title: LIVERcre11

description: Library name: LIVERcre11


title: jc8250_HPAFII_HNF4G_knockout_EV

status: Public on Sep 16 2025

type: SRA

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description:
AN21CUK023250
HNF4G KO-EV

library_source: transcriptomic

data_processing:
STAR, version 2.6.1a, was used to align reads against human hg38 or mouse mm10 reference genome.
The read counting was performed using featureCounts v2.0.4.
For normalized measurement of mRNA expression the read counts were converted into RPKM values.
Differential gene expression analysis was performed using DESeq2 workflow.
Assembly: GRCh38,GRCm38
Supplementary files format and content: text

molecule: total RNA

organism: Homo sapiens

source_name: HNF4G knockout-EV

growth_protocol: Mouse cells were grown in DMEM 10% FBS, Sodium pyruvate. HPAF-II cells were grown in MEM media.  The cells were injected into NSG mice and tumours were monitored using ultra sound. The mice were killed at an humane endpoint and tumours were extracted and processed for RNA seq

extract_protocol:
Maxwell® RSC simplyRNA Cells Kit
RNAseq libraries were prepared using Illumina’s TruSeq mRNA Stranded Sample prep kit.

treatment_protocol: No treatment was performed on these cells. Lentiviral over expression and CRISPR KO's  were generated and this has been indicated in the descriptions.

tag: tissue

value: pancreatic adenocarcinoma

tag: cell line

value: orthotopic xenograft HPAF-II

tag: cell type

value: Tumour 2

tag: genotype

value: CRISPR

tag: treatment

value: CRISPR HNF4G KO-EV


title: LIVERcre12

city: New York

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: LIVERcre12

data_processing:
Reads were aligned to the mouse genome (NCBI37/mm9) with TopHat v1.3.3 and allowed one alignment with up to two mismatches per read. mRNA RPKM values were calculated using Seqmonk’s mRNA quantitation pipeline. A gene was included in the analysis if it met all the following criteria: the maximum RPKM reached four at any time point, the gene length was >200 bp
Differential expression analysis. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment analysis of differentially expressed genes. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway.
Assembly: mm10 (GRCm38)
Supplementary files format and content: DEGs upregulates and downregulated (Normalized abundance-HEATMAPs)

organism: Mus musculus

source_name: LIVER

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen). The aqueous phase containing the RNA was loaded onto a gDNA Eliminator Spin Column (Qiagen, USA) for elimination of genomic DNA, and RNA was isolated using the RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. Total RNA (500 to 1000 ug) was reverse transcribed into cDNA using the M-MLV reverse transcriptase (Invitrogen),
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: LIVER

value: Acypap1r1 floxed/floxed

value: AAV-Cre


title: Sublibrary 2, PlexinB1 Parse-seq

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: SCI-PB1CTRL-KOSublib2

library_source: transcriptomic single cell

data_processing:
The single-nucleus RNA-seq dataset was demultiplexed using the Trailmaker platform. Unfiltered count matrices were uploaded, and background noise was removed by setting a minimum transcript threshold per cell on a per-sample basis (≥ 500 transcripts). Barcodes associated with high mitochondrial gene content (> 0.5%) were excluded to filter out dying or stressed cells. Outliers in gene-to-transcript ratio distributions were removed using spline regression filtering (P values < 0.001). Doublets were identified and removed using the scDblFinder method.
Assembly: mm39
Supplementary files format and content: Processed data is provided in the form of 10x files (barcodes, features, and matrix files), for both the pre- and post-filtering datasets. Additional informative  metadata is provided for the filtered dataset. For the unfiltered dataset, a Seurat object is provided in the form of a RData file (RDS).

molecule: polyA RNA

source_name: Spinal cord

extract_protocol:
To isolate nuclei from spinal cord tissue, approximately 10 mm of spinal cord encompassing the injury site was dissected and finely minced. Nuclei were extracted using a nuclei extraction buffer (Miltenyi Biotec, #130-128-024). The resulting suspension was enriched for nuclei using anti-Nucleus MicroBeads (Miltenyi Biotec, #130-132-997). Nuclei were subsequently fixed using the Evercode Nuclei Fixation Kit v3 (Parse Biosciences, ECFN3300).
Split-seq cDNA libraries 49 were generated by iterative barcoding of nuclei via multiwell plating using the Evercode Whole Transcriptome (WT) v3 kit (ECWT3300; Parse Biosciences).

treatment_protocol: Spinal cord injury

value: Spinal cord

value: neural cells

value: WT and PB1KO

value: uninjured or 7 dpi


title: jc8249_HPAFII_HNF4G_knockout_EV

description:
AN21CUK023250
HNF4G KO-EV

value: Peritoniuem met


title: LIVERctrl9

description: Library name: LIVERctrl9

value: AAV-GFP


title: jc8245_HPAFII_Cas_9_EV

description:
AN21CUK023246
Cas-9-EV

value: CRISPR Cas-9-EV


title: jc6730_AsPC_1_FOXA1

description:
FOXA1 ASPC-1-Rep 2
ASPC-1 FOXA1
untreated

library_source: genomic

data_processing:
Reads were mapped to hg38 or mm10 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.  For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences. Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Assembly: GRCh38,GRCm38
Supplementary files format and content: bed/text

molecule: genomic DNA

source_name: Pancreatic adenocarcinoma

growth_protocol: HPAF-II & ASPC-1 cells were grown in MEM & RPMI High 10% FBS, Sodium pyruvate. KPC mouse cells were grown in DMEM 10% FBS

extract_protocol:
ChIP-Seq was performed at described in Ross-Innes CS et al. Nature. 2012. Antibodies used are specified above FOXA1-ab5089, HNF4G-atlas HPA005438, PRMT1-atlas HPA069769,H3K27Ac-ab4729,flag-sigma-F1804,GATA6-RD-AF1700
DNA was prepared for Illumina sequencing on the Nova Seq 6000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: untreated or CRISPR pertubation

value: Pancreatic adenocarcinoma

value: WT

value: untreated


title: LIVERctrl8

description: Library name: LIVERctrl8


title: jc8251_HPAFII_HNF4G_knockout_EV

description:
AN21CUK023251
HNF4G KO-EV

value: pancreatic adenocarcinoma

value: orthotopic xenograft HPAF-II

value: Tumour 3


title: jc6729_AsPC_1_FOXA1

description:
FOXA1 ASPC-1-Rep 1
ASPC-1 FOXA1
untreated


title: BATcre5

description: Library name: BATcre5

source_name: Brown Adipose Tissue (BAT)

value: Brown Adipose Tissue (BAT)


title: jc6735_AsPC_1_GATA6

description:
GATA6 ASPC-1-Rep 1
ASPC-1 GATA6
untreated


title: BATctrl2

description: Library name: BATctrl2


title: LIVERctrl7

description: Library name: LIVERctrl7

value: LIVER


title: BATctrl1

description: Library name: BATctrl1

value: Acypap1r1 floxed/floxed


title: jc8415_HPAFII_Cas_9_input

description:
input
Cas-9 input
Cas-9 input

value: HPAF-II

value: CRIPSR


title: jc8416_HPAFII_HNF4G_KO_input

description:
input
HNF4G-KO input
HNF4G-KO input


title: BATcre4

description: Library name: BATcre4

value: AAV-Cre


title: jc8414_HPAFII_HNF4G_HNF4G_KO_4_plates

description:
HNF4G -HNF4G-KO-Rep 2
HNF4G-KO
HNF4G HNF4G-KO


title: CITEseq, RO_683(#1)+RO_684(#2), Blood, HTO

city: Leuven

first: Pierre

last: Lemaitre

address: Herestraat 49 - box 902

department: Department of Chronic Diseases, Metabolism and Ageing (CHROMETA)

country: Belgium

institute: KU Leuven

description:
Library name: GSA024_HTO
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Raw sequencing reads were de-multiplexed using the Cell Ranger mkfastq
Demultiplexed data was processed using Cell Ranger count pipeline
Assembly: GRCm38.99
Supplementary files format and content: Cell Ranger Raw Feature Barcode Matrices (H5 Format)
Library strategy: CITE-seq

molecule: protein

source_name: Blood

extract_protocol:
CD45+ cells sorted from treated mice, loaded on a GemCode Single-cell Instrument (10x Genomics, Inc., Pleasanton, CA) to generate single-cell GEMs (Gel Bead-in-EMulsions).
Single-cell RNA sequencing libraries were prepared using GemCode Single-cell 3ʹ V3.1 Gel Bead and Library Kit (10x Genomics)
The cDNA amplification mix was modified to include ADT PCR additive primer (5’-CCTTGGCACCCGAGAATT*C*C-3’ where * indicates a phosphonothioate bond) and HTO PCR additive primer (5’-GTGACTGGAGTTCAGACGTGTGC*T*C-3’).

value: Blood

value: CD45+ cell

value: NOD mice

value: No treatment

tag: outcome

value: Recent-Onset

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0301 anti-mouse Hashtag 1(RO_683(#1)), TotalSeq-A0302 anti-mouse Hashtag 2(RO_684(#2))


title: jc8412_HPAFII_HNF4G_HNF4G_KO_4_plates

description:
HNF4G -HNF4G-KO-Rep 1
HNF4G-KO
HNF4G HNF4G-KO

value: Pancreatic adenocarcinoma


title: jc8409_HPAFII_FOXA1_Cas_9_4_plates

description:
FOXA1-Cas-9-Rep 3
Cas-9
FOXA1 Cas-9


title: CITEseq, RO_683(#1)+RO_684(#2), Blood, ADT

description:
Library name: GSA024_ADT
Antibody-derived oligonucleotide (ADT)

value: ADT

tag: adt

value: see feature_reference.csv


title: jc8408_HPAFII_FOXA1_HNF4G_KO_2_plates

description:
FOXA1-HNF4G-KO-Rep 2
HNF4G-KO
FOXA1 HNF4G-KO


title: jc8405_HPAFII_FOXA1_Cas_9_4_plates

description:
FOXA1-Cas-9-Rep 1
Cas-9
FOXA1 Cas-9


title: CITEseq, RO_676(#1)+RO_681(#2), Blood, ADT

description:
Library name: GSA023_ADT
Antibody-derived oligonucleotide (ADT)


title: CITEseq, RO_683(#1)+RO_684(#2), Blood, cDNA

description:
Library name: GSA024_cDNA
polyA RNA

value: mRNA


title: jc6726_AsPC_1_HNF4G

description:
HNF4G ASPC-1-Rep 2
ASPC-1 HNF4G
untreated

value: WT

value: untreated


title: jc8407_HPAFII_FOXA1_Cas_9_2_plates

description:
FOXA1-Cas-9-Rep 2
Cas-9
FOXA1 Cas-9


title: CITEseq, RO_676(#1)+RO_681(#2), Blood, HTO

description:
Library name: GSA023_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-A0301 anti-mouse Hashtag 1(RO_676(#1)), TotalSeq-A0302 anti-mouse Hashtag 2(RO_681(#2))


title: jc8404_HPAFII_FOXA1_HNF4G_KO_4_plates

description:
FOXA1- HNF4G-KO-Rep 1
HNF4G-KO
FOXA1 HNF4G-KO

value: HPAF-II


title: jc8406_HPAFII_FOXA1_HNF4G_KO_4_plates

description:
FOXA1-HNF4G-KO-Rep 1
HNF4G-KO
FOXA1 HNF4G-KO

value: CRIPSR


title: CITEseq, RO_676(#1)+RO_681(#2), Blood, cDNA

description:
Library name: GSA023_cDNA
polyA RNA


title: BATcre6

description: Library name: BATcre6

value: Brown Adipose Tissue (BAT)

value: Acypap1r1 floxed/floxed

value: AAV-Cre


title: CITEseq, RO_683(#1)+RO_684(#2), Pancreas, HTO

description:
Library name: GSA020_HTO
Hashtag-derived oligonucleotide (HTO)

source_name: Pancreas

value: Pancreas

value: CD45+ cell

value: NOD mice


title: CITEseq, RO_683(#1)+RO_684(#2), Pancreas, cDNA

description:
Library name: GSA020_cDNA
polyA RNA

value: No treatment

value: Recent-Onset


title: jc8401_HPAFII_flag_HNF4G_KO_FOXA1

description:
Flag-HNF4G-KO+FOXA1-Rep 2
HNF4G-KO+FOXA1
FLAG HNF4G-KO+FOXA1

value: Pancreatic adenocarcinoma


title: CITEseq, RO_676(#1)+RO_681(#2), Pancreas, HTO

description:
Library name: GSA019_HTO
Hashtag-derived oligonucleotide (HTO)

value: HTO


title: jc8400_HPAFII_flag_Cas_9_FOXA1

description:
Flag-Cas-9-FOXA1-Rep 2
Cas-9-FOXA1
FLAG Cas-9-FOXA1


title: CITEseq, RO_683(#1)+RO_684(#2), Pancreas, ADT

description:
Library name: GSA020_ADT
Antibody-derived oligonucleotide (ADT)

value: ADT

value: see feature_reference.csv


title: jc8399_HPAFII_flag_Cas_9_EV

description:
Flag-Cas-9-EV-Rep 2
Cas-9-EV
FLAG Cas-9-EV


title: jc8398_HPAFII_flag_HNF4G_KO_FOXA1

description:
Flag-HNF4G-KO+FOXA1-Rep 1
HNF4G-KO+FOXA1
FLAG HNF4G-KO+FOXA1


title: CITEseq, RO_676(#1)+RO_681(#2), Pancreas, ADT

description:
Library name: GSA019_ADT
Antibody-derived oligonucleotide (ADT)


title: CITEseq, RO_676(#1)+RO_681(#2), Pancreas, cDNA

description:
Library name: GSA019_cDNA
polyA RNA

value: mRNA


title: jc8396_HPAFII_flag_Cas_9_EV

description:
Flag-Cas-9-EV-Rep 1
Cas-9-EV
FLAG Cas-9-EV


title: jc8395_HPAFII_H3K27Ac_HNF4G_KO_FOXA1

description:
H3K27Ac-HNF4G-KO+FOXA1-Rep 3
HNF4G-KO+FOXA1
H3K27Ac HNF4G-KO+FOXA1


title: jc8397_HPAFII_flag_Cas_9_FOXA1

description:
Flag-Cas-9-FOXA1-Rep 1
Cas-9-FOXA1
FLAG Cas-9-FOXA1


title: CITEseq, aCD3_534(#1)+aCD3_535(#2), Blood, cDNA

description:
Library name: GSA016_cDNA
polyA RNA

value: Blood

value: 2.5 μg anti-CD3 for 5 days

value: Non-Responders


title: CITEseq, aCD3_534(#1)+aCD3_535(#2), Blood, ADT

description:
Library name: GSA016_ADT
Antibody-derived oligonucleotide (ADT)


title: CITEseq, aCD3_534(#1)+aCD3_535(#2), Blood, HTO

description:
Library name: GSA016_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-A0301 anti-mouse Hashtag 1(aCD3_534(#1)), TotalSeq-A0302 anti-mouse Hashtag 2(aCD3_535(#2))


title: jc8394_HPAFII_H3K27Ac_Cas_9_FOXA1

description:
H3K27Ac-Cas-9-FOXA1-Rep 3
Cas-9-FOXA1
H3K27Ac Cas-9-FOXA1

value: HPAF-II

value: CRIPSR


title: jc8391_HPAFII_H3K27Ac_Cas_9_FOXA1

description:
H3K27Ac-Cas-9-FOXA1-Rep 2
Cas-9-FOXA1
H3K27Ac Cas-9-FOXA1


title: jc8393_HPAFII_H3K27Ac_Cas_9_EV

description:
H3K27Ac-Cas-9-EV-Rep 3
Cas-9-EV
H3K27Ac Cas-9-EV


title: CITEseq, aCD3_531(#1)+aCD3_540(#2), Blood, ADT

description:
Library name: GSA015_ADT
Antibody-derived oligonucleotide (ADT)

value: Responders


title: CITEseq, aCD3_534(#1)+aCD3_535(#2), Pancreas, HTO

description:
Library name: GSA012_HTO
Hashtag-derived oligonucleotide (HTO)

value: Pancreas


title: CITEseq, aCD3_531(#1)+aCD3_540(#2), Blood, HTO

description:
Library name: GSA015_HTO
Hashtag-derived oligonucleotide (HTO)

value: CD45+ cell

value: TotalSeq-A0301 anti-mouse Hashtag 1(aCD3_531(#1)), TotalSeq-A0302 anti-mouse Hashtag 2(aCD3_540(#2))


title: CITEseq, aCD3_531(#1)+aCD3_540(#2), Blood, cDNA

description:
Library name: GSA015_cDNA
polyA RNA

value: NOD mice


title: jc8392_HPAFII_H3K27Ac_HNF4G_KO_FOXA1

description:
H3K27Ac-HNF4G-KO+FOXA1-Rep 2
HNF4G-KO+FOXA1
H3K27Ac HNF4G-KO+FOXA1


title: jc8389_HPAFII_HNF4G_KO_FOXA1_input

description:
input
HNF4G-KO+FOXA1 input
HNF4G-KO+FOXA1  input


title: CITEseq, aCD3_531(#1)+aCD3_540(#2), Pancreas, HTO

description:
Library name: GSA011_HTO
Hashtag-derived oligonucleotide (HTO)


title: jc8390_HPAFII_H3K27Ac_Cas_9_EV

description:
H3K27Ac-Cas-9-EV-Rep 2
Cas-9-EV
H3K27Ac Cas-9-EV


title: CITEseq, aCD3_534(#1)+aCD3_535(#2), Pancreas, ADT

description:
Library name: GSA012_ADT
Antibody-derived oligonucleotide (ADT)


title: jc8386_HPAFII_H3K27Ac_HNF4G_KO_FOXA1

description:
H3K27Ac-HNF4G-KO+FOXA1-Rep 1
HNF4G-KO+FOXA1
H3K27Ac HNF4G-KO+FOXA1


title: jc8384_HPAFII_H3K27Ac_Cas_9_EV

description:
H3K27Ac-Cas-9-EV-Rep 1
Cas-9-EV
H3K27Ac Cas-9-EV


title: jc8388_HPAFII_Cas_9_FOXA1_input

description:
input
Cas-9+FOXA1 input
Cas-9+FOXA1 input


title: CITEseq, aCD3_534(#1)+aCD3_535(#2), Pancreas, cDNA

description:
Library name: GSA012_cDNA
polyA RNA


title: jc8387_HPAFII_Cas_9_EV_input

description:
input
Cas-9-EV input
Cas-9-EV input


title: CITEseq, aCD3_531(#1)+aCD3_540(#2), Pancreas, ADT

description:
Library name: GSA011_ADT
Antibody-derived oligonucleotide (ADT)


title: jc8382_HPAFII_HNF4G_Cas_9_EV

description:
HNF4G -Cas-9-EV- Rep 3
Cas-9-EV
HNF4G Cas-9-EV


title: jc8381_HPAFII_HNF4G_Cas_9_FOXA1

description:
HNF4G -Cas-9-FOXA1-Rep 3
Cas-9-FOXA1
HNF4G Cas-9-FOXA1


title: CITEseq, aCD3_531(#1)+aCD3_540(#2), Pancreas, cDNA

description:
Library name: GSA011_cDNA
polyA RNA


title: CITEseq, aCD3_801(no#), Blood, ADT

description:
Library name: GSA006_ADT
Antibody-derived oligonucleotide (ADT)


title: CITEseq, aCD3_807(#1)+aCD3_818(#2), Blood, cDNA

description:
Library name: GSA005_cDNA
polyA RNA


title: CITEseq, aCD3_807(#1)+aCD3_818(#2), Blood, ADT

description:
Library name: GSA005_ADT
Antibody-derived oligonucleotide (ADT)


title: jc8376_HPAFII_HNF4G_Cas_9_FOXA1

description:
HNF4G -Cas-9-FOXA1-Rep 1
Cas-9-FOXA1
HNF4G Cas-9-FOXA1


title: CITEseq, aCD3_801(no#), Blood, cDNA

description:
Library name: GSA006_cDNA
polyA RNA


title: jc8373_HPAFII_FOXA1_Cas_9_FOXA1

description:
FOXA1-Cas-9-FOXA1-Rep 4
Cas-9-FOXA1
FOXA1 Cas-9-FOXA1


title: CITEseq, aCD3_801(no#), Pancreas, cDNA

description:
Library name: GSA002_cDNA
polyA RNA


title: CITEseq, aCD3_807(#1)+aCD3_818(#2), Pancreas, ADT

description:
Library name: GSA001_ADT
Antibody-derived oligonucleotide (ADT)


title: jc8379_HPAFII_HNF4G_Cas_9_FOXA1

description:
HNF4G -Cas-9-FOXA1-Rep 2
Cas-9-FOXA1
HNF4G Cas-9-FOXA1


title: CITEseq, aCD3_801(no#), Pancreas, ADT

description:
Library name: GSA002_ADT
Antibody-derived oligonucleotide (ADT)


title: CITEseq, aCD3_807(#1)+aCD3_818(#2), Pancreas, HTO

description:
Library name: GSA001_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-A0301 anti-mouse Hashtag 1(aCD3_807(#1)), TotalSeq-A0302 anti-mouse Hashtag 2(aCD3_818(#2))


title: jc8377_HPAFII_HNF4G_HNF4G_KO_FOXA1

description:
HNF4G -HNF4G-KO+FOXA1-Rep 1
HNF4G-KO+FOXA1
HNF4G-KO+FOXA1

value: Pancreatic adenocarcinoma


title: jc8385_HPAFII_H3K27Ac_Cas_9_FOXA1

description:
H3K27Ac-Cas-9-FOXA1-Rep 1
Cas-9-FOXA1
H3K27Ac Cas-9-FOXA1


title: CITEseq, aCD3_807(#1)+aCD3_818(#2), Pancreas, cDNA

description:
Library name: GSA001_cDNA
polyA RNA


title: jc8371_HPAFII_FOXA1_HNF4G_KO_FOXA1

description:
FOXA1-HNF4G-KO+FOXA1-Rep 3
HNF4G-KO+FOXA1
FOXA1 HNF4G-KO+FOXA1


title: jc8370_HPAFII_FOXA1_Cas_9_FOXA1

description:
FOXA1-Cas-9-FOXA1-Rep 3
Cas-9-FOXA1
FOXA1 Cas-9-FOXA1


title: jc8368_HPAFII_FOXA1_HNF4G_KO_FOXA1

description:
FOXA1-HNF4G-KO+FOXA1-Rep 2
HNF4G-KO+FOXA1
FOXA1 HNF4G-KO+FOXA1


title: CITEseq, aCD3_807(#1)+aCD3_818(#2), Blood, HTO

description:
Library name: GSA005_HTO
Hashtag-derived oligonucleotide (HTO)

value: HTO


title: BPRNF SI Tumour scRNA-Seq Rep2

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

description:
Library name: VBPRNF_RKBG32_3a_S4
10x Genomics

data_processing:
Sequence alignment of single cell data to the mm10 genome was performed using the count tool from the Cellranger package (version 6.1.2) according to the developers’ instructions.
Assembly: Mouse mm10
Supplementary files format and content: h5 matrix files

source_name: Small Intestine Tumour

growth_protocol: Mice were induced with a single 70uL injection of 100uM 4-OH tamoxifen into the colonic submucosa

extract_protocol:
Colonic tumour samples were collected in PBS and processed immediately for scRNAseq. Briefly, samples were chopped to achieve a paste-like consistency using a Mcllwain Tissue Chopper. Samples were transferred to GentleMACS C tubes (Miltenyi Biotec, 130-093-237) for tissue homogenisation using the GentleMACS Octo Dissociator with heaters (Miltenyi Biotec, 130-096-427) in combination with the Mouse tumour dissociation kit (Miltenyi Biotec, 130-096-730). Following tissue digestion, samples were resuspended in RPMI + 10% FBS + 2mM EDTA and filtered through 70μm and 40μm strainers respectively. The cell suspension was centrifuged at 400g for 3 mins and washed with RPMI + 0.4% BSA. The sample suspensions were centrifuged at 400g for 3 mins and the resultant pellets resuspended in 2% FCS + 25 mM HEPES + 2 mM EDTA + PBS for cell sorting. Cells were sorted using a BD FACSAria sorter (BD Biosciences) and DAPI (Invitrogen, D1306) to remove dead cells.
Live sorted single cells were loaded onto a Chromium Chip G using reagents from the 10x Chromium Single-Cell 3’ v3 Gel Bead Kit and Library (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: Mice were treated twice  daily with MRTX1133 IP AM and PM (MRTX1133 100uL 7.5mg/kg) or vehicle (100uL10% hydroxpropyl beta cyclodextrin in 50mM citrate buffer ph5) for 4 days and sampled two hours post AM dose on the fourth day.

value: Small Intestine Tumour

tag: Sex

value: Male

value: VilCreER BrafV600E/+ P53fl/fl Rnf43fl/fl


title: BPRNF SI Tumour scRNA-Seq Rep1

description:
Library name: VBPRNF_RKBG_28_1g_S25
10x Genomics

value: Female


title: jc8364_HPAFII_FOXA1_Cas_9_FOXA1

description:
FOXA1-Cas-9-FOXA1-Rep 1
Cas-9-FOXA1
FOXA1 Cas-9-FOXA1


title: BPNA Colon Tumour Vehicle scRNA-Seq Rep2

description:
Library name: VANP_RKF90_6c_S3
10x Genomics

source_name: Colon Tumour

value: Colon Tumour

value: VilCreER BrafV600E/+ P53fl/fl Notch1Tg Alk5fl/fl

value: HPMC-Tween-Vehicle


title: jc8366_HPAFII_FOXA1_Cas_9_EV

description:
FOXA1-Cas-9-EV-Rep 2
Cas-9-EV
FOXA1 Cas-9-EV

value: HPAF-II


title: BPNA Colon Tumour Vehicle scRNA-Seq Rep3

description:
Library name: VANP_RKF90_6e_S5
10x Genomics


title: jc8380_HPAFII_HNF4G_Cas_9_EV

description:
HNF4G -Cas-9-EV-Rep 2
Cas-9-EV
HNF4G Cas-9-EV

value: CRIPSR


title: BPRNF SI Tumour scRNA-Seq Rep3

description:
Library name: VBPRNF_RKBG37_1e_S6
10x Genomics


title: jc8378_HPAFII_HNF4G_Cas_9_EV

description:
HNF4G -Cas-9-EV-Rep 1
Cas-9-EV
HNF4G Cas-9-EV


title: BPNA Colon Tumour Vehicle scRNA-Seq Rep4

description:
Library name: RKF106_1b_S6
10x Genomics


title: jc8372_HPAFII_FOXA1_Cas_9_EV

description:
FOXA1-Cas-9-EV-Rep 3
Cas-9-EV
FOXA1 Cas-9-EV


title: BPNA Colon Tumour Vehicle scRNA-Seq Rep1

description:
Library name: VANP_RKF89_4b_S32
10x Genomics


title: BPNA Colon Tumour Combination Treatment scRNA-Seq Rep4

description:
Library name: VANP_RKF93_1e_S7
10x Genomics

value: Dabrafenib+Erlotinib


title: BPNA Colon Tumour Combination Treatment scRNA-Seq Rep3

description:
Library name: VANP_RKF93_1a_S6
10x Genomics


title: BPNA Colon Tumour Combination Treatment scRNA-Seq Rep2

description:
Library name: VANP_RKF89_5c_S34
10x Genomics


title: jc8150_HPAFII_PRMT1_Input_HNF4G_KO

description:
PRMT1-HNF4G-KO-Rep 2
HNF4G-KO
HNF4G-KO input


title: jc8363_HPAFII_FOXA1_Cas_9_EV

description:
FOXA1-Cas-9-EV-Rep 1
Cas-9-EV
FOXA1 Cas-9-EV


title: jc8149_HPAFII_PRMT1_Input_HNF4G_KO_Rescue

description:
PRMT1-HNF4G-KO+Rescue-Rep 3
HNF4G-KO+Rescue
HNF4G-KO+Rescue input


title: jc8148_HPAFII_PRMT1_Input_Cas_9_EV

description:
PRMT1-Cas-9-EV-Rep 1
Cas-9-EV
Cas-9-EV input


title: BPNA Colon Tumour Combination Treatment scRNA-Seq Rep1

description:
Library name: VANP_RKF89_4c_S33
10x Genomics


title: jc8147_HPAFII_PRMT1_Cas_9_FOXA1_siRNA

description:
PRMT1-FOXA1-siRNA-Rep 3
Cas-9-FOXA1-siRNA
PRMT1 Cas-9-FOXA1-siRNA

value: WT


title: BPNA Colon Tumour scRNA-Seq Rep6

description:
Library name: VANP_RKF94_3e_S3
10x Genomics


title: jc8146_HPAFII_PRMT1_Cas_9_FOXA1_siRNA

description:
PRMT1-FOXA1-siRNA-Rep 2
Cas-9-FOXA1-siRNA
PRMT1 Cas-9-FOXA1-siRNA


title: BPNA Colon Tumour scRNA-Seq Rep5

description:
Library name: VANP_RKF94_2e_S2
10x Genomics


title: jc8145_HPAFII_PRMT1_Cas_9_FOXA1_siRNA

description:
PRMT1-FOXA1-siRNA-Rep 1
Cas-9-FOXA1-siRNA
PRMT1 Cas-9-FOXA1-siRNA


title: jc8367_HPAFII_FOXA1_Cas_9_FOXA1

description:
FOXA1-Cas-9-FOXA1-Rep 2
Cas-9-FOXA1
FOXA1 Cas-9-FOXA1


title: BPNA Colon Tumour scRNA-Seq Rep4

description:
Library name: VANP_RKF100_1c_S10
10x Genomics


title: jc8144_HPAFII_PRMT1_Cas_9_NT

description:
PRMT1-Cas-9-NT-Rep 3
Cas-9-NT
PRMT1 Cas-9-NT

value: siRNA-NT


title: BPNA Colon Tumour scRNA-Seq Rep3

description:
Library name: VANP_RKF100_1b_S9
10x Genomics


title: jc8143_HPAFII_PRMT1_Cas_9_NT

description:
PRMT1-Cas-9-NT-Rep 2
Cas-9-NT
PRMT1 Cas-9-NT


title: BPNA Colon Tumour scRNA-Seq Rep2

description:
Library name: 19_66
10x Genomics


title: BPNA Colon Tumour scRNA-Seq Rep1

description:
Library name: 19_65
10x Genomics


title: jc8365_HPAFII_FOXA1_HNF4G_KO_FOXA1

description:
FOXA1-HNF4G-KO+FOXA1-Rep 1
HNF4G-KO+FOXA1
FOXA1 HNF4G-KO+FOXA1


title: jc8142_HPAFII_PRMT1_Cas_9_NT

description:
PRMT1-Cas-9-NT-Rep 1
Cas-9-NT
PRMT1 Cas-9-NT


title: jc8139_HPAFII_PRMT1_HNF4G_KO_Rescue

description:
PRMT1-HNF4G-KO+Rescue-Rep 2
HNF4G-KO+Rescue
PRMT1 HNF4G-KO+Rescue


title: jc8140_HPAFII_PRMT1_HNF4G_KO_Rescue

description:
PRMT1-HNF4G-KO-Rep 1
HNF4G-KO
PRMT1 HNF4G-KO+Rescue


title: BP SI Tumour scRNA-Seq Rep2

description:
Library name: VBPNOT_RKV72_1e_S5
10x Genomics

value: VilCreER BrafV600E/+ P53fl/fl


title: BP SI Tumour scRNA-Seq Rep1

description:
Library name: 19_52
10x Genomics


title: Apc Colon Tumour scRNA-Seq Rep2

description:
Library name: RZF133_2a_S2
10x Genomics

source_name: Intracolonic Transplant Colon Tumour

value: Intracolonic Transplant Colon Tumour

value: VilCreER Apcfl/fl


title: jc8137_HPAFII_PRMT1_Cas_9

description:
PRMT1-Cas-9-Rep 3
Cas-9
PRMT1 Cas-9

value: Pancreatic adenocarcinoma


title: AKG12D Colon Tumour MRTX1133 Vehicle scRNA-Seq Rep3

description:
Library name: BVAR_RZF125_1c_S19
10x Genomics

value: VilCreER Apcfl/fl KRasG12D/+

value: MRTX1133 Vehicle


title: jc8136_HPAFII_PRMT1_Cas_9

description:
PRMT1-Cas-9-Rep 2
Cas-9
PRMT1 Cas-9


title: jc8135_HPAFII_PRMT1_Cas_9

description:
PRMT1-Cas-9-Rep 1
Cas-9
PRMT1 Cas-9


title: Apc Colon Tumour scRNA-Seq Rep1

description:
Library name: RZF131_2b_S1
10x Genomics

value: Male


title: AKG12D Colon Tumour MRTX1133 Vehicle scRNA-Seq Rep2

description:
Library name: BVAR_RZF122_2a_S17
10x Genomics


title: hpaf50_HPAFII_Input_Inputs

description:
Input
Inputs
HPAFII Input

value: Inputs


title: hpaf49_HPAFII_Input_Inputs

description:
Input
Inputs
HPAFII Input


title: AKG12D Colon Tumour MRTX1133 scRNA-Seq Rep5

description:
Library name: BVAR_RZF122_3d_S6
10x Genomics


title: hpaf48_HPAFII_Input_Inputs

description:
Input
Inputs
HPAFII Input


title: AKG12D Colon Tumour MRTX1133 scRNA-Seq Rep3

description:
Library name: BVAR_RZF124_1a_S20
10x Genomics


title: jc8138_HPAFII_PRMT1_HNF4G_KO_Rescue

description:
PRMT1-HNF4G-KO+Rescue-Rep 1
HNF4G-KO+Rescue
PRMT1 HNF4G-KO+Rescue


title: hpaf46_HPAFII_H3K27Ac_FOXA1_sirna

description:
H3K27Ac-FOXA1-sirna-Rep 4
FOXA1-sirna
FOXA1-sirna


title: AKG12D Colon Tumour MRTX1133 scRNA-Seq Rep4

description:
Library name: BVAR_RZF122_1c_S37
10x Genomics

value: Female


title: AKG12D Colon Tumour MRTX1133 scRNA-Seq Rep2

description:
Library name: BVAR_RZF124_2a_S15
10x Genomics


title: hpaf47_HPAFII_Input_Inputs

description:
Input
Inputs
HPAFII Input


title: BPRNF SI Tumour Rep4

description: Library name: VBPRNF.RKBG18.1h.BPRNF.SI.T.12.09.2023.P3.H12

data_processing:
Trimmed sequences were aligned to mouse genome build GRCm38.98 (mm10) using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Batch correction for Gold Standard sets 1 and 2 was performed in R, using the ComBat_seq function from the sva package.
Assembly: GRCm38
Supplementary files format and content: Matrix of batch corrected raw counts

source_name: Small Intestine

extract_protocol:
After sampling, tissues were stored in RNAlater. RNA was then extracted with an RNeasy Mini Kit according to the manufacturer’s instructions, and then homogenised using a Precellys Evolution machine. RNA quality was assessed by TapeStation and samples were only used if RIN >7.
Library preparation was performed by Azenta using an Illumina mRNA with PolyA selection kit. Libraries were then sequenced using a Novaseq 6000 sequencer.

value: Small Intestine

tag: sample type

value: Tumour

value: VilCreER BrafV600E/+ P53fl/fl Rnf43fl/fl

tag: induction method

value: 2mg intraperitoneal injection of Tamoxifen

tag: intervention timepoint

tag: batch


title: BPRNF SI Tumour Rep3

description: Library name: VBPRNF.RKBG18.1g.BPRNF.SI.T.12.09.2023.P2.A11


title: BPRNF SI Tumour Rep1

description: Library name: VBPRNF.RKBG16.1g.BPRNF.SI.T.12.09.2023.P5.D10


title: hpaf45_HPAFII_H3K27Ac_Non_targetting_siRNA

description:
H3K27Ac-Non-targetting siRNA-Rep 4
Non-targetting siRNA
Non-targetting siRNA

value: HPAF-II


title: hpaf40_HPAFII_H3K27Ac_FOXA1_sirna

description:
H3K27Ac-FOXA1-sirna-Rep 1
FOXA1-sirna
FOXA1-sirna


title: hpaf44_HPAFII_H3K27Ac_FOXA1_sirna

description:
H3K27Ac-FOXA1-sirna-Rep3
FOXA1-sirna
FOXA1-sirna


title: BPRNF SI Tumour Rep5

description: Library name: VBPRNF.RKBG19.1d.BPRNF.SI.T.12.09.2023.P6.C8


title: hpaf43_HPAFII_H3K27Ac_Non_targetting_siRNA

description:
H3K27Ac-Non-targetting siRNA-Rep 3
Non-targetting siRNA
Non-targetting siRNA


title: hpaf42_HPAFII_H3K27Ac_FOXA1_sirna

description:
H3K27Ac-FOXA1-sirna-Rep 2
FOXA1-sirna
FOXA1-sirna


title: hpaf39_HPAFII_H3K27Ac_Non_targetting_siRNA

description:
H3K27Ac-Non-targetting siRNA-Rep 1
Non-targetting siRNA
Non-targetting siRNA


title: hpaf41_HPAFII_H3K27Ac_Non_targetting_siRNA

description:
H3K27Ac-Non-targetting siRNA-Rep 2
Non-targetting siRNA
Non-targetting siRNA


title: BPRNF SI Tumour, LGK974 Vehicle Rep6

description: Library name: VBPRNF-RKBG28-2d-BPRNF-SI-T-D130-LGK974-Vehicle-29-07-2024-P1-F9

value: Day 130


title: hpaf36_HPAFII_H3K27Ac_HNF4G_KO

description:
H3K27Ac-HNF4G-KO-Rep2
HNF4G-KO
HNF4G-KO

value: CRIPSR


title: BPRNF SI Tumour Rep2

description: Library name: VBPRNF.RKBG18.1e.BPRNF.SI.T.12.09.2023.P2.F5


title: BPRNF SI Tumour, LGK974 Vehicle Rep3

description: Library name: VBPRNF-RKBG32-1g-BPRNF-SI-T-D130-LGK974-Vehicle-29-07-2024-P1-C6


title: BPRNF SI Tumour, LGK974 Vehicle Rep5

description: Library name: VBPRNF-RKBG28-1d-BPRNF-SI-T-D130-LGK974-Vehicle-29-07-2024-P1-D5


title: hpaf34_HPAFII_H3K27Ac_Cas_9

description:
H3K27Ac-Cas-9-Rep 4
Cas-9
Cas-9


title: BPRNF SI Tumour, LGK974 Vehicle Rep2

description: Library name: VBPRNF-RKBG28-1c-BPRNF-SI-T-D130-LGK974-Vehicle-29-07-2024-P1-B10


title: AKG12D Colon Tumour MRTX1133 scRNA-Seq Rep1

description:
Library name: BVAR_RZF119_5b_S14
10x Genomics


title: BPRNF SI Tumour, LGK974 Vehicle Rep1

description: Library name: VBPRNF-RKBG32-1e-BPRNF-SI-T-D130-LGK974-Vehicle-29-07-2024-P1-B3


title: AKG12D Colon Tumour MRTX1133 Vehicle scRNA-Seq Rep1

description:
Library name: BVAR_RZF118_6c_S16
10x Genomics


title: hpaf35_HPAFII_H3K27Ac_HNF4G_KO

description:
H3K27Ac-HNF4G-KO-Rep1
HNF4G-KO
HNF4G-KO


title: BPRNF SI Tumour, LGK974 Treated Rep5

description: Library name: VBPRNF-RKBG29-3d-BPRNF-SI-T-D130-LGK974-29-07-2024-P1-F10


title: hpaf31_HPAFII_H3K27Ac_Cas_9

description:
H3K27Ac-Cas-9-Rep 1
Cas-9
Cas-9


title: hpaf37_HPAFII_H3K27Ac_HNF4G_KO

description:
H3K27Ac-HNF4G-KO-Rep3
HNF4G-KO
HNF4G-KO


title: hpaf33_HPAFII_H3K27Ac_Cas_9

description:
H3K27Ac-Cas-9-Rep 3
Cas-9
Cas-9


title: BPRNF SI Tumour, LGK974 Vehicle Rep4

description: Library name: VBPRNF-RKBG21-4a-BPRNF-SI-T-D130-LGK974-Vehicle-29-07-2024-P1-D3


title: hpaf32_HPAFII_H3K27Ac_Cas_9

description:
H3K27Ac-Cas-9-Rep 2
Cas-9
Cas-9


title: hpaf30_HPAFII_HNF4G_FOXA1_sirna

description:
HNF4G FOXA1-sirna-Rep 4
FOXA1-sirna
FOXA1-sirna

value: WT


title: hpaf28_HPAFII_HNF4G_FOXA1_sirna

description:
HNF4G FOXA1-sirna-Rep 3
FOXA1-sirna
FOXA1-sirna


title: BPRNF SI Tumour, LGK974 Treated Rep2

description: Library name: VBPRNF-RKBG21-3k-BPRNF-SI-T-D130-LGK974-29-07-2024-P1-A6


title: BPRNF SI Tumour, LGK974 Treated Rep1

description: Library name: VBPRNF-RKBG21-3f-BPRNF-SI-T-D130-LGK974-29-07-2024-P1-A1


title: BPRNF SI Tumour, LGK974 Treated Rep4

description: Library name: VBPRNF-RKBG32-1c-BPRNF-SI-T-D130-LGK974-29-07-2024-P1-E9


title: hpaf26_HPAFII_HNF4G_FOXA1_sirna

description:
HNF4G FOXA1-sirna-Rep 2
FOXA1-sirna
FOXA1-sirna


title: BPRNF SI Tumour Vehicle Rep10

description: Library name: VBPRNF.RKBG31.2a.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.A12

value: HPMC-Tween-Vehicle


title: hpaf27_HPAFII_HNF4G_Non_targetting_siRNA

description:
HNF4G Non-targetting siRNA-Rep 3
Non-targetting siRNA
Non-targetting siRNA

value: siRNA-NT


title: BPRNF SI Tumour Vehicle Rep9

description: Library name: VBPRNF.RKBG24.2h.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.F7


title: hpaf23_HPAFII_HNF4G_Non_targetting_siRNA

description:
HNF4G Non-targetting siRNA-Rep 1
Non-targetting siRNA
Non-targetting siRNA


title: hpaf25_HPAFII_HNF4G_Non_targetting_siRNA

description:
HNF4G Non-targetting siRNA-Rep 2
Non-targetting siRNA
Non-targetting siRNA


title: hpaf24_HPAFII_HNF4G_FOXA1_sirna

description:
HNF4G FOXA1-sirna-Rep 1
FOXA1-sirna
FOXA1-sirna


title: hpaf21_HPAFII_PRMT1_HNF4G_KO

description:
PRMT1 HNF4G-KO-Rep 2
HNF4G-KO
HNF4G-KO


title: BPRNF SI Tumour Vehicle Rep7

description: Library name: VBPRNF.RKBG24.2f.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.E11


title: BPRNF SI Tumour Vehicle Rep8

description: Library name: VBPRNF.RKBG24.2g.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.E7


title: hpaf22_HPAFII_PRMT1_HNF4G_KO

description:
PRMT1 HNF4G-KO-Rep 3
HNF4G-KO
HNF4G-KO


title: BPRNF SI Tumour Vehicle Rep3

description: Library name: VBPRNF.RKBG21.2a.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.G12


title: BPRNF SI Tumour Vehicle Rep5

description: Library name: VBPRNF.RKBG22.2b.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.D9


title: hpaf20_HPAFII_PRMT1_HNF4G_KO

description:
PRMT1 HNF4G-KO-Rep 1
HNF4G-KO
HNF4G-KO


title: hpaf18_HPAFII_PRMT1_Cas_9

description:
PRMT1 Cas-9-Rep2
Cas-9
Cas-9


title: BPRNF SI Tumour Vehicle Rep4

description: Library name: VBPRNF.RKBG22.2a.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.B9


title: BPRNF SI Tumour, LGK974 Treated Rep3

description: Library name: VBPRNF-RKBG28-2c-BPRNF-SI-T-D130-LGK974-29-07-2024-P1-D11


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep10

description: Library name: VBPRNF.RKBG24.1f.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.B4

value: Dabrafenib-Erlotinib


title: hpaf8_HPAFII_FOXA1_HNF4G_KO

description:
FOXA1-HNF4G-KO-Rep 3
HNF4G-KO
HNF4G-KO

value: Pancreatic adenocarcinoma


title: hpaf19_HPAFII_PRMT1_Cas_9

description:
PRMT1 Cas-9-Rep3
Cas-9
Cas-9


title: BPRNF SI Tumour Vehicle Rep6

description: Library name: VBPRNF.RKBG24.2a.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.G2


title: hpaf7_HPAFII_FOXA1_HNF4G_KO

description:
FOXA1-HNF4G-KO-Rep 2
HNF4G-KO
HNF4G-KO


title: BPRNF SI Tumour Vehicle Rep1

description: Library name: VBPRNF.RKBG17.1e.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.A4


title: hpaf6_HPAFII_FOXA1_HNF4G_KO

description:
FOXA1-HNF4G-KO-Rep 1
HNF4G-KO
HNF4G-KO


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep9

description: Library name: VBPRNF.RKBG24.1e.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.G9


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep7

description: Library name: VBPRNF.RKBG24.1a.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.H2


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep8

description: Library name: VBPRNF.RKBG24.1c.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.G1


title: hpaf3_HPAFII_FOXA1_Cas_9

description:
FOXA1-Cas-9-Rep2
Cas-9
Cas-9


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep6

description: Library name: VBPRNF.RKBG22.2f.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.D1


title: hpaf1_HPAFII_FOXA1_Cas_9

description:
FOXA1-Cas-9-Rep1
Cas-9
Cas-9


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep5

description: Library name: VBPRNF.RKBG22.2e.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.C5


title: jc7852_INPUT_Tumour

description:
input
normal
clinical samples input

source_name: Whipple biopsy samples

value: untreated


title: jc7851_INPUT_normal

description:
input
normal
clinical samples input


title: jc7850_INPUT_normal

description:
input
normal
clinical samples input


title: hpaf17_HPAFII_PRMT1_Cas_9

description:
PRMT1 Cas-9-Rep1
Cas-9
Cas-9


title: BPRNF SI Tumour Vehicle Rep2

description: Library name: VBPRNF.RKBG20.5f.BPRNF.SI.T.D130.HPMC.Tween.Vehicle.29.07.2024.P1.B1


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep2

description: Library name: VBPRNF.RKBG20.6i.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.D12


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep1

description: Library name: VBPRNF.RKBG20.6e.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.F2


title: jc7846_INPUT_Tumour

description:
input
Tumour
clinical samples input


title: BPNA Colon Tumour Rep11

description: Library name: VANP.RKF52.1e.BPNA.Col.T.12.09.2023.P3.A7

source_name: Colon

value: Colon

value: VilCreER BrafV600E/+ P53fl/fl Notch1Tg Alk5fl/fl


title: jc7845_INPUT_Tumour

description:
input
Tumour
clinical samples input


title: BPNA Colon Tumour Rep9

description: Library name: VANP.RKF52.1c.BPNA.Col.T.12.09.2023.P1.H3


title: hpaf4_HPAFII_FOXA1_Cas_9

description:
FOXA1-Cas-9-Rep3
Cas-9
Cas-9


title: BPNA Colon Tumour Rep8

description: Library name: VANP.RKF52.1b.BPNA.Col.T.12.09.2023.P3.F7


title: BPNA Colon Tumour Rep7

description: Library name: VANP.RKF50.1g.BPNA.Col.T.12.09.2023.P5.C11


title: BPNA Colon Tumour Rep6

description: Library name: VANP.RKF50.1c.BPNA.Col.T.12.09.2023.P6.C6

value: Male


title: jc7841_H3K27Ac_Tumour

description:
H3K27Ac
normal
clinical samples


title: BPNA Colon Tumour Rep5

description: Library name: VANP.RKF50.1b.BPNA.Col.T.12.09.2023.P2.A1


title: jc7840_H3K27Ac_normal

description:
H3K27Ac
normal
clinical samples


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep4

description: Library name: VBPRNF.RKBG22.1e.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.B2

value: Female


title: BPNA Colon Tumour Rep4

description: Library name: VANP.RKF81.5d.BPNA.Col.T.01.05.2023.P3.H11

value: VilCreER BrafV600E/+ P53fl/fl ALK5fl/fl Notch1Tg


title: BPRNF SI Tumour, Dabrafenib-Erlotinib Treated Rep3

description: Library name: VBPRNF.RKBG21.1g.BPRNF.SI.T.D130.Dabrafenib.Erlotinib.29.07.2024.P1.E1

value: Small Intestine

value: Tumour


title: jc7839_H3K27Ac_normal

description:
H3K27Ac
normal
clinical samples


title: jc7849_INPUT_normal

description:
input
normal
clinical samples input


title: jc7838_H3K27Ac_normal

description:
H3K27Ac
normal
clinical samples


title: jc7842_INPUT_Tumour

description:
H3K27Ac
Tumour
clinical samples input


title: BPNA Colon Tumour Rep3

description: Library name: VANP.RKF5.5a.BPNA.Col.T.01.05.2023.P1.F7

value: 2mg intraperitoneal injection of Tamoxifen


title: BPNA Colon Tumour Rep12

description: Library name: VANP.RKF61.1b.BPNA.Col.T.12.09.2023.P3.G9


title: BPNA Colon Tumour Rep2

description: Library name: VANP.RKF35.3a.BPNA.Col.T.01.05.2023.P6.D3


title: BPNA Colon Tumour Rep1

description: Library name: VANP.RKF31.1d.BPNA.Col.T.01.05.2023.P8.D10


title: jc7837_H3K27Ac_normal

description:
H3K27Ac
Tumour
clinical samples


title: jc7847_INPUT_Tumour

description:
input
Tumour
clinical samples input


title: jc7848_INPUT_normal

description:
input
Tumour
clinical samples input


title: BPNA Colon Tumour Rep10

description: Library name: VANP.RKF52.1d.BPNA.Col.T.12.09.2023.P4.C9


title: BPNA Colon Tumour Vehicle Rep16

description: Library name: VANP.RKF52.3a.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P3.F12

value: Day 20


title: jc7836_H3K27Ac_Tumour

description:
H3K27Ac
Tumour
clinical samples


title: BPNA Colon Tumour Vehicle Rep14

description: Library name: VANP.RKF45.4h.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P3.A11


title: BPNA Colon Tumour Vehicle Rep15

description: Library name: VANP.RKF49.1h.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P4.G7


title: jc7844_INPUT_Tumour

description:
input
Tumour
clinical samples input


title: jc7835_H3K27Ac_Tumour

description:
H3K27Ac
Tumour
clinical samples


title: jc7843_INPUT_Tumour

description:
input
Tumour
clinical samples input


title: jc7833_H3K27Ac_Tumour

description:
H3K27Ac
Tumour
clinical samples


title: BPNA Colon Tumour Vehicle Rep13

description: Library name: VANP.RKF45.4e.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P4.C5


title: jc7832_H3K27Ac_Tumour

description:
H3K27Ac
Tumour
clinical samples


title: BPNA Colon Tumour Vehicle Rep12

description: Library name: VANP.RKF45.4d.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P3.F11


title: BPNA Colon Tumour Vehicle Rep11

description: Library name: VANP.RKF45.3h.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P4.G9


title: jc8014_PRMT1_Tumour

description:
PRMT1
430008
clinical samples


title: jc8013_PRMT1_Tumour

description:
PRMT1
432928
clinical samples


title: BPNA Colon Tumour Vehicle Rep9

description: Library name: VANP.RKF45.3e.BPNA.Col.T2.D20.HPMC.Tween.Vehicle.12.09.2023.P6.D5


title: BPNA Colon Tumour Vehicle Rep10

description: Library name: VANP.RKF45.3g.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P5.G8


title: jc8011_PRMT1_Tumour

description:
PRMT1
445016
clinical samples


title: BPNA Colon Tumour Vehicle Rep7

description: Library name: VANP.RKF45.3b.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P3.G3


title: jc8009_PRMT1_Tumour

description:
PRMT1
430254
clinical samples


title: BPNA Colon Tumour Vehicle Rep6

description: Library name: VANP.RKF43.4f.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P3.D10


title: jc7495_INPUT

description:
INPUT
TB17.0395
clinical samples input


title: BPNA Colon Tumour Vehicle Rep4

description: Library name: VANP.RKF43.2f.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P3.G4


title: jc7496_INPUT

description:
INPUT
TB17.0297
clinical samples input


title: BPNA Colon Tumour Vehicle Rep8

description: Library name: VANP.RKF45.3e.BPNA.Col.T1.D20.HPMC.Tween.Vehicle.12.09.2023.P3.A2


title: BPNA Colon Tumour Vehicle Rep5

description: Library name: VANP.RKF43.2f.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P5.B4


title: jc8010_PRMT1_Tumour

description:
PRMT1
436513
clinical samples


title: BPNA Colon Tumour Vehicle Rep3

description: Library name: VANP.RKF43.1c.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P6.D8


title: BPNA Colon Tumour Vehicle Rep2

description: Library name: VANP.RKF35.4d.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P2.G3


title: jc7834_H3K27Ac_Tumour

description:
H3K27Ac
Tumour
clinical samples


title: jc7493_INPUT

description:
INPUT
TB17.0277
clinical samples input


title: jc7492_H3K27Ac

description:
H3K27Ac
TB17.0102
clinical samples


title: BPNA Colon Tumour Vehicle Rep1

description: Library name: VANP.RKF33.2i.BPNA.Col.T.D20.HPMC.Tween.Vehicle.12.09.2023.P3.D1


title: jc7491_H3K27Ac

description:
H3K27Ac
TB17.0297
clinical samples


title: BPNA Colon Tumour, Erlotinib Treated Rep5

description: Library name: VANP.RKF83.2g.BPNA.Col.T.D20.Erlotinib.12.09.2023.P5.E6

value: Erlotinib


title: jc7494_INPUT

description:
INPUT
TB17.1768
clinical samples input


title: jc7490_H3K27Ac

description:
H3K27Ac
TB17.0395
clinical samples


title: jc8012_PRMT1_Tumour

description:
PRMT1
448234
clinical samples


title: BPNA Colon Tumour, Erlotinib Treated Rep4

description: Library name: VANP.RKF83.2f.BPNA.Col.T.D20.Erlotinib.12.09.2023.P2.D2


title: BPNA Colon Tumour, Erlotinib Treated Rep2

description: Library name: VANP.RKF61.6b.BPNA.Col.T.D20.Erlotinib.12.09.2023.P3.D9


title: jc7488_H3K27Ac

description:
H3K27Ac
TB17.0277
clinical samples


title: jc7489_H3K27Ac

description:
H3K27Ac
TB17.1768
clinical samples


title: BPNA Colon Tumour, Erlotinib Treated Rep1

description: Library name: VANP.RKF60.3c.BPNA.Col.T.D20.Erlotinib.12.09.2023.P4.B11


title: jc7497_INPUT

description:
INPUT
TB17.0102
clinical samples input


title: BPNA Colon Tumour, Dabrafenib-Erlotinib Treated Rep2

description: Library name: VANP.RKF52.5d.BPNA.Col.T.D20.Dabrafenib.Erlotinib.12.09.2023.P3.H1


title: jc7486_INPUT

description:
Input
TB17.0297
clinical samples input


title: jc7487_INPUT

description:
Input
TB17.0102
clinical samples input


title: BPNA Colon Tumour, Dabrafenib-Erlotinib Treated Rep3

description: Library name: VANP.RKF56.1d.BPNA.Col.T.D20.Dabrafenib.Erlotinib.12.09.2023.P5.B11


title: BPNA Colon Tumour, Dabrafenib Treated, Rep8

description: Library name: VANP.RKF51.4e.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P3.G12

value: Dabrafenib


title: BPNA Colon Tumour, Dabrafenib-Erlotinib Treated Rep1

description: Library name: VANP.RKF45.2h.BPNA.Col.T.D20.Dabrafenib.Erlotinib.12.09.2023.P3.H3


title: jc7485_INPUT

description:
Input
TB17.0395
clinical samples input

value: WT


title: jc7484_INPUT

description:
Input
TB17.0804
clinical samples input


title: jc7482_INPUT

description:
Input
TB17.0277
clinical samples input


title: BPNA Colon Tumour, Dabrafenib Treated, Rep7

description: Library name: VANP.RKF51.3c.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P6.C5


title: jc7481_HNF4g

description:
HNF4G
TB17.0102
clinical samples


title: jc7483_INPUT

description:
Input
TB17.1768
clinical samples input


title: BPNA Colon Tumour, Dabrafenib Treated, Rep6

description: Library name: VANP.RKF49.1g.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P1.H6


title: BPNA Colon Tumour, Dabrafenib Treated, Rep3

description: Library name: VANP.RKF32.1f.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P3.B6


title: jc7479_FOXA1

description:
FOXA1
TB17.0102
clinical samples


title: BPNA Colon Tumour, Dabrafenib Treated, Rep5

description: Library name: VANP.RKF43.7f.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P3.G5


title: jc7480_HNF4a

description:
HNF4A
TB17.0102
clinical samples


title: jc7478_HNF4g

description:
HNF4G
TB17.0297
clinical samples


title: BPNA Colon Tumour, Dabrafenib Treated, Rep2

description: Library name: VANP.RKF30.1b.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P6.A10


title: jc7477_HNF4a

description:
HNF4A
TB17.0297
clinical samples


title: BPNA Colon Tumour, Erlotinib Treated Rep3

description: Library name: VANP.RKF83.2d.BPNA.Col.T.D20.Erlotinib.12.09.2023.P5.H10


title: BPNA Colon Tumour, Dabrafenib Treated, Rep1

description: Library name: VANP.RKF29.1d.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P5.C6


title: BPN SI Tumour Rep30

description: Library name: BVBPN.RKAY8.5d.BPN.SI.T.01.05.2023.P5.E1

value: VilCreER BrafV600E/+ P53fl/fl Notch1Tg


title: BPN SI Tumour Rep29

description: Library name: BVBPN.RKAY8.4d.BPN.SI.T.01.05.2023.P6.B10


title: jc7476_FOXA1

description:
FOXA1
TB17.0297
clinical samples


title: jc7475_HNF4g

description:
HNF4G
TB17.0395
clinical samples


title: jc7474_HNF4a

description:
HNF4A
TB17.0395
clinical samples


title: jc7473_FOXA1

description:
FOXA1
TB17.0395
clinical samples


title: BPN SI Tumour Rep26

description: Library name: BVBPN.RKAY7.5b.BPN.SI.T.01.05.2023.P6.G7


title: BPN SI Tumour Rep27

description: Library name: BVBPN.RKAY8.1b.BPN.SI.T.01.05.2023.P6.F2


title: jc7472_HNF4g

description:
HNF4G
TB17.0804
clinical samples


title: jc7471_HNF4a

description:
HNF4A
TB17.0804
clinical samples


title: BPN SI Tumour Rep25

description: Library name: BVBPN.RKAY7.1c.BPN.SI.T.01.05.2023.P5.D11


title: BPN SI Tumour Rep24

description: Library name: BVBPN.RKAY7.1b.BPN.SI.T.01.05.2023.P7.B9


title: jc7470_FOXA1

description:
FOXA1
TB17.0804
clinical samples


title: BPNA Colon Tumour, Dabrafenib Treated, Rep4

description: Library name: VANP.RKF32.1g.BPNA.Col.T.D20.Dabrafenib.12.09.2023.P2.E9


title: jc7469_HNF4g

description:
HNF4G
TB17.1768
clinical samples


title: BPN SI Tumour Rep23

description: Library name: BVBPN.RKAY6.1c.BPN.SI.T.01.05.2023.P2.E12


title: BPN SI Tumour Rep21

description: Library name: BVBPN.RKAY12.1b.BPN.SI.T.01.05.2023.P7.A7


title: jc7468_HNF4a

description:
HNF4A
TB17.1768
clinical samples


title: BPN SI Tumour Rep22

description: Library name: BVBPN.RKAY12.3c.BPN.SI.T.01.05.2023.P5.G4


title: HPAFII-HNF4G KO rep 4

description: HPAFII-HNF4G KO

data_processing:
Reads were mapped to hg38 or mm10 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library.
The peaks were called with MACS2, version 2.1.1.20160309, using following parameters:  -g hs -f BAM --nomodel --shift -100 --extsize 200.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Assembly: GRCh38,GRCm38
Supplementary files format and content: bed/text

source_name: HPAF-II

growth_protocol: HPAF-II cells were grown in MEM 10% FBS, Sodium pyruvate. KPC cells were grown in DMEM +10% FCS

extract_protocol:
Omni ATAC-seq protocol was performed from Corces et al., 2017, Nature Methods. Transposase and buffers were purchased from Illumina Nextera kits.
DNA was prepared for Illumina sequencing on the NovaSeq 6000.

treatment_protocol: Untreated or CRISPR pertubation

value: HPAF-II

value: Pancreatic cancer cells

value: KO


title: jc7464_FOXA1

description:
FOXA1
TB17.0277
clinical samples

value: Pancreatic adenocarcinoma

value: untreated


title: BPN SI Tumour Rep16

description: Library name: VBPNOT.RKV37.1c.BPN.SI.T.01.05.2023.P5.H8


title: jc7467_FOXA1

description:
FOXA1
TB17.1768
clinical samples


title: jc7466_HNF4g

description:
HNF4G
TB17.0277
clinical samples


title: BPN SI Tumour Rep15

description: Library name: VBPNOT.RKV37.1a.BPN.SI.T.01.05.2023.P4.F4


title: BPN SI Tumour Rep28

description: Library name: BVBPN.RKAY8.1h.BPN.SI.T.01.05.2023.P2.F10


title: BPN SI Tumour Rep20

description: Library name: BVBPN.RKAY11.1g.BPN.SI.T.01.05.2023.P7.G3


title: BPN SI Tumour Rep19

description: Library name: BVBPN.RKAY10.1f.BPN.SI.T.01.05.2023.P6.H12


title: BPN SI Tumour Rep14

description: Library name: VBPNOT.RKV31.1e.BPN.SI.T.01.05.2023.P1.D7


title: BPN SI Tumour Rep17

description: Library name: VBPNOT.RKV39.3c.BPN.SI.T.01.05.2023.P6.F7


title: BPN SI Tumour Rep18

description: Library name: VBPNOT.RKV60.2b.BPN.SI.T.01.05.2023.P4.B7


title: HPAFII-Cas-9 rep 4

description: HPAFII-Control


title: BPN SI Tumour Rep13

description: Library name: VBPNOT.RKV8.3g.BPN.SI.T.01.05.2023.P5.H11


title: jc7465_HNF4a

description:
HNF4A
TB17.0277
clinical samples


title: HPAFII-Cas-9 rep 2

description: HPAFII-Control


title: HPAFII-Cas-9 rep 3

description: HPAFII-Control


title: HPAFII-Cas-9 rep 1

description: HPAFII-Control


title: ABI122

type: genomic

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
minfi
normalized Average Beta (ssNoob)

label: Cy5 and Cy3

source_name: Adolescent Brain Imaging

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the prepIT®•L2P reagent (DNA Genotek).

value: saliva

tag: gender

value: male

tag: age

tag: group

value: child maltreatment

tag: nationality

value: Japanese


title: HPAFII-HNF4G KO rep 2

description: HPAFII-HNF4G KO

tag: tissue

tag: cell line


title: ABI120

value: female


title: ABI123

value: typically developing


title: BPN SI Tumour Rep6

description: Library name: VBPNOT.RKV21.4e.BPN.SI.T.01.05.2023.P5.E2

value: Small Intestine

value: Tumour

value: Male

tag: genotype

value: 2mg intraperitoneal injection of Tamoxifen


title: BPN SI Tumour Rep12

description: Library name: VBPNOT.RKV8.3d.BPN.SI.T.01.05.2023.P6.H4

value: Female

tag: treatment


title: HPAFII-HNF4G KO rep 1

description: HPAFII-HNF4G KO

tag: cell type


title: HPAFII-HNF4G KO rep 3

description: HPAFII-HNF4G KO


title: BPN SI Tumour Rep11

description: Library name: VBPNOT.RKV7.2a.BPN.SI.T.01.05.2023.P5.F12

value: VilCreER BrafV600E/+ P53fl/fl Notch1Tg


title: ABI115


title: BPN SI Tumour Rep9

description: Library name: VBPNOT.RKV5.4g.BPN.SI.T.01.05.2023.P2.G7


title: BPN SI Tumour Rep10

description: Library name: VBPNOT.RKV5.5a.BPN.SI.T.01.05.2023.P7.B4


title: ABI121


title: BPN SI Tumour Rep2

description: Library name: VBPNBN.RKAX31.4i.BPN.SI.T.01.05.2023.P1.A11


title: ABI114


title: BPBCL SI Tumour Vehicle Rep7

description: Library name: VBPNBN.RKAX55.4f.BP9.9l.SI.T.Signs.HPMC.Tween.Vehicle.12.09.2023.P1.F12

value: VilCreER BrafV600E/+ P53fl/fl Bcl9fl/fl Bcl9lfl/fl

value: HPMC-Tween-Vehicle

value: Signs


title: ABI113


title: ABI112


title: BPN SI Tumour Rep7

description: Library name: VBPNOT.RKV29.1a.BPN.SI.T.01.05.2023.P8.C5


title: ABI119


title: BPN SI Tumour Rep5

description: Library name: VBPNOT.RKV21.4c.BPN.SI.T.01.05.2023.P7.D1


title: BPN SI Tumour Rep4

description: Library name: VBPNOT.RKV21.4b.BPN.SI.T.01.05.2023.P6.D5


title: ABI118


title: ABI116


title: ABI117


title: BPN SI Tumour Rep1

description: Library name: VBPNBN.RKAX27.1d.BPN.SI.T.01.05.2023.P1.C5


title: BPN SI Tumour Rep3

description: Library name: VBPNOT.RKV20.2d.BPN.SI.T.01.05.2023.P2.F4


title: ABI110


title: BPN SI Tumour Rep8

description: Library name: VBPNOT.RKV5.2c.BPN.SI.T.01.05.2023.P5.H12


title: ABI108


title: BPBCL SI Tumour Vehicle Rep6

description: Library name: VBPNBN.RKAX55.4a.BP9.9l.SI.T.Signs.HPMC.Tween.Vehicle.12.09.2023.P3.A1


title: BPBCL SI Tumour Vehicle Rep1

description: Library name: VBPNBN.RKAX48.4a.BP9.9l.SI.T.Signs.HPMC.Tween.Vehicle.12.09.2023.P5.G4


title: BPBCL SI Tumour Vehicle Rep5

description: Library name: VBPNBN.RKAX54.5c.BP9.9l.SI.T3.Signs.HPMC.Tween.Vehicle.12.09.2023.P3.A8


title: ABI111


title: ABI109


title: BPBCL SI Tumour Vehicle Rep3

description: Library name: VBPNBN.RKAX54.1b.BP9.9l.SI.T.Signs.HPMC.Tween.Vehicle.12.09.2023.P3.E5


title: BPBCL SI Tumour Vehicle Rep2

description: Library name: VBPNBN.RKAX48.4d.BP9.9l.SI.T.Signs.HPMC.Tween.Vehicle.12.09.2023.P6.D2


title: BPBCL SI Tumour Vehicle Rep4

description: Library name: VBPNBN.RKAX54.5c.BP9.9l.SI.T2.Signs.HPMC.Tween.Vehicle.12.09.2023.P4.H4


title: ABI106


title: ABI107


title: BPBCL SI Tumour, Dabrafenib-Erlotinib Treated Rep6

description: Library name: VBPNBN.RKAX55.3d.BP9.9l.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P4.F9

value: Dabrafenib-Erlotinib


title: BPBCL SI Tumour, Dabrafenib-Erlotinib Treated Rep5

description: Library name: VBPNBN.RKAX49.2g.BP9.9l.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P2.A4


title: ABI105


title: BPBCL SI Tumour, Dabrafenib-Erlotinib Treated Rep7

description: Library name: VBPNBN.RKAX61.1d.BP9.9l.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P5.D7


title: BPBCL SI Tumour, Dabrafenib-Erlotinib Treated Rep4

description: Library name: VBPNBN.RKAX48.6a.BP9.9l.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P2.G12


title: ABI104


title: ABI103


title: ABI100


title: ABI102


title: BPBCL SI Tumour, Dabrafenib-Erlotinib Treated Rep2

description: Library name: VBPNBN.RKAX42.1b.BP.9.9l.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P2.H5


title: ABI101


title: BPBCL SI Tumour, Dabrafenib-Erlotinib Treated Rep1

description: Library name: VBPNBN.RKAX37.5a.BP.9.9l.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P6.B11


title: ABI099


title: BP SI Tumour Rep6

description: Library name: BVBPN.RKAY12.3i.BP.SI.T.01.05.2023.P5.F9

value: VilCreER BrafV600E/+ P53fl/fl


title: ABI097

value: saliva


title: ABI098

value: male


title: BP SI Tumour Rep5

description: Library name: BVBPN.RKAY12.2g.BP.SI.T.01.05.2023.P6.E12


title: BP SI Tumour Rep3

description: Library name: VBP.RKAF1.1b.BP.SI.T1.01.05.2023.P2.G6


title: BP SI Tumour Rep2

description: Library name: VBPNOT.RKV25.2c.BP.SI.T.01.05.2023.P5.G7


title: BPBCL SI Tumour, Dabrafenib-Erlotinib Treated Rep3

description: Library name: VBPNBN.RKAX42.1c.BP9.9l.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P5.A8


title: BP SI Tumour Rep4

description: Library name: VBP.RKAF1.1b.BP.SI.T2.01.05.2023.P5.B9


title: BP SI Tumour Rep1

description: Library name: VBPNBN.RKAX31.4c.BP.SI.T.01.05.2023.P1.B1


title: BP SI Tumour Vehicle Rep6

description: Library name: VBPNBN.RKAX59.1c.BP.SI.T5.Signs.HPMC.Tween.Vehicle.12.09.2023.P3.H6


title: ABI093


title: ABI094

value: child maltreatment


title: BP SI Tumour Vehicle Rep5

description: Library name: VBPNBN.RKAX59.1c.BP.SI.T2.Signs.HPMC.Tween.Vehicle.12.09.2023.P5.H2


title: ABI092

value: Japanese


title: ABI091

value: female


title: BP SI Tumour Vehicle Rep4

description: Library name: VBPNBN.RKAX57.4c.BP.SI.T2.Signs.HPMC.Tween.Vehicle.12.09.2023.P2.D9


title: ABI096


title: ABI090


title: ABI089

value: typically developing


title: ABI087


title: BP SI Tumour, Dabrafenib-Erlotinib Treated, Rep2

description: Library name: VBPNBN.RKAX47.3e.BP.SI.T2.Signs.Dabrafenib.Erlotinib.12.09.2023.P5.E4

value: Small Intestine


title: BP SI Tumour Vehicle Rep2

description: Library name: VBPNBN.RKAX57.4b.BP.SI.T.Signs.HPMC.Tween.Vehicle.12.09.2023.P5.F6

value: Tumour


title: ABI086


title: ABI085


title: ABI083


title: ABI084


title: BPA Colon Tumour Rep9

description: Library name: VANP.RKF80.2f.BAP.Col.T.01.05.2023.P3.B8

value: Colon

value: VilCreER BrafV600E/+ P53fl/fl ALK5fl/fl


title: BPA Colon Tumour Rep7

description: Library name: VANP.RKF48.6e.BAP.Col.T.01.05.2023.P6.G8

value: Female

value: 2mg intraperitoneal injection of Tamoxifen


title: BP SI Tumour, Dabrafenib-Erlotinib Treated, Rep1

description: Library name: VBPNBN.RKAX47.3e.BP.SI.T1.Signs.Dabrafenib.Erlotinib.12.09.2023.P1.E10


title: BPA Colon Tumour Rep10

description: Library name: VANP.RKF42.1a.BAP.Col.T.12.09.2023.P6.D10

value: Male

value: VilCreER BrafV600E/+ P53fl/fl Alk5fl/fl


title: BP SI Tumour, Dabrafenib-Erlotinib Treated, Rep3

description: Library name: VBPNBN.RKAX57.1b.BP.SI.T.Signs.Dabrafenib.Erlotinib.12.09.2023.P3.C10

value: Signs


title: BPA Colon Tumour Rep8

description: Library name: VANP.RKF48.6f.BAP.Col.T.01.05.2023.P4.E3


title: BPA Colon Tumour Rep6

description: Library name: VANP.RKF40.2a.BAP.Col.T.01.05.2023.P8.F11


title: ABI080


title: BP SI Tumour Vehicle Rep3

description: Library name: VBPNBN.RKAX57.4c.BP.SI.T1.Signs.HPMC.Tween.Vehicle.12.09.2023.P2.D6

value: HPMC-Tween-Vehicle


title: ABI081


title: ABI082


title: ABI078


title: BPA Colon Tumour Rep4

description: Library name: VANP.RKF39.2e.BAP.Col.T.01.05.2023.P7.B1


title: BP SI Tumour Vehicle Rep1

description: Library name: VBPNBN.RKAX53.3c.BP.SI.T.Signs.HPMC.Tween.Vehicle.12.09.2023.P2.A9

value: VilCreER BrafV600E/+ P53fl/fl


title: ABI079

value: saliva


title: ABI088

value: male


title: ABI077


title: BPA Colon Tumour Rep3

description: Library name: VANP.RKF11.3d.BAP.Col.T.01.05.2023.P6.F5


title: ABI076

value: child maltreatment


title: BPA Colon Tumour Rep2

description: Library name: VANP.RKF11.3c.BAP.Col.T.01.05.2023.P5.D4


title: ABI075

value: Japanese


title: BPA Colon Tumour Rep1

description: Library name: VANP.RKF11.2f.BAP.Col.T.01.05.2023.P5.E11


title: BA Colon Tumour Rep4

description: Library name: BVBALK.RAH36.1g.BA.Col.T.01.05.2023.P1.A10

value: VilCreER BrafV600E/+ Alk5fl/fl


title: ABI073

value: female


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_AGB1_Rep3

city: Chicago

first: SHASHANK

last: SRIVASTAVA

state: IL

address: 303 E Superior St, SQE Lab 7-400

institute: Northwestern University

description: Library name: SS9

data_processing:
Cleaned and filtered reads were aligned to hg38 using HISAT2.
Quantitative comparisons between conditions were carried out using the DESeq2 R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: DMEM, 5% CO2, 37°C

extract_protocol:
Qiagen Rneasy Kit
1ug total RNA was submitted to Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: 500nM dTAG47 or AGB1 treatment  for 24 hours before total RNA isolation

value: Epithelial


title: ABI074

value: typically developing


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_AGB1_Rep2

description: Library name: SS8


title: BA Colon Tumour Rep3

description: Library name: BVBALK.RAH31.2c.BA.Col.T.01.05.2023.P2.G9

value: Colon

value: Tumour


title: ABI072


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_AGB1_Rep1

description: Library name: SS7


title: BA Colon Tumour Rep2

description: Library name: VBAPT.RFAJ16.3b.BA.Col.T.01.05.2023.P1.A3


title: BA Colon Tumour Rep1

description: Library name: VBALKY.RAL1.1c.BA.Col.T1.01.05.2023.P1.H5


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_dTAG47_Rep2

description: Library name: SS5


title: BPA Colon Tumour Rep5

description: Library name: VANP.RKF6.6c.BAP.Col.T.01.05.2023.P1.E8

value: VilCreER BrafV600E/+ P53fl/fl ALK5fl/fl


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_dTAG47_Rep3

description: Library name: SS6


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_DMSO_Rep3

description: Library name: SS3

value: DMSO


title: ABI071


title: ABI070


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_dTAG47_Rep1

description: Library name: SS4


title: ABI095


title: AK Colon Tumour Rep9

description: Library name: BVAR.RZF70.2e.AK.Intra.Col.T.01.05.2023.P1.G1

value: Female

value: VilCreER Apcfl/fl KRasG12D/+

value: Intracolonic 2 x 70ul 4-OHT 100um in PBS


title: MCF7-ABER cells, SUVASO2M_2, repeat2

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

country: China

institute: yangzhou university

description: Library name: SUVASO2M_2, ATAC

data_processing:
Raw sequencing reads were processed using Trimmomatic (v0.39) to remove low-quality sequences and adapter contamination.And summarized with fastQC (v0.11.9)
Alignment to the human reference genome (GRCh38.p14_NCBI_GCF000001405.40) was performed using Bowtie2 (v2.4.5; parameters: -X 2000)
Use filtering for low-quality alignments (MAPQ=30), PCR duplicates (Picard) (version: 2.27.5; parameters: default), and mitochondrial contamination (samtools).
Peaks were called using macs2 (v2.2.9.1; parameters:–SPMR –nomodel –shift -75 –extsize 150) .
Bigwig files were produced for each sample using deeptools（v3.5.4.post1; parameters: default)
Assembly: hg38
Supplementary files format and content: bw; narrowpeak

source_name: breast cancer

growth_protocol: Phenored-free RPMI1640, 10% Charcoal Stripped FBS

extract_protocol:
MCF7-ABER cells were collected from cultures.Subsequently,follow the manufacturer's instructions to perform cell lysis, fragmentation, and DNA extraction of the fragmented products using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (cat.TD711).
ATAC-seq library preparation was performed using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (cat.TD711) according to the manufacturer instructions.

treatment_protocol: cells were treated with CtrASOM or SUVASO2M

value: breast cancer

value: breast cancer cells

value: WT


title: ABI069

value: saliva


title: MCF7-ABER cells, CtrASOM_2, repeat2

description: Library name: CtrASOM_2, ATAC

value: CtrASOM


title: MCF7-ABER cells, SUVASO2M_1, repeat1

description: Library name: SUVASO2M_1, ATAC


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_DMSO_Rep1

description: Library name: SS1


title: mRNA-Seq of HEK293T cells with ZNF207-FL and siZNF207, Replicate 2

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

institute: National Cancer Institute

description: Library name: 293T_FLAG_ZNF207_FL_siZNF207_Rep2

data_processing:
Raw FASTQ file reads were trimmed with Cutadapt tool and mapped with STAR aligner. Differential splicing analysis was performed using Whippet tool.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with a single sheet containing dPSI and probability values from differential splicing analysis with Whippet tool for all the alternative splicing events that are detected in the  siZNF207 rescue samples (e.g., siZNF207 KD sample and the sapmple with overexpression of ZNF207-FL in the siZNF207 KD background).

growth_protocol: HEK293 cells were maintained in Dulbecco’s Modified Eagle’s Medium (supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin).

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads.
Library construction was carried out following the TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: HEK293 Flp-In stable cell lines were transfected with siRNA targeting ZNF207 or a non-targeting control. Six hours post-transfection, doxycycline was added to induce ZNF207 expression. Forty-eight hours after transfection, the cells were harvested, and total RNA was extracted.

value: Human embryonic kidney cell line


title: AK Colon Tumour Rep7

description: Library name: BVAR.RZF62.2c.AK.Intra.Col.T.01.05.2023.P2.H12

value: Intracolonic 1 x 70ul 4-OHT 100um in PBS


title: AK Colon Tumour Rep8

description: Library name: BVAR.RZF63.3d.AK.Intra.Col.T.01.05.2023.P1.F4


title: ABI068

value: female

value: Japanese


title: MCF7-ABER cells, CtrASOM_1, repeat1

description: Library name: CtrASOM_1, ATAC


title: AK Colon Tumour Rep6

description: Library name: BVAR.RZF62.2b.AK.Intra.Col.T.01.05.2023.P7.A12


title: mRNA-Seq of HEK293T cells with ZNF207-FL and siZNF207, Replicate 1

description: Library name: 293T_FLAG_ZNF207_FL_siZNF207_Rep1


title: AK Colon Tumour Rep5

description: Library name: BVAR.RZF62.2a.AK.Intra.Col.T.01.05.2023.P1.F11


title: mRNA-Seq of HEK293T cells with ZNF207-FL and siNT, Replicate 2

description: Library name: 293T_FLAG_ZNF207_FL_siCTL_Rep2

value: siNT


title: mRNA-Seq of HEK293T cells with ZNF207-FL and siNT, Replicate 1

description: Library name: 293T_FLAG_ZNF207_FL_siCTL_Rep1


title: mRNA-Seq of HEK293T cells with EV and siZNF207, Replicate 2

description: Library name: 293T_FLAG_EV_siZNF207_Rep2


title: HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag_DMSO_Rep2

description: Library name: SS2

value: Epithelial


title: ABI067

value: child maltreatment


title: AK Colon Tumour Rep4

description: Library name: BVAR.RZF62.1b.AK.Intra.Col.T.01.05.2023.P4.C12

value: Colon

value: Tumour

value: Male


title: mRNA-Seq of HEK293T cells with EV and siNT, Replicate 2

description: Library name: 293T_FLAG_EV_siCTL_Rep2


title: mRNA-Seq of HEK293T cells with EV and siNT, Replicate 1

description: Library name: 293T_FLAG_EV_siCTL_Rep1


title: mRNA-Seq of HEK293T cells with EV and siZNF207, Replicate 1

description: Library name: 293T_FLAG_EV_siZNF207_Rep1


title: mRNA-Seq of HEK293T cells with siZNF207 - 3, Replicate 2

description: Library name: 293T_siZNF207_8_Rep2

data_processing:
Raw FASTQ file reads were trimmed with Cutadapt tool and mapped with STAR aligner. Differential splicing analysis was performed using Whippet tool.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with a single sheet containing dPSI and probability values from differential splicing analysis with Whippet tool for all the alternative splicing events that are commonly found across 3 independent siRNA treatments targeting ZNF207.

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads
Library construction was carried out following the TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: HEK293T cells were transfected with three independent siRNAs targeting ZNF207 or a non-targeting control. Forty-eight hours after transfection, the cells were harvested, and total RNA was extracted.

value: siZNF207 - 3


title: ABI065

value: male


title: AK Colon Tumour Rep3

description: Library name: BVAR.RZF62.1a.AK.Intra.Col.T.01.05.2023.P5.D6

value: VilCreER Apcfl/fl KRasG12D/+


title: ABI064

value: typically developing


title: mRNA-Seq of HEK293T cells with siZNF207 - 3, Replicate 1

description: Library name: 293T_siZNF207_8_Rep1


title: AK Colon Tumour Rep2

description: Library name: VARDR.RJO6.2f.AK.Intra.Col.T.01.05.2023.P6.H3

value: Female


title: ABI063

value: saliva


title: mRNA-Seq of HEK293T cells with siZNF207 - 2, Replicate 2

description: Library name: 293T_siZNF207_6_Rep2

value: siZNF207 - 2


title: AK Colon Tumour Rep1

description: Library name: VARDR.RJO5.2j.AK.Intra.Col.T.01.05.2023.P5.E10


title: ABI062


title: mRNA-Seq of HEK293T cells with siZNF207 - 1, Replicate 2

description: Library name: 293T_siZNF207_5_Rep2

value: Human embryonic kidney cell line

value: siZNF207 - 1


title: mRNA-Seq of HEK293T cells with siZNF207 - 2, Replicate 1

description: Library name: 293T_siZNF207_6_Rep1


title: ABI066

value: female


title: mRNA-Seq of HEK293T cells with siNT, Replicate 2

description: Library name: 293T_siNT_Rep2


title: Apc Colon Tumour Rep13

description: Library name: BVAR.RZF87.3e.A.Intra.Col.T.01.05.2023.P6.H10

value: VilCreER Apcfl/fl

value: Intracolonic 1 x 70ul 4-OHT 100um in PBS


title: ABI061

value: Japanese


title: Apc Colon Tumour Rep12

description: Library name: BVAR.RZF87.3a.A.Intra.Col.T.01.05.2023.P2.F9


title: mRNA-Seq for LMNA splicing reporter base editor screen in HAP1 cells, iC

description: Library name: BE_LMNA_RPE1_iC

data_processing:
(1) The sequencing reads (R1) from FASTQ files were analyzed with a custom bioinformatics pipeline, which involves STAR aligner tool for mapping to annotate CRISPR guides. Cell Barcode (CBC) and Unique Molecular Identifier (UMI) sequences were retrieved based on the adjacent plasmid vector regions and used to exclude PCR duplicates from the samples. Splicing outcomes were assessed from the R2 reads to link the phenotype to gene knockout perturbation to understand regulatory influence.
(2) PSI (Percent Spliced In) was calculated and analyzed across a particular CRASP-Seq library to identify gene hits in a specific sample with a 10% FDR intergenic control threshold. We also considered guide proportion of more than or equal to 0.5 for a gene to be a hit. Additionally, every sample was technically segregrated into two replicates based on single cell lineage (SCL) groups. Any hit consistently appearing in both the technical replicates were considered as valid regulators ensruring a stringent selection.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with separate sheets containing (1) Whole library guide dPSI values across all the splicing reporter screens, (2) All identified hits across all the reporters and their respective gene dPSI values, (3)-(7) Individual splicing reporter hits and their respective gene dPSI values.
Library strategy: CRISPR Screen

growth_protocol: HAP1, and RPE1 cells were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. HepG2 cells were cultured in Eagle's Minimum Essential Medium with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads
cDNA synthesis was performed using primers with Unique Molecular Identifier (UMI) sequences.  cDNAs were PCR amplified using illumina sequencing indexes such as i7,P7,i5, and P5 for paired-end sequencing. Next-generation sequencing was performed on an Illumina NovaSeq 6000 platform (200 cycles kit) except for LMNA Base Editor screens which were performed on an Illumina NovaSeq X Plus platform.

treatment_protocol: For the SRSF7 CRASP-Seq screens, cells were treated with 100 µg/mL cycloheximide four hours before cell harvesting and RNA extraction.

value: Near-haploid cell line derived from KBM-7 human CML cell line

value: UNT


title: ABI059


title: ABI060

value: child maltreatment


title: mRNA-Seq of HEK293T cells with siZNF207 - 1, Replicate 1

description: Library name: 293T_siZNF207_5_Rep1


title: mRNA-Seq of HEK293T cells with siNT, Replicate 1

description: Library name: 293T_siNT_Rep1

value: siNT


title: Apc Colon Tumour Rep11

description: Library name: BVAR.RZF84.2b.A.Intra.Col.T.01.05.2023.P7.F2

value: Colon

value: Tumour


title: Apc Colon Tumour Rep10

description: Library name: BVAR.RZF82.3a.A.Intra.Col.T.01.05.2023.P4.C6

value: Male


title: ABI058

value: male

value: typically developing


title: MONO3,5_CO1,6

city: Zurich

first: Magdalini

last: Kanari

address: Lengstrasse 30

department: Oncology

country: Switzerland

institute: University Children's Hospital Zurich

description: Library name: mono3

data_processing:
Cell Ranger multi (v7.1, 10x Genomics) as used to demultiplex, align the raw data and to generate the count matrix
Assembly: GRCh38.p13
Supplementary files format and content: Tab separated values files and matrix files

source_name: mesenchymal stromal cells, human umbilical vein endothelial cells, acute lymphoblastic leukemia cells

extract_protocol:
Enzymatic digestion of the hydrogel for extraction of cellular contents. Cocutures and their respecitve single cell controls were used. Samples were fixed based on the manufacturer's protocol for fixed scRNA-seq.
Samples were multiplexed and pooled to a total of 10000 cells per run. Then, they were loaded and sequenced with the use of an Illumina platform. The standard library protocol for 10x genomics single cell RNA sequencing for fixed cells was followed based on the manufacturer’s instructions


title: CO4,5_MONO4,6

description: Library name: co4

value: mesenchymal stromal cells, human umbilical vein endothelial cells, acute lymphoblastic leukemia cells


title: MSC-HUVEC_CO2,3_MONO2

description: Library name: MSC-HUVEC


title: ABI057

value: saliva


title: MSC_HUVEC_2D_MONO1

description: Library name: MSC


title: HCC827-3

city: Shenyang

first: sihong

last: chen

address: Wenhua Road

institute: Shenyang Pharmaceutical University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters.
The clean reads were separately aligned to GRCh38.p14 with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg19
Supplementary files format and content: gene_FPKM.txt

source_name: lung

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. The total amount of RNA required for a single library construction is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is ≥1.8, and OD260/230 is ≥1.0.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacture's protocols.

value: lung

value: Human non-small cell lung cancer cells


title: Apc Colon Tumour Rep8

description: Library name: BVAR.RZF71.1a.A.Intra.Col.T.01.05.2023.P3.F6


title: HCC827-2


title: Apc Colon Tumour Rep7

description: Library name: BVAR.RZF68.3a.A.Intra.Col.T.01.05.2023.P4.D2


title: ABI056

value: female


title: HCC827-1


title: KOAP2XII5,HDAC3,biol rep 3

city: wuhan

first: xue

last: lilan

state: 请选择...

address: shizishan

institute: huazhong agriculture university

data_processing:
Raw sequencing data were initially filtered using fastp (version 0.23.1) to remove low-quality reads and trim adaptor-contaminated sequences
Clean reads were mapped to the T. gondii reference genome (TGME49) using Bowtie2 (version 2.2.6) with default parameters
RSeQC (version 2.6) was used for read distribution analysis, and insert lengths were calculated using Picard’s Collect Insert Size Metrics tool (version 2.8.2).
DeepTools (version 2.4.1) was used to visualize read distribution upstream and downstream of transcription start sites (TSS).
MACS2 (version 2.2.7.1) was used for peak calling, and bedtools (version 2.30.0) for peak annotation and distribution analysis
Assembly: T. gondii reference genome (TGME49)
Supplementary files format and content: bw, sortedByCoord.out.bam
Library strategy: CUT&Tag

organism: Toxoplasma gondii

source_name: ME49 delta_XII-5

growth_protocol: ME49 and ME49ΔXII-5  were cultured in human foreskin fibroblasts (HFF), in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma-Aldrich, USA), supplemented with 2% heat-inactivated fetal bovine serum (FBS) (Gibco, USA), 1% penicillin-streptomycin, and 5 mM L-glutamine.

extract_protocol:
Intracellular parasites were released by needle passage and purified through filtration with 3 μm pore-size membranes. Approximately 5 x 10⁶ tachyzoites were collected and processed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China), following the manufacturer’s instructions.
The resulting DNA was amplified for library construction using the TD202 TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China). The libraries were enriched, quantified, and sequenced on a NovaSeq 6000 sequencer (Illumina) using the PE150 model.

tag: strain

value: ME49 delta_XII-5

tag: chip antibody

value: rabbit anti-TgHDAC3(generated by immunizing rabbit with the synthetic peptide sequence 'CPYRIRRKDYANDFE' conjugated to KLH)


title: ABI055

value: Japanese


title: Apc Colon Tumour Rep6

description: Library name: BVAR.RZF47.3e.A.Intra.Col.T.01.05.2023.P6.D10

value: Female

value: VilCreER Apcfl/fl

value: Intracolonic 1 x 70ul 4-OHT 100um in PBS


title: ABI054

value: child maltreatment


title: mRNA-Seq for LMNA splicing reporter base editor screen in HAP1 cells, iA

description: Library name: BE_LMNA_HAP1_iA

value: Near-haploid cell line derived from KBM-7 human CML cell line

value: UNT


title: KOAP2XII5,HDAC3,biol rep 2


title: HCC827_Er-2


title: HCC827_Er-1


title: HCC827_Er-3


title: ABI053


title: Apc Colon Tumour Rep5

description: Library name: VELP.RLAF16.2g.A.Intra.Col.T.01.05.2023.P3.C1

value: Colon

value: Tumour


title: Apc Colon Tumour Rep4

description: Library name: VELP.RLAF16.2f.A.Intra.Col.T.01.05.2023.P3.B10


title: Apc Colon Tumour Rep3

description: Library name: VELP.RLAF16.2a.A.Intra.Col.T.01.05.2023.P2.D11

value: Male


title: UT,HDAC3,biol rep 3


title: Apc Colon Tumour Rep9

description: Library name: BVAR.RZF82.2b.A.Intra.Col.T.01.05.2023.P4.C10


title: ABI051

value: male

value: typically developing


title: Apc Colon Tumour Rep2

description: Library name: VARSDH.REAE24.4i.A.Intra.Col.T.01.05.2023.P3.G4


title: UT,HDAC3,biol rep 1


title: xh3k9me2_1051

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

description: Library name: h3k9me2_1051

data_processing:
Read trimming (trimmomatic – for short reads, and porechop + nanofilt – for long reads
short read alignment (using hisat2 on RNA-seq reads, and bowtie2 – for ChIP-seq reads)
counting of exon-spanning reads with featureCounts (for RNA-seq)
calling enriched genomic regions with MACS2 (for ChIP-seq)
de novo genomic assembly with Flye (for long Nanopore reads)
Supplementary files format and content: featureCounts expression matrix (RNA-seq), MACS2-called peaks in broad mode (ChIP-seq)

organism: Drosophila virilis

source_name: ovary

extract_protocol:
Females of the 101 and 1051.47 strains were collected for DNA extraction and aged for 10-15 days. Genomic DNA was isolated from thirty pairs of ovaries using high-salt denaturing buffer containing 100 mM Tris-HCl (pH = 8), 10 mM EDTA (pH = 8), 350 mM NaCl, 2% SDS, and 7 M Urea following phenol-chloroform extraction. Before sequencing, we performed a size selection of high molecular weight DNA by depleting short DNA fragments below 10 kb using the Short Read Eliminator Kit (Circulomics, USA)
The preparation of DNA libraries for sequencing was carried out using the 1D ligation SQK-LSK109 kit (Oxford Nanopore Technologies (ONT), UK), by the recommended protocol from ONT. Sequencing was performed on a flow cell FLO-MIN-106D r9.4 (ONT, UK). The result was an average of 9.5 billion bases sequenced, with a median length of sequenced fragments from 20 to 40 kb for different libraries.

value: ovary


title: SD rat1, Right  Ear skin,OE-Fgf7

city: shanghai

first: Xinhua

middle: hong

last: Liao

state: shanghai

address: No. 333 Nanchen Road

institute: shanghai university

description:
Library name: Sample3
Column name in raw_counts_All Samples.txt: Treated1

data_processing:
RNA-seq data were normalized as FPKM. DEGs were identified, and GO and KKEGG enrichment analyses were performed using the ClusterProfiler package.
Assembly: Rnor_6.0 (rn6）
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Ear skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA w as used for the construction of sequencing libraries.
Total RNA was extracted from samples using standard methods, and RNA integrity was assessed with Agilent Bioanalyzer. Poly(A)+ mRNA was enriched using oligo(dT) beads (or rRNA was depleted, depending on experiment). The purified RNA was fragmented and reverse-transcribed to cDNA. After end repair, A-tailing, and adaptor ligation, cDNA fragments were PCR-amplified to generate sequencing libraries. The final libraries were quality-checked and sequenced on the Illumina NovaSeq X Plus platform.

value: Ear skin

value: Fgf7 overexpression


title: SD rat2, Left Ear skin,Control

description:
Library name: Sample2
Column name in raw_counts_All Samples.txt: Ctrl2

value: wt

value: AAV-control


title: Apc Colon Tumour Rep1

description: Library name: VARSDH.REAE23.4e.A.Intra.Col.T.01.05.2023.P4.B10


title: ABI049

value: saliva

value: female

value: Japanese


title: SD rat2, Right  Ear skin,OE-Fgf7

description:
Library name: Sample4
Column name in raw_counts_All Samples.txt: Treated1


title: ABI050


title: SD rat1, Left Ear skin,Control

description:
Library name: Sample1
Column name in raw_counts_All Samples.txt: Ctrl1


title: ABI048


title: KOAP2XII5,HDAC3,biol rep 1

value: ME49 delta_XII-5

value: rabbit anti-TgHDAC3(generated by immunizing rabbit with the synthetic peptide sequence 'CPYRIRRKDYANDFE' conjugated to KLH)


title: ABI052

value: child maltreatment


title: UT,HDAC3,biol rep 2


title: ABI046


title: ABI045


title: h+ cft1-L249Q biol_rep_3

first: Ana

middle: M

last: Sanchez

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: cft1_L249Q_biol_rep_3

data_processing:
Base calls from Illumina NovaSeq X Plus (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2-2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicated were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source 'ensembl')
Differential expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: Haploid

growth_protocol: Log phase cultures grown at 30˚C in YES medium

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the NEB Ultra II Directional RNA library prep plus PolyA isolation module kit according to manufacturer's protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq X-Plus instrument at the Weill Cornell Medicine Genome Core Facility (in New York).

value: Haploid

tag: growth condition

value: log phase culture, YES (Yeast Extract with Supplements)

tag: developmental stage

value: haploid


title: h+ cft1-L249Q biol_rep_1

description: Library name: cft1_L249Q_biol_rep_1


title: xh3k9_1051_rep2

description: Library name: h3k9_1051_rep2


title: ABI044


title: xinput_101N_rep2

description: Library name: input_101N_rep2


title: xinput_1051_rep2

description: Library name: input_1051_rep2


title: h+ cft1-L249Q biol_rep_2

description: Library name: cft1_L249Q_biol_rep_2


title: h- pla1-Y86L::kanMX biol_rep_3

description: Library name: pla1_Y86L_biol_rep_3


title: GL261, PT2385, mixed pooled of mice 7 and 8

city: Lausanne

first: Felipe

last: Espinoza

address: Rue du Bugnon 7

department: Department of Biomedical Sciences

institute: University of Lausanne

description: Library name: Sample3_07_08

data_processing:
Raw count matrices were generated using CellRanger 2.2.0 (10x Genomics) with a custom reference package based on mouse reference genome GRCm39 and GENCODE63 gene models. Individual count tables were merged using CellRanger aggr to reduce batch effects. A total of 40,144 cells from all merged samples were analyzed. The average of the mean reads per cell across all gene expression libraries was 41,118, with an average of the median genes per cell of 3083, calculated by Cell Ranger. All scRNAseq data were merged, and the analysis was performed in R using the Seurat v5 package. Data was filtered for potential empty droplets, cell aggregates, and cells with > 2500 or < 200 transcripts were excluded from the analysis. Additionally, low-quality/dying cells with > 5% of transcripts corresponding to mitochondrial genes were excluded. Raw counts were normalized in Seurat by a global-scaling normalization and log-transform method (LogNormalize) that normalizes the gene expression measurements for each cell by the total expression and multiplies it by a scale factor (10,000) and log-transforms the result. High-variable genes were detected in Seurat, and the data were scaled by a linear transformation. Subsequently, the highly variable genes were used for unsupervised dimensionality reduction. Dimensionality was determined using a heuristic method that ranks the principal components using the ElbowPlot function. Differential expression analysis between cell clusters was performed using the Wilcoxon rank-sum test through the Seurat FindMarkers function. Clustering was visualized in UMAP two-dimensional scatter plots using the Seurat v5 package.
Assembly: GRCm39
Supplementary files format and content: tab-separated values files and matrix files

source_name: tumor-bearing brain left hemisphere

extract_protocol:
Tumors were harvested at day 21 p.i. and tumor infiltrating leukocytes were sorted (CD45+ DRAQ7-). From four individual mice from each treatment group, cells were suspended in Stain buffer (BD Pharmigen) at a density of 1 million per 100μL and stained with anti-mouse CD16/CD32 Fc Block (BD Pharmigen) for 10 min. Next, an anti-mouse CD45 antibody (Clone 30-F11, BD Pharmigen) was added, and cells were incubated for 20 min at 4 °C, washed with PBS, and sorted in PBS 1% BSA. Sorting was performed on a MoFlo Astrios (Beckman Coulter). Directly after sorting, cell quantity and viability of CD45+DRAQ7- cells were measured, and two pools were prepared from each treatment group comprised of 5000 cells from each of two individual mice.
Each cell suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit according to manufacturer’s protocol. Library quantification and quality assessment was performed using a Qubit fluorometer and a Tapestation (DNA High sensitivity chip, Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode.

treatment_protocol: PT2385 (MedChem) was dissolved in 30% PEG400 (Merck), 10% ethanol (Merck), and 60% aqueous solution (0.5% Tween 80 (MedChem) and 0.5% methylcellulose (Sigma-Aldrich)). PT2385 was administered at 10 mg/kg every day and twice per day in half of the animals; the other half received vehicle. The drug was administered for 21 days from day seven post-implantation. Antibodies were purchased from Bio X Cell. αPD-1 (RPM1-14), αTIM-3 (B8.2C12), rat IgG2a isotype control (2A3), and rat IgG2b isotype control (HRPN) were diluted with sterile PBS and injected intraperitoneally (i.p.).

value: tumor-bearing brain left hemisphere

value: CD45+, DRAQ7- sorted cells

value: WT

tag: Sex

value: 8-9 weeks old


title: xinput_101N_rep1

description: Library name: input_101N_rep1

value: ovary


title: GL261, PT2385/ICB, mixed pooled of mice 15 and 16

description: Library name: Sample7_15_16

value: PT2385/ ICB (aPD-1, aTIM-3)


title: xinput_1051_rep1

description: Library name: input_1051_rep1


title: xh3k9_101N_rep2

description: Library name: h3k9_101N_rep2


title: h- pla1-Y86L::kanMX biol_rep_1

description: Library name: pla1_Y86L_biol_rep_1


title: ABI043

value: male

value: typically developing


title: GL261, PT2385, mixed pooled of mice 5 and 6

description: Library name: Sample2_05_06


title: h- pla1-Y86L::kanMX biol_rep_2

description: Library name: pla1_Y86L_biol_rep_2


title: ABI042

value: saliva


title: xh3k9_101N_rep1

description: Library name: h3k9_101N_rep1


title: GL261, PT2385/ICB, mixed pooled of mice 13 and 14

description: Library name: Sample6_13_14

value: female


title: GL261, untreated, mixed pooled of mice 1 and 2

description: Library name: Sample1_01_02

value: Untreated


title: h- ysh1-L74F asp1-WT::kanMX biol_rep_3

description: Library name: ysh1_L74F_biol_rep_3


title: ABI047

value: Japanese


title: T cells, WT, Allo stimulation-3

city: Milwaukee

first: Qiao

middle: cheng

last: Cheng

state: Wisconsin

institute: Medical College of Wisconsin

description: Library name: ReAl_WT3

data_processing:
The sequenced reads (raw reads) often contain low quality reads and adapters, which will affect the analysis quality. The raw reads were filtered as follows: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Assembly: Mouse mm10
Supplementary files format and content: raw_counts_All_Samples.txt

source_name: Spleen

growth_protocol: T cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using TRIZOL (invitrogen). 0.5ug of total RNA was used to construct sequence libraries.
First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: T cells were treated with anti-CD3 and anti-CD28 antibodies or allogeneic antigen presenting cells (APCs)

value: Spleen

value: T cells

value: Allo stimulation


title: ABI041


title: xh3k9_1051_rep1

description: Library name: h3k9_1051_rep1


title: GL261, ICB, mixed pooled of mice 9 and 10

description: Library name: Sample4_09_10

value: ICB (aPD-1, aTIM-3)


title: xsmallrna_9

description: Library name: smallrna_9


title: T cells, WT, Allo stimulation-2

description: Library name: ReAl_WT2


title: h- ysh1-L74F asp1-WT::kanMX biol_rep_2

description: Library name: ysh1_L74F_biol_rep_2

value: Haploid

value: log phase culture, YES (Yeast Extract with Supplements)

value: haploid


title: ABI040

value: child maltreatment


title: xsmallrna_160

description: Library name: smallrna_160


title: GL261, ICB, mixed pooled of mice 11 and 12

description: Library name: Sample5_11_12

value: tumor-bearing brain left hemisphere

value: CD45+, DRAQ7- sorted cells

value: WT

value: 8-9 weeks old


title: h- ysh1-L74F asp1-WT::kanMX biol_rep_1

description: Library name: ysh1_L74F_biol_rep_1


title: ABI039

value: male

value: typically developing


title: T cells, PERK-KO, Allo stimulation-3

description: Library name: ReAl_PK3

value: PERK-KO


title: xsmallrna_140

description: Library name: smallrna_140

value: ovary


title: h- pta1-T524M asp1-WT::kanMX biol_rep_3

description: Library name: pta1_T524M_biol_rep_3


title: ABI038

value: saliva

value: Japanese


title: T cells, PERK-KO, Allo stimulation-2

description: Library name: ReAl_PK2

value: Spleen

value: T cells


title: xsmallrna_1051

description: Library name: smallrna_1051


title: xsmallrna_101N

description: Library name: smallrna_101N


title: xrna_160_rep2

description: Library name: rna_160_rep2


title: T cells, WT, Ploy stimulation-3

description: Library name: Poly_WT3

value: Poly stimulation


title: h- pfs2-V180F asp1-WT::kanMX biol_rep_3

description: Library name: pfs2_V180F_biol_rep_3

value: Haploid


title: h- pta1-T524M asp1-WT::kanMX biol_rep_2

description: Library name: pta1_T524M_biol_rep_2

value: log phase culture, YES (Yeast Extract with Supplements)


title: ABI035


title: ABI036

value: female


title: h- pta1-T524M asp1-WT::kanMX biol_rep_1

description: Library name: pta1_T524M_biol_rep_1

value: haploid


title: xrna_160_rep1

description: Library name: rna_160_rep1


title: T cells, WT, Ploy stimulation-2

description: Library name: Poly_WT2


title: xrna_1051_rep2

description: Library name: rna_1051_rep2


title: T cells, WT, Ploy stimulation-1

description: Library name: Poly_WT1


title: h- pfs2-V180F asp1-WT::kanMX biol_rep_1

description: Library name: pfs2_V180F_biol_rep_1


title: ABI034


title: ABI033

value: child maltreatment


title: T cells, WT, Allo stimulation-1

description: Library name: ReAl_WT1

value: Allo stimulation


title: h- pfs2-V180F asp1-WT::kanMX biol_rep_2

description: Library name: pfs2_V180F_biol_rep_2


title: T cells, PERK-KO, Ploy stimulation-3

description: Library name: Poly_PK3


title: ABI032


title: xrna_101N_rep2

description: Library name: rna_101N_rep2


title: h- pfs2-E104A asp1-WT::kanMX biol_rep_3

description: Library name: pfs2_E104A_biol_rep_3


title: h- pfs2-E104A asp1-WT::kanMX biol_rep_2

description: Library name: pfs2_E104A_biol_rep_2


title: ABI031


title: xrna_101N_rep1

description: Library name: rna_101N_rep1


title: ABI037


title: T cells, PERK-KO, Allo stimulation-1

description: Library name: ReAl_PK1


title: T cells, PERK-KO, Ploy stimulation-1

description: Library name: Poly_PK1


title: h- pfs2-E104A asp1-WT::kanMX biol_rep_1

description: Library name: pfs2_E104A_biol_rep_1


title: ABI030


title: HEK293T-PRPS1-HA-dTAG, dTAG47, rep2

description: Library name: PRPS1_REP2

data_processing:
Data was processed using the nf-core/atacseq pipeline (https://nf-co.re/atacseq/2.1.2)
Base calls were performed using bcl2fastq2.20 for HiSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with TrimGalore and then reads were aligned to GRCh38 with BWA
Bigwig files were produced using bedtools
Assembly: GRCh38
Supplementary files format and content: bigWig for each sample

source_name: NA, cell line used

extract_protocol:
Transposition was conducted with Tagment DNA Enzyme and Buffer Kit from Illumina and purified using Qiagen MinElute Reaction Cleanup Kit
ATAC seq. Transposed DNA was PCR amplified and library prepped using Nextera adaptors from Illumina

treatment_protocol: DMSO or 500nM dTG47 treatment for 24 hours, cells collected for ATAC seq

value: NA, cell line used

value: epithelial


title: HEK293T-PRPS1-HA-dTAG, dTAG47, rep1

description: Library name: PRPS1_REP1


title: h- msi2-G252E asp1-WT::kanMX biol_rep_2

description: Library name: msi2_G252E_biol_rep_2


title: ABI029


title: ABI028

value: male