title: IMR-90 SV40-T cells, D68N, rep 1

description: Library name: IMR90_SV40T_D68N_rep1


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.5, GEX

status: Public on Mar 02 2026

type: SRA

city: San Francisco

first: Alex

last: Pollen

address: 651 4th Street

country: USA

institute: UCSF

description: Library name: D16_M0-5_GEX

library_source: transcriptomic single cell

data_processing:
Demultiplexing of species and cell line identity was done using cellbouncer (https://github.com/nkschaefer/cellbouncer)
snRNA-seq and snATAC-seq library FASTQs were pre-processed using cellranger-arc version 2.0.2 (10x Genomics) and aligned to either an ancestral genome or to individual species genomes hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque)
For snRNA-seq data: cell doublets were deteced and removed based on species and individual demultiplexing. During the processign of the GEX data, cells with more than 15% mitochondrial reads or more then 10% ribosomal reads were removed. Cells were also filtered based on the number of genes (< 1,000 or > 7,500 for D40-100, and <500 or > 7,500 for D16) and reads (< 1,000) and any gene detected in less than 10 cells was removed. Counts in cells were then normalized by read depth (CPM normalization), log transformed and then scaled to unit variance and zero mean, with a max value of 10.
To obtain clusters with merged species identities, we applied Batch Integration of batch-balanced k-nearest neighbors (BBKNN) to the developmental data sets. Because rotenone exposure reduced cell type marker gene expression and made it more difficult to delineate homologous cell types across species, we used a slightly different approach to integrate and cluster the rotenone data set. we performed reciprocal PCA (rPCA)-based integration to integrate data from each sequencing library for each species and rotenone time point using Seurat default rPCA parameters.We classified cells as DA neurons if they belonged to subclusters with marker expression of established DA markers, including TH, NR4A2, EN1 and LMX1A.
For snATAC-seq data: Signac v1.13.9003152 was used to quantify counts for each species for the original peak set called for each species (after merging across cell types), CrossPeak consensus peaks, and CrossPeak species-only peaks in each species’ own genome coordinates. Cells that passed snRNA-seq quality filters and had cell type identities assigned based on snRNA-seq were included, and further filtered (quality metrics calculated based on each species’ original peak set) to retain cells with TSSenrichment (as calculated with Signac function TSSEnrichment()) > 2 and counts > 1000.
Fragment count matrix for scATAC-seq was generated using PycisTopic from the fragments files output by cellranger using consensus peak set defined in each species.
MULTIseq library FASTQs were processed using py-multi-seq (https://github.com/mtvector/py-multi-seq)
Assembly: Individual species' genomes:hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque). Ancestral genome: our reference data were aligned and annotated in a prior study (Mao et al. 2021, PMID: 33953399).The authors aligned many human and nonhuman primate genomes using Progressive Cactus (Armstrong et al. 2020, PMID: 33177663) and annotated them using the Comparative Annotation Toolkit (CAT) (Fiddes et al. 2018, PMID: 29884752) with the human Gencode annotation v33 (Frankish et al. 2021, PMID: 33270111) as the source for homology-based annotations. The genome assembly versions that we used from this alignment were hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque). As part of its alignment strategy, Progressive Cactus imputes the genome of the most recent common ancestor of each group of genomes it aligns, and we chose to use the Homo/Pan most recent common ancestor (MRCA) for snRNA-seq alignment to mitigate reference bias toward either the human or chimpanzee lineage.
Supplementary files format and content: GEX_pre-QC.h5ad files contain GEX data with RNA counts after alignments on each species’ reference genome. It includs all cells before quality control and filtering.
Supplementary files format and content: GEX_processed-clustered.h5ad files contain GEX data with RNA counts after alignments on each species’ reference genome. It includs cells that passed quality control and filtering and that were used for clustering.
Supplementary files format and content: GEX_ancestral_sce.rds files are SingleCellExperiment objects with RNA counts after alignments to the ancestral genome
Supplementary files format and content: D80-rotenone-exp_GEX.h5ad contains GEX data from the rotenone experiment, before subsetting DA lineage cells
Supplementary files format and content: D80-rotenone-exp_GEX_DA_subset.h5ad contains GEX data from the rotenone expeiement, after subsetting the DA lineage cells that were used for the analysis in Figure 7
Supplementary files format and content: D40-100_ATAC_human_specific_sce.rds and D40-100_ATAC_chimp_specific_sce.rds files are SingleCellExperiment objects with human-specific or chimp-specific ATAC peaks counts
Supplementary files format and content: D40-100_ATAC_consensus_sce.rds is a SingleCellExperiment object with consensus ATAC peaks counts for  human, chimp, and rhesus
Supplementary files format and content: D40-100_ATAC_seurat.rds is a Seurat object with consensus ATAC peaks - data integrated across species including the UMAP calculated
Supplementary files format and content: cistopic_obj.pk files are fragment count matrices for scATAC-seq
Supplementary files format and content: multiseq_calls.csv list the MULTIseq call assignment after demultiplexing with py-multi-seq
Supplementary files format and content: MULTIseq_counts.txt are MULTIseq count tables after demultiplexing with py-multi-seq

molecule: polyA RNA

organism:
Macaca mulatta
Pan troglodytes
Pongo abelii
Homo sapiens

extract_protocol:
D16 ventral midbrain progenitors were dissociated for 10 min in Accutase, counted and distributed into Eppendorf tubes at 1-2 million cells per tube. The cells were centrifuged at 400 x g for 5 min and all liquid was removed before the tubes were dipped into an isopentane bath on dry ice for flash freezing To isolate the nuclei from D16 progenitors, the 10x Genomics demonstrated protocol 'Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing' (CG000365 - Rev B) was used with a few modifications. The cells were incubated for 4 min on ice in 0.1x lysis buffer and washed in wash buffer containing 2% BSA.  After the final wash, nuclei were passed through a 40 μm Flowmi Cell Strainer. For MULTIseq labeling, the nuclei were incubated with the barcode-Anchor LMO mix at a concentration of 50 nM and subsequently incubated with the Co-Anchor LMO at 50 nM. D40, 80 and 100 organoids were cut into smaller pieces under a dissection microscope using scalpels (halves or quarters depending on time point). For the D40 time point, 20 organoids were placed in each tube and for D80-100, 10-15 organoids were used. The tubes were centrifuged at 100x g for 2 min to remove all the liquid and then dipped into an isopentane bath on dry ice for flash freezing. To isolate nuclei from organoids, the 10x demonstrated protocol Nuclei Isolation from Embryonic Mouse Brain for 'Single Cell Multiome ATAC + Gene Expression Sequencing' (CG000366 - Rev C) was used and the organoid pieces were incubated for 5 + 5 min on ice in 0.1x lysis buffer and then washed in wash buffer containing 2% BSA. For the D80 and D100 organoid samples, two additional x washes were added to the procedure to remove as much debris as possible. After the final wash, nuclei were passed through a 40 μm Flowmi Cell Strainer. For MULTIseq labeling, the nuclei were incubated with the barcode-Anchor LMO mix at a concentration of 50 nM and subsequently incubated with the Co-Anchor LMO at 50 nM.
Library was constructed according to manufacturer's instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev C). To prepare the MULTIseq library, 10 μl of the product from ‘Pre-Amplification SPRI Cleanup’ (Step 4.3 in above protocol) portion of the 10x was used and libraries were constructed as described in McGinnis et al. 2019 [PMID: 31209384]

tag: cell line

tag: cell type

value: PSC-derived midbrain progenitors


title: Easy-Sci RNA co-proccessed human cultured cancer cell lines EXP 20230107

city: New York

first: Aileen

last: Ugurbil

state: NY

address: 87 Bedford St, Apt 4

institute: The Rockefeller University

description:
Library name: 20230107_CellLine
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-RNA protocol. Reverse transcription, ligation-based barcoding, and indexed PCR amplification generated single-cell transcriptome libraries, sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_RNA_processed_UMAP.scanpy.h5ad
Pan_Cancer_RNA_metadata.csv

data_processing:
EasySci-RNA and EasySci-ATAC data were processed using custom pipelines as described previously (1). For RNA, cell barcodes and UMIs were extracted, adapters trimmed with Trim Galore, and reads aligned to the human genome with STAR; PCR duplicates were removed based on UMI and genomic coordinates to generate single-cell expression matrices. For ATAC, N5/N7 and cell barcodes were extracted, reads trimmed and aligned with STAR, and duplicates removed with Picard to produce fragment BED files. Single-cell RNA data were analyzed in Scanpy (v1.11.0) with Scrublet (v0.2.3) for doublet detection, normalization, scaling, PCA, and UMAP visualization. Single-cell ATAC data were analyzed in SnapATAC2 (v2.8); cells with ≥1,000 fragments and TSS enrichment ≥3 were retained, peaks were called with macs3 (q < 1e−3), blacklist regions removed, and UMAPs generated from spectral embeddings of the most variable peaks.
Assembly: hg38
Supplementary files format and content: h5ad file include an anndata object containing a peak x count matrix with cell meta data
Supplementary files format and content: h5ad file include an anndata object containing a gene x count matrix with cell meta data

molecule: total RNA

organism: Homo sapiens

source_name: cultured cell line

growth_protocol: All cell lines were maintained at 37 °C with 5% CO₂, and cultured in cell-line specific media.

extract_protocol:
Cells were trypsinized (2 mL, 37 °C, 1–5 min), quenched with 8 mL growth medium (10% FBS + 1% Pen-Strep), dissociated by pipetting, and counted using a hemocytometer. Cells were pelleted at 300 × g for 5 min (4 °C), washed once with 10 mL cold PBS, and transferred to 1.5 mL tubes. Pellets were washed again with 1 mL PBS and lysed in 1 mL ice-cold cell lysis buffer for 5 min on ice. Nuclei were pelleted at 500 × g for 5 min, resuspended in 500 µL nuclei isolation buffer, filtered through a 20 µm filter, and pelleted again. Final nuclei were resuspended in 500 µL NIB for counting or 500 µL Sort Buffer with 0.25 mg/mL DAPI for sorting, then used immediately or snap-frozen at –80 °C.
ATAC libraries were prepared following the EasySci-ATAC protocol, adapted from TrackerSci-ATAC. Nuclei isolated from cultured cell lines were tagmented with indexed Tn5 transposase for 30 min at 37 °C, quenched, pooled, and ligated with plate-specific barcodes. After cleanup and indexed PCR amplification, libraries were purified, quality-checked, and sequenced on an Illumina NextSeq 1000 (paired-end ~60 bp; dual 10 bp index reads). RNA libraries were generated using the EasySci-RNA protocol. Nuclei from cultured cell lines were distributed across 96-well plates (≤20,000 nuclei per well) in Nuclear Suspension Buffer. Reverse transcription was performed with mixed short-dT and random primers using a temperature-ramped program. Post-RT nuclei were pooled, washed, and ligated with well-specific DNA barcodes. Second-strand synthesis and AMPure cleanup were followed by Tn5 tagmentation, indexing PCR, and purification. Final libraries were quantified and sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).

tag: tissue

value: cultured cell line

value: breast, lung, melanoma

tag: batch


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 2, MULTISEQ

description: Library name: D16_M2_MULTISEQ

library_source: other

molecule: other


title: IMR-90 SV40-T cells, E76K, rep 2

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: Library name: IMR90_SV40T_E76K_rep2

library_source: transcriptomic

data_processing:
Reads were trimmed using Trimmomatic. Alignment was performed using HISAT2 to human genome hg38. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with raw counts per gene per sample from DESeq2.

growth_protocol: IMR-90 SV40-T cells were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin/streptomycin at 37°C in 5% CO₂ and 5% O₂.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
NEBNext Ultra II DNA Library Prep Kit (E7645) with NEBNext Multiplex Oligos (E6609)

treatment_protocol: No treatment was applied prior to RNA extraction.

value: fibroblast

tag: genotype

value: H2B E76K


title: CUMC_E27

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 2.1.7) was used to convert BCL to fastq format, coupled with adaptor trimming
Salmon v1.3.0 was used to quantify transcript abundance after generating a full decoy-aware transcriptome index.
tximport v1.18.0 was used to import transcript level count estimates from Salmon and summarize them at the gene level using the "lengthScaledTPM" option for the countsFromAbundance argument.
Genome_build: GENCODE Release 34 (GRCh38.p5)
Supplementary_files_format_and_content: tab-delimited text file containing estimated counts per gene for each sample

source_name: PDAC

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2

tag: compartment

value: Epithelium

tag: group

value: Primary


title: CUMC_E28


title: CUMC_E26


title: CUMC_E31


title: IMR-90 SV40-T cells, WT, rep 3

description: Library name: IMR90_SV40T_WT_rep3

value: H2B WT


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 72h with DOX, rep3

city: Guangzhou

first: Qifeng

last: Yang

state: Guangdong

address: Jingxi Subdistrict

country: China

institute: Southern Medical University

description: Library name: KOHD_induHD_72h_DOX_rep3

data_processing:
The raw sequencing data were processed using fastp (v0.20.0) to remove adapter sequences, filter low-quality reads, and eliminate reads with excessive N bases, generating high-quality clean data with subsequent statistical analysis of read counts and base composition. Clean reads were then aligned to the GRCh38 reference genome using STAR (v2.7.6a), and the resulting BAM files were sorted, deduplicated, and filtered for low-quality alignments using SAMtools (v1.1). RSeQC (v2.6.4) was employed to calculate insert fragment length distribution and assess read coverage uniformity across genes. Potential rRNA contamination was evaluated by aligning reads to rRNA sequences using bowtie2 (v2.3.5.1), followed by quantification of rRNA content and distribution of mapped reads across exonic, intronic, and intergenic regions. Finally, stringtie(v2.0.4) was used to count the reads numbers mapped to each gene, and the FPKM methods were used to standardize the expression level.
Assembly: GRCh38
Supplementary files format and content: The processed data files are in TXT format, containing RNA-seq expression matrices of raw counts and FPKM values.

source_name: hPSCs-derived TSCs, TRIzol RNA extraction

growth_protocol: hPSCs were cultured in human pluripotent stem cell medium. TSCs derived from hPSCs were cultured in trophoblast medium. All cells were maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
RNA was extracted from samples using a standardized extraction method, followed by stringent quality control (QC) of RNA samples, including three key assessments: 1. Concentration assessment: RNA concentration and total yield were quantified using Qubit 4.0 Fluorometer (Thermo Fisher Scientific). 2. Integrity assessment: RNA integrity was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies) using the RNA Integrity Number (RIN) metric. 3. Purity assessment: Sample purity was verified via absorbance ratios (A260/A280 and A260/A230) measured by a NanoDrop spectrophotometer (Thermo Fisher Scientific).
mRNA with polyA tails was enriched using Oligo(dT) magnetic beads, followed by fragmentation at an optimized temperature and duration based on the desired fragment size, using a metal ion solution.The fragmented mRNA was used as a template to synthesize the first strand of cDNA with random oligonucleotide primers in the M-MuLV reverse transcriptase system.After first-strand synthesis, second-strand synthesis was performed, followed by end repair and A-tailing.T4 DNA ligase was used to catalyze the ligation of double-stranded DNA sticky ends with short adapters.Adapter-ligated products were purified using AMPure XP beads, and cDNA fragments of 300–350 bp were selected to ensure fragment uniformity.PCR amplification was performed to add sample index tags, followed by additional purification using AMPure XP beads to obtain the final library. After library construction, the libraries were initially quantified and diluted, followed by fragment size distribution analysis using the Agilent 2100 Bioanalyzer DNA 1000 kit. Qualified libraries were then accurately quantified via qRT-PCR to determine the effective concentration and ensure quality. The prepared DNA nanoballs (DNBs) were loaded onto a patterned array chip, and sequencing was performed using combinatorial probe-anchor synthesis (cPAS) technology. Sequencing primers, anchor molecules, and fluorescent probes were polymerized on the DNBs. A high-resolution imaging system was used to capture, read, and identify optical signals, generating single-base sequence information. This process was repeated in cycles to obtain the full sequence data.

treatment_protocol: Wild-type (WT) and HAND1-knockout (HAND1-KO) hPSCs were differentiated into TSCs using TSC differentiation medium. For the HAND1-KO ROSA26-integrated DOX-inducible HAND1 hPSCs, TSC differentiation was performed in the same medium with or without doxycycline (DOX) treatment. DOX-induced samples were collected at 24, 48, and 72 hours post-induction.

value: trophoblast stem cells

tag: treatment

value: Differentiated in trophoblast medium with 72h DOX induction


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 72h without DOX, rep3

description: Library name: KOHD_induHD_72h_noDOX_rep3

value: Differentiated in trophoblast medium


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 72h without DOX, rep1

description: Library name: KOHD_induHD_72h_noDOX_rep1


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 72h without DOX, rep2

description: Library name: KOHD_induHD_72h_noDOX_rep2


title: IMR-90 SV40-T cells, WT, rep 2

description: Library name: IMR90_SV40T_WT_rep2


title: CUMC_E23


title: IMR-90 SV40-T cells, WT, rep 1

description: Library name: IMR90_SV40T_WT_rep1


title: CUMC_E24


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8,  replicate 1, GEX

description: Library name: D16_M_GEX


title: CUMC_E25


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8,  replicate 2, GEX

description: Library name: D16_M2_GEX


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h without DOX, rep3

description: Library name: KOHD_induHD_48h_noDOX_rep3


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 72h with DOX, rep1

description: Library name: KOHD_induHD_72h_DOX_rep1


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 72h with DOX, rep2

description: Library name: KOHD_induHD_72h_DOX_rep2


title: IMR-90 SV40-T cells, Empty, rep 3

description: Library name: IMR90_SV40T_Empty_rep3

value: Empty


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 1, ATAC

description: Library name: D16_M_ATAC

library_source: genomic single cell

molecule: genomic DNA


title: CUMC_E22


title: CUMC_E21


title: Human dermal fibroblast, young, age 33, male

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: Library name: TM18_CKC15_Y_CTRL

data_processing:
Raw FASTQ files were mapped to hg19 (https://www.ncbi.nlm.nih.gov/grc/human) by STAR (v2.5.3a), and DEG analysis was performed with HOMER pipeline (v4.11.1).
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw counts and normalized TPM values for each sample

source_name: Skin

growth_protocol: Cells were cultured in DMEM (Gibco, 11965092) supplemented with 10% fetal bovine serum (Corning, 45000-736), 1% non-essential amino acids (Gibco, 11140050) and 1% GlutaMAX (Gibco, 35050061) at 37 °C, 5% CO₂, and ambient O₂.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104), according to the manufacturer’s instructions.
PolyA library prep was performed by the Salk Institute for Biological Studies Next Generation Sequencing and Genomics Core.

value: Skin

value: Dermal fibroblast

value: young

tag: age

tag: Sex

value: male


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 1, MULTISEQ

description: Library name: D16_M_MULTISEQ


title: IMR-90 SV40-T cells, Empty, rep 1

description: Library name: IMR90_SV40T_Empty_rep1


title: CUMC_E20


title: IMR-90 SV40-T cells, Empty, rep 2

description: Library name: IMR90_SV40T_Empty_rep2


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h without DOX, rep2

description: Library name: KOHD_induHD_48h_noDOX_rep2


title: Human dermal fibroblast, old, age 64, male

description: Library name: TM19_CKC16_O_CTRL

value: old


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 2, ATAC

description: Library name: D16_M2_ATAC

value: PSC-derived midbrain progenitors


title: Human dermal fibroblast, old, age 64, female

description: Library name: TM17_CKC14_O_CTRL

value: female


title: CUMC_E2


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h without DOX, rep1

description: Library name: KOHD_induHD_48h_noDOX_rep1


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h with DOX, rep3

description: Library name: KOHD_induHD_48h_DOX_rep3

value: Differentiated in trophoblast medium with 48h DOX induction


title: CUMC_E19


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h with DOX, rep2

description: Library name: KOHD_induHD_48h_DOX_rep2


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h with DOX, rep1

description: Library name: KOHD_induHD_48h_DOX_rep1


title: Human dermal fibroblast, young, age 23, male

description: Library name: TM16_CKC8_Y_CTRL


title: Top2-Anchor away 3' READS  Rep B

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description:
Library name: 76
3' READS

data_processing:
Prep fastq files for mapping (discard reads with ambiguous base calls, remove of library adapters, count/remove of initial Ts in each read) python
Map to Sac cer 3 genome, using first 17 nt after adapter and initial T removal; no mismatches allowed, keeping only uniquely mapped reads, Bowtie
Discard reads for which the number of initial Ts could be explained by A residues in the genome adjacent to the mapped position, python
Tally remaining read starts by strand and genomic position, scaling each replicate to 25M total reads (or combined reps scaled to 50M), python
Assembly: Sac cer 3
Supplementary files format and content: Tab-delimited text files giving relative 3' isoform end frequencies by coordinate in the 400nt downstream of each CDS
Supplementary files format and content: Tab-delimited text files of merged A and B replicates giving relative isoform frequencies by genomic coordinate  in the 400nt downstream of each CDS

organism: Saccharomyces cerevisiae

source_name: log phase yeast cells

growth_protocol: Growth to mid-log phase in YPD medium at 30°C

extract_protocol:
Hot acid phenol method to isolate total RNA, followed by purfcation using Qiagen RNEasy with Dnase treatment
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

treatment_protocol: The anchor-away strains were treated for 1hr with 1µM rapamycin before harvesting cells; cells from deletion strains were harvested without treatment

tag: strain

value: tor1hyphen1 fpr1 colon colon NAT RPL13Ahyphen2xFKBP12 DBP2hyphenFRB

value: mid-log YPD culture treated with 1µM rapamycin for 1 hr

value: log phase yeast cells


title: CUMC_E17

value: Epithelium

value: Primary


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h without DOX, rep2

description: Library name: KOHD_induHD_24h_noDOX_rep2

value: trophoblast stem cells


title: CUMC_E18


title: Human dermal fibroblast, old, age 70, female

description: Library name: TM4_CKC6_O_CTRL


title: Human dermal fibroblast, old, age 69, female

description: Library name: TM15_CKC7_O_CTRL


title: miR-30e-3p inhibitor

type: RNA

city: Manchester

first: Bernadette

middle: Carolyn

last: Baker

state: Lancashire

address: Oxford Road

department: Maternal and Fetal Health Research Centre

country: United Kingdom

institute: University of Manchester

description: pooled RNA from 3 placentas, 2 female+1male, IBC 58-92, Gestation 38-40 weeks, all elective c-section, maternal BMI 26-28

hyb_protocol: Standard Affymetrix protocol carried out by Genomics Technology Department at the University of Manchester

scan_protocol: Gene chips scanned in Genomics Technology Department at University of Manchester on GeneArray® Scanner

data_processing: Data analysis was performed by Genomic technologies including quality control and normalisation using Affymetrix default analysis settings

label: biotin

source_name: primary trophoblast cells 48hr post transfection with miR-30e-3p inhibitor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Isolated primary term cytotrophoblast cultured for 18hrs DMEM:F12+ 10% FBS at 37°C in a 5% CO2/95% air gas mixture.

extract_protocol: Trizol extraction of total RNA was performed following manufacturer's protocol with the mirVana miRNA isolation kit with subsequent DNAse treatment

treatment_protocol: 40nM control or inhibitor transfected into cytotrophoblast at 18hr using Dharmafect 2 in antibiotic free media. Media changed at 24hr post-transfection. Total RNA harvested at 48hr post transfection (66hr total incubation time).

value: term placenta, pool of 3 individual isolates

tag: subject status

value: miR-30e-3p inhibitor


title: Human dermal fibroblast, old, age 72, male

description: Library name: TM3_CKC5_O_CTRL


title: Human dermal fibroblast, young, age 26, female

description: Library name: TM2_CKC4_Y_CTRL


title: Non targeting control

source_name: primary trophoblast cells 48hr post transfection with non-targeting miRNA

value: 2 female+1male, IBC 58-92, Gestation 38-40 weeks, all elective c-section, maternal BMI 26-28

value: Non targeting control


title: CUMC_E15


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h without DOX, rep1

description: Library name: KOHD_induHD_24h_noDOX_rep1

value: Differentiated in trophoblast medium


title: miR-34b-5p inhibitor

source_name: primary trophoblast cells 48hr post transfection with miR-34b-5p inhibitor

value: miR-34b-5p inhibitor


title: xrn1∆ 3' READS  Rep B

description:
Library name: 72
3' READS

value: xrn1 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h with DOX, rep2

description: Library name: KOHD_induHD_24h_DOX_rep2

value: Differentiated in trophoblast medium with 24h DOX induction


title: xrn1∆ 3' READS  Rep A

description:
Library name: 71
3' READS


title: Top2-Anchor away 3' READS  Rep A

description:
Library name: 75
3' READS


title: vps34∆ 3' READS  Rep B

description:
Library name: 70
3' READS

value: vps34 deletion in JGY2000 parental strain


title: CUMC_E14


title: Human dermal fibroblast, young, age 23, female

description: Library name: TM1_CKC3_Y_CTRL

value: Skin

value: Dermal fibroblast

value: young

value: female


title: CUMC_E13

value: Epithelium


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h without DOX, rep3

description: Library name: KOHD_induHD_24h_noDOX_rep3


title: Lung squamous cell carcinoma with usual interstitial pneumonia pattern, scRNA-seq, Multi plex

city: Okayama

first: Atsushi

last: Matsuoka

state: Okayama

address: 2-5-1 SHIKATA-CHO, KITAKU, OKAYAMA 700-8558 JAPAN

country: Japan

institute: Okayama University

description: Library name: LUSQ-UIP

data_processing:
The raw FASTQ files generated from sequencing were processed with Cell Ranger (v8.0.1) using the cellranger-multi pipeline. The reference files used were the Human Transcriptome Reference (GRCh38 - 2024-A) and the Human Transcriptome Probe Set v1.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matlix files.
Supplementary files format and content: The barcodes.tsv, features.tsv, mtx, csv, and h5 files with patients ID at the beginning were demultiplexed and generated by Cell Ranger multi.
Supplementary files format and content: sample_config.csv: Configuration file used as input for cellranger-multi. It defines the reference, probe set, FASTQ paths, and sample metadata

source_name: Lung squamous cell carcinoma and adjacent non-tumor lung tissue

extract_protocol:
Tissues (51–55 mg) were minced, fixed in fixation buffer for 24 hours at 4 °C, and dissociated using the gentleMACS Octo Dissociator (Miltenyi Biotec) following the Chromium Next GEM Fixed RNA Sample Preparation Kit protocol (10x Genomics).
Fixed single-cell suspensions were hybridized with probe barcodes using the Chromium Fixed RNA Kit, Human Transcriptome (10x Genomics). Equal numbers of cells from each sample were pooled prior to library construction. GEMs were generated using the Chromium iX and Chip Q. Probe ligation, pre-amplification, and library construction were performed according to the manufacturer’s protocol. Libraries were indexed using the Dual Index Kit TS Set A and sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp), generating approximately 1.6 billion reads in total.

value: surgical resection


title: Dbp2-Anchor away 3' READS  Rep A

description:
Library name: 73
3' READS

value: tor1hyphen1 fpr1 colon colon NAT RPL13Ahyphen2xFKBP12 DBP2hyphenFRB

value: mid-log YPD culture treated with 1µM rapamycin for 1 hr

value: log phase yeast cells


title: vps34∆ 3' READS  Rep A

description:
Library name: 69
3' READS


title: LUSC-IPF,Pt51,out,normal,DSP-1001660021451-G-H11

description: Library name: DSP-1001660021451-G-H11

data_processing:
FASTQ files were converted into DCC files using GeoMx NGS Pipeline (v2.3.3.10).
Assembly: hg38
Supplementary files format and content: Hs_R_NGS_WTA_v1.0.pkc: PKC file
Library strategy: Spatial Transcriptomics

source_name: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

extract_protocol:
FFPE tissue sections were processed using the BOND RXm system (Leica Biosystems) for deparaffinization, antigen retrieval, and enzymatic digestion, following the GeoMx DSP Automated Slide Preparation User Manual (NanoString Technologies). ROIs were selected based on morphology markers, and slides were scanned using the GeoMx DSP to capture high-resolution images.
Hybridization was performed using the GeoMx Human Whole Transcriptome Atlas for Illumina Systems, targeting human protein-coding genes. UV light was applied to release oligonucleotide tags from selected ROIs, which were collected into 96-well plates. Libraries were constructed using the GeoMx Seq Code Pack: G & H Compatible with Illumina Systems (NanoString Technologies), amplified by PCR, purified with AMPure XP beads (Beckman Coulter), and quality-checked with TapeStation (Agilent Technologies). Sequencing was performed as 150 bp paired-end reads on an Illumina NovaSeq 6000, with depth proportional to total ROI area.

tag: patientid

value: male

tag: smoker

value: yes

tag: uip in/out

value: out

value: normal

tag: slide name

tag: scan name

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: segment

value: Full ROI

tag: aoi

value: Full ROI-aoi-001

tag: area

tag: nuclei


title: Dbp2-Anchor away 3' READS  Rep B

description:
Library name: 74
3' READS

tag: genotype

tag: cell type


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, rep3

description: Library name: KOHD_induHD_0h_rep3

source_name: hPSCs, TRIzol RNA extraction

tag: cell line

value: pluripotent stem cells

tag: treatment

value: Cultured in human pluripotent stem cell medium

tag: batch


title: CUMC_E11

tag: compartment

tag: group

value: Primary


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, rep2

description: Library name: KOHD_induHD_0h_rep2


title: CUMC_E16


title: vps15∆ 3' READS  Rep B

description:
Library name: 68
3' READS

tag: strain

value: vps15 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD


title: CUMC_E12

value: Epithelium


title: LUSC-IPF,Pt51,out,normal,DSP-1001660021451-G-H09

description: Library name: DSP-1001660021451-G-H09

tag: tissue

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: patientid

tag: Sex

tag: smoker

value: surgical resection


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h with DOX, rep1

description: Library name: KOHD_induHD_24h_DOX_rep1

value: trophoblast stem cells

value: Differentiated in trophoblast medium with 24h DOX induction


title: vps15∆ 3' READS  Rep A

description:
Library name: 67
3' READS

value: log phase yeast cells


title: CUMC_E10


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, rep1

description: Library name: KOHD_induHD_0h_rep1


title: CUMC_E1


title: M1, HAND1-knockout, Day8, rep3

description: Library name: KOHD_P0_rep3

value: Differentiated in trophoblast medium


title: trf5∆ 3' READS  Rep B

description:
Library name: 66
3' READS

value: trf5 deletion in JGY2000 parental strain


title: LUSC-IPF,Pt51,out,stroma_interface,DSP-1001660021451-G-H07

description: Library name: DSP-1001660021451-G-H07

value: male

value: yes

tag: uip in/out

value: out

value: Sq

tag: slide name

tag: scan name

tag: panel

value: PanCK-


title: LUSC-IPF,Pt51,out,normal,DSP-1001660021451-G-H08

description: Library name: DSP-1001660021451-G-H08

value: normal

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: segment

value: Full ROI

tag: aoi

value: Full ROI-aoi-001

tag: area

tag: nuclei


title: M1, HAND1-knockout, Day8, rep2

description: Library name: KOHD_P0_rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: trf4∆ 3' READS  Rep B

description:
Library name: 64
3' READS

tag: strain

value: trf4 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD


title: CUMC_EP26

tag: compartment

value: Epithelium

tag: group

value: PanIN


title: trf5∆ 3' READS  Rep A

description:
Library name: 65
3' READS


title: LUSC-IPF,Pt51,out,tumor_interface,DSP-1001660021451-G-H06

description: Library name: DSP-1001660021451-G-H06

tag: tissue

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: patientid

tag: Sex

value: surgical resection

value: PanCK+


title: CUMC_EP24


title: M1, Wild-type, Day8, rep3

description: Library name: G3M_P0_rep3

value: trophoblast stem cells

value: Wild-type

value: Differentiated in trophoblast medium

tag: batch


title: M1, HAND1-knockout, Day8, rep1

description: Library name: KOHD_P0_rep1


title: LUSC-IPF,Pt51,out,normal,DSP-1001660021451-G-H10

description: Library name: DSP-1001660021451-G-H10

value: male

tag: smoker

value: yes

tag: uip in/out

value: out

tag: slide name

tag: scan name


title: M1, Wild-type, Day8, rep2

description: Library name: G3M_P0_rep2


title: LUSC-IPF,Pt51,out,core_tumor,DSP-1001660021451-G-H04

description: Library name: DSP-1001660021451-G-H04

value: Sq

tag: panel

tag: segment

tag: aoi

tag: area


title: LUSC-IPF,Pt51,out,tumor_stroma_interface_fullroi,DSP-1001660021451-G-H05

description: Library name: DSP-1001660021451-G-H05

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: nuclei


title: CUMC_EP23


title: CUMC_EP25


title: syc1∆ 3' READS  Rep B

description:
Library name: 62
3' READS

tag: genotype

value: syc1 deletion in JGY2000 parental strain

tag: treatment

tag: cell type

value: log phase yeast cells


title: trf4∆ 3' READS  Rep A

description:
Library name: 63
3' READS

tag: strain

value: trf4 deletion in JGY2000 parental strain


title: sub1∆ 3' READS  Rep B

description:
Library name: 60
3' READS

value: sub1 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD


title: LUSC-IPF,Pt51,out,core_tumor,DSP-1001660021451-G-H03

description: Library name: DSP-1001660021451-G-H03

tag: tissue

value: Full ROI

value: Full ROI-aoi-001


title: syc1∆ 3' READS  Rep A

description:
Library name: 61
3' READS


title: M1, Wild-type, Day8, rep1

description: Library name: G3M_P0_rep1

tag: cell line


title: CUMC_EP22

tag: compartment

value: Epithelium

tag: group

value: PanIN


title: sub1∆ 3' READS  Rep A

description:
Library name: 59
3' READS


title: HAND1-3HA knock-in, TSCs, Day6, rep3

first: Chao

last: Li

description: Library name: Sample3

library_source: genomic

data_processing:
Sequencing reads were trimmed by cutadapt (v 4.3) to get high quality reads. High quality reads were aligned to the human reference genome hg19 using Bowtie2 (v 2.2.5) with the parameter of "-X 2000". The mapped reads were sorted using Samtools (v 1.13), retaining any reads with a MAPQ less than 30. Duplicated reads were removed by Picard (v 2.7). Peaks were called by MACS2 (v 2.2.7.1).  Bigwig files were generated from bam files using deeptools (v 3.5.1) bamCoverage. All samples were normalized to 10 million reads with binsize as 50-bp by "--scaleFactor --binSize 50" parameters.
Assembly: hg19
Supplementary files format and content: The processed files were bigwig files and bed files.

growth_protocol: HAND1-3HA knock-in PSCs were cultured in human pluripotent stem cell medium and maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
In summary, the fixed cells underwent three times washing with 0.1% BSA/PBS. The cells were then resuspended in 80 µl of Antibody Buffer (a mixture of 4 µl 0.5 M EDTA and 1 ml 0.01% Digitonin-Wash Buffer (Dig-Wash Buffer), supplemented with cocktail, 10 mM sodium butyrate, and 0.05% Triton X-100) that contained 1.6 µg of the primary antibody. This mixture was incubated at 4°C for 4 hours on a rotator with 16 rpm. The cells were subsequently washed twice with 180 µl of Dig-Wash Buffer. The secondary antibody (used at a 1:500 ratio) was incubated under the same conditions, except for a shorter duration of 10 minutes. After two times washing with Dig-Wash Buffer, the cells were suspended in 80 µl of Dig-Wash Buffer (containing 0.05% Triton-X, cocktail, and 10 mM sodium butyrate) that also contained 0.83 µM PAT-MEA/B. This was done at 4°C for 1 hour. The free PAT-MEA/B were then dislodged with 180 µl Dig-Wash Buffer containing 0.05% Triton X-100 three times at 5 min each time. The reaction was activated by suspending the cells with 10 µl Reaction Buffer (10 mM TAPS-NaOH pH 8.3, 5 mM MgCl2, 10% DMF, 300 mM NaCl, 0.05% Triton-X, 0.01% Digtonin and supplemented with cocktail, 10 mM sodium butyrate), followed by gently flicking and incubating at 37°C for 1 h in an Eppendorf ThermoMixer with 300 rpm. The reaction was gently mixed once after 30 min incubation and was halted by adding 10 µl of 40 mM EDTA, followed by further incubation at 4°C for 10 min. The samples were then washed with 0.1% BSA/PBS and finally resuspended in 5 µl of Lysis Buffer (0.1 mg/ml Proteinase K, 10 mM Tris-HCl pH 8.5, and 0.05% SDS), and lysed at 55°C for 3 hours in a PCR cycler. Finally, 1.8% Triton X-100 with 5 mM PMSF was added to the cell lysate and incubated at room temperature for 10 minutes to inactivate the proteinase K. This was followed by a 5-minute incubation at 55°C to quench the SDS in the reaction.
After PCR enrichment using 2x KAPA master mix,fragments larger than 1 kb were first eliminated using 0.4x AMPure beads, after which the library was purified using the Zymo DNA Clean and Concentrator-5 Kit.

treatment_protocol: HAND1-3HA knock-in PSCs were performed TSCs differentiation for 6 days in trophoblast medium according to the Hiroaki Okae's protocol, and then in situ ChIP-seq was performed.

value: trophoblast stem cells

value: HAND1-3HA knock-in

tag: chip antibody


title: CUMC_EP21


title: CUMC_EP20


title: M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h with DOX, rep3

description: Library name: KOHD_induHD_24h_DOX_rep3

value: Differentiated in trophoblast medium with 24h DOX induction

tag: batch


title: LUSC-IPF,Pt47,in,tumor_stroma_interface_fullroi,DSP-1001660021451-G-G12

description: Library name: DSP-1001660021451-G-G12

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: patientid

tag: Sex

value: male

tag: smoker

tag: uip in/out

value: in

value: surgical resection

tag: slide name


title: CUMC_EP19


title: HAND1-3HA knock-in, TSCs, Day6, rep2

description: Library name: Sample2

value: Differentiated in trophoblast medium


title: HAND1-3HA knock-in, TSCs, Day6, rep1

description: Library name: Sample1


title: sto1∆ 3' READS  Rep B

description:
Library name: 58
3' READS

value: sto1 deletion in JGY2000 parental strain


title: CUMC_EP18


title: LUSC-IPF,Pt47,in,core_tumor,DSP-1001660021451-G-G11

description: Library name: DSP-1001660021451-G-G11

value: yes

value: Sq

tag: scan name

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: segment

tag: aoi

tag: area


title: LUSC-IPF,Pt47,in,fibrosis,DSP-1001660021451-G-G09

description: Library name: DSP-1001660021451-G-G09

value: fibrosis

tag: treatment

tag: nuclei


title: LUSC-IPF,Pt47,in,core_tumor,DSP-1001660021451-G-G10

description: Library name: DSP-1001660021451-G-G10

tag: tissue

value: Full ROI


title: LUSC-IPF,Pt47,in,stroma_interface,DSP-1001660021451-G-H02

description: Library name: DSP-1001660021451-G-H02

value: PanCK-


title: ssn3∆ 3' READS  Rep A

description:
Library name: 55
3' READS

tag: strain

tag: genotype

value: ssn3 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD

tag: cell type

value: log phase yeast cells


title: ssn3∆ 3' READS  Rep B

description:
Library name: 56
3' READS


title: TT-SI-M4

city: Madison

first: Marienela

middle: Yaritza

last: Heredia

state: WI

address: 1550 Linden Drive

department: Medical Microbiology & Immunology

institute: University of Wisconsin-Madison

description: Library name: Sample 58

data_processing:
Raw FASTQ files were trimmed to remove adapter content, filter out low-quality reads, and group paired reads using Trimmomatic (v0.39)
Trimmed reads were aligned to the Mus musculus strain C57BL/6 genome (GRCm38.p6, release 38; NCBI) using STAR (v2.7.5c). Default parameters were used with the following exceptions: maximum mismatch (2 bp), minimum intron length (20 bp), and maximum intron length (100,000 bp).
Quantification of mapped reads and counts table generation was performed using RSEM (v1.3.1)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text results files containing RSEM outputs, including counts tables, TPM, and FPKM values.

organism: Mus musculus

source_name: distal small intestine

extract_protocol:
Approximately 3-cm-long distal ileal and 2cm proximal colonic tissue fragments were harvested beginning 1 cm upstream and downstream from each cecal junction. Tissues were immediately placed in Buffer RLT (Qiagen) on ice and homogenized using a gentleMACS Octo Dissociator (Miltenyi Biotec). RNA isolation and purification were performed using the RNeasy Mini Kit (Qiagen, cat. 74104), following manufacturer’s instructions.
Bulk RNA library preparation was performed by the University of Wisconsin-Madison Biotechnology Center’s Gene Expression Center using the Illumina TruSeq Stranded mRNA kit for poly(A) enrichment.

treatment_protocol: Tritrichomonas recipients (mono- and co-infected) were gavage-fed 1.5 × 104 Tritrichomonas trophozoites isolated from cecal content. E. muris recipients (mono- and co-infected) were gavage fed 5 × 103 E. muris fecal cysts. Uninfected control mice received 1X PBS by oral gavage.

value: distal small intestine

tag: infection

value: Tritrichomonas


title: LUSC-IPF,Pt47,in,fibrosis,DSP-1001660021451-G-G08

description: Library name: DSP-1001660021451-G-G08

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: patientid

value: Full ROI-aoi-001


title: snf2∆ 3' READS  Rep A

description:
Library name: 53
3' READS

value: snf2 deletion in JGY2000 parental strain


title: LUSC-IPF,Pt47,in,fibrosis,DSP-1001660021451-G-G07

description: Library name: DSP-1001660021451-G-G07

tag: Sex

value: male

value: in

value: surgical resection


title: CUMC_EP14

tag: compartment

value: Epithelium

tag: group

value: PanIN


title: snf2∆ 3' READS  Rep B

description:
Library name: 54
3' READS


title: TT-SI-M2

description: Library name: Sample 57


title: CUMC_EP13


title: LUSC-IPF,Pt47,in,tumor_interface,DSP-1001660021451-G-H01

description: Library name: DSP-1001660021451-G-H01

tag: smoker

value: yes

tag: uip in/out

value: Sq

tag: slide name

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: PanCK+


title: TT-SI-F3

description: Library name: Sample 54

value: female


title: set2∆ 3' READS  Rep A

description:
Library name: 51
3' READS

value: set2 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD


title: LUSC-IPF,Pt38,in,stroma_interface,DSP-1001660021451-G-F07

description: Library name: DSP-1001660021451-G-F07

tag: scan name

tag: panel

tag: segment

value: PanCK-


title: LUSC-IPF,Pt38,in,tumor_interface,DSP-1001660021451-G-F06

description: Library name: DSP-1001660021451-G-F06

tag: treatment

tag: aoi

tag: area


title: TT-SI-F4

description: Library name: Sample 55

tag: tissue

value: distal small intestine

value: Tritrichomonas


title: TT-SI-F5

description: Library name: Sample 56

tag: genotype


title: set2∆ 3' READS  Rep B

description:
Library name: 52
3' READS

tag: strain

tag: cell type

value: log phase yeast cells


title: TT-SI-M5

description: Library name: Sample 59

tag: infection


title: CUMC_EP17


title: CUMC_EP16


title: CUMC_EP11


title: TT-CO-M5

description: Library name: Sample 52

source_name: proximal colon

value: proximal colon

tag: Sex


title: CUMC_EP15

tag: compartment


title: CUMC_EP12

tag: group


title: sto1∆ 3' READS  Rep A

description:
Library name: 57
3' READS

value: sto1 deletion in JGY2000 parental strain


title: rtt103∆ 3' READS  Rep B

description:
Library name: 48
3' READS

value: rtt103 deletion in JGY2000 parental strain


title: TT-SI-F2

description: Library name: Sample 53


title: LUSC-IPF,Pt38,in,tumor_stroma_interface_fullroi,DSP-1001660021451-G-F05

description: Library name: DSP-1001660021451-G-F05

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: patientid

value: male

tag: smoker

value: in

value: surgical resection

value: Full ROI

value: Full ROI-aoi-001

tag: nuclei


title: TT-CO-M3

description: Library name: Sample 50


title: set1∆ 3' READS  Rep B

description:
Library name: 50
3' READS

value: set1 deletion in JGY2000 parental strain


title: set1∆ 3' READS  Rep A

description:
Library name: 49
3' READS


title: CUMC_EP10

value: Epithelium

value: PanIN


title: CUMC_EP9


title: TT-CO-M4

description: Library name: Sample 51


title: rtr1∆ 3' READS  Rep B

description:
Library name: 46
3' READS

value: rtr1 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD


title: LUSC-IPF,Pt38,in,core_tumor,DSP-1001660021451-G-F04

description: Library name: DSP-1001660021451-G-F04

value: yes

tag: uip in/out

value: Sq

tag: slide name

tag: scan name

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: TT-CO-M1

description: Library name: Sample 48

value: proximal colon

value: Tritrichomonas


title: rtt103∆ 3' READS  Rep A

description:
Library name: 47
3' READS

value: rtt103 deletion in JGY2000 parental strain

tag: treatment

value: log phase yeast cells


title: TT-CO-F4

description: Library name: Sample 47

value: female


title: rrp6∆ 3' READS  Rep B

description:
Library name: 44
3' READS

value: rrp6 deletion in JGY2000 parental strain


title: LUSC-IPF,Pt38,in,fibrosis,DSP-1001660021451-G-F01

description: Library name: DSP-1001660021451-G-F01

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

value: male

value: in

value: fibrosis

value: surgical resection

tag: panel

tag: segment

tag: aoi


title: LUSC-IPF,Pt38,in,fibrosis,DSP-1001660021451-G-F02

description: Library name: DSP-1001660021451-G-F02

tag: tissue

value: Full ROI

value: Full ROI-aoi-001

tag: area


title: CUMC_EP7

value: Epithelium

value: PanIN


title: CUMC_EP8


title: LUSC-IPF,Pt38,in,fibrosis,DSP-1001660021451-G-E12

description: Library name: DSP-1001660021451-G-E12

value: yes


title: rtr1∆ 3' READS  Rep A

description:
Library name: 45
3' READS

tag: strain

tag: genotype

value: rtr1 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD

tag: cell type


title: LUSC-IPF,Pt38,in,core_tumor,DSP-1001660021451-G-F03

description: Library name: DSP-1001660021451-G-F03

tag: Sex

value: Sq

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: CUMC_EP6

tag: compartment

tag: group


title: LUSC-IPF,Pt35,in,tumor_interface,DSP-1001660021451-G-E10

description: Library name: DSP-1001660021451-G-E10

tag: patientid

tag: smoker

value: PanCK+


title: TT-CO-M2

description: Library name: Sample 49

value: proximal colon

tag: infection

value: Tritrichomonas


title: LUSC-IPF,Pt35,in,stroma_interface,DSP-1001660021451-G-E11

description: Library name: DSP-1001660021451-G-E11

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: uip in/out

tag: slide name

value: PanCK-

tag: nuclei


title: CUMC_EP5


title: rrp6∆ 3' READS  Rep A

description:
Library name: 43
3' READS

value: rrp6 deletion in JGY2000 parental strain

tag: treatment

value: log phase yeast cells


title: TT-CO-F1

description: Library name: Sample 44

value: female


title: CUMC_EP4


title: TT-CO-F2

description: Library name: Sample 45


title: LUSC-IPF,Pt35,in,tumor_stroma_interface_fullroi,DSP-1001660021451-G-E09

description: Library name: DSP-1001660021451-G-E09

value: male

value: in

value: surgical resection

tag: scan name

tag: panel

tag: segment

value: Full ROI


title: TT-CO-F3

description: Library name: Sample 46

tag: tissue


title: CUMC_EP3

value: Epithelium

value: PanIN


title: rai1∆ 3' READS  Rep B

description:
Library name: 42
3' READS

tag: strain

value: rai1 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD


title: pfd1∆ 3' READS  Rep B

description:
Library name: 40
3' READS

tag: genotype

value: pfd1 deletion in JGY2000 parental strain


title: LUSC-IPF,Pt35,in,tumor_interface,DSP-1001660021451-G-E07

description: Library name: DSP-1001660021451-G-E07

value: yes

value: Sq

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: PanCK+

tag: aoi

tag: area


title: EMU-SI-M5

description: Library name: Sample 43

value: distal small intestine

value: E. muris

tag: Sex


title: CUMC_EP2

tag: compartment

tag: group


title: rai1∆ 3' READS  Rep A

description:
Library name: 41
3' READS

tag: cell type

value: log phase yeast cells


title: EMU-SI-M3

description: Library name: Sample 42

tag: infection


title: LUSC-IPF,Pt35,in,stroma_interface,DSP-1001660021451-G-E08

description: Library name: DSP-1001660021451-G-E08

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: patientid

tag: smoker

tag: uip in/out

value: PanCK-


title: CUMC_EP1


title: CUMC_S99

value: Stroma

value: Primary


title: nhp6a∆,nhp6b∆ 3' READS  Rep B

description:
Library name: 38
3' READS

value: nhp6a,nhp6b double deletion in BY4741 strain background

tag: treatment


title: EMU-SI-M1

description: Library name: Sample 40

value: male


title: LUSC-IPF,Pt35,in,core_tumor,DSP-1001660021451-G-E05

description: Library name: DSP-1001660021451-G-E05

value: in

value: surgical resection

tag: slide name

tag: scan name

value: Full ROI

value: Full ROI-aoi-001

tag: nuclei


title: nhp6a∆,nhp6b∆ 3' READS  Rep A

description:
Library name: 37
3' READS

value: growth to mid-log phase in YPD


title: LUSC-IPF,Pt35,in,tumor_stroma_interface_fullroi,DSP-1001660021451-G-E06

description: Library name: DSP-1001660021451-G-E06

tag: tissue

value: yes

value: Sq

tag: panel

tag: segment


title: LUSC-IPF,Pt35,in,core_tumor,DSP-1001660021451-G-E04

description: Library name: DSP-1001660021451-G-E04

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: aoi


title: pfd1∆ 3' READS  Rep A

description:
Library name: 39
3' READS

tag: strain

tag: genotype

value: pfd1 deletion in JGY2000 parental strain


title: EMU-SI-M2

description: Library name: Sample 41

value: distal small intestine

value: E. muris

tag: Sex


title: CUMC_S97

tag: compartment

tag: group


title: CUMC_S98


title: JGY2000 2022 3' READS  Rep B

description:
Library name: 36
3' READS

value: Parental strain rpb1 colon colon RPB hyphen FRB, rpl13 colon colon RPL13 hyphen FKBP12

tag: cell type

value: log phase yeast cells


title: EMU-SI-F3

description: Library name: Sample 39

tag: infection

value: female


title: CUMC_S96

value: Stroma

value: Primary


title: EMU-SI-F1

description: Library name: Sample 38


title: LUSC-IPF,Pt35,in,fibrosis,DSP-1001660021451-G-E02

description: Library name: DSP-1001660021451-G-E02

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: patientid

value: male

tag: smoker

value: fibrosis

tag: area


title: JGY2000 2022 3' READS  Rep A

description:
Library name: 35
3' READS

tag: treatment


title: CUMC_S94


title: EMU-CO-M4

description: Library name: Sample 36

value: proximal colon


title: LUSC-IPF,Pt35,in,fibrosis,DSP-1001660021451-G-E01

description: Library name: DSP-1001660021451-G-E01

tag: uip in/out

value: in

value: surgical resection

tag: slide name

tag: scan name

value: Full ROI

value: Full ROI-aoi-001


title: CUMC_S95


title: EMU-CO-M5

description: Library name: Sample 37

tag: tissue


title: JGY2000 2018 3' READS  Rep B

description:
Library name: 34
3' READS

value: growth to mid-log phase in YPD


title: LUSC-IPF,Pt50,out,tumor_interface,DSP-1001660021451-G-D11

description: Library name: DSP-1001660021451-G-D11

value: yes

value: out

value: Sq

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: segment

value: PanCK+

tag: nuclei


title: CUMC_S93


title: isy1∆ 3' READS  Rep B

description:
Library name: 32
3' READS

tag: strain

tag: genotype

value: isy1 deletion in JGY2000 parental strain

value: log phase yeast cells


title: isy1∆ 3' READS  Rep A

description:
Library name: 31
3' READS


title: CUMC_S91

tag: compartment

value: Stroma

value: Primary


title: EMU-CO-M1

description: Library name: Sample 34

value: E. muris

tag: Sex

value: male


title: LUSC-IPF,Pt50,out,tumor_stroma_interface_fullroi,DSP-1001660021451-G-D10

description: Library name: DSP-1001660021451-G-D10

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: aoi


title: CUMC_S90

tag: group


title: LUSC-IPF,Pt35,in,fibrosis,DSP-1001660021451-G-E03

description: Library name: DSP-1001660021451-G-E03

tag: patientid

value: in

value: fibrosis


title: CUMC_S9


title: CUMC_S92


title: isw1∆ 3' READS  Rep B

description:
Library name: 30
3' READS

value: isw1 deletion in JGY2000 parental strain

tag: cell type


title: isw1∆ 3' READS  Rep A

description:
Library name: 29
3' READS


title: EMU-CO-F3

description: Library name: Sample 33

value: proximal colon

tag: infection

value: female


title: CTL-SI-M5

description: Library name: Sample 31

value: distal small intestine

value: Uninfected


title: LUSC-IPF,Pt50,out,core_tumor,DSP-1001660021451-G-D09

description: Library name: DSP-1001660021451-G-D09

tag: smoker

value: yes

value: out

value: Sq

tag: treatment

value: surgical resection

value: Full ROI

value: Full ROI-aoi-001

tag: area


title: hbs1∆,ski1∆ 3' READS  Rep A

description:
Library name: 27
3' READS

value: hbs1,ski1 double deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD

value: log phase yeast cells


title: EMU-CO-F2

description: Library name: Sample 32

value: E. muris


title: hbs1∆,ski1∆ 3' READS  Rep B

description:
Library name: 28
3' READS


title: CUMC_S89

value: Stroma

value: Primary


title: CTL-SI-M4

description: Library name: Sample 30

value: male


title: LUSC-IPF,Pt50,out,core_tumor,DSP-1001660021451-G-D08

description: Library name: DSP-1001660021451-G-D08

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: uip in/out

tag: slide name

tag: scan name

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: LUSC-IPF,Pt50,out,normal,DSP-1001660021451-G-D07

description: Library name: DSP-1001660021451-G-D07

tag: tissue

value: normal

tag: panel

tag: segment


title: EMU-CO-M2

description: Library name: Sample 35

value: proximal colon

tag: genotype


title: JGY2000 2018 3' READS  Rep A

description:
Library name: 33
3' READS

tag: strain

value: Parental strain rpb1 colon colon RPB hyphen FRB, rpl13 colon colon RPL13 hyphen FKBP12


title: CTL-SI-M3

description: Library name: Sample 29

value: distal small intestine

value: Uninfected

tag: Sex


title: LUSC-IPF,Pt50,out,normal,DSP-1001660021451-G-D06

description: Library name: DSP-1001660021451-G-D06

value: yes

value: out

value: surgical resection

tag: aoi

tag: nuclei


title: gcn5∆ 3' READS  Rep B

description:
Library name: 26
3' READS

value: gcn5 deletion in JGY2000 parental strain


title: CUMC_S88

tag: compartment

tag: group


title: CTL-SI-M2

description: Library name: Sample 28

tag: infection


title: LUSC-IPF,Pt44,out,tumor_interface,DSP-1001660021451-G-C04

description: Library name: DSP-1001660021451-G-C04

tag: patientid

tag: smoker

value: Sq

value: PanCK+


title: CUMC_S86


title: LUSC-IPF,Pt44,out,stroma_interface,DSP-1001660021451-G-C05

description: Library name: DSP-1001660021451-G-C05

tag: treatment

value: PanCK-

tag: area


title: gcn5∆ 3' READS  Rep A

description:
Library name: 25
3' READS

value: growth to mid-log phase in YPD

tag: cell type

value: log phase yeast cells


title: CTL-SI-F5

description: Library name: Sample 27

value: female


title: CUMC_S87

value: Stroma

value: Primary


title: CUMC_S85


title: CTL-SI-F4

description: Library name: Sample 26


title: elf1∆ 3' READS  Rep A

description:
Library name: 23
3' READS

value: elf1 deletion in JGY2000 parental strain


title: LUSC-IPF,Pt44,out,core_tumor,DSP-1001660021451-G-C02

description: Library name: DSP-1001660021451-G-C02

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

value: male

tag: uip in/out

tag: slide name

tag: scan name

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: Full ROI

value: Full ROI-aoi-001


title: CUMC_S84


title: LUSC-IPF,Pt44,out,tumor_stroma_interface_fullroi,DSP-1001660021451-G-C03

description: Library name: DSP-1001660021451-G-C03

tag: tissue

value: yes

value: out

tag: panel

tag: segment


title: elf1∆ 3' READS  Rep B

description:
Library name: 24
3' READS

tag: strain

tag: genotype


title: CTL-SI-F3

description: Library name: Sample 25

value: distal small intestine

value: Uninfected

tag: Sex


title: CUMC_S83

tag: compartment


title: eaf3∆ 3' READS  Rep B

description:
Library name: 22
3' READS

value: eaf3 deletion in JGY2000 parental strain


title: LUSC-IPF,Pt44,out,core_tumor,DSP-1001660021451-G-B12

description: Library name: DSP-1001660021451-G-B12

value: Sq

value: surgical resection

tag: aoi

tag: nuclei


title: LUSC-IPF,Pt44,out,core_tumor,DSP-1001660021451-G-C01

description: Library name: DSP-1001660021451-G-C01

tag: patientid


title: eaf3∆ 3' READS  Rep A

description:
Library name: 21
3' READS

value: growth to mid-log phase in YPD

value: log phase yeast cells


title: CUMC_S82

value: Stroma

tag: group


title: dom34∆ 3' READS  Rep A

description:
Library name: 19
3' READS

value: dom34 deletion in JGY2000 parental strain

tag: treatment


title: LUSC-IPF,Pt44,out,normal,DSP-1001660021451-G-B11

description: Library name: DSP-1001660021451-G-B11

tag: smoker

value: normal

tag: area


title: CUMC_S81

value: Primary


title: dhh1∆ 3' READS  Rep B

description:
Library name: 18
3' READS

value: dhh1 deletion in JGY2000 parental strain

tag: cell type


title: dom34∆ 3' READS  Rep B

description:
Library name: 20
3' READS


title: CTL-CO-M5

description: Library name: Sample 23

value: proximal colon

tag: infection

value: male


title: CTL-CO-M3

description: Library name: Sample 22


title: LUSC-IPF,Pt44,out,normal,DSP-1001660021451-G-B10

description: Library name: DSP-1001660021451-G-B10

value: Lung squamous cell carcinoma associated with idiopathic pulmonary fibrosis

tag: uip in/out

tag: slide name

tag: scan name

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: Full ROI

value: Full ROI-aoi-001


title: CTL-CO-M2

description: Library name: Sample 21

tag: tissue

value: Uninfected


title: CUMC_S80


title: CUMC_S8


title: CUMC_S79


title: A549 cells, dexamethasone treated, rep 5

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

description:
Library name: A549_dexa_5
column name in genes_counts_A549_dexa_5.csv:  A549_dexa_5

data_processing:
Raw reads were quality-checked using FastQC (v0.11.9), adapter sequences were trimmed using Cutadapt (v3.4), and resulting reads were aligned to the human reference genome (GRCh38) using STAR aligner (v2.7.9a).
Gene expression was quantified with featureCounts (Subread package v2.0.3) and differential expression analysis was performed using DESeq2 (v1.32.0) with Phantasus.
Assembly: GRCh38
Supplementary files format and content: csv files include DESeq2-normalized values for each sample and gene annotation

source_name: lung

growth_protocol: A549 cells (human lung adenocarcinoma epithelial cell line, ATCC CCL-185 were cultured Dulbecco's modified eagle medium (DMEM)+glutamax + 5%FBS.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher), purified on Direct-zol RNA miniprep kit (Zymo Research).
Libraries were prepared using after ribosomal RNA depletion (Ribo-Zero Gold rRNA Removal Kit, Illumina), fragmentated and first-strand cDNA synthesized using random hexamer primers, second-strand cDNA synthesized and remaining overhangs were converted into blunt ends. Adapoters were ligated to after adenylation of 3' ends and cDNA fragments of preferentially 370-420 bp length were purified with AMPure XP system. After PCR and quality assessment libraries were sequenced using a Illumina NovaSeq 6000 platform in 150 bp paired-end configuration to a depth of 40-50 million read pairs per sample.

treatment_protocol: Cells were treated with or without dexamethasone (n= 4 wells) for 48 h at 1 µM concentration. Identical sets of samples were prepared in parallel for RNA-seq and proteomics analysis

value: lung

tag: cell line

value: epithelial cell

value: WT

value: dexamethasone for 48 h at 1 µM concentration

tag: batch


title: CTL-CO-M1

description: Library name: Sample 20

tag: genotype

tag: Sex


title: chd1∆ 3' READS  Rep A

description:
Library name: 15
3' READS

tag: strain

value: chd1 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD

value: log phase yeast cells


title: A549 cells, NT, rep 5

description:
Library name: A549_NT_5
column name in genes_counts_A549_NT_5.csv:  A549_NT_5


title: CTL-CO-F4

description: Library name: Sample 18

value: female


title: dhh1∆ 3' READS  Rep A

description:
Library name: 17
3' READS


title: CTL-SI-F1

description: Library name: Sample 24

value: distal small intestine


title: A549 cells, dexamethasone treated, rep 4

description:
Library name: A549_dexa_4
column name in genes_counts_A549_dexa_4.csv:  A549_dexa_4


title: chd1∆ 3' READS  Rep B

description:
Library name: 16
3' READS


title: LUSC-IPF,Pt44,out,normal,DSP-1001660021451-G-B09

description: Library name: DSP-1001660021451-G-B09

value: yes

value: out

value: normal

value: surgical resection

tag: panel

tag: segment

tag: aoi

tag: nuclei


title: CUMC_S77

tag: compartment

value: Stroma

tag: group

value: Primary


title: CUMC_S78


title: ccr4∆ 3' READS  Rep B

description:
Library name: 14
3' READS

value: ccr4 deletion in JGY2000 parental strain

tag: treatment

tag: cell type


title: CUMC_S76


title: CTL-CO-F3

description: Library name: Sample 17

value: proximal colon

tag: infection

value: Uninfected


title: A549 cells, NT, rep 4

description:
Library name: A549_NT_4
column name in genes_counts_A549_NT_4.csv:  A549_NT_4

value: lung

value: epithelial cell


title: CTL-CO-F2

description: Library name: Sample 16


title: ccr4∆ 3' READS  Rep A

description:
Library name: 13
3' READS


title: bye1∆ 3' READS  Rep B

description:
Library name: 12
3' READS

value: bye1 deletion in JGY2000 parental strain


title: A549 cells, dexamethasone treated, rep 3

description:
Library name: A549_dexa_3
column name in genes_counts_A549_dexa_3.csv:  A549_dexa_3

value: WT

value: dexamethasone for 48 h at 1 µM concentration


title: CoINF-SI-M4

description: Library name: Sample 15

value: E. muris and Tritrichomonas

value: male


title: CUMC_S74


title: CTL-CO-F5

description: Library name: Sample 19

value: female


title: A549 cells, NT, rep 3

description:
Library name: A549_NT_3
column name in genes_counts_A549_NT_3.csv:  A549_NT_3


title: bye1∆ 3' READS  Rep A

description:
Library name: 11
3' READS

value: growth to mid-log phase in YPD

value: log phase yeast cells


title: CoINF-SI-M1

description: Library name: Sample 13

value: distal small intestine


title: BY4741 3' READS  Rep B

description:
Library name: 10
3' READS

value: BY4741 wild-type strain


title: A549 cells, NT, rep 1

description:
Library name: A549_NT_1
column name in genes_counts_A549_NT_1.csv:  A549_NT_1


title: CUMC_S72

value: Stroma


title: CoINF-SI-F4

description: Library name: Sample 12


title: CUMC_S71

value: Primary


title: SK-N-BE(2) cells, NC control, replicate 1

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

description: Library name: Sample 3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome and GENCODE v29 using STAR 2.7.10a with parameters --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using stringtie v2.1.7. Gene differential expression were calculated using DESeq2 v1.40.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and expression values of each gene for each sample and differential expression values between knockdown group and NC group.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells

value: NC control


title: SK-N-BE(2) cells, NC control, replicate 2

description: Library name: Sample 4


title: CoINF-SI-M3

description: Library name: Sample 14


title: CUMC_S73


title: CoINF-SI-F3

description: Library name: Sample 11


title: A549 cells, dexamethasone treated, rep 1

description:
Library name: A549_dexa_1
column name in genes_counts_A549_dexa_1.csv:  A549_dexa_1


title: CUMC_S7


title: CUMC_S70


title: bud31∆ 3' READS  Rep A

description:
Library name: 7
3' READS

value: bud31 deletion  in JGY2000 parental strain


title: BY4741 3' READS  Rep A

description:
Library name: 9
3' READS


title: CUMC_S75


title: CoINF-SI-F1

description: Library name: Sample 9


title: bud31∆ 3' READS  Rep B

description:
Library name: 8
3' READS


title: SK-N-BE(2) cells, knockdown MAB21L2, replicate 1

description: Library name: Sample 1

value: Knockdown MAB21L2


title: CUMC_S69


title: bre1∆ 3' READS  Rep B

description:
Library name: 6
3' READS

value: bre1 deletion in JGY2000 parental strain


title: CoINF-SI-F2

description: Library name: Sample 10


title: SK-N-BE(2) cells, knockdown MAB21L2, replicate 2

description: Library name: Sample 2


title: bre1∆ 3' READS  Rep A

description:
Library name: 5
3' READS


title: CTRL5

city: London

first: Yazead

last: Buhidma

state: London

address: 1 Wakefield Street

department: Department of Neurodegenerative Diseases

institute: University College London

description:
Library name: Sample 16
10X Genomics

data_processing:
The resulting gene count table was analysed using the Seurat package (version 4.4). Quality control was performed to remove low-quality cells based on the number of detected genes and unique molecular identifiers (UMIs). Cells with an unusually high number of UMIs, suggesting potential doublet events, were also excluded using scDblFinder. Using SCTransform, gene expression data were normalised to adjust for differences in sequencing depth between cells and scaled to correct for cell-to-cell variation in total UMI count. Data were also normalised to remove confounding sources of variation such as mitochondrial mapping percentage, post-mortem delay, age of death, and batch number.
Assembly: hg38
Supplementary files format and content: Lashley_seurat_object is an RDS file containing barcodes and gene counts for each nuclei sequenced. The data within has been preprocessed for mitochondrial gene %, features above and below standard limits, as well as being scaled, normalised, and centred.  Unprocessed data files (i.e. Lashley_barcodes, features & matrix) only contain features & gene counts.

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Tissue was transferred directly onto ice-cold sucrose buffer and homogenised by hand. The homogenate was layered on top of a sucrose cushion and nuclei were recovered after centrifugation. Nuclei were resuspended in PBS containing BSA (to prevent clumping) and RNase inhibitors, counted and diluted to 1,000 nuclei/μl.
Sequencing libraries were prepared using the “single cell 3’ library kit v3” with the Chromium instrument (10X Genomics). Aiming to obtain libraries for ~5,000 independent nuclei per sample. Libraries were sequenced on an Illumina NovaSeq6000 instrument (UCL Genomics), to an average of at least 100,000 reads/nucleus. Raw sequencing data were processed through the software CellRanger (10X Genomics) to assign each transcript read to its respective nucleus, we performed alignment to the transcriptome, counting reads, and processing of the unique molecular identifier tag to reduce PCR bias

value: Brain

value: Male


title: CoINF-CO-M4

description: Library name: Sample 7

value: proximal colon


title: CTRL4

description:
Library name: Sample 15
10X Genomics


title: CoINF-CO-M5

description: Library name: Sample 8

value: E. muris and Tritrichomonas


title: CUMC_S67


title: CoINF-CO-M3

description: Library name: Sample 6

value: male


title: CUMC_S68


title: asf1∆ 3' READS  Rep A

description:
Library name: 3
3' READS

value: asf1 deletion in JGY2000 parental strain


title: CoINF-CO-M2

description: Library name: Sample 5


title: C9 TDPA3

description:
Library name: Sample 14
10X Genomics

value: Female


title: CTRL3

description:
Library name: Sample 13
10X Genomics


title: CoINF-CO-M1

description: Library name: Sample 4


title: CUMC_S65


title: CUMC_S66


title: air1∆,air2∆ 3' READS  Rep B

description:
Library name: 2
3' READS

value: air1,air2 double deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD

value: log phase yeast cells


title: TDPA3

description:
Library name: Sample 12
10X Genomics


title: CUMC_S64

value: Stroma


title: CoINF-CO-F4

description: Library name: Sample 3

value: female


title: CUMC_S63

value: Primary


title: air1∆,air2∆ 3' READS  Rep A

description:
Library name: 1
3' READS


title: CoINF-CO-F3

description: Library name: Sample 2


title: CUMC_S62


title: TDPC4

description:
Library name: Sample 10
10X Genomics


title: CoINF-CO-F2

description: Library name: Sample 1


title: HSJ019, K27M, inputForCTCF

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Raw sequences were first trimmed using fastp v0.22.0 with default settings before alignment using bwa-mem2 v2.2.1 to a combined reference of hg38+dm6 or mm10+dm6 with default settings
After identification of duplicates using picard v2.26.2’s “MarkDuplicates” module with default settings, alignments with MAPQ>3 mapping to each species was extracted into separate BAM files using samtools v1.14’s “view” module
Depth-normalized coverage tracks were generated using deepTools v3.5.1’s bamCoverage module with parameters “--normalizeUsing CPM --centerReads -e 200”
Regions with focal ChIP-seq enrichment with respect to input controls were identified using MACS v2.2.7.1 with settings “—broad --broad-cutoff 0.1”
Assembly: hg38, mm10, and dm6
Supplementary files format and content: BW files correspond to count-per-million normalized coverage tracks
Supplementary files format and content: broadPeak files correspond to enriched regions identified by MACS

extract_protocol:
Cells (cell lines or dissociated tumor cells) were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 18-30 cycles, 30s on 30s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below).  ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Dynabeads Protein A beads (Invitrogen) Dynabaeds M-280 Sheep anti-Mouse IgG beads (Invitrogen) were washed and then incubated with antibodies (anti-H3K27me3 (1:40, CST 9733), anti-H3K4me3 (1:40, CST 9751), anti-H2AK119ub (1:40, CST 8240), anti-H3K27ac (1:100, Diagenode C15410196), anti-H3K36me2 (1:50, CST 2901)). One-two million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers.   ChIP reactions for SUZ12, RING1B, CBX2 and CTCF were performed as follows: antibodies (anti-SUZ12 (1:150, CST 3737), anti-RING1B (1:200, Active Motif 39663), anti-CBX2 (Bethyl A302-524 1:200), anti-CTCF (1:400, Diagenode C15410210)) were conjugated by incubating with 40ul protein A or G beads at 4°C for 6 hours, then chromatin from 5-10 million cells was added in RIPA buffer, incubated at 4°C o/n, washed using buffers from Ideal ChIP-seq Kit (1 wash with each buffer, corresponding to RIPA, RIPA+500mM NaCl, LiCl, TE), eluted from beads by incubating with Elution buffer for 30 minutes at room temperature.   Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked, and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: chip antibody

value: Glioma cell line


title: HSJ019, K27M, inputForK4me3


title: Hepatic stellate cells isolated from p16-Alb-LRTD mice

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

description:
Library name: HSC_D1
10x Genomics 3' v3.1

data_processing:
The demultiplexing, barcoded processing, and gene counting were performed by conducting CellRanger software v7.0.1.
Assembly: Mouse mm10
Supplementary files format and content: TSV files for barcodes, features, and count matrix

source_name: Liver

extract_protocol:
The method and solution compositions for hepatic stellate cells were previously described.(PMID: 25612230) Mice were anesthetized, and the portal vein was transected after inserting a 22G indwelling needle into the inferior vena cava. The EGTA, pronase, and collagenase solutions were perfused sequentially at a flow rate of 5 mL/min for 3, 5, and 7 minutes, respectively. The liver tissue was collected and stirred at 37°C in pronase/collagenase solution for 25 minutes maintaining a pH of 7.4. The digested tissue was filtered through a 100 μm cell strainer. After washing with GBSS/B solution (Sigma), the hepatic stellate cells were isolated by density gradient separation using Nycodenz (Serumwerk) solution.
For the hepatic stellate cells isolation from p16-Alb-LRTD and p16-LRTD mice, the library preparation followed the manufacturer's protocol for the Single Cell 3’ Reagent Kit v3.1 (10x Genomics). Quality control and sequencing of the samples were performed by Novogene Inc. (China). Library sequencing was conducted using the NovaSeq X Plus system (Illumina) with 150-bp paired-end reads. Gene expression matrices were generated using the cellranger count of CellRanger (v7.0.1) with the mm10 reference genome.

value: Liver

value: CCl4+Tamoxifen+Diphtheria toxin


title: TDPC3

description:
Library name: Sample 8
10X Genomics


title: TDPC5

description:
Library name: Sample 11
10X Genomics


title: C9 TDPA2

description:
Library name: Sample 9
10X Genomics


title: CUMC_S61


title: CUMC_S60


title: DIPGXIII, K27M, inputForSMC1RING1B

source_name: DIPGXIII

value: DIPGXIII


title: Hepatic stellate cells isolated from p16-LRTD mice

description:
Library name: HSC_C1
10x Genomics 3' v3.1


title: DIPGXIII, K27M, inputForH33


title: CUMC_S59


title: DIPGXIII, K27M, inputForK27M


title: HSJ019, K27M, H3K4me3


title: E11.5 embryos, C3-T2 trunks

first: Jennifer

last: Mansfield

address: 3009 Broadway

department: Biology

institute: Barnard College

description: Library name: JJ005

data_processing:
FastQ files were processed and aligned to the mouse reference transcriptome (GRCm39-2024-A) using Cell Ranger 8.0.1 software.
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole trunks C3-T2

extract_protocol:
Tissue was dissected into sterile PBS. Cells were dissociated by incubation in TrypLE Express (Gibco 12605010) for 15 minutes at 37˚ C, gently pipetting with a siliconized wide bore pipette every 5 minutes. All steps after dissociation were performed on ice. Dissociated cells were filtered through a FlowMi Cell Strainer (Sigma BAH136800040), and centrifuged at 184 RCF for 2 minutes at 4˚ C.  Cells were resuspended in DMEM/20% FBS,  preparations from 3 littermates were then pooled at each timepoint, cells were centrifuged again as above and resuspended in DMEM/20% FBS.
Cells were encapsulated and libraries produced using the using 10x Genomics Chromium method with the Chromium Single Cell 3’ Reagent Kit (version 3.1).

value: whole trunks C3-T2

tag: developmental stage

value: E11.5 embryos


title: TDPA2

description:
Library name: Sample 7
10X Genomics

tag: tissue

value: Brain


title: C9 TDPA1

description:
Library name: Sample 5
10X Genomics

value: Male


title: E13.5 embryos, C3-T2 trunks

description: Library name: JJ003

value: E13.5 embryos


title: DIPGXIII, K27M, inputForCTCF

tag: cell line


title: TDPA1

description:
Library name: Sample 6
10X Genomics


title: CUMC_S58

source_name: PDAC


title: E12.5 embryos, C3-T2 trunks

description: Library name: JJ004

value: E12.5 embryos


title: DIPGXIII, K27M, SMC1


title: CUMC_S6


title: CUMC_S56


title: DIPGXIII, K27M, RING1B

value: RING1B (Active Motif 39663)


title: TDPC2

description:
Library name: Sample 3
10X Genomics


title: TDPC1

description:
Library name: Sample 2
10X Genomics

value: Female


title: DIPGXIII, K27M, K27M

value: K27M (Millipore ABE419)


title: CUMC_S57


title: DIPGXIII, K27M, H33

value: H33 (Millipore 09-838)


title: CTRL2

description:
Library name: Sample 4
10X Genomics


title: CUMC_S55

value: Stroma


title: CUMC_S54


title: CTRL1

description:
Library name: Sample 1
10X Genomics


title: CUMC_S53


title: BT245, K27M, inputForSMC1RING1B


title: Xenograft Cord Blood CD34+ TNF ATAC

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

description: Dicklab_Xenograft_Updated_Filtered_RNA_ATAC.rds

data_processing:
Data was processed using Cell Ranger 2.0.0 using default parameters. RNA reads were aligned to the human reference genome. Downstream analysis and QC done on Seurat v.4. Doublet filtering using scdblfinder and souporcell on select samples. Peak calling using MACS2.
Assembly: hg38
Supplementary files format and content: RDS file containing seurat object with quality controlled raw data
Supplementary files format and content: RDS object containing metadata for which genetic clade the cells in this dataset belong to. Genetic clades were inferred from SouporCell analysis as described in Zeng et al. 2026

source_name: Cord Blood

extract_protocol:
Per manufacturer's instructions for 10x genomics Multiome (RNA+ATAC) kit. Either low input or standard protocols were followed for the samples sequenced on the 10x platform.
Per manufacturer's instructions for 10x genomics Multiome (RNA+ATAC) kit.

value: Cord Blood

value: TNF


title: BT245, K27M, inputForK27M

value: Glioma cell line


title: CUMC_S52

value: Primary


title: Control 05

city: Riyadh

first: Ghaida

last: Almuneef

address: KSA-Riyadh

country: Saudi Arabia

institute: King Abdullah International Medical Research Center

description: Total RNA labeled with FlashTag Biotin HSR and hybridized to Affymetrix GeneChip miRNA 4.0.

hyb_protocol: Labeled RNA was hybridized to the Affymetrix GeneChip miRNA 4.0 array at 48°C with rotation at 60 rpm for 16–18 hours using the GeneChip Hybridization Oven 645

scan_protocol: Arrays were washed and stained on the GeneChip Fluidics Station 450 according to the manufacturer’s protocol and scanned on the GeneChip Scanner 3000 7G. CEL files were generated using Affymetrix GeneChip Command Console (AGCC) or equivalent software

data_processing: CEL files were imported into R and normalized using Robust Multi-array Average (RMA) implemented in oligo (fallback: affy), producing log2 expression values. Probes were filtered by IQR ≥ 0.25 and retained if expression ≥ 5 (log2) in at least 20% of samples. Differential expression (ALL vs CTRL) was tested using limma with empirical Bayes moderation, p-values were adjusted by Benjamini–Hochberg FDR

source_name: bone marrow, peripheral blood, plasma/serum

label_protocol: 130 ng total RNA was labeled using the Affymetrix FlashTag™ Biotin HSR RNA Labeling Kit following the manufacturer’s protocol, including tailing and ligation of a biotinylated signal molecule.

growth_protocol: Not applicable. Clinical human specimens were analyzed (no cell culture)

extract_protocol: Total RNA was extracted from isolated peripheral blood mononuclear cells (PBMCs) using the RNeasy Mini Kit™ (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. Briefly, PBMCs were lysed using the kit reagents, RNA quantity and purity were assessed using NanoDrop ND-1000. Input RNA amount for labeling was 130 ng per sample.

treatment_protocol: Not applicable. This is an observational case–control study; no experimental treatment was applied prior to RNA extraction

value: CTRL

tag: subtype

tag: age

tag: response.eoi(bone marrow)


title: Xenograft Cord Blood CD34+ PBS ATAC

value: PBS


title: CUMC_S51

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 2.1.7) was used to convert BCL to fastq format, coupled with adaptor trimming
Salmon v1.3.0 was used to quantify transcript abundance after generating a full decoy-aware transcriptome index.
tximport v1.18.0 was used to import transcript level count estimates from Salmon and summarize them at the gene level using the "lengthScaledTPM" option for the countsFromAbundance argument.
Genome_build: GENCODE Release 34 (GRCh38.p5)
Supplementary_files_format_and_content: tab-delimited text file containing estimated counts per gene for each sample

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2


title: BT245, K27M, inputForCTCF

tag: genotype


title: Xenograft Cord Blood CD34+ LPS ATAC

value: LPS


title: Control 02


title: CUMC_S50


title: Control 03


title: Xenograft Cord Blood CD34+ LPS RNA


title: Control 01


title: Xenograft Cord Blood CD34+ TNF RNA


title: Control 04


title: CUMC_S49


title: CUMC_S5


title: BT245, K27M, SMC1


title: ALL patient 17

value: ALL

value: pre B ALL

value: CNS 1

value: M1 < 5% blasts


title: ALL patient 18

value: UKALL Relapsing ALL

value: M3 >25% blasts


title: BT245, K27M, RING1B

value: RING1B (Active Motif 39663)


title: BT245, K27M, inputForH33


title: Xenograft Cord Blood CD34+ PBS RNA


title: BT245, K27M, K27M

value: K27M (Millipore ABE419)


title: Sorted Cord Blood LT-HSC RNA

data_processing:
Data was processed using Cell Ranger 2.0.0 using default parameters. RNA reads were aligned to the human reference genome. Downstream analysis and QC done on Seurat v.4. Doublet filtering using scdblfinder.
Assembly: hg38
Supplementary files format and content: RDS file containing seurat object with quality controlled raw data

extract_protocol: Per manufacturer's instructions for the BD Rhapsody platform.


title: CUMC_S48


title: ALL patient 15


title: Cord Blood CD34+ Pool B ATAC

data_processing:
Data was processed using Cell Ranger 2.0.0 using default parameters. RNA reads were aligned to the human reference genome. Downstream analysis and QC done on Seurat v.4. Doublet filtering using scdblfinder and souporcell on select samples. Peak calling using MACS2.
Assembly: hg38
Supplementary files format and content: RDS file containing seurat object with quality controlled raw data
Supplementary files format and content: Cell Ranger output files: barcodes.tsv, features.tsv, matrix.mtx


title: BT245, K27M, H33

value: H33 (Millipore 09-838)


title: CUMC_S47

value: Stroma


title: Cord Blood CD34+ Pool A ATAC

value: Cord Blood


title: ALL patient 14


title: G477, WT

data_processing:
Raw sequences were processed using Juicer v1.6 with default parameters against hg38 or mm10
Juicer .hic files were converted to cooler .mcool files using hic2cool v0.8.3
Bias vectors were re-computed using the balance module of cooler v0.8.11 with default settings
CNV-aware bias vectors were determined using OneD with default parameters
Boundary scores were calcualted using RobusTAD with default parameters
Compartment scores were computed using cooltools with GC content as the sign-orienting signal
Assembly: hg38
Supplementary files format and content: MCOOL files contain multi-resolution contact maps in the Cooler format
Supplementary files format and content: CSV files contain the first eigenvector of 100-kb balanced matrices (i.e., compartment score)
Supplementary files format and content: TSV files contain RobusTAD boundary scores computed using 50-kb balanced matrices

extract_protocol:
Cells were crosslinked using formaldehyde, after which proximity-ligated DNA was digested using a 4-base cutter restriction enzyme (DpnII) with intact permeabilized nuclei. Following fill in and biotinylation of the resulting 5' overhangs and ligation of the blunt ends, DNA was sheared and then pulled down using streptavidin beads
Libraries were prepared following manufacturer guidelines using the NEB kit, and the amplified libraries were ultimately sequenced in paired-end mode

value: H3 WT


title: DIPGXIII, K27M

value: DIPGXIII

value: Glioma cell line


title: CUMC_S46

value: Primary


title: ALL patient 13


title: CUMC_S45


title: Cord Blood CD34+ Pool B RNA


title: CUMC_S44


title: CUMC_S43


title: DIPGXIII, KO, inputForH2Aub


title: hNPC, Input

value: Neural progenitor cell

value: WT NSD1


title: ALL patient 12

value: ALL

value: T ALL


title: Cord Blood CD34+ Pool A RNA


title: HSJ019, K27M-KO, replicate 2

description: 10X Genomics

data_processing:
Cell Ranger (10X Genomics, v3.1.0) was used with default parameters to demultiplex and align sequencing reads, distinguish cells from background, and obtain gene counts per cell
Alignment was performed using a joint hg19+mm10 genome reference build, coupled with Ensembl transcriptome build GRCh37 v.82 for hg19 and GRCm38 v.84 for mm10, excluding intronic counts
Human cells were extracted if cells were either assigned as human by Cell Ranger or the cell contained greater than 75% of total reads mapping to hg19 in order to obtain adequate numbers of cells per sample
Assembly: hg19 and mm10
Supplementary files format and content: TSV files contain feature and barcode information as generated by CellRanger
Supplementary files format and content: MTX files contain count matrices produced by CellRanger

extract_protocol:
The concentration of the single-cell suspension was assessed with a Trypan blue count. Approximately 5000 cells per sample were loaded on the Chromium Single Cell 3′ system (10X Genomics). GEM-RT, DynaBeads cleanup, PCR amplification and SPRIselect beads cleanup were performed using Chromium Single Cell 3′ Gel The concentration of the single-cell suspension was assessed with a Trypan blue count. Approximately 5000 cells per sample were loaded on the Chromium Single Cell 3′ system (10X Genomics). GEM-RT, DynaBeads cleanup, PCR amplification and SPRIselect beads cleanup were performed using Chromium Single Cell 3′ Gel Bead kit
Indexed single-cell libraries were generated using the Chromium Single Cell 3′ Library kit and the Chromium i7 Multiplex kit

tag: mouse strain

value: NOD SCID

value: patient-derived orthotopic xenograft


title: BT245, K27M


title: ALL patient 16

value: pre B ALL

value: CNS 1

value: M1 < 5% blasts


title: HSJ019, K27M-KO, replicate 3

description: 10X Genomics


title: CUMC_S40


title: ALL patient 10

value: CNS 3


title: HSJ019, K27M, replicate 2

description: 10X Genomics


title: CUMC_S41


title: CUMC_EI18

value: Epithelium

value: IPMN


title: CUMC_S42

value: Stroma


title: CUMC_EI19


title: DIPG13, K27M-KO, replicate 2

description: 10X Genomics


title: CUMC_S4


title: CUMC_EI17


title: HSJ019, K27M, replicate 1

description: 10X Genomics


title: ALL patient 09


title: ALL patient 11

value: UKALL Relapsing ALL


title: hNPC, H3K27me3


title: ALL patient 07

value: Interfant -06


title: ALL patient 08


title: ALL patient 05


title: CUMC_EI16


title: DIPG13, K27M-KO, replicate 1

description: 10X Genomics

value: DIPGXIII


title: ALL patient 06


title: ALL patient 04


title: CUMC_S37

value: Primary


title: CUMC_EI15


title: ALL patient 03

value: palliative chemo

value: not done


title: CUMC_S39


title: DIPG13, K27M, replicate 1

description: 10X Genomics


title: CUMC_S38


title: DIPG13, K27M, replicate 2

description: 10X Genomics


title: CUMC_EI14


title: CUMC_EI13


title: CUMC_S36


title: BT245, K27M-KO, replicate 1

description: 10X Genomics


title: Wild-type, 3 weeks of age (2)

city: St. Louis

first: Jeffrey

middle: Wade

last: Brown

state: MO

address: 660 S. Euclid

department: Medicine

institute: Washington University in St. Louis

description:
Library name: b6m2-3wks
Wild-type, 3 weeks of age (2)

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3

Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts is .xlsx format
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3

Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts is .xlsx format

source_name: stomach

extract_protocol:
RNA was isolated using RNeasy (Qiagen) per the manufacturer’s protocol
Total RNA integrity was determined using Agilent 4200 Tapestation.  Library preparation was performed with 5ug of total RNA with a RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 16 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq 6000 using paired end reads extending 150 bases.

value: stomach


title: Wild-type, 3 weeks of age

description:
Library name: b6m1-3wks
Wild-type, 3 weeks of age

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3

Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts is .xlsx format


title: HSJ019, K27M-KO, replicate 1

description: 10X Genomics


title: BT245, K27M, replicate 1

description: 10X Genomics


title: CUMC_S35

first: Hans

last: Maurer


title: ALL patient 02

value: ALL


title: CUMC_S34


title: CUMC_EI12


title: Wild-type, 8 weeks of age (2)

description:
Library name: b6m1-8wks
Wild-type, 8 weeks of age (2)


title: CUMC_S33


title: ALL patient 01

value: St Jude protocol

value: M3 >25% blasts


title: CUMC_EI11


title: CUMC_EI10


title: Wild-type, 8 weeks of age

description:
Library name: b6m-8wks
Wild-type, 8 weeks of age


title: hiPSC, WT, R1

data_processing:
Raw sequences were trimmed using fastp with default settings
Expression quantification was performed using salmon v1.4.0 with default settings against GENCODE annotations (v36/vM25)
Assembly: mm10 or hg38
Supplementary files format and content: quant.sf are TSV files generated by salmon containing transcript abundances

extract_protocol:
Total RNA was extracted from cell pellets and mouse tumors using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts

value: Induced pluripotent stem cell

value: WT NSD1


title: Galectin-8 KO, 3 weeks of age (2)

description:
Library name: gal8m2-3wks
Galectin-8 KO, 3 weeks of age (2)

value: Lgals8 null


title: CUMC_EI9


title: hiPSC, WT, R2


title: CUMC_EI8


title: CUMC_S31


title: Galectin-8 KO, 3 weeks of age

description:
Library name: gal8m1-3wks
Galectin-8 KO, 3 weeks of age


title: hiPSC, NSD1het, R2


title: Galectin-8 KO, 8 weeks of age (2)

description:
Library name: gal8m3-8wks
Galectin-8 KO, 8 weeks of age (2)


title: CUMC_S32


title: CUMC_S30


title: hiPSC, NSD1het, R1


title: CUMC_EI7


title: HSJ019, KO, DM, R1

value: Glioma cell line

value: DMSO


title: HSJ019, KO, DM, R2


title: Galectin-8 KO, 8 weeks of age

description:
Library name: gal8m2-8wks
Galectin-8 KO, 8 weeks of age


title: CUMC_EI5

value: Epithelium

value: IPMN


title: CUMC_EI6