title: Hepa 1-6 cell, WT4

city: Hangzhou

first: xinxin

last: chai

state: State...

address: Zhejiang，Hangzhou

institute: Zhejiang University

description: Library name: WT4

data_processing:
Quality control of raw sequence data was performed using FastQC, and adapters and low-quality bases were trimmed using Trimmomatic. Clean reads were aligned to the Ensembl mouse reference genome (GCF_000001635.26_GRCm38.p6) using HISAT2 with default parameters.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: txt files inculde counts of each samples

source_name: Liver

extract_protocol:
Total RNA was extracted from cells and tissues using TRIzol reagent according to the manufacturer's instruction. 1 μg of total RNA was used for the consturction of sequceing libraries
RNA-seq libraries were constructed from purified RNA using the SMARTer mRNA-Seq Library Prep Kit according to the manufacturer’s instructions, including poly-A selection, cDNA synthesis, fragmentation, adapter ligation, and PCR amplification.)

value: Liver

value: Hepa 1-6

value: Liver cancer cell


title: A549 cells, RELA ChIP, I+B, 1h, rep 1

status: Public on Oct 31 2025

type: SRA

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

description: Library name: Sample 15

library_source: genomic

data_processing:
Demultiplexing was performed using bcl2fastq conversion software (v2.18.0.12) and read quality was assessed using FastQC (v0.10.1).
Good-quality reads were mapped to GRCh38 reference genome using bowtie2 (v2.4.4) and the resultant BAM files were sorted and indexed using samtools (v) prior to peak calling using MACS2 (v2.2.7.1). MACS-identified peaks for GR and RELA were assessed by DiffBind R package (v3.2) to calculate differential binding in response to each treatment compared to no stimulation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes peak names, locations, binding intensity, and behaviour by treatment.
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The human pulmonary type II cell line, A549, was grown under standard culture condition using Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine. Cells were incubated at 37°C in 5% CO2 and were grown to confluence either in 100mm, or 6/12/24-well plates, as appropriate. Prior to experiments, cells were incubated overnight in basal media that was serum- and additive-free.

extract_protocol:
Protein-DNA cross-linking was performed by adding methanol-free formaldehyde to 1% in the culture medium and incubating for 10 min at room temperature. Formaldehyde was then quenched at room temperature for 5 min with 125mM glycine prior to washing cells for 5 min with ice-cold PBS and scraping into ice-cold lysis buffer (5mM PIPES pH 8.0, 1mM EDTA, 85mM KCl, 5% glycerol, 0.5% NP-40) supplemented with protease inhibitor cocktail (PIC). Cell suspensions were incubated at 4°C for 3 h with continuous agitation. Nuclei were collected by centrifugation (600 g, 5 min, 4°C) and resuspended in ice-cold nuclei lysis buffer (NLB) (1xPBS containing 1mM EDTA, 5% glycerol, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40) supplemented with PIC. Samples were sonicated at 4°C using a Bioruptor set for 28 – 30 high-power bursts with 30 s on-off cycles. Lysates were cleared by centrifugation (maximum speed for 15 min at 4°C) and supernatants used for immunoprecipitation. Protein G magnetic Dynabeads were preincubated with primary antibody (2.5µl/sample) overnight at 4 °C in NLB supplemented with PIC and 5 mg/ml BSA. After washing twice with ice-cold NLB plus PIC, the Dynabeads were incubated with cleared lysates overnight at 4°C in NLB supplemented with PIC and BSA. Beads were given 4 washes with ice-cold NLB containing 500mM NaCl, followed by 4 washes with ice-cold LiCl buffer (20mM Tris at pH 8.0, 1 mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate). Crosslinks were reversed by incubation in TE buffer (10mM Tris-HCl,1mM EDTA, pH 8.0) supplemented with 0.7% SDS and 0.2 mg/ml proteinase K for 3h at 55 °C, then 16 h at 65°C. DNA was purified with a ChIP DNA Clean & Concentrator kit.
ChIP-seq libraries were prepared using the NEB Ultra II kit.

treatment_protocol: Budesonide was dissolved in DMSO as a 10mM stock. Unless specifically indicated, budesonide was used at 300nM on cells, representing a concentration that was maximally effective/near maximal on a 2×GRE reporter and gene expression in A549 cells. Final DMSO concentrations on cells were ≤ 0.1%. Recombinant human IL1B was dissolved in phosphate-buffered saline (PBS) containing 0.1% bovine serum albumin (BSA). IL1B was previously found to be maximally or near maximally effective on NF-κB reporters and gene expression at 1ng/ml and this concentration was used in all experiments unless specifically indicated. Following overnight incubation in serum free medium, cells were changed to fresh serum free medium and either not stimulated (NS) or treated with, IL1B, budesonide (Bud) or IL1B plus budesonide (I+B) for the indicated times prior to harvesting for RNA extraction. Data are from two independent experiments.

tag: cell line

tag: cell type

value: lung carcinoma epithelial cells

tag: genotype

value: WT

tag: treatment

value: I+B

tag: chip antibody

value: RELA (Cell Signaling, #8242S)


title: A549 cells, RELA ChIP, I+B, 1h, rep 2

description: Library name: Sample 16


title: Hepa 1-6 cell, WT3

country: China

description: Library name: WT3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: A549 cells, RELA ChIP, Bud, 1h, rep 1

description: Library name: Sample 13

value: Bud


title: A549 cells, RELA ChIP, IL1B, 1h, rep 2

description: Library name: Sample 12


title: Hepa 1-6 cell, WT2

description: Library name: WT2


title: Hepa 1-6 cell, WT1

description: Library name: WT1


title: A549 cells, RELA ChIP, NS, 1h, rep 2

description: Library name: Sample 10

value: NS


title: Hepa 1-6 cell, G9a knockout4

description: Library name: A494

value: G9a knockout


title: A549 cells, GR ChIP, I+B, 1h, rep 1

description: Library name: Sample 7

value: GR356 (Sasse et al., 2019)


title: Hepa 1-6 cell, G9a knockout2

description: Library name: A492


title: Hepa 1-6 cell, G9a knockout3

description: Library name: A493


title: A549 cells, GR ChIP, I+B, 1h, rep 2

description: Library name: Sample 8


title: A549 cells, GR ChIP, Bud, 1h, rep 2

description: Library name: Sample 6


title: 3_39877, tumor, OSE-BPR GEMM

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

country: USA

institute: Frederick National Laboratory for Cancer Research

description: Library name: 3_39877

data_processing:
32 mRNA-Seq samples were pooled and sequenced on NovaSeq 6000 SP using Illumina® Stranded mRNA Prep and paired-end sequencing. The samples have 37 to 56 million pass filter reads with more than 91% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. The average mapping rate of all samples is 93%. Unique alignment is above 83%. There are 5.13 to 7.10% unmapped reads. The mapping statistics are calculated using Picard software. The samples have 0.32% ribosomal bases. Percent coding bases are between 45-52%. Percent UTR bases are 34-37%, and mRNA bases are between 80-88% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 77-88% non-duplicate reads.
Basecalling RTA v3.4.4 Illumina instrument run time analysis software
Illumina bcl2fastq2.20 was used to demultiplex and convert binary base calls and quality scores to fastq format
The sequencing reads were trimmed of adapters and low quality bases using Cutadapt (version 1.18).
The trimmed reads were mapped to mouse reference genome (GRCm38/mm10) and Gencode annotation M21 using  STAR aligner (version 2.7.0f) with two-pass alignment option.
RSEM (version 1.3.1) was used for gene and transcript quantification based on GENCODE annotation file.
Assembly: Mouse_mm10
Supplementary files format and content: tab-delimited text files include raw count  values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: tumor

growth_protocol: mouse ovarian tumors developed in vivo

extract_protocol:
total RNA extracted with RNAeasy mini kit Qiagen
RNAseq

value: tumor

tag: strain

value: FVB

tag: model

value: OSE-BPR GEMM

value: Brca1 fl/fl, Trp53 fl/fl, K18GT121 Tg/+

tag: Sex

value: female


title: Hepa 1-6 cell, G9a knockout1

description: Library name: A491


title: A549 cells, GR ChIP, IL1B, 1h, rep 2

description: Library name: Sample 4


title: A549 cells, GR ChIP, Bud, 1h, rep 1

description: Library name: Sample 5


title: A549 cells, GR ChIP, IL1B, 1h, rep 1

description: Library name: Sample 3


title: Transcriptome of v-3w-169

city: Tsu

first: Kazuaki

last: Maruyama

state: Mie

address: 2-174, Edobashi

country: Japan

institute: Mie University, Graduate school of medicine, Department of Pathology and Matrix Biology

description:
Library name: v-3w-169
Illumina NovaSeq 6000

data_processing:
FASTQ files were processed using Trim Galore v0.6.10 for adapter trimming, aligned to GRCm39 with STAR v2.7.10a, and quantified with featureCounts (Subread v2.0.1). Differential expression analysis was performed using DESeq2 (v1.38.3), and visualization was done with iDEP (v2.01).
Assembly: GRCm39 (Ensembl Release 108)
Supplementary files format and content: The file "processed_counts_for_GEO.tsv" contains log-normalized gene expression values generated from DESeq2 analysis. Rows correspond to genes (Ensembl IDs or symbols), and columns correspond to each sample (library name). Values represent log-transformed normalized counts.

source_name: Heart

growth_protocol: Mice (BALB/cAJcl, 10 weeks old) were housed in specific pathogen-free conditions in the Mie University animal facility. Both male and female mice were used for initial assessments; only males were used for RNA-seq experiments.

extract_protocol:
Total RNA was extracted from heart tissues using Isogen reagent (Nippon Gene) following the manufacturer's instructions. RNA quality was assessed by NanoDrop and 2100 Bioanalyzer (Agilent). Samples with RIN > 8.0 were used for downstream processing.
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on the Illumina NovaSeq 6000 platform (Osaka University NGS Core Facility).

treatment_protocol: Mice were treated with VEGF-C C156S (1 μg/day) or PBS via intraperitoneal injection from Day 7 to Day 10 following cardiac myosin immunization.

value: Heart

value: VEGF-C


title: Transcriptome of v-3w-165

description:
Library name: v-3w-165
Illumina NovaSeq 6000


title: Transcriptome of v-3w-164

description:
Library name: v-3w-164
Illumina NovaSeq 6000


title: Transcriptome of c-3w-256

description:
Library name: c-3w-256
Illumina NovaSeq 6000

value: PBS


title: A549 cells, GR ChIP, NS, 1h, rep 2

description: Library name: Sample 2


title: Transcriptome of c-3w-254

description:
Library name: c-3w-254
Illumina NovaSeq 6000


title: Transcriptome of c-3w-255

description:
Library name: c-3w-255
Illumina NovaSeq 6000


title: A549 cells, GR ChIP, NS, 1h, rep 1

description: Library name: Sample 1


title: L15_SiLacZ

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr.Homi Bhaba road, Pashan

country: India

institute: INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH,Pune

description: Library name: Sample 2

data_processing:
Reference-based RNA-Seq data analysis on Galaxy
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: Colorectal

growth_protocol: For a 75 cm² flask, the specified volumes should be adjusted proportionally for different culture vessel sizes. Begin by removing and discarding the culture medium, followed by a brief rinse with 0.25% (w/v) Trypsin-0.53 mM EDTA solution to eliminate any residual serum, which may inhibit trypsin activity. Next, add 2.0 to 3.0 mL of Trypsin-EDTA solution and monitor cell detachment under an inverted microscope, typically occurring within 5 to 15 minutes. To prevent clumping, avoid agitating the flask by shaking or tapping. If cells are resistant to detachment, incubating at 37°C may aid dispersal. Once detached, add 6.0 to 8.0 mL of complete growth medium and resuspend cells by gentle pipetting. Transfer appropriate aliquots of the cell suspension to new culture vessels and incubate at 37°C to promote growth.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: siRNA transfection (50nM, final concentration) was done for 72h and cell were harvested in TRIzol

value: Colorectal

value: Transformed


title: F15_SiFBL

description: Library name: Sample 4


title: Transcriptome of v-3w-168

description:
Library name: v-3w-168
Illumina NovaSeq 6000


title: A549 cells, RELA ChIP, IL1B, 1h, rep 1

description: Library name: Sample 11

value: lung carcinoma epithelial cells

value: WT


title: Transcriptome of c-3w-250

description:
Library name: c-3w-250
Illumina NovaSeq 6000


title: A549 cells, RELA ChIP, NS, 1h, rep 1

description: Library name: Sample 9

value: RELA (Cell Signaling, #8242S)


title: L13_SiLacZ

description: Library name: Sample 1


title: group3_SCI+CX546_rep2

city: Toronto

first: Laureen

last: Hachem

state: Ontario

address: 60 Leonard Ave

institute: University of Toronto

description:
Library name: LM25
group 3 (SCI+CX546)_rep2

library_source: transcriptomic single cell

data_processing:
Droplet libraries were processed using cellranger pipeline. Sequencing reads were aligned to the mm10 mouse reference genome, and transcript counts were quantified for each annotated gene within every cell.
Assembly: mm10
Supplementary files format and content: An h5 file containing Cell Ranger count pipeline output for raw or filtered cell-feature data: columns contain UMI counts across cells; rows contain features.

source_name: spinal cord

extract_protocol:
Mice used for snRNAseq were perfused with sterile PBS and a 0.6cm section of spinal cord tissue centered on the injury epicenter (or corresponding C6/7 level in uninjured animals) was extracted and snap frozen in liquid nitrogen. Tissue was cut into 1-2mm3 pieces, lysis buffer was applied and then tissue homogenized. Samples were centrifuged and washed then filtered with a 40um strainer. Nuclei were stained with DAPI and FACS sorted to remove debris and dead nuclei.
snRNAseq library preparation was carried out using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit Version 3.

value: spinal cord


title: U2OS, IFNb, 8h, rep6

city: Princeton

first: Cameron

last: Myhrvold

state: NJ

address: Washington Street, Moffett, 161

department: Molecular Biology

institute: Princeton University

description: Library name: sAB0018

data_processing:
Reads were demultiplexed with Picard v2.25.6 (from within viral-core v.2.3.1) using Q20M1 mismatch tolerance and the read structure flag '112T16S8B2S'
Demultiplexed reads were mapped to the human genome hg38 with STAR v2.7.11b
Uniquely maped reads to the comprehensive gene annotation on the primary assembly with htseq-count v2.0.5.
Assembly: hg38, GENCODE release 39
Supplementary files format and content: raw counts, csv

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using a Quick-RNA MidiPrep kit.
Purified total RNA samples were first examined on Bioanalyzer 2100 using RNA 6000 Pico chip to evaluate the integrity and concentration (Agilent Technologies, CA), then normalized onto 96-well plates.  The poly-A containing RNA transcripts in these samples were converted to cDNA using barcoded oligo-dT primers in the reverse transcription reaction to index each sample following the drop-seq method (Macosko EZ et al, Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214). The pooled barcoded cDNA samples were amplified by PCR and purified, then turned into sequencing libraries using the Illumina Tagment DNA Enzyme and Buffer kit (Illumina, CA) to include only the poly-A tail adjacent 3’ ends of RNA transcripts.  These libraries were examined on the Bioanalyzer (Agilent, CA) DNA HS chips for size distribution and quantified by Qubit fluorometer (Invitrogen, CA), then sequenced on Illumina NovaSeq 6000 S Prime flowcell using the 100 cycle v1.5 kit.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: U2OS cells were plated at 250,000 in 6 well plates and the following day treated with 1000 IU/ml IFN-beta for 0, 4, 8h.

value: osteosarcoma

value: naive

value: IFNb

tag: replicate

tag: time

value: 8 hours


title: U2OS, IFNb, 8h, rep5

description: Library name: sAB0017


title: group3_SCI+CX546_rep1

description:
Library name: LM16
group 3 (SCI+CX546)_rep1


title: group2_SCI_rep4

description:
Library name: LM32
group 2 (SCI)_rep4

value: SCI


title: group2_SCI_rep3

description:
Library name: LM29
group 2 (SCI)_rep3


title: F13_SiFBL

description: Library name: Sample 3


title: U2OS, IFNb, 8h, rep2

description: Library name: sAB0014


title: U2OS, IFNb, 8h, rep1

description: Library name: sAB0013


title: U2OS, IFNb, 4h, rep6

description: Library name: sAB0012

value: 4 hours


title: group2_SCI_rep1

description:
Library name: LM15
group 2 (SCI)_rep1


title: U2OS, IFNb, 4h, rep5

description: Library name: sAB0011


title: group1_no SCI_rep2

description:
Library name: LM41
group 1 (no SCI)_rep2

value: no SCI


title: U2OS, IFNb, 4h, rep3

description: Library name: sAB0009


title: group3_SCI+CX546_rep4

description:
Library name: LM37
group 3 (SCI+CX546)_rep4


title: U2OS, IFNb, 4h, rep4

description: Library name: sAB0010


title: group1_no SCI_rep4

description:
Library name: LM47
group 1 (no SCI)_rep4


title: JLA_M3_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

description: Library name: JLA_M3_SPN_48H_inconclusive_infection

data_processing:
FASTQ files were mapped to the Mus musculus reference genome using HISAT.
Gene expression counts for all samples were estimated using HTseq
Supplementary files format and content: Tab-delimited raw HTSeq counts of gene expression for Mus musculus.
Assembly: GRCm38.p3

source_name: Whole lung homogenate

growth_protocol: Male and female 9-week-old C57BL/6J mice were purchased from The Jackson Laboratory (Bar Harbor, ME). Mice were housed at 21°C in a 12-hour light/dark cycle and administered food and water ad libitum.

extract_protocol:
Samples were incubated in 100 μL of lysis buffer (10 μL of mutanolysin, 20 μL of proteinase K, 30 μL of lysozyme, 40 μL of TE buffer) for 10 minutes. Followed by mechanical disruption in 600 μL RLT buffer (RNeasy Mini Kit, Qiagen) containing 1% ß-mercaptoethanol, using a motorized pestle for 30 seconds (36). RNA was then captured on the RNeasy Mini Kit columns with DNase treatment on column (Qiagen protocol).Extracted RNA was quantitated using a Bioanalyzer.
300 bp-insert RNA-seq Illumina libraries were constructed using ~1.0 μg of enriched mRNA that was fragmented then used for synthesis of strand-specific cDNA using the NEBnext Ultra Directional RNA Library Prep Kit (NEB-E7420L). The cDNA was purified between enzymatic reactions and the size selection of the library performed with AMPure SpriSelect Beads (Beckman Coulter Genomics). The titer and size of the libraries was assessed on the LabChip GX (Perkin Elmer) and with the Library Quantification Kit (Kapa Biosciences). RNA-seq was conducted on 150 nt paired-end runs of the Illumina NovaSeq 6000 platform using two or three biological replicates for each condition

treatment_protocol: Mice were anesthetized with 2.5% vaporized isoflurane in oxygen. Mice were intranasally infected by dropwise instillation into the nares with 250 plaque-forming units (PFU) of Influenza A virus PR8 (H1N1 A/Puerto Rico/8/1934) in 50 ul of phosphate buffered saline (PBS). Between 7-9 days post-infection (dpi), or after each animal had lost ~10% of their original body weight pre-infection, mice were anesthetized and challenged intratracheally with 107 CFU in 100 ul of PBS of Spn strain EF3030 (serotype 19F) by forced tracheal aspiration (1). Infected mice were monitored daily throughout, and euthanized post Spn infection at 12, 24, and 48 hours. For the collection of lung samples, lungs were first perfused with 3 mL of ice-cold PBS using a 27-gauge needle via the cardiac route (2) and then excised. The middle lung lobe was homogenized in 1 mL of PBS, serially diluted, and plated onto 5% sheep’s blood agar plates for colony-forming unit (CFU) enumeration. The remaining tissue was cut into small pieces and placed into 5 mL of RNAprotect® Bacteria Reagent (Qiagen, #76506) and stored at -20 C°.

value: Whole lung homogenate

value: Male

value: Streptococcus pneumoniae EF3030


title: group1_no SCI_rep1

description:
Library name: LM40
group 1 (no SCI)_rep1


title: U2OS, untreated, n/a, rep6

description: Library name: sAB0006

value: Untreated


title: JLA_M3_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M3_SPN_24H_inconclusive_infection


title: U2OS, IFNb, 4h, rep1

description: Library name: sAB0007


title: JLA_M3_SPN_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_M3_SPN_12H_inconclusive_infection


title: U2OS, untreated, n/a, rep5

description: Library name: sAB0005


title: group3_SCI+CX546_rep3

description:
Library name: LM30
group 3 (SCI+CX546)_rep3


title: U2OS, IFNb, 8h, rep4

description: Library name: sAB0016


title: U2OS, IFNb, 8h, rep3

description: Library name: sAB0015


title: JLA_M3_PBS_48H_inconclusive_mock_infection, lung harvested 48 hours post infection

description: Library name: JLA_M3_PBS_48H_inconclusive_infection


title: group2_SCI_rep2

description:
Library name: LM26
group 2 (SCI)_rep2


title: JLA_M3_IAV_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M3_IAV_SPN_24H_inconclusive_infection

value: Streptococcus pneumoniae EF3030, Influenza A virus (A/California/07/2009(H1N1))


title: JLA_M3_IAV_SPN_48H, lung harvested 48 hours post infection

description: Library name: JLA_M3_IAV_SPN_48H


title: U2OS, untreated, n/a, rep3

description: Library name: sAB0003


title: JLA_M3_IAV_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_M3_IAV_48H_inconclusive_infection

value: Influenza A virus (A/California/07/2009(H1N1))


title: group1_no SCI_rep3

description:
Library name: LM46
group 1 (no SCI)_rep3


title: JLA_M3_IAV_SPN_12H, lung harvested 12 hours post infection

description: Library name: JLA_M3_IAV_SPN_12H


title: U2OS, untreated, n/a, rep1

description: Library name: sAB0001


title: P780L_3

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

country: France

institute: UMR1078 - Université de Bretagne Occidentale

description: Library name: P780L_3

data_processing:
After sequencing, raw data were obtained in the fastq format. The software FastQC (was used for validating the quality of the data and Trimmomatic was used for trimming of the adaptor content and over-represented sequences. The alignment of the trimmed sequences to the human transcriptome, was performed with the Kallisto tool.
Assembly: Hs.Ensembl104_transgene
Supplementary files format and content: Final normalization was performed using the Relative Log Expression (RLE) method, the R-package Tximport was used to convert the transcript quantifications to gene quantifications  and differential expressed genes were identified with R-package DESeq2

extract_protocol:
RNA was extracted using Nucleospin RNA kit (Macherey-Nagel). RNA Integrity Numbers ranged from 9.1 to 9.8.
rRNA removal and Directional library preparation.


title: U2OS, IFNb, 4h, rep2

description: Library name: sAB0008


title: U2OS, untreated, n/a, rep2

description: Library name: sAB0002


title: JLA_M3_IAV_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M3_IAV_24H_inconclusive_infection


title: P780L_2

description: Library name: P780L_2


title: JLA_M2_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_M2_SPN_48H_inconclusive_infection


title: P780L_1

description: Library name: P780L_1


title: JLA_M3_IAV_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_M3_IAV_12H_inconclusive_infection


title: N829S_1

description: Library name: N829S_1


title: JLA_M2_PBS_48H_inconclusive_mock_infection, lung harvested 48 hours post infection

description: Library name: JLA_M2_PBS_48H_inconclusive_infection


title: U2OS, untreated, n/a, rep4

description: Library name: sAB0004


title: E722K_2

description: Library name: E722K_2


title: JLA_M2_IAV_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_M2_IAV_SPN_48H_inconclusive_infection


title: JLA_M2_IAV_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M2_IAV_SPN_24H_inconclusive_infection


title: E722K_1

description: Library name: E722K_1


title: K700E_3

description: Library name: K700E_3


title: JLA_M2_IAV_SPN_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_M2_IAV_SPN_12H_inconclusive_infection


title: JLA_M2_IAV_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_M2_IAV_48H_inconclusive_infection


title: JLA_M2_IAV_24H, lung harvested 24 hours post infection

description: Library name: JLA_M2_IAV_24H


title: K700E_2

description: Library name: K700E_2


title: K700E_1

description: Library name: K700E_1


title: WT_3

description: Library name: WT_3


title: WT_2

description: Library name: WT_2


title: N829S_3

description: Library name: N829S_3


title: WT_1

description: Library name: WT_1


title: N829S_2

description: Library name: N829S_2


title: JLA_M2_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M2_SPN_24H_inconclusive_infection


title: JLA_M1_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_M1_SPN_48H_inconclusive_infection


title: JLA_M1_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M1_SPN_24H_inconclusive_infection


title: MUT3_IM5_1

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

data_processing:
Raw sequencing reads were processed using the Rsubread package (version 2.10.4) for alignment and quantification.
Assembly: hg19
Supplementary files format and content: feature_counts.txt

source_name: microglia

growth_protocol: Macrophage precursors were harvested bi-weekly. 50.000 or 1x106 macrophage precursors were plated in either 96 or 6 well plates. Cells were cultured in basal microglia differentiation medium consisting of Advanced DMEM/F12 (ThermoFisher Scientific, 35050061), 1x N2 (ThermoFisher Scientific, 17502001), 1x Pen/Strep (Invitrogen, 15140122), 1x GlutaMax (ThermoFisher Scientific, 35050061), 50 µM β-Mercaptoethanol (ThermoFisher Scientific, 31350-010) supplemented with 100 ng/ml IL-34 (Biolegend, 577906), and 10 ng/ml GM-CSF (Biolegend, 572905) as described previously. The protocol was adapted from a previousl publication (Sabate Soler, 2022).

extract_protocol:
RNA was extracted using Qiazol (QIAGEN #79306). 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using Novogene’s property library prep protocols (Novogene NGS RNA Library Prep Set PT042 for 250-300 bp insert cDNA library). Indices were incorporated to multiplex multiple samples. mRNA was purified using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by a second strand cDNA synthesis. Library preparation was finalized following end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, insert size of the library was validated on an Agilent 2100 and quantified using RT-PCR. Libraries were sequenced using Illumina NovaSeq 6000 S4 flowcell with PE150.

treatment_protocol: Untreated

value: microglia

value: human induced pluripotent stem cells

value: Microglia

tag: disease state

value: Parkinson’s disease


title: JLA_M1_IAV_SPN_48H, lung harvested 48 hours post infection

description: Library name: JLA_M1_IAV_SPN_48H


title: JLA_M1_SPN_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_M1_SPN_12H_inconclusive_infection


title: E722K_3

description: Library name: E722K_3


title: JLA_M2_SPN_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_M2_SPN_12H_inconclusive_infection


title: JLA_M1_IAV_SPN_12H, lung harvested 12 hours post infection

description: Library name: JLA_M1_IAV_SPN_12H


title: JLA_M1_IAV_48H, lung harvested 48 hours post infection

description: Library name: JLA_M1_IAV_48H


title: WT3_201_1

value: WT

value: healthy


title: JLA_M1_IAV_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M1_IAV_24H_inconclusive_infection


title: JLA_M2_IAV_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_M2_IAV_12H_inconclusive_infection


title: WT2_BIL_1


title: JLA_F3_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_F3_SPN_48H_inconclusive_infection

value: Female


title: JLA_M1_PBS_48H_inconclusive_mock_infection, lung harvested 48 hours post infection

description: Library name: JLA_M1_PBS_48H_inconclusive_infection


title: MUT4_T46_1


title: WT4_262_1


title: JLA_F3_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_F3_SPN_24H_inconclusive_infection


title: WT1_389_1


title: SW480 cells, MUCP1-FLAG, biol rep2

city: Philadelphia

first: Junjie

last: Nie

state: PA

address: 4119 Powelton Avenue

institute: university of Pennsylvania

data_processing:
Quality control was performed using fastp to remove low-quality reads and adapter sequences.
Clean reads were mapped to the reference genome GRCh38 using HISAT2.
Gene expression was quantified using featureCounts, obtaining raw counts for each gene.
Expression values were normalized using FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Differential expression analysis was conducted using DESeq2, identifying genes with |log2FC| > 1 and FDR < 0.05.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Tab-delimited text files containing raw counts and FPKM values for each gene across all samples.

growth_protocol: SW480 cells (LV-NC and MUCP1-FLAG) were maintained in L-15 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Technologies) following the manufacturer’s protocol. The aqueous phase was separated with chloroform, and RNA was precipitated using isopropanol. RNA quality and concentration were measured using Nanodrop 2000.
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (12309ES,Yeasen)  following manufacturer’s protocols.

value: colon adenocarcinoma cells

value: MUCP1-Flag overexpression


title: MUT2_222_1


title: JLA_F3_SPN_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_F3_SPN_12H_inconclusive_infection


title: MUT1_226_1


title: JLA_M1_IAV_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_M1_IAV_12H_inconclusive_infection


title: SW480 cells, LV-NC, biol rep3

value: None / LV-NC


title: SW480 cells, LV-NC, biol rep1


title: JLA_F3_PBS_48H_inconclusive_mock_infection, lung harvested 48 hours post infection

description: Library name: JLA_F3_PBS_48H_inconclusive_infection


title: JLA_F3_IAV_SPN_12H, lung harvested 12 hours post infection

description: Library name: JLA_F3_IAV_SPN_12H


title: JLA_M1_IAV_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_M1_IAV_SPN_24H_inconclusive_infection


title: SW480 cells, MUCP1-FLAG, biol rep1


title: JLA_F3_IAV_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_F3_IAV_SPN_48H_inconclusive_infection


title: SW480 cells, LV-NC, biol rep2


title: Huh7.5cells, si01419

city: Iksan

first: Ju-Hee

last: Yang

country: South Korea

institute: Jeon-buk national university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRch38
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

growth_protocol: Huh7.5 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) , 1x NEAA and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: epithelial-like, tumorigenic cells

value: LINC01419 Knockdwon


title: JLA_F3_IAV_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_F3_IAV_48H_inconclusive_infection

value: Whole lung homogenate


title: Huh7.5cells, siNC


title: JLA_F3_IAV_24H, lung harvested 24 hours post infection

description: Library name: JLA_F3_IAV_24H


title: UOK146

city: Boston

first: Karl

last: Semaan

state: MA

address: Brookline Ave 450

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq and MeDIP-seq reads were aligned to the hg19 human genome build using Burrows–Wheeler Aligner version 0.7.1740. Non-uniquely mapping and redundant reads were discarded. MACS version 2.1.1.2014061641 was used for ChIP-seq peak calling with a q value (false discovery rate (FDR)) threshold of 0.01. Fragment locations were converted to BED files using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set. For analyses involving overlap with genomic regions, fragments were imported as GRanges objects and collapsed to 1 bp at the center of the fragment location to ensure that a fragment can map to only one site. LPWGS data were used to estimate ctDNA using ichorCNA with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

source_name: Cell line

extract_protocol:
MeDIP was performed using the MagMeDIP kit from Diagenode.Samples were purified using the iPure Kit v2 from Diagenode
ChIP-seq libraries were generated from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit from TakaraBio. Libraries were sequenced using 150-base paired-end reads on an Illumina platform. MeDIP-Seq libraries were generated using the KAPA HyperPrep Kit, complemented by end-repair, A-tailing, and ligation of NEBNext adaptors. 10 ng of DNA was used as starting material.Libraries were sequenced using 150-base paired-end reads on an Illumina platform.

value: Cell line

tag: experiment type

value: MeDIP-seq

tag: genome build


title: SW480 cells, MUCP1-FLAG, biol rep3


title: JLA_F2_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_F2_SPN_48H_inconclusive_infection

value: Streptococcus pneumoniae EF3030


title: JLA_F3_IAV_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_F3_IAV_12H_inconclusive_infection

value: Influenza A virus (A/California/07/2009(H1N1))


title: UOK109


title: sTFE

value: sTFE


title: JLA_F2_PBS_48H_inconclusive_mock_infection, lung harvested 48 hours post infection

description: Library name: JLA_F2_PBS_48H_inconclusive_infection


title: FUUR1


title: KMRC1


title: JLA_F2_SPN_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_F2_SPN_12H_inconclusive_infection


title: CAKI1


title: JLA_F3_IAV_SPN_24H, lung harvested 24 hours post infection

description: Library name: JLA_F3_IAV_SPN_24H

value: Streptococcus pneumoniae EF3030, Influenza A virus (A/California/07/2009(H1N1))


title: JLA_F2_IAV_SPN_12H, lung harvested 12 hours post infection

description: Library name: JLA_F2_IAV_SPN_12H


title: 786O


title: JLA_F2_IAV_48H, lung harvested 48 hours post infection

description: Library name: JLA_F2_IAV_48H


title: JLA_F2_IAV_SPN_24H, lung harvested 24 hours post infection

description: Library name: JLA_F2_IAV_SPN_24H


title: JLA_F2_IAV_SPN_48H, lung harvested 48 hours post infection

description: Library name: JLA_F2_IAV_SPN_48H


title: wTRCC_5

data_processing:
ChIP-seq and MeDIP-seq reads were aligned to the hg19 human genome build using Burrows–Wheeler Aligner version 0.7.1740. Non-uniquely mapping and redundant reads were discarded. MACS version 2.1.1.2014061641 was used for ChIP-seq peak calling with a q value (false discovery rate (FDR)) threshold of 0.01. Fragment locations were converted to BED files using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set. For analyses involving overlap with genomic regions, fragments were imported as GRanges objects and collapsed to 1 bp at the center of the fragment location to ensure that a fragment can map to only one site. LPWGS data were used to estimate ctDNA using ichorCNA with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak
Library strategy: low pass whole genome sequencing (LPWGS)

source_name: Plasma

value: Plasma

value: LPWGS


title: A498


title: JLA_F1_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_F1_SPN_48H_inconclusive_infection


title: 769P


title: wTRCC_26


title: JLA_F2_IAV_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_F2_IAV_12H_inconclusive_infection


title: wTRCC_27


title: JLA_F1_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_F1_SPN_24H_inconclusive_infection


title: wTRCC_8


title: JLA_F1_SPN_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_F1_SPN_12H_inconclusive_infection


title: wTRCC_25


title: wTRCC_24


title: JLA_F2_SPN_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_F2_SPN_24H_inconclusive_infection


title: wTRCC_22


title: JLA_F1_IAV_SPN_48H_inconclusive_infection, lung harvested 48 hours post infection

description: Library name: JLA_F1_IAV_SPN_48H_inconclusive_infection


title: JLA_F1_PBS_48H_inconclusive_mock_infection, lung harvested 48 hours post infection

description: Library name: JLA_F1_PBS_48H_inconclusive_infection


title: JLA_F1_IAV_SPN_24H, lung harvested 24 hours post infection

description: Library name: JLA_F1_IAV_SPN_24H


title: wTRCC_13_6


title: wTRCC_13_5


title: wTRCC_13_4


title: JLA_F1_IAV_SPN_12H, lung harvested 12 hours post infection

description: Library name: JLA_F1_IAV_SPN_12H


title: JLA_F1_IAV_48H, lung harvested 48 hours post infection

description: Library name: JLA_F1_IAV_48H


title: JLA_F2_IAV_24H, lung harvested 24 hours post infection

description: Library name: JLA_F2_IAV_24H


title: wTRCC_13_3


title: wTRCC_13_2


title: JLA_F1_IAV_24H_inconclusive_infection, lung harvested 24 hours post infection

description: Library name: JLA_F1_IAV_24H_inconclusive_infection


title: JLA_F1_IAV_12H_inconclusive_infection, lung harvested 12 hours post infection

description: Library name: JLA_F1_IAV_12H_inconclusive_infection


title: wTRCC_13_1


title: wTRCC_12_9


title: FKHM+Ran Input FoxP3 Rep 2

first: Sun

last: Hur

address: 3 Blackfan St

department: Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

description:
Library name: PD_Random_6
Prepared by Wenxiang Zhang, analyzed by Ryan Clark

library_source: other

data_processing:
Paired-end reads were merged using BBmerge v38.84.
All reads (paired-end and single-end) were trimmed using Biopython v1.85.
Trimmed reads were processed in Python using Pandas, where unique sequences were collapsed and counted. Final DataFrame contains one unique sequence per row, with columns representing read counts per sample.
Supplementary files format and content: FASTQ files containing paired-end reads, 150 bp, demultiplexed.
Supplementary files format and content: FASTQ files containing single-end reads, 130 bp, demultiplexed.
Supplementary files format and content: csv files

molecule: other

source_name: In vitro assay (recombinant FoxP3 protein)

extract_protocol:
DNA eluted from FoxP3-protein-DNA complexes using proteinase K and purified via QIAquick Nucleotide Removal Kit.
Amplified with barcoded Illumina-compatible primers and pooled for sequencing.


title: FKHM+Ran Input FoxP3 Rep 1

description:
Library name: PD_Random_5
Prepared by Wenxiang Zhang, analyzed by Ryan Clark

value: In vitro assay (recombinant FoxP3 protein)


title: wTRCC_12_8


title: FKHM+Ran Input FoxP1 Rep 2

description:
Library name: PD_Random_4
Prepared by Wenxiang Zhang, analyzed by Ryan Clark

source_name: In vitro assay (recombinant FoxP1 protein)


title: FKHM+Ran Input FoxP1 Rep 1

description:
Library name: PD_Random_3
Prepared by Wenxiang Zhang, analyzed by Ryan Clark

value: In vitro assay (recombinant FoxP1 protein)


title: wTRCC_12_6


title: FKHM+Ran Input Rep 2

description:
Library name: PD_Random_2
Prepared by Wenxiang Zhang, analyzed by Ryan Clark

source_name: Synthetic DNA library

value: Synthetic DNA library


title: wTRCC_12_5


title: wTRCC_12_7


title: wTRCC_12_4


title: Mrc2 KO mouse lung fibroblasts at baseline (bio rep 5)

city: Madison

first: Lynn

middle: M

last: Schnapp

state: WI

address: 1685 Highland Ave, Suite 5000

department: Medicine

institute: University of Wisconsin-Madison

description: Library name: U5303

data_processing:
Reads mapping: Reads were aligned to the reference genome using STAR software version 2.5 (parameter - mismatch = 2)
Quantification: Gene expression quantification was performed using HTSeq version 0.6.1 (parameter: -m union)
Differential expression analysis: Differential gene expression was analyzed using DESeq2 (version 2_1.6.3) with adjusted p-value threshold (padj) < 0.05
Assembly: Mus musculus reference genome: mm10
Supplementary files format and content: .xlsx file containing gene counts

source_name: Primary cells

growth_protocol: Mouse lung fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Bio-Rad Aurum kit. 2828 to 5490 ng of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were prepared using poly(A)-selected mRNA isolation and standard Illumina library preparation protocols. cDNA synthesis and library construction were performed, followed by sequencing on an Illumina NovaSeq 6000 platform.

value: Lung

value: Fibroblasts

value: Mrc2 knockout

tag: batch

value: Batch 1


title: Mrc2 KO mouse lung fibroblasts at baseline (bio rep 4)

description: Library name: U5286


title: FKHM+Ran Input Rep 1

description:
Library name: PD_Random_1
Prepared by Wenxiang Zhang, analyzed by Ryan Clark


title: wTRCC_12_3


title: Mrc2 KO mouse lung fibroblasts at baseline (bio rep 3)

description: Library name: U5285


title: wTRCC_12_13


title: wTRCC_12_12


title: WT mouse lung fibroblasts at baseline (bio rep 5)

description: Library name: W5402

value: WT


title: Mrc2 KO mouse lung fibroblasts at baseline (bio rep 2)

description: Library name: U5284


title: wTRCC_12_10


title: wTRCC_12_2


title: WT mouse lung fibroblasts at baseline (bio rep 4)

description: Library name: W5401


title: wTRCC_12_11


title: wTRCC_12_1


title: Mrc2 KO mouse lung fibroblasts at baseline (bio rep 1)

description: Library name: U5283


title: wTRCC_10_4


title: WT mouse lung fibroblasts at baseline (bio rep 2)

description: Library name: W5399


title: WT mouse lung fibroblasts at baseline (bio rep 3)

description: Library name: W5400


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9+ssp6 strain, rep 3

city: Dundee

first: Megan

last: Bergkessel

state: Dundee

address: Dow Street

department: School of Life Sciences

country: United Kingdom

institute: University of Dundee

description: Library name: GM103_3

data_processing:
Samples were de-multiplexed and fastq files generated by Illumina DRAGEN Host Software Version 07.021.602.3.8.4. Reads from  fastq files were were processed for analysis using the Tn-Seq Pre-Processor (TPP) tool from the Transit package (v3.2.1). This identifies the end of the transposon sequence in each read, then maps the adjacent genome sequence to a reference genome using the bwa package (version 0.7.17-r1188, "bwa alg mem"), producing a .sam file and a .wig file.
The featureCounts function (v1.6.4) of the subread package was used to summarise the number of transposon-genome junctions detected in each gene, for each sample, using the "-- read2pos 5" option.
Read counts were normalised by dividing each read count value by the number of millions of reads assigned to all features in the genome, as reported by the featureCounts summary output.
The average read count value for the three replicates in each treatment was calculated, and average ratios between treatment types were calculated and log2-transformed.
Assembly: The genome sequence of Pseudomonas fluorescens (renamed simiae) 55 has been deposited, with the accesion CP179688, BioProject ID PRJNA1199885, and BioSample ID SAMN45889088. The annotation used in this analysis was generated using Prodigal v2.6 by MicrobesNG, who performed the sequencing.
Supplementary files format and content: A summary file containing raw read counts per gene, normalised read counts per gene, and log2-transformed average ratios between samples attacked by  the ssp4 or ssp6 expression strains and the D9 strain of S. marcescens, is included as an .xslx spreadsheet.

organism: Pseudomonas simiae

source_name: bacteria; originally Pseudomonas fluorescens but now Pseudomonas simiae 55

growth_protocol: Cultures of the P. fluorescens 55 transposon mutant library (target) and the indicated S. marcescens strain (attacker) were normalised  to OD 0.5 in lysogeny broth (LB).

extract_protocol:
All cells were recovered from each plate in 1 ml PBS and genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen).
Genomic DNA (~10 µg) was sheared into 250 bp fragments by sonication using the QSonica Q800R sonicator (Amplitude 25%: 20x cycles of 15s on/off) and end repaired using the NEBNext End Repair Module (New England Biolabs). A polyC tail was added to 1 µg of end repaired DNA using Terminal Deoxynucleotidyl Transferase (NEB) with a mixture of 95% dCTP and 5% ddCTP as a substrate. Residual C-tailing reagents were removed using NucleoSeq gel filtration columns (Macherey-Nagel) and DNA fragments containing transposon insertion sites were amplified by PCR using Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs) and oligonucleotide primers directed against the transposon sequence and the polyC tail. Size selection was performed using AMPure XP beads (Beckman) to enrich for an average fragment size of approximately 250 bp. Sequencing and index primers (NEB) were added by an additional round of PCR.

treatment_protocol: The normalised cultures were combined at a ratio of 1:2 (attacker:target) and spotted as 2 x 25 ul spots on a pre-warmed LB agar plate for each biological replicate. The co-culture spots were incubated at 30 degrees C for 4 hours

value: WT plus random Tn5 transposon insertion

value: attacked by S. marcescens Db10 D9+ssp6 strain


title: WT mouse lung fibroblasts at baseline (bio rep 1)

description: Library name: W5398


title: wTRCC_10_3


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9+ssp6 strain, rep 2

description: Library name: GM103_2

value: bacteria; originally Pseudomonas fluorescens but now Pseudomonas simiae 55


title: wTRCC_10_2


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9+ssp4 strain, rep 3

description: Library name: YL57_3

value: attacked by S. marcescens Db10 D9 +ssp4 strain


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9+ssp6 strain, rep 1

description: Library name: GM103_1


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9+ssp4 strain, rep 2

description: Library name: YL57_2


title: DKD mouse, immune cell

city: Hwasung

first: Peong Gang

last: Park

address: Dongtansibumhanbi-gil 38, 215-502

institute: Ajou University School of Medicine

description: 10x genomics

data_processing:
The generation of count tables were performed using CellRanger v7.1.0 (10x Genomics) from the fastq files.
Assembly: mm10
Supplementary files format and content: .mtx

source_name: kidney

extract_protocol:
Mouse kidney tissue was finely chopped and incubated in a 37°C water bath for 30 minutes to facilitate dissociation. After incubation, the tissue was mechanically dissociated using a wide-bore pipette tip to obtain a single-cell suspension. The resulting cells were then filtered through a cell strainer to remove debris and subsequently centrifuged to pellet the cells. Finally, immune cells were isolated by performing CD45 FACS to obtain a population of immune cells for further analysis.
Sequencing adapters were ligated to the cDNA fragments, and the libraries were purified and quantified, making them ready for sequencing.

treatment_protocol: Protocol to Induce Type 2 Diabetic Kidney Disease (T2DKD): A T2DKD model was induced by feeding the mice a high-fat diet consisting of 60% standard laboratory chow and 20% carbohydrates (Research Diets) for 24 weeks. Four weeks into the high-fat diet, streptozotocin was intraperitoneally injected at a dose of 50 mg/kg per day for five consecutive days. The control group was fed a standard diet and injected with sodium citrate (the vehicle for streptozotocin) for five days.

value: kidney

value: induced type 2 DKD

value: immune cells

tag: age

value: 6 months


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9+ssp4 strain, rep 1

description: Library name: YL57_1


title: control mouse, immune cell

description: 10x genomics

value: control


title: wTRCC_10_1

value: Plasma

value: LPWGS


title: wCCRCC2975


title: WT-IEC_NR3C2

city: Tokyo

first: Kenichiro

last: Kinouchi

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University School of Medicine

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: mm10
Supplementary files format and content: Files with extension *.bam. Binary files containing reads and alignment information.

source_name: Colon

extract_protocol:
An aliquot of chromatin (30 ug) was precleared with protein G agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 6ul of antibody against BMAL1 (Abcam cat# ab93806) and 8ul of antibody against Mineralocorticoid Receptor (Abcam cat# ab64457).  Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries (a custom type, using the same paired read adapter oligonucleotides described by Bentley et al., (2008)) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: Colon

value: male

value: wild-type


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9 strain, rep 3

description: Library name: YL37_3

value: attacked by S. marcescens Db10 D9 strain


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9 strain, rep 2

description: Library name: YL37_2


title: wCCRCC2974


title: P. fluorescens 55 transposon mutant library attached by S. marcescens Db10 D9 strain, rep 1

description: Library name: YL37_1


title: WT-IEC_BMAL1


title: Colon biopsy from Inactive UC patient, sample G

city: Chicago

first: Ronen

last: Sumagin

state: Illinois

address: 303 E Chicago Ave

institute: Northwestern University

description:
Library name: G_Inactive_UC
10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were generated using Cell Ranger (v7.0.1)
Assembly: GRCh38(, GRCm38
Supplementary files format and content: tab-delimited text file includes cell and gene unique identifiers
Supplementary files format and content: mtx file contains counts for each sample

source_name: colon biopsy

extract_protocol:
Colons were excised opened longitudinally, washed of fecal content with HBSS and cut into ~5mm pieces. Epithelium was separated from the LP by placing the tissue on a shaker for 15 minutes (150RPM, 37°C) using 10% FBS and 2mM EDTA HBSS solution. Remining LP tissue was minced and digested into single cell solution by shaking (200 RPM, 10-15 minutes) in collagenase solution (5% FBS, 1.5 mg/ml, collagenase type VIII and 40μg/ml DNase in HBSS), resulting cell suspensions were washed and filtered through a 40µm filter to ensure single cell separation.  Human colonic biopsies were obtained from consented inactive UC patients (Mayo endoscopic scores of 0) during routine screening and processed into single cell suspensions in a Liberase TH (0.1WU/mL), DNase I (0.5U/mL) in HBSS solution for 3 rounds of 10 min incubations at 37°C at 800RPM. Cell suspensions were washed and passed through a 40 strainer to ensure single cell separation.
Libraries for both human and mouse samples were generated using Genomics Single Cell 3’ Reagents kit (v3) in accordance with the manufacturer’s protocols. Single cell suspensions were diluted in PBS 2%BSA targeting approximately 10,000 cells per sample. Single cells were sequenced to a read depth of ~ 20,000 reads per cell. Libraries were sequenced on an Illumina NovaSeq X Plus platform

treatment_protocol: Mice were given 2.5% DSS in drinking water for 6 days (cycle1), afterwards they were switched to regular drinking water for 14 days (recovery phase),  followed by a second administration of 2.5%DSS in drinking water for 6 days (cycle2).

value: colon biopsy

value: Inactive UC


title: WT-IEC-2T12-1_Input


title: Colon biopsy from Inactive UC patient, sample F

description:
Library name: F_Inactive_UC
10x genomics


title: wCCRCC2971


title: wCCRCC2973


title: Colon biopsy from Inactive UC patient, sample D

description:
Library name: D_Inactive_UC
10x genomics


title: Colon biopsy from Inactive UC patient, sample E

description:
Library name: E_Inactive_UC
10x genomics


title: wCCRCC2970


title: wild type age 6 weeks wt249

city: Jerusalem

first: Eithan

last: Galun

address: Hadassah Ein Kerem

country: Israel

institute: Hadassah Medical Organization

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using 10X Genomics Cell Ranger software pipeline version V6.1.2
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files

source_name: Liver

growth_protocol: miR-122 knockout (KO) mice (C57BL/6miR-122em2Hhtg) were generated in collaboration with Prof. Dr. Nicola Gagliani and Prof. Samuel Huber at the University Medical Center Hamburg-Eppendorf, Hamburg, Germany. The genomic region of miR-122 (chr18:65,381,932-65,381,997) was targeted with 2 sgRNA guide sequences (sgRNA1:AACAGACGTCAAGTCACGCGTGG, sgRNA2:AGTGTGATAATGGCGTTTGATGG) generating a 60bp deletion. All mice were screened by genotyping the miR-122 genomic region by PCR analysis (for primer sequences, see table S1). Two separate colonies generated by separate founders were maintained for experimentation. Male mice were used in all the experiments. Mice were maintained under specific pathogen-free (SPF) conditions in an animal facility with a temperature of approximately 23°C in a 12-hour light-dark cycle and received sterile commercial rodent chow and water ad libitum unless otherwise indicated. Maintenance of mice and all experimental procedures were performed by the Institutional Animal Care and Use Committee approved animal treatment protocols (license number OPRR-A01– 5011). All animal experiments were performed after a stringent ethical consideration and approval by the Hebrew University Of Jerusalem, Israel. The experiments were regulated by veterinarian specialists.

extract_protocol:
Livers were perfused with PBS and harvested in cold PBS. A 50mg portion was collected in disassociation buffer (0.15% Collagenase P (Roche) in HBSS) and incubated at 37˚c until complete disassociation. Cells were treated with ACK for the removal of red blood cells. Cells were washed and strained and kept in full growth medium (DMEM supplemented with 10% fetal calf serum (FCS) (Thermo Scientific, Waltham, MA, USA)). Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec, Auburn, USA) according to the manufacturer protocol. Cells were counted manually, and dead cell percentages were calculated using trypan blue. Only samples with less than 10% dead cells were used for sequencing.
The cells were subjected to the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10× Genomics, CA, USA) and libraries were prepared for sequencing following manufacturer company instructions. Sequencing was done using NovaSeq 6000 system machine (Illumina) with the following sequencing conditions: 28 bp (Read1) and 90 bp (Read2) using the NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) (Illumina).

value: Liver

value: WT

value: 6 weeks


title: miR-122 KO age 6 weeks b414

value: miR-122 KO


title: Colon biopsy from Inactive UC patient, sample B

description:
Library name: B_Inactive_UC
10x genomics


title: H1-YP-D5-ATAC-2

city: Guangzhou

first: Qifan

last: Jiang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

description: Library name: W08241228279

data_processing:
Illumina sequencing adapters were trimmed using BBDuk (BBMap v37.87) with parameters specified in the Lexogen data analysis protocol. High-quality reads were aligned to the human reference genome (GRCh38/hg38) using RSEM with the Bowtie2 aligner. Gene expression levels were normalized using EDASeq and read counts per gene were calculated using SAMtools (v1.3.1) and HTSeq-count (v0.6.0). Genes with a mean count of less than 20 across all samples were removed to reduce noise. For ATAC-seq, raw sequencing reads underwent quality control (QC) filtering using FastQC (v0.11.9) to assess read quality, adapter contamination, and duplication rates. High-quality reads were trimmed using Cutadapt (v1.13) to remove adapter sequences and low-quality bases. For genome alignment, trimmed reads were mapped to the human reference genome (UCSC hg38) using Bowtie2 (v2.2.5) with default parameters optimized for ATAC-Seq analysis. Mapped reads were further processed by SAMtools (v1.3.1) for sorting and indexing, followed by de-duplication using Picard Tools (v1.90) to remove PCR duplicates and ensure data accuracy. To identify open chromatin regions, peak calling was performed using MACS2 (v2.2.7.1) with the callpeak function, and the bdgcmp function was applied to remove duplicate reads and improve peak specificity. Differential peak analysis between conditions was conducted using MACS2 bdgdiff, allowing for the identification of chromatin regions with significant accessibility differences
Assembly: GRCh38
Supplementary files format and content: For ATAC-seq, the file format is signal.ext.RPGC.bigwig, contains processed normalized signal track. For RNA-seq, the file format is excel, contains the normalized counts.

source_name: human embryonic stem cell H1 derived cells

extract_protocol:
Total RNA was extracted from two independent biological replicates using the TRIzol reagent (Invitrogen) following the manufacturer's protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer to ensure high-quality RNA (RNA integrity number, RIN > 7.0) before proceeding with library preparation. ATAC-Seq was performed to assess chromatin accessibility following the protocol provided by the ATAC-Seq Assay Library Construction Kit (Vazyme, Cat# TD502-02).
For RNA sequencing library construction, RNA was sheared and purified using the TruSeq RNA Sample Preparation Kit v2 (Illumina), followed by reverse transcription into double-stranded cDNA (ds-cDNA). The cDNA was purified using the QIAquick Gel Extraction Kit (QIAGEN) and AMPure XP beads (Beckman Coulter) to obtain DNA fragments of 250–300 bp in length. DNA concentrations were quantified using the dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific), ensuring a minimum concentration of 1 ng/μL. Transposase-mediated tagmentation was conducted to fragment open chromatin regions, and DNA libraries were prepared using the TruePrep DNA Library Preparation Kit V2 for Illumina (Vazyme, Cat# TD503-01). Constructed ATAC-Seq libraries were quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851)

tag: time point

value: human trophoblast stem cells


title: wCCRCC1570


title: H1-YP-D5-ATAC-1

description: Library name: W08241228278

tag: cell line

value: human embryonic stem cell H1 derived cells


title: Colon biopsy from Inactive UC patient, sample C

description:
Library name: C_Inactive_UC
10x genomics


title: H1-TS-D5-ATAC-2

description: Library name: W08241228277

tag: cell type


title: H1-TS-D5-ATAC-1

description: Library name: W08241228276


title: K4me3_TRCC_8

value: H3K4me3 ChIP-seq


title: miR-122 KO age 3 weeks b360

tag: genotype

value: 3 weeks


title: TS-YP-1

description: Library name: R02TR241239741-1-932-661


title: TS-YP-2

description: Library name: R02TR241239742-1-933-660


title: wild type age 3 weeks wt154


title: YP-D5-2

description: Library name: R02TR241239732-1-923-670


title: K4me3_TRCC_5


title: wild type age 2 weeks wt153

value: 2 weeks


title: YP-D5-1

description: Library name: R02TR241239731-1-922-671


title: TS-D5-2

description: Library name: R02TR241239730-1-921-672


title: miR-122 KO age 2 weeks b359


title: wild type age 2 weeks


title: TS-D5-1

description: Library name: R02TR241239729-1-920-673


title: K4me3_TRCC_26

value: Plasma


title: YP-D10-2

description: Library name: R02R241084297-1-958-635


title: K4me3_TRCC_27


title: YP-D10-1

description: Library name: R02R241084296-1-957-636


title: miR-122 KO age 2 weeks


title: K4me3_TRCC_25


title: TPD-D10-2

description: Library name: R02R241084295-1-956-637


title: K4me3_TRCC_24


title: TS-D10-2

description: Library name: R02R241084293-1-954-639


title: TS-D10-1

description: Library name: R02R241084292-1-953-640


title: OT-1-caIL12_TCR

city: Bethesda

first: Jay

middle: A

last: Berzofsky

address: Building 41 Room D702D

department: Center for Immuno-Oncology

institute: National Cancer Institute

description: 5’ gene expression and TCR V(D)J profiling with Feature Barcode enrichment.

data_processing:
Base calling was performed using RTA 3.4.4
demultiplexing was performed using cellranger v7.1.0 (Bcl2fastq 2.20.0)
alignment was performed using cellranger v7.1.0 (STAR 2.7.2a
Sequenced reads were aligned to the 10x provided mouse reference sequence (refdata-gex-mm10-2020-A).
Sequenced reads were also aligned to the following Total Seq C hashtags: HTO_1, HTO_2, and HTO_3
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: SCAF3694_OT-1-MSaV1_filtered_feature_bc_matrix.h5: procesed data is formated as an H5 file containing gene counts for single cell RNA-seq data organized by HTO index as well as associated counts for TCR V(D)J clonotypes
Supplementary files format and content: SCAF3695_OT-1-CaIL12_filtered_feature_bc_matrix.h5: procesed data is formated as an H5 file containing gene counts for single cell RNA-seq data organized by HTO index as well as associated counts for TCR V(D)J clonotypes

source_name: B16 melanoma

growth_protocol: Tumor resected from mouse

extract_protocol:
For TIL isolation, the tumors were resected, placed into complete RPMI medium, and kept on ice. After weighing, the tumors were processed into single cells using a tumor cell isolation kit (130-110-187, Miltenyi Biotech, Auburn, CA, USA) following the manufacturer’s instructions. A debris removal step was incorporated following the manufacturer’s protocol (130-109-398, Miltenyi Biotech, Auburn, CA, USA). After this step, the Dead Cell Removal Kit (130-090-101, Miltenyi Biotech, Auburn, CA, USA) protocol was combined with a Pan T Cell Isolation Kit II (130-095-130, Miltenyi Biotech, Auburn, CA, USA), and an additional 1 µL of anti-Ter119-biotin (130-112-915, Miltenyi Biotech, Auburn, CA, USA) and anti-CD105-biotin (130-112-637, Miltenyi Biotech, Auburn, CA, USA )were added to the antibody cocktail.
Libraries werePrepared according to the 10x Genomics Chromium Next GEM Single Cell 5’v2 (Dual Index) Kit User Guide

treatment_protocol: Tumor bearing mice received OT-I TCR T cell  genetically modified with/without caIL-12

value: Tumor

tag: library type

value: TCR V(D)J

tag: treatment

value: OT-I -caIL-12 T cell


title: K4me3_TRCC_22

tag: tissue


title: H1-ES-2

description: Library name: R02R241084299-1-960-633

source_name: human embryonic stem cell H1

value: human embryonic stem cell H1

value: human embryonic stem cells


title: TPD-D10-1

description: Library name: R02R241084294-1-955-638


title: OT-1-caIL12_FBC

value: Feature Barcode


title: Gamma Delta T cell Donor 5

first: Prithvi

last: Sinha

address: 3400 Civic Center Bvld

institute: University of Pennsylvania

description: Library name: GDT 5

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification. Reads were pseudo-aligned with Kallisto (version 0.46.1, b = 100) against the human genome (GRCh38 assembly)
In R (version 4.0.5), transcripts were collapsed to genes using package tximport (version 1.22.0) 75, and then normalized and filtered by edgeR 76 (version 3.36.0) to generate counts per million mapped reads (CPM) for each gene
Assembly: GRCh38 assembly
Supplementary files format and content: Xls file contains cpm values for each sample

source_name: T cells

extract_protocol:
Total RNA was isolated using the Rneasy Minikit (Qiagen) and quality and conc were determined using TapeStation (Agilent)
NEBNext Ultra II RNA Library Prep Kit.Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: T cells


title: K4me3_TRCC_13_6


title: H1-ES-1

description: Library name: R02R241084298-1-959-634


title: K4me3_TRCC_13_5


title: Gamma Delta T cell Donor 4

description: Library name: GDT 4


title: OT-1-control_TCR

value: OT-I TCR T cell


title: OT-1-caIL12_GEX

value: Gene Expression


title: Gamma Delta T cell Donor 3

description: Library name: GDT 3


title: Gamma Delta T cell Donor 2

description: Library name: GDT 2


title: K4me3_TRCC_13_4


title: OT-1-control_FBC


title: Gamma Delta T cell Donor 1

description: Library name: GDT 1


title: Alpha Beta T cell Donor 5

description: Library name: ABT 5


title: Alpha Beta T cell Donor 4

description: Library name: ABT 4


title: K4me3_TRCC_13_3


title: K4me3_TRCC_13_2


title: Alpha Beta T cell Donor 2

description: Library name: ABT 2


title: Alpha Beta T cell Donor 1

description: Library name: ABT 1


title: Alpha Beta T cell Donor 3

description: Library name: ABT 3


title: K4me3_TRCC_13_1


title: Donor D shPERK

description: Library name: shPERK D

data_processing:
Reads were pseudo-aligned with Kallisto (version 0.46.1, b = 100) against the human genome (GRCh38 assembly)
In R (version 4.0.5), transcripts were collapsed to genes using package tximport (version 1.22.0) 75, and then normalized and filtered by edgeR 76 (version 3.36.0) to generate counts per million mapped reads (CPM) for each gene
Assembly: GRCh38 assembly
Supplementary files format and content: Xls file contains cpm values for each sample

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

extract_protocol:
Total RNA was isolated using the Rneasy Minikit (Qiagen) and quality and conc were determined using TapeStation (Agilent)
NEBNext Ultra II RNA Library Prep Kit. Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Human Gamma Delta T cells


title: K4me3_TRCC_12_9


title: HSC, rep1

city: San Francisco

first: Sixuan

last: Pan

state: California

address: 1450 3rd Street

department: Bioengineering

institute: UCSF

description:
PIP-seq
HSC_1

data_processing:
Library demultiplexing, read alignment, identification of empty droplets, and UMI quantification were performed with PIPseeker 1.0.0 (Fluent Biosciences) with default parameters.
Assembly: GRCh38, GRCm39
Supplementary files format and content: barcodes.tsv.gz contains the barcode sequences, features.tsv.gz contains the gene names, and the matrix.mtx.gz contains the gene expression matrix table. All files are after filtering.

source_name: bone marrow

growth_protocol: Human HEK 293T and mouse NIH 3T3 cells (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher, 11995073) supplemented with 10% fetal bovine serum (FBS; Gibco, 10082147) and 1× Antibiotic-Antimycotic (Gibco, 15240062) at 37°C and 5% CO2.

extract_protocol:
Mice were humanely euthanized using CO2. BM cells from their limb bones were isolated and resuspended in FACS buffer (PBS + 2% FBS) by centrifugation at 8,000 × g for 1 minute. After removing red blood cells (RBC) with a commercial lysis buffer (BioLegend, 420302), diluted to 1X with distilled water, single-cell suspensions were depleted of hematopoietic cells committed to a specific lineage using a Lineage Cell Depletion Kit (EasySep, StemCell Technologies, Inc., 19856A). To label LT-HSC cells, the following fluorophore-conjugated antibodies were used at the indicated dilutions: CD117 (c-Kit) BV785 (clone 2B8, BioLegend; 1:200 dilution), Ly-6A/E (Sca-1) PE/Cy7 (clone D7, BioLegend; 1:1000 dilution), CD48 PerCP/Cy5.5 (clone HM48-1, BioLegend; 1:100 dilution) and CD150 (SLAM) APC (clone TC15-12F12.2, BioLegend; 1:50 dilution). After adding the rat serum and isolation cocktail of the Lineage Cell Depletion Kit, the LT-HSC-labeling antibodies were also added for a 30-minute-long incubation in the dark at 4°C. Following the removal of lineage-positive cells, samples were spun down in FACS buffer and subsequently resuspended in 200-300 μL of FACS buffer containing DAPI at a final concentration of 1 μg/mL. Cells from 2/3 age-matched mice were combined to generate each pool sample, with a total of 2 replicates for the young condition and 3 replicates for the middle-aged and old conditions, respectively (total n=10 mice).
Single cells were processed for scRNA-seq using the PIP-seq T2 3’ Single Cell RNA kit (v3.0) according to the manufacturer's protocol (Fluent Biosciences, FB0001026).

treatment_protocol: HEK or 3T3 cells were treated with 0.05% Trypsin-EDTA with Phenol red (Gibco, 25200114) for 3 min, quenched with growth medium, and centrifuged for 3 min at 300g. The supernatant was removed, and the cells were resuspended in 1X DPBS without calcium or magnesium. Fresh-frozen human peripheral blood mononuclear cells (PBMCs) were obtained from STEMCELL Technologies. DMEM with 10% FBS was warmed up to 37°C, and the frozen PBMCs were thawed by adding 1 mL of warm media on top of the frozen cells and immediately transferring the media to a 15-mL conical. This process was repeated until all PBMCs were thawed and transferred. Cells were centrifuged for 3 min at 300g and resuspended in 1X DPBS. For the 10-3, 10-4, and 10-5 target cell fraction samples, human HEK 293T cells were the target population mixed with mouse NIH 3T3 cells background population. For the 10-6 target cell fraction sample, mouse NIH 3T3 cells were the target population mixed with the human PBMCs background population. The target population was treated with 1 μg/mL Calcein Red-Orange (Invitrogen, C34851), and the background population was treated with 1 μg/mL Calcein Green (Invitrogen, C34852) for 15 min at 37°C, followed by washing and dilution to the final concentration in 1× DPBS with 0.1% BSA. The viability and cell concentration were evaluated by an automated cell counter (Bio-Rad, TC20) after adding Trypan Blue (Gibco, 15250061). The mixed cell suspension was filtered through a 40 µm cell strainer (Flowmi, BAH136800040) and processed through the PURE-seq workflow described above to enrich for Calcein Red-Orange labeled cells.

value: bone marrow

value: HSC


title: Donor D shControl

description: Library name: Control D

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: Donor C shControl

description: Library name: Control C


title: Donor C shPERK

description: Library name: shPERK C


title: LT-HSC, old, rep2

description:
PIP-seq
Old_2

value: LT-HSC


title: Donor B shControl

description: Library name: Control B


title: K4me3_TRCC_12_7

value: H3K4me3 ChIP-seq


title: Donor B shPERK

description: Library name: shPERK B


title: K4me3_TRCC_12_6


title: Donor A shControl

description: Library name: Control A


title: OT-1-control_GEX


title: LT-HSC, middle-aged, rep3

description:
PIP-seq
MA_3


title: LT-HSC, old, rep1

description:
PIP-seq
Old_1


title: K4me3_TRCC_12_5


title: HeLa cells, VPgEMCV-treated for 24 h, sample 1

city: Kyoto

first: Takashi

last: Fujita

state: Kyoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Biosystems Science

institute: Kyoto University

description: Library name: VPgEMCV-1

data_processing:
DRAGEN Bio-IT Platform (Illumina) was used to generate gene expression data (conducted by Takara Bio).
Bioinformatics analyses were further conducted using OlvTools (BxINFO). Transcript abundances were estimated using Salmon against human transcriptome GRCh39. Gene abundances were then calculated from transcript abundances using tximport package. Differential expression analysis was performed using edgeR package after filterByExpr function was applied to remove low expressed genes. The genes with |FC| > 1 and FDR < 0.05 were considered differentially expressed.
Assembly: GRCh38, GRCh39 (OlvTools)
Supplementary files format and content: Gene expression, transcript expression, mapping info
Supplementary files format and content: Supplementary files contain the datasheet provided by Takara Bio (xlsx), and DEG listed by FDR ranking, created using OlvTools used in the study (csv)

source_name: HeLa

growth_protocol: HeLa cells (ATCC) were grown in DMEM (Nacalai Tesque) supplied with 10% FBS (Sigma-Aldrich) and 1% Antibiotic-Antimycotic Mix (Nacalai Tesque).

extract_protocol:
RNA was isolated from cells using TRIzol reagent (Invitrogen), and standard methods of chloroform/phenol extraction-ethanol precipitation were conducted for purification of RNA. DNase I (Roche) was treated according to the protocol for complete removal of DNA.
The library was created using SMART-seq v4 Ultra Low Input RNA Kit (Takara Bio), conducted by Takara Bio, following their own kit protocol.

treatment_protocol: HeLa cells (ATCC) were seeded at 1x10^5 cells/mL overnight, and treated with 1000 U/mL IFN-b (PeproTech), 10 ng/mL IFN-g (PeproTech), or 1 ng/mL VPgEMCV for 24 h. Non-treated (NT) conditions were also prepared.

value: HeLa

value: Cervial cancer cell line

value: WT

value: treated for 24 h


title: HeLa cells, VPgEMCV-treated for 24 h, sample 2

description: Library name: VPgEMCV-2


title: HSC, rep2

description:
PIP-seq
HSC_2


title: LT-HSC, middle-aged, rep2

description:
PIP-seq
MA_2


title: Donor A shPERK

description: Library name: shPERK A


title: HeLa cells, IFN-g-treated for 24 h, sample 2

description: Library name: IFNg-2


title: K4me3_TRCC_12_4

source_name: Plasma

value: Plasma


title: HeLa cells, IFN-g-treated for 24 h, sample 1

description: Library name: IFNg-1


title: LT-HSC, old, rep3

description:
PIP-seq
Old_3


title: K4me3_TRCC_12_3


title: LT-HSC, middle-aged, rep1

description:
PIP-seq
MA_1


title: HeLa cells, IFN-b-treated for 24h, sample 2

description: Library name: IFNb-2


title: K4me3_TRCC_12_8


title: LT-HSC, young, rep2

description:
PIP-seq
Young_2


title: HeLa cells, IFN-b-treated for 24 h, sample 1

description: Library name: IFNb-1


title: HeLa cells, non-treated (N.T.) for 24 h, sample 2

description: Library name: NT-2

value: no treatment


title: K4me3_TRCC_12_13


title: HeLa cells, non-treated (N.T.) for 24 h, sample 1

description: Library name: NT-1


title: Ran+Ran FoxP3

description:
Library name: PD_Random_8
Prepared by Wenxiang Zhang, analyzed by Ryan Clark

source_name: In vitro assay (recombinant FoxP3 protein)


title: LT-HSC, young, rep1

description:
PIP-seq
Young_1


title: K4me3_TRCC_12_12


title: Ran+Ran FoxP1

description:
Library name: PD_Random_7
Prepared by Wenxiang Zhang, analyzed by Ryan Clark

source_name: In vitro assay (recombinant FoxP1 protein)


title: K4me3_TRCC_12_10


title: GFP IP, rep2

city: Poznan

first: IHG PAS

last: Bioinfo Team

state: Greater Poland

address: Strzeszynska 32

department: Bioinformatics Team

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

description: Library name: GFP4_IP

data_processing:
The eCLIP experiment was performed by Eclipse BioInnovations’ standard RBP-eCLIP pipeline as previously described. Raw sequencing reads were trimmed of UMIs and adapters, filtered out of reads that mapped to repeat elements, aligned to the reference genome (hg38) with STAR, and filtered of PCR duplicates.
Clusters (regions within the IP sample that contain a pileup of reads) were identified using CLIPper (https://github.com/YeoLab/clipper). Each cluster was normalized against the paired input sample. Final peaks for each sample were filtered for enrichment over the input (|log2FC| ≥ 2) and statistical significance (adjusted p-value ≤ 0.01). Replicated peaks were then identified by positionally intersecting peaks of each replicate of the same condition with the intersect command of bedtools, with the -s option. Aspecific peaks (i.e. those also found in GFP samples) were then filtered out from RBMXL3_FLAG peaks by positional intersection in the same way. Peaks were annotated using the GenomeRanges and wavClusteR R packages.
Assembly: GRCh38/hg38, Gencode v44
Supplementary files format and content: bigWig peaks for positive and negative strand

growth_protocol: TCam-2 cells were cultured at 37 °C and 5% CO2 in Roswell Park Memorial Institute 1640 Medium (RPMI 1640 Medium, GlutaMAX™ Supplement Thermo Fisher Scientific, 61870044) supplemented with 10% heat-inactivated Fetal Bovine Serum (Cytiva, HYCLSV30160.03) and 1% Antibiotic-Antimycotic solution (100X) (Thermo Fisher Scientific, 15240062).

extract_protocol:
Two biological replicates of 20 million cells (TCam-2 transfected with RBMXL3_FLAG and GFP_FLAG) were used in eCLIP-seq. Briefly, 48 hours after transfection, TCam-2 cells grown on culture dishes were crosslinked at 254 nm UV with an energy setting of 400 mJ/cm² (Analytik Jena, CL-3000). The cells were then harvested in ice-cold DPBS, and the pellets were flash-frozen in liquid nitrogen and stored at -80°C before the IP reaction with an anti-FLAG antibody, performed by Eclipse BioInnovations (USA). During IP reaction Dynabeads M-280 Sheep Anti-Mouse IgG (Thermo Fisher cat. 11201D) and antibody Anti-FLAG M2 (Sigma Aldrich cat. F1804-1MG) were used.
Libraries were constructed using the eCLIP protocol as previously described (van Nostrand et al, 2016).

value: human testicular cancer cell line

value: GFP overexpression


title: Ncr1-cre+polyIC

city: Hefei

first: Qi

middle: wu

last: Bian

state: Anhui

address: Division of Life Sciences and Medicine, 443 Huangshan Road

department: Life sciences and medicine

institute: University of Science and Technology of China

description: 10x Genomics

data_processing:
Reads were processed using the Cell Ranger 3.0.1 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version mm10, using the STAR algorithm.
Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes.
Assembly: mm10
Supplementary files format and content: Saline_barcodes.tsv.gz, Saline_features.tsv.gz, Saline_matrix.mtx.gz
Supplementary files format and content: polyIC_barcodes.tsv.gz, polyIC_features.tsv.gz, polyIC_matrix.mtx.gz
Supplementary files format and content: ko_barcodes.tsv.gz, ko_features.tsv.gz, ko_matrix.mtx.gz

source_name: fetal brain

extract_protocol:
Fetal brains were gathered, minced and filtered through a 200-gauge stainless steel mesh. Subsequently, cell isolation was achieved through gradient centrifugation using 37% and 70% Percoll. CD11b+ cells were further purified using CD11b microbeads from Miltenyi with a magnetic-activated cell sorter (MACS) (Miltenyi Biotec).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation,so that each cell was paired with a bead in a Gel Beads-in emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.The library construction and sequencing was performed at Shanghai Biotechnology Corporation.

value: fetal brain

value: CD11b+ cells

value: polyIC


title: GFP IP, rep1

description: Library name: GFP3_IP


title: GFP INPUT, rep2

description: Library name: GFP4_INP


title: K4me3_TRCC_10_4

data_processing:
ChIP-seq and MeDIP-seq reads were aligned to the hg19 human genome build using Burrows–Wheeler Aligner version 0.7.1740. Non-uniquely mapping and redundant reads were discarded. MACS version 2.1.1.2014061641 was used for ChIP-seq peak calling with a q value (false discovery rate (FDR)) threshold of 0.01. Fragment locations were converted to BED files using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set. For analyses involving overlap with genomic regions, fragments were imported as GRanges objects and collapsed to 1 bp at the center of the fragment location to ensure that a fragment can map to only one site. LPWGS data were used to estimate ctDNA using ichorCNA with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak


title: K4me3_TCRCC_10_3


title: mutant, RV, replicate3

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
All datasets were processed using Cellranger 2.0.2.
FASTQ files were generated using the mkfastq function
Reads were aligned to a custom mm9 reference containing tdTomato and ZsGreen reporter genes.
Cellranger aggr was used to aggregate individual libraries after read depth normalization.
Data was analyzed using Seurat v3
Assembly: mm9
Supplementary files format and content: Seurat object

source_name: mouse embryonic heart

extract_protocol:
Embryonic hearts were dissected from pregnant dams at E13.5 in 1% FBS in PBS. Yolk sacs were used for genotyping. Hearts were then microdissected to obtain the interventricular septum (IVS), left ventricular (LV) and right ventricular (RV) tissue. Tissues were singularized with TryplE at 37C, quenched with 1% FBS in PBS, filtered and centrifuged at 300g for 5 minutes. The resulting pellet was resuspended in 1% FBS in PBS and counted using an automated cell counter. A 30μL aliquot of the cell suspension was used for library generation.
Single cell droplet libraries were generated with the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, accoring to manufacturer's instructions.

value: mouse embryonic heart

tag: developmental stage

value: mutant


title: K4me3_TCRCC_10_2

extract_protocol:
MeDIP was performed using the MagMeDIP kit from Diagenode.Samples were purified using the iPure Kit v2 from Diagenode
ChIP-seq libraries were generated from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit from TakaraBio. Libraries were sequenced using 150-base paired-end reads on an Illumina platform. MeDIP-Seq libraries were generated using the KAPA HyperPrep Kit, complemented by end-repair, A-tailing, and ligation of NEBNext adaptors. 10 ng of DNA was used as starting material.Libraries were sequenced using 150-base paired-end reads on an Illumina platform.


title: RBMXL3 IP, rep1

description: Library name: R1-RBMXL3_IP

value: RBMXL3 overexpression


title: RBMXL3 INPUT, rep1

description: Library name: R1-RBMXL3_INP


title: Gzmb-cko+polyIC

description: 10x Genomics


title: Ncr1-cre+Saline

description: 10x Genomics

value: Saline


title: mutant, RV, replicate2


title: K4me3_TCRCC_10_1


title: mutant, RV, replicate1


title: normal diet 20 weeks, No.7

city: DAEGU

first: Soyoung

last: Kwak

address: Myeongdeok-ro 16-gil

department: Nuclear Medicine

institute: Keimyung University Dongsan Hospital

description: Library name: B2_con3

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012).
Bowtie2  indices were either generated from genome assembly sequence or the representative transcript  sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.  Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020)  using Bioconductor (Gentleman et al.,2004).
Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Assembly: mm10
Supplementary files format and content: FASTQC files include raw counts for each sample

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. In brief, each 500ng total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components.

value: epididymal white adipose tissue

value: Wild type

value: normal diet


title: normal diet 20 weeks, No.8

description: Library name: B2_con4


title: RBMXL3 INPUT, rep2

description: Library name: R4_INP


title: normal diet 20 weeks, No.9

description: Library name: B2_con5


title: K4me3_CCRCC2999

first: Karl

last: Semaan

address: Brookline Ave 450

institute: Dana-Farber Cancer Institute

value: H3K4me3 ChIP-seq


title: normal diet 20 weeks, No.5

description: Library name: B2_con1


title: Western diet 20 weeks, No.5

description: Library name: B1_WD5

value: western diet


title: K4me3_CCRCC2997


title: mutant, LV, replicate2, techrep2


title: Western diet 20 weeks, No.4

description: Library name: B1_WD4


title: GFP INPUT, rep1

description: Library name: GFP3_INP


title: RBMXL3 IP, rep2

description: Library name: R4_IP


title: mutant, LV, replicate2, techrep1


title: Western diet 20 weeks, No.1

description: Library name: B1_WD1


title: Western diet 20 weeks, No.2

description: Library name: B1_WD2


title: Western diet 20 weeks, No.3

description: Library name: B1_WD3


title: K4me3_CCRCC2974


title: mutant, LV, replicate1


title: normal diet 20 weeks, No.4

description: Library name: B1_con4


title: mutant, IVS, replicate2


title: K4me3_CCRCC2971


title: normal diet 20 weeks, No.6

description: Library name: B2_con2


title: mutant, LV, replicate3


title: ATAC-seq on CRISPR mESC R1 cells, proximal Sox2 at Akr1cl enhancer mutated, replicate 2

city: Kansas City

first: Melanie

last: Weilert

state: MO

institute: Stowers Institute for Medical Research

description: Library name: mesc_Akr1cl_scenario_context_mut_B_atac_2

data_processing:
Reads were pre-trimmed for adapters using Cutadapt (v.4.2) and aligned to the mouse genome assembly mm10 using bowtie2 (v.2.3.5.1).
Any CRISPR ATAC-seq experiments were aligned to a custom mm10 genome assembly modified to contain the expected CRISPR mutations. Duplicated alignments were marked using Picard (v.2.23.8) (Broad Institute n.d.). Alignments were then deduplicated, filtered for fragment lengths exceeding 600 bp, corrected for dovetailed alignment pairs, and end-adjusted to accommodate the Tn5 enzymatic cut correction of -4/+4.
Normalized read-per-million (RPM) ATAC-seq tracks were generated by scaling the aligned coverage to the weighted total reads.
Cut site ATAC-seq coverage used for training ChromBPNet models were generated by isolating the bases on each end of an aligned fragment, consolidating those “cut events” into coverage tracks. ATAC-seq peaks were mapped using MACS2 (v.2.2.7.1) with default settings.
Assembly: UCSC mm10
Supplementary files format and content: BigWig coverage of ATAC-seq cutsites

growth_protocol: R1 ESCs were cultured on 0.1% gelatin-coated plates without feeder cells in N2B27 medium (DMEM/F12 with 1:1 mix of GlutaMax/N2 and Neurobasal medium/B27, Invitrogen) supplemented with 2 mM L-glutamine (Stemcell Technologies), 1x 2-mercaptoethanol (Millipore), 1x NEAA (Stemcell Technologies), 3 µM CHIR99021 (Stemcell Technologies), 1 µM PD0325901 (Stemcell Technologies), 0.033% BSA solution (Invitrogen) and 107 U/mL LIF (Millipore).

extract_protocol:
For each ATAC-seq experiment, 100,000 R1 wildtype or CRISPR-edited mouse embryonic stem cells were used. Cells were washed once in cold PBS, with centrifugation at 500 x g and 4 °C for 5 minutes. The cell pellets were then resuspended in 50 µL of cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% Digitonin (Promega, G9441). After a 3 minute incubation on ice, 1 mL of cold ATAC Resuspension Buffer supplemented with 0.1% Tween-20 was added and the samples were centrifuged at 500 x g and 4°C for 10 minutes. Tagmentation was performed at 1000 rpm and 37 °C for 30 minutes in a 50 μL reaction volume containing 10 μL of 5x Tagment DNA Buffer (50 mM Tris-HCl pH 7.4, 25 mM MgCl2, 50% DMF), 0.5 μL 10% Tween-20, 0.5 μL 1% Digitonin,1 µL of 20 µM Tn5 transposase loaded with oligonucleotides, and 38 µL water. For all experiments, the Tn5 used was purified in-house using pETM11-Sumo3-Tn5 and His6-tagged SenP2 protease plasmids.
DNA fragments were purified using the Monarch PCR & DNA Cleanup Kit (NEB, #T1030) and used as input for library preparation using Illumina Nextera Dual Indexing. During library preparation, qPCR was performed to prevent over-amplification, and libraries were purified using a 2% agarose gel and the Monarch DNA Gel Extraction kit (NEB, #T1020). Paired-end sequencing was performed on an Illumina NextSeq 500 and 2000 instruments (2 x 75 bp cycles).

treatment_protocol: For each of the five candidate mutations across two genomic loci  (Akr1cl and Btbd11 enhancers), crRNA target sites were designed using the IDT target predictor tool by evaluating the predicted on-target efficiency score and off-target potential. Alt-R CRISPR-Cas9 crRNA was designed to contain ∼40 bases of homology from the targeted cut site. Equimolar amounts (stock of 100 μm) of Alt-R crRNA and tracrRNA-ATTO550 were mixed to form gRNA at a final concentration of 50 μM. The mixture was heated at 95°C for 5 min and cooled at RT. The single-stranded donor oligonucleotides (ssODN) were designed to contain ∼40 bases of homology from the targeted cut site (crRNA and ssODN sequences were designed using the IDT software tool). A ribonucleoprotein (RNP) complex was formed by combining 150 pmol of gRNA (crRNA+tracrRNA) and 125 pmol of Cas9 HiFi v3 protein (IDT) with hybridization for 20 min at RT. The RNP was combined with 100 pmol of ssODN donor and 100 pmol of electroporation enhancer v2 and delivered to 1.5e5 cells by Neon electroporation (1,400 V, 10 m, 3 pulses; Neon Transfection System, MPK5000, Life Technologies). Immediately after electroporation, cells were cultured in 0.5 μM Alt-R HDR enhancer V2 of 0.69 mM. After 24 h, cells were washed with PBS before FACS sorting on S6 FACSymphony. Single cells were directly sorted into 96-well plates. Cells were screened for the expected mutations through paired-end sequencing on an Illumina MiSeq instrument (250 cycles).

value: CRISPR proximal Sox2 mutation at Akr1cl enhancer


title: normal diet 20 weeks, No.1

description: Library name: B1_con1


title: normal diet 20 weeks, No.2

description: Library name: B1_con2


title: mutant, IVS, replicate1, techrep2


title: ATAC-seq on CRISPR mESC R1 cells, proximal Sox2 at Akr1cl enhancer mutated, replicate 1

description: Library name: mesc_Akr1cl_scenario_context_mut_B_atac_1


title: K4me3_CCRCC1730

value: Plasma


title: mutant, IVS, replicate1, techrep1


title: ATAC-seq on CRISPR mESC R1 cells, distal Sox2 at Akr1cl enhancer mutated, replicate 2

description: Library name: mesc_Akr1cl_scenario_context_mut_A_atac_2

value: CRISPR distal Sox2 mutation at Akr1cl enhancer


title: K4me3_CCRCC170


title: K4me3_CCRCC2975


title: ATAC-seq on CRISPR mESC R1 cells, Sox2 and Oct4-Sox2 at Btbd11 enhancer mutated, replicate 1

description: Library name: mesc_Btbd11_scenario_WT_coop_mut_null_atac_1

value: CRISPR Sox2 and Oct4-Sox2 simultaneous mutation at Btbd11 enhancer


title: ATAC-seq on CRISPR mESC R1 cells, Sox2 and Oct4-Sox2 at Btbd11 enhancer mutated, replicate 2

description: Library name: mesc_Btbd11_scenario_WT_coop_mut_null_atac_2


title: control, RV, replicate4

value: control