title: A2-Molm14-DMSO-R2

description: Library name: A2

value: myeloid cells


title: individual MA_14501, untreated

status: Public on Jul 04 2025

type: SRA

city: Montreal

first: Guy

last: Rouleau

state: Quebec

address: 3801 Rue University

department: Neurology

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Trimmomatic 0.39: Sequence reads were trimmed for adaptor sequence/low-quality sequence. Parameters: ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:36
star 2.7.9a: Trimmed sequence reads were mapped to GRCh38 with default parameters
rsem 1.3.3: read count extraction was performed using default parameters
edgeR 3.34.1: read count normalization was done with a cutoff of >1CPM in >80% of samples. Values are log2(CPM)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include log2(CPM) values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: iPSC-derived neurons, 4 weeks old

growth_protocol: see section " iPSC line generation and neuronal differentiation" in Method of the manuscript

extract_protocol:
Total RNA was extracted from ~3x106 cells for each condition using miRNeasy kit (Qiagen, USA) according to the manufacturer’s instructions. RNA was resuspended in RNAse-free water
Library preparation was done using the TruSeq Stranded Total RNA Kit (Ilumina) with Ribo-Zero depletion. Sequencing was done on the NovaSeq 6000 at 150bp paired end reads with a total of 113M reads (~17Gb/sample).

treatment_protocol: Li treatment 1.5mM (Sigma)

tag: cell type

value: iPSC-derived neurons, 4 weeks old

tag: genotype

value: wildtype

tag: phenotype

tag: treatment

value: untreated


title: myb110-2-SAM

city: Nanjing

first: Yi

last: Jin

address: No. 666, Binjiang Avenue, Jiangbei New District

country: China

institute: Nanjing Agricultural University

description: Library name: sample11

data_processing:
To ensure data quality, it is necessary to perform data filtering on the raw data before information analysis to reduce the analytical interference caused by invalid data. Firstly, we use fastp to conduct quality control on the raw reads obtained from the sequencer, filtering out low-quality data (the filtering criteria are detailed below), and obtain clean reads.After the data is filtered, we will analyze the composition of bases and the distribution of quality to visually present the quality of the data. The more balanced the base composition and the higher the quality, the more accurate the subsequent analysis will be.
Assembly: The Rice Annotation Project Database （RAP-DB, http://rapdb.dna.affrc.go.jp/）
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Oryza sativa

source_name: SAM

extract_protocol:
Total RNA was isolated by TRIzol reagent (Invitrogen) and purified by RNeasy Plant Mini Kit (Qiagen)
After enriching eukaryotic mRNA with polyA tails using magnetic beads with Oligo(dT), the mRNA was fragmented with buffer. Using the fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized in an M-MuLV reverse transcriptase system. Subsequently, the RNA strand was degraded with RNaseH, and the second strand of cDNA was synthesized in a DNA polymerase I system using dNTPs as raw materials. The purified double-stranded cDNA was subjected to end repair, addition of an A tail, and ligation of sequencing adapters. AMPure XP beads were used to select cDNA of approximately 200bp, followed by PCR amplification and purification of the PCR products with AMPure XP beads. Finally, the library was obtained.

tag: tissue

value: SAM

tag: cell line

value: no


title: myb110-1-blade

description: Library name: sample4

source_name: blade

value: blade


title: WT-2-SAM

description: Library name: sample8


title: myb110-2-blade

description: Library name: sample5


title: WT-1-SAM

description: Library name: sample7


title: WT3-Blade

description: Library name: sample3


title: myb110-3-SAM

description: Library name: sample12


title: WT2-Blade

description: Library name: sample2


title: WT-3-SAM

description: Library name: sample9


title: WT1-Blade

description: Library name: sample1


title: myb110-1-SAM

description: Library name: sample10


title: individual MA_20026, lithium-treated

value: Lithium


title: 10N

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Library name: F1

data_processing:
FastQ files were aligned against the Mus musculus mm10 genome with STAR 2.5.2b using default options.
Aligned reads were used to obtain expression quantification at mm10 NCBI RefSeq gene level using featureCounts with options minMQS=1 (unique hits).
Assembly: mm10
Supplementary files format and content: Raw counts in excel format

organism: Mus musculus

source_name: Interscapular Brown adipose tissue

growth_protocol: Mice were kept under a 12 h dark/light cycle and provided a standard chow diet and water ad libitum.

extract_protocol:
RNA was harvested using RNAeasy minikit columns (Qiagen). mRNA was isolated from 1.2 μg of total RNA using the kit NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
NGS libraries for RNA-seq were prepared from the purified mRNA using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

value: Interscapular Brown adipose tissue


title: myb110-3-blade

description: Library name: sample6


title: 8N

description: Library name: H12


title: 5N

description: Library name: G12


title: individual MA_20026, untreated


title: SETD2CI_H3K79me1

city: Cleveland

first: Kaixiang

last: Cao

state: Ohio

address: 10900 Euclid Avenue

country: USA

institute: Case Western Reserve University

description: Library name: Sample 39

library_source: genomic

data_processing:
ChIP-Rx mapping and peak calling were performed using the ENCODE ChIP-seq analysis pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” and then aligned to the mouse mm9 and human hg19 genome assemblies using Bowtie v2.4.4 or BWA v0.7.17 with default parameters.  All unmapped reads, low mapping quality reads (MAPQ < 30), and PCR duplicates were removed using SAMtools v1.14 and Picard v2.21.4 (https://broadinstitute.github.io/picard/). The number of spike-in hg19 reads was counted with SAMtools v1.14 and normalization factor alpha = 1e6/hg19_count was calculated. Normalized bigwig was generated with bamCoverage function from deepTools v3.5.1 using scale factors calculated above and reads mapped to the ENCODE blacklist regions were removed using BEDTools v2.17.0.
Assembly: mm9
Supplementary files format and content: Bigwig files

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: ESCs were grown in N2B27 based serum free medium containing MEK inhibitor PD0325901 and GSK inhibitor CHIR99021 (2i), and LIF (Sigma).

extract_protocol:
ESCs were fixed with 1% formaldehyde (Thermo Fisher) and sheared with E220 focused ultrasonicator (Covaris), respectively. Sheared chromatins were mixed with lysate from HEK293T cells processed identically as spike-in for normalization. Mixed chromatin were incubated at 4℃ overnight with antibodies. Protein A/G beads (Santa Cruz Biotechnology) were then incubated with the chromatin and antibody mixture for 2 hours at 4℃. Beads were washed, reverse-crosslinked, and DNA were purified with Qiaquick PCR purification kit (Qiagen).
KAPA HyperPrep Kit (Roche) was used to prepare ChIP-Rx libraries.

value: Embryonic stem cells

value: SETD2 CI


title: DCI_H3K79me1

description: Library name: Sample 40

value: DCI


title: DOT1LCI_H3K79me1

description: Library name: Sample 38

value: DOT1L CI


title: individual PE0050M, lithium-treated


title: 4N

description: Library name: F12


title: WT_H3K79me1

description: Library name: Sample 37

value: WT


title: DCI_RNAPII_2

description: Library name: Sample 36


title: 3N

description: Library name: E12


title: WT_RNAPII_2

description: Library name: Sample 35


title: DCI_TEAD4

description: Library name: Sample 34


title: DCI_RNAPIISer5

description: Library name: Sample 42


title: WT_RNAPIISer5

description: Library name: Sample 41


title: DOT1LCI_input_2

description: Library name: Sample 29


title: individual NS0405R, untreated


title: SETD2CI_input_2

description: Library name: Sample 28


title: WT_YAP1

description: Library name: Sample 31


title: individual NS0405R, lithium-treated


title: 10C

description: Library name: D12


title: DCI_input_2

description: Library name: Sample 30


title: WT_input_2

description: Library name: Sample 27


title: WT_TEAD4

description: Library name: Sample 32


title: DCI_YAP1

description: Library name: Sample 33


title: 8C

description: Library name: C12


title: 6C

description: Library name: B12


title: individual MA_35794, lithium-treated


title: scATAC_Control_ivposi

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: Library name: scATAC_Control_ivposi

library_source: genomic single cell

data_processing:
Basecalls and mapping performed using Cell Ranger ver v4.3.2 and 7.0.1
Assembly: mm10, GRCh38
Supplementary files format and content: Matrix.h5 including barcodes, features and matrix tsv files

source_name: Lung

extract_protocol:
Single-cell suspensions were prepared from mouse lung tissues by isolating CD4(iv)-negative tissue-resident and CD4(iv)-positive circulating CD4⁺ T cells via FACS (BD FACS Aria III), with 10,000 viable cells (>98% viability) collected per subset; human nasal polyps were finely minced and enzymatically digested in RPMI 1640 containing collagenase III, hyaluronidase, and DNase I, followed by mononuclear cell isolation through Percoll density gradient centrifugation and 70-μm nylon mesh filtration, while peripheral blood mononuclear cells were isolated using Ficoll-Paque Plus and similarly filtered to ensure high-quality single-cell suspensions.
Single-cell RNA-seq libraries for both mouse and human (nasal polyps and PBMCs) samples were generated using the Chromium Single Cell 3’ Reagent Kits v3.1 with dual indexing (10x Genomics), and single-cell ATAC-seq libraries for mouse samples were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics), followed by sequencing on a NovaSeq 6000 system (Illumina) with appropriate read settings and achieving a minimum depth of 20,000–25,000 read pairs per cell or nucleus according to assay type.

treatment_protocol: Mouse models were sensitized by intranasal administration of Aspergillus fumigatus antigen (Greer, Lenoir, NC, USA) over a 7-week period using a modified protocol: 50 μg of antigen was delivered once weekly for the initial 3 weeks, followed by 20 μg twice weekly for the remaining 4 weeks; assays were typically conducted 24 hours after the final antigen exposure, though in some experiments, mice were analyzed at specific time points—days 0, 8, 22, and 36 during sensitization, or 7 weeks post-final antigen administration.

value: Lung

value: Control

tag: term

tag: iv staining

value: positive


title: WT_RNAPIISer2

description: Library name: Sample 25


title: individual MA_21868, lithium-treated


title: DCI_RNAPIISer2

description: Library name: Sample 26


title: individual MA_21868, untreated


title: DCI_H3K79me3

description: Library name: Sample 24


title: DOT1LCI_H3K79me3

description: Library name: Sample 23


title: 1C

description: Library name: A12


title: SETD2CI_H3K79me3

description: Library name: Sample 22


title: individual PE0050M, untreated


title: individual MA_7762, lithium-treated


title: scATAC_Control_ivnega

description: Library name: scATAC_Control_ivnega

value: negative


title: scATAC_7w_Asp_ivposi

description: Library name: scATAC_7w_Asp_ivposi

value: Asp-Ag


title: individual MA_35794, untreated

value: iPSC-derived neurons, 4 weeks old

value: wildtype


title: DCI_H3K79me2

description: Library name: Sample 20


title: individual MA_7762, untreated

value: untreated


title: WT_H3K79me3

description: Library name: Sample 21


title: DOT1LCI_H3K79me2

description: Library name: Sample 19


title: scATAC_7w_Asp_ivnega

description: Library name: scATAC_7w_Asp_ivnega


title: SETD2CI_H3K79me2

description: Library name: Sample 18


title: individual MA_40064, lithium-treated


title: WT_H3K79me2

description: Library name: Sample 17


title: scRNA_14w_Asp_ivnega

description: Library name: scRNA_14w_Asp_ivnega

library_source: transcriptomic single cell


title: DCI_H3K27ac

description: Library name: Sample 16


title: WT_H3K27ac

description: Library name: Sample 15


title: individual MA_40064, untreated


title: WT_H3K4me1

description: Library name: Sample 13


title: DCI_RNAPII

description: Library name: Sample 12


title: individual MA_7158, lithium-treated


title: DCI_H3K4me1

description: Library name: Sample 14


title: scRNA_Control_ivnega

description: Library name: scRNA_Control_ivnega


title: DCI_input

description: Library name: Sample 10


title: scRNA_Control_ivposi

description: Library name: scRNA_Control_ivposi


title: individual MA_7158, untreated


title: SETD2CI_RNAPII

description: Library name: Sample 9


title: DCI_H3K36me3

description: Library name: Sample 11


title: scRNA_7w_Asp_ivposi_rep2

description: Library name: scRNA_7w_Asp_ivposi_rep2


title: SETD2CI_H3K36me3

description: Library name: Sample 8


title: individual MNI_EEDU_3448, untreated


title: individual MNI_EEDU_3448, lithium-treated


title: SETD2CI_input

description: Library name: Sample 7


title: scRNA_7w_Asp_ivposi_rep1

description: Library name: scRNA_7w_Asp_ivposi_rep1


title: DOT1LCI_RNAPII

description: Library name: Sample 6


title: scRNA_14w_Asp_ivposi

description: Library name: scRNA_14w_Asp_ivposi


title: individual MA_37014, lithium-treated


title: DOT1LCI_H3K36me3

description: Library name: Sample 5


title: scRNA_7w_Asp_ivnega_rep2

description: Library name: scRNA_7w_Asp_ivnega_rep2


title: WT_RNAPII

description: Library name: Sample 3


title: WT_H3K36me3

description: Library name: Sample 2


title: DCI_VP8h_ATAC_2

description: Library name: Sample 8

data_processing:
Raw reads from ATAC-seq were trimmed as described in ChIP-Rx and aligned to the mm9 genome assembly using Bowtie v2.4.4 with parameter “-N 1 -L 25 -X 2000 --no-mixed --no-discordant”. Mitochondrial reads and PCR duplicates were then filtered using SAMtools v1.12 and Picard Tools v2.25.5 (https://broadinstitute.github.io/picard/). Finally, the reads were shifted to compensate for the offset in the tagmentation site relative to the Tn5 binding site using the alignmentSieve function of deepTools v3.5.1 with the ‘--ATACshift’ option. Reads were normalized to total read counts per million (cpm) and visualized as bigwig-formatted coverage tracks using deepTools v3.5.1.
Assembly: mm9
Supplementary files format and content: Bigwig files

extract_protocol:
Cells were washed with PBS and lysed with ATAC lysis buffer. 50K nuclei were tagmented at 37 °C for 30 minutes. Tagmented DNA was then cleaned up with the MinElute Reaction Clean-up Kit (Qiagen) and subject to library preparation.
Tagmented DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay.

value: VP


title: DCI_DMSO8h_ATAC_2

description: Library name: Sample 7

value: DMSO


title: individual MNI_EEDU_L2131, lithium-treated

value: Lithium


title: DCI_VP8h_ATAC

description: Library name: Sample 6


title: scRNA_7w_Asp_ivnega_rep1

description: Library name: scRNA_7w_Asp_ivnega_rep1


title: DCI_DMSO8h_ATAC

description: Library name: Sample 5


title: AML-06-postTx-Live_GoT_IDH2_R140_runS62

city: New York

first: Maria

last: Sirenko

state: NY

address: 550 1st Avenue

institute: NYU Langone

description:
Library name: AML-06-postTx-Live_GoT_IDH2_R140_runS62
GoT

library_source: other

data_processing:
FASTQs were aligned to GRCh38 and cell by gene count matrices were generated using CellRanger 5.0.1 with default parameters. CellRanger quality control metrics are provided in Table S1. Gene expression analysis was conducted using Seurat v4 in R4.2.2.
Assembly: GRCh38 - default CellRanger reference
Supplementary files format and content: cellranger filtered barcode matrices provided
Supplementary files format and content: seurat object in rds format

molecule: other

source_name: Peripheral Blood

extract_protocol:
Samples from AML-01, AML-02, AML-03, AML-04, AML-05, AML-06, CH-01, CH-02 were processed as follows. Frozen bone marrow and peripheral blood samples were thawed under standard procedures and prepared for sorting by flow cytometry. Briefly, cryopreserved samples were thawed and transferred to 15 ml conical tubes containing 10 ml of RPMI media with 10% fetal bovine serum (FBS) and 0.1mL of a 1 mg/mL DNAse I solution. Cells were centrifuged at 300 x g for 4 minutes at 4°C, and supernatant was removed. Cells were resuspended in FACS buffer and incubated with Fc blocker for 15 minutes. Next, cells were stained with PE-conjugated CD45, and FITC-conjugated CD3, CD19, and CD56 to enable lymphoid-depleted sorting. Cells were stained for 15 minutes and resuspended in FACS-DAPI to enable enrichment for live cells. Cells were then sorted for DAPI-, CD3-/CD19-/CD56- cells using the BD Influx at the Weill Cornell Medicine flow cytometry core.
Sorted cells were processed using the 10X Genomics Chromium controller with the Single Cell Gene Expression 5’ V1 protocol (except sample CH-05 which was processed on 5’ V2 after V1 was discontinued). The 5’ kit was selected to maximize genotyping efficiency because most mutations, including IDH1, IDH2, NRAS, and SRSF2, were closer to the 5’ end of the mRNA. Single cell gene expression libraries were sequenced on a Nova-seq 6000 with R1:R2:I1 27:176:8bp paired end format where R1 contains the 10X barcode and UMI, R2 contains the transcript sequence, and I1 the sample index. Single cell genotyping was applied to 13 patients/donors (AML-01, AML-02, AML-03, AML-04, AML-05, AML-06, AML-16, AML-17, AML-18, AML-19, AML-20, CH-01, CH-02). Somatic mutations detected by clinical targeted DNA sequencing informed the design of multiplexed single cell genotyping using Genotyping of Transcriptomes (GoT).25 GoT targets were prioritized to capture mutations representative of distinct subclones with greater than 5% VAF in targeted DNA sequencing and sufficient gene expression in 10X data. Cells were profiled using the 5’ 10X Genomics kit to maximize GoT efficiency, as most mutations were within 1000bp of the 5’ end (IDH1/2, NRAS, NPM1, and SRSF2) (Figures S4B and S4C). GoT libraries were prepared for IDH1, IDH2, NRAS, NPM1, FLT3 and SRSF2 as described in Nam et al.25 We did not genotype DNMT3A which is often clonal and co-occurring within the same cells as IDH mutations, due to technical limitations of low gene expression (Average expression in single cell data: 0.19; comparable to IDH1 0.15) and >2000 base pair mutation distance from 5’ end. Primers used for GoT are provided in Table S1. GoT Libraries were pooled and sequenced on Illumina MiniSeq 300 cycle mid-output kit in 147:8:147 paired end configuration or spiked in at 1-2% of gene expression library sequencing runs on NovaSeqX Plus with configuration as described above.

value: Peripheral Blood

value: postTx

value: Live

value: Post-Treatment

tag: batch

value: GoT


title: RelAcKO3

city: Niigata City

first: Norihisa

last: Bizen

address: 757 Ichibancho, Asahimachi-dori, Chuo Ward

department: Graduate School of Medical and Dental Sciences

institute: Niigata University

description: Library name: RelAcKO3

data_processing:
alignment with STAR
to have BAM file
transcript level  with RSEM
Assembly: mm39
Supplementary files format and content: .txt, gene_id, gene_symbol, raw count

source_name: cerebral cortex including hippocampas

growth_protocol: RelA knock-out mice, RelAflox/flox mice were crossed with Cnp-Cre knockin mice.

extract_protocol:
Total RNA was extracted from the cerebral cortices including hippocampi of control and RelA cKO mice at P14, with three independent biological replicates for each group. RNA extraction was performed using QIAzol reagent, and mRNA libraries were subsequently constructed by Novogene using the Illumina TruSeq RNA Sample Prep Kit v2.
TruSeq RNA Sample Prep Kit v2

value: cerebral cortex including hippocampas

value: RelA cKO


title: RelAcKO1

description: Library name: RelAcKO1


title: AML-06-postTx-Live_GoT_SRSF2_P95_runS62

description:
Library name: AML-06-postTx-Live_GoT_SRSF2_P95_runS62
GoT


title: WT_ATAC_2

description: Library name: Sample 3

value: Embryonic stem cells

value: WT


title: RelAcKO2

description: Library name: RelAcKO2


title: DCI_ATAC_2

description: Library name: Sample 4

value: DCI


title: Ctrl3

description: Library name: Ctrl3

value: Control


description:
Library name: AML-06-Dx-LymphDepleted_GoT_SRSF2_P95_runS62
GoT

value: Dx

value: LymphDepleted

value: Diagnosis


title: DCI_ATAC

description: Library name: Sample 2


title: WT_ATAC

description: Library name: Sample 1


title: Ctrl2

description: Library name: Ctrl2


title: DCI_serumLIF_RNA_2

description: Library name: Sample 44

data_processing:
Raw reads were processed with Trimmomatic v0.39 to remove adaptors and low-quality reads with the parameter “-q 30”. The cleaned reads were aligned to the mm9 genome assembly using STAR v2.5.1 with default parameter. Reads were normalized to total read counts per million (cpm) and visualized as bigwig-formatted coverage tracks using deepTools v3.5.6.
Assembly: mm9
Supplementary files format and content: bigwig files for plus and minus strands

extract_protocol:
RNA was extracted and purified with Trizol reagent (Life Technologies) following manufacturer’s instructions. RNA was further treated with DnaseI (Sigma) and then purified with RNeasy mini kit (Qiagen).
NEBNext rRNA Depletion Kit (New England BioLabs) and NEBNext Ultra II Directional RNA Kit (New England BioLabs) were used to deplete ribosomal RNA and prepare RNA-seq libraries, respectively.


description:
Library name: AML-06-Dx-LymphDepleted_GoT_IDH2_R140_runS62
GoT


title: DCI_serumLIF_RNA

description: Library name: Sample 43


title: individual MA_37014, untreated

value: iPSC-derived neurons, 4 weeks old

value: wildtype

value: untreated


title: DOT1LCI_input

description: Library name: Sample 4

value: DOT1L CI


title: SETD2CI_serumLIF_RNA_2

description: Library name: Sample 42

value: SETD2 CI


description:
Library name: AML-05-postTx-Live_GoT_SRSF2_P95_runS216
GoT

value: Peripheral Blood

value: postTx

value: Live


title: Ctrl1

description: Library name: Ctrl1

value: cerebral cortex including hippocampas


title: individual MNI_EEDU_L2131, untreated


title: WT_input

description: Library name: Sample 1


title: Luc-V2_TCR

city: Bethesda

first: Peng

last: Jiang

state: Maryland

address: 41 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

description:
Library name: Luc-V2_TCR
HCC tumor 8 induced by MYC-Luc with vector overexpression

data_processing:
We first run “cellranger multi” (v7.2.0) with default parameters to jointly processed the 5RNA, BCR, and TCR sequencing data.
We used the R package Seurat 5.0.1 to process and merge eight scRNA-seq samples from hepatocellular carcinoma tumors. Quality control was conducted to filter out the cells with unique feature counts > 4000 or <500, or >15% mitochondrial counts. We then normalized the total counts in each cell to 10,000, followed by log transformation to generate the normalized data. We applied Uniform Manifold Approximation and Projection (UMAP) analysis to the first 30 principal components (PCs) for dimensional reduction and data visualization. We clustered the cells using FindClusters from Seurat, which is a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm. We used Scrublet 0.2.2 to calculate doublet scores. The marker genes of major lineage and sub-lineage are adapted from https://www.cellsignal.com/pathways/immune-cell-markers-mouse.
Further analysis details are available in our manuscript Methods section.
Assembly: mm39
Supplementary files format and content: cellranger outputs
Supplementary files format and content: cell type annotations in tab-delimited txt files.
Library strategy: TCR-Seq

molecule: polyA RNA

source_name: spontaneous hepatocellular carcinoma tumor

extract_protocol:
Tumor samples were harvest and dissociated into single-cell suspension using Liberase (Sigma) and DNase I (Sigma). The CD45+ tumor-infiltrating lymphocytes were then isolated from the single-cell mixture by using the EasySep™ Mouse CD45 Positive Selection Kit (Stem cell technologies) and resuspended in sterile PBS. The CD45+ TILs were sent to HKU CPOS for further processing.
Fresh single-cell suspensions prepared in the previous step were processed using the Chromium Single Cell 5’ Library + TCR/BCR Library (10× Genomics) to generate uniquely barcoded RNA, which was then reverse-transcribed into cDNA, PCR-amplified, and used to construct sequencing libraries. The uniquely barcoded cDNA was sequenced on the Illumina NovaSeq 6000 platform. Quality control was performed with Cell Ranger, and the sequencing data were aligned to the mouse genome (mm39), resulting in Cell Ranger output files.

treatment_protocol: For the anti-PD1 experiment, treatments were initiated 8-9 days after hydrodynamic delivery of plasmids, a time point that already presents malignant tumor cells. Anti-PD1 (BioXCell, #BE0146, 200 μg/dose) was given twice per week for a total of 4 doses. Bioluminescence imaging was taken twice a week.


title: Luc-V1_TCR

description:
Library name: Luc-V1_TCR
HCC tumor 7 induced by MYC-Luc with vector overexpression

value: spontaneous hepatocellular carcinoma tumor


title: DOT1LCI_serumLIF_RNA_2

description: Library name: Sample 40

value: Embryonic stem cells


title: DOT1LCI_serumLIF_RNA

description: Library name: Sample 39


title: WT_serumLIF_RNA_2

description: Library name: Sample 38

value: WT


title: WT_SGC0946_72h_RNA_2

description: Library name: Sample 35


title: LucOS-V2_TCR

description:
Library name: LucOS-V2_TCR
HCC tumor 6 induced by MYC-LucOS (antigen) with vector overexpression


description:
Library name: AML-05-Dx-LymphDepleted_GoT_IDH2_R140_runS62
GoT

value: GoT


title: WT_serumLIF_RNA

description: Library name: Sample 37


title: LucOS-V1_TCR

description:
Library name: LucOS-V1_TCR
HCC tumor 5 induced by MYC-LucOS (antigen) with vector overexpression


title: WT_SGC0946_EPZ719_72h_RNA_2

description: Library name: Sample 36


description:
Library name: AML-05-Dx-LymphDepleted_GoT_SRSF2_P95_runS216
GoT


title: WT_SGC0946_EPZ719_72h_RNA

description: Library name: Sample 33


description:
Library name: AML-04-postTxD84-Live_GoT_SRSF2_P95_runS216
GoT

value: Post-Treatment


title: WT_DMSO_72h_RNA_4

description: Library name: Sample 34

value: DMSO


description:
Library name: AML-04-postTxD84-Live_GoT_IDH2_R172_runS203
GoT


title: WT_SGC0946_72h_RNA

description: Library name: Sample 32


title: WT_DMSO_72h_RNA_3

description: Library name: Sample 31


title: SETD2CI_serumLIF_RNA

description: Library name: Sample 41


description:
Library name: AML-04-postTxD28-LymphDepleted_GoT_IDH2_R172_runS62
GoT

value: LymphDepleted


title: LucOS-A1_TCR

description:
Library name: LucOS-A1_TCR
HCC tumor 3 induced by MYC-LucOS (antigen) with Aoah overexpression


title: WT_DMSO_72h_RNA_2

description: Library name: Sample 30


title: WT_EPZ719_72h_RNA_2

description: Library name: Sample 29


description:
Library name: AML-04-postTxD28-LymphDepleted_GoT_SRSF2_P95_runS62
GoT


title: WT_DMSO_72h_RNA

description: Library name: Sample 28


title: Luc-A2_TCR

description:
Library name: Luc-A2_TCR
HCC tumor 2 induced by MYC-Luc with Aoah overexpression


title: LucOS-A2_TCR

description:
Library name: LucOS-A2_TCR
HCC tumor 4 induced by MYC-LucOS (antigen) with Aoah overexpression


title: AML-05-postTx-Live_GoT_IDH2_R140_runS62

description:
Library name: AML-05-postTx-Live_GoT_IDH2_R140_runS62
GoT


title: Luc-A1_TCR

description:
Library name: Luc-A1_TCR
HCC tumor 1 induced by MYC-Luc with Aoah overexpression


title: WT_EPZ719_72h_RNA

description: Library name: Sample 27


title: DCI_VP24h_RNA_2

description: Library name: Sample 26

value: DCI

value: VP


title: DCI_VP8h_RNA_2

description: Library name: Sample 25


title: Luc-V2_BCR

description:
Library name: Luc-V2_BCR
HCC tumor 8 induced by MYC-Luc with vector overexpression

data_processing:
We first run “cellranger multi” (v7.2.0) with default parameters to jointly processed the 5RNA, BCR, and TCR sequencing data.
We used the R package Seurat 5.0.1 to process and merge eight scRNA-seq samples from hepatocellular carcinoma tumors. Quality control was conducted to filter out the cells with unique feature counts > 4000 or <500, or >15% mitochondrial counts. We then normalized the total counts in each cell to 10,000, followed by log transformation to generate the normalized data. We applied Uniform Manifold Approximation and Projection (UMAP) analysis to the first 30 principal components (PCs) for dimensional reduction and data visualization. We clustered the cells using FindClusters from Seurat, which is a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm. We used Scrublet 0.2.2 to calculate doublet scores. The marker genes of major lineage and sub-lineage are adapted from https://www.cellsignal.com/pathways/immune-cell-markers-mouse.
Further analysis details are available in our manuscript Methods section.
Assembly: mm39
Supplementary files format and content: cellranger outputs
Supplementary files format and content: cell type annotations in tab-delimited txt files.
Library strategy: BCR-Seq


title: DCI_DMSO8h_RNA_2

description: Library name: Sample 23


description:
Library name: AML-04-postTxD28-Live_GoT_SRSF2_P95_runS216
GoT


title: Luc-V1_BCR

description:
Library name: Luc-V1_BCR
HCC tumor 7 induced by MYC-Luc with vector overexpression


title: DCI_VP8h_RNA

description: Library name: Sample 21


title: DCI_VP24h_RNA

description: Library name: Sample 22


title: DCI_DMSO24h_RNA

description: Library name: Sample 20


description:
Library name: AML-04-Dx-LymphDepleted_GoT_IDH2_R172_runS62
GoT

value: Dx

value: Diagnosis


description:
Library name: AML-03-postTx-LymphDepleted_GoT_NPM1_W288_runS62
GoT

source_name: Bone Marrow

value: Bone Marrow


title: Ewing3_GEX

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

description: Library name: sample3

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.
Gene expression libraries were aligned to GRCh38 using CellRanger v7.0.1.
Assembly: GRCh38
Supplementary files format and content: Gzipped tar archive file containing tab-delimited barcodes, features, and matrix files.

source_name: tumor

extract_protocol:
Freshly resected Ewing sarcoma tumors were mechanically disrupted/ Single-cell RNAseq was performed using 10X Genomics and libraries were sequenced on an Illumina NovaSeq500 instrument.
The library generation strategy was as per the manufacturer's instructions for 10X Genomics 5' based chemistries.

value: tumor

tag: disease state

value: Ewing sarcoma


title: LucOS-A2_BCR

description:
Library name: LucOS-A2_BCR
HCC tumor 4 induced by MYC-LucOS (antigen) with Aoah overexpression


title: LucOS-A1_BCR

description:
Library name: LucOS-A1_BCR
HCC tumor 3 induced by MYC-LucOS (antigen) with Aoah overexpression


title: DCI_neural_day21_RNA_3

description: Library name: Sample 18


description:
Library name: AML-03-postTx-LymphDepleted_GoT_NPM1_W288_runS45
GoT

value: postTx


title: CD34+, sgRNA68, rep1

city: Cambridge

first: Heejin

last: Roh

state: MA

address: 12 Oxford St

institute: Harvard

description: Library name: HBG_68_r1

data_processing:
After removing adapters using NGmerge, the ATAC-seq data was aligned using bowtie2, and duplicates were removed by using picard MarkDuplicates.
Bam files were converted into fragments files by using bedtools bamtobed.
The genomic region of interest was divided into 1 bp bins and the number of Tn5 fragment ends overlapping with each bin was quantified as the Tn5 insertion density. Then the insertion density track was smoothed by a 250 bp window to obtain the final coverage track. The coverage tracks were exported to bigwig format and visualize in IGV
Assembly: hg38
Supplementary files format and content: XXX.frags.gz: ATAC fragments files. Containing 5 columns corresponding to the chromosome, start, end, sample ID, and count of each fragment.

source_name: Blood

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 10%. CD34+ HSPCs were cultured in hematopoietic stem cell expansion media consisting of StemSpan SFEM II supplemented CC100 cytokine cocktail, 50 ng/mL human TPO, 1% L-Glutamine, 1% penicillin/streptomycin, and 35 nM UM171.

extract_protocol:
DNA was purified with the Qiagen MinElute PCR Purification Kit
Cells were washed twice with PBS and resuspended in PBS. 10, 000 cells in 5 µL PBS were mixed 42.5 µL of transposition buffer. The reaction was incubated at room temperature for 10 minutes, followed by the addition of 2.5 µL of assembled Tn5 transposase, and then incubated at 37 °C for 30 minutes in a Thermomixer set to 300 rpm. DNA was subsequently purified with the Qiagen MinElute PCR Purification Kit and minimally amplified for sequencing. Final libraries were purified again with the MinElute PCR Purification Kit.

treatment_protocol: Cells were transduced with lentiviral particles carrying the sgRNA plasmid and selected with puromycin. Subsequently, cells were electroporated with Cas9. For CD34+ cells, erythroid differentiation was initiated 2 days after electroporation by switching to EDM media.

value: Blood

value: CD34+ HSPC

value: Hematopoietic stem and progenitor cells

value: sgRNA-68 HBG deletion

value: sgRNA transduction, Cas9 electroportaion, erythroid differentiation

tag: time

value: Day 5 after differentiation induction


title: DCI_DMSO8h_RNA

description: Library name: Sample 19

value: Embryonic stem cells


title: CD34+, sgRNA68, rep2

description: Library name: HBG_68_r2


title: Luc-A2_BCR

description:
Library name: Luc-A2_BCR
HCC tumor 2 induced by MYC-Luc with Aoah overexpression

value: spontaneous hepatocellular carcinoma tumor


title: DCI_neural_day21_RNA_2

description: Library name: Sample 16


description:
Library name: AML-03-postTx-LymphDepleted_GoT_IDH1_R132_runS62
GoT

value: LymphDepleted

value: Post-Treatment

value: GoT


title: DCI_DMSO24h_RNA_2

description: Library name: Sample 24

value: DCI

value: DMSO


title: CD34+, Non-targeting sgRNA, rep1

description: Library name: HBG_nc_r1

value: WT


description:
Library name: AML-03-postTx-LymphDepleted_GoT_IDH1_R132_runS45
GoT

value: Bone Marrow


title: CD34+, Non-targeting sgRNA, rep2

description: Library name: HBG_nc_r2


title: WT_neural_day21_RNA_2

description: Library name: Sample 15


title: Luc-A1_BCR

description:
Library name: Luc-A1_BCR
HCC tumor 1 induced by MYC-Luc with Aoah overexpression


description:
Library name: AML-04-Dx-LymphDepleted_GoT_SRSF2_P95_runS62
GoT

value: Peripheral Blood

value: Dx

value: Diagnosis


title: LucOS-V2_BCR

description:
Library name: LucOS-V2_BCR
HCC tumor 6 induced by MYC-LucOS (antigen) with vector overexpression


description:
Library name: AML-04-postTxD28-Live_GoT_IDH2_R172_runS203
GoT

value: Live


title: KO 5 CSDS

city: Jerusalem

first: Hadas

last: Hovav

address: Hadassah Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Fastp v3 (with default parameters) was used for the quality control and preprocessing of raw reads.
The processed reads were mapped to the mouse mm10 genome using STAR 4 (with default parameters).
The systemPipeR v5 was employed to build the workflow for calculating gene expression of the mapped reads per kilobase of transcript per million (RPKM).
Assembly: mm10 genome
Supplementary files format and content: txt format. Content as RPKM

source_name: hippocampi

extract_protocol:
RNA was extracted from mice hippocampi using RNeasy Lipid Tissue Mini Kit
Libraries were constructed using Truseq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA).
poly A RNA-seq. 75 bp long, single-end fragments were sequenced

treatment_protocol: For 10 consecutive days, the experimental mice were placed for 5 min in the home cage of a previously screened, unfamiliar, aggressive CD-1 mouse. Following this physical stress, the two mice were separated by a perforated transparent divider for the remaining 24 h until the next defeat session. Each day, the experimental mouse was exposed to a different aggressor.

value: hippocampi

value: CSDS


description:
Library name: AML-03-postTx-LymphDepleted_GoT_IDH1_R132_runS123
GoT

value: postTx


title: DCI_neural_day21_RNA

description: Library name: Sample 14


title: LucOS-V1_BCR

description:
Library name: LucOS-V1_BCR
HCC tumor 5 induced by MYC-LucOS (antigen) with vector overexpression


title: Luc-V2_5RNA

description:
Library name: Luc-V2_5RNA
HCC tumor 8 induced by MYC-Luc with vector overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt

data_processing:
We first run “cellranger multi” (v7.2.0) with default parameters to jointly processed the 5RNA, BCR, and TCR sequencing data.
We used the R package Seurat 5.0.1 to process and merge eight scRNA-seq samples from hepatocellular carcinoma tumors. Quality control was conducted to filter out the cells with unique feature counts > 4000 or <500, or >15% mitochondrial counts. We then normalized the total counts in each cell to 10,000, followed by log transformation to generate the normalized data. We applied Uniform Manifold Approximation and Projection (UMAP) analysis to the first 30 principal components (PCs) for dimensional reduction and data visualization. We clustered the cells using FindClusters from Seurat, which is a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm. We used Scrublet 0.2.2 to calculate doublet scores. The marker genes of major lineage and sub-lineage are adapted from https://www.cellsignal.com/pathways/immune-cell-markers-mouse.
Further analysis details are available in our manuscript Methods section.
Assembly: mm39
Supplementary files format and content: cellranger outputs
Supplementary files format and content: cell type annotations in tab-delimited txt files.


title: WT_neural_day21_RNA_3

description: Library name: Sample 17


description:
Library name: AML-03-Dx-LymphDepleted_GoT_NPM1_W288_runS45
GoT


description:
Library name: AML-03-Dx-LymphDepleted_GoT_IDH1_R132_runS62
GoT


title: KO 4 CSDS


title: WT_neural_day21_RNA

description: Library name: Sample 13


title: KO 3 CSDS


title: LucOS-V2_5RNA

description:
Library name: LucOS-V2_5RNA
HCC tumor 6 induced by MYC-LucOS (antigen) with vector overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt


title: KO 2 CSDS


title: LucOS-V1_5RNA

description:
Library name: LucOS-V1_5RNA
HCC tumor 5 induced by MYC-LucOS (antigen) with vector overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt


title: DCI_RNA_3

description: Library name: Sample 12


description:
Library name: AML-03-Dx-LymphDepleted_GoT_IDH1_R132_runS45
GoT


title: SETD2CI_RNA_3

description: Library name: Sample 11

value: SETD2 CI


title: KO 1 CSDS


title: DOT1LCI_RNA_3

description: Library name: Sample 10

value: Embryonic stem cells

value: DOT1L CI


title: LucOS-A2_5RNA

description:
Library name: LucOS-A2_5RNA
HCC tumor 4 induced by MYC-LucOS (antigen) with Aoah overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt

value: spontaneous hepatocellular carcinoma tumor


description:
Library name: AML-03-Dx-LymphDepleted_GoT_IDH1_R132_runS123_2
GoT

value: LymphDepleted


title: KO 10B control


title: LucOS-A1_5RNA

description:
Library name: LucOS-A1_5RNA
HCC tumor 3 induced by MYC-LucOS (antigen) with Aoah overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt


description:
Library name: AML-03-Dx-LymphDepleted_GoT_NPM1_W288_runS62
GoT

value: GoT


description:
Library name: AML-03-Dx-LymphDepleted_GoT_IDH1_R132_runS123
GoT


title: WT_RNA_3

description: Library name: Sample 9


title: DCI_RNA_2

description: Library name: Sample 8

value: DCI


title: KO 11 control


description:
Library name: AML-02-postTx-LymphDepleted_GoT_NRAS_G12_runS35
GoT

value: NRAS

value: Post-Treatment


title: Luc-A2_5RNA

description:
Library name: Luc-A2_5RNA
HCC tumor 2 induced by MYC-Luc with Aoah overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt


title: KO 10 control

value: control


title: Luc-V1_5RNA

description:
Library name: Luc-V1_5RNA
HCC tumor 7 induced by MYC-Luc with vector overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt


title: Luc-A1_5RNA

description:
Library name: Luc-A1_5RNA
HCC tumor 1 induced by MYC-Luc with Aoah overexpression
meta_sc.combined.txt
meta_sc.combined.T.txt


description:
Library name: AML-02-postTx-LymphDepleted_GoT_IDH1_R132_runS35
GoT

value: Bone Marrow


description:
Library name: AML-02-Dx-LymphDepleted_GoT_IDH1_R132_runS35
GoT

value: Dx


title: KO 9 control


title: DOT1LCI_RNA_2

description: Library name: Sample 6


title: SETD2CI_RNA_2

description: Library name: Sample 7


title: Luc-V4

description:
Library name: Luc-V4
HCC tumor 14 induced by MYC-Luc with vector overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt

data_processing:
Raw fastq files were processed using the RNA-seq data-processing pipeline described in our publication.
Assembly: mm39
Supplementary files format and content: RSEM TPM values, tab delimited gzip file
Supplementary files format and content: DESeq2, Tab delimited text file
Supplementary files format and content: MiXCR summary, Tab delimited text file

extract_protocol:
Tumors samples were ground in a homogenizer and lysed using the TRIzol method (Takara) to release total RNA. The RNA was then extracted with chloroform, precipitated with isopropanol, washed with 75% ethanol, and finally dissolved in RNase-free water for quantification and quality control.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A tailing, adapter ligation, size selection, USER enzyme digestion, amplification and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: bulk tumor


title: DCI_RNA

description: Library name: Sample 4


title: Luc-V3

description:
Library name: Luc-V3
HCC tumor 13 induced by MYC-Luc with vector overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt


title: WT_RNA_2

description: Library name: Sample 5

value: WT


description:
Library name: AML-02-Dx-LymphDepleted_GoT_NRAS_G12_runS35
GoT

value: Diagnosis


title: AML-02-Dx-Blasts_GoT_NRAS_G12_runS35

description:
Library name: AML-02-Dx-Blasts_GoT_NRAS_G12_runS35
GoT

value: Blasts


title: KO 7 control

value: hippocampi


title: Luc-V2

description:
Library name: Luc-V2
HCC tumor 12 induced by MYC-Luc with vector overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt


title: KO 6 control


title: SETD2CI_RNA

description: Library name: Sample 3

value: SETD2 CI


title: LucOS-V3

description:
Library name: LucOS-V3
HCC tumor 10 induced by MYC-LucOS (antigen) with vector overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
LucOS.DESeq.txt


title: AML-02-Dx-Blasts_GoT_IDH1_R132_runS35

description:
Library name: AML-02-Dx-Blasts_GoT_IDH1_R132_runS35
GoT


title: Luc-V1

description:
Library name: Luc-V1
HCC tumor 11 induced by MYC-Luc with vector overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt


title: DOT1LCI_RNA

description: Library name: Sample 2

value: Embryonic stem cells


title: WT 5 CSDS

value: CSDS


description:
Library name: AML-01-postTx-LymphDepleted_GoT_NPM1_W288_runS35
GoT

value: postTx


title: WT 4 CSDS


description:
Library name: AML-01-postTx-LymphDepleted_GoT_IDH1_R132_runS75
GoT

value: LymphDepleted


title: LucOS-V1

description:
Library name: LucOS-V1
HCC tumor 8 induced by MYC-LucOS (antigen) with vector overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
LucOS.DESeq.txt

value: spontaneous hepatocellular carcinoma tumor


title: LucOS-V2

description:
Library name: LucOS-V2
HCC tumor 9 induced by MYC-LucOS (antigen) with vector overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
LucOS.DESeq.txt


title: WT 3 CSDS


title: WT_RNA

description: Library name: Sample 1


title: Time 6 Control_B (rep3)

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

description:
Library name: Sample B12
mRNA seq
Time6_Control_B_Time0_B_normalized_counts.txt
Time6_Control_B_Time0_B_results_differential_gene_expression.txt

data_processing:
Clean reads were obtained from the original sequencing data (raw reads) after removing the low-quality reads, mismatches, and adaptor sequences.The quality reads of the samples were mapped to Lactuca sativa reference genome (NCBI RefSeq assembly: GCF_002870075.2, cv. Salinas) using the STAR RNA-Seq aligner tool. Assignment of mapped reads to genomic features (counting) was performed with feature Counts version 1.6.3. The normalized counts per sample were calculated using the TPM method that takes into account the gene length and the sequencing library size. Then assembled reads of control and treated samples were merged together for differential expression analysis of genes.
Assembly: NCBI RefSeq assembly: GCF_002870075.2, Variety "Salinas"
Supplementary files format and content: text files  including normalized counts
Supplementary files format and content: text files including differential expression data

organism: Lactuca sativa

source_name: leaves

growth_protocol: variety "Luna Bionda" or "Falstaff"

extract_protocol:
Total RNA was isolated from the leaves (100mg) following a TRIZOL based method with modifications as previously described (Leonetti et al. 2021,  https://doi.org/10.1111/nph.16932). The quality of the RNA for each sample has been assured through Spectrophotometric evaluation (Nanodrop OneC, Thermo Fisher Scientific) and RNA integration Number (RIN) using Bio analyzer (Agilent Technologies Inc., USA), and qualified samples were proceeded to library construction. RNA amplification and cDNA library was prepared using the Nextera XT (Illumina, San Diego, CA, USA) by random fragmentation of the cDNA samples, followed by 5' and 3' adapter ligation. Each fragment was then amplified into distinct, clonal clusters through bridge amplification. The purified amplification products were sequenced on a Novaseq-PE 150 platform.
RNA amplification and cDNA library was prepared using the Nextera XT (Illumina, San Diego, CA, USA) by random fragmentation of the cDNA samples, followed by 5' and 3' adapter ligation. Each fragment was then amplified into distinct, clonal clusters through bridge amplification. The purified amplification products were sequenced on a Novaseq-PE 150 platform.

value: leaves

value: Wild type, Variety "Falstaff"

value: visible light only; Time day 6


description:
Library name: AML-01-postTx-LymphDepleted_GoT_IDH1_R132_runS35
GoT

value: Post-Treatment

value: GoT


title: KO 8 control

value: control


title: LucOS-A3

description:
Library name: LucOS-A3
HCC tumor 7 induced by MYC-LucOS (antigen) with Aoah overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
LucOS.DESeq.txt

value: bulk tumor


title: WT 2 CSDS

value: WT


title: WT 1 CSDS


title: Time 6 Control_B (rep2)

description:
Library name: Sample B11
mRNA seq
Time6_Control_B_Time0_B_normalized_counts.txt
Time6_Control_B_Time0_B_results_differential_gene_expression.txt


description:
Library name: AML-01-Dx-LymphDepleted_GoT_IDH1_R132_runS35
GoT

value: Bone Marrow

value: Dx

value: Diagnosis


title: AML-01-Dx-Blasts_GoT_NPM1_W288_runS35

description:
Library name: AML-01-Dx-Blasts_GoT_NPM1_W288_runS35
GoT

value: Blasts


title: Time 6 Control_B (rep1)

description:
Library name: Sample B10
mRNA seq
Time6_Control_B_Time0_B_normalized_counts.txt
Time6_Control_B_Time0_B_results_differential_gene_expression.txt


title: WT 9B control

value: hippocampi


title: LucOS-A1

description:
Library name: LucOS-A1
HCC tumor 5 induced by MYC-LucOS (antigen) with Aoah overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
LucOS.DESeq.txt


title: WT 10 control


title: AML-01-Dx-Blasts_GoT_IDH1_R132_runS35

description:
Library name: AML-01-Dx-Blasts_GoT_IDH1_R132_runS35
GoT


title: Time 6 UVA (rep3)

description:
Library name: Sample B9
mRNA seq
Time6_UVB2_B_Time0_B_normalized_counts.txt
Time6_UVB2_B_Time0_B_results_differential_gene_expression.txt


title: Time 6 UVA (rep2)

description:
Library name: Sample B8
mRNA seq
Time6_UVB2_B_Time0_B_normalized_counts.txt
Time6_UVB2_B_Time0_B_results_differential_gene_expression.txt


title: Luc-A4

description:
Library name: Luc-A4
HCC tumor 4 induced by MYC-Luc with Aoah overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt


title: CH-02_GoT_SRSF2_P95_runS224

description:
Library name: CH-02_GoT_SRSF2_P95_runS224
GoT

value: Peripheral Blood


title: Luc-A3

description:
Library name: Luc-A3
HCC tumor 3 induced by MYC-Luc with Aoah overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt


title: Time 6 UVA (rep1)

description:
Library name: Sample B7
mRNA seq
Time6_UVB2_B_Time0_B_normalized_counts.txt
Time6_UVB2_B_Time0_B_results_differential_gene_expression.txt


title: Time 6 UVB1_B (rep3)

description:
Library name: Sample B6
mRNA seq
Time6_UVB1_B_Time0_B_normalized_counts.txt
Time6_UVB1_B_Time0_B_results_differential_gene_expression.txt


title: WT 7 control


title: CH-02_GoT_IDH2_R140_runS224

description:
Library name: CH-02_GoT_IDH2_R140_runS224
GoT


title: Luc-A1

description:
Library name: Luc-A1
HCC tumor 1 induced by MYC-Luc with Aoah overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt


title: Time 6 UVB1_B (rep2)

description:
Library name: Sample B5
mRNA seq
Time6_UVB1_B_Time0_B_normalized_counts.txt
Time6_UVB1_B_Time0_B_results_differential_gene_expression.txt


title: CH-01_01_GoT_IDH2_R140_runS203

description:
Library name: CH-01_01_GoT_IDH2_R140_runS203
GoT


title: LucOS-A2

description:
Library name: LucOS-A2
HCC tumor 6 induced by MYC-LucOS (antigen) with Aoah overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
LucOS.DESeq.txt


title: Vec22

description:
Library name: Vec22
B16mghp100 tumor 7 with vector over-expression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
DESeq.Cr1l.txt

source_name: Subcutaneous implanted tumor

extract_protocol:
Tumors samples were ground in a homogenizer and lysed using the TRIzol method (Takara) to release total RNA. The RNA was then extracted with chloroform, precipitated with isopropanol, washed with 75% ethanol, and finally dissolved in RNase-free water for quantification and quality control.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: 10 days after the inoculation of tumor cells, anti-PD1 (BioXCell, #BE0146, 200 μg/dose) was given to the tumor-bearing mice twice per week for a total of 4 doses. One day after the last dose, tumor samples were harvested from the mice and used to RNA extraction.

value: Subcutaneous implanted tumor


title: Time 6 UVB1_B (rep1)

description:
Library name: Sample B4
mRNA seq
Time6_UVB1_B_Time0_B_normalized_counts.txt
Time6_UVB1_B_Time0_B_results_differential_gene_expression.txt


title: Time 0_B (rep3)

description:
Library name: Sample B3
mRNA seq
Time0_A_Time0_B_normalized_counts.txt
Time0_A_Time0_B_results_differential_gene_expression.txt

value: visible light only; Time day 0


title: Blood, scrapie_preclinical, 5

city: Zaragoza

first: Sonia

last: Pérez-Lázaro

address: Miguel Servet 177

institute: Universidad de Zaragoza

description: Library name: PC_25_03931AAC_TCGGCA

data_processing:
Each sample was sequenced twice and data from both files were merged to achieve a unique file per sample.
Sequencing adapters and reads for quality and length were trimmed using Skewer v0.2.2, applying default parameters.
Reads of length between 15 and 30 bases were aligned to the sheep reference genome using ShortStack v3.8.5, based on Bowtie 1 v1.2.2.
MiRNAs were annotated using Ovis aries miRNAs in miRBase v22;  reads not assigned were subjected to de novo prediction using Infernal v1.1.4 and miRDeep2 v2.0.1.2.
Infernal and miRDeep2 predictions were joined to the annotated miRNAs in Ovis aries from miRBase and filtered for removing redundancy using Bedtools v2.27.1
Merged annotation reads were quantified using HTSeq-count and filtered to retain miRNAs with at least one read per sample per group.
Assembly: Oar_v4.0
Supplementary files format and content: tab-delimited text file includes read counts after normalisation by DESEQ2

organism: Ovis aries

extract_protocol:
2.5 mL of blood were collected by jugular vein puncture into PAXgene Blood RNA Tubes (PreAnalytiX) and total RNA was extracted using the PAXgene Blood RNA kit (PreAnalytix), following the manufacturer's steps.
Sequencing libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (New England Biolabs), following the manufacturer’s protocol.

value: Blood


title: Vec21

description:
Library name: Vec21
B16mghp100 tumor 6 with vector over-expression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
DESeq.Cr1l.txt


title: Vec

description:
Library name: Vec
B16mghp100 tumor 5 with vector over-expression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
DESeq.Cr1l.txt


title: Blood, scrapie_preclinical, 4

description: Library name: PC_24_03930AAC_TCCCGA


title: E72, 29538, section 6

first: Gayani

last: Senevirathne

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

description: 10X Genomics

data_processing:
The raw files were mapped to the Human genome Hg38 using the Space Ranger v.2.0 software, available via the 10X Genomics website.
Assembly: hg38
Supplementary files format and content: space ranger output files: fragments, matrix and barcodes are provided.
Library strategy: Spatial transcriptomics

source_name: ilium

extract_protocol:
Fresh ilium tissues were dissected, flash frozen in OCT, sectioned at 10um, permeabalized, and follwed the 10X Genomics Multiomics manufactureres protocol. cDNA was made, amplified and the DNA was purified using Ampure beads.
Libraries were constructed following 10X Genomics visium manufactures protocols. Quality was checked using the tapestation, libraries were pooled and eventually sequenced using the NovaSeq X.
These are spatial transcriptomics datasets, performed on transverse or sagittal sections.

value: ilium


title: WT 9 control


title: Luc-A2

description:
Library name: Luc-A2
HCC tumor 2 induced by MYC-Luc with Aoah overexpression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
Luc.DESeq.txt

value: spontaneous hepatocellular carcinoma tumor


title: WT 8 control


title: E72, 29538, section 5

description: 10X Genomics


title: Time 0_B (rep2)

description:
Library name: Sample B2
mRNA seq
Time0_A_Time0_B_normalized_counts.txt
Time0_A_Time0_B_results_differential_gene_expression.txt

value: leaves

value: Wild type, Variety "Falstaff"


title: CH-01_02_GoT_IDH2_R140_runS203

description:
Library name: CH-01_02_GoT_IDH2_R140_runS203
GoT

value: LymphDepleted

value: GoT


title: Blood, scrapie_preclinical, 3

description: Library name: PC_23_04136AAC_TACAGC


title: Blood, scrapie_preclinical, 2

description: Library name: PC_22_04135AAC_CGGAAT


title: Cr1l4

description:
Library name: Cr1l4
B16mghp100 tumor 4 with Cr1l over-expression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
DESeq.Cr1l.txt

value: bulk tumor


title: Blood, scrapie_preclinical, 1

description: Library name: PC_21_04134AAC_CATTTT


title: E72, 29538, section 4

description: 10X Genomics


title: Cr1l2

description:
Library name: Cr1l2
B16mghp100 tumor 2 with Cr1l over-expression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
DESeq.Cr1l.txt


title: Time 0_B (rep1)

description:
Library name: Sample B1
mRNA seq
Time0_A_Time0_B_normalized_counts.txt
Time0_A_Time0_B_results_differential_gene_expression.txt


title: Time 6 Control_A (rep3)

description:
Library name: Sample A12
mRNA seq
Time6_Control_A_Time0_A_normalized_counts.txt
Time6_Control_A_Time0_A_results_differential_gene_expression.txt

value: Wild type, Variety "Luna bionda"

value: visible light only; Time day 6


title: Cr1l3

description:
Library name: Cr1l3
B16mghp100 tumor 3 with Cr1l over-expression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
DESeq.Cr1l.txt


title: Time 6 UVB2_A (rep1)

description:
Library name: Sample A11
mRNA seq
Time6_UVB2_A_Time0_A_normalized_counts.txt
Time6_UVB2_A_Time0_A_results_differential_gene_expression.txt


title: Blood, healthy, 10

description: Library name: N_20_04133AAC_CAACTA


title: WT 6 control

value: WT

value: control


title: E72, 29538, section 2

description: 10X Genomics


title: Cr1l1

description:
Library name: Cr1l1
B16mghp100 tumor 1 with Cr1l over-expression
RSEM.TPM.processed.txt.gz
MiXCR.Repertoire.txt
DESeq.Cr1l.txt


title: E72,29538, section 7

description: 10X Genomics


title: Time 6 Control_A (rep2)

description:
Library name: Sample A10
mRNA seq
Time6_Control_A_Time0_A_normalized_counts.txt
Time6_Control_A_Time0_A_results_differential_gene_expression.txt


title: Blood, healthy, 9

description: Library name: N_19_04132AAC_GAGTGG


title: E72, 29538, section 1

description: 10X Genomics


title: Vector_3_1

description:
Library name: Vector_3_1
B16mghp100 tumor 6 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: Blood, healthy, 8

description: Library name: N_18_04131AAC_CGTACG


title: Time 0_A (rep3)

description:
Library name: Sample A9
mRNA seq
Time0_A_Time0_B_normalized_counts.txt
Time0_A_Time0_B_results_differential_gene_expression.txt


title: Vector_2_2

description:
Library name: Vector_2_2
B16mghp100 tumor 5 portion 2 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: Blood, healthy, 7

description: Library name: N_17_03929AAC_GTCCGC


title: Time 0_A (rep2)

description:
Library name: Sample A8
mRNA seq
Time0_A_Time0_B_normalized_counts.txt
Time0_A_Time0_B_results_differential_gene_expression.txt


title: E72, 29538, section 3

description: 10X Genomics


title: E57, 29507, section 4

description: 10X Genomics


title: Vector_1_2

description:
Library name: Vector_1_2
B16mghp100 tumor 4 portion 2 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: Vector_2_1

description:
Library name: Vector_2_1
B16mghp100 tumor 5 portion 1 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: E57, 29507, section 3

description: 10X Genomics


title: Time 6 UVB2_A (rep3)

description:
Library name: Sample A6
mRNA seq
Time6_UVB2_A_Time0_A_normalized_counts.txt
Time6_UVB2_A_Time0_A_results_differential_gene_expression.txt


title: Time 6 UVB2_A (rep2)

description:
Library name: Sample A5
mRNA seq
Time6_UVB2_A_Time0_A_normalized_counts.txt
Time6_UVB2_A_Time0_A_results_differential_gene_expression.txt


title: E57, 29507, section 2

description: 10X Genomics


title: Blood, healthy, 4

description: Library name: N_14_04129AAC_ATGTCA


title: Vector_1_1

description:
Library name: Vector_1_1
B16mghp100 tumor 4 portion 1 with vector over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: Colq_3

description:
Library name: Colq_3
B16mghp100 tumor 3 with Colq over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: Blood, healthy, 5

description: Library name: N_15_04130AAC_CCGTCC


title: Time 6 Control_A (rep1)

description:
Library name: Sample A4
mRNA seq
Time6_Control_A_Time0_A_normalized_counts.txt
Time6_Control_A_Time0_A_results_differential_gene_expression.txt


title: Blood, healthy, 3

description: Library name: N_13_04128AAC_AGTTCC


title: 53, 29271, section 8

description: 10X Genomics


title: E57, 29507, section 1

description: 10X Genomics


title: 53, 29271, section 6

description: 10X Genomics


title: Colq_2

description:
Library name: Colq_2
B16mghp100 tumor 2 with Colq over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: Time 6 UVB1_A (rep3)

description:
Library name: Sample A3
mRNA seq
Time6_UVB1_A_Time0_A_normalized_counts.txt
Time6_UVB1_A_Time0_A_results_differential_gene_expression.txt


title: 53, 29271, section 2

description: 10X Genomics


title: Blood, healthy, 2

description: Library name: N_12_04127AAC_CTTGTA


title: Colq_1

description:
Library name: Colq_1
B16mghp100 tumor 1 with Colq over-expression
RSEM.TPM.processed.gz
MiXCR.Repertoire
DESeq.Colq


title: Time 6 UVB1_A (rep2)

description:
Library name: SampleA2
mRNA seq
Time6_UVB1_A_Time0_A_normalized_counts.txt
Time6_UVB1_A_Time0_A_results_differential_gene_expression.txt


title: Blood, healthy, 6

description: Library name: N_16_03928AAC_GTAGAG


title: Time 0_A (rep1)

description:
Library name: Sample A7
mRNA seq
Time0_A_Time0_B_normalized_counts.txt
Time0_A_Time0_B_results_differential_gene_expression.txt


title: Brain 12

city: Hamilton

first: Sheila

middle: K

last: Singh

state: ON

address: 1280 Main St. West

department: Surgery

institute: McMaster University

data_processing:
Demultiplexed samples were then input into Galaxy to make use of Cutadapt and Trimgalore features
20 nucleotide sequences corresponding to sgRNA detected in each sample were aligned to an index file of all sgRNA and corresponding target genes contained within the Calabrese A library
Aligned reads from each sample were combined into a read matrix file in R and normalized to 1 million reads per sample
Normalized reads were then utilized to determine sgRNA abundance in the lungs and brains
Assembly: Human Calabrese libaray A index file
Supplementary files format and content: each processed data file type consists of the 20 nucleotide sgRNA sequences amplified from each mouse lung or brain.  These will need to be aligned to the library index file in order to obtain raw sgRNA counts.

source_name: brain

growth_protocol: 2x10^6 CRUK0748-GLD cells transduced with the Calabrese "A" library were inoculated into the lung of an NSG mice.  This was repeated for 29 other mice.  At endpoint, lungs and brains were extracted and sequenced for sgRNA abundance

extract_protocol:
Genomic DNA was extracted from each tissue using the Gentra Puregene tissue kit (Qiagen #158689) and DNA pellets were resuspended in nuclease-free water.  DNA was phenol:chloroform extracted and ethanol precipitated before proceeding
sgRNA were amplified from DNA extracts from lung or brain tissue.  Amplicons were then amplified with a mix p5 (including stagger for diversity) and uniquely barcoded p7 primers to add illumina adapters to each sample
amplicon sequencing

treatment_protocol: No treatment was used in this experiment

value: brain

value: Lung adenocarcinoma cell line modified to express dCas9, GFP and luciferase


title: E53, 29607, section 3

description: 10X Genomics


title: Blood, healthy, 1

description: Library name: N_11_04126AAC_GGCTAC


title: Blood, scrapie_clinical, 10

description: Library name: C_10_04125AAC_TAGCTT


title: Time 6 UVB1_A (rep1)

description:
Library name: Sample A1
mRNA seq
Time6_UVB1_A_Time0_A_normalized_counts.txt
Time6_UVB1_A_Time0_A_results_differential_gene_expression.txt


title: E53, 29607, section 2

description: 10X Genomics


title: Blood, scrapie_clinical, 9

description: Library name: C_9_04124AAC_GATCAG


title: Brain 10


title: Brain 9


title: E53, 29607, section 1

description: 10X Genomics


title: Blood, scrapie_clinical, 7

description: Library name: C_7_03926AAC_CAGATC


title: Brain 8


title: phot1 gl1, 15C, ZT24, rep1

city: La Jolla

first: Adam

last: Seluzicki

state: CA

address: 10010 N. Torrey Pines Rd.

department: Plant Biology Laboratory

institute: HHMI, Salk Institute for Biological Studies

data_processing:
Cyverse
Tophat2-SE_Stranded version 2.0.9
BowTie version 2.1.0
HTSeq-0.6.1 : strand specificity: none, MODE: intersect_strict
edgeR 3.16.5, retained genes with cumulative CPM >2 across all samples
Assembly: TAIR10
Supplementary files format and content: tab delimited text file with raw counts for nuclear genes
Supplementary files format and content: tab-delimited text file with normalized Counts per million reads (CPM) for all samples – one column per sample

organism: Arabidopsis thaliana

source_name: 14-day-old Shoot (above-ground)

growth_protocol: seeds germinated on 1/2x Linsmaier & Skoog medium, grown for two days, transplanted to soil and moved to chambers with light intensity ~100umol m-2 s-1 at noted growth temperature. Above-ground (shoot) tissue from three plants per sample were harvested at the indicated time.

extract_protocol:
RNA was extracted using the RNeasy Plant Mini Kit (Qiagen)
Stranded mRNA

value: 14-day-old Shoot (above-ground)

value: phot1-5 gl1

value: 16h light, 8h dark, 15C

tag: time (zeitgeber_time-zt)


title: 67, 29597, section 8

description: 10X Genomics


title: Blood, scrapie_clinical, 8

description: Library name: C_8_03927AAC_ACTTGA

value: Blood


title: phot1 gl1, 15C, ZT24, rep2


title: 67, 29597, section 7

description: 10X Genomics

value: ilium


title: 67, 29597, section 6

description: 10X Genomics


title: Brain 7


title: Blood, scrapie_clinical, 6

description: Library name: C_6_04123AAC_GCCAAT


title: gl1, 15C, ZT24, rep2


title: Blood, scrapie_clinical, 5

description: Library name: C_5_04122AAC_ACAGTG


title: gl1, 15C, ZT24, rep1


title: Brain 11


title: 67, 29597, section 3

description: 10X Genomics


title: Blood, scrapie_clinical, 4

description: Library name: C_4_04121AAC_TGACCA


title: 57, 29508, section 9

description: 10X Genomics


title: Brain 5


title: Brain 6


title: phot2 gl1, 20C, ZT24, rep2

value: phot2-1 gl1

value: 16h light, 8h dark, 20C


title: Blood, scrapie_clinical, 3

description: Library name: C_3_04120AAC_TTAGGC


title: Brain 4


title: phot2 gl1, 15C, ZT24, rep1


title: 57, 29508, section 5

description: 10X Genomics


title: phot2 gl1, 20C, ZT24, rep1


title: Brain 3


title: Blood, scrapie_clinical, 2

description: Library name: C_2_04119AAC_CGATGT


title: 54, 29166, section 6

description: 10X Genomics


title: phot1 gl1, 20C, ZT24, rep1


title: Blood, scrapie_clinical, 1

description: Library name: C_1_04140AAC_ATCACG


title: Brain 2


title: KO7

description: Library name: 133 2020

data_processing:
FastQ files were aligned against the Mus musculus mm10 genome with STAR 2.5.2b using default options.
Aligned reads were used to obtain expression quantification at mm10 NCBI RefSeq gene level using featureCounts with options minMQS=1 (unique hits).
Assembly: mm10
Supplementary files format and content: Raw counts in excel format

extract_protocol:
RNA was harvested using RNAeasy minikit columns (Qiagen). mRNA was isolated from 1.2 μg of total RNA using the kit NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
NGS libraries for RNA-seq were prepared from the purified mRNA using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

value: Interscapular Brown adipose tissue

value: HETEROZYGOUS RAP250


title: phot2 gl1, 15C, ZT24, rep2


title: 54, 29166, section 5

description: 10X Genomics


title: gl1, 20C, ZT24, rep2


title: Brain 1


title: E59, 29133, section 1

description: 10X Genomics


title: E57, 29074, section3

description: 10X Genomics


title: KO6

description: Library name: 132 2020


title: Lung 13

source_name: lung

value: lung


title: KO4

description: Library name: 130 2020


title: KO3

description: Library name: 129 2020


title: Lung 11


title: Lung 12


title: E72,29190 ilium, scMultiomics,ATAC

description: 10X Genomics

data_processing:
The raw files were mapped to the Human genome Hg38 using the Cell Ranger v.2.0 software, available via the 10X Genomics website.
Assembly: hg38
Supplementary files format and content: cell ranger output files: fragments, matrix and barcodes are provided. These output files are same for the both RNA and ATAC.

extract_protocol:
Fresh ilium tissues were extracted, digested using Collagenese type II, filtered and the cell count was calculated prior to moving on to following the 10X Genomics Multiomics protocol. cDNA was made, amplified and the DNA was purified using Ampure beads.
Libraries were constructed following 10X Genomics multiomics manufactures protocols. Quality was checked using the tapestation, libraries were pooled and eventually sequenced using the NovaSeq X.
These are sc-multiomics samples: a combination of scRNA+scATAC seq has been perfomed on the same set of cells.

value: Chondrocytes, muscles etc

tag: library

value: DNA


title: phot2 gl1, 15C, ZT16, rep2


title: phot2 gl1, 15C, ZT16, rep1


title: Lung 10


title: E45,29029,section1

description: 10X Genomics


title: WT4

description: Library name: 127 2020


title: E72,29190 ilium, scMultiomics,RNA

description: 10X Genomics

value: RNA


title: phot1 gl1, 15C, ZT16, rep2


title: phot1 gl1, 20C, ZT24, rep2


title: E59,  ilium, scMultiomics, ATAC

description: 10X Genomics


title: WT3

description: Library name: 126 2020

value: WT


title: Lung 9


title: phot1 gl1, 15C, ZT16, rep1


title: Lung 8


title: E59,  ilium, scMultiomics,RNA

description: 10X Genomics


title: gl1, 15C, ZT16, rep2


title: gl1, 20C, ZT24, rep1


title: WT2

description: Library name: 125 2020


title: gl1, 15C, ZT16, rep1


title: CD3 T cells Isolated from 23 week old fetal thymus

city: Singapore

first: Pavanish

last: Kumar

state: Not Applicable

address: 20 collage road, The Academia, Discovery Tower, Level-8 Translation Immunology Institute (TII)

country: Singapore

institute: Translational Immunology Institute (TII), SingHealth-DukeNUS

description: Library name: FT_23week

data_processing:
Cellranger v4.0.8 (10x genomics) was used for barcode proccessing, feature counting and gene aggregation.
Assembly: Human Hg38
Supplementary files format and content: Tab seperated features, barcode information and count matrix mtx file.

source_name: Fetal thymus

growth_protocol: 10% Human Serum, 1% PSG, RPMI

extract_protocol: 10x Genomics Chromium Next GEM Single Cell Single Cell 5’ Reagent Kits v2 (Dual Index)

treatment_protocol: Immune cells were stained and sorted for CD45+ live cells. No stimulation performed

value: Fetal thymus

value: Primary human Lymphocytes

value: Lymphocytes


title: E72, ilium, scMultiomics,RNA

description: 10X Genomics


title: Lung 7

value: Lung adenocarcinoma cell line modified to express dCas9, GFP and luciferase


title: CD3 T cells Isolated from 16 week old fetal thymus

description: Library name: FT_16week


title: Lung 6


title: phot2 gl1, 20C, ZT16, rep2

value: 14-day-old Shoot (above-ground)


title: E67, ilium, scMultiomics,ATAC

description: 10X Genomics


title: phot2 gl1, 20C, ZT16, rep1


title: CD3 T cells Isolated from 14 week old fetal thymus

description: Library name: FT_14week


title: E67, ilium, scMultiomics,RNA

description: 10X Genomics


title: Lung 4


title: E57, ilium, scMultiomics,ATAC

description: 10X Genomics


title: CD3 T cells Isolated from 23 week old fetal liver

description: Library name: FL_23week

source_name: Fetal Liver

value: Fetal Liver


title: phot1 gl1, 20C, ZT16, rep2

value: phot1-5 gl1


title: E57, ilium, scMultiomics,RNA

description: 10X Genomics

value: ilium


title: CD3 T cells Isolated from 16 week old fetal liver

description: Library name: FL_16week


title: phot1 gl1, 20C, ZT16, rep1


title: Lung 3


title: gl1, 20C, ZT16, rep2


title: CD3 T cells Isolated from 15 week old fetal liver

description: Library name: FL_15week


title: E53, ilium, scMultiomics, ATAC

description: 10X Genomics


title: Lung 1


title: E53, ilium, scMultiomics,RNA

description: 10X Genomics


title: E72, ilium, scMultiomics, ATAC

description: 10X Genomics


title: CD3 T cells Isolated from 14 week old fetal liver

description: Library name: FL_14week


title: gl1, 20C, ZT16, rep1


title: CD3 T cells Isolated from 15 week old fetal thymus

description: Library name: FT_15week


title: MT3, CCD-1, dDAVP-3, 5 days, RNA-seq

status: Public on Jul 03 2025

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

description:
Library name: Sample 35
20210922_tpm_betacat_noAVP_annotated.txt

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 104). Transcript per million (TPM) and expected counts were generated by RSEM. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform. For ATAC-seq processing, adapter sequences were trimmed for both forward and reverse reads using cutadapt (version 3.4, parameters: minimum length = 36, -- q = 30). Read quality was assessed using fastQC. Trimmed sequences were aligned to the mouse reference genome mm10 using bowtie2 (parameters : X = 2000, -- no-mixed, -- no-discordant). The resulting SAM files were converted to a binary format (BAM), sorted by queryname, and indexed using samtools (function used; samtools view, samtools sort and samtools index). Reads that mapped to the mitochondrial genome were removed using samtools (function used; samtools idxstats). Identically mapping read duplicates were marked using Picard MarkDuplicates (Broad Institute. Picard toolkit. Broad Institute, GitHub repository (2019)), and removed using samtools (parameters: -F 1804, -f =2, -q =30). BAM files were converted to BED format using BedTools (version: v2.30.0). Narrow open chromatin peaks were identified using MACS2 with parameter –nomodel --shift -75 –extsize 150. Reads mapping to ENCODE blacklist regions were discarded using BedTools (i.e., empirically identified genomic regions that produce artifactual high signal in functional genomic experiments). For visualization, bigwig files were generated using bamCoverage. Read distribution was visualized on the UCSC genome browser. As ATAC-seq-specific quality control, fragment size distribution was evaluated by the bamQC function under the R package ATACseqQC. Differentially accessible regions (DAR) between vehicle infusion and dDAVP-infusion were identified using R package DiffBind with a statistical cutoff of FDR < 0.01.
Assembly: Ensemble release 104
Supplementary files format and content: text file includes TPM valus for RNAs-eq

source_name: Kidney

extract_protocol:
RNA was extracted using Direct-zol RNA MicroPrep kit
For RNA-seq: Trizol-extracted RNA was proceeded to cDNA generation using the SMARTer V4 Ultra Low RNA Kit (Takara Bio). cDNA was generated with 8 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform. For ATAC-seq: ATAC-seq was performed using a the method of Corces et al. Three manually dissected cortical collecting ducts (300-600 μm each) were lysed and transposed simultaneously in 25 μl of transposition mix (0.1% NP40, 0.1% Tween-20, 0.01% digitonin and 5% Tn5 enzyme [Illumina # 15027865] in Tagment DNA Buffer [FC-121–1030; Illumina]). The transposition reaction was incubated at 37 °C for 30 mins in a thermomixer with shaking at 1,000 rpm. After 11 tagmentation, the reactions were stopped with addition of 80 μl of water, 3 μl of 0.5% EDTA, 1.5 μl of 20% SDS and 5 μl of proteinase K (20 mg/mL stock, Fisher Scientific #25530049). The transposed DNA fragments were purified by DNA Purification Kits (Zymo Research, # D4014), and amplified by PCR. The final libraries were purified using AmPure XP magnetic beads (Beckman Coulter, Indianapolis, IN). Mitochondrial DNA were depleted from the purified libraries using a CRISPR/Cas9-based method.46 The DNA content of the final library was quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA). Purified DNA libraries were sequenced on an Illumina Novaseq platform.

value: Kidney

tag: group

value: WT mouse with dDAVP infusion

value: microdissected CCD

value: dDAVP


title: MT3, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 33
20210922_tpm_betacat_noAVP_annotated.txt


title: MT4, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 36
20210922_tpm_betacat_noAVP_annotated.txt


title: MT4, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 37
20210922_tpm_betacat_noAVP_annotated.txt


title: Lung 5

value: lung


title: MT3, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 34
20210922_tpm_betacat_noAVP_annotated.txt


title: MT2, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 31
20210922_tpm_betacat_noAVP_annotated.txt


title: MT2, CCD-1, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 32
20210922_tpm_betacat_noAVP_annotated.txt


title: MT1, CCD-1, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 29
20210922_tpm_betacat_noAVP_annotated.txt


title: MT2, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 30
20210922_tpm_betacat_noAVP_annotated.txt


title: MT1, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 28
20210922_tpm_betacat_noAVP_annotated.txt


title: WT4, CCD-1, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 26
20210922_tpm_betacat_noAVP_annotated.txt


title: WT4, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 25
20210922_tpm_betacat_noAVP_annotated.txt


title: Lung 2


title: WT3, CCD-1, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 23
20210922_tpm_betacat_noAVP_annotated.txt


title: WT4, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 24
20210922_tpm_betacat_noAVP_annotated.txt


title: WT3, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 22
20210922_tpm_betacat_noAVP_annotated.txt


title: WT3, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 21
20210922_tpm_betacat_noAVP_annotated.txt


title: WT2, CCD-1, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 20
20210922_tpm_betacat_noAVP_annotated.txt


title: MT4, CCD-1, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 38
20210922_tpm_betacat_noAVP_annotated.txt


title: WT1, CCD-1, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 17
20210922_tpm_betacat_noAVP_annotated.txt


title: WT2, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 18
20210922_tpm_betacat_noAVP_annotated.txt


title: WT1, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 16
20210922_tpm_betacat_noAVP_annotated.txt


title: WT, CCD-4, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 14
WT-dDAVP-infusion.txt


title: WT1, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 15
20210922_tpm_betacat_noAVP_annotated.txt


title: WT, CCD-2, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 12
WT-dDAVP-infusion.txt


title: WT, CCD-3, dDAVP-3, 5 days, RNA-seq

description:
Library name: Sample 13
WT-dDAVP-infusion.txt


title: WT, CCD-4, Vehicle, 5 days, RNA-seq

description:
Library name: Sample 10
WT-dDAVP-infusion.txt

value: WT mouse with Saline infusion

value: Saline


title: MT1, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 27
20210922_tpm_betacat_noAVP_annotated.txt


title: WT, CCD-1, Vehicle, 5 days, RNA-seq

description:
Library name: Sample 7
WT-dDAVP-infusion.txt


title: WT, CCD-1, dDAVP-1, 5 days, RNA-seq

description:
Library name: Sample 11
WT-dDAVP-infusion.txt


title: WT, CCD-2, Vehicle, 5 days, RNA-seq

description:
Library name: Sample 8
WT-dDAVP-infusion.txt


title: WT, CCD-3, Vehicle, 5 days, RNA-seq

description:
Library name: Sample 9
WT-dDAVP-infusion.txt


title: WT, CCD-3, Vehicle, 5 days, ATAC-seq

description:
Library name: Sample 3
ATAC_CCD_veh_vs_dDAVP_5days.txt


title: WT, CCD-2, Vehicle, 5 days, ATAC-seq

description:
Library name: Sample 2
ATAC_CCD_veh_vs_dDAVP_5days.txt


title: WT, CCD-1, dDAVP-1, 5 days, ATAC-seq

description:
Library name: Sample 4
ATAC_CCD_veh_vs_dDAVP_5days.txt


title: WT, CCD-2, dDAVP-2, 5 days, ATAC-seq

description:
Library name: Sample 5
ATAC_CCD_veh_vs_dDAVP_5days.txt


title: WT, CCD-3, dDAVP-3, 5 days, ATAC-seq

description:
Library name: Sample 6
ATAC_CCD_veh_vs_dDAVP_5days.txt


title: CDC50A KD4

city: Memphis

first: Douglas

middle: R

last: Green

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
Library name: sh50A_4
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686027_sh50A_4

data_processing:
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse mm10 assembly using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function.
Transcript quantification was calculated using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for all sample

source_name: Myeloid

growth_protocol: RAW264.7 cells were plated on 6-well plates in complete media and harvested in cold PBS the next day

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen), quantified by RiboGreen (ThermoFisher), and quality-checked on a 4200 TapeStation HS RNA ScreenTape (Agilent)
Libraries were prepared from 500 ng total RNA with the TruSeq Stranded mRNA Kit (Illumina), with insert sizes verified on TapeStation D1000 and concentrations measured by PicoGreen (ThermoFisher)

value: Myeloid

value: CDC50A KD


title: CDC50A KD3

description:
Library name: sh50A_3
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686026_sh50A_3


title: CDC50A KD2

description:
Library name: sh50A_2
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686025_sh50A_2


title: WT, CCD-1, Vehicle, 5 days, ATAC-seq

description:
Library name: Sample 1
ATAC_CCD_veh_vs_dDAVP_5days.txt


title: CDC50A KD1

description:
Library name: sh50A_1
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686024_sh50A_1


title: WT2, CCD-1, dDAVP-2, 5 days, RNA-seq

description:
Library name: Sample 19
20210922_tpm_betacat_noAVP_annotated.txt


title: ATP11A/C KD4

description:
Library name: shA-C_4
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686023_shA-C_4

value: ATP11A/C KD


title: ATP11A/C KD2

description:
Library name: shA-C_2
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686021_shA-C_2


title: ATP11A/C KD3

description:
Library name: shA-C_3
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686022_shA-C_3


title: ATP11A/C KD1

description:
Library name: shA-C_1
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt :2686020_shA-C_1


title: ORP5/8 KD4

description:
Library name: sh5-8_4
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686019_sh5-8_4

value: ORP5/8 KD


title: ORP5/8 KD3

description:
Library name: sh5-8_3
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686018_sh5-8_3


title: ORP5/8 KD2

description:
Library name: sh5-8_2
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686017_sh5-8_2


title: Parental4

description:
Library name: Ctrl_4
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686015_Ctrl_4

value: Parental


title: ORP5/8 KD1

description:
Library name: sh5-8_1
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686016_sh5-8_1


title: Parental3

description:
Library name: Ctrl_3
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686013_Ctrl_3


title: Parental2

description:
Library name: Ctrl_2
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686013_Ctrl_2


title: Skeletal muscle, CC_NaB1

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

description: RNA-seq

data_processing:
RNA-seq raw files (fastq, PE150) were aligned to the GRCm38/mm10 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided (tab-delimited file).

source_name: Skeletal muscle

growth_protocol: Mice were maintained under standard housing conditions and received a regular diet.

extract_protocol:
Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.
The RNA-seq library preparation was followed by the instructions of LC Bio Technology CO., Ltd.

treatment_protocol: The cancer cachexia model was established according to the literature. A cancer cachexia model was established by subcutaneous injection of a cell suspension containing a specific number of tumor cells at a concentration of 500,000 cells/100 μL per mouse into the flank of mice. The cachexia phenotype typically manifested within 2 to 3 weeks. Mice were then randomized into four groups: control (NC), cachexia (C26), cachexia with sodium butyrate (CNaB), and sodium butyrate only (NaB). Cachexia was induced by injecting either C26 cells (5×105 cells/mouse) into BALB/c mice or LLC cells (5×105 cells/mouse) into C57BL/6J mice. Starting on day 7 after inoculation, mice were administered sodium butyrate (50 mg/kg) or sterile water by gavage daily. Body weight and food consumption were monitored daily, and after 14 days, mice were euthanized for tissue collection.

value: Skeletal muscle

tag: strain

value: BALB/c

value: WT

tag: Sex

value: Male

value: 500000 C26 cell injection and NaB supplementation


title: Eosinophil, EV treated, Biol rep 2

city: Nashville

first: Heather

middle: H.

last: Pua

state: Tennessee

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

data_processing:
For pipeline details please see https://github.com/parkdj1/RNASeq-Pipeline
FastQC was used to quality control data
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequence reads were mapped to mouse genome and counts extracted using Salmon
Read count normalization and differential expression analysis were performed using DESeq2
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes DESeq differential gene expression analysis between Th2 cell EV- and media-treated eosinophils.
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Bone marrow-derived eosinophil

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). ~0.5-1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) selection kit by the Vanderbilt Technologies for Advanced Genomics Core

treatment_protocol: Eosinophils were differentiated from bone marrow and treated with EVs purified from Th2 cell culture by size exclusion chromatography or parallelly processed non-conditioned media as a control for 24 hours.

value: Bone marrow-derived eosinophil

value: Th2 cell EV, 24 hrs


title: Eosinophil, EV treated, Biol rep 3


title: Eosinophil, Media treated, Biol rep 3

value: Media, 24 hrs


title: Eosinophil, Media treated, Biol rep 2


title: Eosinophil, Media treated, Biol rep 1


title: small intestine tissue, KO

city: Beijing

first: Jiali

last: Wang

address: Hai Dian

institute: Tsinghua University

data_processing:
Remove the contaminated reads for adapters and remove the low-quality reads.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HIAST2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then estimate the expression level of genes.
DEGseq was used for differential gene expression analysis between two samples with non biological replicates.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

source_name: small intestine

extract_protocol:
The RNA of small intestine tissues  was extracted by TRIzol reagent (Invitrogen).
RNA-Seq library construction uses amplification of cDNA via SMART-SeqII.

value: small intestine

value: Spibfl/flVillin-Cre


title: KO, tuft cell, Spib

data_processing:
After removing adapters (Trim Galore!), reads were aligned to mouse reference genome (mm10) using bowtie2.
Peak calling was performed using SEACR (v1.2) in  stringent mode.
The distribution of peaks was annotated with ChIPseeker.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Sorted tuft cells were incubated with Con-A-coaed beads and Spi-B antibody (CST).
CUT&Tag seq libraries were prepared using HyperactiveTM In-situ ChIP library Prep Kit for Illumina according to the manufacturer’s protocol.

value: tuft cells


title: WT, tuft cell, Spib

value: Spib+Villin-Cre


title: Skeletal muscle, CC2

city: Nanjing

data_processing:
RNA-seq raw files (fastq, PE150) were aligned to the GRCm38/mm10 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).

value: 500000 C26 cells injection


title: small intestine tissue, WT


title: Skeletal muscle, NC3

value: PBS injection


title: Skeletal muscle, NC2


title: Skeletal muscle, CC1


title: male offspring / control mother library#7

city: Grand Rapids

first: Adelheid

last: Lempradl

state: Michigan

address: 333 Bostwick Ave NE

department: Metabolism and Nutritional Programing

institute: Van Andel Institute

data_processing:
Adapter and low-quality sequences were trimmed from the reads using Trim Galore v0.6.0 (Krueger et al., 2021) with the ‘--paired’ parameter.
Trimmed reads were aligned to the mm10 genome with GENCODE M24 gene annotations (Frankish et al., 2019), using STAR v2.7.8a (Dobin et al., 2013) with the parameters ‘--twopassMode Basic’, and ‘--quantMode GeneCounts’ to generate the read counts per gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited files containing per-gene read counts as calculated by STAR.

source_name: hypothalamus

extract_protocol:
Prior to RNA extraction, tissue samples were stored in RNAlater at -80°C. 1 mL TRIzol Reagent (Life Technologies, 15596026) was added per 50-100 mg of tissue in screw cap tubes containing 3 mm Zirconium Beads (OPS Diagnostics, BAWZ 3000-300-23). Tissue was homogenized using the FastPrep-24 system on high for 30 seconds and visually observed for tissue disruption, performing additional homogenizations as needed. 200 ul chloroform (Sigma-Aldrich, 319988) was added and samples were centrifuged at 12,000 x g for 15 minutes at 4°C. The upper aqueous phase was transferred to new Eppendorf tubes followed by RNA precipitation using 500 ul ice cold isopropanol (Sigma-Aldrich, 190764) and 2 ul GlycoBlue (ThermoFisher, AM9516) for pellet visualization. Samples were then centrifuged at 12,000 x g for 15 minutes at 4°C. Supernatant was removed and discarded. The samples were washed twice with 75% ethanol (Fisher Scientific, 111000200), using a 5-minute 7,500 x g centrifugation each round for pellet collection. The pellet was air dried for 10 minutes and resuspended in 20 ul RNase-free water (Life Technologies, AM9938). Samples were incubated at 60°C for 5 minutes, then stored at -80°C.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA). Ribosomal RNA material was reduced using the QIAseq FastSelect –rRNA HMR Kit (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA)). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer to an average depth of 30M raw paired-reads per transcriptome.

value: hypothalamus

tag: litter

value: Control


title: Skeletal muscle, NC1


title: male offspring / control mother library#31


title: male offspring / control mother library#22


title: male offspring / control mother library#2


title: Skeletal muscle, CC_NaB3

description: RNA-seq


title: Parental1

description:
Library name: Ctrl_1
Column names in GREEN-318289-STRANDED_RSEM_gene_count.2024-01-10_03-09-06.txt : 2686012_Ctrl_1

value: Myeloid

value: Parental


title: male offspring / control mother library#19


title: Skeletal muscle, CC_NaB2

description: RNA-seq

value: Skeletal muscle

value: BALB/c


title: male offspring / control mother library#21

value: Male


title: male offspring / control mother library#10


title: Eosinophil, EV treated, Biol rep 1

tag: cell type


title: female offspring / control mother library#8

tag: genotype

value: Female


title: female offspring / control mother library#30


title: female offspring / control mother library#33


title: female offspring / control mother library#28


title: Skeletal muscle, CC3

value: WT


title: female offspring / control mother library#11


title: female offspring / control mother library#15


title: female offspring / control mother library#1


title: male offspring / benzene exposed mother library#32

value: Benzene


title: female offspring / benzene exposed mother library#4


title: male offspring / control mother library#24


title: male offspring / benzene exposed mother library#3


title: male offspring / benzene exposed mother library#27


title: female offspring / benzene exposed mother library#20


title: male offspring / benzene exposed mother library#13


title: male offspring / benzene exposed mother library#12


title: female offspring / benzene exposed mother library#9


title: male offspring / control mother library#18


title: female offspring / benzene exposed mother library#6


title: male offspring / benzene exposed mother library#5


title: female offspring / benzene exposed mother library#26


title: female offspring / benzene exposed mother library#23


title: female offspring / benzene exposed mother library#16


title: female offspring / benzene exposed mother library#25