title: D3TA-02

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

description:
Library name: Sample 4
10X Genomics

data_processing:
Cell Ranger was used for demultiplexing, barcode processing, gene counting, and aggregation analysis.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Spleen

extract_protocol:
Spleen were mechanically digested using a scalpel and passed sequentially through 16G × 1" and 19G × 1½" needles. Single-cell suspensions were filtered through a 70 µm cell strainer, followed by red blood cell lysis using BD Pharm Lyse buffer (BD Biosciences, Cat# 555899) for 15 minutes. Cells were then washed with PBS and filtered through a 35 µm cell strainer.
Single cells were loaded onto 10X Genomics GEM-X chips targeting 10,000 cells per sample, and barcoded cDNA transcripts were generated using the 10X Genomics Chromium X platform. Sample-labeled cDNA libraries were constructed according to the manufacturer's protocol and sequenced on an Illumina NovaSeq X sequencer

treatment_protocol: A global, constitutive heterozygous knock-in of the CCND3 gene resulting in a Thr283Ala substitution was generated in the C57BL/6J background using CRISPR/Cas9 genome editing

value: Spleen

value: spleenocytes


title: D1408T24

status: Public on May 01 2026

type: SRA

city: Paris

first: Alessandro

last: Donada

address: 11 rue Pierre et Marie Curie, Batiment Curie, RDC, R12, UMR168 - Equipe Perie

country: France

institute: Institut Curie

description: Library name: Dataset_B_24

library_source: transcriptomic single cell

data_processing:
FASTQ files for each single cell were generated using bcl2fastq (version 2.20.0), with default parameters. The Read 1 contain the TSO (constant tag sequence and a UMI) followed by cDNA or only cDNA.  The Read 2 contain cDNA only. Index1 and index2 reads correspond to cell-specific barcode. The scRNA-SmartSeq3 pipeline v1.2.1 (https://doi.org/10.5281/zenodo.15056215) was used to generate UMI count tables from FASTQ files. Briefly, reads were aligned to the human genome (hg38) using STAR (version 2.7.8a) and assigned to genes using FeatureCounts (deeptools version 3.5.0). UMIs were extracted, deduplicated and counted for each gene using umiTools (version 1.1.1). Low-quality cells were filtered out based on a minimum of 500 genes detected and a percentage of mitochondrial RNA lower than 20. Families composed of only one cell were also removed. Counts were normalised using SCTransform function with default parameters from R Seurat package (version 4.3.0).  CITE-seq: Raw sequencing reads were processed using Cellranger v3.1.0. To obtain a reads/cell/gene count table, reads were mapped to the human GRCh38 reference genome. Cells with less than 1000 genes per cell and with a high percentage (> 30%) of mitochondrial genes were removed from downstream analyses. Following our filtering procedures, the average UMI count per cell was 4406. The median number of genes detected per cell was 1662, 2.2% mapped to mitochondrial genes. Data normalization and integration were performed using the default Seurat v4 approach FindIntegrationAnchors() followed by IntegrateData(), and differentially expressed genes were determined using a logistic regression in Seurat on the non-integrated data using the FindConservedMarkers() function. Pathway based analyses were performed using the enrichR package. Unsupervised clustering was performed on the significant variable genes using the 10 first PCA followed by the nonlinear dimensionality reduction technique UMAP. Annotation of the data was obtained by mapping published signatures using the AddModuleScore() method of Seurat.
Assembly: Human hg38
Supplementary files format and content: html/raw data QC for SMART-seq3
Supplementary files format and content: mtx and h5/matrix count for CITE-seq

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
SMART-seq3: Single cell distribution of individual cell families has been performed using the cellenONE platform (Cellenion). Briefly, we selected individual wells of 96-wells plates displaying at least four cells, harvested the entire well, centrifugated for 8’ at 300g and resuspended in 6 µL of PBS 1X (Sigma). Then, the whole volume was loaded into the machine, but due to the dead volume, effectively only 4 µL of this cell suspension could be redistributed. Individual cells were each sorted directly into single wells of 96-wells plates (90 cells per plate) at 4 °C, each well containing 3 µL of lysis buffer. The lysis buffer contains 0.03 µL Triton X100 (ThermoFisher Scientific), 0.0375 µL Recombinant RNAse Inhibitor (Takara Bio), 0.2 µL dNTP 10mM (ThermoFisher Scientific), 0.5 µL PEG 40% (Sigma), 0.04 µL SMARTseq3 oligo-dT 100 μM (/5BiosG/ACGAGCATCAGCAGCATACGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN; IDT) and ultrapure RNAse water (Invitrogen).  CITE-seq: Magnetic sorted CD34+ cells from umbilical cord blood were plated at a cell density of 1x105 cells/mL, using the same culture condition described for the condition Diff. Cells were harvested after 96 hours, counted with a haemocytometer, and resuspended in cold PBS 1X (ThermoFisher Scientific) containing 2% Bovine Serum Albumin (BSA, Euromedex) and 0.01% Tween 20 (Sigma), to a final concentration of 106 cells/mL. 100 µL of this cell suspension was incubated with a mix of previously prepared CITE-seq antibodies. Cells were incubated for 30 minutes at 4 °C, washed three times with the same solution used for the incubation and resuspended in 16.5 µL, at a final concentration of 1000 cells/mL.
SMART-seq3: Reverse transcription (RT) and the subsequent steps were performed accordingly to the SMART-seq3 technique40. Briefly, lysates in each well underwent RT (42 °C for 90 mins, 10 cycles at 50 °C 2 mins + 42 °C 2 mins, and finally 85 °C for 5 mins) on ice, in presence of template switch oligonucleotide at 100 µM (/5BiosG/AGAGACAGATTGCGCAATGNNNNNNNNrGrGrGIDT), 0.04 µL Maxima H minus reverse transcriptase (ThermoFisher Scientific), TRIS-HCl 1M PH 8.3 (Invitrogen), 0.12µL NaCl 1M (Invitrogen), 0.04 µL GTP 100mM (ThermoFisher Scientific), 0,32 µL DTT 100mM (ThermoFisher Scientific), 0.1 µL MgCl2 50mM (ThermoFisher Scientific) and 0.05 µL Recombinant RNAse Inhibitor (Takara Bio) and water. The following PCR step was performed immediately after, using the Kapa Hifi HotStart Ready Mix (Roche), and forward (100 µM TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTGCGCAATG) and reverse (25 µM ACGAGCATCAGCAGCATACGA) primers (IDT technologies) for 25 cycles. After DNA purification using AMPure XP microbeads (ratio 0.8:1) (Beckman Coulter, A63881), the cDNA was tagmented in a final volume of 2 µL, using the Nextera XT DNA Library preparation kit (Illumina). The following library amplification was performed adding 1.5 µL of UDI primers and 2,5 µL of PCR mix including the Phusion High Fidelity DNA polymerase (ThermoFisher Scientific). After tagmentation, the different samples were pooled, purified using AMPure XP microbeads (ratio 0.9:1) and sequenced at 100-bp paired end on a high-output flow cell, using a NovaSeq SP, 800M reads (Illumina).  CITE-seq: Approximately 1.65x104 cells were loaded, to obtain a final yield of 1x104 recovered cells. Cells were processed accordingly to the Chromium Single Cell 3’ library v3.1 (10x Genomics). Libraries were sequenced using a Novaseq s1 (Illumina), allocating at least 20,000 reads per cell for the mRNA library, and 5,000 reads for the Antibody Derived Tags (ADT) library

tag: tissue

value: Blood

tag: cell type

value: Haematopoietic stem and progenitors


title: RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, dTAG13, 24h, replicate 3

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: RNAseq_ADNP-FKBP12_CTCF-FKBP12_dTAG13_24h_r3

library_source: transcriptomic

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 and repeat sensitive settings according to Teissandier et al (Mobile DNA, 2019) (--outFilterType BySJout --outFilterMultimapNmax 100000  --outFilterMismatchNmax 3 --winAnchorMultimapNmax 20000 --alignMatesGapMax 350 --seedSearchStartLmax 30 alignTranscriptsPerReadNmax 30000  --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300  --seedNoneLociPerWindow 1000--outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax --limitBAMsortRAM 10000000000).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by using samtools and bedtools to calculate per base coverage, then counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
For RNA-seq, RNA was collected using Absolutely RNA miniprep kit (Agilent) according to manufacturer's instructions. For TT-seq, RNA was isolated using Trizol according to manufacturer's instructions.
Libraries were prepared using TruSeq Ilumina total RNA-seq

tag: strain

value: hybrid 129-C57BL/6

tag: cell line

value: embryonic stem cells (ESC)

tag: genotype

tag: treatment


title: D1408T25

description: Library name: Dataset_B_25


title: Patient 26 intrahepathic cholangiocarcinoma

city: Montpellier

first: Simon

last: Cabello-Aguilar

address: Avenue du doyen Gaston Giraud

institute: CHU Montpellier

description: Library name: L26

data_processing:
Raw counts matrix were obtained using the DRAGEN RNA pipeline (v4.2.7, Illumina).
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing the raw counts

molecule: polyA RNA

source_name: bile duct

extract_protocol:
Total RNA were extracted using Maxwell® RSC FFPE RNA kit (Promega), following the manufacturer’s instructions. Concentrations were measured using Qubit RNA HS assays (Thermo Fisher Scientific).
RNA sequencing was performed using the RNA Prep with Enrichment, (L) Tagmentation in combination with the RNA Pan-cancer panel (1,362 genes, Illumina) according to the manufacturer’s recommendations. Libraries were sequenced on a NextSeq 500 instrument (2×150 cycles, Illumina).

value: bile duct


title: D3TA-01

country: USA

description:
Library name: Sample 3
10X Genomics


title: D1408T23

description: Library name: Dataset_B_23


title: RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, dTAG13, 24h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_CTCF-FKBP12_dTAG13_24h_r1


title: Patient 21 intrahepathic cholangiocarcinoma

description: Library name: L21


title: WT-02

description:
Library name: Sample 2
10X Genomics

value: WT


title: D1408T22

description: Library name: Dataset_B_22


title: Patient 27 extrahepathic cholangiocarcinoma

description: Library name: L27


title: RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, ctrl, 24h, replicate 3

description: Library name: RNAseq_ADNP-FKBP12_CTCF-FKBP12_ctrl_24h_r3

value: 24h DMSO ctrl


title: RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, dTAG13, 24h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_CTCF-FKBP12_dTAG13_24h_r2


title: WT-3

description:
Library name: WT_10
Column name in raw_counts_All_samples.txt: WT_10

data_processing:
Base calling and generation of FASTQ files were performed using standard CASAVA pipeline.
RNA-seq quality was checked by running FastQC, and TrimGalore was used for adapter and quality trimming. RNA-seq reads were mapped against mm10 genome using HISAT2 aligner with default parameters.
Differential gene expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing raw counts for each samples.

extract_protocol:
RNA was isolated using the RNeasy Plus kit following the manufacturer's instructions.
mRNA 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. The end repair, A-tailing, adapter ligation, size selection, amplification, and purification were performed.


title: D1408T21

description: Library name: Dataset_B_21


title: WT-2

description:
Library name: WT_16
Column name in raw_counts_All_samples.txt: WT_16


title: RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, ctrl, 24h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_CTCF-FKBP12_ctrl_24h_r2


title: Patient 20 extrahepathic cholangiocarcinoma

description: Library name: L20


title: WT-01

description:
Library name: Sample 1
10X Genomics


title: D1408T20

description: Library name: Dataset_B_20


title: RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, ctrl, 24h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_CTCF-FKBP12_ctrl_24h_r1


title: WT-1

description:
Library name: WT_51
Column name in raw_counts_All_samples.txt: WT_51


title: Patient 17 intrahepathic cholangiocarcinoma

description: Library name: L17


title: D1408T19

description: Library name: Dataset_B_19


title: Patient 15 intrahepathic cholangiocarcinoma

description: Library name: L15


title: D1408T18

description: Library name: Dataset_B_18


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_4h_r2


title: D3TA-3

description:
Library name: D3TA_3ILE
Column name in raw_counts_All_samples.txt: D3TA_3ILE


title: D1408T16

description: Library name: Dataset_B_16


title: Patient 12 intrahepathic cholangiocarcinoma

description: Library name: L12


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 3

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_24h_r3


title: Patient 16 intrahepathic cholangiocarcinoma

description: Library name: L16


title: D1408T17

description: Library name: Dataset_B_17


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 3

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_4h_r3


title: Patient 13 extrahepathic cholangiocarcinoma

description: Library name: L13


title: D3TA-1

description:
Library name: D3TA_15F
Column name in raw_counts_All_samples.txt: D3TA_15F


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_4h_r1


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_24h_r2


title: D3TA-2

description:
Library name: D3TA_8F
Column name in raw_counts_All_samples.txt: D3TA_8F


title: Patient 10 intra hepathic cholangiocarcinoma

description: Library name: L10


title: Patient 11 intrahepathic cholangiocarcinoma

description: Library name: L11


title: D1408T14

description: Library name: Dataset_B_14


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_24h_r1


title: Pt6_Bx_I1D118_XEN

type: RNA

city: Seattle

first: Aude

last: Chapuis

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: 10x Genomics

hyb_protocol: Custom 480-gene probe panel was hybridized, ligated, and amplified according to 10x Genomics Xenium in situ gene expression protocols.

scan_protocol: Slides were imaged on the Xenium instrument following manufacturer instructions after autofluorescence quenching and nuclear staining.

data_processing: Raw data were processed using 10x Genomics Xenium Ranger. Downstream analysis including quality control, normalization, clustering, and cell type annotation was performed using Scanpy v1.10.0 and scikit-learn v1.4.0. Processed files include gene × cell matrices, cell metadata, and cell/nucleus boundaries.

label: Xenium probe set

source_name: Tumor

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE tumor tissue sections were mounted on Xenium slides, deparaffinized, rehydrated, and decrosslinked following 10x Genomics FFPE tissue preparation guide.

tag: patient id

tag: infusion

tag: day

value: Tumor

tag: collection site

value: Pelvic lymph node

tag: treatment group

tag: tissue preservation method

value: FFPE


title: Chicken yolk sac membrane cells at embryonic day 7 (scRNA-seq)

city: Taipei

first: Jie Ci

last: Wu

address: Roosevelt Rd.

country: Taiwan

institute: National Taiwan Unviersity

description:
Library name: E7_YSM_scRNA
Single-cell RNA sequencing of yolk sac membrane endodermal epithelial cells at embryonic day 7

data_processing:
Raw sequencing reads were processed to generate gene expression count matrices.
Cells with low gene counts or low sequencing depth were removed during quality control filtering.
Gene expression data were normalized and scaled for downstream analysis.
Dimensionality reduction and clustering were performed to identify distinct cell populations.
Cell clusters were annotated based on known marker gene expression.
Assembly: Gallus gallus (GRCg6a)
Supplementary files format and content: Processed data include filtered gene expression matrices in Matrix Market format (MTX), cell barcode annotations, gene feature annotations, and cell-level metadata including sequencing depth, gene counts, and clustering assignments.
Supplementary files format and content: Data are provided separately for each sample (E4 and E7), with matching matrix, barcode, feature, and metadata files.

molecule: cytoplasmic RNA

organism: Gallus gallus

source_name: yolk sac membrane

growth_protocol: Fertilized chicken eggs were incubated under standard conditions until embryonic day 4 (E4) and embryonic day 7 (E7).

extract_protocol:
Yolk sac membrane (YSM) tissues were dissected from chicken embryos. Single-cell suspensions were prepared by enzymatic dissociation, followed by filtration to remove debris and obtain viable cells.
Single-cell RNA-seq libraries were prepared using the BD Rhapsody system according to the manufacturer's instructions. cDNA libraries were constructed and sequenced on an Illumina NovaSeq X platform.

treatment_protocol: No treatment was applied. Samples were collected directly from developing embryos.

value: yolk sac membrane

value: mixed cell population from yolk sac membrane

value: wild type

tag: batch


title: Chicken yolk sac membrane cells at embryonic day 4 (scRNA-seq)

description:
Library name: E4_YSM_scRNA
Single-cell RNA sequencing of yolk sac membrane endodermal epithelial cells at embryonic day 4


title: D1408T13

description: Library name: Dataset_B_13


title: Pt6_Bx_I1D052_XEN

description: 10x Genomics


title: Patient 94 intrahepathic cholangiocarcinoma

description: Library name: L94


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 1h, replicate 3

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_1h_r3


title: RNA-seq in ADNP-FKBP12 mESC, dTAG13, 1h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_1h_r2


title: Patient 92 extrahepathic cholangiocarcinoma

description: Library name: L92


title: D1408T12

description: Library name: Dataset_B_12


title: Pt6_Bx_I1D014_XEN

description: 10x Genomics


title: Patient 90 intrahepathic cholangiocarcinoma

description: Library name: L90


title: D1408T11

description: Library name: Dataset_B_11


title: Patient 89 intrahepathic cholangiocarcinoma

description: Library name: L89


title: Pt2_Bx_I1D105_XEN

description: 10x Genomics

value: Skin

value: SFRT


title: Pt6_Bx_PreIFNg_XEN

description: 10x Genomics

value: PreIFNg (-11)


title: D1408T9

description: Library name: Dataset_B_9


title: RNA-seq in ADNP-FKBP12 mESC,  dTAG13, 1h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_dTAG13_1h_r1


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 4h, replicate 3

description: Library name: RNAseq_ADNP-FKBP12_ctrl_4h_r3

value: 4h DMSO ctrl


title: D1408T10

description: Library name: Dataset_B_10

value: Blood


title: Patient 86 intrahepathic cholangiocarcinoma

description: Library name: L86


title: D1408T8

description: Library name: Dataset_B_8

value: Haematopoietic stem and progenitors


title: Patient 87 intrahepathic cholangiocarcinoma

description: Library name: L87


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 4h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_ctrl_4h_r1

value: hybrid 129-C57BL/6


title: Pt2_Bx_PreTx_XEN

description: 10x Genomics

value: PreTx (0)


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 4h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_ctrl_4h_r2

value: embryonic stem cells (ESC)


title: D1408T34

description: Library name: Dataset_B_34


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 3

description: Library name: RNAseq_ADNP-FKBP12_ctrl_24h_r3


title: D1408T6

description: Library name: Dataset_B_6


title: Patient 08 extrahepathic cholangiocarcinoma

description: Library name: L08

value: bile duct


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_ctrl_24h_r2

value: 24h DMSO ctrl


title: Patient 80 intrahepathic cholangiocarcinoma

description: Library name: L80


title: D1408T7

description: Library name: Dataset_B_7


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_ctrl_24h_r1


title: D1408T5

description: Library name: Dataset_B_5


title: Atg14_flox mice1, naive

city: Beijing

first: Siwei

last: Feng

address: No.30,Shuangqing street

country: China

institute: Siwei Feng

description: Library name: sample5

data_processing:
Reads were aligned to the GRCm38.p2 assembly of the mouse genome using STAR aligner. Additional options were "- outFilterMultimapNmax 15 - outFilterMismatchNmax 6-quantMode TranscriptomeSAM".
Aligned reads were quantified using quant3p script (github.com/ctlab/quant3p) to account for specifics of 3' sequencing: higher dependency on good 3' annotation and lower level of sequence specificity close to 3' end.
RefSeq genome annotation was used. Using MACS2 peak caller around 70000 putative exons were identified (peaks in rna-seq alignment not overlapping with known exons). Around 6600 of them were assigned to a gene located within 5000 bp and added into the annotation.
For on average 1 million reads per sample that mapped to multiple genome positions there were only one exonic alignment. For these reads multimapper flags were removed for read counting purposes.
Actual read counting were carried out by ht-seq with enriched genome annotation and alignment with fixed multimapper flags. DESeq2 was used for differential gene expression analysis which was used as ranked list in preranked GSEA analysis to identify pathway enrichments
Assembly: GRCm38.p2
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes CPM values for each sample

source_name: lung

extract_protocol:
Lung cells were harvested PBS perfusion, placed in DMEM containing 10% FBS, minced finely, and digested at 37 ⁰C for an hour with mechanical disruption with a stir bar and enzymatic digestion with Liberase Blendzyme III (Roche), hyaluronidase (Sigma), and DNase I (Sigma).RNA was isolated from cells using the RNeasy minikit (QIAGEN) in accordance with the manufacturer’s instructions.
mRNA was extracted from cell lysates by means of oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrid was degraded with consecutive acid-alkali treatment. Then, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI (Solid Phase Reversible Immobilisation) clean-up. The mixture then was PCR enriched 12 cycles and SPRI purified to yield final strand-specific RNA-seq libraries.

value: lung


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 1h, replicate 3

description: Library name: RNAseq_ADNP-FKBP12_ctrl_1h_r3

value: 1h DMSO ctrl


title: Patient 77 extrahepathic cholangiocarcinoma

description: Library name: L77


title: Atg14_flox mice4, naive

description: Library name: sample8


title: Atg14_flox mice2, naive

description: Library name: sample6


title: Patient 79 intrahepathic cholangiocarcinoma

description: Library name: L79


title: Atg14_flox mice3, naive

description: Library name: sample7


title: D1408T4

description: Library name: Dataset_B_4


title: D1408T3

description: Library name: Dataset_B_3


title: D1408T2

description: Library name: Dataset_B_2


title: Patient 05 intrahepathic cholangiocarcinoma

description: Library name: L05


title: Atg14_lysmcre mice4, naïve

description: Library name: sample4


title: Atg14_lysmcre mice3, naïve

description: Library name: sample3


title: Atg14_lysmcre mice2, naïve

description: Library name: sample2


title: Patient 75 intrahepathic cholangiocarcinoma

description: Library name: L75


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 1h, replicate 2

description: Library name: RNAseq_ADNP-FKBP12_ctrl_1h_r2


title: D1408T1

description: Library name: Dataset_B_1


title: Atg14_lysmcre mice1, naïve

description: Library name: sample1


title: Patient 03 intrahepathic cholangiocarcinoma

description: Library name: L03


title: RNA-seq in ADNP-FKBP12 mESC, ctrl, 1h, replicate 1

description: Library name: RNAseq_ADNP-FKBP12_ctrl_1h_r1


title: D920T288

description: Library name: Dataset_A_81


title: AAV2-scramble-4 transcriptome analysis

city: Changsha

first: Duan

last: peiyun

address: 139 Renmin Zhong Lu,

institute: The second xiangya hospital of central south university

description:
Library name: AAV2-scramble-4
AAV2-shScramble 4

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Subsequently, approximately 48M clean reads per sample were preserved for further analysis. The clean reads were aligned to the reference genome via HISAT2.
The FPKM for each gene was calculated, and gene read counts were acquired through HTSeq-count. PCA analysis was undertaken using R (version 3.2.0) to assess the biological replication of samples. Differential expression analysis was executed employing DESeq2, with a q-value < 0.05 and fold change > 2 designated as the criteria for significantly differentially expressed genes (DEGs).
Hierarchical clustering analysis of DEGs was conducted using R (version 3.2.0) to elucidate the expression patterns of genes across various groups and samples.
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text (.txt); Content: Gene-level TPM expression matrix with 8 samples (4 shCX36 and 4 scramble)

source_name: Retina

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Micro Kit according to the manufacturer’s protocol.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

value: Retina

value: RGCs


title: AAV2-scramble-2 transcriptome analysis

description:
Library name: AAV2-scramble-2
AAV2-shScramble 2


title: D920T287

description: Library name: Dataset_A_80


title: D920T286

description: Library name: Dataset_A_79


title: AAV2-scramble-3 transcriptome analysis

description:
Library name: AAV2-scramble-3
AAV2-shScramble 3


title: AAV2-scramble-1 transcriptome analysis

description:
Library name: AAV2-scramble-1
AAV2-shScramble 1


title: NPM1 patient 10, diagnosis+relapse sample replicate 2,TotalSeq-A1-2 hash tag oligos

city: Napels

first: Wout

last: Megchelenbrink

address: Vico de Crecchio 7

department: Precision Medicine

country: Italy

institute: University of Campania "Luigi Vanvitelli”

description: Library name: NPM1_10_rep2_HTO

library_source: other

data_processing:
scRNA-seq data analysis. FASTQ files were aligned to the human GRCh38 reference using CellRanger v5.0 (10x Genomics). Pooled samples were demultiplexed into patients using germline SNPs and subsequently into DX vs RL samples using sample-specific HTOs. First, BAM generated by Cell Ranger were used as input for cellsnp-lite23 to count the REF and ALT occurrences per cell barcode across ~13 million known SNPs from gnomAD with minor allele frequency ≥ 0.01. Next, vireoSNP24 was used to assign cells to donors using the donor-matched WXS samples (DX timepoint) as a reference. Next, the hashtag count matrix was generated from a FASTQ file using CITE-seq-Count followed by DX vs RL demultiplexing with Seurat v5.025. Cells with fewer than 200 unique molecular identifiers (UMIs), more than 5,000 UMIs, or more than 15% mitochondrial reads were discarded.
Assembly: GRCh38 (v37)
Supplementary files format and content: R/Seurat object of the single cell RNA-seq data without batch correction. Raw and normalized counts can be extracted from the Seurat object.

molecule: other

source_name: bone marrow mononuclear cells

extract_protocol:
Cryopreserved AML samples were thawed at 37°C. Viable cells were enriched using an Annexin V MicroBead Kit (Miltenyi Biotec). After washing with cold PBS, cells were resuspended in 500 μl 0.5% PBA (0.5% BSA, 1 x PBS) with 0.2% human serum and incubated for 10 min on ice. After centrifugation and removal of the supernatant, cells were resuspended in 100 μl cold 0.5% PBA with 1 μl of unique cell hashing antibody (Biolegend, TotalSeq-A1-4) and incubated for 20 min on ice. Subsequently, cells were washed after spinning down and resuspended with an appropriate amount of 0.04% PBA (0.04% BSA, PBS) for the following procedures.
Libraries were processed using a GemCode Single-Cell instrument and a Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics), according to the manufacturer’s instructions, until the cDNA amplification step. Hashtag oligo (HTO) primers were added during the cDNA amplification PCR, and cDNA was generated following the 10x Single Cell 3’ v2 protocol. Hashed cells were diluted to 1 million cells/ml and pooled together immediately before loading. Four samples (2 pairs) were pooled and loaded into one lane of a 10x Genomics Chromium Chip. Following PCR, 0.6X volume of SPRI beads were used to separate larger cDNA fragments (retained on beads) from cellular mRNA from the HTO-containing fraction (in supernatant). The cDNA fraction derived from cellular mRNA was processed according to the 10x Single Cell 3’ v2 protocol. An additional 1.4X volume of SPRI beads was added to the HTO fraction to obtain a final SPRI volume of 2X SPRI. After cleanup and final elution, a separate PCR program was set up to generate HTO libraries.

value: bone marrow mononuclear cells


title: NPM1 patient 10, diagnosis+relapse sample replicate 1,TotalSeq-A1-2 hash tag oligos

description: Library name: NPM1_10_rep1_HTO


title: HTVi of Akt/Nras/SBT, snRNA-seq

city: Shanghai

first: Lu

last: Li

state: Shanghai

address: No. 650, Xinsongjiang Road, Songjiang District, Shanghai, China

department: Shanghai General Hospital

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample_sn5
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Liver

extract_protocol:
For snRNA-seq, the 10× chromium pipeline was applied. Mice were perfused with 0.9% NaCl solution to remove blood cells. Mouse livers were immediately snap-frozen in liquid nitrogen and stored at -80°C before use. Nuclear isolation was performed on ice using nuclear lysis buffer followed by filtration, centrifugation, and washing.
After nuclear isolation and quality control, single-nucleus libraries were prepared according to manufacturer protocol of Chromium Next GEM Automated Chip G Single Cell Kit (10× Genomics).

value: Liver

tag: Sex

value: male

value: Epithelial cells

value: WT

tag: age

value: 9-12 weeks old


title: D920T285

description: Library name: Dataset_A_78

value: Blood


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 4,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_08_09_rep4_HTO


title: CRS and HTVi of Akt/Nras/SBT, snRNA-seq

description:
Library name: Sample_sn6
10x Genomics


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 3,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_08_09_rep3_HTO


title: AAV2-shCX36-3 transcriptome analysis

description:
Library name: AAV2-shCX36-3
AAV2-shCX36 3


title: D920T283

description: Library name: Dataset_A_77

value: Haematopoietic stem and progenitors


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 2,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_08_09_rep2_HTO


title: CRS and HTVi of ΔN90-β-Catenin/c-Met/SBT, snRNA-seq

description:
Library name: Sample_sn4
10x Genomics


title: CRS-exposed liver, snRNA-seq

description:
Library name: Sample_sn2
10x Genomics

value: 8-10 weeks old


title: HTVi of ΔN90-β-Catenin/c-Met/SBT, snRNA-seq

description:
Library name: Sample_sn3
10x Genomics


title: AAV2-shCX36-4 transcriptome analysis

description:
Library name: AAV2-shCX36-4
AAV2-shCX36 4


title: D920T282

description: Library name: Dataset_A_76


title: AAV2-shCX36-2 transcriptome analysis

description:
Library name: AAV2-shCX36-2
AAV2-shCX36 2


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 1,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_08_09_rep1_HTO


title: D920T280

description: Library name: Dataset_A_75


title: Healthy liver, snRNA-seq

description:
Library name: Sample_sn1
10x Genomics


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 4,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_06_07_rep4_HTO


title: D920T279

description: Library name: Dataset_A_74


title: AAV2-shCX36-1 transcriptome analysis

description:
Library name: AAV2-shCX36-1
AAV2-shCX36 1


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 3,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_06_07_rep3_HTO


title: D920T278

description: Library name: Dataset_A_73


title: Liver cancer, rep2

description: Library name: Sample 59

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q less than or equal to 19. For paired-end sequencing, both reads will be filtered if either end is low-quality). Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The sequencing reads were mapped to the mm10 using STAR algorithm.
The RSEM was used to estimate the number of reads mapped to each gene.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes counts values of each gene symbol for each sample.

extract_protocol:
Total RNA of all liver cells or hepatocytes was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. Sequencing library was prepared from one microgram of total RNA.
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Sample Prep Kit following manufacturer's protocols

value: Male

value: HTVi of Akt/Nras/SBT


title: Liver cancer, rep3

description: Library name: Sample 60


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 1,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_06_07_rep1_HTO


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 2,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_06_07_rep2_HTO


title: Liver cancer, rep1

description: Library name: Sample 58


title: Liver cancer and CRS, rep3

description: Library name: Sample 57

value: CRS and HTVi of Akt/Nras/SBT


title: D920T277

description: Library name: Dataset_A_72


title: DRG_LCMV04

city: shanghai

first: GuoFeng

last: Fang

address: No. 1630 Dongfang Road, Pudong New Area

department: Shanghai Institute of Immunotherapy Innovation, Renji Hospital

description:
Library name: DRG_LCMV04
DRG (left T8-T13) at 7 days post-LCMV infection

data_processing:
Raw reads were processed using Trim Galore/Fastp, aligned with STAR/HISAT2, and quantified via FeatureCounts (v2.0.3).
Assembly: GRCm39/mm39
Supplementary files format and content: comma-delimited csv file includes raw counts for each Sample

source_name: DRG (left T8-T13)

growth_protocol: C57BL/6 mice were intraperitoneally injected with 2 × 105 plaque-forming units (PFU) of the Armstrong strain of LCMV on day 0. Simultaneously, 2 × 105 wild-type SMARTA cells were intravenously injected. After 7 days,  DRG (left T8-T13) tissues were used for RNA-seq analysis.

extract_protocol:
polyA RNA
Cell samples were snap-frozen in liquid nitrogen, and total RNA was isolated using the RNeasy Mini Kit (Qiagen, 74104). RNA integrity was validated via Agilent 2100 Bioanalyzer (RIN ≥8). Libraries were size-selected (300–500 bp) and PCR-amplified, followed by sequencing on an Illumina NovaSeq 6000 with S4 flow cells (PE150).

value: DRG (left T8-T13)

value: DRG (left T8-T13) tissue

value: post-LCMV infection


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 4,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_04_05_rep4_HTO


title: DRG_LCMV02

description:
Library name: DRG_LCMV02
DRG (left T8-T13) at 7 days post-LCMV infection


title: D920T275

description: Library name: Dataset_A_71


title: DRG_LCMV01

description:
Library name: DRG_LCMV01
DRG (left T8-T13) at 7 days post-LCMV infection


title: Patient 45 intrahepathic cholangiocarcinoma

description: Library name: L45

value: bile duct


title: DRG_LCMV05

description:
Library name: DRG_LCMV05
DRG (left T8-T13) at 7 days post-LCMV infection


title: D1408T15

description: Library name: Dataset_B_15


title: D920T274

description: Library name: Dataset_A_70


title: DRG_noninfec05

description:
Library name: DRG_noninfec05
DRG (left T8-T13) at 7 days post-LCMV infection

value: non-infection


title: Liver cancer and CRS, rep2

description: Library name: Sample 56


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 2,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_04_05_rep2_HTO

value: bone marrow mononuclear cells


title: DRG_noninfec03

description:
Library name: DRG_noninfec03
DRG (left T8-T13) at 7 days post-LCMV infection


title: Liver cancer and CRS, rep1

description: Library name: Sample 55

value: Liver


title: HCC and CRS, rep4

description: Library name: Sample 54

value: CRS and HTVi of ΔN90-β-Catenin/c-Met/SBT


title: D920T273

description: Library name: Dataset_A_69


title: D920T272

description: Library name: Dataset_A_68


title: D920T270

description: Library name: Dataset_A_66


title: HCC and CRS, rep2

description: Library name: Sample 52

value: Epithelial cells


title: D920T269

description: Library name: Dataset_A_65


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 2, TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_02_03_rep2_HTO


title: RNA-seq of mouse: adult female uterus E18.5_2

city: Boone County

first: Amanda

last: Patterson

state: MO

address: 1030 Hitt St

institute: university of Missouri

description: Library name: P-Ai14-94

data_processing:
The untrimmed sequencing files    were aligned to a customized mm10 reference genome using Cell Ranger (version 7.0.1) by 10x Genomics.
Following alignment, the raw count matrices were input to CellBender (version 0.3.0.) (50) for ambient RNA decontamination.
The filtered count matrices were loaded into Seurat (version 5.1.0.)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples

source_name: uterus

extract_protocol:
Nuclei from the uterus extracted using Singulator 100.
Library constructed with Chromium Next GEM Single Cell 3 Reagent Kits v3.1

value: uterus

tag: time point

value: female

value: 4-5 months


title: Patient 22 intrahepathic cholangiocarcinoma

description: Library name: L22


title: RNA-seq of mouse: adult female uterus E18.5_1

description: Library name: P-Ai14-143


title: D920T268

description: Library name: Dataset_A_64

value: Blood

value: Haematopoietic stem and progenitors


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 3,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_04_05_rep3_HTO


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 1,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_04_05_rep1_HTO


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 1, TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_02_03_rep1_HTO


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 3,TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_02_03_rep3_HTO


title: DRG_noninfec01

description:
Library name: DRG_noninfec01
DRG (left T8-T13) at 7 days post-LCMV infection


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 4, TotalSeq-A1-4 hash tag oligos

description: Library name: NPM1_02_03_rep4_HTO


title: D920T271

description: Library name: Dataset_A_67


title: HCC and CRS, rep3

description: Library name: Sample 53

value: Male

value: WT


title: HCC, rep3

description: Library name: Sample 50

value: HTVi of ΔN90-β-Catenin/c-Met/SBT


title: HCC and CRS, rep1

description: Library name: Sample 51


title: D920T267

description: Library name: Dataset_A_63


title: HCC, rep2

description: Library name: Sample 49


title: HCC, rep1

description: Library name: Sample 48


title: RNA-seq of mouse: adult female uterus PPD1_2

description: Library name: P-Ai14-81


title: NPM1 patient 10, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]

description:
Library name: NPM1_10_rep1_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: RNA-seq of mouse: adult female uterus PPD1_1

description: Library name: P-Ai14-38


title: Adrb2-deficient hepatocytes, rep3

description: Library name: Sample 46


title: RNA-seq of mouse: adult female uterus PPD28_2

description: Library name: P-Ai14-360


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]

description:
Library name: NPM1_08_09_rep3_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Adrb2-deficient hepatocytes, rep4

description: Library name: Sample 47


title: Adrb2-deficient hepatocytes, rep2

description: Library name: Sample 45


title: D920T264

description: Library name: Dataset_A_60


title: NPM1 patient 10, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]

description:
Library name: NPM1_10_rep2_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T265

description: Library name: Dataset_A_61


title: D920T263

description: Library name: Dataset_A_59


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]

description:
Library name: NPM1_06_07_rep4_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: RNA-seq of mouse: adult female uterus PPD2_1

description: Library name: P-Ai14-153


title: RNA-seq of mouse: adult female uterus PPD28_1

description: Library name: P-Ai14-372


title: Adrb2-deficient hepatocytes, rep1

description: Library name: Sample 44


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]

description:
Library name: NPM1_08_09_rep1_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T262

description: Library name: Dataset_A_58


title: Adrb2-control hepatocytes, rep3

description: Library name: Sample 42


title: RNA-seq of mouse: adult female uterus PPD3_2

description: Library name: P-Ai14-51


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]

description:
Library name: NPM1_08_09_rep2_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: RNA-seq of mouse: adult female uterus PPD4_2

description: Library name: P-Ai14-97


title: D920T266

description: Library name: Dataset_A_62


title: D920T261

description: Library name: Dataset_A_57


title: Adrb2-control hepatocytes, rep4

description: Library name: Sample 43


title: RNA-seq of mouse: adult female uterus PPD3_1

description: Library name: P-Ai14-162


title: D920T260

description: Library name: Dataset_A_56


title: RNA-seq of mouse: adult female uterus PPD2_2

description: Library name: P-Ai14-55


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]

description:
Library name: NPM1_06_07_rep3_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: RNA-seq of mouse: adult female uterus PPD4_1

description: Library name: P-Ai14-105


title: Adrb2-control hepatocytes, rep2

description: Library name: Sample 41


title: D920T259

description: Library name: Dataset_A_55


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]

description:
Library name: NPM1_06_07_rep2_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Adrb2-control hepatocytes, rep1

description: Library name: Sample 40


title: overlap-3

city: Suzhou

first: Qiuying

last: Zhao

address: No. 199 Ren'ai Road, Suzhou Industrial Park, Xietang Street

institute: Soochow University

description: Library name: Sample 9

data_processing:
Trim_galore, Adapter and PolyA cut-off
STAR, align reads to mm9 genome
umi_homopolymer.py(UMI extraction)/umi_tools (Deduplication) provided by Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.
FeatureCounts, Align reads preferentially to 3'end and calculate the strand-specific reads counts
RSeQC, Show reads distribution on the gene bodies
Assembly: mm9
Supplementary files format and content: csv files include count values for each sample

source_name: PFA-fixed frozen tissue

extract_protocol:
RNA was released directly in PCR tube during lysis from spermatocytes, which were collected from FFPE testicular biopsy tissue using laser capture microdissection systembased on Smart-3SEQ method(Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.).
each library was constructed using Smart-3SEQ protocol (Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.)

value: PFA-fixed frozen tissue

value: spermatocytes

value: overlap


title: D920T257

description: Library name: Dataset_A_54


title: overlap-2

description: Library name: Sample 8


title: Liver, 4 week liver cancer, rep3

description: Library name: Sample 39

value: HTVi of Akt/Nras/SBT


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]

description:
Library name: NPM1_04_05_rep4_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, 4 week liver cancer, rep2

description: Library name: Sample 38


title: D920T256

description: Library name: Dataset_A_53


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]

description:
Library name: NPM1_04_05_rep3_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T255

description: Library name: Dataset_A_52


title: Liver, 4 week liver cancer, rep1

description: Library name: Sample 37


title: c-fos-3

description: Library name: Sample 6

value: c-fos


title: D920T254

description: Library name: Dataset_A_51


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]

description:
Library name: NPM1_06_07_rep1_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000

value: bone marrow mononuclear cells


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]

description:
Library name: NPM1_04_05_rep2_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: overlap-1

description: Library name: Sample 7


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]

description:
Library name: NPM1_04_05_rep1_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T253

description: Library name: Dataset_A_50


title: c-fos-1

description: Library name: Sample 4


title: mCHerry-3

description: Library name: Sample 3

value: mCHerry


title: c-fos-2

description: Library name: Sample 5


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]

description:
Library name: NPM1_02_03_rep3_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T252

description: Library name: Dataset_A_49


title: Kidney, Treated with EpSAZT 21, Sample 3

city: Qingdao

first: Yanjun

last: Liu

state: Shandong

address: Yushan road 5

institute: JIANGNAN

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt

data_processing:
Sequencing was performed on an Illumina Novaseq platform using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.
Assembly: Rawdata files
Supplementary files format and content: RPKM

source_name: Kidney

growth_protocol: Six-week-old male C57BL/6 mice were housed with a 12 h/12 h light/dark cycle

extract_protocol:
Spin Column Animal Total RNA Purification Kit
1 μg total RNA was used for following library preparation. Sequencing was performed on an Illumina Novaseq platform using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: Six-week-old mice fed a standard chow diet, a high-fat diet, or a high-fat diet containing 3% EpSA for 14 weeks

value: Kidney

value: EpSA

value: male


title: Kidney, Treated with EpSAZT 25, Sample 2

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]

description:
Library name: NPM1_02_03_rep4_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T250

description: Library name: Dataset_A_47


title: Kidney, Treated with EpSAZT 25, Sample 3

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Kidney, Treated with EpSAZT 25, Sample 1

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: mCHerry-2

description: Library name: Sample 2


title: mCHerry-1

description: Library name: Sample 1


title: Kidney, Treated with EpSAZT 21, Sample 2

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]

description:
Library name: NPM1_02_03_rep2_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T251

description: Library name: Dataset_A_48


title: D920T249

description: Library name: Dataset_A_46


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]

description:
Library name: NPM1_02_03_rep1_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Kidney, Treated with EpSAZT 17, Sample 3

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: NPM1 patient 01, relapse sample [Illumina Nextseq 500 ]

description:
Library name: NPM1_01_RL_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: D920T248

description: Library name: Dataset_A_45


title: D920T247

description: Library name: Dataset_A_44


title: Kidney, Treated with EpSAZT 21, Sample 1

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: NPM1 patient 01, diagnosis sample [Illumina Nextseq 500 ]

description:
Library name: NPM1_01_DX_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Muscle,IMQ-induced,Tcn2-deficient (Tcn2-/-),T2ho_3

first: Jingkai

last: Xu

address: No.2, Cherry Blossom Garden East Street, Chaoyang District

institute: China-Japan Friendship Hospital

description: Library name: T2ho_3

data_processing:
alignment of sequencing reads to a reference genome: GRCm39.112;calculate gene/transcript expression (TPM/FPKM)
Assembly: GRCm39.112
Supplementary files format and content: annotated Expression Matrix,integration of raw expression data with gene function annotation

source_name: skin

extract_protocol:
Specific eukaryotic mRNAs were captured from total RNAs using magnetic beads with Oligo(dT);Oligo(dT) on the surface of the beads binded complementarily to the poly(A) tails of the mRNAs, and non-targeted RNAs, such as rRNAs, were removed by magnetic separation.
The mRNA was cleaved into short fragments by addition of fragmentation buffer and single-stranded cDNA was synthesised using mRNA as template with six base random hexamers, then double-stranded cDNA was synthesised by addition of buffer, dNTPs, DNA polymerase I and RNase H. The purified double-stranded cDNA was first subjected to end repair, A-tail addition and ligation of sequencing junctions, followed by fragment size selection using AMPure XP beads. The purified double-stranded cDNA was first subjected to end repair, A-tail addition and ligation to sequencing junctions, followed by fragment size selection using AMPure XP beads. Finally, PCR amplification was performed and the PCR products were purified using AMPure XP beads to obtain the final sequencing library.

value: skin


title: Muscle,IMQ-induced,Tcn2-deficient (Tcn2-/-),T2ho_4

description: Library name: T2ho_4


title: D920T246

description: Library name: Dataset_A_43


title: Kidney, Treated with EpSAZT 17, Sample 2

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Muscle,IMQ-induced,Tcn2-deficient (Tcn2-/-),T2ho_2

description: Library name: T2ho_2


title: Muscle,IMQ-induced,Tcn2-deficient (Tcn2-/-),T2ho_1

description: Library name: T2ho_1


title: Kidney, Treated with EpSAZT 17, Sample 1

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Muscle,IMQ-induced,Pso_5

description: Library name: Pso_5


title: Input for H3K27ac ChIP-seq in DMSO-treated cells, control for 24hr dTAG13 treatment

city: Oxford

first: I-Jun

last: Lau

address: Old Rd

department: Botnar Research Centre

country: United Kingdom

institute: University of Oxford

description: Library name: SEM-DMSO-24hr_K27-INPUT

library_source: genomic

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome hg38 using bowtie2 vbowtie2-align-s version 2.5.1 with with default parameters.
Duplicate reads were removed using Picard MarkDuplicates v3.1.1 with with default parameters
BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Supplementary files format and content: Peak calling and annotation using Homer v4.11

molecule: genomic DNA

source_name: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (TFs). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).

value: DMSO


title: D920T245

description: Library name: Dataset_A_42

data_processing:
FASTQ files for each single cell were generated using bcl2fastq (version 2.20.0), with default parameters. The Read 1 contain the TSO (constant tag sequence and a UMI) followed by cDNA or only cDNA.  The Read 2 contain cDNA only. Index1 and index2 reads correspond to cell-specific barcode. The scRNA-SmartSeq3 pipeline v1.2.1 (https://doi.org/10.5281/zenodo.15056215) was used to generate UMI count tables from FASTQ files. Briefly, reads were aligned to the human genome (hg38) using STAR (version 2.7.8a) and assigned to genes using FeatureCounts (deeptools version 3.5.0). UMIs were extracted, deduplicated and counted for each gene using umiTools (version 1.1.1). Low-quality cells were filtered out based on a minimum of 500 genes detected and a percentage of mitochondrial RNA lower than 20. Families composed of only one cell were also removed. Counts were normalised using SCTransform function with default parameters from R Seurat package (version 4.3.0).  CITE-seq: Raw sequencing reads were processed using Cellranger v3.1.0. To obtain a reads/cell/gene count table, reads were mapped to the human GRCh38 reference genome. Cells with less than 1000 genes per cell and with a high percentage (> 30%) of mitochondrial genes were removed from downstream analyses. Following our filtering procedures, the average UMI count per cell was 4406. The median number of genes detected per cell was 1662, 2.2% mapped to mitochondrial genes. Data normalization and integration were performed using the default Seurat v4 approach FindIntegrationAnchors() followed by IntegrateData(), and differentially expressed genes were determined using a logistic regression in Seurat on the non-integrated data using the FindConservedMarkers() function. Pathway based analyses were performed using the enrichR package. Unsupervised clustering was performed on the significant variable genes using the 10 first PCA followed by the nonlinear dimensionality reduction technique UMAP. Annotation of the data was obtained by mapping published signatures using the AddModuleScore() method of Seurat.
Assembly: Human hg38
Supplementary files format and content: html/raw data QC for SMART-seq3
Supplementary files format and content: mtx and h5/matrix count for CITE-seq

extract_protocol:
SMART-seq3: Single cell distribution of individual cell families has been performed using the cellenONE platform (Cellenion). Briefly, we selected individual wells of 96-wells plates displaying at least four cells, harvested the entire well, centrifugated for 8’ at 300g and resuspended in 6 µL of PBS 1X (Sigma). Then, the whole volume was loaded into the machine, but due to the dead volume, effectively only 4 µL of this cell suspension could be redistributed. Individual cells were each sorted directly into single wells of 96-wells plates (90 cells per plate) at 4 °C, each well containing 3 µL of lysis buffer. The lysis buffer contains 0.03 µL Triton X100 (ThermoFisher Scientific), 0.0375 µL Recombinant RNAse Inhibitor (Takara Bio), 0.2 µL dNTP 10mM (ThermoFisher Scientific), 0.5 µL PEG 40% (Sigma), 0.04 µL SMARTseq3 oligo-dT 100 μM (/5BiosG/ACGAGCATCAGCAGCATACGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN; IDT) and ultrapure RNAse water (Invitrogen).  CITE-seq: Magnetic sorted CD34+ cells from umbilical cord blood were plated at a cell density of 1x105 cells/mL, using the same culture condition described for the condition Diff. Cells were harvested after 96 hours, counted with a haemocytometer, and resuspended in cold PBS 1X (ThermoFisher Scientific) containing 2% Bovine Serum Albumin (BSA, Euromedex) and 0.01% Tween 20 (Sigma), to a final concentration of 106 cells/mL. 100 µL of this cell suspension was incubated with a mix of previously prepared CITE-seq antibodies. Cells were incubated for 30 minutes at 4 °C, washed three times with the same solution used for the incubation and resuspended in 16.5 µL, at a final concentration of 1000 cells/mL.
SMART-seq3: Reverse transcription (RT) and the subsequent steps were performed accordingly to the SMART-seq3 technique40. Briefly, lysates in each well underwent RT (42 °C for 90 mins, 10 cycles at 50 °C 2 mins + 42 °C 2 mins, and finally 85 °C for 5 mins) on ice, in presence of template switch oligonucleotide at 100 µM (/5BiosG/AGAGACAGATTGCGCAATGNNNNNNNNrGrGrGIDT), 0.04 µL Maxima H minus reverse transcriptase (ThermoFisher Scientific), TRIS-HCl 1M PH 8.3 (Invitrogen), 0.12µL NaCl 1M (Invitrogen), 0.04 µL GTP 100mM (ThermoFisher Scientific), 0,32 µL DTT 100mM (ThermoFisher Scientific), 0.1 µL MgCl2 50mM (ThermoFisher Scientific) and 0.05 µL Recombinant RNAse Inhibitor (Takara Bio) and water. The following PCR step was performed immediately after, using the Kapa Hifi HotStart Ready Mix (Roche), and forward (100 µM TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTGCGCAATG) and reverse (25 µM ACGAGCATCAGCAGCATACGA) primers (IDT technologies) for 25 cycles. After DNA purification using AMPure XP microbeads (ratio 0.8:1) (Beckman Coulter, A63881), the cDNA was tagmented in a final volume of 2 µL, using the Nextera XT DNA Library preparation kit (Illumina). The following library amplification was performed adding 1.5 µL of UDI primers and 2,5 µL of PCR mix including the Phusion High Fidelity DNA polymerase (ThermoFisher Scientific). After tagmentation, the different samples were pooled, purified using AMPure XP microbeads (ratio 0.9:1) and sequenced at 100-bp paired end on a high-output flow cell, using a NovaSeq SP, 800M reads (Illumina).  CITE-seq: Approximately 1.65x104 cells were loaded, to obtain a final yield of 1x104 recovered cells. Cells were processed accordingly to the Chromium Single Cell 3’ library v3.1 (10x Genomics). Libraries were sequenced using a Novaseq s1 (Illumina), allocating at least 20,000 reads per cell for the mRNA library, and 5,000 reads for the Antibody Derived Tags (ADT) library

value: Blood


title: Input for H3K27ac ChIP-seq in dTAG13-treated (24hr) SEM cells with MYB endogenously tagged with FKBP12(F36V)

description: Library name: SEM-dTAG13-24hr_K27-INPUT

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

value: 0.5µM dTAG13 for 24hr


title: D920T244

description: Library name: Dataset_A_41

value: Haematopoietic stem and progenitors


title: Muscle,IMQ-induced,Pso_4

description: Library name: Pso_4


title: Kidney, Treated with EpSAZT 13, Sample 2

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt

value: WT


title: Kidney, Treated with EpSAZT 13, Sample 3

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: H3K27ac ChIP-seq in dTAG13-treated (24hr) SEM cells with MYB endogenously tagged with FKBP12(F36V)

description: Library name: SEM-dTAG13-24hr_H3K27ac

value: Diagenode C15410196


title: D920T243

description: Library name: Dataset_A_40


title: Kidney, Treated with EpSAZT 13, Sample 1

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: D920T242

description: Library name: Dataset_A_39


title: Kidney, Treated with EpSAZT 9, Sample 3

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Muscle,IMQ-induced,Pso_1

description: Library name: Pso_1


title: Kidney, Treated with EpSAZT 9, Sample 2

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Muscle,IMQ-induced,Pso_2

description: Library name: Pso_2


title: D920T241

description: Library name: Dataset_A_38


title: TT-seq in dTAG13-treated (24hr) SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 2

description: Library name: SEM-dTAG-24hr-2

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome hg38 using STAR v2.7.11a with the following parameters: --quantMode TranscriptomeSAM GeneCounts --outSAMunmapped Within --outSAMattributes Standard.
BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: -bs 1 --normalizeUsing CPM.
Strands were separated using the --filterRNAstrand option. Alignments were quantified using featureCounts v2.0.6 with the following parameters: -s 0 -p --countReadPairs -t exon -g gene_id
Assembly: hg38
Supplementary files format and content: Read counts were determined using featureCounts (Subread package)
Supplementary files format and content: Differential gene expression analysis was conducted using edgeR

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
5e7 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. RNA was mildly fragmented by sonication. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7760).

treatment_protocol: see sample table


title: TT-seq in dTAG13-treated (24hr) SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 3

description: Library name: SEM-dTAG-24hr-3


title: Muscle,IMQ-induced,Pso_3

description: Library name: Pso_3


title: D920T239

description: Library name: Dataset_A_36


title: Muscle,wild-type,Ctr_2

description: Library name: Ctr_2


title: TT-seq in DMSO-treated SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 3

description: Library name: SEM-DMSO-24hr-3


title: TT-seq in dTAG13-treated (24hr) SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 1

description: Library name: SEM-dTAG-24hr-1


title: D920T237

description: Library name: Dataset_A_34


title: Muscle,wild-type,Ctr_3

description: Library name: Ctr_3


title: Kidney, Treated with EpSAZT 5, Sample 3

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: D920T240

description: Library name: Dataset_A_37


title: Kidney, Treated with EpSAZT 5, Sample 2

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Muscle,wild-type,Ctr_1

description: Library name: Ctr_1


title: Kidney, Treated with EpSAZT 9, Sample 1

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Kidney, Treated with EpSAZT 5, Sample 1

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: TT-seq in DMSO-treated SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 2

description: Library name: SEM-DMSO-24hr-2


title: Kidney, Treated with EpSAZT 1, Sample 3

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: JiaMut, scRNAseq

city: San Francisco

first: John

last: Rubenstein

state: CA

address: Box 2611 , Mission Bay 284C

institute: University of California, San Francisco

description:
Library name: JiaMut, scRNAseq
10x chromium

data_processing:
Raw FASTQ files were processed using Cell Ranger, which aligned the data to the mm10 genome and generated feature-barcode matrices (both filtered and raw). The RData file integrating data from all samples was generated using Seurat in R. Detailed processing steps, including integration, normalization, dimensionality reduction, clustering, and annotation, are described in the associated publication.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files are provided for each sample, including barcodes.tsv, genes.tsv, and matrix.mtx files for both filtered and raw. Each of the RData files contains one Seurat object. AllCells.so.RData contains cells from the full dataset, while DlxSubclust.so.RData corresponds to specific subclusters. Detailed information on clustering and annotation is available in the associated publication.

source_name: neocortical

extract_protocol:
Neocortices were incubated with a prewarmed solution of Papain (Worthington; prepared according to manufacturer’s protocol) for 15 minutes at 37°C. After Papain incubation, tissues were washed multiple times with DMEM/10% FBS (Thermo Fisher) and were then gentle triturated. The tissue was allowed to settle for about 1 minute. The cell-containing supernatant was filtered (30 μm MACS SmartStrainer) into new conical tubes. Conical tubes containing cells were centrifuged at 200 rcf for 2–3 minutes. The supernatant was removed without disturbing the cell pellets. The pellets were resuspended in cold Hibernate buffer (BrainBits) to achieve a concentration of 2,000 cells per microliter.
Library preparation was performed by the UCSF Institute of Human Genetics Core (IHG), using 10X Chromium Single 3’ Reagent Kits Version 2 (10X Genomics). The library length and concentration were quantified using a Bioanalyzer (Agilent) according to the manufacturer's protocol.
Paired-end sequencing was performed on the Illumina NovaSeq at Center for Advanced Technology (UCSF).

value: mixed

value: neocortical


title: D920T235

description: Library name: Dataset_A_32


title: D920T234

description: Library name: Dataset_A_31


title: JiaHet, scRNAseq

description:
Library name: JiaHet, scRNAseq
10x chromium


title: JiaWT, scRNAseq

description:
Library name: JiaWT, scRNAseq
10x chromium


title: Kidney, Treated with EpSAZT 1, Sample 2

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: Kidney, Treated with EpSAZT 1, Sample 1

description:
Dataanalysis.txt
meta2d_LEOA.exp.txt


title: H3K27ac ChIP-seq in DMSO-treated cells, control for 24hr dTAG13 treatment

description: Library name: SEM-DMSO-24hr_H3K27ac


title: D920T236

description: Library name: Dataset_A_33


title: emilycKO, scRNAseq

description:
Library name: emilycKO, scRNAseq
10x chromium


title: D920T232

description: Library name: Dataset_A_29


title: D920T233

description: Library name: Dataset_A_30


title: Kidney, ZT 25, Sample 3

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

value: Chow diet


title: emilycHet, scRNAseq

description:
Library name: emilycHet, scRNAseq
10x chromium


title: D920T231

description: Library name: Dataset_A_28


title: Exosomes from WJ-MSCs hypoxia 2

city: Delhi

first: Sujata

last: Mohanty

state: Delhi

address: Ansari nagar

department: Stem Cell Facility

country: India

institute: AIIMS, New Delhi

description: Library name: ED2

data_processing:
The size selected and purified libraries were analyzed in 4200 Tape Station system (Agilent Technologies) using High sensitivity D1000 Screen tape as per manufacturer instructions
The sequenced raw reads often contain low quality reads with adapters, which will affect the quality of downstream analysis. To avoid this, raw reads containing ambiguous base (Ns), poly (A) tails and the reads lacking 3’ adapter were removed using Cutadapt v1.18. Finally, low quality bases were trimmed to get high quality reads using Trimmomatic v0.39 in single-end mode with quality cut-off of 20 wherever applicable.
The high-quality reads were mapped to the reference genome using bowtie v1.3.1 aligner with default parameters. Unmapped reads were discarded and reads mapped on genome were considered for downstream analysis.
SmallRNA sequencing data is known to include reads from other category of small non-coding RNAs such as tRNA, snoRNA, snRNA and piRNA ect. Sample-wise reads were mapped against the customized database of Rfam (Database built after removing miRNA and their precursor sequences from the Rfam) using Bowtie v1.3.1 aligner with default parameters. The unmapped against Rfam database were considered for downstream analysis
Reads which are not mapped to Rfam, were mapped to known repeat sequences i.e. Repbase (v22) using Bowtie v1.3.1 aligner with default parameters. Reads mapped on Repbase database were discarded and unmapped reads were considered for downstream analysis.
Reads having length less than 18 nts and greater than 30 nts were excluded from the analysis. The reads which have length between 18-30 bases were considered for miRNA identification.
Assembly: The high-quality reads were mapped to the reference genome using bowtie v1.3.1 aligner with default parameters. Unmapped reads were discarded and reads mapped on genome were considered for downstream analysis.
Supplementary files format and content: 1 PDF file-EGI_Final Report_Dr. Sujata Mohanty_GA243209_Small RNA Seq_17-10-2024.pdf containing all the processed data along with the respective graphs

source_name: umbilical cord

growth_protocol: standard cell culture treatment

extract_protocol:
Trizol chloroform extraction was performed and total RNA was isolated
The small RNA sequencing libraries were prepared from the received total RNA samples using illumina NEBNext® Multiplex Small RNA Library Prep Kit for Illumina (NEB) as per the manufacturer’s instruction. Briefly, approximately 1ug of RNA was processed for 3' adapter ligation followed by 5’ adaptor ligation. The adaptor ligated RNA samples were then converted to cDNA using reverse transcriptase followed by PCR amplification using common primer and indexed primer. The enriched library was then purified using Spin column followed by AMPureXP bead-based size selection.

treatment_protocol: hypoxia and normoxia

value: umbilical cord

value: primary MSCs

value: Stem Cell


title: Kidney, ZT 25, Sample 2

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

value: Kidney


title: BM-MSCs Normoxia 2

description: Library name: CA2

source_name: bone marrow

value: bone marrow


title: Exosomes from WJ-MSCs Normoxia 2

description: Library name: EC2


title: Input E16 OB

description: Library name: input_e16_OB_S12

data_processing:
Raw FASTQ files were first adapter- and quality-trimmed using Trimmomatic. Trimmed reads were aligned to the mm10 reference genome using Bowtie2. With PCR duplicates removed using Samtools markdup, then Peak calling was performed using MACS2.
Assembly: mm10
Supplementary files format and content: Processed data files in narrowPeak format are provided, one per sample, from macs2 output.

source_name: Olfactory Bulb

extract_protocol:
Both OB, BG and Cortices were fixed in 1.5 % formaldehyde and lysed with a hypotonic buffer to obtain the nuclei; these were then lysed in 1% SDS buffer and the chromatin was sheared into 300-1000 bp fragments by sonicating using a bioruptor (Diagenode). Immunoprecipitation (IP) reactions were performed with the sheared chromatin diluted 1/10 times with “dilution buffer” and 5 µg DLX2 specific Ab was added. Negative control ChIP reactions were set-up with a rabbit IgG (5µg). Antibody/chromatin complexes were purified using Dynabeads (Invitrogen) and washed extensively in “wash buffers” (low salt, high salt, LiCl, and TE).Complexes were eluted in 1% SDS, 10mM Sodium bicarbonate buffer at 65˚C for 10 min.
Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen) and QC tested on a Bioanalyzer (Agilent).
The libraries were sequenced as single-ended 50 nucleotide reads on a HiSeq 4000 or NovaSeq  (Illumina) at Center for Advanced Technology (UCSF).

value: Olfactory Bulb


title: Kidney, ZT 25, Sample 1

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

value: male


title: Exosomes from BM-MSCs Hypoxia 2

description: Library name: EB 2


title: Input E16 Cx

description: Library name: input_e16_Cx_S9

source_name: Cortex

value: Cortex


title: D920T238

first: Alessandro

last: Donada

address: 11 rue Pierre et Marie Curie, Batiment Curie, RDC, R12, UMR168 - Equipe Perie

description: Library name: Dataset_A_35

source_name: Blood

value: Blood


title: D920T230

description: Library name: Dataset_A_27


title: D920T229

description: Library name: Dataset_A_26


title: emilyWT, scRNAseq

description:
Library name: emilyWT, scRNAseq
10x chromium


title: Kidney, ZT 21, Sample 3

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: Exosomes from BM-MSCs Normoxia 2

description: Library name: EA 2


title: Input P3 OB

description: Library name: input_P3_OB_S18


title: D920T228

description: Library name: Dataset_A_25


title: WJ-MSCs hypoxia

description: Library name: CD1


title: Input P3 Cx

description: Library name: input_P3_Cx_S15


title: Kidney, ZT 21, Sample 2

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: Kidney, ZT 21, Sample 1

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: WJ-MSCs hypoxia 2

description: Library name: CD2


title: Input BG E16

description: Library name: input_BG_e16_rep3_S1

source_name: Basal Ganglia

value: Basal Ganglia


title: D920T227

description: Library name: Dataset_A_24


title: WJ-MSCs Normoxia

description: Library name: CC1


title: Kidney, ZT 17, Sample 3

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: D920T226

description: Library name: Dataset_A_23


title: Kidney, ZT 17, Sample 2

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: Dlx2 ChIP CX P3

description: Library name: Dlx2 CX p3

tag: chip antibody


title: D920T224

description: Library name: Dataset_A_21

tag: tissue


title: Kidney, ZT 17, Sample 1

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: Exosomes from WJ-MSCs hypoxia

description: Library name: ED1

tag: cell type


title: D920T223

description: Library name: Dataset_A_20


title: BM-MSCs Normoxia

description: Library name: CA1


title: Dlx2 ChIP OB P3

description: Library name: Dlx2 OB p3


title: Exosomes from WJ-MSCs Normoxia

description: Library name: EC1


title: Dlx2 ChIP CX E16

description: Library name: Dlx2 CX e16


title: BM-MSCs Hypoxia

description: Library name: CB1


title: D920T222

description: Library name: Dataset_A_19


title: Kidney, ZT 13, Sample 3

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

tag: strain


title: Kidney, ZT 13, Sample 2

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: Dlx2 ChIP OB E16

description: Library name: Dlx2 OB e16


title: TT-seq in DMSO-treated SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 1

description: Library name: SEM-DMSO-24hr-1

tag: cell line

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

value: DMSO


title: D920T221

description: Library name: Dataset_A_18

value: Haematopoietic stem and progenitors


title: Exosomes from BM-MSCs Hypoxia

description: Library name: EB1


title: Dlx2 ChIP BG E16

description: Library name: Dlx2 BG e16


title: Kidney, ZT 9, Sample 3

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

tag: genotype

value: WT


title: Exosomes from BM-MSCs Normoxia

description: Library name: EA1


title: control_M4_hypothalamus

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

description:
Library name: hypothalamus_control_rep3
control_M4_hypothalamus

data_processing:
RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.5.1a
Aligned reads were imported to Partek Flow software for downstream analysis
DEGs were identified with DESeq2 package implemented in Partek Flow
Assembly: Ensembl release 101
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample

source_name: hypothalamus

growth_protocol: Tissues were stored in RNALater (Thermofisher) in 4 degree overnight and transferred to -20 degree until RNA extraction

extract_protocol:
RNA was extracted with the magnetic bead based MaxwellRSC 48 instrument using the Maxwell RSC simply RNA Tissue kit
For muscle, library was prepared according to manufacturer’s protocol with Clontech SMARTer method kit; for fat and hypothalamus, library was prepared with RiboErase method kit

value: hypothalamus

tag: treatment

value: vehicle


title: D920T220

city: Paris

institute: Institut Curie

description: Library name: Dataset_A_17


title: D920T219

description: Library name: Dataset_A_16


title: Kidney, ZT 9, Sample 2

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

value: Chow diet


title: control_M2_hypothalamus

description:
Library name: hypothalamus_control_rep2
control_M2_hypothalamus


title: Kidney, ZT 13, Sample 1

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: control_M1_hypothalamus

description:
Library name: hypothalamus_control_rep1
control_M1_hypothalamus


title: D920T225

description: Library name: Dataset_A_22


title: D920T218

description: Library name: Dataset_A_15


title: Kidney, ZT 9, Sample 1

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: 10mg_M5_hypothalamus

description:
Library name: hypothalamus_10mg_rep4
10mg_M5_hypothalamus

value: 10mg/kg oxaliplatin


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]

description:
Library name: NPM1_08_09_rep4_scRNA_Seq, NextSeq 500
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000

value: bone marrow mononuclear cells


title: mre11_null_amplicon_3

city: Ann Arbor

first: Agnieszka

last: Lukaszewicz

address: 1241 East Catherine Street

department: Human Genetics

institute: University of Michigan Medical School

description: Library name: Sample 3

data_processing:
FASTQ sequencing files were analyzed using a pipeline, svAmplicon, an extension of the svx-mdi-tools suite repository (Wilson et al., 2023 NAR Genom Bioinform). Paired-read FASTQ sequencing files were quality filtered and merged when sufficiently overlapping into single reads by fastp version 0.23.2. Prepared reads were aligned to the mm10 reference genome using bwa mem version 0.7.17 (https://arxiv.org/abs/1303.3997) to identify the best match for each read while allowing for off-target alignment. The outer endpoints of reads were used to perform ab initio identification of apparent amplicons present in the pooled data, which consistently met expectations of the PCR reactions performed. Reads were grouped into unique sequences per amplicon, keeping the best base quality observed over all equivalent reads, and realigned to the genome as individual best. Structural variant (SV) breakpoint nodes were first identified from discontinuous, i.e. supplementary alignments, and then by extracting small inline node pairs from the CIGAR string of individual alignments representing deletions 10 bp or larger. An important class of artifactual false junctions can arise when a low-quality segment of a read fails to align in an otherwise continuous amplicon, leading to an insertion and deletion of roughly equal length. Such non-SV indels were identified and discarded, resulting in called SVs with a net deletion of ≥10 bp. Read sequences were parsed to infer the microhomologous or inserted bases at each junction (Wilson et al., 2024 Nat Commun). Amplicon reads were grouped into unique alignment paths to allow potential PCR duplicates to be identified. Final junction validation was performed in the interactive svAmplicon R Shiny app. First, filters required that the best read representing a molecule path had an average Phred-scaled base quality of 25 and a mapping quality (MAPQ) of 55 for each alignment. Deletion SVs as defined above were individually examined, allowing correlation of local base quality, indel lengths, and microhomology spans to ensure that only true novel junctions were tabulated in processed data files.
The svAmplicon pipeline and app code are available as part of the svx-mdi-tools repository (GitHub: https://github.com/wilsontelab/svx-mdi-tools; documentation: https://wilsontelab.github.io/svx-mdi-tools), linked to Zenodo DOI (https://doi.org/10.5281/zenodo.7871676).
Assembly: mm10
Supplementary files format and content: One txt file for each sample contains reads with deletions. Columns A–R represent svAmplicon output, and columns S–U indicate deletion sizes and positions adjusted to be consistent with previous Atm–/– amplicon analyses (Lukaszewicz et al., 2021 Cell). Deletion breakpoint positions (pos1, pos2) refer to the last aligned bases to the reference genome. Deletion sizes (eventSize) indicate the number of deleted bases, calculated as pos2 − pos1 − 1. Deletion breakpoint positions (pos1, pos2) were renumbered to indicate the genomic positions of the deleted bases (delpos1, delpos2), as calculated: (1) for deletion events with inserted bases at junctions (insertSize > 0), Delpos1 = pos1 + 1; Delpos2 = pos2 – 1; (2) for deletion events with ≥0 bp microhomology (insertSize < 1), Delpos1 = pos1 + 1 + insertSize; Delpos2 = pos2 – 1. In the case of microhomologies present at breakpoints, position 1 is arbitrarily adjusted. For renumbered deletion breakpoint positions (delpos1, delpos2), deletion sizes are calculated as delpos2 – delpos1 + 1.

source_name: testis

extract_protocol:
DNA was isolated from testicular single-cell suspensions according to the previously published protocol (Lukaszewicz et al., 2021 Cell). Mre11 conditional knockout mice, here referred to as Mre11–/–, were used (Buis et al., 2008 Cell; Kim et al., 2025 Nat Commun). Generation of amplicons and deep sequencing were performed as previously described (Lukaszewicz et al., 2021 Cell). Briefly, four overlapping ~580-bp amplicons of the Chr1 single hotspot were amplified using published primers (Lukaszewicz et al., 2021 Cell). PCRs were carried out in 96-well plates in 50 µl reactions, each containing 50 ng input genomic DNA, 1.5 U Taq DNA polymerase, and 0.3 U Pfu Turbo DNA polymerase in the in the Jeffreys buffer (Cole et al., 2010 Molecular Cell). For each amplicon, PCR conditions were the same: denaturation (2 min at 96°C), followed by 22 cycles of amplification (20 s at 96°C, 30 s at 59°C, and 35 s at 65°C). Testis DNA was isolated from three Mre11–/– mice and amplified independently. A total of 576 PCRs were performed for each amplicon, with input DNA equivalent to 9.6 million haploid genomes. Next, for each amplicon, PCR products were pooled, and a 1200-ml aliquot was purified and concentrated on spin columns (Lukaszewicz et al., 2021 Cell). Approximately 60 µl of DNA at a concentration of 1–2 ng/µl was used for library preparation and deep sequencing.
The library was prepared by ligation of indexed adapter sequences using the KAPA HyperPrep Kit (Roche). Sequencing was performed using Illumina MiSeq (2 x 300-bp paired-end reads). In a single run, libraries from amplicons 1–4 were mixed with 5% PhiX DNA control library.

value: testis

value: spermatocytes

value: 5–7 weeks old


title: mre11_null_amplicon_4

description: Library name: Sample 4


title: D920T217

description: Library name: Dataset_A_14


title: mre11_null_amplicon_2

description: Library name: Sample 2


title: 10mg_M4_hypothalamus

description:
Library name: hypothalamus_10mg_rep3
10mg_M4_hypothalamus


title: D920T216

description: Library name: Dataset_A_13


title: Kidney, ZT 5, Sample 3

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

value: Kidney


title: mre11_null_amplicon_1

description: Library name: Sample 1


title: Kidney, ZT 5, Sample 1

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt

value: male


title: cc_022725_wt_bmal1_female4

city: St. Louis

first: India

last: Reiss

address: 660 S. Euclid Ave.

department: Genetics

description:
Library name: cc_022725_wt_bmal1_female4
Calling Cards Lib Prep, rep8

data_processing:
Calling Cards FASTQ reads were processed with a custom bash pipeline to generate per-sample insertion files for peak calling. Briefly, reads were first adapter-trimmed and demultiplexed by requiring an exact 5′ match to the OM-piggyBac transposon sequence using cutadapt with zero mismatches/indels and discarding untrimmed reads, then SRT barcodes were extracted with umi_tools extract, followed by an additional exact-match trim of the transposon sequence and trimming of trailing Nextera adapters (cutadapt).  Trimmed reads were aligned to the reference genome with Bowtie2 and converted to BAM; mapped reads were retained, then sorted and indexed. Transposon insertion sites were then computed per read by assigning the insertion point to the alignment start (forward reads) or end (reverse reads), correcting for soft clipping, and encoding the genomic interval immediately preceding the insertion. For piggyBac, reads were optionally filtered to those matching the expected “TTAA” insertion motif.  Finally, unique insertions were aggregated into an insertion table (“qbed” file)  by counting identical insertion sites; these insertion files were then used as input for downstream peak calling.
Differential Calling Cards peak sets were generated using a custom pipeline that (i) defines a unified candidate peak set and (ii) classifies those peaks as condition-enriched (CLN3-specific/WT-specific) or shared. For each condition, peaks were called with PyCallingCards using the MACCs (“cctools”) framework with the parameters  pvalue_cutoffbg=0.05, window_size=800, step_size=400, pvalue_cutoffTTAA=0.005, lam_win_size=1,000,000, pseudocounts=0.4. Peaks from the two TF conditions were then concatenated and collapsed into a nonredundant “union” peak set by sorting and merging intervals with bedtools merge using a 1 kb merge distance (-d 1000).  To call differential peaks, we quantified insertions from the two TF qbed files across the union peak set using pycallingcards.pp.make_Anndata, then tested TF_C1 vs TF_C2 per peak with Fisher’s exact test and ranked peaks by multiple-testing–adjusted p-values. Peaks with adjusted p < 0.05 enriched in TF_C1 were designated CLN3-specific peaks, and peaks enriched in TF_C2 were designated WT-specific peaks (written as separate BED files). Finally, “shared” peaks were defined as the remaining union peaks not assigned to either differential class, implemented with bedtools intersect -v against the condition-specific BED files.
Paired-end MNase-seq FASTQ files were aligned to the mm10 reference genome using Bowtie2 v2.3.5. Alignments were performed in paired-end mode with an expected insert-size range of 110-210 bp (-I 110 -X 210), requiring properly paired reads, and reads were trimmed to 40 bp prior to alignment. SAM files were converted to BAM and unmapped reads were removed, followed by coordinate sorting and indexing. To restrict analyses to canonical chromosomes, BAMs were filtered to chr1-chr19, chrX, chrY, name-sorted, and processed with samtools fixmate.  BAMs were then coordinate-sorted and PCR duplicates were removed with samtools markdup -r.
To generate genome-browser tracks, processed replicate BAMs for each condition were supplied to DANPOS3 for differential analysis using the standard danpos.py. DANPOS3 outputs included pooled per-condition WIG tracks (normalized/smoothed signal) and a differential WIG track (Poisson-based difference). Finally, WIG files were converted to bigWig format using the UCSC wigToBigWig utility. This produced bigWig tracks for each condition’s normalized/smoothed MNase signal and for the DANPOS differential signal.
RNA-seq counts tables produced by GTAC.
Assembly: mm10, hg38
Supplementary files format and content: Calling Cards: qBED, BED. Mnase-seq: bigWig. RNA-seq: counts  csv and metadata csv

source_name: astrocytes

growth_protocol: Hepg2 cells were maintained in DMEM+10% FBS, 1x Penstrep in 6 well plates.

extract_protocol:
For MNase-seq, MNase digestion was performed immediately following astrocyte isolation. Cells were fixed for 10 minutes in 1% formaldehyde and the reaction was quenched for 5 minutes with 2.5 M glycine, added to a final concentration of 0.125 M. The cells were then washed twice in 1x PBS. Nuclei were prepared by adding 100 μl of Nuclei Prep Buffer (Zymo EZ Nucleosome DNA Prep Kit, D5220) per 1 million cells. After centrifugation, the cells were resuspended in 1x Takara MNase Digestion Buffer. Chromatin was digested with 4 units of Takara MNase (2910A) per 1,000,000 cells. The reaction was stopped by adding 5x MN stop buffer from the EZ kit. Subsequently, 4.8 μl of 5 M NaCl and 2 μl of proteinase K were added per 1 million cells, and samples were incubated at 65°C overnight. The following day, DNA was isolated using the EZ kit according to the manufacturer’s instructions. For Calling Cards and RNA-seq, total RNA extraction after MACS was done using the Qiagen RNeasy Plus Mini Kit (Cat no. 74134) according to the manufacturer's protocol. All of the total RNA was used for reverse transcription.
For Calling Cards, First-strand cDNA was generated by oligo(dT) priming with the SMART_dT18VN primer and Maxima H Minus reverse transcriptase in the presence of RNase inhibitor, followed by heat inactivation and RNase H treatment to remove the RNA strand, yielding cDNA for downstream library construction. Self-reporting transposon (SRT) transcripts were then PCR-amplified from cDNA using KAPA HiFi HotStart with a reporter specific primer (tdtomato or puromycin) and SMART reverse primers (cycle number minimized/optimized to avoid over-amplification; typical program uses ~20 cycles with 98°C denaturation, 65°C annealing, and long 72°C extension), and amplicons were size-selected/cleaned with a 0.6× AMPure XP bead cleanup and QC’d by Qubit. Purified SRT PCR products were converted into sequencing-ready libraries by Nextera XT tagmentation (ATM + TD buffer at 55°C), neutralization, and an indexing PCR using a barcoded piggyBac (OM-PB) primer together with a Nextera N7 index primer to enable multiplexing, followed by a final 0.6× bead cleanup and fragment distribution QC prior to pooling and Illumina sequencing. A fraction of the samples were checked for sequencing quality using WashU’s DNA Sequencing Innovation Lab (DSIL)’s spike in program with the Illumina MiSeq or Illumina Miniseq. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. All sequencing data was combined at the end for each sample. MNase-seq libraries were prepared using the NEBNext Ultra end repair and A-tailing module (NEBNext End Prep, E7442), followed by adapter ligation using the NEBNext Ultra Ligation Module with Quick Ligation (E7445). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63880). Adapter-ligated DNA was PCR-amplified using Phusion High-Fidelity DNA Polymerase with NEB primers (NEB, E6440S), followed by a second cleanup with Agencourt AMPure XP beads. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. RNA-seq libraries were prepared in-house from total RNA using the NEBNext UltraExpress® RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Indexes used from NEBNext Multiplex Oligos for Illumina® (E6440S).  Final libraries were quantified, pooled, and submitted to the Washington University Genome Technology Access Center (GTAC) for sequencing. GTAC performed sequencing on the Illumina NovaSeq X Plus (paired end reads extending 150 bases) and generated gene-level RNA-seq count tables from the resulting sequencing data using their standard RNA-seq processing workflow; these GTAC-provided count tables were used to assemble the final count matrix for downstream analyses.

treatment_protocol: AAV injections were performed as described in (Yen et al. 2023). Viral titers (viral genomes [vg] per milliliter) were ∼1.0 × 10. Neonatal mice (P0-P1) received intracerebroventricular (ICV) injections of Calling Cards AAVs encoding the piggyBac transposase (unfused or BMAL1 fusion) and donor/self-reporting transposon. AAV stocks were mixed 1:1 immediately prior to injection (6 µL total per pup). Pups were anesthetized by hypothermia on ice (5-8 min; ≤15 min maximum) and injected bilaterally using a Hamilton syringe fitted with a depth guard to ensure a consistent 2 mm insertion depth. Virus was delivered at 1 µL per site at three sites per hemisphere (1 µL/s); after each injection, the needle was held in place for 5 s before withdrawal to minimize backflow. Following injection, pups were placed on a low warming pad for recovery (5-10 min) and returned to the home cage with the dam. For HepG2 cells, calling card constructs (with puro as the marker gene) transfected through neon electroporation (2*10^6 cells/well). Puro selection performed with 3ug/mL puro. Puro selection done over 5 days to allow for cells without insertions to die off, a non-transfected well was used to determine that all cells without insertions had died at that point.

value: astrocytes

value: injected w/ bmal1 cc aav


title: 10mg_M3_hypothalamus

description:
Library name: hypothalamus_10mg_rep2
10mg_M3_hypothalamus


title: 10mg_M2_hypothalamus

description:
Library name: hypothalamus_10mg_rep1
10mg_M2_hypothalamus


title: D920T215

description: Library name: Dataset_A_12

value: Blood


title: cc_022725_wt_bmal1_female3

description:
Library name: cc_022725_wt_bmal1_female3
Calling Cards Lib Prep, rep7


title: D920T214

description: Library name: Dataset_A_11


title: cc_022725_wt_bmal1_female2

description:
Library name: cc_022725_wt_bmal1_female2
Calling Cards Lib Prep, rep6


title: cc_022725_wt_bmal1_female1

description:
Library name: cc_022725_wt_bmal1_female1
Calling Cards Lib Prep, rep5


title: Kidney, ZT 1, Sample 3

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: control_M4_fat

description:
Library name: Fat_control_rep3
control_M4_fat

source_name: white adipose tissue

value: white adipose tissue


title: Kidney, ZT 5, Sample 2

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: Kidney, ZT 1, Sample 1

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: D920T213

description: Library name: Dataset_A_10


title: Kidney, ZT 1, Sample 2

description:
Dataanalysis.txt
meta2d_Ctrl.exp.txt


title: control_M2_fat

description:
Library name: Fat_control_rep2
control_M2_fat


title: cc_022525_wt_bmal1_male4

description:
Library name: cc_022525_wt_bmal1_male4
Calling Cards Lib Prep, rep4


title: D920T212

description: Library name: Dataset_A_9