional Sciences and Wellness

institute: The University of Arizona

data_processing:
FastQ files were converted into expression matrices using the limma-voom workflow
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

value: Blood

value: GDs

value: PreEX


title: GD, during-ISO, subject 2

value: ISO


title: E. coli O104:H4 rpoS ATG>ATA_log_Rep2

description:
75 bp read length
O104_T2

source_name: log growth phase (OD600 = 0.4- 0.5)

value: log growth phase (OD600 = 0.4- 0.5)


title: colorectal cancer tissue sample AUS2_750_T3


title: colorectal cancer tissue sample AUS2_750_T2


title: GD, during-ISO, subject 1


title: GD, pre-ISO, subject 1

value: PreISO


title: Col-0_cyt_FC1_rep2

description: UMIs in header

source_name: rosette


title: E. coli O104:H4 _log_Rep3

description:
75 bp read length
O104_L3

value: serotype O104:H4

value: strain LB226692


title: Col-0_nuc_FC1_rep4

description: UMIs in header

value: rosette

value: nucleus


title: GD, during-EX, subject 1

value: EX


title: GD, pre-ISO, subject 2


title: Col-0_nuc_FC1_rep2

description: UMIs in header


title: Col-0_nuc_FC1_rep1

description: UMIs in header


title: Col-0_cyt_FC1_rep1

description: UMIs in header

value: cytoplasm


title: E. coli O104:H4 rpoS ATG>ATA_log_Rep3

description:
75 bp read length
O104_T3

value: rpoS ATG>ATA


title: colorectal cancer tissue sample AUS2_748_T

value: colorectal cancer tissue sample

value: no

value: T


title: colorectal cancer tissue sample AUS2_748_T2


title: colorectal cancer tissue sample AUS2_746_T3


title: E. coli O104:H4 rpoS ATG>ATA_log_Rep1

description:
75 bp read length
O104_T1


title: GD, during-EX, subject 2


title: Col-0_nuc_FC1_rep3

description: UMIs in header


title: GD, pre-EX, subject 1


title: E. coli O104:H4 _transition_Rep1

description:
75 bp read length
rpoSATA_L1

value: transition to stationary phase (OD600 = 3.0-3.4)

value: wild type


title: E. coli O104:H4 _log_Rep2

description:
75 bp read length
O104_L2


title: colorectal cancer tissue sample A286_AUS2_760


title: E. coli O104:H4 _log_Rep1

description:
75 bp read length
O104_L1


title: colorectal cancer tissue sample AUS2_746_T2


title: saline_SNI1_S33

status: Public on Apr 03 2024

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using htseq-counts software against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing counts

source_name: spinal cord

extract_protocol:
L3-6 DRGs were harvested from male C57Bl6/J mice (one mouse per sample) and flash frozen on dry ice. RNA was isolated using a TRIzol:Chloroform phase separation protocol.
RNA libraries were generated using the Stranded mRNA Prep Kit (Illumina).

value: spinal cord

tag: Sex

value: male

value: dorsal root ganglia

tag: group

value: SNI

tag: agent

value: saline


title: colorectal cancer tissue sample A287_AUS2_760

tag: tissue


title: saline_SNI2_S34


title: dystrophic mouse quadriceps, Cre-/mdx control, biological replicate 2

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

hyb_protocol: Labeled cDNA targets were hybridized to Affymetrix GeneChip® Clariom D array, Mouse for 16 h at 45 ⁰C rotating at 60 rpm

scan_protocol: The arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000.

data_processing: For gene expression analysis, arrays were normalized using Gene Level SST RMA algorithm in Expression Console and comparisons made in Transcriptome Analysis Console (Affymetrix).

source_name: MR flox/flox;mdx

label_protocol: 5.5 µg of cDNA was labeled and fragmented using the GeneChip WT PLUS reagent kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: Mouse quadriceps muscles dissected from 8-week-old dystrophic mice.

extract_protocol: RNA was isolated using TRIzol reagent (Life Technologies), according to manufacturer’s instructions. RNA concentration was determined spectrophotometrically using a NanoDrop 2000c (Thermo Scientific). Samples were DNAse treated using RQ1 DNAse (Promega) for 30 minutes at 37⁰C, reaction was stopped with a 25:24:1 phenol: chloroform: isoamyl alcohol mixture (Invitrogen) and centrifuged 5 minutes (14,000 x g; room temperature). A chloroform phase separation was performed; the aqueous layer was removed and ethanol (Fisher) precipitated. The pellet was washed (75% ethanol), centrifuged (14,000 x g, 10 minutes, 4⁰C), air dried (5 minutes) and re-suspended in autoclaved millipore filtered water. DNAse treated RNA concentration was determined spectrophotometrically and samples were stored at -80⁰C. Samples for microarray analysis were further purified using the RNeasy mini kit (Qiagen) RNA cleanup protocol and final RNA concentrations were determined. RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). A 100 ng aliquot of total mRNA was linearly amplified.

value: dystrophic mouse quadriceps

tag: genotype

value: Cre -/- MR flox/flox;mdx

value: 8 weeks

value: female


title: dystrophic mouse quadriceps, myeloid cell MRcko/mdx, biological replicate2

source_name: LysM-Cre+/MR flox/flox;mdx

value: myeloid cell mineralocorticoid receptor conditional knockout (LysM-Cre+/- MR flox/flox;mdx)


title: dystrophic mouse quadriceps, Cre-/mdx control, biological replicate 3


title: dystrophic mouse quadriceps, myeloid cell MRcko/mdx, biological replicate 3


title: saline_SNI3_S35


title: colorectal cancer tissue sample AUS2_746_T


title: dystrophic mouse quadriceps, Cre-/mdx control, biological replicate 1


title: dystrophic mouse quadriceps, myeloid cell MRcko/mdx, biological replicate 1


title: colorectal cancer tissue sample A285_AUS2_760


title: dystrophic mouse quadriceps, myofiber MRcko/mdx, biological replicate 3

source_name: MCK-Cre+/MR flox/flox;mdx

value: myofiber mineralocorticoid receptor conditional knockout (MCK-Cre+/- MR flox/flox;mdx)


title: dystrophic mouse quadriceps, myofiber MRcko/mdx, biological replicate 1


title: dystrophic mouse quadriceps, myofiber MRcko/mdx, biological replicate2


title: saline_sham3_S39

value: sham


title: saline_SNI4_S36


title: saline_sham1_S37


title: saline_sham4_S40


title: DMI_sham3_S19

value: DMI


title: saline_sham2_S38


title: DMI_SNI1_S21


title: DMI_SNI3_S23


title: DMI_SNI4_S24


title: DMI_sham4_S20


title: DMI_sham1_S17


title: Seronegative MG pre-treatment_9

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

library_source: transcriptomic single cell

data_processing:
Base calling and making fastq files were performed using software provided with the 10X Genomics Cell Ranger (cellranger mkfastq v3.0).
Count data were calculated from fastq files using software provided with the 10X Genomics Cell Ranger (cellranger count v3.0).
Count data were normalized to compare across samples using software provided with the 10X Genomics Cell Ranger (cellranger aggr v3.0).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include gene symbol and gene expression (read count) for each cell.

source_name: PBMC

extract_protocol: A single-cell RNA-seq library was prepared from PBMC using Chromium Single Cell 3' Library Kit v2 (10x Genomics) following the manufacturer’s instructions.

tag: disease state

value: Seronegative MG pre-treatment

value: PBMC


title: Seronegative MG post-treatment_9

value: Seronegative MG post-treatment

tag: cell type


title: Seronegative MG post-treatment_7


title: Seronegative MG post-treatment_6


title: Seronegative MG pre-treatment_7


title: Seronegative MG pre-treatment_8


title: Seronegative MG pre-treatment_6


title: Seronegative MG post-treatment_5


title: DMI_sham2_S18


title: Seronegative MG post-treatment_8


title: Seronegative MG post-treatment_4


title: Seronegative MG pre-treatment_4


title: Seronegative MG pre-treatment_5


title: Seronegative MG post-treatment_3


title: Seronegative MG pre-treatment_3


title: Seronegative MG pre-treatment_2


title: Seronegative MG pre-treatment_1


title: Seronegative MG post-treatment_2


title: Seronegative MG post-treatment_1


title: Seronegative MG pre-treatment_10


title: Seronegative MG post-treatment_10


title: Healthy control_8

value: Healthy control


title: Healthy control_7


title: Healthy control_5


title: Healthy control_9


title: Healthy control_6


title: N0S0(32.3)

type: genomic

city: Minneapolis

first: David

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC v2.0 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio, minfi

source_name: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.3

label_protocol: Standard Illumina Protocol

growth_protocol: Cell lines were maintained and passaged at 37°C with 5% CO2 in DMEM high glucose media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: Genomic DNA was extracted and purified from samples using Thermo Scientific GeneJET Genomic DNA Purification Kit according to standard instructions

treatment_protocol: No treatment was performed after cell line generation.

tag: cell line


title: Healthy control_4


title: Healthy control_3


title: Healthy control_2


title: AChR-positive MG_8

value: AChR-positive MG


title: AChR-positive MG_7


title: N0(32.3)

source_name: eihsc, NF1 deficient,  origin 32.3


title: Healthy control_10


title: Healthy control_1


title: AChR-positive MG_9


title: AChR-positive MG_4


title: AChR-positive MG_3


title: AChR-positive MG_2


title: N0S0(32.9)

source_name: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.9


title: N1S1(3.3)

source_name: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.3


title: N1S0(3.14)

source_name: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.14


title: AChR-positive MG_6


title: AChR-positive MG_1


title: AChR-positive MG_5


title: HUVEC p2

city: Chicago

first: Emily

last: Pinheiro

state: IL

address: 320 East Superior St

institute: Northwestern University

data_processing:
Reads were mapped to the GRCh38 reference human genome using Subread software
Gene expression levels were estimated using featureCounts function in the Subread software
Gene expression data was log2 normalized

source_name: cell line

extract_protocol:
RNA was extracted using 350 µL/well of TRIzol Reagent. RNA was then purified using the Direct-zol RNA MicroPrep kit, including on-column Dnase digestion to remove genomic DNA
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic strand-specific mRNA library protocol.

value: cell line

value: HUVEC

value: WT


title: N1E0(3.8)

source_name: eihsc, NF1 proficient; EED deficient,  origin 3.8


title: N1S1(3.1)

source_name: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.1


title: AChR-positive MG_10


title: HCAEC p2

value: HCAEC


title: N1S0(3.15)

source_name: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.15


title: 442333 MEC d6

value: hiPSC-MEC


title: N0E0(32.12)

source_name: eihsc, NF1 deficient; EED deficient,  origin 32.12


title: N0(32.1)

source_name: eihsc, NF1 deficient,  origin 32.1


title: 441227 MEC d6


title: 26-3 EC p2

value: hiPSC-EC


title: 25-3 EC p2


title: 19-3 EC p2


title: DMI_SNI2_S22

value: spinal cord

value: male

value: dorsal root ganglia

value: SNI


title: 26-3 CM d30

value: hiPSC-CM


title: 19-3 CM d30


title: 132-2B hiPSC

value: hiPSC


title: 19-3 hiPSC


title: 22-10 CM d30


title: 124-9 hiPSC


title: 25-3 CM d30


title: N1E0(3.9)


title: N0E0(32.13)

source_name: eihsc, NF1 deficient; EED deficient,  origin 32.13


title: 441228 MEC d6


title: N1S0(3.7)

source_name: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.7


title: Trauma T16

city: Gainesville

first: Rob

last: Maile

state: FL

department: Surgery

institute: University of Florida

hyb_protocol: Standard nanostring miRNA hybridisation protocols.

data_processing: nsolver v3

label: NanoString

source_name: peripheral blood plasma exosomes

extract_protocol: Collected peripheral blood was centrifuged at 2,000g for 30 minutes for plasma separation. Exosomes were isolated from plasma with the Invitrogen Total Exosome Isolation Kit and RNA was isolated using a miRNeasy Mini Kit


title: Trauma T15

label_protocol: Standard nanostring miRNA hybridisation protocols.


title: N0S0(32.4)

source_name: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.4


title: Trauma T14

value: female


title: Trauma T13


title: Trauma T11


title: Trauma T12


title: N0(32.2)

source_name: eihsc, NF1 deficient,  origin 32.2


title: Trauma T10


title: N1S1(3.2)

source_name: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.2


title: Trauma T8


title: Trauma T6


title: Trauma T9


title: Trauma T7


title: Trauma T4


title: Trauma T2


title: Trauma T3


title: Healthy H8


title: Sample_734_1

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: Sodium bisulfite treated gDNA was amplified and enzymatically fragmented before hybridization to the microarray. After washing and staining, the microarray was scanned using the iScan device (Illumina).

scan_protocol: Infinium MethylationEPIC microarray platform

data_processing:
Raw red/green channel *.idat files were imported into R using the RnBeads packages for initial quality  control, data normalization (SWAN) and extraction of β-values representing the percentage of  methylation for each CpG site on the microarray. SNP-enriched, cross-reactive, non-CpG  and sex chromosome specific probes were removed from further analyses. Differential methylation  was calculated using limma and RnBead´s rank cutoff. The top 500 differentially methylated  CpG sites were used for further analyses.
Normalized Average Beta

label: cy3, cy5

label_protocol: 500ng of gDNA was sodium bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen, Germantown, MD, USA), processed using the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, CA, USA) and processed for microarray hybridization using Infinium MethylationEPIC Kit.

extract_protocol: Genomic DNA (gDNA) was extracted using the Maxwell FFPE Plus Kit (Promega, Madison, Wisconsin, USA).

value: NR

tag: localisation


title: Trauma T1


title: Sample_550_2


title: Healthy H7


title: Healthy H5


title: Healthy H6


title: Healthy H4


title: Sample_38_1


title: Sample_250_1


title: Healthy H3


title: Sample_575


title: Sample_36_2


title: Healthy H2


title: Sample_255


title: Healthy H1


title: Sample_85

value: R


title: Trauma T5


title: Sample_248


title: Sample_555


title: Sample_243


title: Sample_71


title: Sample_783


title: Sample_797


title: Sample_553


title: Sample_782


title: Sample_568


title: Sample_543


title: Sample_574


title: Sample_249


title: Sample_83


title: Sample_76


title: Sample_247


title: Sample_91


title: Sample_551


title: Sample_734_2


title: Sample_93


title: Sample_554_2


title: Sample_541


title: Sample_36_1


title: Sample_561


title: Sample_242_1


title: Sample_205_1


title: Sample_38_2


title: Sample_253


title: Sample_252


title: Sample_36_4


title: Sample_206


title: Sample_203


title: Sample_191


title: Sample_194


title: Sample_192


title: Sample_204


title: Sample_78


title: Sample_77


title: Sample_92


title: Sample_74


title: Sample_554_1

value: LN


title: Sample_73


title: Sample_37


title: Sample_550_1


title: Sample_72


title: Sample_35


title: Sample_36_3


title: Sample_621


title: Sample_250_2


title: Sample_205_2


title: Sample_622


title: Sample_775


title: Sample_619


title: Sample_623


title: Sample_617


title: Sample_242_2


title: Sample_571


title: Sample_618


title: Sample_565


title: Sample_620


title: Sample_84


title: Sample_570


title: Sample_558


title: Sample_557


title: Sample_556


title: Sample_552


title: Sample_549


title: Sample_75


title: Sample_544


title: Sample_86


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.3, ChiP H3K27me3

data_processing:
Aligning via BWA
Quality filtering via picard
Wig file generation via bedtools
Peak calling with MACS2 for narrow Peaks, which generates encodePeak file
Peak calling with SICER for broad Peaks which generates islands-summary file
Read quality analysis via fastqc
Assembly: Homo sapiens hg38
Supplementary files format and content: Wig, encodePeak (for narrow peaks), islands-summary (tab-delimited file for broad peaks)

extract_protocol:
Lysed cells were treated with 100 gel units of MNase in MNase digestion buffer (20 min, 37°C, continuous thermal mixing). Following sonication in Diagenode Bioruptor pico (Denville, NJ), supernatant was subjected to ChIP with antibody overnight
Chip and library preparation were performed following the description of Caride et al. (2023) BMC Genomic. Titration-based normalization of antibody amount improves consistency of ChIP-seq experiments

value: Engineered immortalized human Schwann cells

value: NF1 proficient; SUZ12 proficient

value: anti-H3K27me3 antibody (CST, Cat. #9733)


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.4, ChiP none

value: cell line

value: NF1 deficient; SUZ12 deficient


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.2, ChiP H3K27me3


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.1, ChiP H3K27me3


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.3, ChiP H3K27ac

value: anti-H3K27ac (CST, cat # 8173)


title: Sample_573


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.2, ChiP none


title: eihsc, NF1 proficient; EED deficient, origin 3.9, ChiP H3K27ac

value: NF1 proficient; EED deficient


title: Sample_566


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.1, ChiP none


title: eihsc, NF1 proficient; EED deficient, origin 3.9, ChiP H3K27me3


title: Sample_560


title: eihsc, NF1 proficient; EED deficient, origin 3.8, ChiP H3K27ac


title: Sample_559


title: eihsc, NF1 proficient; EED deficient, origin 3.8, ChiP none


title: eihsc, NF1 deficient, origin 32.3, ChiP H3K27me3

value: NF1 deficient


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.3, ChiP none


title: eihsc, NF1 proficient; EED deficient, origin 3.9, ChiP none


title: eihsc, NF1 deficient, origin 32.3, ChiP none


title: eihsc, NF1 deficient; EED deficient, origin 32.13, ChiP H3K27ac

value: NF1 deficient; EED deficient


title: eihsc, NF1 deficient, origin 32.2, ChiP H3K27me3


title: eihsc, NF1 deficient, origin 32.2, ChiP H3K27ac


title: eihsc, NF1 deficient, origin 32.1, ChiP H3K27me3


title: eihsc, NF1 deficient, origin 32.1, ChiP H3K27ac


title: eihsc, NF1 proficient; EED deficient, origin 3.8, ChiP H3K27me3


title: eihsc, NF1 deficient, origin 32.3, ChiP H3K27ac


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.1, ChiP H3K27ac


title: eihsc, NF1 deficient; EED deficient, origin 32.12, ChiP H3K27me3


title: eihsc, NF1 deficient; EED deficient, origin 32.13, ChiP none


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.9, ChiP H3K27ac


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.9, ChiP H3K27me3


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.9, ChiP none


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.4, ChiP H3K27me3


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.4, ChiP H3K27ac


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.3, ChiP none


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.7, ChiP none

value: NF1 proficient; SUZ12 deficient


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.7, ChiP H3K27ac


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.15, ChiP none


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.15, ChiP H3K27me3


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.3, ChiP H3K27ac


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.14, ChiP H3K27me3


title: eihsc, NF1 deficient; SUZ12 deficient, origin 32.3, ChiP H3K27me3


title: eihsc, NF1 deficient, origin 32.2, ChiP none


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.15, ChiP H3K27ac


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.14, ChIP none


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.14, ChiP H3K27ac


title: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.15, tech rep 2

data_processing:
Quality and adapter trimming via Trimmomatic
Mapping via RNAStar to ensembl annotation GRCh38
Gene Count Quantification via subread
Read quality analysis via fastqc
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested from cells using Qiagen RNEasy mini purification kits and subjected to TURBO DNAse to remove any residual genomic DNA contamination.
TruSeq stranded mRNA


title: eihsc, NF1 deficient, origin 32.1, ChiP none


title: eihsc, NF1 deficient; EED deficient, origin 32.13, ChiP H3K27me3


title: eihsc, NF1 deficient; EED deficient, origin 32.12, ChiP none


title: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.4, tech rep 1


title: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.4, tech rep 2


title: eihsc, NF1 proficient; SUZ12 deficient, origin 3.7, ChiP H3K27me3


title: eihsc, NF1 deficient,  origin 32.2, tech rep 2


title: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.7, tech rep 2


title: eihsc, NF1 deficient,  origin 32.2, tech rep 1


title: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.7, tech rep 1


title: eihsc, NF1 deficient,  origin 32.1, tech rep 2


title: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.1, tech rep 1


title: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.1, tech rep 2


title: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.3, tech rep 1


title: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.2, tech rep 2


title: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.2, tech rep 1


title: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.14, tech rep 1


title: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.3, tech rep 1


title: eihsc, NF1 proficient; SUZ12 proficient, origin 3.2, ChiP H3K27ac


title: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.15, tech rep 1


title: eihsc, NF1 deficient,  origin 32.3, tech rep 1


title: eihsc, NF1 deficient,  origin 32.3, tech rep 2


title: eihsc, NF1 proficient; EED deficient,  origin 3.9, tech rep 2


title: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.3, tech rep 2


title: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.9, tech rep 1


title: eihsc, NF1 proficient; EED deficient,  origin 3.8, tech rep 1


title: eihsc, NF1 proficient; EED deficient,  origin 3.8, tech rep 2


title: eihsc, NF1 deficient; EED deficient,  origin 32.12, tech rep 1


title: eihsc, NF1 proficient; SUZ12 proficient,  origin 3.3, tech rep 2


title: eihsc, NF1 proficient; EED deficient,  origin 3.9, tech rep 1


title: eihsc, NF1 deficient; EED deficient,  origin 32.12, tech rep 2


title: eihsc, NF1 deficient,  origin 32.1, tech rep 1


title: eihsc, NF1 deficient; SUZ12 deficient,  origin 32.9, tech rep 2


title: eihsc, NF1 deficient; EED deficient, origin 32.12, ChiP H3K27ac


title: eihsc, NF1 deficient; EED deficient,  origin 32.13, tech rep 2


title: eihsc, NF1 proficient; SUZ12 deficient,  origin 3.14, tech rep 2


title: Cal27 cells transfected with plasmids contained ACLY-2

city: Beijing

first: Qiaoshi

last: Xu

address: No. 4 Tian Tan Xi Li, Dongcheng District

institute: Beijing Stomatological Hospital, Capital Medical University

data_processing:
The image data measured by the high-throughput sequencer are convertedintosequence data (reads) by CASAVA base recognition. Raw data (rawreads) of fastqformat were firstly processed through in-house perl scripts. In this step, cleandata(clean reads) were obtained by removing reads containing adapter, reads containingNbase and low quality reads from raw data. At the same time, Q20, Q30 andGCcontent the clean data were calculated. All the downstream analyses were basedonthe clean data with high quality
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the reference genome usingHisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generateadatabase of splice junctions based on the gene model annotation file and thus a bettermapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene. FPKM, expected number of Fragments PerKilobase of transcript sequence per Millions base pairs sequenced, considers theeffect of sequencing depth and gene length for the reads count at the same time, andiscurrently the most commonly used method for estimating gene expression levels.
Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed usingtheDESeq2 R package (1.20.0). DESeq2 provide statistical routines for determiningdifferential expression in digital gene expression data using a model based onthenegative binomial distribution. The resulting P-values were adjusted usingtheBenjamini and Hochberg’s approach for controlling the false discovery rate. padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantlydifferential expression
Assembly: hg38
Supplementary files format and content: Tab-delimited txt file includes raw count for each sample

source_name: human head and neck squamous cell carcinoma

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, USA) supplemented with 10% exosome-depleted fetal bovine serum (FBS; A27208-03, Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin at 37 °C in a standard humidified atmosphere of 5% CO2.

extract_protocol:
RNA was extracted fromcells using TRIzol reagent (Invitrogen).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized usingrandom hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseHtodegrade the RNA. Second strand cDNA synthesis was subsequently performed usingDNA Polymerase I and dNTP. Remaining overhangs were converted into blunt endsvia exonuclease/polymerase activities. After adenylation of 3’ ends of DNAfragments, Adaptor with hairpin loop structure were ligated to prepare forhybridization. In order to select cDNA fragments of preferentially 370~420 bpinlength, the library fragments were purified with AMPure XP system(BeckmanCoulter, Beverly, USA). Then PCR amplification, the PCR product was purifiedbyAMPure XP beads, and the library was finally obtained

treatment_protocol:
HNSCC cells were treated with 100 ng/ml IL-8 for 24h
HNSCC cells were transfected with plasmids containing ACLY or vector

value: Malignant cells

tag: treatment


title: Cal27 cells transfected with plasmids contained ACLY-3

value: human head and neck squamous cell carcinoma


title: Cal27 cells transfected with plasmids contained ACLY-1


title: Cal27 cells transfected with vector plasmids-2


title: Cal27 cells transfected with vector plasmids-1


title: HN6 cells transfected with plasmids contained ACLY-1


title: HN6 cells transfected with plasmids contained ACLY-2


title: HN6 cells transfected with plasmids contained ACLY-3


title: HN6 cells transfected with vector plasmids-3


title: HN6 cells transfected with vector plasmids-2


title: HN6 cells transfected with vector plasmids-1


title: HN4 cells transfected with plasmids contained ACLY-3


title: HN4 cells transfected with plasmids contained ACLY-2


title: HN4 cells transfected with vector plasmids-3


title: HN4 cells transfected with vector plasmids-2


title: Yak_dsx_neurons

city: Philadelphia

first: Justin

last: Walsh

state: PA

address: 3740 Hamilton Walk

institute: University of Pennsylvania

description:
10X Genomics
Global_Trimmed_MelYak.Rds
TN1OnlyMelYak.Rds

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using CellRanger software v7.1.0
Assembly: GCA_000001215.4
Assembly: GCA_016746365.2
Supplementary files format and content: tab-separated value files, matrix files, and Rds files

organism: Drosophila yakuba

source_name: neurons

extract_protocol:
The central nervous system of approximately 100 doublesex-GAL4 x UAS-nls::tdTomato flies were dissected in ice cold Schneider's medium and digested in a solution containing Liberase DH for 45 mins. The tissue was washed with Schneider's medium and broken apart via pipetting before FACS sorting out the tdTomato+ cells.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol, 10X Genomics)

value: neurons

value: male

tag: age

value: 4-8 day old adults


title: HN4 cells transfected with vector plasmids-1


title: Cal27 cells treated with IL-8-2

value: Cal27 cells treated with IL-8


title: eihsc, NF1 deficient; EED deficient,  origin 32.13, tech rep 1


title: Cal27 cells treated with IL-8-3


title: Cal27 cells, without treatment-2

value: Cal27 cells, without treatment


title: Cal27 cells, without treatment-1


title: Cal27 cells treated with IL-8-1


title: Cal27 cells transfected with vector plasmids-3


title: HN6 cells treated with IL-8-2

value: HN6 cells treated with IL-8


title: HN6 cells treated with IL-8-1


title: HN6 cells, without treatment-3

value: HN6 cells, without treatment


title: HN6 cells, without treatment-1


title: HN6 cells, without treatment-2


title: HN4 cells treated with IL-8-2

value: HN4 cells treated with IL-8


title: HN4 cells, without treatment-2

value: HN4 cells, without treatment


title: HN4 cells, without treatment-3


title: HN4 cells, without treatment-1


title: HN4 cells treated with IL-8-1


title: 8992-RP-0074

city: Frederick

first: Himanshu

last: Goel

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description: Treatment

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Homo sapiens (108) transcriptome downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Assembly: Homo sapiens (version 108)
Supplementary files format and content: tab-delimited text files, including abundance measurements

source_name: Liver

extract_protocol:
Total RNA was isolated from all human liver samples obtained from Sekisui XenoTech.These RNA samples were submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for quantity and quality check before sequencing.
VUMC successfully identified and purchased from a supplier, Sekisui XenoTech, these 5 collections (lots) of pooled plateable cryopreserved human hepatocytes with 3 lots composed of cells derived from 10 different donors per lot and 2 lots derived from 5 different donors per lot. Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: in vitro hepatocytes

value: Liver

tag: duration

tag: dose

value: High (12 mM Thioacetamide)


title: 8992-RP-0075

description: Treatment


title: 8992-RP-0070

description: Treatment

value: Low (1.33 mM Thioacetamide)


title: HN4 cells transfected with plasmids contained ACLY-1


title: 8992-RP-0073

description: Treatment


title: 8992-RP-0072

description: Treatment


title: 8992-RP-0071

description: Treatment


title: Cal27 cells, without treatment-3


title: HN6 cells treated with IL-8-3


title: 8992-RP-0069

description: Treatment


title: 8992-RP-0067

description: Treatment


title: 8992-RP-0066

description: Treatment


title: 8992-RP-0065

description: Control

value: Vehicle


title: HN4 cells treated with IL-8-3


title: 8992-RP-0061

description: Control


title: 8992-RP-0068

description: Treatment


title: 8992-RP-0062

description: Control


title: 8992-RP-0060

description: Treatment


title: 8992-RP-0063

description: Control


title: 8992-RP-0058

description: Treatment


title: 8992-RP-0064

description: Control


title: 8992-RP-0057

description: Treatment


title: 8992-RP-0059

description: Treatment


title: 8992-RP-0056

description: Treatment


title: Saline, Rep3

city: Charlottesville

first: Joshua

last: Danoff

state: VA

address: 485 McCormick Road

institute: University of Virginia

description:
Lib32_S16
IOL_GeneCounts.csv
IOL_IsoformCounts.csv

data_processing:
Trimgalore was used for adapter trimming and quality control
Kallisto was used for pseudo-alignment and quantification followed by DESeq2 for gene-level differential expression
STAR2 and Stringtie were used for splice-aware alignment and subsequent novel transcript identification, followed by IsoformSwitchAnalyzeR for differential transcript usage
Assembly: MicOch v1.0, Ensembl release version 96
Supplementary files format and content: IOL_GeneCounts.csv (kallisto-based gene-level quantification)
Supplementary files format and content: IOL_IsoformCounts.csv (novel transcript quantification)
Supplementary files format and content: MicOch_stringtie_merged_transcripts.gtf (StringTie novel transcript assembly)

organism: Microtus ochrogaster

source_name: nucleus accumbens

extract_protocol:
Qiagen AllPrep
NEBNext Ultra Directional RNA with magnetic mRNA isolation

value: nucleus accumbens

value: Saline


title: 8992-RP-0054

description: Treatment


title: 8992-RP-0055

description: Treatment


title: Saline, Rep2

description:
Lib30_S14
IOL_GeneCounts.csv
IOL_IsoformCounts.csv


title: Saline, Rep1

description:
Lib29_S13
IOL_GeneCounts.csv
IOL_IsoformCounts.csv


title: Oxytocin, Rep2

description:
Lib28_S12
IOL_GeneCounts.csv
IOL_IsoformCounts.csv

value: Oxytocin


title: 8992-RP-0053

description: Treatment


title: Oxytocin, Rep1

description:
Lib27_S11
IOL_GeneCounts.csv
IOL_IsoformCounts.csv


title: 8992-RP-0050

description: Control


title: 8992-RP-0052

description: Treatment


title: 8992-RP-0049

description: Control


title: 8992-RP-0051

description: Treatment


title: WT_Rep3

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

institute: IPBLN-CSIC

description: Trypanosomes (wild-type) were isolated from the blood of infected mice at 5 dpi

data_processing:
The miARma‐Seq pipeline by Andrés-León et al. 2016 (PMID: 27167008) was used for all analyses
First, it uses fastqc to perform quality control, then alignment proceeds with hisat2
Quantification of the aligned reads was performed by featureCounts
All differential gene expression analyses over the counts were performed using edgeR, as well as normalization and computation of RPKM counts
Genes transcripts fromTbSUMOallKR versus WT parasites with [log2FC] ≥ 0.58 (log2 of Fold Change) and a pValue ≤ 0.05 were considered differentially expressed
Assembly: Trypanosoma brucei Lister Strain 427 2018 (TriTrypDB-61)
Supplementary files format and content: The processed data files are tables (xls) containing the quantification of the expression in the samples (RPKM values) and the output of the differential gene expression analyses by edgeR (log2 Fold Change and P-values)

organism: Trypanosoma brucei

source_name: blood of infected mice

growth_protocol: Female BALB/c mice were inoculated intraperitoneally with 5,000 parasites obtained from axenic culture in exponential growth. Two mice were used

extract_protocol:
Trypanosomes were isolated from the blood of infected mice at 5 dpi (peak of higher parasitemia). Total RNA was isolated from parasites of the first peak of parasitemia, obtained by differential centrifugation. Extraction and sequencing of at least two independent biological samples for each sample proceeded as described by Saura et al. (PMID: 31693280).
Libraries from mRNA were prepared using the Illumina stranded mRNA Prep Ligation kit (Illumina, CA, USA) according to the manufacturer’s protocol. Quality (RNA integrity) and size distribution of indexed mRNA libraries were validated through Bioanalyzer High Sensitivity DNA assay in a Bioanalyzer 2100. Concentration was measured on the Qubit fluorometer. Final libraries were pooled in an equimolecular manner and then diluted and denatured as recommended

treatment_protocol: Parasitemias were obtained by counting cell number in blood with 0,83 %w/v ammonium chloride by quadruplicate in a Neubauer chamber under the light microscope (×400). They ranged from 3,4E8 to 1,46E9 in the two mice

tag: time

value: 5 dpi

value: wild-type (WT)

tag: replicate

value: replicate 2

tag: read length


title: WT_Rep2

value: replicate 1


title: SUMO_chain_mutant_Rep2

description: Trypanosomes (SUMO chain mutant) were isolated from the blood of infected mice at 5 dpi

value: SUMO chain mutant (TbSUMOallKR)


title: SUMO_chain_mutant_Rep3


title: 8992-RP-0047

description: Control

tag: strain


title: 8992-RP-0048

description: Control


title: 8992-RP-0045

description: Treatment


title: 8992-RP-0046

description: Control


title: 8992-RP-0044

description: Treatment


title: Oxytocin, Rep3

description:
Lib31_S15
IOL_GeneCounts.csv
IOL_IsoformCounts.csv


title: 8992-RP-0041

description: Treatment


title: 8992-RP-0043

description: Treatment


title: 8992-RP-0040

description: Treatment


title: 8992-RP-0042

description: Treatment


title: 8992-RP-0039

description: Treatment


title: 8992-RP-0037

description: Treatment


title: 8992-RP-0038

description: Treatment


title: 8992-RP-0034

description: Control


title: 8992-RP-0036

description: Treatment


title: 8992-RP-0032

description: Control


title: 8992-RP-0035

description: Control


title: 8992-RP-0033

description: Control


title: 8992-RP-0031

description: Control


title: 8992-RP-0029

description: Treatment


title: 8992-RP-0028

description: Treatment


title: 8992-RP-0030

description: Treatment


title: T lymphocytes, sWAT infiltrating, obese individual 11

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

hyb_protocol: Labeled cDNAs were hybridized onto Clariom D Human Assay Microarrays, which include probe sets enabling transcriptome-wide gene- and exon-level expression profiling (Affymetrix, ThermoFisher Scientific).

scan_protocol: The arrays were scanned using the GeneChip 3000 system (Affymetrix).

data_processing: Transcript Analysis Console (TAC v4.0; Affymetrix, ThermoFisher) software was used for initial hybridization quality assessment and data inspection. All statistical analyses of microarray data were performed using R-based software environment. Quality control was done with the array QualityMetrics package. Background correction, probe set summarization and normalization were performed with the oligo package using the most up to date annotation in Bioconductor. Subsequent differential expression analysis was performed using the Limma package at the gene level taking the average of all probe sets for a particular gene and focusing on known genes (with assigned gene symbols).

source_name: T-lymphocytes from white adipose tissue

label_protocol: CD3+ cell extracted RNA was reverse transcribed into cDNA and amplified and biotinylated by in vitro transcription (MultiScribe TaqMan Reverse Transcription Reagents; ThermoFisher Scientific, Waltham, MA, USA).

growth_protocol: The study was approved by the Ethical Committee of the Hospital Germans Trias i Pujol (Badalona, Spain) and follow the guidelines of Helsinki convention. Participants of both Cohorts 1 and 2 gave their written informed consent before clinical data collection.Two different cohorts of patients were enrolled in this study. All patients were evaluated by the same endocrinologist (S.P.) following the institutional protocol for bariatric surgery between October 2015 and September 2021, according to criteria for bariatric surgery formulated in Spanish Position Statement between Obesity, Endocrinology, Diabetes and Surgery Societies. For Cohort 1, 11 patients with obesity (BMI>35 kg/m2) and different metabolic status were enrolled, and vWAT and sWAT from the same patient were collected on occasion of bariatric surgery. For Cohort 2, 27 patients with or without severe obesity (BMI>35 kg/m2 or BMI<27 kg/m2, respectively) were enrolled; for individuals with obesity, they attended to bariatric surgery, while for normal-weight individuals on occasion of consultation/minor surgery. Then, vWAT and sWAT were collected during the surgical procedures. The inclusion criterion for individuals with obesity was exhibiting a BMI higher than 35 kg/m2. Exclusion criteria for all cohorts were having active infectious or inflammatory pathologies other than those related to obesity and treatment with immunosuppressant drugs, since these conditions could alter the results of the study.

extract_protocol: Total RNA was then extracted using affinity column-based methodology suitable for small amounts of biological material (NucleoSpin RNA XS; Mecherey-Nagel, Duren, Germany). RNA yield and purity were determined by spectrophotometry and RNA integrities were assessed with the Nano 6000 assay on Agilent's 2100 Bioanalyzer. Samples with RNA integrity number (RIN) values mostly above 6.7 were used as input for subsequent microarray gene expression profiling assays.

treatment_protocol: vWAT and sWAT samples (n = 22 in total) were obtained from these 11 patients from Cohort 1 during bariatric surgery. Fresh WAT collected during surgeries was transferred into two 50 mL tubes containing a 2% fetal bovine serum (FBS) in phosphate saline buffer (PBS) solution and placed on separate multiwell plate wells submerged in collagenase and Hank's Balanced Salt Solution (pH=7.1). The tissue was then minced into small pieces followed by several centrifugation and supernatant removal steps as previously published (19,20). CD3+ cells were then labeled with anti-CD3+ MicroBeads and magnetically separated from the unlabeled cells by a magnetic-activated cell sorting (MACS) Column supplied by Miltenyi Biotec (Miltenyi Biotec S.L Madrid). Briefly, the cell suspension was centrifuged at 300 x g for 10 min and the supernatant was completely discarded. Second, the pellet was resuspended in 82 µL of MACS buffer and 2 µL were diluted by adding 18 µl of MACS buffer and reserved at 4º C to evaluate percentage of CD3+ cells. Then, 20 µL of CD3+ MicroBeads were added to 80 µL of cell suspension, mixed and incubated for 15 min in ice. Next, the cells were washed by adding 2 mL of MACS buffer and centrifugated at 300 g for 10 minutes at 4ºC. Then the pellet was resuspended in 500 µL of MACS buffer and maintained in ice. Meanwhile, the separation column was prepared. For this, the LS column was placed in the magnetic field, on the MidiMACS™ Separator and rinsed with 3 mL of MACS buffer. Once the column reservoir was empty, the cell suspension was added into the column. When all the suspension passed, the column was washed by adding 3 mL of MACS buffer, twice. After that, the column was removed from the magnetic field, and placed onto a new 15 mL conical tube (collection tube). Then, 5 mL of MACS buffer was added and the fraction with the magnetically labeled cells was immediately flushed out applying the plunger supplied with the column. 20 µL of the eluted fraction was reserved in ice. Next, the CD3+ fraction of cells was centrifuged at 300 g for 7 min at 4º C, 4 mL of the supernatant was discarded, and the pellet was resuspended in the remaining volume, which was transferred into 1.5 mL conical tube and centrifuged at 11000g for 5 min, the resulting pellet was used to perform RNA extraction. The reserved aliquots from sWAT and vWAT were labeled to quantify the viability and the number of infiltrated CD3+ cells, respectively. For this purpose, 10 µL of cell sample were mixed with 48 µL of MACS Buffer, 2 µL of 7-AAD and 0.5 µL of CD3+, the prepared mix was incubated in darkness for 10 min and then 10 µL of Counting beads were added. Isolated T-cells were detected by the flow cytometer FACSCanto II by BD Biosciences. The optic consists of an excitation source and a three-laser system: blue (488 nm, air-cooled, 20-mV solid state), red (633 nm, 17-mV HeNe) and violet (405 nm, 30-mV solid state) allowing measurement of 8 parameters (FSC, SSC and 6 fluorescence detectors) with carrousel acquisition option for tubes. For quantification analysis the FACSDiva software were used, and FlowJo Software (Tree Star Inc.) was used for the graphs and the gating strategy. Cells are being separated based on their size and fluorescence. Viability, percent, and concentration (cells/μL) of T-cells (CD3+) in each tissue (vWAT and sWAT) was measured at the flow cytometer.

tag: gender

value: female

value: subcutaneous white adipose tissue (sWAT)

value: T lymphocytes /CD3+

tag: health status

value: Obese

tag: individual

value: Individual 11

tag: batch


title: T lymphocytes, sWAT infiltrating, obese individual 10

value: male

tag: tissue

value: Individual 10


title: T lymphocytes, vWAT infiltrating, obese individual 8

value: visceral white adipose tissue (vWAT)

value: Individual 8


title: 8992-RP-0026

description: Treatment

value: in vitro hepatocytes

value: Liver

value: High (12 mM Thioacetamide)


title: 8992-RP-0025

description: Treatment

value: Low (1.33 mM Thioacetamide)


title: MKN74.Hp_3

city: Porto

first: Marina

last: Leite

state: Porto

address: Rua Alfredo Allen, 208

country: Portugal

institute: i3S - Instituto de Investigação e Inovação em Saúde

data_processing:
Sequencing data were analyzed primarily within the Torrent Suite™ software using the AmpliSeq™ plug-in according to manufacturer's instructions. Raw sequencing reads (FASTQ files) were aligned in the Torrent Mapping Alignment Program (TMAP) against the reference sequence set containing all transcripts. targeted by the AmpliSeq kit.
Assembly: aligned to hg19 AmpliSeq Transcriptome ERCC v1
Supplementary files format and content: tab-delimited text files include Raw Count values for each Sample

source_name: Helicobacter pylori-infected cells

growth_protocol: For in vitro challenge conditions, MKN74 cells were seeded in 12-well plates (300,000 cells) with antibiotic-free RPMI medium supplemented with stable glutamine and 10% of heat-inactivated fetal bovine serum, at 37 °C under a 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted from MKN74 co-cultures using the SPLIT RNA Extraction Kit (Lexogen GmbH, Vienna, Austria). 100 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Ion AmpliSeq™template preparation kit in the Ion Chef™ system, following manufacturer's protocols.

treatment_protocol: Twenty-four hours after seeding, a fresh antibiotic-free medium was added and MKN74 cells were challenged with saline (control), OMVs and H.pylori

value: Stomach gastric cell line

value: Infected


title: 8992-RP-0024

description: Treatment


title: T lymphocytes, sWAT infiltrating, obese individual 7

value: Individual 7


title: T lymphocytes, vWAT infiltrating, obese individual 6

value: Individual 6


title: T lymphocytes, sWAT infiltrating, obese individual 6


title: 8992-RP-0027

description: Treatment


title: T lymphocytes, vWAT infiltrating, obese individual 10


title: MKN74.Hp_1


title: T lymphocytes, vWAT infiltrating, obese individual 9

value: Individual 9


title: T lymphocytes, sWAT infiltrating, obese individual 8

value: female

value: subcutaneous white adipose tissue (sWAT)


title: T lymphocytes, vWAT infiltrating, obese individual 5

value: T lymphocytes /CD3+

value: Obese

value: Individual 5


title: T lymphocytes, vWAT infiltrating, obese individual 7


title: T lymphocytes, sWAT infiltrating, obese individual 4

value: Individual 4


title: 8992-RP-0022

description: Treatment


title: 8992-RP-0023

description: Treatment


title: T lymphocytes, sWAT infiltrating, obese individual 3

value: Individual 3


title: T lymphocytes, vWAT infiltrating, obese individual 3

value: visceral white adipose tissue (vWAT)


title: MKN74.OMVs_6

source_name: Cells exposed to Helicobacter pylori-derived OMVs

value: OMVs treated


title: T lymphocytes, sWAT infiltrating, obese individual 2

value: Individual 2


title: MKN74.OMVs_5


title: T lymphocytes, sWAT infiltrating, obese individual 5


title: 8992-RP-0020

description: Control

value: in vitro hepatocytes

value: Liver

value: Vehicle


title: MKN74.OMVs_4

value: Stomach gastric cell line


title: 8992-RP-0021

description: Treatment

value: Low (1.33 mM Thioacetamide)


title: MKN74.OMVs_3


title: T lymphocytes, vWAT infiltrating, obese individual 1

value: male

value: Individual 1


title: 8992-RP-0019

description: Control


title: T lymphocytes, sWAT infiltrating, obese individual 1


title: T lymphocytes, sWAT infiltrating, obese individual 9

value: Individual 9


title: T lymphocytes, vWAT infiltrating, obese individual 11

value: female

value: Individual 11


title: T lymphocytes, vWAT infiltrating, obese individual 4

value: T lymphocytes /CD3+

value: Obese


title: MKN74.OMVs_1


title: 8992-RP-0018

description: Control


title: MKN74.OMVs_2


title: MKN74_3

source_name: Saline-treated cells

value: Control


title: 8992-RP-0017

description: Control


title: 8992-RP-0015

description: Treatment

value: High (12 mM Thioacetamide)


title: MKN74_2


title: 8992-RP-0016

description: Control


title: 8992-RP-0014

description: Treatment


title: MKN74_1


title: 8992-RP-0013

description: Treatment


title: Paerugionsa Capture Rep3

city: Bethesda

first: Pedro

middle: J

last: Batista

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

description: WT_Paeruginosa_MTSEA-Capture_collated_processed.csv

data_processing:
Raw fastqs were mapped using bowtie2 2.5.1
samtools 1.17 was used to extract tRNA reads containing the 3'CCA
Assembly: Custom transcriptomes for E. Coli and P. Aeruginosa
Supplementary files format and content: Mapped and subsetted BAM files containing mature tRNA reads

organism: Pseudomonas aeruginosa PA14

source_name: bacterial cell

extract_protocol:
RNA isolation with Trizol reagent, precipitation with GlycoBlue
Sequencing libraries were prepared from inputs and captured s4u-containing RNA. 3’ end adaptors (Table 6) were ligated 100 ng of RNA in an overnight reaction at 16C (250 nM adaptor, 1x T4 RNA ligase buffer, 1 ml of T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (M0437M), 50 mM DTT (Sigma 43816-10mL), 6 ml of 50% PEG 8000 (NEB B1004A), 40 units of Ribolock RNase inhibitor EO0382). All samples were then gel purified on a denaturing 10% polyacrylamide gel (National Diagnostics, EC-829). Gels were cut between 60 to 200 nt and purified via crush and soak overnight tumble at 4C (crush gel through needle punched bottom of 500 ml tubes into 1.7 mL Eppendorf tubes, soak in 10 mM Tris pH 7.5 (15567-027), 500 mM NaCl (AM9759), 1 mM EDTA (AM9261), 0.1% SDS (351-032-101). Gel buffer mix is then transferred to SpinX columns (CLS8162-96EA) to remove remaining gel. Three volumes of 100% ethanol are added to the RNA-containing buffer for precipitation.

value: bacterial cell

tag: genotype

value: WT

tag: media condition

value: chemically defined media

tag: fraction

value: captured s4u-containing RNA


title: 8992-RP-0011

description: Treatment

value: in vitro hepatocytes

value: Liver


title: Paerugionsa Capture Rep2

tag: cell type


title: T lymphocytes, vWAT infiltrating, obese individual 2

value: visceral white adipose tissue (vWAT)

value: Individual 2


title: 8992-RP-0010

description: Treatment

value: Low (1.33 mM Thioacetamide)


title: Paeruginosa Input Rep1

description: WT_Paeruginosa_Input_collated_processed.csv

value: Input


title: Paeruginosa Input Rep3


title: 8992-RP-0007

description: Treatment


title: 8992-RP-0008

description: Treatment


title: 8992-RP-0005

description: Control

value: Vehicle


title: Paeruginosa Input Rep2


title: 8992-RP-0009

description: Treatment


title: M_T_cell_1

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
Raw reads were filtered by removing reads containing adapter and reads containing N>10% and for Phred scores >30. The filtered reads were analyzed using Partek Flow software version 7.0. Filtered reads were aligned with STAR 2.73a CanFam3.1 genome assembly. Aligned reads were annotated and counted using HTseq
Assembly: CanFam3.1
Supplementary files format and content: txt files contain CPM normalized data

organism: Canis lupus familiaris

source_name: T cell

growth_protocol: Non-tissue culture treated plates were coated with 24 µg/mL Retronectin (Tankara) according to the manufacture’s protocol. Frozen B7-H3 retroviral supernatant was thawed in a 37˚ C water bath and aliquoted into Retronectin coated 6-well plates at 2 ml/well and centrifuged at 32˚ C for 2.5 hours at 2,000 G. Viral supernatant was discarded after centrifugation and activated PBLs were plated onto retroviral bound plates at a concentration of 5.05 cells/mL and 2 mL per well and incubated overnight. The T cells were transduced once before being rescued from virus and expanded in fresh cTCM media and cytokines. The CAR T cells were transduced twice before being rescued from virus and put into fresh cTCM with fresh cytokines. Half of the medium was changed, and fresh cytokines are added every 2-3 days. The CAR T cells were used for analysis on day 10-14 of culture.

extract_protocol:
RNA was extracted with a RNeasy mini kit (Qiagen, Hilden Germany).
Libraries were prepared with SMART-Seq v4 3’ DE Kit (Takarabio, Japan)

tag: biological replicate

value: M

value: T cell

tag: breed

value: mixed breed

tag: treatment

value: Untransduced


title: 8992-RP-0004

description: Control

tag: duration

tag: dose


title: 8992-RP-0002

description: Control


title: 8992-RP-0003

description: Control


title: M_B7H3_CAR_T_1


title: M_BC_CAR_T_1


title: 8992-RP-0001

description: Control


title: E_B7H3_CAR_T_1

value: E


title: 8992-RP-0006

description: Treatment


title: E_BC_CAR_T_1


title: MKN74.Hp_2

tag: cell line

value: Stomach gastric cell line

value: Infected


title: HBE cells, ATAC seq

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
ATAC-seq data were separately processed by AIAP package that contained an optimized ATAC-seq data QC and analysis pipeline with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig for visulization
Supplementary files format and content: ATAC-seq peak calling results

growth_protocol: HBE and B2B cell lines were grown in LHC-8 (Gibco) and BEGM, respectively. 16HBE cell lines were grown in alpha-MEM based medium with 10% serum according to manufacturer protocol (Millipore). Cells were cultured in 2D submerged format on collagen-coated plastic and maintained at 37°C 5% CO2.

extract_protocol: Cells were grown to 70-90% confluence on 150mm tissue culture plates and cells were subsequently lysed and the nuclear extract was obtained using a Nuclear Extraction Kit (Signosis) according to manufacturer protocol.

value: Human Bronchial Epithelial


title: Paerugionsa Capture Rep1

value: bacterial cell

value: WT

value: chemically defined media


title: B_B7H3_CAR_T_1

value: B


title: B_BC_CAR_T_1


title: B2B cells, ATAC seq


title: 16HBE cells, ATAC seq


title: CT26-iPSC-Vac

city: Taichung City

first: Kevin

middle: Chih-Yang

last: Huang

address: No. 91, Xueshi Road, North District

department: Department of Biomedical Imaging and Radiological Science

country: Taiwan

institute: China Medical University

data_processing:
The trimming of sequence reads was performed by Trimmomatic (v0.39).
RNA-seq reads were aligned to the mouse genome (mm10) using HISAT2 (v2.1.0) software.
eads that overlapped with exon coordinates were counted using featureCounts (v2.0.3).
The read count matrix was normalized by converting the counts to counts per million (CPM). Subsequently, a statistical analysis was performed using edgeR (v4.2.2) to identify genes that were significantly expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and CPM for each sample

source_name: resected tumors

extract_protocol:
Total RNA was extracted from the cell lines and resected tumor tissues with TRIzol (Thermo Fisher Scientific, CA, USA), quantified by measuring the absorbance at 260 nm, and then reverse-transcribed into cDNA by iScript™ Reverse Transcription Supermix (Bio-Rad, CA, USA).
Utilizing 1 microgram of total RNA as the starting material, eukaryotic mRNA was captured using magnetic beads coated with Oligo (dT), followed by mRNA fragmentation through heat treatment. Subsequently, fragmented mRNA served as a template for the synthesis of the first-strand cDNA using random primers and reverse transcriptase. The resulting single-stranded cDNA was then subjected to the addition of reaction reagents, dNTPs, RNaseH, and DNA polymerase to synthesize double-stranded cDNA products. The double-stranded cDNA products, purified via AMPure XP (Beckman Coulter, Beverly, USA) magnetic beads, underwent end repair and 3' adenylation, followed by ligation with sequencing adaptors. Finally, library construction was completed by PCR amplification of the products and subsequent magnetic bead purification.

value: resected tumors

value: colon cancer cells

value: mouse irradiated iPSC vaccination


title: CT26

value: No treatment


title: 12M_CO_3_ATAC

city: New York

first: James

last: Nicholson

address: 413 East 69th Street

institute: Weill Cornell Medicine

data_processing:
The Cell Ranger 2.0.1 pipeline was used to align reads to the GRCh38 human reference genome and produce count matrices for downstream preprocessing and analysis using the Seurat v4.0 R package
For quality control, cells with fewer than 750 genes detected or greater than 10% mitochondrial gene expression were removed
Raw Multiome sequencing data were converted to fastq format and subsequently aligned to the GRCh38 genome using “cellranger-arc mkfastq” and “cellranger-arc count” (10X Genomics, v2.0.0).
Assembly: GRCh38 human reference genome
Supplementary files format and content: Cellranger output series matrix files for scRNAseq; filtered_feature_bc_matrix.h5 & atac_fragments.tsv.gz for paired scRNA/ATACseq

source_name: Cerebral Organoid

growth_protocol: Cerebral Organoids and GSCs lines were generated and maintained as previosuly described (Linklous et al. 2019, Cell Reports)

extract_protocol:
COs were dissociated into single-cell suspensions using the Papain Dissociation System following manufacturers instructions (Worthington Biochemical, LK003150). Cells were filtered through a 40um strainer and resuspended on ice-cold PBS/2%BSA. For GLICO samples, GFP-positive/DAPInegative spGSCs were sorted by FACS (Becton-Dickinson Aria II) and collected on PBS/2%BSA for Single-cell ATAC-/ RNA-sequencing.
Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (10x Genomics, PN-120237)

value: Cerebral Organoid

tag: time


title: E_T_cell_1


title: 9M_CO_3_ATAC


title: B_T_cell_1


title: 12M_CO_2_ATAC


title: 9M_CO_2_ATAC


title: 12M_CO_3_GEX