title: IaD_1

description:
Library name: Sample 35
Iα deletion in non-coding IgH Sμ-Sα deletion cells

value: IaDel


title: testicular cells, low chorus at 30 hrs, biol rep 6

status: Public on Mar 14 2026

type: SRA

city: Ottawa

first: Jeffrey

last: Ethier

state: Ontario

address: 75 Laurier Ave E

department: Biology

country: Canada

institute: University of Ottawa

description: Library name: L_30_6

library_source: transcriptomic

data_processing:
De novo assembly was produced by LC Sciences. Cutadapt 45 and custom Perl scripts (https://www.perl.org/about.html) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was then verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
De novo assembly of the transcriptome was performed with Trinity 2.4.0 46. Trinity groups transcripts into clusters, loosely defined as a ‘gene’, based on shared sequence content.
Assembly: De novo assembly
Supplementary files format and content: xlsx files include raw counts and TPM each all samples

molecule: total RNA

organism: Pseudacris maculata

source_name: testicular cells

extract_protocol:
total RNA was purified from the homogenates using NucleoZOL reagents with NucleoSpin RNA columns (Macherey-Nagel, Germany). RNA concentrations were measured with a Qubit 4 Fluorometer (Invitrogen™, Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity (RIN) was assessed using an Agilent 4150 TapeStation system (Agilent Technologies, Inc., Santa Clara, CA, USA).
RNA sequencing library was performed by LC Sciences Inc. (https://lcsciences.com, Houston, TX, USA) and was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

tag: tissue

value: testicular cells

tag: cell line

value: WT

tag: cell type

tag: genotype

tag: treatment

value: low chorus


title: IaD_3

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

country: China

institute: Peking University

description:
Library name: Sample 37
Iα deletion in non-coding IgH Sμ-Sα deletion cells

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
DNA was extracted overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using CSR-HTGTS-Seq (Dong et al., 2015)

treatment_protocol: CH12F3 cell lines were cultured in R15 medium and stimulated with anti-CD40+IL4+TGF-β for 72 hrs.

value: aCD40/IL4/TGFb stimulation


title: IaD_2

description:
Library name: Sample 36
Iα deletion in non-coding IgH Sμ-Sα deletion cells


title: SCR_1

type: RNA

city: Ube

first: MITSUKAI

last: FUJIMOTO

state: Yamaguchi

address: 1-1-1 Minami-Kogushi

department: Graduate School of Medicine

country: Japan

institute: Yamaguchi University

description: Gene expression data from MeWo cells treated with scrambled shRNA (SCR)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom S Array  human. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: Human melanoma MeWo cells

label_protocol: Biotinylated cDNA were prepared from 100 ng total RNA with WT PLUS Reagent Kit (Thermo Fisher).

growth_protocol: DMEM containing 10% fetal boviine serum at 37C

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: No

value: Human melanoma MeWo cells

value: SCR (Control)


title: Muscle, F1: CC037/TauUnc x CC019/TauUnc, male - rep3

city: Baltimore

first: Adam

last: Davidovich

state: Maryland

address: 855 N. Wolfe Street

country: USA

institute: Johns Hopkins University

description: Library name: 3719-106M

data_processing:
ONT reads were canonical and modified base (5mCG_5hmCG) called using the super high accuracy model of Dorado (v0.8.3).
Basecalled reads were aligned to the CC019 and CC037 reference genomes separately using MiniMap2 (v2.28) and reads with a MAPQ of < 20 were filtered.
Aligned reads were phased separately with CC019 and CC037 as the reference genomes using WhatsHap (v2.3) with SNPs between CC019 and CC037 identified via MUMmer4 (v4.0.0rc1).
Methylation data was extracted from the phased BAM files using the modkit (v0.4.1) pileup command with strain-specific reference genomes provided.
Assembly: CC019 and CC037 reference genomes from the Collaborative Cross Graphical Genome (v2.0).
Supplementary files format and content: Modkit bedMethyl file with phased CC019 allele-specific methylation information for each CpG in each sample (zero-based, half-open).
Supplementary files format and content: Modkit bedMethyl file with phased CC037 allele-specific methylation information for each CpG in each sample (zero-based, half-open).

source_name: Muscle

extract_protocol:
High molecular weight (HMW) DNA was extracted from ~35mg of flash-frozen right femoral muscle using the Nanobind PanDNA Kit (PacBio SKU 103-260-000) following to the manufacturer’s instructions. Homogenization was performed using the TissueRuptor II (Qiagen Cat. 9002755) at maximum speed for 10s.
DNA was sheared to 20-30kb. Libraries were prepared using Ligation Sequencing Kit LSK114 and sequenced on R10.4.1 flow cells.

value: Muscle

tag: strain

value: F1:CC037/TauUnc x CC019/TauUnc

tag: Sex

value: male

tag: age

value: 4 months


title: γ3IRD_1

description:
Library name: Sample 44
intergenic regions deletion between Cγ3 and Cμ  in Iα deletion cells


title: γ3Inv_1

description:
Library name: Sample 38
γ3 inversion to next to Cμ in Iα deletion cells


title: γ3_αInv_αInv _3

description:
Library name: Sample 34
α inversion in γ3-αInv cells


title: testicular cells, low chorus at 30 hrs, biol rep 4

description: Library name: L_30_4


title: testicular cells, low chorus at 30 hrs, biol rep 7

description: Library name: L_30_7


title: γ3_αInv_αInv _1

description:
Library name: Sample 32
α inversion in γ3-αInv cells


title: Muscle, F1: CC037/TauUnc x CC019/TauUnc, male - rep2

description: Library name: 3719-103M

value: 5 months


title: γ3_αInv_αInv _2

description:
Library name: Sample 33
α inversion in γ3-αInv cells


title: testicular cells, low chorus at 30 hrs, biol rep 5

description: Library name: L_30_5


title: SCR_2


title: γ1Inv_3

description:
Library name: Sample 31
γ1 inversion in  IaD cells


title: testicular cells, low chorus at 30 hrs, biol rep 2

description: Library name: L_30_2


title: Muscle, F1: CC019/TauUnc x CC037/TauUnc, male - rep3

description: Library name: 1937-111M

value: F1:CC019/TauUnc x CC037/TauUnc


title: Muscle, F1: CC037/TauUnc x CC019/TauUnc, male - rep1

description: Library name: 3719-102M


title: testicular cells, low chorus at 30 hrs, biol rep 3

description: Library name: L_30_3


title: Muscle, F1: CC019/TauUnc x CC037/TauUnc, male - rep2

description: Library name: 1937-110M


title: γ1Inv_1

description:
Library name: Sample 29
γ1 inversion in  IaD cells


title: IaD_6

description:
Library name: Sample 25
Iα deletion in non-coding IgH Sμ-Sα deletion cells


title: γ1Inv_2

description:
Library name: Sample 30
γ1 inversion in  IaD cells


title: testicular cells, low chorus at 24 hrs, biol rep 8

description: Library name: L_24_8


title: UP36 leaf RNA-seq at 48 h after Xoo inoculation, replicate 3

first: Muhammad

last: Sohaib Shafique

state: Beijing

address: 12-Zhongguancun south street, Haidian District

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

description: Library name: UP36_48h_rep3

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
Adapter sequences and low-quality bases were removed to obtain clean reads.
Clean reads were aligned to the rice reference genome using STAR aligner.
Aligned reads were processed to generate gene-level read counts for each sample.
Gene expression matrices were used for downstream differential expression
Assembly: Rice reference genome R498 (Oryza sativa indica).
Supplementary files format and content: The file normCounts_UP36.csv contains normalized gene expression values for all RNA-seq samples. Rows represent gene IDs and columns represent individual samples (UP36_0h and UP36_48h replicates).

organism: Oryza rufipogon

source_name: leaf

growth_protocol: Plants of Oryza rufipogon accession UP36 were grown under standard greenhouse conditions until the maximum tillering stage.

extract_protocol:
Total RNA was isolated from rice leaf tissues using RNAiso Plus reagent (Takara) following the manufacturer’s protocol. RNA quality was checked before library construction.
RNA-seq libraries were prepared from total RNA using a standard Illumina protocol and sequenced as paired-end reads.

treatment_protocol: Plants were inoculated with Xanthomonas oryzae pv. oryzae (PXO99A) using the leaf-clipping method. Leaf tissues were collected at 0 h and 48 h after inoculation.

value: leaf

value: Xoo PXO99A infection


title: IaD_5

description:
Library name: Sample 24
Iα deletion in non-coding IgH Sμ-Sα deletion cells


title: IaD_4

description:
Library name: Sample 23
Iα deletion in non-coding IgH Sμ-Sα deletion cells


title: Muscle, F1: CC019/TauUnc x CC037/TauUnc, female - rep3

description: Library name: 1937-106M

value: female


title: αInv_5

description:
Library name: Sample 22
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells

value: aInv


title: Muscle, F1: CC019/TauUnc x CC037/TauUnc, female - rep2

description: Library name: 1937-104M


title: testicular cells, low chorus at 24 hrs, biol rep 6

description: Library name: L_24_6


title: UP36 leaf RNA-seq at 48 h after Xoo inoculation, replicate 1

description: Library name: UP36_48h_rep1


title: UP36 leaf RNA-seq at 48 h after Xoo inoculation, replicate 2

description: Library name: UP36_48h_rep2


title: Muscle, F1: CC019/TauUnc x CC037/TauUnc, male - rep1

description: Library name: 1937-101M


title: testicular cells, low chorus at 24 hrs, biol rep 5

description: Library name: L_24_5


title: Muscle, F1: CC019/TauUnc x CC037/TauUnc, female - rep1

description: Library name: 1937-102M


title: γ2aInv_3

description:
Library name: Sample 28
γ2a inversion in  IaD cells


title: γ2aInv_1

description:
Library name: Sample 26
γ2a inversion in IaD cells


title: testicular cells, low chorus at 30 hrs, biol rep 1

description: Library name: L_30_1


title: testicular cells, low chorus at 24 hrs, biol rep 7

description: Library name: L_24_7


title: αInv_2

description:
Library name: Sample 19
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells


title: testicular cells, low chorus at 24 hrs, biol rep 4

description: Library name: L_24_4


title: Muscle, CC037/TauUnc, male - rep2

description: Library name: 37-107M

data_processing:
ONT reads were canonical and modified base (5mCG_5hmCG) called using the super high accuracy model of Dorado (v0.8.3).
Basecalled reads were aligned to the CC019 and CC037 reference genomes separately using MiniMap2 (v2.28) and reads with a MAPQ of < 20 were filtered.
Aligned reads were phased separately with CC019 and CC037 as the reference genomes using WhatsHap (v2.3) with SNPs between CC019 and CC037 identified via MUMmer4 (v4.0.0rc1).
Methylation data was extracted from the phased BAM files using the modkit (v0.4.1) pileup command with strain-specific reference genomes provided.
Assembly: CC019 and CC037 reference genomes from the Collaborative Cross Graphical Genome (v2.0).
Supplementary files format and content: Modkit bedMethyl file with phased CC037 allele-specific methylation information for each CpG in each sample (zero-based, half-open).

value: 3 months


title: αInv_3

description:
Library name: Sample 20
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells


title: Muscle, CC037/TauUnc, male - rep3

description: Library name: 37-110M


title: UP36 leaf RNA-seq at 0 h after Xoo inoculation, replicate 3

description: Library name: UP36_0h_rep3


title: testicular cells, low chorus at 24 hrs, biol rep 3

description: Library name: L_24_3

value: testicular cells


title: γ2aInv_2

description:
Library name: Sample 27
γ2a inversion in  IaD cells


title: UP36 leaf RNA-seq at 0 h after Xoo inoculation, replicate 2

description: Library name: UP36_0h_rep2


title: testicular cells, low chorus at 24 hrs, biol rep 2

description: Library name: L_24_2

value: WT


title: αInv_1

description:
Library name: Sample 18
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells


title: Muscle, CC037/TauUnc, female - rep3

description: Library name: 37-105M


title: UP36 leaf RNA-seq at 0 h after Xoo inoculation, replicate 1

description: Library name: UP36_0h_rep1


title: CH12F3PO_11

description:
Library name: Sample 17
non-coding IgH VH-3'BCEs deletion


title: testicular cells, high chorus at 30 hrs, biol rep 8

description: Library name: H_30_8

value: high chorus


title: αInv_4

description:
Library name: Sample 21
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells

value: aCD40/IL4/TGFb stimulation


title: Muscle, CC037/TauUnc, female - rep2

description: Library name: 37-104M


title: CH12F3PO_10

description:
Library name: Sample 16
non-coding IgH VH-3'BCEs deletion


title: CH12F3PO_9

description:
Library name: Sample 15
non-coding IgH VH-3'BCEs deletion


title: Muscle, CC037/TauUnc, female - rep1

description: Library name: 37-103M


title: testicular cells, low chorus at 24 hrs, biol rep 1

description: Library name: L_24_1

value: low chorus


title: COMBO_7d_3

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Library name: MR556

data_processing:
Raw fastq files were aligned using STAR v2.6.0. Raw counts were calculated by STAR, FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt files of raw counts and FPKM values

molecule: polyA RNA

source_name: Prostate

growth_protocol: C4-2B prostate cancer  cell line was maintained in RPMI culture media supplemented with 10% fetal bovine serum (FBS), penicillin sodium (100 U/mL), and streptomycin sulfate (100 µg/mL).

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA) following the manufacturer’s instructions.
RNA-seq libraries were prepared from 0.5 μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: C4-2B cells were treated with either DMSO as vehicle, VIC-1911 (0.1µM), olaparib (1uM) or both for either 2 days or 7 days, the sampales were collected post treatment for RNA analysis.

value: Prostate

value: Prostate cancer cell

value: Combination 7days


title: CH12F3PO_7

description:
Library name: Sample 13
non-coding IgH VH-3'BCEs deletion


title: testicular cells, high chorus at 30 hrs, biol rep 7

description: Library name: H_30_7


title: CH12F3PO_8

description:
Library name: Sample 14
non-coding IgH VH-3'BCEs deletion


title: Muscle, CC019/TauUnc, male - rep2

description: Library name: 19-105M

data_processing:
ONT reads were canonical and modified base (5mCG_5hmCG) called using the super high accuracy model of Dorado (v0.8.3).
Basecalled reads were aligned to the CC019 and CC037 reference genomes separately using MiniMap2 (v2.28) and reads with a MAPQ of < 20 were filtered.
Aligned reads were phased separately with CC019 and CC037 as the reference genomes using WhatsHap (v2.3) with SNPs between CC019 and CC037 identified via MUMmer4 (v4.0.0rc1).
Methylation data was extracted from the phased BAM files using the modkit (v0.4.1) pileup command with strain-specific reference genomes provided.
Assembly: CC019 and CC037 reference genomes from the Collaborative Cross Graphical Genome (v2.0).
Supplementary files format and content: Modkit bedMethyl file with phased CC019 allele-specific methylation information for each CpG in each sample (zero-based, half-open).

value: Muscle

value: male


title: Muscle, CC019/TauUnc, male - rep1

description: Library name: 19-104M

value: 4 months


title: OLA_7d_3

description: Library name: MR553

value: olaparib 1uM 7days


title: OLA_7d_2

description: Library name: MR552


title: γ3_αInv_6

description:
Library name: Sample 12
γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: Muscle, CC019/TauUnc, female - rep3

description: Library name: 19-103M


title: testicular cells, high chorus at 30 hrs, biol rep 5

description: Library name: H_30_5


title: testicular cells, high chorus at 30 hrs, biol rep 3

description: Library name: H_30_3


title: testicular cells, high chorus at 30 hrs, biol rep 6

description: Library name: H_30_6


title: testicular cells, high chorus at 30 hrs, biol rep 4

description: Library name: H_30_4


title: COMBO_7d_1

description: Library name: MR554


title: Muscle, CC019/TauUnc, female - rep2

description: Library name: 19-102M


title: OLA_7d_1

description: Library name: MR551


title: γ3_αInv_5

description:
Library name: Sample 11
γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: VIC_7d_3

description: Library name: MR544

value: VIC-1911 0.1uM 7days


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep12

data_processing:
ONT reads were basecalled using the super high accuracy model of Guppy (v6.1.2).
Basecalled reads were aligned to the CC019 and CC037 reference genomes separately using MiniMap2 (v2.24).
Aligned reads were phased separately with CC019 and CC037 as the reference genomes using WhatsHap (v1.6) with SNPs between CC019 and CC037 identified via MUMmer4 (v4.0.0rc1).
Methylation was called using the Nanopolish (v0.14.0) call-methylation function for all reads phased to the same genome independent of the reference genome used. Methylation was called in the reference genome to which the read was phased.
Phased methylation calls were converted to allele-specific methylation frequency values for each CpG using the Nanopolish calculate_methylation_frequency.py script.
Assembly: CC019 and CC037 reference genomes from the Collaborative Cross Graphical Genome (v2.0).
Supplementary files format and content: Tab-delimited file with phased CC019 allele-specific methylation frequency data for each CpG in each sample. Data includes CpG location (CC019 reference genome, zero-based), methylation call and frequency data, and local sequence group information (number of CpGs and sequence).
Supplementary files format and content: Tab-delimited file with phased CC037 allele-specific methylation frequency data for each CpG in each sample. Data includes CpG location (CC037 reference genome, zero-based), methylation call and frequency data, and local sequence group information (number of CpGs and sequence).
Supplementary files format and content: Guppy sequencing summary file containing read-level sequencing and basecalling information.
Library strategy: ONT sequencing (targeted - adaptive sampling)

source_name: Liver

extract_protocol:
High molecular weight (HMW) DNA was extracted from ~20mg of flash-frozen median liver lobe using the Nanobind Tissue Kit (PacBio SKU 102-302-100) following to the manufacturer’s instructions. Homogenization was performed using the TissueRuptor II (Qiagen Cat. 9002755) at maximum speed for 10s.
DNA was sheared to 20-30kb. Libraries were prepared using Ligation Sequencing Kit LSK110 and sequenced on R9.4.1 flow cells. Adaptive sampling was utilized to enrich for 84 target regions selected for additional characterization.

value: Liver

value: F2:CC019/TauUnc, CC037/TauUnc


title: Muscle, CC019/TauUnc, female - rep1

description: Library name: 19-101M

value: female


title: COMBO_7d_2

description: Library name: MR555


title: γ3_αInv_4

description:
Library name: Sample 10
γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: Muscle, CC037/TauUnc, male - rep1

description: Library name: 37-101M


title: VIC_7d_1

description: Library name: MR542


title: γ3_αInv_3

description:
Library name: Sample 9
γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: testicular cells, high chorus at 30 hrs, biol rep 2

description: Library name: H_30_2


title: γ3_αInv_1

description:
Library name: Sample 7
γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, female - rep7


title: γ3_αInv_2

description:
Library name: Sample 8
γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: testicular cells, high chorus at 30 hrs, biol rep 1

description: Library name: H_30_1


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, female - rep6


title: VEH_7d_3

description: Library name: MR541

value: DMSO 7days


title: VEH_7d_2

description: Library name: MR540


title: testicular cells, high chorus at 24 hrs, biol rep 7

description: Library name: H_24_7

value: testicular cells


title: CH12F3PO_6

description:
Library name: Sample 6
non-coding IgH VH-3'BCEs deletion


title: VEH_7d_1

description: Library name: MR539

value: WT


title: testicular cells, high chorus at 24 hrs, biol rep 8

description: Library name: H_24_8

value: high chorus


title: testicular cells, high chorus at 24 hrs, biol rep 6

description: Library name: H_24_6


title: VIC_7d_2

description: Library name: MR543


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, female - rep4


title: CH12F3PO_5

description:
Library name: Sample 5
non-coding IgH VH-3'BCEs deletion

value: aCD40/IL4/TGFb stimulation


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, female - rep5


title: VIC_2d_3

description: Library name: MR722

value: VIC-1911 0.1uM 2days


title: CH12F3PO_4

description:
Library name: Sample 4
non-coding IgH VH-3'BCEs deletion


title: testicular cells, high chorus at 24 hrs, biol rep 4

description: Library name: H_24_4


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep11


title: VIC_2d_2

description: Library name: MR721

value: Prostate


title: VIC_2d_1

description: Library name: MR720

value: Prostate cancer cell


title: CH12F3PO_3

description:
Library name: Sample 3
non-coding IgH VH-3'BCEs deletion


title: testicular cells, high chorus at 24 hrs, biol rep 3

description: Library name: H_24_3


title: testicular cells, high chorus at 24 hrs, biol rep 2

description: Library name: H_24_2


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep9


title: CH12F3PO_2

description:
Library name: Sample 2
non-coding IgH VH-3'BCEs deletion


title: VEH_2d_3

description: Library name: MR719

value: DMSO 2days


title: CH12F3PO_1

description:
Library name: Sample 1
non-coding IgH VH-3'BCEs deletion


title: VEH_2d_2

description: Library name: MR718


title: testicular cells, high chorus at 6 hrs, biol rep 8

description: Library name: H_6_8


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, female - rep3


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep8


title: VEH_2d_1

description: Library name: MR717


title: testicular cells, high chorus at 24 hrs, biol rep 1

description: Library name: H_24_1


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, female - rep2


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep10


title: Ig3_PS_Ia_sti_Rad21_2

description:
Library name: Sample8
Iγ3-PS-Iα-AID-/-

data_processing:
Reads were aligned using bowtie 2.4.4 with --very-sensitive flag
reads were quantified for specific loci using samtools 1.15.1
wig files were produced using bamCoverage 3.5.1 and normalized using RPKM
peak files were produced using MACS2 2.2.7.1
Assembly: mm9
Supplementary files format and content: wig files contain peak information for samples
Supplementary files format and content: peak files contain enriched peak information for samples using MACS2

source_name: CH12F3 murine lymphoma cells

extract_protocol:
10 million CH12F3 cell lines treated with  anti-CD40+IL4+TGF-β for 72 hrs. were collected and cross-linked with 1% formaldehyde, followed by quenching with glycine. The cross-linked cells were sonicated in sonication buffer (10 mM Tris pH 8.0, 0.25% SDS, 2 mM EDTA and protease inhibitors) to get chromatin fragments with the size between 200bp to 700bp. Equal amount of chromatin was used for immunoprecipitation with specific antibodies including anti-Rad21(abcam, ab992). After incubating the antibodies with sonicated chromatin at 4℃overnight, Protein A magnetic beads (ThermoFisher, 10002D) were added into the chromatin for another 2 hours to enrich antibody-bound chromatin. After 3 times of wash to remove unspecific binding of chromatin to the antibodies, the chromatin on beads was tagmented by Tn5 transponsase and eluted from beads.
Eluted ChIP DNA was subjected to constructing libraries using NEBNext High-Fidelity PCR Master Mix (New England Biolabs, M0541) and illumina index primers. The final ChIP-seq libraries were size-selected by SPRIselect beads (Beckman Coulter, B23318) and sequenced via paired-end 150bp sequencing on Novoseq 6000.

value: CH12F3 murine lymphoma cells

value: Sg3-Sa deletion while retaining partial Sg3 and Sa regions  in aInv cells

value: Rad21 antibody(ab992), aCD40/IL4/TGFb for 3 days


title: testicular cells, high chorus at 6 hrs, biol rep 7

description: Library name: H_6_7


title: testicular cells, high chorus at 24 hrs, biol rep 5

description: Library name: H_24_5


title: Ig3_PS_Ia_sti_Rad21_1

description:
Library name: Sample7
Iγ3-PS-Iα-AID-/-


title: testicular cells, high chorus at 6 hrs, biol rep 6

description: Library name: H_6_6


title: Ig3_PS_Ca_sti_Rad21_2

description:
Library name: Sample6
Iγ3-PS-Cα-AID-/-

value: Sg3-Sa deletion while retaining partial Sg3 and Sa regions in non-coding IgH VH-3'BCEs deletion cells


title: BT549 cells, siWFDC21P-2, rep3

city: Foshan

first: Yi

last: Wang

state: Guangdong

address: Guicheng Street

institute: Sun Yat-Sen University

description:
Library name: BT549si4
Column name in fpkm_siWFDC21P-2_ rep3.txt: BT549si4

data_processing:
Raw data (raw reads) of fastq format were processed through in-house Perl scripts.
Index of the reference genome was built using Bowtie2 v2.2.3.
Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample.
Assembly: Assembly: hg38
Supplementary files format and content: Matrix files include FPKM values for each Sample

growth_protocol: BT549 was grown in RPMI 1640 medium (Gibco) supplemented with 0.023 U/ml insulin and 10% fetal bovine serum (FBS, Vigonob). BT549 was cultured in the incubator at 37˚C with 5% CO2.

extract_protocol:
RNA was extracted by TRIzol (GK20008, GLPBIO), homogenized in chloroform, and then purified by isopropanol and ethanol. Total 1 ug RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard lllumina protocols.

treatment_protocol: BT549 (4*105) cells were seeded in 6-well plates, after 24 hours incubation, cells were transfected with 5 μl siRNA (10 μM; RiboBio, Guangzhou, China). 48 hours after transfection, cells were harvested to extract RNA.

value: breast cancer cell

value: WFDC21P kmockdown


title: BT549 cells, siWFDC21P-2, rep2

description:
Library name: BT549si3
Column name in fpkm_siWFDC21P-2_ rep2.txt: BT549si3


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep7

value: Liver

value: F2:CC019/TauUnc, CC037/TauUnc

value: male

value: 4 months


title: BT549 cells, siWFDC21P-2, rep1

description:
Library name: BT549si2
Column name in fpkm_siWFDC21P-2_ rep1.txt: BT549si2


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep6


title: Ig3_PS_Ca_sti_Rad21_1

description:
Library name: Sample5
Iγ3-PS-Cα-AID-/-


title: testicular cells, high chorus at 6 hrs, biol rep 5

description: Library name: H_6_5

value: testicular cells

value: WT


title: Ig3_FS_Ia_sti_Rad21_2

description:
Library name: Sample4
Iγ3-FS-Iα-AID-/-

value: Cg3-Ca deletion while retaining the full-length Sg3 and Sa regions in aInv cells


title: Ig3_FS_Ia_sti_Rad21_1

description:
Library name: Sample3
Iγ3-FS-Iα-AID-/-


title: testicular cells, high chorus at 6 hrs, biol rep 4

description: Library name: H_6_4

value: high chorus


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep5


title: BT549 cells, siWFDC21P-1, rep3

description:
Library name: BT549-siWFDC21P-1-2
Column name in fpkm_siWFDC21P-1_rep3.txt: BT549-siWFDC21P-1-2


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep4


title: testicular cells, high chorus at 6 hrs, biol rep 3

description: Library name: H_6_3


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep3


title: BT549 cells, siWFDC21P-1, rep2

description:
Library name: BT549-siWFDC21P-1
Column name in fpkm_siWFDC21P-1_ rep2.txt: BT549-siWFDC21P-1


title: Ig3_FS_Ca_sti_Rad21_2

description:
Library name: Sample2
Iγ3-FS-Cα-AID-/-

value: Cg3-Ia deletion while retaining the full-length Sg3 and Sa regions in non-coding IgH VH-3'BCEs deletion cells


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, female - rep1

value: female


title: BT549 cells, siWFDC21P-1, rep1

description:
Library name: BT549-siWFDC21P-1-a
Column name in fpkm_rep1.txt:BT549-siWFDC21P-1-a


title: testicular cells, high chorus at 6 hrs, biol rep 2

description: Library name: H_6_2


title: testicular cells, low chorus at 6 hrs, biol rep 8

description: Library name: L_6_8

value: low chorus


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep2


title: testicular cells, high chorus at 6 hrs, biol rep 1

description: Library name: H_6_1


title: BT549 cells, siNC, rep2

description:
Library name: BT549-siNC-b
Column name in fpkm_ siNC_rep2.txt: BT549-siNC-b


title: Setx del14 ABLki 45h rep3

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

description: Library name: S14KO2Rep3

data_processing:
Reads were trimmed using Alientrimmer, aligned using RNA STAR on mm10. Read counts were extracted using featurecounts.
Differential gene expression was assessed using DESeq2
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file with the normalized count matrix

source_name: v-Abl Pro B

growth_protocol: v-Abl pro-B cells were grown in RPMI-based medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere (5% CO2) at 37°C

extract_protocol:
RNA was harvested using Rneasy kit and column Dnase digestion. 1ug of total RNA was used was library preparation
directional library preparation by Novogene in march 2023

treatment_protocol: Cells were treated with 3 microM ABLki for 45h to undergo G1 phase arrest, Rag expression and rearrangement of the Igk endogenous locus

value: v-Abl Pro B


title: Liver, F2: CC019/TauUnc, CC037/TauUnc, male - rep1


title: SKBr3 cells, TVB-3166 250 nmol/L, refeed day 3, day 7, rep3

city: Salt

first: Javier

middle: Abel

last: Menendez

state: Girona

address: Dr Castany s/n. Parc hospitalari Marti i Julia

country: Spain

institute: Girona Biomedical Research Institute

description:
Library name: SKBr3_TVB-3166_rep3
colum name in Read_counts_ALL_samples: SKBr3_TVB3166_R3_Read_Count

data_processing:
BCL/cBCL (base call) binary files are converted into FASTQ files using bcl2fastq
Trimmed reads are mapped to reference genome with HISAT2
Stringtie was used for transcript assembly
read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes read counts for each sample

extract_protocol:
Total RNA was extracted from cells using the NucleoSpin RNA Plus kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit acording to standard Illumina protocols. Reference Guide # 1000000040498 v00

value: Breast cells

tag: time

value: Day 7


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep7

data_processing:
ONT reads were basecalled using the super high accuracy model of Guppy (v6.1.2).
Basecalled reads were aligned to the CC019 and CC037 reference genomes separately using MiniMap2 (v2.24).
Aligned reads were phased separately with CC019 and CC037 as the reference genomes using WhatsHap (v1.6) with SNPs between CC019 and CC037 identified via MUMmer4 (v4.0.0rc1).
Methylation was called using the Nanopolish (v0.14.0) call-methylation function for all reads phased to the same genome independent of the reference genome used. Methylation was called in the reference genome to which the read was phased.
Phased methylation calls were converted to allele-specific methylation frequency values for each CpG using the Nanopolish calculate_methylation_frequency.py script.
Assembly: CC019 and CC037 reference genomes from the Collaborative Cross Graphical Genome (v2.0).
Supplementary files format and content: Tab-delimited file with phased CC019 allele-specific methylation frequency data for each CpG in each sample. Data includes CpG location (CC019 reference genome, zero-based), methylation call and frequency data, and local sequence group information (number of CpGs and sequence).
Supplementary files format and content: Guppy sequencing summary file containing read-level sequencing and basecalling information.

extract_protocol:
High molecular weight (HMW) DNA was extracted from ~20mg of flash-frozen median liver lobe using the Nanobind Tissue Kit (PacBio SKU 102-302-100) following to the manufacturer’s instructions. Homogenization was performed using the TissueRuptor II (Qiagen Cat. 9002755) at maximum speed for 10s.
DNA was sheared to 10kb. Libraries were prepared using Ligation Sequencing Kit LSK109 and sequenced on R9.4.1 flow cells.

value: F1:CC037/TauUnc x CC019/TauUnc


title: testicular cells, low chorus at 6 hrs, biol rep 6

description: Library name: L_6_6


title: BT549 cells, siNC, rep1

description:
Library name: BT549-siNC-a
Column name in fpkm_ siNC_rep1.txt: BT549-siNC-a

value: breast cancer cell


title: Setx del14 ABLki 45h rep1

description: Library name: S14KO2Rep1


title: Ig3_FS_Ca_sti_Rad21_1

description:
Library name: Sample1
Iγ3-FS-Cα-AID-/-

value: CH12F3 murine lymphoma cells

value: Rad21 antibody(ab992), aCD40/IL4/TGFb for 3 days


title: BT549 cells, siNC, rep3

description:
Library name: BT549NC
Column name in fpkm_ siNC_rep3.txt: BT549NC


title: Setx del14 ABLki 45h rep2

description: Library name: S14KO2Rep2


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, male - rep6

value: Liver


title: testicular cells, low chorus at 6 hrs, biol rep 7

description: Library name: L_6_7


title: SKBr3 cells, TVB-3166 250 nmol/L, refeed day 3, day 7, rep1

description:
Library name: SKBr3_TVB-3166_rep1
colum name in Read_counts_ALL_samples: SKBr3_TVB3166_R1_Read_Count


title: SKBr3 cells, TVB-3166 250 nmol/L, refeed day 3, day 7, rep2

description:
Library name: SKBr3_TVB-3166_rep2
colum name in Read_counts_ALL_samples: SKBr3_TVB3166_R2_Read_Count


title: WT ABLki 45h rep3

description: Library name: WTRep3


title: testicular cells, low chorus at 6 hrs, biol rep 4

description: Library name: L_6_4


title: testicular cells, low chorus at 6 hrs, biol rep 5

description: Library name: L_6_5


title: testicular cells, low chorus at 6 hrs, biol rep 3

description: Library name: L_6_3


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, male - rep5

value: male


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep5

extract_protocol:
High molecular weight (HMW) DNA was extracted from ~20mg of flash-frozen median liver lobe using the Nanobind Tissue Kit (PacBio SKU 102-302-100) following to the manufacturer’s instructions. Homogenization was performed using the TissueRuptor II (Qiagen Cat. 9002755) at maximum speed for 10s.
DNA was sheared to 20-30kb. Libraries were prepared using Ligation Sequencing Kit LSK110 and sequenced on R9.4.1 flow cells.

value: 4 months


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep6


title: testicular cells, low chorus at 6 hrs, biol rep 2

description: Library name: L_6_2

value: testicular cells


title: WT ABLki 45h rep1

description: Library name: WTRep1


title: WT ABLki 45h rep2

description: Library name: WTRep2


title: SKBr3 cells, Palboclib 1 umol/L, refeed day 3, day 7, rep3

description:
Library name: SKBr3_palboclib_rep3
colum name in Read_counts_ALL_samples: SKBr3_PALBO_R3_Read_Count

value: Palboclib 1 umol/L


title: Setx del3 ABLki 45h rep3

description: Library name: S3KO1Rep3


title: testicular cells, wind control at 6 hrs, biol rep 8

description: Library name: W_6_8

value: WT

value: wind


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep3


title: SKBr3 cells, ND-646 250 nmol/L, refeed day 3, day 7, rep3

description:
Library name: SKBr3_ND-646_rep3
colum name in Read_counts_ALL_samples: SKBr3_ND646_R3_Read_Count


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep4


title: testicular cells, wind control at 6 hrs, biol rep 7

description: Library name: W_6_7


title: SKBr3 cells, ND-646 250 nmol/L, refeed day 3, day 7, rep2

description:
Library name: SKBr3_ND-646_rep2
colum name in Read_counts_ALL_samples: SKBr3_ND646_R2_Read_Count


title: SKBr3 cells, Palboclib 1 umol/L, refeed day 3, day 7, rep2

description:
Library name: SKBr3_palboclib_rep2
colum name in Read_counts_ALL_samples: SKBr3_PALBO_R2_Read_Count


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, male - rep4


title: Setx del3 ABLki 45h rep1

description: Library name: S3KO1Rep1


data_processing:
Sequenced reads were mapped to a diploid transcriptome made from CC019 and CC037 strain-specific transcriptomes and allelic expression levels were quantified using the Salmon (v1.9.0) quant function.
Allelic expression values were then calculated in R using the fishpond (v2.8.0) importAllelicCounts function.
Assembly: Diploid transcriptome made from CC019 and CC037 strain-specific transcriptomes. Strain-specific transcriptomes were generated using the gffread (v0.12.7) function with strain-specific genomes and strain-specific genome annotation files from the Collaborative Cross Graphical Genome (v2.0).
Supplementary files format and content: Tab-delimited file with allele-specific gene counts for each sample. Each file containes one column each for CC019 and CC037 allelic counts.
Supplementary files format and content: Salmon quantification file containing allelic expression information.

extract_protocol:
RNA was extracted from ~10-20mg of flash-frozen median liver lobe using the RNeasy Mini kit (Qiagen Cat. 74104) following the manufacturer’s instructions with on-column DNase digestion. Disruption and homogenization were performed using the TissueRuptor II (Qiagen Cat. 9002755) at maximum speed for 10s.
Strand-specific mRNA libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs #E7760), and mRNA isolation was performed using the Poly(A) mRNA Magnetic Isolation Module (New England BioLabs #E7490). The stranded mRNA libraries were sequenced on an Illumina NovaSeq 6000 using v1.5 chemistry with S4 flow cell, generating 150 bp paired-end dual-indexed reads.


title: SKBr3 cells, Palboclib 1 umol/L, refeed day 3, day 7, rep1

description:
Library name: SKBr3_palboclib_rep1
colum name in Read_counts_ALL_samples: SKBr3_PALBO_R1_Read_Count


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep2


title: testicular cells, low chorus at 6 hrs, biol rep 1

description: Library name: L_6_1


title: Setx del3 ABLki 45h rep2

description: Library name: S3KO1Rep2


title: testicular cells, wind control at 6 hrs, biol rep 5

description: Library name: W_6_5


title: SKBr3 cells, Doxorubicin 10 nmol/L, refeed day 3, day 7, rep3

description:
Library name: SKBr3_doxorubicin_rep3
colum name in Read_counts_ALL_samples: SKBr3_DOXO_R3_Read_Count

value: Doxorubicin 10 nmol/L


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep1

value: female


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, male - rep2


title: testicular cells, wind control at 6 hrs, biol rep 4

description: Library name: W_6_4


title: testicular cells, wind control at 6 hrs, biol rep 3

description: Library name: W_6_3


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, male - rep1


title: testicular cells, wind control at 6 hrs, biol rep 6

description: Library name: W_6_6


title: testicular cells, wind control at 6 hrs, biol rep 2

description: Library name: W_6_2


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, female - rep5


title: SKBr3 cells, Doxorubicin 10 nmol/L, refeed day 3, day 7, rep1

description:
Library name: SKBr3_doxorubicin_rep1
colum name in Read_counts_ALL_samples: SKBr3_DOXO_R1_Read_Count


title: SKBr3 cells, proliferative control, rep2

description:
Library name: SKBr3_proliferative_rep2
colum name in Read_counts_ALL_samples: SKBr3_proliferative_R2_Read_Count

value: Day 0

value: no treatment


title: SKBr3 cells, ND-646 250 nmol/L, refeed day 3, day 7, rep1

description:
Library name: SKBr3_ND-646_rep1
colum name in Read_counts_ALL_samples: SKBr3_ND646_R1_Read_Count

value: Breast cells


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, female - rep2

value: F1:CC019/TauUnc x CC037/TauUnc


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, male - rep3

value: F1:CC037/TauUnc x CC019/TauUnc


title: SKBr3 cells, control cells, day 7, rep3

description:
Library name: SKBr3_control_rep3
colum name in Read_counts_ALL_samples: SKBr3_CT_R3_Read_Count

value: Day 7


title: SKBr3 cells, Doxorubicin 10 nmol/L, refeed day 3, day 7, rep2

description:
Library name: SKBr3_doxorubicin_rep2
colum name in Read_counts_ALL_samples: SKBr3_DOXO_R2_Read_Count


title: SKBr3 cells, proliferative control, rep1

description:
Library name: SKBr3_proliferative_rep1
colum name in Read_counts_ALL_samples: SKBr3_proliferative_R1_Read_Count


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 5

description: Library name: A_6_5

value: amphiplex


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, female - rep5


title: testicular cells, wind control at 6 hrs, biol rep 1

description: Library name: W_6_1


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, female - rep4


title: SKBr3 cells, proliferative control, rep3

description:
Library name: SKBr3_proliferative_rep3
colum name in Read_counts_ALL_samples: SKBr3_proliferative_R3_Read_Count


title: Liver, F1: CC037/TauUnc x CC019/TauUnc, male - rep2


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 6

description: Library name: A_6_6


title: SKBr3 cells, control cells, day 7, rep2

description:
Library name: SKBr3_control_rep2
colum name in Read_counts_ALL_samples: SKBr3_CT_R2_Read_Count


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, female - rep1


title: SKBr3 cells, control cells, day 7, rep1

description:
Library name: SKBr3_control_rep1
colum name in Read_counts_ALL_samples: SKBr3_CT_R1_Read_Count


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, female - rep3


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 8

description: Library name: A_6_8


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 7

description: Library name: A_6_7


title: SKBr3 cells, bleomycin 10 umol/L, refeed day 3, day 7, rep2

description:
Library name: SKBr3_bleomycin_rep2
colum name in Read_counts_ALL_samples: SKBr3_BLEO_R2_Read_Count

value: bleomycin 10 umol/L


value: Liver


title: SKBr3 cells, bleomycin 10 umol/L, refeed day 3, day 7, rep3

description:
Library name: SKBr3_bleomycin_rep3
colum name in Read_counts_ALL_samples: SKBr3_BLEO_R3_Read_Count


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 4

description: Library name: A_6_4


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, male - rep1

value: male


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, male - rep3

value: 4 months


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, male - rep4


title: Liver, CC037/TauUnc, female - rep5


title: Liver, CC037/TauUnc, female - rep5


title: Liver, CC037/TauUnc, male - rep4


title: Liver, F1: CC019/TauUnc x CC037/TauUnc, male - rep2


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 3

description: Library name: A_6_3

value: testicular cells


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 2

description: Library name: A_6_2


title: SKBr3 cells, alisertib 500 nmol/L, refeed day 3, day 7, rep1

description:
Library name: SKBr3_alisertib_rep1
colum name in Read_counts_ALL_samples: SKBr3_ALI_R1_Read_Count

value: alisertib 500 nmol/L


title: SKBr3 cells, alisertib 500 nmol/L, refeed day 3, day 7, rep3

description:
Library name: SKBr3_alisertib_rep3
colum name in Read_counts_ALL_samples: SKBr3_ALI_R3_Read_Count


title: Liver, CC037/TauUnc, female - rep4


title: testicular cells, saline control at 6 hrs, biol rep 8

description: Library name: S_6_8

value: WT

value: saline


title: Liver, CC037/TauUnc, male - rep2


title: SKBr3 cells, alisertib 500 nmol/L, refeed day 3, day 7, rep2

description:
Library name: SKBr3_alisertib_rep2
colum name in Read_counts_ALL_samples: SKBr3_ALI_R2_Read_Count


title: testicular cells, saline control at 6 hrs, biol rep 7

description: Library name: S_6_7


title: Liver, CC037/TauUnc, male - rep4


title: Liver, CC037/TauUnc, male - rep3


title: testicular cells, saline control at 6 hrs, biol rep 6

description: Library name: S_6_6


title: testicular cells, saline control at 6 hrs, biol rep 5

description: Library name: S_6_5


title: testicular cells, amphiplex mixture at 6 hrs, biol rep 1

description: Library name: A_6_1


title: SKBr3 cells, bleomycin 10 umol/L, refeed day 3, day 7, rep1

description:
Library name: SKBr3_bleomycin_rep1
colum name in Read_counts_ALL_samples: SKBr3_BLEO_R1_Read_Count


title: Liver, CC037/TauUnc, male - rep3


title: Immortalized Human Nasal Epithelial Cells, Negative control overexpression, EV 3

city: Pamplona

first: Paz

last: Cartas Cejudo

address: Irunlarrea, 3

institute: Navarrabiomed

description: Library name: Sample 9

data_processing:
RNA-seq data quality was first assessed using FastQC v0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC v1.9 (http://multiqc.info/). Raw reads were trimmed and filtered to retain sequences with a Phred quality score ≥25, and adapter sequences were removed using TrimGalore v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). To eliminate residual rRNA reads, trimmed sequences were processed with SortMeRNA v2.1 (https://bioinfo.lifl.fr/RNA/sortmerna/) [22] to remove 18S and 28S rRNA fragments that might remain after depletion. High-quality reads were aligned to the Homo sapiens reference genome (GRCm38.p6/GCA_000001635.8, ftp://ftp.ensembl.org) using HISAT2 v2.2.1 (https://daehwankimlab.github.io/hisat2/) under default parameters. Alignment quality was evaluated with Qualimap2 (http://qualimap.bioinfo.cipf.es), and resulting BAM files were sorted and indexed using Samtools v1.18.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Immortalized Human Nasal Epithelial Cells - SV48

extract_protocol:
Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Sequencing libraries were generated using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina Inc., San Diego, CA, USA) from 100 ng of total RNA, following the depletion procedure as instructed. Libraries were sequenced on a HiSeq1500 system (Illumina) in PE100 rapid mode and pooled in equimolar proportions to a final concentration of 10 nM. Library concentrations were quantified using a Qubit 3.0 fluorometer (Invitrogen, Waltham, MA, USA), and fragment size distributions were verified by capillary electrophoresis on a Fragment Analyzer (AATI).

value: Negative control overexpression


title: Liver, CC037/TauUnc, male - rep1


title: Liver, CC037/TauUnc, female - rep3

value: female


title: Liver, CC037/TauUnc, male - rep2


title: testicular cells, saline control at 6 hrs, biol rep 4

description: Library name: S_6_4


title: Immortalized Human Nasal Epithelial Cells, overexpression SIRT3, OE SIRT3 3

description: Library name: Sample 12

source_name: Immortalized Human Nasal Epithelial Cells - SV51

value: overexpression SIRT3


title: testicular cells, saline control at 6 hrs, biol rep 2

description: Library name: S_6_2


title: Liver, CC037/TauUnc, female - rep4


title: Liver, CC037/TauUnc, male - rep1


title: Liver, CC037/TauUnc, female - rep2


title: Liver, CC037/TauUnc, female - rep1


title: testicular cells, saline control at 6 hrs, biol rep 3

description: Library name: S_6_3


title: Immortalized Human Nasal Epithelial Cells, overexpression SIRT3, OE SIRT3 1

description: Library name: Sample 10

source_name: Immortalized Human Nasal Epithelial Cells - SV49


title: Liver, CC037/TauUnc, female - rep2


title: α_3CBEInv_sti_1

description:
Library name: Sample 10
AID-/-; Cα-3'CBE inversion in Iα-Cα inversion cells

data_processing:
Reads were aligned using bowtie 2.2.8 with --local flag
reads were quantified for specific loci using samtools version 1.8
wig files were produced using RseqQ package
Assembly: mm9
Supplementary files format and content: wig files contain peak information for samples

molecule: nuclear RNA

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with permeabilization buffer. The permeabilized cells were resuspended in 100 ml of storage buffer for nuclear run-on with 2X run-on mix at 37℃ for 5 min. RNA was extracted by Trizol and followed by hybrolyzation. The RNA was incubated with streptavidin C1 beads (Thermo Fisher Scientific, #65001) and the enriched run-on samples were incubated with hydroxyl repair with T4 PNK (NEB, M0201S) and RppH (NEB, M0356S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA.
The cDNA was subjected to making PRO-seq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318). PRO-seq libraries were sequenced via single end 50bp or paired end 150bp sequencing on a Nova-seq 6000 (Illumina) sequencer and normalized to a coverage of 10 million 100nt reads for display.

value: CH12F3 murine lymphoma cells

value: aCD40/IL4/TGFb stimulation


title: Immortalized Human Nasal Epithelial Cells, Negative control overexpression, EV 1

description: Library name: Sample 7

source_name: Immortalized Human Nasal Epithelial Cells - SV46


title: Liver, CC037/TauUnc, female - rep3


title: Immortalized Human Nasal Epithelial Cells, overexpression SIRT3, OE SIRT3 2

description: Library name: Sample 11

source_name: Immortalized Human Nasal Epithelial Cells - SV50


title: Immortalized Human Nasal Epithelial Cells, Negative control overexpression, EV 2

description: Library name: Sample 8

source_name: Immortalized Human Nasal Epithelial Cells - SV47


title: Immortalized Human Nasal Epithelial Cells, silencing SIRT3, si SIRT3 1

description: Library name: Sample 4

source_name: Immortalized Human Nasal Epithelial Cells - SV43

value: silencing SIRT3


title: testicular cells, saline control at 6 hrs, biol rep 1

description: Library name: S_6_1

data_processing:
De novo assembly was produced by LC Sciences. Cutadapt 45 and custom Perl scripts (https://www.perl.org/about.html) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was then verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
De novo assembly of the transcriptome was performed with Trinity 2.4.0 46. Trinity groups transcripts into clusters, loosely defined as a ‘gene’, based on shared sequence content.
Assembly: De novo assembly
Supplementary files format and content: xlsx files include raw counts and TPM each all samples


title: Immortalized Human Nasal Epithelial Cells, silencing SIRT3, si SIRT3 3

description: Library name: Sample 6

source_name: Immortalized Human Nasal Epithelial Cells - SV45


title: Liver, CC019/TauUnc, female - rep2


title: High-Dose Tamoxifen (HDT) Group

city: New York

first: Hualong

last: Zheng

state: NY

department: Department of Medicine

institute: Columbia University Medical Center

description: Library name: Sample2

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using Cell Ranger v8.0.1.
Alignment to the mouse reference genome (GRCm39-2024-A).
Barcodes and UMIs were filtered and counted to generate feature-barcode matrices.
Assembly: Reference genome: GRCm39-2024-A
Supplementary files format and content: Filtered and raw gene expression matrices in MTX format.

source_name: Stomach

extract_protocol:
Gastric corpus tissues were harvested and dissociated into single-cell suspensions. Tissues were enzymatically digested using collagenase IV (2 mg/ml) and DNase I (40 U/ml) at 37°C for 30 minutes. Cells were then filtered, washed, and stained with viability dyes for live-cell sorting. Fluorescence-activated cell sorting (FACS) was performed using a BD FACSAria system, based on CD326+ and tdTomato+ expression for lineage tracing. Sorted cells were resuspended in PBS with 0.04% BSA for downstream processing.
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ v4 kit, following the manufacturer’s protocol. Cells were encapsulated in a gel bead-in-emulsion (GEM) system, and poly-A RNA transcripts were reverse-transcribed into cDNA containing Illumina R1 primer sequences, Unique Molecular Identifiers (UMIs), and 10x barcodes. Post-amplification cDNA was purified using SPRIselect beads, and libraries were constructed with Illumina R2 sequencing adapters and sample indices for paired-end sequencing.

treatment_protocol: Low-dose (LDT) and high-dose (HDT) tamoxifen groups were used to induce Tff2+ progenitors at different time points.

value: Stomach

value: Projenitors

value: Tff2+ projenitors

value: High-Dose Tamoxifen (HDT) Group


title: Liver, CC037/TauUnc, female - rep1

value: Liver


title: Low-Dose Tamoxifen (LDT) Group

description: Library name: Sample1

value: Low-Dose Tamoxifen (LDT) Group


title: Liver, CC019/TauUnc, female - rep1

value: 4 months


title: Immortalized Human Nasal Epithelial Cells, Negative control siRNA, SCR1

description: Library name: Sample 1

source_name: Immortalized Human Nasal Epithelial Cells - SV40

value: Negative control siRNA


title: γ3_αInv_sti_1

description:
Library name: Sample 4
AID-/-; γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: Immortalized Human Nasal Epithelial Cells, silencing SIRT3, si SIRT3 2

description: Library name: Sample 5

source_name: Immortalized Human Nasal Epithelial Cells - SV44


title: Liver, CC019/TauUnc, female - rep1


title: Liver, CC019/TauUnc, female - rep3


title: Liver, CC019/TauUnc, male - rep3

value: male


title: Liver, CC019/TauUnc, female - rep2


title: αInv_sti_1

description:
Library name: Sample 7
AID-/-; Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells

value: aInv-AID-/-


title: Immortalized Human Nasal Epithelial Cells, Negative control siRNA, SCR3

description: Library name: Sample 3

source_name: Immortalized Human Nasal Epithelial Cells - SV42


title: Liver, CC019/TauUnc, male - rep2


title: Liver, CC019/TauUnc, male - rep2


title: Immortalized Human Nasal Epithelial Cells, Negative control siRNA, SCR2

description: Library name: Sample 2

source_name: Immortalized Human Nasal Epithelial Cells - SV41


title: Liver, CC019/TauUnc, male - rep1


title: CH12F3PO_sti_1

description:
Library name: Sample 1
AID-/-; non-coding IgH VH-3'BCEs deletion


title: Liver, CC019/TauUnc, male - rep3


title: Liver, CC019/TauUnc, female - rep3


title: C. major, stress, rep5, T08 (FH5T08)

status: Public on Mar 13 2026

city: Vienna

first: Hannes

middle: M.

last: Kramml

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

description: Library name: FH5T08

data_processing:
Sample preprocessing was conducted using fastp (v0.23.2) with following parameters: -q 30, -l 80, --detect_adapter_for_pe
STAR (v2.7.10b) and RSEM utilized read alignment and polyploid/allele-aware estimation of normalized transcripts per million (TPM) for each sample
Data matrices for downstream analyses were constructed and integrated via custom scripts in R (Clusia panomics database)
Assembly: CmuV2.3_predom, CmuV2.3_alt
Supplementary files format and content: tab-delimited file of TPM values for all samples combined per species
Supplementary files format and content: tab-delimited file includes raw counts, normalized counts, TPM, and FPKM values for each sample separately

organism: Clusia major

source_name: Leaf

extract_protocol:
Total RNA was extracted according to the protocol of Oliveira, R. R. et al. (2015) with an adapted extraction buffer (2.5 M NaCl, 2.5% PVP, 100 mM Tris, 25 mM EDTA, 2.5% -mercaptoethanol and 2% SDS). Purification was done using AMPure beads, mRNA enrichment and cDNA synthesis via NEB polyA kit.
Standard RNA library preparation was conducted for 150 bp paired-end Illumina sequencing on a NovaSeq S4 XP system.

value: Leaf

tag: condition

value: Stress


title: C. major, stress, rep2, T19 (FH2T19)

description: Library name: FH2T19


title: Liver, CC019/TauUnc, male - rep1

source_name: Liver


title: C. major, stress, rep3, T19 (FH3T19)

description: Library name: FH3T19


title: C. major, control, rep2, T08 (FD2T08)

description: Library name: FD2T08

value: Control


title: HS-19 Heat Stroke T0

city: Thuwal

first: Maria

middle: de los Angeles

last: Gomez

address: 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia

department: Bioengineering

country: Saudi Arabia

institute: KAUST

description: Library name: TREATMENT_19

data_processing:
Raw FASTQ files were processed using the Nextflow smrnaseq pipeline (v2.2.4), beginning with quality control and adapter trimming via FastQC (v0.12.0) and fastp (v0.23.2). Contaminant sequences were filtered out using Bowtie2 (v2.5.1), followed by UMI deduplication with UMI-tools (v1.1.4). Filtered reads were aligned to miRBase mature miRNAs and hairpins (v22) using Bowtie1 (v1.3.1) and SAMtools (v1.16.1), with optional alignment to the GRCh38 human genome to identify known and novel miRNAs via MiRDeep2 (v0.1.3). Following alignment, Mirtop (v0.4.25) was used for read collapsing and isomiR annotation, EdgeR (v4.2.0) handled hairpin count analysis and TMM normalization, and the overall pipeline quality was assessed using MultiQC (v1.14).
Assembly: GRCh38
Supplementary files format and content: A CSV (Comma Separated Values) file with TMM normalized counts of reads aligned to mature miRNAs/miRNA precursors (hairpins)

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using Leucosep seperation tube. RNA was extracted using TRIzol Reagent (Invitrogen) and the SV Total RNA Isolation System (Promega, USA) following the company protocol.
Small RNA libraries were prepared using the QIAseq miRNA Library Kit. The procedure consisted of the following steps: Ligation of a pre-adenylated DNA adapter to the 3′ ends and an RNA adapter to the 5′ ends of mature miRNAs. Reverse transcription using a UMI-integrated primer to tag individual molecules and introduce a universal sequence. PCR amplification using plate index kits to assign a Unique Dual Index (UDI) to each sample. Library purification using a magnetic bead-based cleanup method. Quality control assessment using an Agilent Bioanalyzer and quantification via Qubit Fluorometer. Equimolar pooling of the final libraries for sequencing on an Illumina MiSeq platform.

value: Blood

value: Peripheral blood mononuclear cells

tag: subject status

value: heat stroke patient

tag: batch

tag: gender

value: Female

value: Old


title: C. major, stress, rep2, T08 (FH2T08)

description: Library name: FH2T08


title: HS-18 Heat Stroke T0

description: Library name: TREATMENT_18

value: Young


title: HS-15 Heat Stroke T0

description: Library name: TREATMENT_15

value: Male


title: C. major, stress, rep5, T13 (FH5T13)

description: Library name: FH5T13


title: C. major, control, rep3, T13 (FD3T13)

description: Library name: FD3T13


title: C. major, stress, rep5, T04 (FH5T04)

description: Library name: FH5T04


title: C. major, stress, rep3, T13 (FH3T13)

description: Library name: FH3T13


title: C. major, stress, rep2, T04 (FH2T04)

description: Library name: FH2T04


title: C. major, control, rep2, T04 (FD2T04)

description: Library name: FD2T04


title: C. major, control, rep1, T13 (FD1T13)

description: Library name: FD1T13


title: C. major, stress, rep5, T19 (FH5T19)

description: Library name: FH5T19


title: C. major, control, rep3, T19 (FD3T19)

description: Library name: FD3T19


title: HS-11 Heat Stroke T0

description: Library name: TREATMENT_11


title: C. major, stress, rep3, T08 (FH3T08)

description: Library name: FH3T08


title: C. major, stress, rep3, T04 (FH3T04)

description: Library name: FH3T04


title: HS-10 Heat Stroke T0

description: Library name: TREATMENT_10


title: HS-16 Heat Stroke T0

description: Library name: TREATMENT_16


title: HS-17 Heat Stroke T0

description: Library name: TREATMENT_17


title: C. major, control, rep2, T13 (FD2T13)

description: Library name: FD2T13


title: C. major, stress, rep2, T13 (FH2T13)

description: Library name: FH2T13


title: DKO, scATAC

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

description:
Library name: DKO-scATAC
BD Rhapsody ATAC + WTA

library_source: genomic single cell

data_processing:
RNA and ATAC raw reads were processed using BD Rhapsody sequence analysis pipeline to map RNA transcripts and ATAC peaks to mm39 reference genome.
Assembly: mm39
Supplementary files format and content: Tab separated matrix files for scRNA andFragments bed files for scATAC data

source_name: spleen

extract_protocol:
Cells were pelleted for 5 mins at 300 × g followed by nuclei isolation by incubating cells with chilled cell lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% tween-20, 0.1% IGEPAL CA-630, 0.01% digitonin, 1mM dithiothreitol, 1 U/μL RNase inhibitor and 1% BSA) for 3 min. Nuclei were washed twice in 1 ml of wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1 mM dithiothreitol and 1 U/µL RNase inhibitor and 1% BSA) by centrifuging at 500 × g for 5 min. After centrifugation, cells were resuspended in chilled Nuclei Buffer (1× Nuclei Buffer, 1 mM dithiothreitol and 1 U/µL RNase inhibitor).
Nuclei were incubated in transposition mix according to the BD Rhapsody single-cell ATAC-seq and mRNA whole transcriptome analysis protocol version 23-24474(01). Following tagmentation, cells were loaded onto BD Rhapsody cartridge. Library preparation was performed according to the BD Rhapsody single-cell ATAC-seq and mRNA whole transcriptome analysis protocol version 23-24474(01).

treatment_protocol: NK cells were FAC-sorted from spleen of naïve NcriCreT/+, NcriCreT/+Gfi1fl/fl, NcriCreT/+Foxo1fl/fl and NcriCreT/+Gfi1fl/flFoxo1fl/fl mice. NK cells were pooled from 3-5 mice and ~1×105 cells were used for nuclei isolation.

value: spleen

value: NK cells


title: C. major, control, rep1, T08 (FD1T08)

description: Library name: FD1T08


title: C. major, control, rep2, T19 (FD2T19)

description: Library name: FD2T19


title: HS-04 Heat Stroke T0

description: Library name: TREATMENT_04


title: C. major, control, rep1, T19 (FD1T19)

description: Library name: FD1T19


title: C. major, control, rep3, T08 (FD3T08)

description: Library name: FD3T08


title: HS-12 Heat Stroke T0

description: Library name: TREATMENT_12


title: GFI1-KO, scRNA

description:
Library name: GFI1-KO-scRNA
BD Rhapsody ATAC + WTA


title: WT, scRNA

description:
Library name: Ncr1-scRNA
BD Rhapsody ATAC + WTA


title: FOXO1-KO, scATAC

description:
Library name: FOXO1-KO-scATAC
BD Rhapsody ATAC + WTA


title: HS-11_2 Heat Stroke T0

description: Library name: TREATMENT_11_2


title: HS-08 Heat Stroke T0

description: Library name: TREATMENT_08


title: WT, scATAC

description:
Library name: Ncr1-scATAC
BD Rhapsody ATAC + WTA


title: HS-13 Heat Stroke T0

description: Library name: TREATMENT_13


title: C. major, control, rep3, T04 (FD3T04)

description: Library name: FD3T04


title: HT-16 Control

description: Library name: CONTROL_16

value: control


title: C. major, control, rep1, T04 (FD1T04)

description: Library name: FD1T04


title: HT-15 Control

description: Library name: CONTROL_15


title: HT-19 Control

description: Library name: CONTROL_19


title: WT-Female-3

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

description:
Library name: G0866
G0866

data_processing:
Rsubread v2.16.1
Assembly: mm10
Supplementary files format and content: aligned gene expression matrix from fastq file in csv format.

source_name: brain vessel

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen, Germany) and integrity measured with an Agilent RNA Pico Bioanalyzer assay (Agilent Technologies).
Libraries were generated using TruSeq standard mRNA kit (Illumina) according to manufactures instruction in with 200ng RNA input. Sequencing was performed at the Health Sciences Sequencing Core at UPMC Children’s Hospital of Pittsburgh on NextSeq 2000 (Illumina).

value: brain vessel

value: WT


title: HS-14 Heat Stroke T0

description: Library name: TREATMENT_14


title: HT-12 Control

description: Library name: CONTROL_12


title: HS-09 Heat Stroke T0

description: Library name: TREATMENT_09


title: HS-05 Heat Stroke T0

description: Library name: TREATMENT_05


title: DKO, scRNA

description:
Library name: DKO-scRNA
BD Rhapsody ATAC + WTA


title: WT-Female-1

description:
Library name: A3174
A3174


title: WT-Female-4

description:
Library name: G0867
G0867


title: WT-Female-6

description:
Library name: C3067
C3067


title: HS-02 Heat Stroke T0

description: Library name: TREATMENT_02


title: FOXO1-KO, scRNA

description:
Library name: FOXO1-KO-scRNA
BD Rhapsody ATAC + WTA


title: WT-Female-5

description:
Library name: X0443
X0443


title: HS-06 Heat Stroke T0

description: Library name: TREATMENT_06


title: WT-Male-3

description:
Library name: W3
W3


title: WT-Female-2

description:
Library name: A3178
A3178


title: WT-Male-2

description:
Library name: W2
W2


title: WT-Male-6

description:
Library name: W6
W6


title: HT-10 Control

description: Library name: CONTROL_10


title: HS-03 Heat Stroke T0

description: Library name: TREATMENT_03


title: WT-Male-5

description:
Library name: W5
W5


title: APP-Female-6

description:
Library name: A12
A12

value: APP/PS+


title: HT-11 Control

description: Library name: CONTROL_11


title: HT-08 Control

description: Library name: CONTROL_08


title: HT-06 Control

description: Library name: CONTROL_06


title: HT-13 Control

description: Library name: CONTROL_13


title: HT-07 Control

description: Library name: CONTROL_07


title: WT-Male-1

description:
Library name: W1
W1


title: HT-04 Control

description: Library name: CONTROL_04


title: HT-05 Control

description: Library name: CONTROL_05


title: APP-Female-5

description:
Library name: A11
A11


title: HT-03 Control

description: Library name: CONTROL_03


title: HT-01 Control

description: Library name: CONTROL_01


title: HT-09 Control

description: Library name: CONTROL_09


title: APP-Female-3

description:
Library name: A9
A9


title: HT-02 Control

description: Library name: CONTROL_02


title: APP-Female-1

description:
Library name: A3139
A3139


title: APP-Female-2

description:
Library name: A3140
A3140


title: APP-Male-6

description:
Library name: E7967
E7967


title: K. lactis, Heat 39C, biorep1

city: Berkeley

first: Kaylee

middle: Elizabeth

last: Christensen

state: CA

address: Koshland Hall rm 321

department: Plant and Microbial Biology

institute: UC Berkeley

description: Library name: Kl 39C 1

data_processing:
mapped to genome with TopHat with default parameters, input to Htseq for raw read counts
Assembly: custom pseudogenomes for our lab strains of K. marxianus Km31 and K. lactis yLB72
Supplementary files format and content: column 1 lists gene name, column 2 lists raw read count

organism: Kluyveromyces lactis

source_name: yeast

growth_protocol: colonies from YPD plates picked into YPD for overnight growth, back-diluted to 0.05 OD in 50mL

extract_protocol:
Direct-Zol RNA MicroPrep RNA kit (Zymo Research)
mRNA enrichment with Poly (A) capture; RNA fragmentation with Covaris; cDNA reverse transcription; RNA library preparation done by Novogene, Inc.

treatment_protocol: grown at condition listed in 50mL back-diluted culture until reached 0.4-0.85 OD, 2OD units suspended in 1mL of RNAlater and stored at 4C for <48 hours

value: yeast

value: K. lactis yLB72


title: K. lactis, Heat 39C, biorep2

description: Library name: Kl 39C 2


title: APP-Male-5

description:
Library name: A3172
A3172


title: K. lactis, Control 28C, biorep1

description: Library name: Kl 28C 1


title: K. lactis, Control 28C, biorep3

description: Library name: Kl 28C 3


title: K. lactis, Heat 39C, biorep3

description: Library name: Kl 39C 3


title: K. lactis, Control 28C, biorep2

description: Library name: Kl 28C 2


title: APP-Male-3

description:
Library name: A3
A3


title: K. lactis, MMS, biorep3

description: Library name: Kl MMS 3


title: APP-Male-2

description:
Library name: A2
A2


title: APP-Male-4

description:
Library name: A4
A4


title: K. lactis, MMS, biorep1

description: Library name: Kl MMS 1


title: APP-Female-4

description:
Library name: A10
A10


title: K. lactis, MMS, biorep2

description: Library name: Kl MMS 2


title: NCR-cre M2 NK cells, Exp1, Rep2

data_processing:
Read quality was assessed and low quality reads trimmed with fastp.
Reads were mapped to the mouse genome (mm10) using STAR v2.7.10
After mapping, reads were quantified with featureCounts v2.0.1
Assembly: mm10
Supplementary files format and content: Read counts following mapping to mm10 using featurecount

extract_protocol:
RNA was extracted from NK cells using RNeasy Plus Micro kit (Qiagen)
Libraries were prepared with TruSeq Stranded Total RNA kit (Illumina) or NEBNext Single Cell/low Input Library prep kit (New England Biolabs).


title: APP-Male-1

description:
Library name: A1
A1


title: K. lactis, caffeine, biorep3

description: Library name: Kl caffeine 3


title: GF1-KO M2 NK cells, Exp1, Rep3


title: K. lactis, ethanol, biorep2

description: Library name: Kl ethanol 2


title: GF1-KO M2 NK cells, Exp1, Rep2


title: K. lactis, ethanol, biorep1

description: Library name: Kl ethanol 1


title: WT-Male-4

description:
Library name: W4
W4


title: K. lactis, ethanol, biorep3

description: Library name: Kl ethanol 3


title: NCR-cre M2 NK cells, Exp1, Rep1


title: K. lactis, caffeine, biorep2

description: Library name: Kl caffeine 2


title: NCR-cre M2 NK cells, Exp1, Rep3


title: GF1-KO M1 NK cells, Exp1, Rep2


title: Rectum_noninflamed [267r3327]

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

institute: Northwestern University

description:
Cos3wk6V296R267R3327_exprMat_file.csv
Cos3wk6V296R267R3327_fov_positions_file.csv
Cos3wk6V296R267R3327_metadata_file.csv
Cos3wk6V296R267R3327_tx_file.csv
Cos3wk6V296R267R3327-polygons.csv
fov 1-21

hyb_protocol: CosMx

scan_protocol: CosMx

data_processing: We performed cell quality control (QC) on CosMx multi-tissue, Xenium multi-tissue, Xenium colon-specific, CosMx 6K, and Xenium 5K data. For CosMx multi-tissue, we performed QC by removing the cells with fewer than 20 unique molecular identifiers (UMIs). For Xenium multi-tissue and Xenium colon-specific, we performed QC by removing the cells with fewer than 5 UMIs. For CosMx 6K and Xenium 5K data, we performed QC by excluding the cells with fewer than 50 UMIs. After QC, we normalized and transformed the raw datasets using log normalization (each cell’s gene counts are divided by its total counts, multiplied by 10,000, and log transformed). For CosMx 6K and Xenium 5K data, the top 3,000 highly variable genes were next identified. After further scaling the data, we performed principal component analysis on the normalized data and clustered the cells through a shared nearest neighbor approach.

label: CosMx

source_name: human rectum

label_protocol: CosMx

growth_protocol: Colonic biopsies were obtained with informed consent from healthy and IBD patients during routine screening. All procedures were approved by Northwestern University IRB committee (STU00214234) operating under the main biorepository IRB (STU00203172) at the Digestive Health Center. A standardized biopsy collection protocol was used, and biopsies were targeted for the most inflamed portion of each segment, and if no inflammation was present, they were taken from areas adjacent to where routine care biopsies were taken to most closely align with routine care histology assessments.

extract_protocol: Biopsies were immediately placed in formalin jars fixed and transferred to the Northwestern University Pathology Core for automated embedding, cataloging, and H&E imaging. Formalin-fixed, paraffin-embedded blocks were cut into sections on positively charged slides, and full block sections were used for all experiments.

value: Rectum


title: Rectum_noninflamed [296r3327]

description:
Cos3wk6V296R267R3327_exprMat_file.csv
Cos3wk6V296R267R3327_fov_positions_file.csv
Cos3wk6V296R267R3327_metadata_file.csv
Cos3wk6V296R267R3327_tx_file.csv
Cos3wk6V296R267R3327-polygons.csv
fov 22-41


title: GF1-KO Imm NK cells, Exp1, Rep1


title: GF1-KO M2 NK cells, Exp1, Rep1


title: NCR-cre M1 NK cells, Exp1, Rep1


title: NCR-cre M1 NK cells, Exp1, Rep2


title: GF1-KO M1 NK cells, Exp1, Rep3


title: NCR-cre M1 NK cells, Exp1, Rep3


title: Rectum_inflamed [I0387_RSDF_CosMx2.0]

description:
Cos31KxeniumcosmxI0387RSDF-polygons.csv
Cos31KxeniumcosmxI0387RSDF_exprMat_file.csv
Cos31KxeniumcosmxI0387RSDF_fov_positions_file.csv
Cos31KxeniumcosmxI0387RSDF_metadata_file.csv
Cos31KxeniumcosmxI0387RSDF_tx_file.csv


title: GF1-KO Imm NK cells, Exp1, Rep2


title: Rectum_HC [306r4327]

description:
Cos3wk6V306R309R4327_exprMat_file.csv
Cos3wk6V306R309R4327_fov_positions_file.csv
Cos3wk6V306R309R4327_metadata_file.csv
Cos3wk6V306R309R4327_tx_file.csv
Cos3wk6V306R309R4327-polygons.csv
fov 19-41


title: K. lactis, caffeine, biorep1

description: Library name: Kl caffeine 1


title: Rectum_noninflamed [296r1327]

description:
Cos2wk6D296R267R1327_exprMat_file.csv
Cos2wk6D296R267R1327_fov_positions_file.csv
Cos2wk6D296R267R1327_metadata_file.csv
Cos2wk6D296R267R1327_tx_file.csv
Cos2wk6D296R267R1327-polygons.csv
fov 22-41


title: GF1-KO M1 NK cells, Exp1, Rep1


title: GF1-KO Imm NK cells, Exp1, Rep3


title: Wild-type SOX2+ Neural organoids plate7

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: JvB-198-SOX2-Neural-Organoids-WT-20E-F-pl7
2x100bp

data_processing:
see scEdU-seq (Nature Methods, 2024)
Assembly: hg38
Supplementary files format and content: count tables

source_name: neural

growth_protocol: U2OS cells were cultured in DMEM with Glutamax and 10% FCS plus PenStep (Gibco). IPSC were differentiated into SOX2 neural Organoids

extract_protocol:
Proteinase K digestion
see scEdU-seq (Nature Methods, 2024)

value: neural

value: iPSC

value: Neural Organoids

value: Wild-type


title: Rectum_inflamed [I0380_RSDF_CosMx2.0]

description:
Cos31KxeniumcosmxI0380RSDF-polygons.csv
Cos31KxeniumcosmxI0380RSDF_exprMat_file.csv
Cos31KxeniumcosmxI0380RSDF_fov_positions_file.csv
Cos31KxeniumcosmxI0380RSDF_metadata_file.csv
Cos31KxeniumcosmxI0380RSDF_tx_file.csv


title: NCR-cre Imm NK cells, Exp1, Rep3


title: Rectum_inflamed [309r4327]

description:
Cos3wk6V306R309R4327_exprMat_file.csv
Cos3wk6V306R309R4327_fov_positions_file.csv
Cos3wk6V306R309R4327_metadata_file.csv
Cos3wk6V306R309R4327_tx_file.csv
Cos3wk6V306R309R4327-polygons.csv
fov 1-18


title: Rectum_HC [306r2314]

description:
Cos3wk4D306R309R2314_exprMat_file.csv
Cos3wk4D306R309R2314_fov_positions_file.csv
Cos3wk4D306R309R2314_metadata_file.csv
Cos3wk4D306R309R2314_tx_file.csv
Cos3wk4D306R309R2314-polygons.csv
fov 19-45


title: Rectum_inflamed [309r2327]

description:
Cos2wk6D306R309R2327_exprMat_file.csv
Cos2wk6D306R309R2327_fov_positions_file.csv
Cos2wk6D306R309R2327_metadata_file.csv
Cos2wk6D306R309R2327_tx_file.csv
Cos2wk6D306R309R2327-polygons.csv
fov 1-18


title: Rectum_noninflamed [267r4314]

description:
Cos1wk4V296R267R4314_exprMat_file.csv
Cos1wk4V296R267R4314_fov_positions_file.csv
Cos1wk4V296R267R4314_metadata_file.csv
Cos1wk4V296R267R4314_tx_file.csv
Cos1wk4V296R267R4314-polygons.csv
fov 1-21


title: Wild-type SOX2+ Neural organoids plate3

description:
Library name: JvB-198-SOX2-Neural-Organoids-WT-20E-F-pl3
2x100bp


title: Rectum_HC [306r2327]

description:
Cos2wk6D306R309R2327_exprMat_file.csv
Cos2wk6D306R309R2327_fov_positions_file.csv
Cos2wk6D306R309R2327_metadata_file.csv
Cos2wk6D306R309R2327_tx_file.csv
Cos2wk6D306R309R2327-polygons.csv
fov 19-1


title: NCR-cre Imm NK cells, Exp1, Rep1


title: Wild-type SOX2+ Neural organoids plate2

description:
Library name: JvB-198-SOX2-Neural-Organoids-WT-20E-F-pl2
2x100bp


title: Rectum_noninflamed [296r1314]

description:
Cos3wk4D296R267R1314_exprMat_file.csv
Cos3wk4D296R267R1314_fov_positions_file.csv
Cos3wk4D296R267R1314_metadata_file.csv
Cos3wk4D296R267R1314_tx_file.csv
Cos3wk4D296R267R1314-polygons.csv
fov 22-41


title: Rectum_noninflamed [267r4228]

description:
week2D296R267R4228_exprMat_file.csv
week2D296R267R4228_fov_positions_file.csv
week2D296R267R4228_metadata_file.csv
week2D296R267R4228_tx_file.csv
week2D296R267R4228-polygons.csv
fov 1-21


title: Rectum_noninflamed [267r1327]

description:
Cos2wk6D296R267R1327_exprMat_file.csv
Cos2wk6D296R267R1327_fov_positions_file.csv
Cos2wk6D296R267R1327_metadata_file.csv
Cos2wk6D296R267R1327_tx_file.csv
Cos2wk6D296R267R1327-polygons.csv
fov 1-21


title: Rectum_noninflamed [267r1315]

description:
Cos3wk4D296R267R1314_exprMat_file.csv
Cos3wk4D296R267R1314_fov_positions_file.csv
Cos3wk4D296R267R1314_metadata_file.csv
Cos3wk4D296R267R1314_tx_file.csv
Cos3wk4D296R267R1314-polygons.csv
fov 1-21


title: Rectum_inflamed [309r2314]

description:
Cos3wk4D306R309R2314_exprMat_file.csv
Cos3wk4D306R309R2314_fov_positions_file.csv
Cos3wk4D306R309R2314_metadata_file.csv
Cos3wk4D306R309R2314_tx_file.csv
Cos3wk4D306R309R2314-polygons.csv
fov 1-18


title: Wild-type SOX2+ Neural organoids plate4

description:
Library name: JvB-198-SOX2-Neural-Organoids-WT-20E-F-pl4
2x100bp


title: NCR-cre Imm NK cells, Exp1, Rep2


title: KANSL+/- SOX2+ Neural organoids plate4

description:
Library name: JvB-198-SOX2-Neural-Organoids-KANSL-20E-F-pl4
2x100bp

value: KANSL-


title: Wild-type SOX2+ Neural organoids plate5

description:
Library name: JvB-198-SOX2-Neural-Organoids-WT-20E-F-pl5
2x100bp


title: KANSL+/- SOX2+ Neural organoids plate7

description:
Library name: JvB-198-SOX2-Neural-Organoids-KANSL-20E-F-pl7
2x100bp


title: Rectum_HC [306r3314]

description:
Cos1wk4V306R309R3314_exprMat_file.csv
Cos1wk4V306R309R3314_fov_positions_file.csv
Cos1wk4V306R309R3314_metadata_file.csv
Cos1wk4V306R309R3314_tx_file.csv
Cos1wk4V306R309R3314-polygons.csv
fov 19-46


title: Rectum_HC [306r3228]

description:
week2D306R309R3228_exprMat_file.csv
week2D306R309R3228_fov_positions_file.csv
week2D306R309R3228_metadata_file.csv
week2D306R309R3228_tx_file.csv
week2D306R309R3228-polygons.csv
fov 19-46


title: Rectum_noninflamed [296r4228]

description:
week2D296R267R4228_exprMat_file.csv
week2D296R267R4228_fov_positions_file.csv
week2D296R267R4228_metadata_file.csv
week2D296R267R4228_tx_file.csv
week2D296R267R4228-polygons.csv
fov 22-41


title: KANSL+/- SOX2+ Neural organoids plate3

description:
Library name: JvB-198-SOX2-Neural-Organoids-KANSL-20E-F-pl3
2x100bp


title: Rectum_inflamed [309r1214]

description:
week0D306R309R1214_exprMat_file.csv
week0D306R309R1214_fov_positions_file.csv
week0D306R309R1214_metadata_file.csv
week0D306R309R1214_tx_file.csv
week0D306R309R1214-polygons.csv
fov 1-18


title: KANSL+/- SOX2+ Neural organoids plate2

description:
Library name: JvB-198-SOX2-Neural-Organoids-KANSL-20E-F-pl2
2x100bp


title: Rectum_noninflamed [296r4314]

description:
Cos1wk4V296R267R4314_exprMat_file.csv
Cos1wk4V296R267R4314_fov_positions_file.csv
Cos1wk4V296R267R4314_metadata_file.csv
Cos1wk4V296R267R4314_tx_file.csv
Cos1wk4V296R267R4314-polygons.csv
fov 22-41


title: Rectum_noninflamed [353_6_2138]

description:
353RSDF0624CMX2138_exprMat_file.csv
353RSDF0624CMX2138_fov_positions_file.csv
353RSDF0624CMX2138_metadata_file.csv
353RSDF0624CMX2138_tx_file.csv
353RSDF0624CMX2138-polygons.csv
fov 15-31


title: Rectum_HC [306r1214]

description:
week0D306R309R1214_exprMat_file.csv
week0D306R309R1214_fov_positions_file.csv
week0D306R309R1214_metadata_file.csv
week0D306R309R1214_tx_file.csv
week0D306R309R1214-polygons.csv
fov 19-46


title: Rectum_noninflamed [353_72_3439]

description:
353RSDF4872CMX3438_exprMat_file.csv
353RSDF4872CMX3438_fov_positions_file.csv
353RSDF4872CMX3438_metadata_file.csv
353RSDF4872CMX3438_tx_file.csv
353RSDF4872CMX3438-polygons.csv
fov 1-22


title: Rectum_inflamed [309r3228]

description:
week2D306R309R3228_exprMat_file.csv
week2D306R309R3228_fov_positions_file.csv
week2D306R309R3228_metadata_file.csv
week2D306R309R3228_tx_file.csv
week2D306R309R3228-polygons.csv
fov 1-18


title: Cardiomyocytes RRAGD S76L Diff 4

city: Nijmegen

first: Sara

last: van Katwijk

address: Geert Grooteplein Zuid 28

department: Medical BioSciences

institute: Radboudumc

description:
Library name: CMs-RRAGD-S76L-4
Column name in GRCh38.p13-counts.tsv S76L_diff_4

data_processing:
seq2science pipeline (https://vanheeringen-lab.github.io/seq2science/content/workflows/rna_seq.html)
Assembly: GRCh38.p14
Supplementary files format and content: tsv file of raw counts

source_name: hiPSC-CMs

growth_protocol: hiPSC-derived cardiomyocytes (hiPSC-CMs) were cultured in cardio culture medium (RPMI-1640 Medium with GlutaMAXTM Supplement with HEPES supplemented with B-27 Supplement 50x-serum free (#17504001, Thermo Fisher Scientific, California, USA) in humidified incubator at 37°C and 5% (v/v) CO2

extract_protocol:
Total RNA was extracted from 80-day old hiPSC-CMs using the Trizol Reagent (Invitrogen, Bleiswijk, The Netherlands) according to the manufacturer’s protocol.
RNA-Seq libraries were prepared from total RNA using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Massachusetts, USA). Oligo hybridization, rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to the manufacturer’s protocol.

value: hiPSC-CMs

value: Human induced pluripotent stem cell-derived cardiomyocytes

value: RRAGD WT/S76L

value: Cardiomyogenic differentiation


title: Cardiomyocytes RRAGD WT Diff 3

description:
Library name: CMs-RRAGD-WT-3
Column name in GRCh38.p13-counts.tsv WT_diff_3

value: RRAGD WT/WT


title: Rectum_noninflamed [353_6_3338]

description:
353RSDF0624CMX3338_exprMat_file.csv
353RSDF0624CMX3338_fov_positions_file.csv
353RSDF0624CMX3338_metadata_file.csv
353RSDF0624CMX3338_tx_file.csv
353RSDF0624CMX3338-polygons.csv
fov 17-27


title: Colon_HC [302c8]

description:
7um302628_exprMat_file.csv
7um302628_fov_positions_file.csv
7um302628_metadata_file.csv
7um302628_tx_file.csv
7um302628-polygons.csv
fov 1-13

source_name: human colon

value: Colon


title: Colon_HC [302c7]

description:
7um302628_exprMat_file.csv
7um302628_fov_positions_file.csv
7um302628_metadata_file.csv
7um302628_tx_file.csv
7um302628-polygons.csv
fov 14-26


title: hPA, non-targeting, INPUT, rep 3

city: Durham

first: Samuel

last: Reisman

state: NC

address: 1328 Campus Drive

institute: Duke University

description: Library name: hPA_NT_INPUT_rep3

data_processing:
Reads that aligned to the integrated lentiviral cargo were removed using Bowtie2. Remaining reads were then aligned to the hg38 reference genome, and PCR duplicates were removed using rmdup from SAMtools. Peaks were called in each replicate individually using MACS2. Peaks passing qval < .05 not in hg38 blacklist regions were then input to IDR analysis to identify high-confidence reproducible peaks across replicates. Peaks passing a stringent IDR threshold (IDR < 0.001) in all replicate comparisons within a condition were merged using BEDtools to generate per-gRNA peaksets, then a union peakset was generated by merging across gRNA conditions. BAM files were converted to normalized bigWig tracks using deepTools. For each sample, reads were extended to estimated fragment length and binned at 25 bp resolution. Genome coverage was computed with bamCoverage, applying read-per-genome-coverage (RPGC) normalization to an effective hg38 genome size of 2.91 Gb and masking ENCODE hg38 blacklist regions.
Assembly: hg38
Supplementary files format and content: .bed file of consensus IDR peaks, bigWigs

source_name: astrocyte

growth_protocol: Primary human astrocytes derived from the fetal cerebral cortex were purchased (Sciencell 1800) and routine cell culture was performed following the supplier’s protocol. Upon thawing, cells were seeded on plates coated with poly-D-lysine (PDL), and grown in Astrocyte Medium (Sciencell 1801) supplemented to 10% fetal bovine serum (Gibco) to encourage proliferation. Culture medium was replaced every two days until cultures reached 70% confluence, and subsequently every three days until cultures reached 95% confluence. To passage, cells were rinsed with PBS and dissociated using 0.025% trypsin. To eliminate residual potential progenitor cells and non-proliferative neuronal cells, astrocytes expanded for two passages. All experiments were initiated upon replating after the second passage reached confluence. Astrocytes were subjected to freeze/thaw cycles.

extract_protocol:
Supernatant containing sheared chromatin was incubated at 65°C overnight to reverse DNA-protein crosslinks. ChIP DNA was purified with QIAquick PCR Purification kit (Qiagen).
ChIP-seq libraries were constructed with a KAPA HyperPrep kit (Roche). ChIP DNA was quantified and amplified with 7 PCR cycles after KAPA adapter ligation. Libraries were pooled and sequenced with 1% PhiX spike-in on an Illumina NextSeq with a P4 XLEAP-SBS reagent kit.

treatment_protocol: ChIP experiments were performed in triplicate and harvested 8 days after transduction. For each replicate, 2 x 107 astrocytes were resuspended in Astrocyte Medium with 1% formaldehyde (Pierce) and fixed for 10 minutes at room temperature with gentle rocking. Fixation was blocked with 0.125 M glycine for 5 minutes. Cells were then washed twice with ice-cold PBS and resuspended in cell lysis buffer (5 mM HEPES, 85mM KCl, 0.5% NP-40 pH 8.0) with protease inhibitor. To facilitate nuclei extraction, cells were passed 15 times through a Dounce homogenizer before incubation for 15 minutes at 4°C. Nuclei were then resuspended in nuclear lysis buffer (50 mM Tris HCl, 10 mM EDTA, 0.1% SDS pH 8.1) and sonicated to 200-700 bp fragments using a Diagenode Bioruptor Pico for 15 cycles of 30 seconds on and 30 seconds off. Before IP, a sample was collected for input control. For each replicate, we conjugated 5 µg monoclonal Anti-FLAG M2 (Sigma F1804) to 200 µl Dynabeads M-280 Sheep Anti-Mouse IgG (Invitrogen 11201D). Sheared chromatin was then incubated with antibody-conjugated beads on a rotator overnight at 4°C. Beads were washed five times with a LiCl wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), and remaining ions were removed with a TE wash (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA). Chromatin fragments were eluted in an IP elution buffer (PBS, 1% SDS, 0.1M NaHCO3) at 65°C for 1 hour.

value: astrocyte

value: non-targeting

value: neuronal reprogramming


title: Colon_HC [302c5]

description:
6um302528_exprMat_file.csv
6um302528_fov_positions_file.csv
6um302528_metadata_file.csv
6um302528_tx_file.csv
6um302528-polygons.csv
fov 14-26


title: Cardiomyocytes RRAGD WT Diff 1

description:
Library name: CMs-RRAGD-WT-1
Column name in GRCh38.p13-counts.tsv WT_diff_1


title: Rectum_inflamed [309r3314]

description:
Cos1wk4V306R309R3314_exprMat_file.csv
Cos1wk4V306R309R3314_fov_positions_file.csv
Cos1wk4V306R309R3314_metadata_file.csv
Cos1wk4V306R309R3314_tx_file.csv
Cos1wk4V306R309R3314-polygons.csv
fov 1-18


title: Wild-type SOX2+ Neural organoids plate1

description:
Library name: JvB-198-SOX2-Neural-Organoids-WT-20E-F-pl1
2x100bp


title: KANSL+/- SOX2+ Neural organoids plate6

description:
Library name: JvB-198-SOX2-Neural-Organoids-KANSL-20E-F-pl6
2x100bp


title: Colon_HC [302c3]

description:
5um302428_exprMat_file.csv
5um302428_fov_positions_file.csv
5um302428_metadata_file.csv
5um302428_tx_file.csv
5um302428-polygons.csv
fov 14-26


title: Rectum_noninflamed [267r2214]

description:
week0D296R267R2214_exprMat_file.csv
week0D296R267R2214_fov_positions_file.csv
week0D296R267R2214_metadata_file.csv
week0D296R267R2214_tx_file.csv
week0D296R267R2214-polygons.csv
fov 1-21


title: Wild-type SOX2+ Neural organoids plate6

description:
Library name: JvB-198-SOX2-Neural-Organoids-WT-20E-F-pl6
2x100bp


title: hPA, non-targeting, ChIP, rep 2

description: Library name: hPA_NT_ChIP_rep2


title: KANSL+/- SOX2+ Neural organoids plate1

description:
Library name: JvB-198-SOX2-Neural-Organoids-KANSL-20E-F-pl1
2x100bp


title: KANSL+/- SOX2+ Neural organoids plate5

description:
Library name: JvB-198-SOX2-Neural-Organoids-KANSL-20E-F-pl5
2x100bp


title: Rectum_HC [I0400 RSCF00A CosMx6k]

description:
Cos1400R355RRNA6K4u1716_exprMat_file.csv
Cos1400R355RRNA6K4u1716_fov_positions_file.csv
Cos1400R355RRNA6K4u1716_metadata_file.csv
Cos1400R355RRNA6K4u1716_tx_file.csv
Cos1400R355RRNA6K4u1716-polygons.csv
fov 32-65


title: Rectum_noninflamed [296r2214]

description:
week0D296R267R2214_exprMat_file.csv
week0D296R267R2214_fov_positions_file.csv
week0D296R267R2214_metadata_file.csv
week0D296R267R2214_tx_file.csv
week0D296R267R2214-polygons.csv
fov 22-41


title: Cardiomyocytes RRAGD S76L Diff 3

description:
Library name: CMs-RRAGD-S76L-3
Column name in GRCh38.p13-counts.tsv S76L_diff_3


title: Rectum_noninflamed [353_24_2138]

description:
353RSDF0624CMX2138_exprMat_file.csv
353RSDF0624CMX2138_fov_positions_file.csv
353RSDF0624CMX2138_metadata_file.csv
353RSDF0624CMX2138_tx_file.csv
353RSDF0624CMX2138-polygons.csv
fov 1-14


title: Rectum_UC_Noninflamed [I0276 RSDF00A CosMx1k]

description:
I0284RI0276R2119_exprMat_file.csv
I0284RI0276R2119_fov_positions_file.csv
I0284RI0276R2119_metadata_file.csv
I0284RI0276R2119_tx_file.csv
I0284RI0276R2119-polygons.csv
fov 1-13


title: dHepaRG cells, HDVIL29, rep3

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: Library name: HDVIL29_3

data_processing:
Paired-end clean reads were aligned to the human reference genome (version hg38) using HISAT2 v2.0.5 (Mortazavi et al., 2008).
The mapped reads for each sample were assembled with StringTie v1.3.3b in a reference-guided approach (Pertea et al., 2015).
FeatureCounts v1.5.0-p3 (Liao et al., 2014) was used to count the number of reads mapped to each gene, and FPKM values were calculated
For samples with biological replicates, differential expression analysis was performed using the DESeq2 R package (v1.20.0) (Love et al., 2014).
The resulting p-values were adjusted using the Benjamini-Hochberg method to control the false discovery rate.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each sample, and differential expression results

source_name: dHepaRG cells

extract_protocol:
Total intracellular RNA was purified using the Monarch Nucleic Acid Purification Kit (New England Biolabs)
RNA-seq libraries were prepared with the NEB-Next® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA).Messenger RNA was isolated from total RNA using poly-T oligo-attached magnetic beads. cDNA was synthesized, and libraries were prepared as previously described (Parkhomchuk et al., 2009).

value: dHepaRG cells

value: day 6

value: HDV + IFN-λ1


title: Cardiomyocytes RRAGD WT Diff 4

description:
Library name: CMs-RRAGD-WT-4
Column name in GRCh38.p13-counts.tsv WT_diff_4


title: hPA, non-targeting, ChIP, rep 3

description: Library name: hPA_NT_ChIP_rep3


title: dHepaRG cells, HDVIFNa, rep3

description: Library name: HDVIFNa_3

value: HDV + IFN-α-2a


title: hPA, non-targeting, INPUT, rep 2

description: Library name: hPA_NT_INPUT_rep2


title: Rectum_noninflamed [353_48_3438]

description:
353RSDF4872CMX3438_exprMat_file.csv
353RSDF4872CMX3438_fov_positions_file.csv
353RSDF4872CMX3438_metadata_file.csv
353RSDF4872CMX3438_tx_file.csv
353RSDF4872CMX3438-polygons.csv
fov 23-29

value: Rectum


title: Cardiomyocytes RRAGD S76L Diff 1

description:
Library name: CMs-RRAGD-S76L-1
Column name in GRCh38.p13-counts.tsv S76L_diff_1


title: Cardiomyocytes RRAGD S76L Diff 2

description:
Library name: CMs-RRAGD-S76L-2
Column name in GRCh38.p13-counts.tsv S76L_diff_2


title: Colon_HC [302c1]

description:
4um302328_exprMat_file.csv
4um302328_fov_positions_file.csv
4um302328_metadata_file.csv
4um302328_tx_file.csv
4um302328-polygons.csv
fov 14-26


title: hPA, gRNA-hit, ChIP, rep 2

description: Library name: hPA_gRNAhit_ChIP_rep2

value: gRNA-hit


title: Rectum_noninflamed [353_24_3338]

description:
353RSDF0624CMX3338_exprMat_file.csv
353RSDF0624CMX3338_fov_positions_file.csv
353RSDF0624CMX3338_metadata_file.csv
353RSDF0624CMX3338_tx_file.csv
353RSDF0624CMX3338-polygons.csv
fov 1-16


title: Colon_HC [302c2]

description:
4um302328_exprMat_file.csv
4um302328_fov_positions_file.csv
4um302328_metadata_file.csv
4um302328_tx_file.csv
4um302328-polygons.csv
fov 1-13


title: Ileum_UC_Noninflamed [I0310 ITDF00A CosMx1k]

description:
321I310I128_exprMat_file.csv
321I310I128_fov_positions_file.csv
321I310I128_metadata_file.csv
321I310I128_tx_file.csv
321I310I128-polygons.csv
fov 1-28

source_name: human Ileum

value: Ileum


title: Rectum_UC_Noninflamed [I0355 RSDF00A CosMx6k]

description:
Cos1400R355RRNA6K4u1716_exprMat_file.csv
Cos1400R355RRNA6K4u1716_fov_positions_file.csv
Cos1400R355RRNA6K4u1716_metadata_file.csv
Cos1400R355RRNA6K4u1716_tx_file.csv
Cos1400R355RRNA6K4u1716-polygons.csv
fov 1-31


title: hPA, non-targeting, INPUT, rep 1

description: Library name: hPA_NT_INPUT_rep1


title: Rectum_UC_Inflamed [I0387 RSDF00A CosMx6k]

description:
Cos1380R387RRNA6K4u2716_exprMat_file.csv
Cos1380R387RRNA6K4u2716_fov_positions_file.csv
Cos1380R387RRNA6K4u2716_metadata_file.csv
Cos1380R387RRNA6K4u2716_tx_file.csv
Cos1380R387RRNA6K4u2716-polygons.csv
fov 1-17


title: Colon_HC [302c6]

description:
6um302528_exprMat_file.csv
6um302528_fov_positions_file.csv
6um302528_metadata_file.csv
6um302528_tx_file.csv
6um302528-polygons.csv
fov 1-13


title: hPA, gRNA-hit, ChIP, rep 3

description: Library name: hPA_gRNAhit_ChIP_rep3


title: Rectum_CD_Inflamed [I0294 RSDF00A CosMx1k ]

description:
294R303R1124_exprMat_file.csv
294R303R1124_fov_positions_file.csv
294R303R1124_metadata_file.csv
294R303R1124_tx_file.csv
294R303R1124-polygons.csv
fov 12-29