title: YFP_neg_2, HTO

city: New York

first: Chrysothemis

last: Brown

department: Immuno-Oncology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: YFP_neg_2_HTO
HTO library for dendrititc cell

data_processing:
FASTQ files were aligned to mm10 (Cell Ranger mouse reference genome mm10-2020-A) and counted by Cell Ranger v9.0.1 with default parameters. HTO sequencing data were processed using CellRanger multi pipeline v9.0.1 with default parameters. The singlet barcodes were further filtered based on the number of RNA-seq transcripts (>400), the number of detected genes (>250), and the fraction of mitochondrial transcripts (<8%). Finally, any genes detected in <2 cells in the scRNA-seq data were discarded.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: YFP_pos-gex_matrix.mtx.gz, YFP_pos-gex_features.tsv.gz, YFP_pos-gex_barcodes.tsv.gz, YFP_neg-gex_matrix.mtx.gz, YFP_neg-gex_features.tsv.gz, YFP_neg-gex_barcodes.tsv.gz
Supplementary files format and content: Outpus files for hashtag: YFP_pos-hto_matrix.mtx.gz, YFP_pos-hto_features.tsv.gz, YFP_pos-hto_barcodes.tsv.gz, YFP_neg-hto_matrix.mtx.gz, YFP_neg-hto_features.tsv.gz, YFP_neg-hto_barcodes.tsv.gz
Supplementary files format and content: Analysis results from Scanpy including pheno_louvain clusters, Celltype annotations and UMAP

molecule: protein

source_name: mLN and spleen

extract_protocol:
Mouse DC subsets were enriched from a pool of mesenteric lymph nodes or spleen, obtained from four Tbx21RFP-creERT2Clec9acre/creR26lsl-YFP mice. Lymphoid organs were digested in collagenase in RPMI1640 supplemented with 5% fetal calf serum, 1% L-glutamine, 1% penicillin–streptomycin, 10 mM HEPES, 1 mg ml−1 collagenase A (Sigma, 11088793001) and 1 U ml−1 DNase I (Sigma, 10104159001) for 45 min at 37 °C, 250 rpm. Digested samples were filtered through 100-μm strainers and centrifuged to remove collagenase solution. Cells were depleted of Lin+ (TCRb, TCRγδ, CD19, Ter-119, NK1.1)+ cells by staining with biotinylated antibodies followed by magnetic bead negative selection (M-280 dynabeads; ThermoFisher). Cells were incubated with anti-CD16/32 in sorting buffer (2% FBS in PBS) for 10 minutes at 4°C to block binding to Fc receptors. Extracellular antigens were stained for 30 minutes at RT in sorting buffer. mLN and spleen samples were separately “stained” with different TotalSeqTM oligo-conjugated antibodies consisting of a pool of antibodies directed against CD45 (30-F11) and H2 MHC Class I alloantigens (clone M1/42; Biolegend). Cells were washed and resuspended in sorting buffer with SYTOX blue (Invitrogen) for exclusion of dead cells. Live, Lin (CD19, NK1.1, TCRb, SiglecF)–MHCII+YFP+ or YFP– cells were  sorted into complete RPMI-20% FBS, before being pelleted and resuspended in complete RPMI-2% FBS. YFP+ and YFP– cells were combined as follows: 1,600 mLN and 13,400 splenic YFP+ cells, 9,700 mLN and 5,300 splenic YFP– cells. Cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspensions were loaded onto Chromium GEM-X 3’ Chip (10x Genomics PN 1000690) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 2,300-3,800 cells proceeded using the Chromium GEM-X Single Cell 3’ Kit v4 (10X Genomics PN 1000691) according to the manufacturer’s protocol. cDNA amplification included 11 cycles and 13-35 ng of the material was used to prepare sequencing libraries with 10 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq X in a PE28/88 paired end run using the NovaSeq X 10B Reagent Kit (100 cycles) (Illumina).  An average of 31 thousand paired reads was generated per cell. Amplification products generated using the methods described above included both cDNA and feature barcodes tagged with cell barcodes and unique molecular identifiers. Smaller feature barcode fragments were separated from longer amplified cDNA using a 0.6X cleanup using aMPure XP beads (Beckman Coulter catalog # A63882).  Libraries were constructed using the 3’ Feature Barcode Kit (10X Genomics PN 1000276) according to the manufacturer’s protocol with 10 cycles of PCR.
YFP+ or YFP– cells from different lymph nodes were multiplexed together on one lane of 10X Chromium using Hash Tag Oligonucleotides - HTO following previously published protocol. Final libraries were sequenced on NovaSeq X in a PE28/88 paired end run using the NovaSeq X 10B Reagent Kit (100 cycles) (Illumina)

value: mLN and spleen

value: Dendritic cell

value: 13 weeks

tag: library type

value: HTO


title: A38_HTH

status: Public on Nov 20 2025

type: genomic

city: Hong Kong

first: Andrew

middle: J.

last: Kwok

address: 30-32 Ngan Shing Street, Shatin, New Territories

department: Medicine and Therapeutics

country: Hong Kong

institute: Chinese University of Hong Kong

description:
A38
208114950055_R01C02

hyb_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

data_processing:
Raw data were processed with SeSaMe (v1.16.1)
Processed data are presented in the form of beta values.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Mus musculus

source_name: HTH

extract_protocol: Genomic DNA was extracted with the Quick-DNA Miniprep Plus Kit (D4069, Zymo Research) for blood or EZNA Tissue DNA Kit (D3396-02, Omega Bio-Tek) for solid tissue)

tag: tissue

value: HTH

tag: treatment


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_paBC_DNA_Index1_Rep2

type: SRA

city: Ithaca

first: Haiyuan

last: Yu

state: New York

address: 237 Tower Road

department: Department of Computational Biology, Weill Institute for Cell and Molecular Biology

country: USA

institute: Cornell University

description:
Library name: QUASARRseq_paBC_DNA_Index1_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_paBC_limma_logFC.tsv

library_source: other

data_processing:
QUASARR-seq data preprocessing includes two main parts: 1. eaBC-TRE-paBC index mapping and 2. RNA aBC/DNA aBC activity measurement. Raw sequencing data was first filtered using fastp using the following parameters "--disable_adapter_trimming --trim_poly_g --cut_right", followed by processing using biodatatools. Briefly, sequence information was retrieved according to the library’s corresponding layout; eaBC-TRE-paBC and unique molecular identifiers (UMIs) for index mapping, and RNA aBCs, DNA aBCs, and UMIs for activity measurements. In index mapping, eaBCs and paBCs were clustered by merging all sequences with a maximum Hamming distance of one for sequencing error tolerance. Partial element sequences were aligned to the reference element sequences. eaBCs and paBCs were then assigned to the TREs. For the multiple minP library set, an additional three-bp minP barcode was used to assign aBCs to their associated minPs. eaBCs and paBCs were regarded as a representation of a given TRE(A), if the number of eaBC-TRE(A)-paBC entries were significantly higher than all other eaBC-TRE(X)-paBC entries for any given TRE(X). In activity measurement, eaBCs and paBCs were extracted and matched to the previously clustered eaBCs and paBCs during index mapping and assigned to their corresponding TRE. All counts generated were subjected to UMI correction to collapse identical copies. The resultant RNA and DNA element counts were then normalized using edgeR to calculate the normalized element counts and logFCs.
Assembly: hg38
Supplementary files format and content: Processed QUASARR-seq files contain per-element DNA input counts, RNA output counts, and activity statistics computed using limma. Element (identifier for tested sequence), DNA1/DNA2 and RNA1/RNA2 (normalized counts from two replicates), limma outputs logFC (log2 fold-change), AveExpr (average log2 abundance), t (moderated t-statistic), P.Value (raw P-value), adj.P.Val (FDR-adjusted P-value), and B (log-odds of differential activity).

molecule: other

organism: Homo sapiens

growth_protocol: K-562 (CCL-243; ATCC) cells were cultured in IMDM (30-2005; ATCC) supplemented with 10% FBS (30-2020; ATCC) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol Reagent (15596026; Invitrogen) following the manufacturer’s instructions. Plasmid DNA was extracted from cells as previously described (PMID: 9591124).
QUASARR-seq requires the generation of a pre-transfected DNA eaBC-TRE-paBC index library for barcode-element index generation, as well as a minimum of four libraries per replicate: two RNA libraries targeting the eaBC and paBC transcripts, respectively, and two DNA libraries targeting the eaBC and paBC inputs, respectively. To construct an eaBC-TRE-paBC index, pre-transfected eaBC-TRE-paBC libraries were generated prior to electroporation. Total RNA was extracted from cells using TRIzol Reagent following the manufacturer’s instructions. To remove contaminating plasmid DNA, RNA was treated with DNase I (AM2222; Invitrogen) and subsequently purified using RNeasy Mini Kit (74104; QIAGEN). Reverse transcription was performed with the DNase-treated RNA (for eaBC and paBC quantification libraries) as the template using SuperScript III Reverse Transcriptase (18080093; Invitrogen). Plasmid DNA was extracted from cells as previously described (PMID: 9591124). A first primer extension was performed with the pre-transfected (for eaBC-TRE-paBC index library) and extracted (for eaBC and paBC quantification libraries) DNA as the templates. Reactions were treated with Exonuclease I (M0293; New England Biolabs) to remove unused primer and purified using DNA Clean & Concentrator-5 (D4013; Zymo Research Corp.). A second primer extension was performed with the products of the reverse transcription (RNA libraries) and the first primer extension (DNA libraries) as the templates, respectively. Reactions were again treated with Exonuclease I and purified using DNA Clean & Concentrator-25 (D4033; Zymo Research) and DNA Clean & Concentrator-5 for the RNA and DNA libraires, respectively. Finally, low-cycle PCR was performed to add sequencing adapters, followed by acquisition of 2 × 150 bp reads on an Illumina NovaSeq X Plus.

treatment_protocol: QUASARR-seq input libraries were electroporated into K-562 using Amaxa Cell Line Nucleofector Kit V (VCA-1003; Lonza Group AG) with a Lonza Amaxa Nucleofector II Device using program T-016. The manufacturers’ Amaxa Cell Line Nucleofector Kit V protocol for ATCC K-562 was followed, except for each electroporation, 1 x 10^6 cells received 20 μg of QUASARR-seq library. Five electroporations were carried out per technical replicate, two technical replicates per biological replicate. Cells for different biological replicates were cultured and electroporated on separate days. Following a 6-hour incubation period, cells were harvested by pooling samples for the same technical replicate to remove variance introduced during electroporation. Following three washes with 1X PBS (10010023; Gibco), each technical replicate was parsed out where 4 x 10^6 cells were used for RNA libraries and 1 x 10^6 cells were used for DNA libraries. Cell pellets were snap-frozen with LN2 and stored in −80°C until library preparation.

tag: cell line


title: control_F_5yo_whole_blood

city: Philadelphia

first: Kelly

middle: J

last: Clark

state: PA

address: 3501 Civic Center Blvd

department: Human Genetics

institute: Children's Hospital of Philadelphia

hyb_protocol: Day one consists of denaturing and neutralizing bisulfite converted DNA samples to prepare them for amplification. The denatured DNA is isothermally amplified in an overnight step. Day two begins by fragmenting the amplified product using end-point fragmentation to avoid over-fragmenting the sample. After an isopropanol precipitation, the fragmented DNA is collected by centrifugation at 4 degrees C. The precipitated DNA is then resuspended in hybridization buffer. The array is then prepared for hybridization in a capillary flow-through chamber. Samples are applied to an array; the loaded array is incubated overnight in the Illumina Hybridization Oven. Day three begins with “washing” the hybridized array; unhybridized and non-specifically hybridized DNA is washed away to prepare the chip for staining and extension. Extend and Stain (Xstain) consists of single-base extension of the oligos on the array, using the captured DNA as a template, incorporates detectable labels on the array and determines the genotype call for the sample.

scan_protocol: Beadchips are then loaded into the Illumina iScan, which scans the array using a laser to excite the fluorophore of the single-base extension product on the beads. The scanner records high-resolution images of the light emitted from the fluorophores. The iScan Reader uses a laser to excite the fluor of the single-base extension product on the beads of the BeadChip sections. Light emissions from these fluors are then recorded in high-resolution images of the BeadChip sections.

data_processing:
Data from these images are analyzed using Illumina’s GenomeStudio Methylation Module. IDAT files were processed in R using the minfi package to get beta values. Only probes with detection p-values under 0.05 were used. Probes from X and Y chromosomes and probes with SNPs were filtered out.
minfi-computed beta values

source_name: whole blood

label_protocol: Bisulfite-treated DNA is amplified and loaded onto an Infinium methylation array for the Infinium methylation assay and scanned on the iScan System.

growth_protocol: Fibroblasts were cultured in DMEM. Media was changed every 2-3 days, and cells were split at ~70% confluency.

extract_protocol: Fibroblast DNA was extracted with Qiagen DNeasy Blood and Tissue Kit. Whole blood DNA was extracted on the Biomek FX using the Agencourt Genfind chemistry and methodologies.

tag: cell type

value: whole blood

tag: genotype

value: WT


title: YFP_pos_1, HTO

description:
Library name: YFP_pos_1_HTO
HTO library for dendrititc cell

tag: age


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_paBC_DNA_Index1_Rep1

description:
Library name: QUASARRseq_paBC_DNA_Index1_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_paBC_limma_logFC.tsv


title: YFP_neg_2, GEX

description:
Library name: YFP_neg_2_mRNA
GEX (3' mRNA) library for dendritic cells

library_source: transcriptomic single cell

molecule: polyA RNA

value: mRNA


title: A38_Hippo

description:
A38
208114950055_R06C01

scan_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

source_name: Hippo

value: Hippo


title: YFP_pos_1, GEX

description:
Library name: YFP_pos_1_mRNA
GEX (3' mRNA) library for dendritic cells


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_eaBC_DNA_Index1_Rep1

description:
Library name: QUASARRseq_eaBC_DNA_Index1_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_eaBC_limma_logFC.tsv


title: A38_FCTX

description:
A38
208114950055_R05C01

source_name: FCTX

label_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

value: FCTX


title: control_M_7yo_whole_blood


title: A38_CardiacMuscle

description:
A38
208114950055_R04C01

source_name: CardiacMuscle

value: CardiacMuscle


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_paBC_RNA_Index1_Rep1

description:
Library name: QUASARRseq_paBC_RNA_Index1_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_paBC_limma_logFC.tsv


title: healthy mouse liver-derived liver organoid, TGF-β1-treated in vitro fibrosis organoid,  Sargassum japonica treatment 2

city: Seoul

first: Jiyoung

last: Heo

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

description:
Library name: ND-4
in vitro fibrosis organoid countmatrix.txt

library_source: transcriptomic

data_processing:
Differentially expressed genes were subjected to gene enrichment analysis with the Python.
ShinyGO
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each example

molecule: total RNA

source_name: mouse liver

growth_protocol: Organoids were cultured in Matrigel domes with expansion medium. After initial growth, organoids were differentiated for 4–5 days in differentiation medium.

extract_protocol:
Total RNA was extracted and purified from organoids using the TRIzol reagent. 1.2ug of total RNA was used to construct sequencing library
Libraries were generated using the Illumina TruSeq strand mRNA sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: After differentiation, in vivo fibrosis organoids were treated with Sargassum japonica extract for 24 hours. In vitro fibrosis organoids were first treated with TGF-β1 for 24 hours, followed by Sargassum japonica treatment for an additional 24 hours.

value: mouse liver

tag: sample group

value: TGF-β1, Sargassum japonica


title: H3-3B_Q125R_F_14yo_whole_blood


title: A38_SkeletalMuscle

description:
A38
208114950055_R03C01

source_name: SkeletalMuscle

value: SkeletalMuscle


title: H3-3A_K36E_M_35yo_whole_blood


title: Pre-transfected_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_TRE-paBC_DNA_Index1

description:
Library name: QUASARRseq_TRE-paBC_DNA_Index1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_paBC_limma_logFC.tsv
QUASARR_CNPL-TRE202-MRE_eaBC_limma_logFC.tsv


title: A38_Adipose

description:
A38
208114950055_R02C01

source_name: Adipose

value: Adipose


title: control_F_7yo_whole_blood_1


title: Pre-transfected_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_eaBC-TRE-paBC_DNA_Index1

description:
Library name: QUASARRseq_eaBC-TRE-paBC_DNA_Index1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_paBC_limma_logFC.tsv
QUASARR_CNPL-TRE202-MRE_eaBC_limma_logFC.tsv


title: A38_WBC

description:
A38
208114950055_R01C01

source_name: WBC

value: WBC


title: H3-3A_V46M_M_7yo_whole_blood


title: healthy mouse liver-derived liver organoid, TGF-β1-treated in vitro fibrosis organoid 2

description:
Library name: NP-5
in vitro fibrosis organoid countmatrix.txt


title: healthy mouse liver-derived liver organoid, TGF-β1-treated in vitro fibrosis organoid 3

description:
Library name: NP-6
in vitro fibrosis organoid countmatrix.txt


title: HPAF-II cells, trametinib 24h, IgG, rep2

city: Singapore

first: David

last: Virshup

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Library name: HPAF-II_trametinib_IgG_rep2

library_source: genomic

data_processing:
Adapter sequences were trimmed with Cutadapt v3.5; paired-end reads were discarded if either mate was <15 nt after trimming. Trimmed reads were aligned to the human reference genome (GRCh38/hg38; Ensembl release 110 annotation) with Bowtie2 v2.5.4 using default settings, and only alignments with MAPQ ≥ 20 were retained for downstream analyses. For each biological replicate, JUNB peaks were called against the matched IgG control using MACS2 v2.2.7.1 (q-value/FDR ≤ 0.01). Reproducible peaks were defined as regions with reciprocal overlaps of ≥20% peak length between replicates using bedtools v2.27.0 (intersect -r -f 0.20). Reproducible peaks were used for peak annotation and motif enrichment with the HOMER suite v4.11, using the exact peak widths (-size given).
Assembly: GRCh38/hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Run

source_name: HPAF-II

growth_protocol: HPAF-II cells were cultured in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% FBS, 1 mM sodium pyruvate, 2 mM L-glutamine, and 1% (v/v) penicillin/streptomycin (Gibco, no. 15140122).

extract_protocol:
The Cut&Run assay was performed using the CUT&RUN Assay Kit (CST, no. 86652) following the manufacturer’s protocol. 200,000 cells were used for each reaction. Anti-JUNB antibody (CST, no. 3753) and rabbit IgG isotype from the CUT&RUN Assay Kit were used. DNA was purified by Zymo Oligo Clean & Concentrator column.
The libraries were constructed using the NEBNext Ultra II library preparation kit and NEBNext Multiplex Oligos for Illumina kit.

treatment_protocol: Cells were either untreated or treated with DMSO control (0.1% v/v) or 100 nM trametinib for 24 h before Cut&Run assays.

value: HPAF-II

value: Trametinib (100 nM) for 24 h


title: control_M_1yo_whole_blood


title: A37_HTH

description:
A37
208114950053_R05C02


title: HPAF-II cells, trametinib 24h, IgG, rep1

description: Library name: HPAF-II_trametinib_IgG_rep1


title: healthy mouse liver-derived liver organoid, TGF-β1-treated in vitro fibrosis organoid 1

description:
Library name: NP-4
in vitro fibrosis organoid countmatrix.txt


title: control_F_2yo_whole_blood


title: healthy mouse liver-derived liver organoid 3

description:
Library name: NN-5
in vitro fibrosis organoid countmatrix.txt


title: healthy mouse liver-derived liver organoid, TGF-β1-treated in vitro fibrosis organoid,  Sargassum japonica treatment 3

description:
Library name: ND-5
in vitro fibrosis organoid countmatrix.txt


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_paBC_RNA_Index1_Rep2

description:
Library name: QUASARRseq_paBC_RNA_Index1_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_paBC_limma_logFC.tsv


title: H3-3B_G34V_M_5yo_whole_blood


title: A37_Hippo

description:
A37
208114950053_R04C02


title: HPAF-II cells, trametinib 24h, anti-JUNB, rep1

description: Library name: HPAF-II_trametinib_JUNB_rep1


title: H3-3A_L109R_M_34yo_whole_blood


title: healthy mouse liver-derived liver organoid, TGF-β1-treated in vitro fibrosis organoid,  Sargassum japonica treatment 1

description:
Library name: ND-2
in vitro fibrosis organoid countmatrix.txt


title: HPAF-II cells, DMSO 24h, IgG, rep2

description: Library name: HPAF-II_DMSO_IgG_rep2

value: DMSO control for 24 h


title: A37_FCTX

description:
A37
208114950053_R03C02


title: healthy mouse liver-derived liver organoid 1

description:
Library name: NN-3
in vitro fibrosis organoid countmatrix.txt


title: control_M_37yo_whole_blood


title: HPAF-II cells, DMSO 24h, IgG, rep1

description: Library name: HPAF-II_DMSO_IgG_rep1


title: A37_CardiacMuscle

description:
A37
208114950053_R02C02


title: A37_Colon

description:
A37
208114950053_R06C02

source_name: Colon

value: Colon


title: H3-3A_D81H_F_7yo_whole_blood


title: carbon tetrachloride induced fibrosis mouse liver-derived in vivo liver organoid, Sargassum japonica treatment 3

description:
Library name: XD-10
in vivo fibrosis organoid countmatrix.txt

value: Sargassum japonica


title: HPAF-II cells, DMSO 24h, anti-JUNB, rep2

description: Library name: HPAF-II_DMSO_JUNB_rep2


title: HPAF-II cells, trametinib 24h, anti-JUNB, rep2

description: Library name: HPAF-II_trametinib_JUNB_rep2


title: H3-3A_R128C_F_1yo_whole_blood


title: HPAF-II cells, DMSO 24h, anti-JUNB, rep1

description: Library name: HPAF-II_DMSO_JUNB_rep1


title: carbon tetrachloride induced fibrosis mouse liver-derived in vivo liver organoid, Sargassum japonica treatment 2

description:
Library name: XD-9
in vivo fibrosis organoid countmatrix.txt


title: A37_Adipose

description:
A37
208114950053_R06C01


title: H3-3A_T22I_F_5yo_whole_blood


title: A37_WBC

description:
A37
208114950053_R05C01


title: carbon tetrachloride induced fibrosis mouse liver-derived in vivo liver organoid, Sargassum japonica treatment 1

description:
Library name: XD-8
in vivo fibrosis organoid countmatrix.txt


title: HPAF-II cells, untreated, IgG, rep2

description: Library name: HPAF-II_untreated_IgG_rep2

value: Untreated


title: carbon tetrachloride induced fibrosis mouse liver-derived in vivo fibrosis liver organoid 3

description:
Library name: XP-7
in vivo fibrosis organoid countmatrix.txt


title: HPAF-II cells, untreated, IgG, rep1

description: Library name: HPAF-II_untreated_IgG_rep1


title: A36_Colon

description:
A36
208114950053_R04C01


title: control_F_14yo_whole_blood

value: whole blood


title: carbon tetrachloride induced fibrosis mouse liver-derived in vivo fibrosis liver organoid 2

description:
Library name: XP-5
in vivo fibrosis organoid countmatrix.txt


title: healthy mouse liver-derived liver organoid 2

description:
Library name: NN-4
in vitro fibrosis organoid countmatrix.txt


title: control_M_35yo_whole_blood

value: WT


title: HPAF-II cells, untreated, anti-JUNB, rep2

description: Library name: HPAF-II_untreated_JUNB_rep2


title: H3-3B_P121R_M_18yo_rep2

source_name: dermal fibroblast

value: dermal fibroblast


title: carbon tetrachloride induced fibrosis mouse liver-derived in vivo fibrosis liver organoid 1

description:
Library name: XP-4
in vivo fibrosis organoid countmatrix.txt


title: A36_Hippo

description:
A36
208114950053_R02C01

value: Hippo


title: HPAF-II cells, untreated, anti-JUNB, rep1

description: Library name: HPAF-II_untreated_JUNB_rep1


title: A36_HTH

description:
A36
208114950053_R03C01

value: HTH


title: H3-3B_P121R_M_18yo_rep1


title: A37_SkeletalMuscle

description:
A37
208114950053_R01C02


title: healthy, mineral oil (vehicle control for carbon tetrachloride) treatment mouse liver-derived liver organoid 3

description:
Library name: XN-13
in vivo fibrosis organoid countmatrix.txt


title: A36_FCTX

description:
A36
208114950053_R01C01

value: FCTX


title: S. mansoni, Vitamin C, biol rep 3

city: Shanghai

first: Gongwen

last: Chen

address: 220 Handan Road

country: China

institute: Fudan University

description: Library name: VitC_3

data_processing:
The raw sequencing data (raw reads) were first processed using the fastp software.
The reference genome index was built using HISAT2 (version 2.2.1), and the paired-end clean reads were then aligned to the reference genome using HISAT2.
Gene expression quantification was performed using featureCounts (version 2.0.6) to count the reads mapped to each gene. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value for each gene was then calculated based on the gene's length and the count of reads mapped to it.
Assembly: SM_V10
Supplementary files format and content: tab-delimited text files includes raw counts or FPKM values for each Sample.

organism: Schistosoma mansoni

source_name: whole worm

growth_protocol: worms were perfused from mice 7-9 weeks after infection using DMEM with 5% horse serum and heparin warmed at 37C. Recovered worms were washed several times with perfusion solution and cultured in Basch Medium 169 containing 10% fetal bovine serum (BM169) and 50 µM BATT in 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol (Ambition/Invitrogen, USA).
RNA libraries for RNA-seq were prepared using SMARTer PCR cDNA Synthesis Kit following manufacturer's protocols.

treatment_protocol: The culture medium for the VC treatment group was supplemented with 200 μM Vitamin C , while the Nc group medium received no supplementation.

value: whole worm

tag: Sex

value: female

tag: time

value: day 10

value: Vitamin C


title: S. mansoni, Vitamin C, biol rep 2

description: Library name: VitC_2


title: A36_CardiacMuscle

description:
A36
208114950052_R06C02

value: CardiacMuscle


title: H3-3B_V117V_M_15yo_rep1


title: A36_SkeletalMuscle

description:
A36
208114950052_R05C02

value: SkeletalMuscle


title: H3-3A_G90R_F_8yo_rep2


title: carbon tetrachloride induced fibrosis mouse, Sargassum japonica treatment, liver tissue 3

description:
Library name: CD-3
liver tissue countmatrix.txt

value: mouse liver


title: H3-3B_V117V_M_15yo_rep2


title: S. mansoni, Vitamin C, biol rep 1

description: Library name: VitC_1


title: H3-3A_G90R_F_8yo_rep1


title: A36_Adipose

description:
A36
208114950052_R04C02

value: Adipose


title: carbon tetrachloride induced fibrosis mouse, Sargassum japonica treatment, liver tissue 2

description:
Library name: CD-2
liver tissue countmatrix.txt


title: S. mansoni, control, biol rep 3

description: Library name: Nc_3

value: Control


title: S. mansoni, control, biol rep 2

description: Library name: Nc_2


title: H3-3A_S31F_M_2yo_rep2


title: carbon tetrachloride induced fibrosis mouse, Sargassum japonica treatment, liver tissue 1

description:
Library name: CD-1
liver tissue countmatrix.txt


title: S. mansoni, control, biol rep 1

description: Library name: Nc_1


title: A34_Colon

description:
A34
208114950052_R02C02

value: Colon


title: carbon tetrachloride induced fibrosis mouse, liver tissue 3

description:
Library name: CP-3
liver tissue countmatrix.txt


title: H3-3A_S31F_M_2yo_rep1


title: A34_HTH

description:
A34
208114950052_R01C02


title: healthy, mineral oil (vehicle control for carbon tetrachloride) treatment mouse liver-derived liver organoid 2

description:
Library name: XN-6
in vivo fibrosis organoid countmatrix.txt


title: H3-3A_T6S_M_2yo_rep2

value: H3-3A p.T6S


title: A34_Hippo

description:
A34
208114950052_R06C01


title: carbon tetrachloride induced fibrosis mouse, liver tissue 2

description:
Library name: CP-2
liver tissue countmatrix.txt


title: healthy, mineral oil (vehicle control for carbon tetrachloride) treatment mouse liver-derived liver organoid 1

description:
Library name: XN-5
in vivo fibrosis organoid countmatrix.txt


title: H3-3A_T6S_M_2yo_rep1


title: A34_FCTX

description:
A34
208114950052_R05C01


title: carbon tetrachloride induced fibrosis mouse, liver tissue 1

description:
Library name: CP-1
liver tissue countmatrix.txt


title: Old tumor, Rep5

city: La Jolla

first: Cosimo

last: Commisso

state: CA

address: 10901 N. Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: Old_Rep5

data_processing:
Illumina Truseq adapters and polyA/polyT sequences were trimmed using Cutadapt v2.3. Trimmed reads were aligned to mouse genome version mm10 and Ensembl gene annotations v84 using STAR version 2.7.0d_0221 and ENCODE long RNA-seq pipeline parameters (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). RSEM v1.3.1 was used to obtain gene level estimated counts and transcripts per million.
Assembly: mm10
Supplementary files format and content: Tab-delimited tables of counts and transcripts per million (TPM)

source_name: Pancreatic tumor

extract_protocol:
Total RNA was isolated from tumor pieces (n=6 for young and old) using the PureLink RNA Mini Kit (Invitrogen, Cat# 12183025,) according to the manufacturer's instructions. Isolated RNAs were quality-controlled using Agilent 4200 TapeStation system (Agilent Technologies) and only preparations with RIN > 8 were used to prepare cDNA libraries.
PolyA RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module, and bar-coded libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

value: Pancreatic tumor

value: Epithelial

value: Old tumor


title: Old tumor, Rep4

description: Library name: Old_Rep4


title: healthy mouse, liver tissue 3

description:
Library name: CN-3
liver tissue countmatrix.txt

value: healthy mouse, liver tissue


title: Old tumor, Rep6

description: Library name: Old_Rep6


title: H3-3B_G34V_M_5yo_rep2

value: dermal fibroblast


title: A36_WBC

description:
A36
208114950052_R03C02

value: WBC


title: healthy mouse, liver tissue 2

description:
Library name: CN-2
liver tissue countmatrix.txt


title: A34_CardiacMuscle

description:
A34
208114950052_R04C01


title: H3-3B_G34V_M_5yo_rep1


title: Old tumor, Rep2

description: Library name: Old_Rep2


title: H3-3A_R17G_M_10yo_rep2


title: A34_SkeletalMuscle

description:
A34
208114950052_R03C01


title: healthy mouse, liver tissue 1

description:
Library name: CN-1
liver tissue countmatrix.txt


title: Old tumor, Rep3

description: Library name: Old_Rep3


title: A34_Adipose

description:
A34
208114950052_R02C01


title: A34_WBC

description:
A34
208114950052_R01C01


title: Old tumor, Rep1

description: Library name: Old_Rep1


title: H3-3A_R17G_M_10yo_rep1


title: Young tumor, Rep6

description: Library name: Young_Rep6

value: Young tumor


title: VAS7564A93

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
Library name: VAS7564A93
C5HetVav_male_ileum_IEL_time_6_weeks_1

data_processing:
Trim adapters with Trimmomatic v0.39
Align reads to mm10 with STAR 2.7.11b
Count reads with Salmon 1.10.3
Variance-stabilised counts with DESeq2 (vst)
Assembly: GRCm38 release-95
Supplementary files format and content: csv format – vst normalized data

source_name: IEL

extract_protocol:
Small intestines were cut into small pieces digested and isolated following the instructions provided in Miltenyi Biotec Lamina propria dissociation kit protocol, 130-097-410. lamina propria and intraepithelial cells were resuspended in FACS buffer after centrifugation. Single cell suspensions were stained with lineage exclusion antibodies against CD19, CD3, NK1.1, Ly6G and gated in CD45+, CD11b+, CD64+ then, FACS sorted on an Aria Fusion (BD) with a 100um nozzle.
RNA-seq libraries were made using total RNA made with KAPA RNA HyperPrep with RiboErase following manufacturer’s instructions (Roche, 08098131702). SMART‑Seq libraries were pooled and sequenced on an Illumina NovaSeq 6000 (2 × 100 bp) (Illumina).

value: IEL

value: CTRL

tag: batch


title: VAS7564A94

description:
Library name: VAS7564A94
C5HetVav_male_ileum_IEL_time_6_weeks_2


title: H3-3A_T45I_F_4yo_rep1


title: H3-3A_T45I_F_4yo_rep2


title: Young tumor, Rep5

description: Library name: Young_Rep5


title: Young tumor, Rep4

description: Library name: Young_Rep4


title: A33_HTH

description:
A33
208114950038_R05C02

value: HTH


title: VAS7564A91

description:
Library name: VAS7564A91
C5deltaVav_male_ileum_IEL_time_6_weeks_2

value: KO


title: control_F_11yo_rep2

value: WT


title: VAS7564A90

description:
Library name: VAS7564A90
C5deltaVav_male_ileum_IEL_time_6_weeks_1


title: control_F_11yo_rep1


title: A33_Hippo

description:
A33
208114950038_R04C02

value: Hippo


title: Young tumor, Rep3

description: Library name: Young_Rep3


title: control_M_17yo_rep2


title: VAS7564A9

description:
Library name: VAS7564A9
C5HetVav_female_ileum_IEL_time_8_weeks_1


title: Young tumor, Rep2

description: Library name: Young_Rep2


title: A33_FCTX

description:
A33
208114950038_R03C02

value: FCTX


title: VAS7564A89

description:
Library name: VAS7564A89
C5deltaVav_female_ileum_IEL_time_6_weeks_2


title: A33_CardiacMuscle

description:
A33
208114950038_R02C02

value: CardiacMuscle


title: A33_SkeletalMuscle

description:
A33
208114950038_R01C02

value: SkeletalMuscle


title: HeLa cells ZFC3H1 IP

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner
peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and peak file

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in DMEM medium (Sigma-Aldrich) supplemented with FCS 10% and penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody using ChIP-IT high sensitivity (Active Motif).
Libraries were prepared using Next Gen DNA Library Kit (Active Motif 53216 and 53264).

treatment_protocol: Rad21 chip-seq were supplemented with lentiviral particles for expression of control shRNA, ZFC3H1 shRNA or MTR4 shRNA.

value: HeLa

tag: chip antibody

value: ZFC3H1 (Bethyl A301-457A)

value: untreated


title: control_M_17yo_rep1


title: A33_Colon

description:
A33
208114950038_R06C02

value: Colon


title: PH-2

city: Xiamen

first: aicun

last: li

address: South Xiang'an Road 4221-120, Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

description: Library name: Sample 4

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0)
Cufflinks (v2.2.1) was used to calculate the expression of RefSeq annotated genes
Assembly: hg38
Supplementary files format and content: xls files include FPKM values for each Sample

growth_protocol: A375 cells were cultured in DMEM supplemented with 10% FBS, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were lyzed by trizol.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of NEBNext rRNA Depletion Kit (NEB E6310). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (NEB, E7760), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq X-Ten at Amogene (Xiamen, China) Biotech Co., Ltd following the vendor's recommended protocol.

treatment_protocol: Cells were  treated with indicated drugs.

value: melanoma

value: Paroxetine Hydrochloride


title: PH-1

description: Library name: Sample 3


title: A33_Adipose

description:
A33
208114950038_R06C01

value: Adipose


title: VAS7564A86

description:
Library name: VAS7564A86
C5HetVav_male_ileum_LP_time_6_weeks_2

source_name: LP

value: LP


title: DMSO-2

description: Library name: Sample 2

value: DMSO


title: control_F_13yo_rep1

value: dermal fibroblast


title: VAS7564A92

description:
Library name: VAS7564A92
C5HetVav_female_ileum_IEL_time_6_weeks_1

value: IEL

value: CTRL


title: VAS7564A85

description:
Library name: VAS7564A85
C5HetVav_male_ileum_LP_time_6_weeks_1


title: control_F_13yo_rep2

value: WT


title: control_M_1yo_rep2


title: DMSO-1

description: Library name: Sample 1


title: A33_WBC

description:
A33
208114950038_R05C01

value: WBC


title: A31_Colon

description:
A31
208114950038_R04C01


title: Young tumor, Rep1

description: Library name: Young_Rep1

value: Pancreatic tumor

value: Epithelial

value: Young tumor


title: VAS7564A84

description:
Library name: VAS7564A84
C5HetVav_female_ileum_LP_time_6_weeks_1


title: A31_HTH

description:
A31
208114950038_R03C01

source_name: HTH

value: HTH


title: K4me3-PH

description: Library name: Sample 4

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were aligned to the Hg38 human reference genomes using Bowtie2 (v2.3.4.1) and generated SAM files were converted to BAM files using Samtools (v.1.9)  using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters which were converted to BigWig files using Deeptools. BigWig files were visualized using the Integrative Genomics Viewer (Broad Institute).
HOMER suit of tools was used. Aligned bam files were subjected to peak calling using findPeaks tools with the -style factor.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using deeptools and were visualized using the Integrative Genomics Viewer (Broad Institute).

extract_protocol:
For H3K4me3 (CST, C42D8, 9751S#) and H3-5HT (Beyotime, AG3850) ChIP, cells were fixed with 1% formaldehyde (Thermo, 28908) for 15 min at room temperature (RT). Cells were then washed with PBS and terminated by the addition of 0.125 M glycine. The pellet was resuspended in 1% SDS lysis buffer after removal of cytosolic proteins with cytosolic buffer (50 mM Tris-HCl pH = 8.0, 0.5% NP-40 and 50 mM NaCl). Chromatin DNA was sheared by sonication to an average size of 300-500 bp. The lysates were incubated with IgG or specific antibodies overnight at 4°C and then incubated with protein A/G magnetic beads (MCE, HY-K0202) for 4 hours. After washing, the eluted protein-DNA complex was reversed by heating at 65°C overnight. The immunoprecipitated DNA was purified on QIAquick Spin Columns (Qiagen, 28106) and high-throughput sequencing was performed
Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing. Briefly, Chip DNA was end-blunted and added with an ‘A’ base. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

value: 24 hours


title: control_F_2yo_rep1


title: A31_FCTX

description:
A31
208114950038_R01C01

value: FCTX


title: VAS7564A82

description:
Library name: VAS7564A82
C5deltaVav_male_ileum_LP_time_6_weeks_1

value: KO


title: control_F_2yo_rep2


title: K4me3-DMSO

description: Library name: Sample 3

value: melanoma


title: VAS7564A88

description:
Library name: VAS7564A88
C5deltaVav_female_ileum_IEL_time_6_weeks_1


title: H3-5HT-PH

description: Library name: Sample 2

value: H3K4me3/Q5ser (Beyotime, AG3850)

value: Paroxetine Hydrochloride


title: A31_Hippo

description:
A31
208114950038_R02C01

value: Hippo


title: VAS7564A83

description:
Library name: VAS7564A83
C5deltaVav_male_ileum_LP_time_6_weeks_2

value: LP


title: A31_CardiacMuscle

description:
A31
208114950015_R06C02

value: CardiacMuscle


title: H3-5HT-DMSO

description: Library name: Sample 1

value: DMSO


title: control_M_11yo_rep2

value: dermal fibroblast


title: control_M_11yo_rep1

value: WT


title: VAS7564A81

description:
Library name: VAS7564A81
C5deltaVav_female_ileum_LP_time_6_weeks_2


title: A31_SkeletalMuscle

description:
A31
208114950015_R05C02

value: SkeletalMuscle


title: VAS7564A80

description:
Library name: VAS7564A80
C5deltaVav_female_ileum_LP_time_6_weeks_1


title: dCas9-blockade_rep4

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

description:
Library name: Sample 49
aligned to modified genome: mm9_dCas9_blockade

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same coordinates.
Assembly: mm9 and modified genomes as indicated
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl pro-B lines were maintained in RPIM1640 medium supplemented with 10% FBS, 50 uM 2-Mercaptoethanol, 100 U/ml Penicillin-Streptomycin and 2 mM L-Glutamine.

extract_protocol:
DNA was lysed overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
Genomic DNA was extracted from G1 arrested cells. 2 to 4 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98o 2min, 1cycle; 95o 30sec, 58o 30sec, 72o 90sec, 80 cycles; 72o 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25o 1 hour, 22 o 3 hours, 16 o overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 15 cycles; 72o 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 12 cycles; 72o 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to Mi-Seq machine (Illumina) with paired-end 300 bp sequencing.

treatment_protocol: RAG complementation and 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest. For induction of dCas9-blockade, 2 ug/ml doxycycline was added 4 hours prior to G1 arrest.

value: v-Abl transformed pro-B cell line

value: Wapl-AID2, CTCF(Y226A/F228A), Igk+/-, dCas9-blockade, Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 2 ug/ml doxycycline and 3 uM STI-571 treated for 4 days.


title: A31_Adipose

description:
A31
208114950015_R04C02

value: Adipose


title: VAS7564A78

description:
Library name: VAS7564A78
C5HetVav_male_colon_LP_time_6_weeks_2

value: CTRL


title: S_629_22, Nbl1, WT, PBS

city: Bar Harbor

first: Courtney

last: Willey

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description:
Library name: S_629_22
Counts_S-629-22_GT22-18232; TPM_S-629-22_GT22-18232; FPKM_S-629-22_GT22-18232

data_processing:
JAX RNA-seq Nextflow Pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed using featureCounts
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts, tpm, and fpkm for each sample.

source_name: Kidney

extract_protocol:
RNA was harvested using NucleoMag RNA Kit (Macherey-Nagel). Samples with RIN >8  was used for the construction of sequencing libraries.
RNA libraries for for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (Roche) following manufacturer's protocols.

value: Kidney

value: PBS


title: control_M_1yo_rep1


title: dCas9-blockade_rep3

description:
Library name: Sample 48
aligned to modified genome: mm9_dCas9_blockade


title: A31_WBC

description:
A31
208114950015_R03C02

value: WBC


title: dCas9-blockade_rep2

description:
Library name: Sample 47
aligned to modified genome: mm9_dCas9_blockade


title: S_609_22, Nbl1, WT, PBS

description:
Library name: S_609_22
Counts_S-609-22_GT22-18217; TPM_S-609-22_GT22-18217; FPKM_S-609-22_GT22-18217


title: VAS7564A77

description:
Library name: VAS7564A77
C5HetVav_male_colon_LP_time_6_weeks_1


title: VAS7564A76

description:
Library name: VAS7564A76
C5HetVav_female_colon_LP_time_6_weeks_1


title: S_602_22, Nbl1, WT, PBS

description:
Library name: S_602_22
Counts_S-602-22_GT22-18237; TPM_S-602-22_GT22-18237; FPKM_S-602-22_GT22-18237


title: dCas9-blockade_rep1

description:
Library name: Sample 46
aligned to modified genome: mm9_dCas9_blockade


title: A32_Colon

description:
A32
208114950015_R02C02

value: Colon


title: VAS7564A75

description:
Library name: VAS7564A75
C5deltaVav_male_colon_LP_time_6_weeks_2

value: KO


title: A32_HTH

description:
A32
208114950015_R01C02

value: HTH


title: S_600_22, Nbl1, WT, PBS

description:
Library name: S_600_22
Counts_S-600-22_GT22-18231; TPM_S-600-22_GT22-18231; FPKM_S-600-22_GT22-18231


title: VAS7564A74

description:
Library name: VAS7564A74
C5deltaVav_male_colon_LP_time_6_weeks_1

value: LP


title: A32_Hippo

description:
A32
208114950015_R06C01

source_name: Hippo

value: Hippo


title: S_400_22, Nbl1, WT, PBS

description:
Library name: S_400_22
Counts_S-400-22_GT22-18222; TPM_S-400-22_GT22-18222; FPKM_S-400-22_GT22-18222


title: BS-only_rep1

description:
Library name: Sample 43
aligned to modified genome: mm9_dCas9_blockade

value: Wapl-AID2, CTCF(Y226A/F228A), Igk+/-, dCas9-BS-inserted, Emu-Bcl2+, RAG1(D708A)


title: S_3643_22, Nbl1, WT, PBS

description:
Library name: S_3643_22
Counts_S-3643-22_GT22-18230; TPM_S-3643-22_GT22-18230; FPKM_S-3643-22_GT22-18230


title: BS-only_rep2

description:
Library name: Sample 44
aligned to modified genome: mm9_dCas9_blockade


title: VAS7564A72

description:
Library name: VAS7564A72
C5deltaVav_female_colon_LP_time_6_weeks_1


title: S_2456_22, Nbl1, WT, PBS

description:
Library name: S_2456_22
Counts_S-2456-22_GT22-18234; TPM_S-2456-22_GT22-18234; FPKM_S-2456-22_GT22-18234


title: A32_FCTX

description:
A32
208114950015_R05C01

source_name: FCTX

value: FCTX


title: VAS7564A71

description:
Library name: VAS7564A71
C5HetVav_male_ileum_IEL_time_4_weeks_2

value: IEL


title: A32_CardiacMuscle

description:
A32
208114950015_R04C01

source_name: CardiacMuscle

value: CardiacMuscle


title: Wapl-AID2_CTCF-Nm_5phIAA_rep2

description: Library name: Sample 38

value: v-Abl transformed pro-B cell line

value: Wapl-AID2, CTCF(Y226A/F228A), Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days.


title: Wapl-AID2_CTCF-Nm_5phIAA_rep3

description: Library name: Sample 39


title: VAS7564A70

description:
Library name: VAS7564A70
C5HetVav_male_ileum_IEL_time_4_weeks_1


title: A32_SkeletalMuscle

description:
A32
208114950015_R03C01

source_name: SkeletalMuscle

value: SkeletalMuscle


title: A32_Adipose

description:
A32
208114950015_R02C01

source_name: Adipose

value: Adipose


title: S_625_22, Nbl1, WT, Cisplatin

description:
Library name: S_625_22
Counts_S-625-22_GT22-18219; TPM_S-625-22_GT22-18219; FPKM_S-625-22_GT22-18219

value: Kidney

value: WT

value: Cisplatin


title: Wapl-AID2_CTCF-Nm_5phIAA_rep1

description: Library name: Sample 37


title: A32_WBC

description:
A32
208114950015_R01C01

source_name: WBC

value: WBC


title: VAS7564A69

description:
Library name: VAS7564A69
C5HetVav_female_ileum_IEL_time_4_weeks_2

value: CTRL


title: S_624_22, Nbl1, WT, Cisplatin

description:
Library name: S_624_22
Counts_S-624-22_GT22-18241; TPM_S-624-22_GT22-18241; FPKM_S-624-22_GT22-18241


title: BS-only_rep3

description:
Library name: Sample 45
aligned to modified genome: mm9_dCas9_blockade

value: RAG1 retrovirally complemented, 2 ug/ml doxycycline and 3 uM STI-571 treated for 4 days.


title: VAS7564A68

description:
Library name: VAS7564A68
C5HetVav_female_ileum_IEL_time_4_weeks_1


title: sams1 Day 7 R5

city: Worcester

first: Amy

last: Walker

state: MA

address: 373 Plantation Street

institute: UMass Medical School

description: Library name: Sample 12

data_processing:
Nextflow (Trimmomatic 0.39, STAR 2.710b, RSEM 1.3.3, DESeq2 1.38, WormCat 2.0)
Assembly: WS289 (Wormbase)
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were grown on agar plates on HT115 bacteria.

extract_protocol:
RNA for sequencing was purified using TriReagent, then RNAeasy columns (Qiagen).
RNA library construction was performed by BGI (Hong Kong).

treatment_protocol: Lysis of young adult C. elegans was performed in 0.5% SDS, 5% β-ME, 10 mM EDTA, 10 mM Tris-HCl ph7.4, 0.5 mg/ml Proteinase K

value: whole animal

value: wild type

value: RNAi


title: VAS7564A73

description:
Library name: VAS7564A73
C5deltaVav_female_colon_LP_time_6_weeks_2

value: LP

value: KO


title: VAS7564A67

description:
Library name: VAS7564A67
C5deltaVav_male_ileum_IEL_time_4_weeks_2

value: IEL


title: S_608_22, Nbl1, WT, Cisplatin

description:
Library name: S_608_22
Counts_S-608-22_GT22-18216; TPM_S-608-22_GT22-18216; FPKM_S-608-22_GT22-18216


title: sams1 Day 7 R3

description: Library name: Sample 11


title: S_606_22, Nbl1, WT, Cisplatin

description:
Library name: S_606_22
Counts_S-606-22_GT22-18209; TPM_S-606-22_GT22-18209; FPKM_S-606-22_GT22-18209


title: sams1 Day 7 R1

description: Library name: Sample 10


title: VAS7564A65

description:
Library name: VAS7564A65
C5deltaVav_female_ileum_IEL_time_4_weeks_2


title: VAS7564A64

description:
Library name: VAS7564A64
C5deltaVav_female_ileum_IEL_time_4_weeks_1


title: S_601_22, Nbl1, WT, Cisplatin

description:
Library name: S_601_22
Counts_S-601-22_GT22-18233; TPM_S-601-22_GT22-18233; FPKM_S-601-22_GT22-18233


title: Wapl-AID2_5PhIAA_rep3

description: Library name: Sample 27

value: v-Abl transformed pro-B cell line

value: Wapl-AID2, Emu-Bcl2+, RAG1(D708A)


title: S_2451_22, Nbl1, WT, PBS

description:
Library name: S_2451_22
Counts_S-2451-22_GT22-18228; TPM_S-2451-22_GT22-18228; FPKM_S-2451-22_GT22-18228

value: PBS


title: Wapl-AID2_5PhIAA_rep2

description: Library name: Sample 26

value: RAG1 retrovirally complemented, 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days.


title: S_2453_22, Nbl1, WT, Cisplatin

description:
Library name: S_2453_22
Counts_S-2453-22_GT22-18240; TPM_S-2453-22_GT22-18240; FPKM_S-2453-22_GT22-18240


title: Wapl-AID2_5PhIAA_rep1

description: Library name: Sample 25


title: sams1 Day 1 R1

description: Library name: Sample 7


title: S_619_22, Nbl1, HET, PBS

description:
Library name: S_619_22
Counts_S-619-22_GT22-18225; TPM_S-619-22_GT22-18225; FPKM_S-619-22_GT22-18225

value: HET


title: Wapl-AID2_untreated_rep3

description: Library name: Sample 24

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: S_615_22, Nbl1, HET, PBS

description:
Library name: S_615_22
Counts_S-615-22_GT22-18214; TPM_S-615-22_GT22-18214; FPKM_S-615-22_GT22-18214

value: Kidney


title: VAS7564A61

description:
Library name: VAS7564A61
C5HetVav_female_ileum_LP_time_4_weeks_2


title: wild-type Day 7 R5

description: Library name: Sample 6

value: Control


title: VAS7564A62

description:
Library name: VAS7564A62
C5HetVav_male_ileum_LP_time_4_weeks_1


title: S_618_22, Nbl1, WT, Cisplatin

description:
Library name: S_618_22
Counts_S-618-22_GT22-18220; TPM_S-618-22_GT22-18220; FPKM_S-618-22_GT22-18220

value: WT

value: Cisplatin


title: Wapl-AID2_untreated_rep2

description: Library name: Sample 23


title: wild-type Day 7 R3

description: Library name: Sample 5


title: VAS7564A66

description:
Library name: VAS7564A66
C5deltaVav_male_ileum_IEL_time_4_weeks_1


title: S_610_22, Nbl1, HET, PBS

description:
Library name: S_610_22
Counts_S-610-22_GT22-18238; TPM_S-610-22_GT22-18238; FPKM_S-610-22_GT22-18238


title: Wapl-AID2_CTCF-Nm_untreated_rep3

description: Library name: Sample 18

value: Wapl-AID2, CTCF(Y226A/F228A), Emu-Bcl2+, RAG1(D708A)


title: Wapl-AID2_untreated_rep1

description: Library name: Sample 22


title: sams1 Day 1 R5

description: Library name: Sample 9

value: whole animal


title: S_612_22, Nbl1, HET, PBS

description:
Library name: S_612_22
Counts_S-612-22_GT22-18235; TPM_S-612-22_GT22-18235; FPKM_S-612-22_GT22-18235


title: VAS7564A6

description:
Library name: VAS7564A6
C5deltaVav_female_ileum_LP_time_8_weeks_2


title: S_409_22, Nbl1, HET, PBS

description:
Library name: S_409_22
Counts_S-409-22_GT22_18227; TPM_S-409-22_GT22-18227; FPKM_S-409-22_GT22-18227


title: VAS7564A59

description:
Library name: VAS7564A59
C5deltaVav_male_ileum_LP_time_4_weeks_2


title: S_2457_22, Nbl1, WT, Cisplatin

description:
Library name: S_2457_22
Counts_S-2457-22_GT22-18229; TPM_S-2457-22_GT22-18229; FPKM_S-2457-22_GT22-18229


title: wild-type Day 7 R1

description: Library name: Sample 4

value: wild type


title: wild-type Day 1 R5

description: Library name: Sample 3


title: Wapl-AID2_CTCF-Nm_untreated_rep2

description: Library name: Sample 17


title: sams1 Day 1 R3

description: Library name: Sample 8

value: RNAi


title: VAS7564A58

description:
Library name: VAS7564A58
C5deltaVav_male_ileum_LP_time_4_weeks_1

value: LP


title: VAS7564A63

description:
Library name: VAS7564A63
C5HetVav_male_ileum_LP_time_4_weeks_2

value: CTRL


title: wild-type Day 1 R3

description: Library name: Sample 2


title: S_405_22, Nbl1, HET, PBS

description:
Library name: S_405_22
Counts_S-405-22_GT22-18242; TPM_S-405-22_GT22-18242; FPKM_S-405-22_GT22-18242


title: Wapl-AID2_CTCF-Nm_untreated_rep1

description: Library name: Sample 16


title: wild-type Day 1 R1

description: Library name: Sample 1


title: VAS7564A57

description:
Library name: VAS7564A57
C5deltaVav_female_ileum_LP_time_4_weeks_2

value: KO


title: CTCF-Nm_Vk6-17-inv_rep3

description:
Library name: Sample 15
aligned to modified genome: mm9_Vk6-17-inv

value: v-Abl transformed pro-B cell line


title: S_392_22, Nbl1, HET, PBS

description:
Library name: S_392_22
Counts_S-392-22_GT22-18236; TPM_S-392-22_GT22-18236; FPKM_S-392-22_GT22-18236


title: VAS7564A56

description:
Library name: VAS7564A56
C5deltaVav_female_ileum_LP_time_4_weeks_1


title: S_626_22, Nbl1, HET, Cisplatin

description:
Library name: S_626_22
Counts_S-626-22_GT22-18224; TPM_S-626-22_GT22-18224; FPKM_S-626-22_GT22-18224


title: D7 human perturb-seq targeting ARX and LMO1, illumina, GEX

city: San Francisco

first: Alex

last: Pollen

institute: UCSF

description:
Library name: LMO1_GEX
IN.h5ad

data_processing:
10X gene expression libraries together with sgRNA and STICR libraries were aligned to the hg38 genome obtained from CellRanger (refdata-gex-GRCh38-2024-A) with feature barcode reference using CellRanger-7.2.0. Aligned counts were then processed with Cellbender(Fleming et al. 2023, PMID: 37550580) for ambient removal. The resulting counts were processed by Scanpy (Wolf et al. 2018, PMID: 29409532) to remove low quality cells containing fewer than 1000 genes, a high abundance of mitochondrial reads (greater than 15% of total transcripts), or a high abundance of ribosomal reads (greater than 40% of total transcripts). Illumina Single Cell CRISPR libraries were aligned using DRAGEN Single Cell RNA v4.4.5 with additional arguments --single-cell-barcode-tag and --single-cell-umi-tag to support downstream individual demultiplexing. Low quality cells that had fewer than 500 genes or high abundance of mitochondrial or ribosomal reads were removed. To align 10X runs with pooled human and rhesus macaque individuals, we made a composite genome using CellRanger mkref function with (1) hg38 (CellRanger refdata-gex-GRCh38-2024-A) and (2) a version of rheMac10 included in a hierarchical alignment and annotated with the Comparative Annotation Toolkit as part of Mao et al. (PMID: 33953399), then filtered with litterbox(https://github.com/nkschaefer/litterbox). Cells identified as cross-species multiplets were removed from downstream analyses. STICR barcodes for lineage tracing experiments were aligned and assigned using the NextClone (Putri et al. 2023) workflow. Individual barcodes were filtered by at least 3 reads supporting a single UMI and at least 2 UMI to call cells with a barcode.
Assembly: GRCh38, RheMac10
Supplementary files format and content: Merged anndata object of cells with assigned sgRNA and lineage barcode, including gene count matrix and metadata including individulal, developmental stages, cellt ype annotation, sgRNA assignment and clonal barcode assignment for experiments containing lineage tracing. For lineage tracing experiments, merged anndata objecta at the clone level at the clonexcell type format.
Supplementary files format and content: Csv files contain sgRNA sequences and target gene information used for sgRNA alignment.

source_name: Cortical neural Progenitors

extract_protocol:
Culture of primary human and macaque neural progenitors were dissociated for 20 min in papain, spun down and resuspended in 0.5% BSA, 5% Trehalose in PBS and sorted with FACSAria Fusion cell sorter (BD) based on GFP (and mCherry) expression. Collected cells were resuspended in 0.02%BSA in PBS and captured following manufacture's protocol.
Gene expression library was constructed according to manufacturer's instructions. sgRNA libraries were separately amplified from each cDNA library. To generate STICR barcode libraries, cDNA library was used as template following protocol described in Delgado et al. 2021, PMID: 34912114.

value: Cortical neural Progenitors


title: VAS7564A60

description:
Library name: VAS7564A60
C5HetVav_female_ileum_LP_time_4_weeks_1


title: D12-14 human perturb-seq targeting 5 TFs coupled with lineage tracing, slice culture, 10X lane2, STICR

description:
Library name: SlicePS_L2_STICR
slice.h5ad


title: S_621_22, Nbl1, HET, Cisplatin

description:
Library name: S_621_22
Counts_S-621-22_GT22-18221; TPM_S-621-22_GT22-18221; FPKM_S-621-22_GT22-18221


title: CTCF-Nm_Vk6-17-inv_rep2

description:
Library name: Sample 14
aligned to modified genome: mm9_Vk6-17-inv


title: CTCF-Nm_Vk6-17-inv_rep1

description:
Library name: Sample 13
aligned to modified genome: mm9_Vk6-17-inv


title: S_616_22, Nbl1, HET, Cisplatin

description:
Library name: S_616_22
Counts_S-616-22_GT22-18239; TPM_S-616-22_GT22-18239; FPKM_S-616-22_GT22-18239


title: CTCF-Nm_Igk-377kb-inv_rep3

description:
Library name: Sample 12
aligned to modified genome: mm9_377kb_inv


title: D12-14 human perturb-seq targeting 5 TFs coupled with lineage tracing, slice culture, 10X lane2, sgRNA

description:
Library name: SlicePS_L2_sgRNA
feature_ref.csv


title: VAS7564A53

description:
Library name: VAS7564A53
C5HetVav_female_colon_LP_time_4_weeks_2


title: CTCF-Nm_Igk-377kb-inv_rep2

description:
Library name: Sample 11
aligned to modified genome: mm9_377kb_inv


title: D12-14 human perturb-seq targeting 5 TFs coupled with lineage tracing, slice culture, 10X lane2, GEX

description:
Library name: SlicePS_L2_GEX
slice.h5ad


title: VAS7564A52

description:
Library name: VAS7564A52
C5HetVav_female_colon_LP_time_4_weeks_1


title: VAS7564A54

description:
Library name: VAS7564A54
C5HetVav_male_colon_LP_time_4_weeks_1


title: S_611_22, Nbl1, HET, Cisplatin

description:
Library name: S_611_22
Counts_S-611-22_GT22-18211; TPM_S-611-22_GT22-18211; FPKM_S-611-22_GT22-18211


title: CTCF-Nm_Igk-377kb-inv_rep1

description:
Library name: Sample 10
aligned to modified genome: mm9_377kb_inv


title: D12-14 human perturb-seq targeting 5 TFs coupled with lineage tracing, slice culture, 10X lane1, STICR

description:
Library name: SlicePS_L1_STICR
slice.h5ad


title: S_607_22, Nbl1, HET, Cisplain

description:
Library name: S_607_22
Counts_S-607-22_GT22-18226; TPM_S-607-22_GT22-18226; FPKM_S-607-22_GT22-18226


title: D7 human perturb-seq targeting ARX and LMO1, illumina, sgRNA

description:
Library name: LMO1_sgRNA
feature_ref-illumina.csv


title: D12-14 human perturb-seq targeting 5 TFs coupled with lineage tracing, slice culture, 10X lane1, sgRNA

description:
Library name: SlicePS_L1_sgRNA
feature_ref.csv


title: CTCF-Nm_single-Igk_rep3

description: Library name: Sample 9


title: S_605_22, Nbl1, HET Cisplatin

description:
Library name: S_605_22
Counts_S-605-22_GT22-18245; TPM_S-605-22_GT22-18245; FPKM_S-605-22_GT22-18245


title: VAS7564A50

description:
Library name: VAS7564A50
C5deltaVav_male_colon_LP_time_4_weeks_1


title: S_604_22, Nbl1, HET, Cisplatin

description:
Library name: S_604_22
Counts_S-604-22_GT22-18246; TPM_S-604-22_GT22-18246; FPKM_S-604-22_GT22-18246


title: VAS7564A51

description:
Library name: VAS7564A51
C5deltaVav_male_colon_LP_time_4_weeks_2


title: D12-14 human perturb-seq targeting 5 TFs coupled with lineage tracing, slice culture, 10X lane1, GEX

description:
Library name: SlicePS_L1_GEX
slice.h5ad


title: CTCF-Nm_single-Igk_rep2

description: Library name: Sample 8


title: VAS7564A55

description:
Library name: VAS7564A55
C5HetVav_male_colon_LP_time_4_weeks_2


title: S_603_22, Nbl1, HET, Cisplatin

description:
Library name: S_603_22
Counts_S-603-22_GT22-18213; TPM_S-603-22_GT22-18213; FPKM_S-603-22_GT22-18213


title: VAS7564A5

description:
Library name: VAS7564A5
C5deltaVav_female_ileum_LP_time_8_weeks_1


title: CTCF-Nm_single-Igk_rep1

description: Library name: Sample 7


title: D7 human perturb-seq targeting 5 TFs coupled with lineage tracing , batch2,10X lane2,  STICR

description:
Library name: HM2D_2nd_L2_STICR
clones.h5ad


title: VAS7564A49

description:
Library name: VAS7564A49
C5deltaVav_female_colon_LP_time_4_weeks_2


title: D7 human perturb-seq targeting 5 TFs coupled with lineage tracing, batch2, 10X lane2,  sgRNA

description:
Library name: HM2D_2nd_L2_sgRNA
feature_ref.csv


title: CTCF-Nm_rep3

description: Library name: Sample 6


title: CTL, (Cept1fl/fl Cre-) or control

city: Saint Louis

first: Mohamed

middle: Adel

last: Zayed

email: zayedlab@wustl.edu, zayedm@wustl.edu

state: MO

address: 4940 Children’s place

department: Surgery

institute: Washington University School of Medicine

description:
Library name: Sample 2
10x Genomics

data_processing:
Fastq files were then processed with Cellranger to yield a unique molecular identifier (UMI) matrix, filtering out low-quality barcodes and mapping reads to the mouse genome (mm10), resulting in approximately 15,000 cells and 2,000 genes per cell per group. Datasets from both genotypes were combined using the Cellranger aggr pipeline to equalize the average read depth between samples. Gene expression from both samples were filtered, normalized, and clustered using the R package Seurat. To filter out multiplets, low-quality cells, and empty droplets, features were normalized to include log2 counts between 9.3-14.5, UMI log2 count within 8.5-11, and mitochondrial genes below 15%. Principal component analysis (PCA) was performed to reduce dataset dimensionality, and t-distributed stochastic neighbor embedding (t-SNE) was used to visualize principal components, focusing on the first two dimensions. Unbiased clustering and marker identification defined each cell types, and differentially expressed genes between clusters were identified for pathway analysis in Metascape. Bonferroni-adjusted p-values were used to determine significance at an FDR adjusted p value of <0.05. Genes involved in pathways analysis were represented using module scores based on average expression calculation within a specific cluster. Additional information and files to enhance reproducibility of the data can be found in Zayed Lab GitHub website: https://github.com/Zayedlab/Cept1_Angiogenesis.git
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aorta

extract_protocol:
Male mice were euthanized, and the thoracic and abdominal aorta were surgically micro-dissected from the aortic arch to the distal aortic bifurcation in the pelvis. Aortic tissue (n = 3 per condition) was minced into small pieces using a scalpel and transferred into a glass vial with 1.5 mL of cold digestion buffer (125U/ml Collagenase XI, 60U/ml Hyaluronidase type 1-s, 60U/ml DNase I and 450U/ml Collagenase type I. Tissue was further digested in a shaking (100 rpm) 37 °C water bath for 1 hour. The resulting cell suspension was strained through 70μM cell strainer and treated with ACK lysis buffer to lyse red blood cells. Single-cell suspensions then used for subsequent single-cell sorting.
Transcriptional profiling of Cept1fl/fl Cre− and Cept1fl/fl Cre+ mouse whole aortae was performed using droplet-based massively parallel 10X genomic single-cell RNA sequencing (scRNA-seq) 3’ v3. Single cells for each genotype were individually barcoded and subjected to sequencing, generating Fastq files.

treatment_protocol: A conditional EC-specific Cept1 overexpression mouse model was engineered by breeding Cept1fl/fl mice with VE-cadherin-Cre-ERT2 mice. Male littermates at least 8 weeks of age received tamoxifen (TMX-diluted with sunflower oil) treatment (five daily i.p. injections at 1 mg per mouse) to induce Cre expression and conditional EC-specific Cept1 gene over-expression. Mice were allowed to recover for 5 days post TMX injections before initiating in vivo experimental protocols.

value: Aorta

tag: strain background

value: Cept1fl/fl Cre- (Control)

value: 6-8 week old

value: Male


title: D7 human perturb-seq targeting 5 TFs coupled with lineage tracing, batch2, 10X lane2 , GEX

description:
Library name: HM2D_2nd_L2_GEX
merged.h5ad


title: D7 human perturb-seq targeting 5 TFs coupled with lineage tracing , batch2, 10X lane1,  STICR

description:
Library name: HM2D_2nd_L1_STICR
clones.h5ad


title: CTCF-Nm_rep2

description: Library name: Sample 5

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: VAS7564A48

description:
Library name: VAS7564A48
C5deltaVav_female_colon_LP_time_4_weeks_1


title: CTCF-Nm_rep1

description: Library name: Sample 4


title: CEPT1, endothelial cell-specific,  Cept1 overexpression (Cept1fl/fl Cre+)

description:
Library name: Sample 1
10x Genomics

value: Tamoxifen (TMX)-induced VE-cadherin-Cre-ERT2 expression (Cept1fl/flCre+)


title: D7 human perturb-seq targeting 5 TFs coupled with lineage tracing , batch2, 10X lane1,  sgRNA

description:
Library name: HM2D_2nd_L1_sgRNA
feature_ref.csv


title: VAS7564A47

description:
Library name: VAS7564A47
C5deltaVav_male_colon_LP_time_8_weeks_2


title: WT, treated, 90min, rep3

city: Cambridge

first: Jingxu

last: Guo

address: Papworth Road

department: Medicine

institute: University of Cambridge

description: Library name: L8_90_WT_C

data_processing:
Raw data was processed by Novogene using in-house perl scripts.
Mapping was performed using Hisat2 v2.0.5.
Read counts were extracted using FeatureCounts v1.5.0-p3.
Differential expression analysis was performed using DESeq2 v.1.26.0
Assembly: Ensembl_106_mus_musculus_grcm39_primary
Supplementary files format and content: A csv file with raw count for each sample

source_name: Lung endothelial cells

growth_protocol: Cells were maintained in endothelial growth media MV2 with 10% FBS, 100 μg/ml heparin, 20 U/ml interferon-γ  and 1 μM SB431542.

extract_protocol:
Cells were lysed and RNA was extracted using RNeasy Mini Kit buffers (Qiagen) and Silica Membrane Mini Spin Columns (Geneflow) following the manufacturer’s protocol.
Library was prepared using the Novogene NGS Stranded RNA Library prep Set. 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 using edUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Serum-starved WT cells were treated with 0.2 ng/ml sENG(M):BMP9 (BMP9 GFD concentration) and ENG KO cells were treated with 0.2 ng/ml Pro:BMP9 (BMP9 GFD concentration) for 90 min with untreated controls.

value: Lung endothelial cells

value: MLEC

value: Endothelial cells

value: WT

value: BMP9:sENG(M) trteated


title: D7 human perturb-seq targeting 5 TFs coupled with lineage tracing, batch2, 10X lane1 , GEX

description:
Library name: HM2D_2nd_L1_GEX
merged.h5ad


title: WT, treated, 90min, rep2

description: Library name: L5_90_WT_C


title: WT_rep3

description: Library name: Sample 3

value: Emu-Bcl2+, RAG1(D708A)


title: WT_rep2

description: Library name: Sample 2


title: WT, treated, 90min, rep1

description: Library name: L4_90_WT_C


title: D7 human perturb-seq targeting 44 TFs, 10X lane4 , sgRNA

description:
Library name: 2D_L4_sgRNA
feature_ref.csv


title: VAS7564A46

description:
Library name: VAS7564A46
C5deltaVav_male_colon_LP_time_8_weeks_1

value: LP


title: WT, untreated, 90min, rep4

description: Library name: L10_90_WT_PS

value: PBS-treated


title: D7 human perturb-seq targeting 44 TFs, 10X lane4, GEX

description:
Library name: 2D_L4_GEX
screen.h5ad


title: VAS7564A42

description:
Library name: VAS7564A42
C5deltaVav_male_ileum_LP_time_8_weeks_2

value: KO


title: WT_rep1

description: Library name: Sample 1

value: v-Abl transformed pro-B cell line


title: VAS7564A41

description:
Library name: VAS7564A41
C5deltaVav_male_ileum_LP_time_8_weeks_1


title: VAS7564A45

description:
Library name: VAS7564A45
C5HetVav_male_colon_LP_time_8_weeks_1

value: CTRL


title: D7 human perturb-seq targeting 44 TFs, 10X lane3,  sgRNA

description:
Library name: 2D_L3_sgRNA
feature_ref.csv

value: Cortical neural Progenitors


title: VAS7564A43

description:
Library name: VAS7564A43
C5HetVav_male_ileum_LP_time_8_weeks_1


title: VAS7564A4

description:
Library name: VAS7564A4
C5HetVav_male_ileum_LP_time_8_weeks_2


title: D7 human perturb-seq targeting 44 TFs, 10X lane3 , GEX

description:
Library name: 2D_L3_GEX
screen.h5ad


title: WT, untreated, 90min, rep2

description: Library name: L5_90_WT_PS


title: VAS7564A39

description:
Library name: VAS7564A39
C5deltaVav_male_ileum_IEL_time_8_weeks_2

value: IEL


title: WT, untreated, 90min, rep3

description: Library name: L8_90_WT_PS


title: WT, treated, 90min, rep4

description: Library name: L10_90_WT_C


title: D7 human perturb-seq targeting 44 TFs, 10X lane2 , GEX

description:
Library name: 2D_L2_GEX
screen.h5ad


title: VAS7564A38

description:
Library name: VAS7564A38
C5deltaVav_male_ileum_IEL_time_8_weeks_1


title: KO, treated, 90min, rep4

description: Library name: L10_90_iK_P9

value: ENG KO

value: Pro:BMP9 treated


title: VAS7564A37

description:
Library name: VAS7564A37
C5HetVav_male_ileum_IEL_time_8_weeks_1


title: Patient15 B

city: Houston

middle: Leo

last: Lei

state: TX

address: 1901 East Rd

department: Head and Neck Surgery

institute: The University of Texas M.D. Anderson Cancer Center

description: Library name: Samples 30

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCh38 (ENSEMBL 109), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7 (Ewels et al., 2016)
Assembly: GRCh38
Supplementary files format and content: gene_expected_count.annot.txt was provided for all samples
Supplementary files format and content: gene_FPKM.annot.txt was provided for all samples

source_name: Oral Cancer

growth_protocol: Fresh samples

extract_protocol:
Total RNA was extracted by RNeasy Plus Mini Kit (74136, Qiagen). The RNA concentration was determined using a Nanodrop Spectrophotometer from Thermo Fisher Scientific.
RNA libraries for RNA-seq were prapered by NGS core of University of Michigan .

treatment_protocol: Wash with cold PBS

value: Oral Cancer

value: no


title: VAS7564A3

description:
Library name: VAS7564A3
C5HetVav_male_ileum_LP_time_8_weeks_1


title: Patient15 A

description: Library name: Samples 29


title: KO, treated, 90min, rep2

description: Library name: L5_90_iK_P9

value: Lung endothelial cells


title: KO, untreated, 90min, rep4

description: Library name: L10_90_iK_PS

value: MLEC


title: Patient14 A

description: Library name: Samples 27


title: VAS7564A20

description:
Library name: VAS7564A20
C5HetVav_male_colon_LP_time_8_weeks_2


title: Patient13 B

description: Library name: Samples 26


title: KO, treated, 90min, rep1

description: Library name: L4_90_iK_P9

value: Endothelial cells


title: Patient14 B

description: Library name: Samples 28


title: VAS7564A2

description:
Library name: VAS7564A2
C5HetVav_female_ileum_LP_time_8_weeks_2


title: Patient13 A

description: Library name: Samples 25


title: KO, untreated, 90min, rep2

description: Library name: L5_90_iK_PS


title: Patient12 B

description: Library name: Samples 24


title: VAS7564A19

description:
Library name: VAS7564A19
C5HetVav_male_colon_LP_time_8_weeks_1


title: VAS7564A18

description:
Library name: VAS7564A18
C5HetVav_female_colon_LP_time_8_weeks_2


title: KO, untreated, 90min, rep1

description: Library name: L4_90_iK_PS


title: Patient12 A

description: Library name: Samples 23


title: E14tg2a, P14_d4_rep2

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

description: Library name: P14_d4_rep2

data_processing:
Sequence reads were trimmed using trimgalore (R-package).
Trimed fasq files were aligned by Hisat2 to mm10 genome with defaults setting.
Read counts were extracted using R package FeatureCounts using mm10 KnownGenes.
Read counts were visualized using the iDEP web application (http://bioinformatics.sdstate.edu/idep/).
Assembly: Mus musculus (GRCm38/mm10)
Supplementary files format and content: tab-delimited text files containing read counts

source_name: Pluripotent stem cells

growth_protocol: Mouse embryonic stem cells (ESCs; E14tg2a and ZHBTc4) were cultured on 0.1% gelatin-coated dishes under two conditions: serum + LIF (SL) medium or 2i + LIF (2iL) medium. SL medium consisted of GMEM (WAKO), 10% fetal bovine serum (FBS; Sigma), 0.1 mM non-essential amino acids (NEAA), 0.1 mM β-mercaptoethanol, 1 mM sodium pyruvate, 2 mM L-glutamine, penicillin/streptomycin, and 1000 U/mL LIF. For 2iL conditions, ESCs were cultured in N2B27 medium supplemented with 1 µM PD0325901 (MEK inhibitor), 3 µM CHIR99021 (GSK3β inhibitor), and 1000 U/mL LIF.

extract_protocol:
Total RNAs were extracted using a PureLinkTM RNA Mini Kit (Ambion, Inc.)
RNAseq libraries were contructed using CollibriTM Stranded RNA library prep for ilIuminaTM Systems (ThermoFisher Scientific).

treatment_protocol: For EpiLC induction, ESCs were plated at 1 x10^5 cells per well in a 12-well plate containing N2B27 medium supplemented with 12 ng/mL bFGF on fibronectin-coated dishes.

value: mouse embryonic stem cells

value: embryonic stem cells (E14tg2a)


title: D7 human perturb-seq targeting 44 TFs, 10X lane2 , sgRNA

description:
Library name: 2D_L2_sgRNA
feature_ref.csv


title: WT, untreated, 90min, rep1

description: Library name: L4_90_WT_PS

value: WT


title: VAS7564A17

description:
Library name: VAS7564A17
C5HetVav_female_colon_LP_time_8_weeks_1

value: LP


title: E14tg2a, P14_d4_rep1

description: Library name: P14_d4_rep1


title: VAS7564A14

description:
Library name: VAS7564A14
C5deltaVav_female_ileum_IEL_time_8_weeks_2

source_name: IEL


title: KO, treated, 90min, rep3

description: Library name: L8_90_iK_P9


title: E14tg2a, P14_d2_rep2

description: Library name: P14_d2_rep2


title: Patient11 A

description: Library name: Samples 21


title: VAS7564A22

description:
Library name: VAS7564A22
C5deltaVav_female_colon_LP_time_8_weeks_2

source_name: LP


title: Patient10 B

description: Library name: Samples 20


title: VAS7564A21

description:
Library name: VAS7564A21
C5deltaVav_female_colon_LP_time_8_weeks_1


title: VAS7564A13

description:
Library name: VAS7564A13
C5deltaVav_female_ileum_IEL_time_8_weeks_1


title: VAS7564A12

description:
Library name: VAS7564A12
C5HetVav_male_ileum_IEL_time_8_weeks_2


title: E14tg2a, P14_d2_rep1

description: Library name: P14_d2_rep1


title: KO, untreated, 90min, rep3

description: Library name: L8_90_iK_PS

value: PBS-treated


title: E14tg2a, DKO_d4_rep2

description: Library name: DKO_d4_rep2


title: Patient10 A

description: Library name: Samples 19


title: VAS7564A11

description:
Library name: VAS7564A11
C5HetVav_male_ileum_IEL_time_8_weeks_1


title: E14tg2a, DKO_d4_rep1

description: Library name: DKO_d4_rep1


title: Patient9 B

description: Library name: Samples 18


title: VAS7564A10

description:
Library name: VAS7564A10
C5HetVav_female_ileum_IEL_time_8_weeks_2


title: E14tg2a, DKO_d2_rep2

description: Library name: DKO_d2_rep2


title: Patient9 A

description: Library name: Samples 17


title: VAS7564A1

description:
Library name: VAS7564A1
C5HetVav_female_ileum_LP_time_8_weeks_1


title: E14tg2a, DKO_d2_rep1

description: Library name: DKO_d2_rep1


title: Patient8 B

description: Library name: Samples 16


title: 4sU labeling, scRNA-seq, unsti_J, rep1

city: Bethesda

first: Jun

last: Lyu

state: Maryland

address: 37 Convent Drive

department: Laboratory of Biochemistry and Molecular Biology

institute: National cancer institute

description: Library name: Jurkat_unSti_rep1

data_processing:
Raw sequencing data of scRNA-seq was subjected to fastq calling, reads alignment, and quantification using cellranger7.1.0  with default parameters and standard pipeline.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separate values files and matrix files

source_name: Jurkat T Clone E6-1

extract_protocol:
For single cell RNA sequencing, single cell suspension was prepared for 10X Genomics sample loading. For RNA-seq, RNA was extracted using RNeasy Mini Kit (Qiagen).
For NOTE-seq, Libraries were constructed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E) with serval additional steps detaied in the Method section. For MeOH-4sU-10X, one million eHAP1 cells were fixed in 80% cold methanol and incubated for 30 minutes at –20 °C. For chemical conversion, iodoacetamide (IAA) was added to the fixed cell suspension to a final concentration of 10 mM, followed by incubation for 16 hours at room temperature on a rotator in the dark. Cells were then pelleted by centrifugation at 1000 × g for 5 minutes and resuspended in quenching buffer (PBS, 0.1% BSA, 1 U/µl SUPERase-In, 100 mM DTT) for 5 minutes at room temperature. After a second centrifugation, cells were resuspended in PBS containing 0.1% BSA and 1 U/µl SUPERase-In, passed through a 20 µm strainer, counted, and immediately loaded onto the 10 x Chromium system using the Chromium Next GEM Single Cell 3ʹ Kit v3.1.

value: Jurkat T Clone E6-1


title: Patient11 B

description: Library name: Samples 22


title: marmoset GD135 male thalamus, rep 20-218_fetus2 rep2

first: Margaret

last: Schroeder

address: 77 Massachusetts Avenue

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

description:
Library name: Exp119_cjGD135_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

data_processing:
Demultiplexed fastq files were generated by the Broad Institute Genomics Platform using Illumina software. 10x Genomics Cell Ranger software version 7.1 was used for alignment and counting via the 10x Genomics Cloud Analysis platform. For samples that were sequenced across several library pools, fastq files were grouped prior to alignment to create one cell-by-gene (cell x gene) counts matrix per sample. CellBender (v0.2.0) remove-background (Fleming et al., 2023) was used to remove ambient RNA and call nuclei with default parameters and expected_cells = 10,000, total-droplets-included = 40,000 and the –cuda flag. CellBender-cleaned cell x gene matrix .h5 files were read into Python in the anndata format using a custom function written by Stephen Fleming (https://github.com/broadinstitute/CellBender/issues/57).
Assembly: Reads were aligned to an optimized mouse reference genome based on the mouse GRCm38 primary sequence assembly (version 2, Pool et al. 2024) or or a modified marmoset mCalja1.2.pat.X assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011100555.1/) provided courtesy of Michael DeBerardine and Fenna Krienen (Princeton Neuroscience Institute) in which mitochondrial genes from CM021961.1 (https://www.ncbi.nlm.nih.gov/nuccore/1820101357/) were annotated using MITOS2113. The marmoset reference genome was generated from the .fasta and .gtf files using Cell Ranger “mkref” v7.1.0 using default parameters without filtering for any gene/transcript biotype and is available at: https://doi.org/10.5281/zenodo.16915694.
Supplementary files format and content: Processed data files are cell x gene count matrices in .h5 format without ambient RNA removal.

organism: Callithrix jacchus

source_name: thalamus

growth_protocol: Common marmosets were housed in AAALAC-accredited facilities at MIT, in spacious holding rooms with a 12 hour light/dark cycle, temperature 74.0 ± 2.0°F (23.3 ± 1.1°C), relative humidity of 50 ± 20 %, and unrestricted access to food and water. Cages contained a variety of perches and enrichment devices. Procedures were conducted with prior approval by the MIT Committee for Animal Care (CAC) and following veterinary guidelines. Animal work was performed in accordance with protocols approved by MIT’s Committee on Animal Care and NIH guidelines. All postnatal mice were wild-type C57BL/6J originally obtained from Jackson Laboratories and bred in-house. Timed pregnant C57BL/6J females were either obtained from Jackson Laboratories to arrive between gestation day 11 and 15 or were impregnated in house by setting up overnight mating pairs with females in proestrus or estrus phase. Embryos were harvested at E18.5 (18 days after the plug date). Mice were housed in a facility with a light cycle running from 07:00 to 19:00,  temperature 20-22.2°C, humidity 30-70%, and food and water available ad libitum. Postnatal mice were not derived from timed pregnant females. Instead, age was determined during regular pup checks by experienced researchers based on the Jax Mice Pup Appearance Chart.

extract_protocol:
Nuclei were extracted from frozen tissue using the 10x Genomics Chromium Nuclei Isolation Kit (Protocol CG000505, Rev A).
snRNAseq libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Protocol CG000315 Rev C or Rev D) following manufacturer instructions.

treatment_protocol: None; animals were wild-type and allowed to develop normally.

value: thalamus

value: nuclei


title: 4sU labeling, IAA, scRNA-seq,

description: Library name: K562_4sU


title: Patient8 A

description: Library name: Samples 15


title: E14tg2a, DKO_2i_rep1

description: Library name: DKO_2i_rep1


title: E14tg2a, DKO_2i_rep2

description: Library name: DKO_2i_rep2


title: Patient7 B

description: Library name: Samples 14


title: 4sU labeling, no IAA, SNP background for K562, scRNA-seq

description: Library name: K562bg


title: 4sU labeling, IAA, methanol, scRNA-seq

description: Library name: eHAP_MeOH

source_name: eHAP

value: eHAP


title: E14tg2a, WT_d4_rep2

description: Library name: WT_d4_rep2


title: Patient7 A

description: Library name: Samples 13


title: marmoset GD135 male PFC, rep 20-218_fetus2 rep2

description:
Library name: Exp119_cjGD135_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: PFC

value: PFC


title: Patient6 B

description: Library name: Samples 12


title: marmoset GD135 male striatum, rep 20-218_fetus2 rep2

description:
Library name: Exp119_cjGD135_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: striatum

value: striatum


title: E14tg2a, WT_d4_rep1

description: Library name: WT_d4_rep1


title: marmoset GD135 male thalamus, rep 20-218_fetus2 rep1

description:
Library name: Exp119_cjGD135_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: Tcf21d/d-3

city: Beijing

first: Jie

last: Li

address: No.8 Xishiku Street, Xicheng District, Beijing

institute: Peking University First Hospital

description: Library name: cKO-3

data_processing:
HISAT2, samtools, and featureCounts
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: uterus

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) , 1μg of total RNA was used for the construction of RNA libraries
RNA libraries for RNA-seg were prepared following manufacturer's protocols.

value: uterus


title: Tcf21d/d-2

description: Library name: cKO-2


title: 4sU labeling, scRNA-seq, sti_J, rep1

description: Library name: Jurkat_Sti_rep1

source_name: Jurkat T Clone E6-2

value: Jurkat T Clone E6-2


title: E14tg2a, WT_d2_rep2

description: Library name: WT_d2_rep2


title: E14tg2a, WT_d2_rep1

description: Library name: WT_d2_rep1


title: marmoset GD135 male PFC, rep 20-218_fetus2 rep1

description:
Library name: Exp119_cjGD135_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: Tcf21f/f-3

description: Library name: WT-3


title: Patient6 A

description: Library name: Samples 11

value: Oral Cancer

value: no


title: E14tg2a, WT_2i_rep2

description: Library name: WT_2i_rep2


title: Tcf21f/f-2

description: Library name: WT-2


title: marmoset GD135 female thalamus, rep 19-221_fetus1 rep2

description:
Library name: Exp117_cjGD135_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: E14tg2a, WT_2i_rep1

description: Library name: WT_2i_rep1


title: Tcf21f/f-1

description: Library name: WT-1


title: marmoset GD135 female PFC, rep 19-221_fetus1 rep2

description:
Library name: Exp117_cjGD135_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset GD135 female striatum, rep 19-221_fetus1 rep2

description:
Library name: Exp117_cjGD135_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: HEK293 eGFP-YAP sorbitol replicate 3 Hi-C

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

description:
Library name: HEK293_eGFP_YAP_sorbitol_rep3
Hi-C of HEK293 cells at 1h

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Hi-C contact matrices in .hic format (hg38 reference genome). Files include both individual biological replicates and merged replicates (megaMap) for each condition. Datasets include HCT116 wild-type cells (control and 1h sorbitol treatment), HEK293 wild-type cells from the Phanstiel lab (control and sorbitol treatment), HEK293 eGFP-YAP cells from the Cai lab (control and sorbitol treatment), HEK293 wild-type sorbitol timecourse (10m, 30m, 1h, 3h, 6h, 12h, 24h), and HEK293 eGFP-YAPdTAD cells from the Cai lab (control and sorbitol treatment). MegaMap files represent merged replicates for increased sequencing depth. Spike-in normalized loop calls at 5kb resolution are provided for eGFP-YAP and WT Phanstiel conditions. Differential loop analysis (diffLoops_WT_noDroso_10kb.rds) comparing control vs sorbitol treatment is provided for WT Phanstiel samples.

growth_protocol: HEK293T and HCT116 cells were cultured at 37 °C in a humidified incubator with 5% CO₂. HEK293T cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin. HCT116 cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and penicillin/streptomycin. Cells were routinely monitored for mycoplasma contamination and maintained at ~70–80% confluence to ensure log-phase growth. Cells were harvested for experiments only when healthy and within 5–15 passages from thaw.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
In situ Hi-C libraries were prepared using MboI restriction digestion, fill-in with biotinylated nucleotides, proximity ligation, reverse crosslinking, and DNA purification. Libraries were size-selected and PCR-amplified prior to sequencing.

treatment_protocol: Hyperosmotic stress was induced by adding sorbitol to a final concentration of 200 mM for the indicated timepoints. Untreated samples were collected in parallel as controls. Cells were harvested at the specified time after treatment and processed immediately for downstream library preparation.

value: eGFP-YAP

value: 0.2M sorbitol for 1h


title: Patient4 A

description: Library name: Samples 7


title: Patient4 B

description: Library name: Samples 8


title: Patient5 A

description: Library name: Samples 9


title: HEK293 eGFP-YAP sorbitol replicate 2 Hi-C

description:
Library name: HEK293_eGFP_YAP_sorbitol_rep2
Hi-C of HEK293 cells at 1h


title: Right cervical lymph nodes from two mice pooled, infected, depleted, control, replicate 3

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description:
Library name: b6.ctb1.rcln.dep.3
10X Genomics

data_processing:
Demultiplexing, barcode processing, transcript counting, and aggregation was performed using CellRanger v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest). Only genes detected in at least 3 cells in across the entire dataset were retained. Cells with less than 200 or more than 4000 genes detected genes were discarded as were cells in which more than 5% of reads mapped to mitochondrial transcripts. Cell type annotations were assigned by comparing the transcriptome of each cell with the Immgen database.
Assembly: mm10
Supplementary files format and content: cln.rds: Seurat object containing the counts for each transcript detected in each single cell

source_name: cervical lymph node

extract_protocol:
Lymph nodes were removed by dissection, minced into small pieces, and digested to a single cell suspension in RPMI containing 100 ug/mL DNase, 200 ug/mL Collagenase P, and 64 ug/mL Dispase II at 37 C, pipetting gently every 5 minutes. After 25 minutes, the digestion was stopped by adding EDTA to a final concentration of 10 mM. The suspension was passed through a 70 uM filter to remove undigested tissue and brought to a volume of 5 mL in MACS buffer. Cells were then counted and pelleted at 500g for 5 minutes and resuspended in 100 uL of MACS buffer per 1e7 total cells. T and B cells were then removed by negative magnetic selection using CD3ε-Biotin followed by Anti-Biotin MicroBeads and CD19-MicroBeads (all from Miltenyi) following the manufacturers instructions.
Libraries were prepared according to the manufacturers instructions (10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1). Briefly, CD3/CD19-depleted single-cell suspensions of lymph nodes were resuspended in the master mix and loaded with partitioning oil and gel beads into the chip to generate gel bead-in-emulsions (GEMs). Poly-A RNA from the cell lysate contained in each GEM was retrotranscribed to cDNA containing the Illumina R1 primer sequence, Unique Molecular Identifier (UMI), and 10X Barcode. The pooled, barcoded cDNA was then processed with Silane DynaBeads, amplified by PCR, and size-selected with SPRIselect reagent for library construction. During library construction, the Illumina R2 primer sequence and sample indices were added.

treatment_protocol: CMTB was established by intradermal inoculation of the right ear with 10,000 CFU Mtb (strain H37Rv) in 10 uL of PBS.

value: cervical lymph node

value: intradermal Mtb infection


title: Right cervical lymph nodes from two mice pooled, infected, depleted, control, replicate 2

description:
Library name: b6.ctb1.rcln.dep.2
10X Genomics


title: Right cervical lymph nodes from two mice pooled, infected, depleted, control, replicate 1

description:
Library name: b6.ctb1.rcln.dep.1
10X Genomics


title: marmoset GD135 female striatum, rep 19-221_fetus1 rep1

description:
Library name: Exp117_cjGD135_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset GD135 male striatum, rep 20-218_fetus2 rep1

description:
Library name: Exp119_cjGD135_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: HEK293 eGFP-YAP sorbitol replicate 1 Hi-C

description:
Library name: HEK293_eGFP_YAP_sorbitol_rep1
Hi-C of HEK293 cells at 1h


title: marmoset GD135 female thalamus, rep 19-221_fetus1 rep1

description:
Library name: Exp117_cjGD135_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: Right cervical lymph nodes from four replicate mice pooled, control, depleted, control, replicate 3

description:
Library name: b6.ctl.rcln.dep.3
10X Genomics


title: Patient3 B

description: Library name: Samples 6


title: marmoset GD135 female PFC, rep 19-221_fetus1 rep1

description:
Library name: Exp117_cjGD135_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: Patient3 A

description: Library name: Samples 5


title: HEK293 eGFP-YAP control replicate 3 Hi-C

description:
Library name: HEK293_eGFP_YAP_control_rep3
Hi-C of HEK293 cells at 0h

value: untreated


title: Tcf21d/d-1

description: Library name: cKO-1


title: Patient2 B

description: Library name: Samples 4


title: Patient5 B

description: Library name: Samples 31