title: Repliseq_mBMMSC_S1

value: Mouse Embryonic Stem Cells

value: Asynchronous cells. FACS sorted according to cell cycle. 2nd of six fractions.


title: TX PAX_1108914_04

status: Public on Dec 01 2025

type: RNA

city: La Jolla

first: SUNIL

last: KURIAN

state: CA

address: 10666 N Torrey Pines Rd

country: USA

institute: Scripps Health

description:
TX
GSM2869539

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained in the Affymetrix Gene Titan MC.

scan_protocol: GeneChips were scanned in the Affymetrix Gene Titan MC.

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Whole Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: PAXgene extraction of total RNA was performed using the PAXgene RNA extraction kit according to the manufacturer's instructions.

tag: tag

value: Well Functioning Transplant


title: fWT1A_H4K16bu

type: SRA

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

library_source: genomic

data_processing:
Paired-end sequencing reads were trimmed by cutadapt (version 3.5) with the parameters -a CTGTCTCTTATA -A CTGTCTCTTATA -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=20 and mapped to the reference genome (Mus musculus GRCm38 dna primary assembly) using bowtie2 (version 2.5.1). Reads were filtered by samtools (version 1.17) with the parameter -q 12.
ChIP-seq coverage (bigwig) files created in R (version 4.1.2) using the Bioconductor packages ShortRead (version 1.52.0) and rtracklayer (version 1.54.0) on the unique fragments (read pairs). Coverages were normalized by the total number of fragments and multiplied by a million.
ChIP-seq peaks were called using Homer (version 4.10) findPeaks with parameters -style histone -fragLength 150 -inputFragLength 150 using input libraries as control. Peaks overlapping black list regions were filtered out using bedtools (version 2.31.0) and the black list (mm10-blacklist.v2).
Assembly: GRCm38
Supplementary files format and content: BED peak files
Supplementary files format and content: BW bigwig coverage

molecule: genomic DNA

organism: Mus musculus

source_name: liver

growth_protocol: WT and hypomorphic Pcca-/- (A138T) mice (FVB background) were maintained on standard chow diet in a temperature-controlled environment on a 12/12 h light-dark cycle. Food and water were available ad libitum.

extract_protocol:
We used a native ChIP approach. For this 40-60 mg of frozen liver tissue was homogenized via a tissue grinder. After lysis, the nuclei pellet was digested with 20 U MNase for 15 min at 20 °C.
Libraries from purified DNA were prepared using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s instructions. After PCR enrichment of adaptor-ligated DNA, libraries were size selected at 150-700 bp in length using AMPure XP beads (Beckman Coulter) following the instructions of SPRIselect User Guide. Libraries were controlled via BioAnalyzer (Agilent) measurements using the High Sensitivity DNA

tag: tissue

value: liver

tag: Sex

value: female

tag: age

value: 11 weeks

tag: genotype

value: WT

tag: antibody

value: H4K16bu (in-house)

tag: chip input


title: TX PAX_1108911_04

description:
TX
GSM2869538


title: Repliseq_mBMMSC_G1

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

data_processing:
100-bp single end reads were aligned to the reference mouse genome Human GRCm38/mm10 using bwa v.0.7.17
Only the uniquely mapped reads with mapping quality > 30 Phred score were used as input to generate the coverage bigWig track in 1kb resolution by applying the bins per million mapped reads (BPM) normalization method and smoothing of 4kb.
Assembly: GRCm38/mm10
Supplementary files format and content: 1kb resolution bigWig signal files of RepliSeq experiments
Library strategy: Repli-Seq

source_name: mBM-MSC

growth_protocol: Mouse embryonic stem cells (mESCs) from 129/SVEV strain were purchased from Merck (CMTi-1, passage 11). They were thawed, amplified as per manufacturer instructions for three passages, aliquoted and frozen. This stock of cells was routinely used on gelatin plates (or flasks) for no more than 32 passages. For all experiments, mESC were grown in DMEM+Glutamax (Gibco, 61965-026), 10% ES-FBS (Gibco 16141-079), MEM NEAA (Gibco 11140-035), sodium pyruvate (Gibco, 11360-039), 1mM beta-mercaptoethanol (Gibco, 31350-010), penicillin/streptomycin (P/S, Gibco, 15140-122), 100ng/mL LIF (stocked at 1-2mg/mL; produced at the Protein Production and Purification Platform of the EPFL, Lausanne, Switzerland), 3µM GSK3 inhibitor (Sigma 361559) and MEK inhibitor (PD0325901, Selleckchem). Cells were seeded in T225 flasks and grown for 48 hours after which EdU (40 µM) was added for 30 minutes.

extract_protocol:
After fixation, the cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-it Kit. Purification of genomic DNA was then performed by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina NovaSeq 6000 sequencer.

treatment_protocol: We should aim to collect at least have at least 20 million cells. Cells were collected by trypsinization, pelleted, resuspended in PBS, fixed in methanol added drop-wise (final concentration 90%) and stored at -20ºC until further processing. Cells were centrifuged at 4ºC, 400G for 10’, washed with 2-5 mL PBS and pelleted again, permeabilized in 5 mL 2% triton/PBS for 30 minutes. Cells were pelleted, washed in PBS and passed into a 5 mL low bind tube. They were centrifuged, resuspended in 1-5 mL of Biotin-Azide Reaction cocktail (as in EdU-seq) and incubated for 30 minutes at room temperature. Cells were then centrifuged, washed once in PBS and resuspended in PBS containing 500µg/mL propidium iodide and 500-100U of RNaseA (Thermo EN0531). The sample was incubated for 30 minutes at 37ºC and kept at 4ºC until the day after. The cells were then sorted in six fractions according to the cell cycle PI profile on a MOFLO Astrios EQ (Beckman Coulter) at the Cytometry platform of the University of Geneva. At least one million cells per fraction were sorted directly into low bind centrifuge tubes, which were later centrifuged and processed as in the EdU-seq protocol.

tag: cell line

value: mBM-MSC

tag: cell type

tag: genetic modification

tag: treatment

value: Asynchronous cells. FACS sorted according to cell cycle. 1st of six fractions.


title: EUseq_mESC_G1_rep2

data_processing:
100-bp single end reads were aligned to the reference mouse genome Human GRCm38/mm10 using bwa v.0.7.17
Only the uniquely mapped reads with mapping quality > 30 Phred score were used as input to generate the coverage bigWig track in 1kb resolution by applying the bins per million mapped reads (BPM) normalization method and smoothing of 4kb.
Assembly: GRCm38/mm10
Supplementary files format and content: 1kb resolution bigWig signal files of Euseq experiments
Library strategy: EU-seq

source_name: mESC CMTi-1

growth_protocol: Mouse embryonic stem cells (mESCs) from 129/SVEV strain were purchased from Merck (CMTi-1, passage 11). They were thawed, amplified as per manufacturer instructions for three passages, aliquoted and frozen. This stock of cells was routinely used on gelatin plates (or flasks) for no more than 32 passages. For all experiments, mESC were grown in DMEM+Glutamax (Gibco, 61965-026), 10% ES-FBS (Gibco 16141-079), MEM NEAA (Gibco 11140-035), sodium pyruvate (Gibco, 11360-039), 1mM beta-mercaptoethanol (Gibco, 31350-010), penicillin/streptomycin (P/S, Gibco, 15140-122), 100ng/mL LIF (stocked at 1-2mg/mL; produced at the Protein Production and Purification Platform of the EPFL, Lausanne, Switzerland), 3µM GSK3 inhibitor (Sigma 361559) and MEK inhibitor (PD0325901, Selleckchem). MEF were grown in DMEM with 10% FBS, l-glutamine, pyruvate and penicillin/streptomycin. All cells were routinely checked for mycoplasma.

extract_protocol:
RNA samples were then precipitated by adding 350 µL of water, 16 µL of 5M NaCl, 1 µL of glycogen and 832 µL of cold ethanol, incubating the mix at -70ºC and centrifuging for 30-60 minutes at 4ºC, 16000 G. The RNA pellet was washed twice in a cold solution of 75% ethanol/water, centrifuged and the pellet resuspended in 400 µL of water. Biotinylated RNA was captured using 200 µL of Dynabeads MyOne streptavidin C1 (Invitrogen, 65001) per sample. The beads had been previously washed thrice in buffer W1x (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.5% Tween-20), twice in Solution A (0.1M NaOH, 0.05M NaCl in water) and twice in Solution B (0.1M NaCl in water). The volume of solutions used for washing the beads was calculated as 200 µL per sample and scaled up depending on the total number of samples. After the last wash, the beads were removed from the magnet and resuspended in buffer W2x (same as W1x but two times concentrated) in two times the original volume (400 µL per sample). 400 µL of this washed bead mix were added to each biotinylated RNA sample and incubated 30 minutes at room temperature on a rotating wheel. Afterwards, the bead-RNA samples were washed three times with 800 µL of buffer W1x. Each Biotinylated-RNA sample was eluted by resuspending the beads in a solution containing 55 µL of 10mM Tris pH 8 and 1.1 µL of 2-mercaptoethanol and incubating them for one hour at room temperature.
RNA libraries were generated without the ribodepletion step and sequenced at the Genomics platform of the University of Geneva.

treatment_protocol: For the synchronized 2h EU-seq, two T225 flasks were each seeded with three million mESCs. Two days after, nocodazole was added in the morning and mitotic-shake-off was performed 6 hours later. The lifted cells were seeded on a 10 cm gelatine plate. EU (5-ethynil-uridine, Jena Biosciences, Cat. No. CLK-N002-10) was added at a concentration of 0.5 mM for 30 minutes before collection, which took place two hours after seeding. For FACS sorted EU-seq, one million mESCs or 3 million MEFs were seeded in 10 cm plates and, the following day, EU was added at a concentration of 0.5 mM for 30 minutes before collection by trypsinization. For all experiments, the samples were then processed as in 59, but with certain modifications. Briefly, cell pellets were resuspended in 600 µL of Trizol and total RNA was extracted through chloroform purification and ethanol precipitation. 10-15 µg of EU-labelled RNA were processed with the Click-iT Nascent RNA Capture Kit (Invitrogen, Cat. No. C-10365) but substituting the biotin-azide from the kit with cleavable biotin-azide (Azide-PEG(3+ 3)-S-S-biotin) (Jena Biosciences, CLK-A2112-10). The click reaction took place on a volume of 50 µL for 30 minutes at room temperature.

value: mESC CMTi-1


title: Repliseq_mBMMSC_S2

value: Asynchronous cells. FACS sorted according to cell cycle. 3rd of six fractions.


title: RVA_15, run 1

city: Ann Arbor

first: Marc

middle: B

last: Hershenson

state: MI

address: 1150 W. Medical Center Drive

department: Department of Pediatric Pulmonology

institute: Michigan Medicine

description: Library name: 11119-JK-30

library_source: transcriptomic

data_processing:
The reads were trimmed using Cutadapt v4.8 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCh38 (ENSEMBL 109), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.20 (Ewels et al., 2016).
Assembly: GRCh38 (ENSEMBL 109)
Supplementary files format and content: Tab-deliminated text file includes a complete matrix of gene expected count totals for all samples.

molecule: polyA RNA

source_name: nasal epithelium

extract_protocol:
Total RNA from nasal swab samples was prepared using Trizol extraction. RNA was purified using RNEasy spin columns and enriched for mRNA using a Poly(A) mRNA Magnetic Isolation Module.
A TruSeq-based Takara kit was used during library preparation. This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan.

value: nasal epithelium

tag: host viral_infection

value: RV-A

tag: library batch


title: RVC_26, run 1

description: Library name: 11119-JK-29

value: RV-C


title: TX PAX_1108906_04

description:
TX
GSM2869537


title: fPA2A_H4K16ac

value: PA

value: H4K16ac (Merck Millipore, #17-10101)


title: Repliseq_MEF_S4

source_name: MEF

value: MEF

value: Mouse Embryonic Stem Cells

value: Asynchronous cells. FACS sorted according to cell cycle. 5th of six fractions.


title: TX PAX_1108905_04

description:
TX
GSM2869536

value: Well Functioning Transplant


title: TX PAX_1108900_06

description:
TX
GSM2869535


title: fPA1A_H4K16ac

value: liver

value: female


title: RVA_14, run 1

description: Library name: 11119-JK-28


title: Repliseq_MEF_S3

value: Asynchronous cells. FACS sorted according to cell cycle. 4th of six fractions.


title: fWT2A_H4K16ac

value: 11 weeks

value: WT


title: Repliseq_MEF_S2


title: RVA_13, run 1

description: Library name: 11119-JK-26


title: Repliseq_MEF_S1

value: Asynchronous cells. FACS sorted according to cell cycle. 2nd of six fractions.


title: fWT1A_H4K16ac


title: ADNR PAX_1108708_04

description:
ADNR
_

value: Acute dysfunction no rejection


title: RVC_24, run 1

description: Library name: 11119-JK-25


title: fPA2A_H3K9ac

value: H3K9ac (abcam, ab4441)


title: Repliseq_MEF_G1

value: Asynchronous cells. FACS sorted according to cell cycle. 1st of six fractions.


title: TX PAX_1108899_05

description:
TX
GSM2869534


title: fPA1A_H3K9ac


title: fWT2A_H3K9ac


title: RVC_22, run 1

description: Library name: 11119-JK-23

value: nasal epithelium


title: TX PAX_1108704_04

description:
TX
GSM2869533


title: Repliseq_mESC_Nuc_S3

value: mESC CMTi-1

value: Treated with Embryomax (0.5x). Asynchronous cells. FACS sorted according to cell cycle. 4th of six fractions.


title: RVC_25, run 1

description: Library name: 11119-JK-27

value: RV-C


title: fWT1A_H3K9ac


title: Repliseq_mESC_Nuc_S2

value: Treated with Embryomax (0.5x). Asynchronous cells. FACS sorted according to cell cycle. 3rd of six fractions.


title: RVA_12, run 1

description: Library name: 11119-JK-21

value: RV-A


title: Repliseq_mESC_Nuc_S1

value: Mouse Embryonic Stem Cells

value: Treated with Embryomax (0.5x). Asynchronous cells. FACS sorted according to cell cycle. 2nd of six fractions.


title: TX PAX_1108705_05

description:
TX
GSM2869902

value: Well Functioning Transplant


title: fPA1A_H3K27ac

value: liver

value: female

value: PA

value: H3K27ac (abcam, #ab4729)


title: RVC_20, run 1

description: Library name: 11119-JK-20


title: TX PAX_1108687_04

description:
TX
GSM2869531


title: Repliseq_mESC_Nuc_G1

value: Treated with Embryomax (0.5x). Asynchronous cells. FACS sorted according to cell cycle. 1st of six fractions.


title: RVA_11, run 1

description: Library name: 11119-JK-19


title: RVC_23, run 1

description: Library name: 11119-JK-24


title: TX PAX_1108493_05

description:
TX
_


title: subAR PAX_1107553_04

description:
subAR
GSM2869901

value: Subclinical acute rejection


title: TX PAX_1108497_05

description:
TX
GSM2869530


title: Repliseq_mESC_S4

value: Asynchronous cells. FACS sorted according to cell cycle. 5th of six fractions.


title: TX PAX_1108496_04

description:
TX
GSM2869529


title: cAR PAX_1107552_05

description:
cAR
_

value: Clinical acute rejection


title: ADNR PAX_1107541_05

description:
ADNR
_

value: Acute dysfunction no rejection


title: RVC_21, run 1

description: Library name: 11119-JK-22

value: nasal epithelium


title: fPA2A_H3K27ac

value: 11 weeks


title: subAR PAX_1107538_05

description:
subAR
GSM2869900


title: fPA1A_input


title: fPA2A_input


title: RVC_19, run 1

description: Library name: 11119-JK-14

value: RV-C


title: RVA_9, run 1

description: Library name: 11119-JK-15


title: Repliseq_mESC_S1

value: mESC CMTi-1

value: Asynchronous cells. FACS sorted according to cell cycle. 2nd of six fractions.


title: fWT2A_H3K27ac

value: WT


title: fWT2A_input


title: RVC_18, run 1

description: Library name: 11119-JK-13


title: RVC_17, run 1

description: Library name: 11119-JK-12


title: fWT1A_H3K27ac


title: fWT1A_input


title: Repliseq_mESC_G1

value: Mouse Embryonic Stem Cells

value: Asynchronous cells. FACS sorted according to cell cycle. 1st of six fractions.


title: TX PAX_1107535_04

description:
TX
GSM2869528

value: Well Functioning Transplant


title: RVA_10, run 1

description: Library name: 11119-JK-16

value: RV-A


title: RVC_16, run 1

description: Library name: 11119-JK-10


title: Repliseq_mESC_S3

value: Asynchronous cells. FACS sorted according to cell cycle. 4th of six fractions.


title: Repliseq_mESC_S2

value: Asynchronous cells. FACS sorted according to cell cycle. 3rd of six fractions.


title: TX PAX_1107495_05

description:
TX
GSM2869526


title: ADNR PAX_1107530_06

description:
ADNR
_


title: TX PAX_1107042_05

description:
TX
GSM2869525


title: RVC_15, run 1

description: Library name: 11119-JK-9


title: TX PAX_1106755_04

description:
TX
GSM2869524


title: Control rep1

city: Qingdao

first: Yuning

last: Song

address: 72 Binhai Road

department: School of Life Sciences

country: China

institute: Shandong  University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (three or four biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: cochlear epithelium

extract_protocol:
RNA extraction was performed using RNeasy Micro Kit following the manufacturer’s protocol (QIAGEN, 74004)
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: cochlear epithelium

tag: developmental stage

value: embryonic stage E16

value: cochlear cells

value: Control

value: untreated


title: RVA_8, run 1

description: Library name: 11119-JK-8

value: nasal epithelium


title: Repliseq_mESC_Nuc_S4

value: Treated with Embryomax (0.5x). Asynchronous cells. FACS sorted according to cell cycle. 5th of six fractions.


title: fWT1_ATAC

data_processing:
Paired-end sequencing reads were trimmed by cutadapt (version 3.5) with the parameters -a CTGTCTCTTATA -A CTGTCTCTTATA -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=20.
Reads were mapped to the reference genome (Mus musculus GRCm38 dna primary assembly) using bowtie2 (version 2.5.1).
Mapped reads were filtered by samtools (version 1.17) with the parameter -q 12.
Coverage (bigwig) files created in R (version 4.1.2) using the Bioconductor packages ShortRead (version 1.52.0) and rtracklayer (version 1.54.0) on the unique fragments (read pairs).
Coverages were normalized by the total number of fragments and multiplied by a million.
Peaks were called using Homer (version 4.10) findPeaks with parameters -style factor -fragLength 150 -size 400 -F 6 -L 6.
Peaks overlapping black list regions (mm10-blacklist.v2) were filtered out using bedtools (version 2.31.0).
Assembly: GRCm38
Supplementary files format and content: BED peak files
Supplementary files format and content: BW bigwig coverage

extract_protocol:
We followed the Omni-ATAC protocol. We used the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits and started with 20 mg of frozen liver.
Libraries from purified DNA were prepared using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s instructions. After PCR enrichment of adaptor-ligated DNA, libraries were size selected at 150-700 bp in length using AMPure XP beads (Beckman Coulter) following the instructions of SPRIselect User Guide. Libraries were controlled via BioAnalyzer (Agilent) measurements using the High Sensitivity DNA kit.

value: liver

value: female

value: 11 weeks


title: RVC_14, run 1

description: Library name: 11119-JK-7

value: RV-C


title: Control rep2


title: fWT2_ATAC

value: WT


title: konck out Brg1 rep4

value: Brg1 knockout


title: konck out Brg1 rep3


title: TX PAX_1106743_04

description:
TX
GSM2869521

value: Well Functioning Transplant


title: Control rep3


title: MYC;PMEPA1_10 overexpression, C57BL6/J

city: Barcelona

first: Ana

last: Hernández de Sande

address: C/ del Rosselló, 153

country: Spain

institute: IDIBAPS

data_processing:
We first assessed the quality of paired-end reads with FASTQC  (version 0.11.8).
Next, we filtered reads with BBDUK from BBTOOLS  (version 37.53) to remove adapters, known artefacts and then quality trimmed (PHRED quality score < 10).
Reads that became too short after trimming (N < 60 bp) were discarded. We did not retain singleton reads (i.e., reads whose mate has been discarded). We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (version 1.0.0) by a quasi-mapping on Mus musculus GRCm38.
We estimated the gene-level quantification using tximport  library and converted mouse gene expression to human gene expression using biomaRt  library.
Assembly: GRCm38, Mus_musculus.GRCm38.cds.all.fa.gz (ENSEMBL)
Supplementary files format and content: Counts are provided in csv format including gene id, gene symbol, raw counts, FPKM and TPM normalized counts

source_name: tumor

growth_protocol: hydrodynamic tail vein delivery

extract_protocol:
Trizol® (Invitrogen) followed by digestion with DNase I (Roche) and purification with the RNeasy Kit (Qiagen). TruSeq RNA Sample Preparation
RNA was poly-A selected and multiplexed RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions, at the Icahn School of Medicine at Mount Sinai Genomics Core.

treatment_protocol: no treatment

value: tumor

tag: strain

tag: mutations

tag: passage

value: 8-10 passages


title: RVC_13, run 1

description: Library name: 11119-JK-6


title: TX PAX_1106745_05

description:
TX
GSM2869522

tag: tag


title: konck out Brg1 rep2

tag: tissue


title: TX PAX_1106737_04

description:
TX
GSM2869519


title: fPA2_ATAC

tag: Sex

value: PA


title: fPA1_ATAC

tag: age


title: konck out Brg1 rep1

value: cochlear epithelium

tag: genotype


title: MYC;PMEPA1_5 overexpression, C57BL6/J


title: RVC_11, run 1

description: Library name: 11119-JK-4


title: RVC_12, run 1

description: Library name: 11119-JK-5


title: MitoSnap+, scRNAseq

city: Oxford

first: Mariana

last: Borsa

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Initial data processing was conducted with Cell Ranger 7.2.0.
Assembly: mm10
Supplementary files format and content: matrix files .tsv

source_name: spleen

extract_protocol:
Murine spleens were harvested. Single-cell suspensions were used for naïve CD8+ T cell isolation using EasySep™ Mouse Naïve CD8+ T Cell Isolation Kit (StemcellTM Technologies) following manufacturer’s instructions. Purified populations were cultured (at 37°C, 5% CO2) in T cell medium: RPMI-1640 containing HEPES and l-glutamine (R5158, Sigma-Aldrich) supplemented with 10% filtered fetal bovine serum (Sigma-Aldrich), 1× Penicillin-Streptomycin (Sigma-Aldrich), 1× non-essential amino acids (Gibco), 50 μM β-mercaptoethanol (Gibco), and 1 mM sodium pyruvate (Gibco). T cell activation was done on anti-CD3 (5 μg/ml) (145-2C11, BioLegend), anti-CD28 (5 μg/ml) (37.51, BioLegend) and recombinant human or murine Fc-ICAM-1 (10 μg/ml) (R&D Systems) coated plates. 36h post activation cells were sorted. To determine cell division events, cells were stained with CellTrace VioletTM (Life Technologies) following manufacture’s guidelines. MitoSnap CD8+ T cells were in 3 steps. Labelling of old organelles was done by harvesting CD8+ T cells 16 h post-activation and washing them in PBS (500 xg). Cells were incubated in T cell medium containing the first SnapSubstrate for 30 min at 37°C, washed in PBS and put back in culture in their original wells for further 20h.At 36h post-activation, cells were harvested, washed and incubated with T cell medium containing 5 μM (Snap-Cell Block S9106S, New England Biolabs, NEB) for 30 min at 37°C. After washing, cells rested for 30-60 min in T cell medium and then incubated with the second SnapSubstrate for 30 min at 37°C. After washing, cells rested for 60 min in T cell medium and prepared for sorting. Fluorescent cell permeable Snap-Cell substrates (NEB) were used in the following concentrations: 3 μM (Snap-Cell 647-SiR S9102S), 3 μM (Snap-Cell TMR-Star S9105S), 5 μM (Snap-Cell Oregon Green S9104S).
In short, cell suspensions were encapsulated into Gel Beads in Emulsion (GEMs) using the Chromium Controller. Within each GEM, cell lysis and barcoded reverse transcription of RNA occurred, followed by cDNA amplification. The amplified cDNA underwent library construction via fragmentation, end-repair, A-tailing, adaptor ligation, and index PCR. Final libraries were sequenced on an Illumina NovaSeq 6000 system.

value: spleen

value: CD8+ T cells

value: 6-12 weeks


title: MYC;PMEPA1_1 overexpression, C57BL6/J


title: RVC_10, run 1

description: Library name: 11119-JK-3


title: TX PAX_1106512_04

description:
TX
GSM2869517


title: TX PAX_1106511_04

description:
TX
GSM2869516


title: Air_Pol+Fish_Oil_rep4 [RRBS]

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Demultiplexed fastq files were aligned by BSBlt using  aligner  Bowtie2 against the mm10 referece.
Methylation calling was performed applying call methylation function of BSBolt.  A read pile-up was created using SAMtools and initialized using pysam for each reference contig with aligned reads. Methylation calls were made for all methylatable bases and only CG sites were used for downstream analysis.
further downstream analysis was done using CpGtools
Assembly: mm10
Supplementary files format and content: Methylation Profile  Matrix (.rds file)

source_name: Placental cell at Gestational D19

growth_protocol: C57BL/6J mouse were obtained from Jackson Laboratories housed under dark: light 12:12(h) conditions with free access to water and chow in the University of California Animal Facility

extract_protocol:
Placental samples were colleted  from D19 placenta of  CON or Air Pollution particle exposed mice along with mice fed with Fish oil and Fish oil followed by exposure to Air Pollutant. DNA was extracted  with DNA mini kit from  Qiagen following manufacturer's protocol.
extracted DNA was fragmented using restriction endonuclease MspI
DNA fragments were size-selected using AMPure XP beads (Beckman Coulter) and bisulfite conversion was performed using EpiTect Fast Bisulfite Conversion Kits (Qiagen).
Libraries were prepared according to Illumina's instructions. Libraries  were sequenced by the HiSeq-2000 (Illumina Inc.; San Diego, CA, USA).

treatment_protocol: Female mice were exposed  with SRM1649b particle (resuspend in sterile PBS and sonicated to obtain a concentration of 15μg/µl) intranasally either starting from 2months prior to gestation followed by 18th day of gestation.

value: Placenta

tag: agent

value: Fish Oil + Air Polution


title: MitoSnap-, scRNAseq

description: 10x genomics


title: TX PAX_1106506_04

description:
TX
GSM2869515


title: subAR PAX_1106417_04

description:
subAR
GSM2869899

value: Subclinical acute rejection


title: MYC;PMEPA1_9 overexpression, C57BL6/J


title: 4_D

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

department: SV

institute: EPFL

data_processing:
*library strategy: Spatial transcriptomics
The reads were aligned using SpaceRanger v2.1.1. and the final data matrix is generated as per Spaceranger pipeline.
Assembly: GRCm39.109
Supplementary files format and content: Data were analyzed using Seurat v4

molecule: nuclear RNA

source_name: spinal cord

extract_protocol:
We carried out two separate experiments to study the cytoarchitecture of the lesion microenvironment after SCI. First, we prepared sections from injured young mice, old mice and old mice treated with regeneration protocol. For each experimental condition, we prepared sections from the lesion epicenter of three independent biological replicates. Second, to prepare our four-dimensional spatiotemporal atlas, we collected sections throughout the entire spinal cord of mice from each of the three experimental conditions. The spinal cord injury sites of mice were embedded in OCT and cryosections were generated at 10 µm at −20 °C. For the four-dimensional atlas, every fifth section was collected throughout the entire dorsoventral axis of each spinal cord. Sections were immediately placed on chilled Visium Tissue Optimization Slides or Visium Spatial Gene Expression Slides.
Visium Spatial Gene Expression kit was used to profile the spatial transcriptomics experiments

value: spinal cord

value: Nuclei

value: Spinal cord injury, subjected to autonomic dysreflexia


title: Air_Pol+Fish_Oil_rep3 [RRBS]


title: Air_Pol+Fish_Oil_rep2 [RRBS]


title: TX PAX_1106420_04

description:
TX
GSM2869514


title: uninfected_3, run 2

description: Library name: 10455-JK-11

value: nasal epithelium

value: uninfected


title: 4_C

value: Spinal cord injury


title: Fish_Oil_rep4 [RRBS]

value: Fis Oil


title: uninfected_2, run 2

description: Library name: 10455-JK-10


title: Fish_Oil_rep3 [RRBS]


title: 3_B


title: TX PAX_1106240_04

description:
TX
GSM2869513

value: Well Functioning Transplant


title: RVC_8, run 1

description: Library name: 11119-JK-1

value: RV-C


title: TX PAX_1106238_04

description:
TX
GSM2869512


title: RSV_8, run 1

description: Library name: 10455-JK-8

value: RSV


title: 3_A


title: Fish_Oil_rep2 [RRBS]


title: TX PAX_1106232_04

description:
TX
GSM2869511


title: RVC_9, run 1

description: Library name: 11119-JK-2


title: TX PAX_1105677_04

description:
TX
GSM2869510


title: 2_D


title: Fish_Oil_rep1 [RRBS]


title: ADNR PAX_1105470_04

description:
ADNR
_

value: Acute dysfunction no rejection


title: RSV_7, run 1

description: Library name: 10455-JK-7


title: RSV_6, run 1

description: Library name: 10455-JK-6


title: RSV_5, run 1

description: Library name: 10455-JK-5


title: Air_Pollution_rep3 [RRBS]

value: Air Pollution


title: Air_Pollution_rep4 [RRBS]


title: uninfected_1, run 2

description: Library name: 10455-JK-9


title: TX PAX_1105461_04

description:
TX
GSM2869508


title: Air_Pollution_rep2 [RRBS]


title: RSV_4, run 1

description: Library name: 10455-JK-4


title: 1_B


title: liver, dKO, ZT22, rep2, RNA-seq

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
matrix column name: 6814
mx_rawCounts_swisnf_zt.txt

data_processing:
Reads were aligned to mm10 using STAR (Version 2.7.5c)
Filtering steps were applied to exclude reads with low mapping quality (MAPQ<30), reads/mates that were unmapped, reads failing platform and those not classified as primary alignments (samtools view -q 30 -F 780).
Reads were quantified with featureCounts (v1.6.4-2.0.0)  with GENCODE vM18-25 GTF reference annotation followed by DESeq2 normalization.
Assembly: mm10
Supplementary files format and content: FeatureCounts output tab-delimited text file for each sample
Supplementary files format and content: tab-delimited text file containing the raw counts from each Sample

growth_protocol: Wild type mice: C57BL/6N. Smarca2-/- and Smarca4fl/fl mice on 129/Sv background and backcrossed with C57BL/6N mice and subsequently intercrossed. 8-10 weeks old mice were used for experiments.

extract_protocol:
10 mg of snap-frozen liver tissue was homogenized in 700µL Tri Reagent (Sigma Aldrich, 93289) using the FastPrep-24™ 5G Instrument. 0.2 volume chloroform was added, and the sample was vortexed for 30 sec, incubated for 15 min at RT, and centrifuged at 10,000g for 10 min at 4 °C. The upper phase was transferred to a new tube and 0.6 volume 96% ethanol was added. The sample was loaded into an EconoSpin column (Epoch, 1920-050/250), centrifuged at 13000g for 30 sec. Flowthrough was discarded and the column was washed 3 times with buffer RPE (Qiagen, 1018013) by adding 500µL of buffer RPE, centrifuging, and discarding flowthrough. After washing, the column was centrifuged at 13000g for 2 min at RT to dry. The column was transferred to a new Eppendorf tube and incubated with open lid for 5 min to evaporate remaining ethanol. 30µL of DEPC-treated water was pipetted to the center of the membrane, incubated for 2 min at RT and centrifuged at 16000g for 1 min.  RNA concentration was determined using NanoDrop ND-1000 Spectrophotometer. RNA quality was assessed via a standard sensitivity RNA kit (Agilent, DNF-471) and fragment analyzer. RNA integrity number (RIN) > 8.0 was considered good quality.
Libraries from RNA using NEBNext® reagents and kits for Illumina® Sequencing following manufacturer’s instrcutions. Samples were sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Smarca2-/- mice, Smarca4fl/fl mice, and Smarca2-/-;smarca4fl/fl mice were tail vein injected AAV-TBG-GFP or AAV-TBG-CRE. Ten days after injection the mice were trained to night restricted feeding for another 4 days. Mice were sacrificed by cervical dislocation at different timepoints during the day (ZT 2, 6, 10, 14, 18, and 22).

value: male

value: Smarca2 -/- Smarca4 fl/fl

value: AAV-TBG-CRE

value: liver

tag: zeitgeber time_(zt)


title: liver, dKO, ZT22, rep3, RNA-seq

description:
matrix column name: 6815
mx_rawCounts_swisnf_zt.txt


title: ADNR PAX_1105167_06

description:
ADNR
_


title: Air_Pollution_rep1 [RRBS]

value: Placenta


title: liver, dKO, ZT22, rep1, RNA-seq

description:
matrix column name: 6813
mx_rawCounts_swisnf_zt.txt


title: RSV_2, run 1

description: Library name: 10455-JK-2


title: TX PAX_1104985_04

description:
TX
GSM2869507


title: liver, dKO, ZT22, rep4, RNA-seq

description:
matrix column name: 6816
mx_rawCounts_swisnf_zt.txt


title: RSV_1, run 1

description: Library name: 10455-JK-1


title: CONTROL_rep2 [RRBS]

value: Control


title: liver, BRMKO, ZT22, rep3, RNA-seq

description:
matrix column name: 6811
mx_rawCounts_swisnf_zt.txt

value: AAV-TBG-GFP


title: subAR PAX_1105153_06

description:
subAR
GSM2869897

value: Subclinical acute rejection


title: liver, BRMKO, ZT22, rep4, RNA-seq

description:
matrix column name: 6812
mx_rawCounts_swisnf_zt.txt


title: uninfected_5, run 1

description: Library name: 9400-JK-20

value: nasal epithelium


title: CONTROL_rep1 [RRBS]


title: 4_A

value: spinal cord

value: Nuclei


title: RSV_3, run 1

description: Library name: 10455-JK-3


title: liver, BRMKO, ZT22, rep1, RNA-seq

description:
matrix column name: 6809
mx_rawCounts_swisnf_zt.txt


title: liver, BRMKO, ZT22, rep2, RNA-seq

description:
matrix column name: 6810
mx_rawCounts_swisnf_zt.txt


title: TX PAX_1104905_04

description:
TX
GSM2869506


title: CONTROL_rep4 [RRBS]


title: TX PAX_1104897_04

description:
TX
GSM2869505


title: Air_Pol+Fish_Oil_rep4 [5-hydroxymethylation Sequencing]

data_processing:
Demultiplaxed fastq files obtained from the sequencer were aligned to the mouse reference genome (mm10) using Bowtie2
5hmC peaks were identified using MACS2 (3)  with the following parameters: effective genome size = 1.87e9 bp, Tag size = 50 bp; Bandwidth = 300 bp; Q-value cut-off = 1.00e-02bp with no antibody DNA input as a control.
Further analysis and data visualization were performed by ChIPseeker
Assembly: mm10
Supplementary files format and content: Annotated peaks (.rds)

extract_protocol:
Placental samples were colleted  from D19 placenta of  CON or Air Pollution particle exposed mice along with mice fed with Fish oil and Fish oil followed by exposure to Air Pollutant. DNA was extracted  with DNA mini kit from  Qiagen following manufacturer's protocol.
extracted DNA was fragmented by sonication and 5hmC labelling reactions were performed by transfering UDPG-N3. labelled DNA was purified using the QIAquick PCR purification kit
disulside -biotin linker was added using click chemistry and DNA fragments were precipitated using Pierce Monomeric Avidin Kit (Thermo) following the manufacturer’s recommendations.
Final library was prepared using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina following manufacturer’s protocol.
5-hydroxymethylation Sequencing

value: Fish Oil + Air Polution


title: subAR PAX_1105152_06

description:
subAR
GSM2869896


title: ADNR PAX_1103719_04

description:
ADNR
_


title: uninfected_4, run 1

description: Library name: 9400-JK-19

value: uninfected


title: CONTROL_rep3 [RRBS]


title: cAR PAX_1103476_06

description:
cAR
_

value: Clinical acute rejection


title: liver, dKO, ZT18, rep4, RNA-seq

description:
matrix column name: 6808
mx_rawCounts_swisnf_zt.txt


title: Air_Pol+Fish_Oil_rep3 [5-hydroxymethylation Sequencing]


title: uninfected_3, run 1

description: Library name: 9400-JK-18


title: uninfected_6, run 1

description: Library name: 9400-JK-21


title: liver, dKO, ZT18, rep3, RNA-seq

description:
matrix column name: 6807
mx_rawCounts_swisnf_zt.txt


title: uninfected_2, run 1

description: Library name: 9400-JK-17


title: liver, dKO, ZT18, rep1, RNA-seq

description:
matrix column name: 6805
mx_rawCounts_swisnf_zt.txt


title: Air_Pol+Fish_Oil_rep2 [5-hydroxymethylation Sequencing]


title: ADNR PAX_1003302_06

description:
ADNR
_


title: TX PAX_1103475_06

description:
TX
GSM2869501

value: Well Functioning Transplant


title: RVC_7, run 1

description: Library name: 9400-JK-15

value: RV-C


title: uninfected_1, run 1

description: Library name: 9400-JK-16


title: liver, dKO, ZT18, rep2, RNA-seq

description:
matrix column name: 6806
mx_rawCounts_swisnf_zt.txt


title: Fish_Oil_rep3 [5-hydroxymethylation Sequencing]

value: Fis Oil


title: RVC_6, run 1

description: Library name: 9400-JK-14


title: Fish_Oil_rep2 [5-hydroxymethylation Sequencing]


title: TX PAX_1103713_06

description:
TX
GSM2869502


title: liver, BRMKO, ZT18, rep4, RNA-seq

description:
matrix column name: 6804
mx_rawCounts_swisnf_zt.txt

value: male


title: Air_Pollution_rep4 [5-hydroxymethylation Sequencing]

value: Air Pollution


title: cAR PAX_1003301_05

description:
cAR
_


title: Air_Pollution_rep3 [5-hydroxymethylation Sequencing]


title: RVC_4, run 1

description: Library name: 9400-JK-12


title: liver, BRMKO, ZT18, rep2, RNA-seq

description:
matrix column name: 6802
mx_rawCounts_swisnf_zt.txt

value: Smarca2 -/- Smarca4 fl/fl


title: TX PAX_1003265_06

description:
TX
GSM2869895


title: liver, BRMKO, ZT18, rep1, RNA-seq

description:
matrix column name: 6801
mx_rawCounts_swisnf_zt.txt

value: liver


title: TX PAX_1003266_04

description:
TX
GSM2869496


title: RVC_5, run 1

description: Library name: 9400-JK-13


title: Air_Pollution_rep2 [5-hydroxymethylation Sequencing]

value: Placenta


title: RVC_3, run 1

description: Library name: 9400-JK-11


title: TX BX_1136185_03

description:
TX
_

source_name: Renal Biopsy


title: TX PAX_1003264_06

description:
TX
GSM2869495


title: Air_Pol+Fish_Oil_rep1 [5-hydroxymethylation Sequencing]


title: liver, dKO, ZT14, rep4, RNA-seq

description:
matrix column name: 6800
mx_rawCounts_swisnf_zt.txt

value: AAV-TBG-CRE


title: RVA_7, run 1

description: Library name: 9400-JK-10

value: RV-A


title: Air_Pollution_rep1 [5-hydroxymethylation Sequencing]


title: liver, dKO, ZT14, rep3, RNA-seq

description:
matrix column name: 6799
mx_rawCounts_swisnf_zt.txt


title: CONTROL_rep4 [5-hydroxymethylation Sequencing]

value: Control


title: liver, BRMKO, ZT18, rep3, RNA-seq

description:
matrix column name: 6803
mx_rawCounts_swisnf_zt.txt

value: AAV-TBG-GFP


title: cAR BX_1136158_03

description:
cAR
_


title: RVA_6, run 1

description: Library name: 9400-JK-9

value: nasal epithelium


title: CONTROL_rep3 [5-hydroxymethylation Sequencing]


title: RVA_5, run 1

description: Library name: 9400-JK-8


title: liver, dKO, ZT14, rep2, RNA-seq

description:
matrix column name: 6798
mx_rawCounts_swisnf_zt.txt


title: TX BX_1134586_03

description:
TX
_


title: RVC_2, run 1

description: Library name: 9400-JK-7


title: CONTROL_rep2 [5-hydroxymethylation Sequencing]


title: RVC_1, run 1

description: Library name: 9400-JK-6


title: subAR BX_1134584_03

description:
subAR
_

value: Subclinical acute rejection


title: liver, BRMKO, ZT14, rep3, RNA-seq

description:
matrix column name: 6795
mx_rawCounts_swisnf_zt.txt


title: cAR BX_1134583_03

description:
cAR
_


title: liver, BRMKO, ZT14, rep4, RNA-seq

description:
matrix column name: 6796
mx_rawCounts_swisnf_zt.txt


title: CONTROL_rep1 [5-hydroxymethylation Sequencing]


title: RVA_4, run 1

description: Library name: 9400-JK-4


title: TX BX_1134571_03

description:
TX
_


title: liver, BRMKO, ZT14, rep2, RNA-seq

description:
matrix column name: 6794
mx_rawCounts_swisnf_zt.txt


title: PC3 siMYC rep3

city: Chicago

first: Mihai

middle: Ioan

last: Truica

state: Illinois

address: 303 E Superior

department: Urology

institute: Northwestern University

description: Library name: Sample 24

data_processing:
Raw FASTQ files were processed using the Ceto next‑generation sequencing analysis pipeline developed in the Bartom laboratory (Elizabeth Bartom; https://github.com/ebartom/NGSbartom). Briefly, Ceto’s RNA‑seq module performed initial quality control on raw reads, adapter and quality trimming, after which cleaned paired‑end reads were aligned to the GRCh38 or GRCm39 reference genome using the splice‑aware aligner STAR v2.7.11b with a genome index built from the corresponding GTF gene annotation, followed by generation of gene‑level count tables from uniquely mapped reads. The pipeline produced per‑sample quality metrics (including read quality, mapping statistics, and duplication estimates) and a matrix of raw gene counts that was used for downstream normalization and differential expression analysis in R.
Gene‑level counts were obtained from the STAR‑generated BAM files using featureCounts (Subread), counting properly paired fragments overlapping exons and accounting for strand specificity when applicable
The resulting raw count matrix was used as input for downstream normalization and differential expression analysis in R ( using DESeq2), including filtering of lowly expressed genes, library size and dispersion estimation, and statistical testing for differential expression between conditions
Assembly: GRCh38 and GRCmm39 (for mouse line MycCaP)
Supplementary files format and content: tab-delimited text file includes raw counts for each file

source_name: cell line

growth_protocol: PC-3 and A549 cells were grown in F12K (Gibco) medium and MycCaP cells in DMEM medium (Gibco), all supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco). All cells were cultured in 1% Penicillin-Streptomycin (10,000U/ml, Life Technologies) and 5% CO2 in a humidified incubator at 37 °C.

extract_protocol:
Total RNA was extracted from cell pellet using Qiagen RNeasy Plus kit. 1 μg of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare sequencing libraries. The Kit procedure was performed without modifications. This procedure includes rRNA depletion, remaining RNA purification and fragmentation, cDNA synthesis, end preparation, Illumina adapter ligation, library PCR amplification and validation.

treatment_protocol: All 3 different cell lines were treated with either 5µM HYDRAC or 5 µM scramble control for 24 hours. PC3 cells were also treated with siMYC or siCNT as per the siRNA protocol:  cells were seeded at 3 × 10^5 cells per well in a 6-well plate in 2 mL of antibiotic-free complete medium and allowed to attach for 24 hours. siRNA targeting MYC (siEP300, M-003282-07-0005, Horizon Discovery Biosciences) or a control siRNA (siCTL, D-001210-01-05, Horizon Discovery Biosciences) were reconstituted in nuclease-free water to a final concentration of 10 μM. Transfection was performed using DharmaFect transfection reagent 1 (Horizon Discovery Biosciences) according to the manufacturer’s protocol. After 72 hours of incubation, cells were harvested, and knockdown efficiency was evaluated by Western blot analysis of MYC protein levels.

tag: cell line

value: human prostate epithelial cancer cells

value: WT

value: siMYC


title: ADNR BX_1134570_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: liver, BRMKO, ZT14, rep1, RNA-seq

description:
matrix column name: 6793
mx_rawCounts_swisnf_zt.txt


title: RVA_2, run 1

description: Library name: 9400-JK-2


title: RVA_3, run 1

description: Library name: 9400-JK-3


title: TX BX_1134569_03

description:
TX
_

value: Well Functioning Transplant


title: PC3 siMYC rep1

description: Library name: Sample 22

tag: cell type


title: liver, dKO, ZT14, rep1, RNA-seq

description:
matrix column name: 6797
mx_rawCounts_swisnf_zt.txt


title: liver, dKO, ZT10, rep4, RNA-seq

description:
matrix column name: 6792
mx_rawCounts_swisnf_zt.txt


title: PC3 siCNT rep3

description: Library name: Sample 21

value: siCNT


title: RVA_1, run 1

description: Library name: 9400-JK-1


title: liver, dKO, ZT10, rep3, RNA-seq

description:
matrix column name: 6791
mx_rawCounts_swisnf_zt.txt

value: male


title: PC3 siCNT rep2

description: Library name: Sample 20


title: ADNR BX_1134560_03

description:
ADNR
_


title: Patient 90 Late Passage 3

city: Nottingham

first: Brinda

last: Balasubramanian

address: University Park

institute: University of Nottingham

description:
Library name: P99_6
Column name in raw_counts_PDO.txt: P99_6

data_processing:
Raw paired-end FASTQ files are analyzed using FastQC to evaluate sequencing quality metrics.
Adapter sequences and low-quality bases are removed using Trim Galore!, followed by generation of post-trimming FastQC reports.
Trimmed reads are aligned to the reference genome using HISAT2
Aligned reads are counted against gene annotations using FeatureCounts, producing a gene-level count matrix for downstream analysis.
Gene ID converted and genes with very low expression are removed
Assembly: GRCh38.p12
Supplementary files format and content: raw_counts_PDO.txt

source_name: colon

growth_protocol: Human intestinal crypts were isolated from adult tissues using 25 μg/mL of liberase (Roche), embedded into Matrigel (Corning, Cat 356231) and grown into organoids. Human intestinal organoids were cultured in IntestiCult™ Organoid Human Growth Medium or in-house media and were split once a week by mechanical dissociation and with TryPLE every two weeks.

extract_protocol:
RNA was collected from healthy individuals and IBD patient derived organoids embedded in Matrigel in 48-well plates. RNA was extracted using Qiagen RNeasy kit and RNA quality was assessed with the NanoDrop and the RIN score was checked.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platform NovaSeq XPlus 25B platform, according to effective library concentration and data amount

value: colon

tag: disease state

value: IBD


title: liver, dKO, ZT10, rep2, RNA-seq

description:
matrix column name: 6790
mx_rawCounts_swisnf_zt.txt

value: Smarca2 -/- Smarca4 fl/fl

tag: treatment

value: liver


title: PC3 siCNT rep1

description: Library name: Sample 19


title: liver, dKO, ZT10, rep1, RNA-seq

description:
matrix column name: 6789
mx_rawCounts_swisnf_zt.txt

value: AAV-TBG-CRE


title: PC3 sHR 24hr rep3

description: Library name: Sample 18

value: non-targeting degrading copolymer


title: Patient 90 Late Passage 2

description:
Library name: P99_5
Column name in raw_counts_PDO.txt: P99_5


title: Patient 90 Late Passage 1

description:
Library name: P99_4
Column name in raw_counts_PDO.txt: P99_4


title: TX BX_1133779_03

description:
TX
_


title: liver, BRMKO, ZT10, rep4, RNA-seq

description:
matrix column name: 6788
mx_rawCounts_swisnf_zt.txt


title: PC3 siMYC rep2

description: Library name: Sample 23


title: PC3 sHR 24hr rep2

description: Library name: Sample 17


title: subAR BX_1133645_03

description:
subAR
_


title: Patient 90 Early Passage 3

description:
Library name: P99_3
Column name in raw_counts_PDO.txt: P99_3


title: cAR BX_1133646_03

description:
cAR
_

value: Clinical acute rejection


title: PC3 sHR 24hr rep1

description: Library name: Sample 16


title: Patient 90 Early Passage 2

description:
Library name: P99_2
Column name in raw_counts_PDO.txt: P99_2


title: subAR BX_1133100_03

description:
subAR
_


title: liver, BRMKO, ZT10, rep3, RNA-seq

description:
matrix column name: 6787
mx_rawCounts_swisnf_zt.txt

value: AAV-TBG-GFP


title: ADNR BX_1134564_03

description:
ADNR
_


title: PC3 HYDRAC 24hr rep3

description: Library name: Sample 15

value: MYC-targeting degrading copolymer


title: liver, BRMKO, ZT10, rep2, RNA-seq

description:
matrix column name: 6786
mx_rawCounts_swisnf_zt.txt


title: Patient 90 Early Passage 1

description:
Library name: P99_1
Column name in raw_counts_PDO.txt: P99_1


title: subAR BX_1133109_03

description:
subAR
_

value: Subclinical acute rejection


title: subAR BX_1132806_03

description:
subAR
_


title: PC3 HYDRAC 24hr rep2

description: Library name: Sample 14

value: human prostate epithelial cancer cells


title: liver, dKO, ZT6, rep4, RNA-seq

description:
matrix column name: 6784
mx_rawCounts_swisnf_zt.txt


title: liver, BRMKO, ZT10, rep1, RNA-seq

description:
matrix column name: 6785
mx_rawCounts_swisnf_zt.txt


title: PC3 HYDRAC 24hr rep1

description: Library name: Sample 13

value: WT


title: Patient 90 IBD 3

description:
Library name: P90_3
Column name in raw_counts_PDO.txt: P90_3


title: Patient 90 IBD 2

description:
Library name: P90_2
Column name in raw_counts_PDO.txt: P90_2


title: liver, dKO, ZT6, rep3, RNA-seq

description:
matrix column name: 6783
mx_rawCounts_swisnf_zt.txt


title: subAR BX_1131609_03

description:
subAR
_


title: Patient 90 IBD 1

description:
Library name: P90_1
Column name in raw_counts_PDO.txt: P90_1


title: TX BX_1131615_03

description:
TX
_


title: A549 sHR 24hr rep3

description: Library name: Sample 6

value: human lung alveolar epithelial carcinoma cells


title: subAR BX_1131598_03

description:
subAR
_


title: liver, dKO, ZT6, rep2, RNA-seq

description:
matrix column name: 6782
mx_rawCounts_swisnf_zt.txt


title: liver, dKO, ZT6, rep1, RNA-seq

description:
matrix column name: 6781
mx_rawCounts_swisnf_zt.txt


title: A549 sHR 24hr rep2

description: Library name: Sample 5


title: Patient 89 IBD 4

description:
Library name: P89_4
Column name in raw_counts_PDO.txt: P89_4


title: TX BX_1131595_03

description:
TX
_


title: liver, BRMKO, ZT6, rep4, RNA-seq

description:
matrix column name: 6780
mx_rawCounts_swisnf_zt.txt


title: Patient 89 IBD 3

description:
Library name: P89_3
Column name in raw_counts_PDO.txt: P89_3


title: Patient 89 IBD 2

description:
Library name: P89_2
Column name in raw_counts_PDO.txt: P89_2


title: liver, BRMKO, ZT6, rep3, RNA-seq

description:
matrix column name: 6779
mx_rawCounts_swisnf_zt.txt


title: Patient 89 IBD 1

description:
Library name: P89_1
Column name in raw_counts_PDO.txt: P89_1


title: TX BX_1130347_03

description:
TX
_


title: A549 HYDRAC 24hr rep2

description: Library name: Sample 2


title: subAR BX_1130242_03

description:
subAR
_


title: A549 HYDRAC 24hr rep1

description: Library name: Sample 1


title: liver, BRMKO, ZT6, rep2, RNA-seq

description:
matrix column name: 6778
mx_rawCounts_swisnf_zt.txt


title: Patient 12 Healthy Late Passage 4

description:
Library name: P12_7
Column name in raw_counts_PDO.txt: P12_7

value: normal


title: TX BX_1130240_03

description:
TX
_

value: Well Functioning Transplant


title: RPMI_H3K27ac

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

description: Library name: sample1

data_processing:
cleaning with fastq-mcf
quality control with FastQC
mapping with Bowtie2, further processing with SAMTools
peak calling with MACS2
normalization with deepTools
Assembly: hg38
Supplementary files format and content: bigwig files were generated with the deepTools software package (genome normalization)
Supplementary files format and content: narrowPeak files were generated with the MACS2 peak calling algorithm (FDR<0.01)

growth_protocol: RPMI-8402 cells were maintained in RPMI-1640 medium supplemented with 10% FBS at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Bioruptor NGS (Diagenode) sonicator.
ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody


title: liver, BRMKO, ZT6, rep1, RNA-seq

description:
matrix column name: 6777
mx_rawCounts_swisnf_zt.txt


title: TX BX_1129891_03

description:
TX
_


title: HEK293T, Torin1-treated, Ribo-Seq, rep3

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

description: Library name: HEK_G6_torin_Ribo_3

data_processing:
Read quality control was performed with FastQC v0.11.5. The reads were trimmed with cutadapt v2.10 "-a ATCGTAGATCGGAAGAGCACACGTCTGAA -j 24 --minimum-length 20 --nextseq-trim=20 --trimmed-only". The availability of UMIs allowed pre-alignment deduplication using seqkit v2.6.1 rmdup followed by cutadapt "-u -5" to remove UMIs.
Read mapping was performed to the hg38 genome assembly using STAR v2.7.6a with default parameters and "--quantMode GeneCounts" to estimate the read counts per gene. The supplied genome annotation was GENCODE v38 with spike-in sequences as additional contigs.
Assembly: hg38
Supplementary files format and content: File format: tsv, tab-separated plain text files. File contents: the files contain the read counts per gene (including spike-ins) estimated by STAR.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, and 100 µg streptomycin.

extract_protocol:
Cells were chilled on ice and washed with PBS supplemented with cycloheximide (100 µg/ml), lysed with buffer containing 20 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, and 25 U/ml TURBO DNase (Ambion). The lysate was divided into two parts for Ribo-Seq and RNA-Seq library preparation.
Ribo-Seq libraries were obtained according to (McGlincy 2017, PMID: 28579404) using CircLigase II (Lucigen), custom adapter with UMI-sequence (5 random nucleotides  for deduplication), and NEBNext Multiplex Oligos for Illumina Index Primers Set (NEB). The rRNA depletion was performed using a RiboMinus™ Eukaryote Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s recommendations.

treatment_protocol: Cells were treated with Torin1 (dissolved in DMSO, 250 nM; Tocris Bioscience, Bristol, UK) or with DMSO alone for 2 h.

value: cell line

value: Human Embryonic Kidney

value: wt

value: 250 nM Torin1, 2h


title: A549 sHR 24hr rep1

description: Library name: Sample 4


title: Patient 12 Healthy Late Passage 2

description:
Library name: P12_5
Column name in raw_counts_PDO.txt: P12_5

value: colon


title: Patient 12 Healthy Late Passage 3

description:
Library name: P12_6
Column name in raw_counts_PDO.txt: P12_6


title: ADNR BX_1129886_03

description:
ADNR
_

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

extract_protocol: PAXgene extraction of total RNA was performed using the PAXgene RNA extraction kit according to the manufacturer's instructions.

value: Acute dysfunction no rejection


title: liver, dKO, ZT2, rep4, RNA-seq

description:
matrix column name: 6776
mx_rawCounts_swisnf_zt.txt

value: male

value: Smarca2 -/- Smarca4 fl/fl

value: AAV-TBG-CRE

value: liver


title: liver, dKO, ZT2, rep3, RNA-seq

description:
matrix column name: 6775
mx_rawCounts_swisnf_zt.txt


title: TX BX_1131592_03

description:
TX
_


title: liver, dKO, ZT2, rep2, RNA-seq

description:
matrix column name: 6774
mx_rawCounts_swisnf_zt.txt


title: A549 HYDRAC 24hr rep3

description: Library name: Sample 3

value: MYC-targeting degrading copolymer


title: HEK293T, Torin1-treated, Ribo-Seq, rep1

description: Library name: HEK_G6_torin_Ribo_1


title: Patient 12 Healthy Early Passage 3

description:
Library name: P12_3
Column name in raw_counts_PDO.txt: P12_3


title: liver, dKO, ZT2, rep1, RNA-seq

description:
matrix column name: 6773
mx_rawCounts_swisnf_zt.txt


title: HEK293T, Torin1-treated, Ribo-Seq, rep2

description: Library name: HEK_G6_torin_Ribo_2


title: Patient 12 Healthy Late Passage 1

description:
Library name: P12_4
Column name in raw_counts_PDO.txt: P12_4


title: TX BX_1129681_03

description:
TX
_


title: HEK293T MELL3/14 KD, Torin-treated, Ribo-Seq, rep3

description: Library name: HEK_G6_dd_METTL_torin_Ribo_3

value: METTL3 and METTL14 knockdown


title: Patient 12 Healthy Early Passage 2

description:
Library name: P12_2
Column name in raw_counts_PDO.txt: P12_2


title: TX BX_1129703_03

description:
TX
_


title: liver, BRMKO, ZT2, rep4, RNA-seq

description:
matrix column name: 6772
mx_rawCounts_swisnf_zt.txt

value: AAV-TBG-GFP


title: HEK293T MELL3/14 KD, Torin-treated, Ribo-Seq, rep2

description: Library name: HEK_G6_dd_METTL_torin_Ribo_2


title: Patient 12 Healthy Early Passage 1

description:
Library name: P12_1
Column name in raw_counts_PDO.txt: P12_1


title: TX BX_1129216_03

description:
TX
_


title: liver, BRMKO, ZT2, rep3, RNA-seq

description:
matrix column name: 6771
mx_rawCounts_swisnf_zt.txt


title: ADNR BX_1129334_03

description:
ADNR
_


title: HEK293T MELL3/14 KD, Torin-treated, Ribo-Seq, rep1

description: Library name: HEK_G6_dd_METTL_torin_Ribo_1


title: liver, BRMKO, ZT2, rep2, RNA-seq

description:
matrix column name: 6770
mx_rawCounts_swisnf_zt.txt


title: HEK293T MELL3/14 KD, DMSO-treated, Ribo-Seq, rep3

description: Library name: HEK_G6_dd_METTL_Ribo_3

value: DMSO, 2h


title: Hypoxia + SFN + 5-FU replicate 2

city: Jinan

first: Jinshen

last: Wang

state: Shandong Province

address: Jingwu Weiqi Road, Huaiyin District, Jinan 250021, Shandong, China.

department: Department of Gastrointestinal Surgery

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description: Library name: F_2

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/) to map reads to the reference genome of homo sapiens Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: homo_sapiens Ensembl_v107
Supplementary files format and content: Processed data consist of a tab-delimited text file containing gene-level FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values. Each row represents an Ensembl gene ID (ENSG), and each column represents an individual sample.

source_name: colorectal cancer cells

growth_protocol: SW480 colorectal cancer cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum and cultured under standard conditions (37°C, 5% CO₂).

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 400±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ X Plus (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Cells were exposed to hypoxia (1% O₂) for 48 h. Three groups were included: hypoxia control, hypoxia + sulforaphane (25 μM), and hypoxia + sulforaphiluracil (SFN + 5-FU).

value: colorectal cancer cells

value: Hypoxia, sulforaphane + 5-fluorouracil treatment


title: Hypoxia + SFN + 5-FU replicate 3

description: Library name: F_3


title: liver, BRMKO, ZT2, rep1, RNA-seq

description:
matrix column name: 6769
mx_rawCounts_swisnf_zt.txt


title: TX BX_1129215_03

description:
TX
_

value: Well Functioning Transplant


title: TX BX_1129212_03

description:
TX
_


title: HEK293T MELL3/14 KD, DMSO-treated, Ribo-Seq, rep2

description: Library name: HEK_G6_dd_METTL_Ribo_2

value: cell line


title: TX BX_1128865_03

description:
TX
_


title: Hypoxia + SFN replicate 3

description: Library name: E_3

value: Hypoxia, sulforaphane treatment


title: liver, dKO, rep4, RNA-seq

description:
matrix column name: 8689
mx_rawCounts_genotypes_zt10.txt


title: Hypoxia + SFN + 5-FU replicate 1

description: Library name: F_1


title: HEK293T MELL3/14 KD, DMSO-treated, Ribo-Seq, rep1

description: Library name: HEK_G6_dd_METTL_Ribo_1

value: Human Embryonic Kidney


title: liver, dKO, rep2, RNA-seq

description:
matrix column name: 8687
mx_rawCounts_genotypes_zt10.txt


title: HEK293T, DMSO-treated, Ribo-Seq, rep3

description: Library name: HEK_G6_Ribo_3

value: wt


title: HEK293T, DMSO-treated, Ribo-Seq, rep2

description: Library name: HEK_G6_Ribo_2


title: Hypoxia + SFN replicate 2

description: Library name: E_2


title: liver, dKO, rep1, RNA-seq

description:
matrix column name: 8686
mx_rawCounts_genotypes_zt10.txt


title: Hypoxia control replicate 3

description: Library name: D_3

value: Hypoxia, untreated


title: subAR BX_1128861_03

description:
subAR
_

value: Subclinical acute rejection


title: ADNR BX_1128583_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: subAR BX_1128585_03

description:
subAR
_


title: subAR BX_1127878_03

description:
subAR
_


title: RPMI-8402-WT30-NKX2_1

description:
Library name: sample8
RPMI-8402-WT.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak

value: WT


title: liver, L-BRG1KO, rep4, RNA-seq

description:
matrix column name: 8697
mx_rawCounts_genotypes_zt10.txt

value: male

value: Smarca2 +/+ Smarca4 fl/fl

value: AAV-TBG-CRE


title: Hypoxia control replicate 2

description: Library name: D_2


title: TX BX_1127728_03

description:
TX
_


title: liver, L-BRG1KO, rep3, RNA-seq

description:
matrix column name: 8696
mx_rawCounts_genotypes_zt10.txt

value: liver


title: Hypoxia control replicate 1

description: Library name: D_1


title: RPMI-8402-WT28-NKX2_1

description:
Library name: sample7
RPMI-8402-WT.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak


title: liver, dKO, rep3, RNA-seq

description:
matrix column name: 8688
mx_rawCounts_genotypes_zt10.txt

value: Smarca2 -/- Smarca4 fl/fl


title: liver, L-BRG1KO, rep2, RNA-seq

description:
matrix column name: 8695
mx_rawCounts_genotypes_zt10.txt


title: RPMI-8402-WT13-NKX2_1

description:
Library name: sample6
RPMI-8402-WT.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak


title: non_5

city: Shanghai

first: Jiayao

last: Zhou

address: No. 600,  Yishan Road

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 15
Cells cultured ex vivo from the nasal mucosa of the fifth patient

data_processing:
Raw reads were filtered with Seqtk to remove adaptor sequence and low-quality sequence.
Genome mapping was performed by "splices mapping" algorithm in Hista2 (version:2.0.4).
Annotation genome used was GRCh38.p4 (hg38).
Assembly: GRCh38.p4 (hg38)
Supplementary files format and content: tab-delimited text file includes count and RPKM values for each Sample

source_name: nasal mucosa

growth_protocol: Cells were cultured in DMEM/F12 containing 10% Fetal bovine Serum (FBS), 100 IU/mL penicillin, 100μg/mL streptomycin and 2μg/mL amphotericin B at 37 ℃ with 5% CO2.

extract_protocol:
RNA was extracted using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

treatment_protocol: Cells were treated with 1% polar and non-polar organic components of PM2.5 or  same amount of normal culture medium for 24h.

value: nasal mucosa

value: fibroblasts

value: non-polar organic component


title: RPMI-8402-WT10-NKX2_1

description:
Library name: sample5
RPMI-8402-WT.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak


title: polar_5

description:
Library name: Sample 14
Cells cultured ex vivo from the nasal mucosa of the fifth patient

value: polar organic component


title: TX BX_1127208_03

description:
TX
_

value: Well Functioning Transplant


title: liver, BRMKO, rep4, RNA-seq

description:
matrix column name: 8685
mx_rawCounts_genotypes_zt10.txt

value: AAV-TBG-GFP


title: HEK293T, DMSO-treated, Ribo-Seq, rep1

description: Library name: HEK_G6_Ribo_1

value: cell line

value: Human Embryonic Kidney

value: DMSO, 2h


title: Hypoxia + SFN replicate 1

description: Library name: E_1

value: colorectal cancer cells

value: Hypoxia, sulforaphane treatment


title: RPMI-8402-S36-NKX2_1

description:
Library name: sample4
RPMI-8402-NKX21.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak


title: liver, BRMKO, rep3, RNA-seq

description:
matrix column name: 8684
mx_rawCounts_genotypes_zt10.txt


title: ct_5

description:
Library name: Sample 13
Cells cultured ex vivo from the nasal mucosa of the fifth patient

value: control


title: subAR BX_1126940_03

description:
subAR
_

value: Subclinical acute rejection


title: non_4

description:
Library name: Sample 12
Cells cultured ex vivo from the nasal mucosa of a fourth patient


title: subAR BX_1126487_03

description:
subAR
_


title: RPMI-8402-C15-NKX2_1

description:
Library name: sample2
RPMI-8402-NKX21.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak


title: liver, BRMKO, rep2, RNA-seq

description:
matrix column name: 8683
mx_rawCounts_genotypes_zt10.txt

value: male


title: ADNR BX_1126921_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: ADNR BX_1126325_03

description:
ADNR
_


title: polar_4

description:
Library name: Sample 11
Cells cultured ex vivo from the nasal mucosa of a fourth patient


title: WT30

description: Library name: sample8

data_processing:
cleaning with fastq-mcf
quality control with FastQC
mapping with Tophat2, further processing with SAMTools
counting abundances with subread
Assembly: hg38
Supplementary files format and content: comma seperated file with the raw counts per gene and per sample

extract_protocol:
Total RNA was harvested using the Rneasy mini kit (Qiagen). 10 µL of total RNA was used for the construction of the RNA-sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: WT


title: liver, L-BRG1KO, rep1, RNA-seq

description:
matrix column name: 8694
mx_rawCounts_genotypes_zt10.txt

value: Smarca2 +/+ Smarca4 fl/fl

value: AAV-TBG-CRE

value: liver


title: ADNR BX_1126318_03

description:
ADNR
_


title: ct_4

description:
Library name: Sample 10
Cells cultured ex vivo from the nasal mucosa of a fourth patient

value: nasal mucosa

value: fibroblasts


title: liver, BRG1/BRM, rep4, RNA-seq

description:
matrix column name: 8693
mx_rawCounts_genotypes_zt10.txt


title: RPMI-8402-C12-NKX2_1

description:
Library name: sample1
RPMI-8402-NKX21.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak


title: non_3

description:
Library name: Sample 9
Cells cultured ex vivo from the nasal mucosa of a third patient

value: non-polar organic component


title: subAR BX_1125904_03

description:
subAR
_


title: polar_3

description:
Library name: Sample 8
Cells cultured ex vivo from the nasal mucosa of a third patient

value: polar organic component


title: liver, BRG1/BRM, rep2, RNA-seq

description:
matrix column name: 8691
mx_rawCounts_genotypes_zt10.txt

value: AAV-TBG-GFP


title: liver, BRG1/BRM, rep3, RNA-seq

description:
matrix column name: 8692
mx_rawCounts_genotypes_zt10.txt


title: RPMI-8402-S04-NKX2_1

description:
Library name: sample3
RPMI-8402-NKX21.bigwig
RPMI-NKX2-1-peaks_peaks.narrowPeak


title: WT13

description: Library name: sample6


title: liver, BRG1/BRM, rep1, RNA-seq

description:
matrix column name: 8690
mx_rawCounts_genotypes_zt10.txt


title: WT10

description: Library name: sample5


title: ct_3

description:
Library name: Sample 7
Cells cultured ex vivo from the nasal mucosa of a third patient


title: non_2

description:
Library name: Sample 6
Cells cultured ex vivo from the nasal mucosa of the second patient


title: liver, BRMKO, rep1, RNA-seq

description:
matrix column name: 8682
mx_rawCounts_genotypes_zt10.txt

value: Smarca2 -/- Smarca4 fl/fl


title: S36

description: Library name: sample4


title: ADNR BX_1125899_03

description:
ADNR
_


title: subAR BX_1125795_03

description:
subAR
_


title: liver, WT, ZT22, rep3, RNA-seq

description:
matrix column name: SM4491
mx_rawCounts_wt_zt.txt


title: polar_2

description:
Library name: Sample 5
Cells cultured ex vivo from the nasal mucosa of the second patient


title: liver, WT, ZT22, rep2, RNA-seq

description:
matrix column name: SM4490
mx_rawCounts_wt_zt.txt


title: ADNR BX_1125365_03

description:
ADNR
_


title: S04

description: Library name: sample3


title: C15

description: Library name: sample2


title: liver, WT, ZT22, rep1, RNA-seq

description:
matrix column name: SM4489
mx_rawCounts_wt_zt.txt


title: non_1

description:
Library name: Sample 3
Cells cultured ex vivo from the nasal mucosa of the first patient


title: liver, WT, ZT18, rep3, RNA-seq

description:
matrix column name: SM4485
mx_rawCounts_wt_zt.txt


title: C12

description: Library name: sample1


title: WT28

description: Library name: sample7


title: cAR BX_1124952_03

description:
cAR
_

value: Clinical acute rejection


title: TX BX_1124951_03

description:
TX
_

value: Well Functioning Transplant


title: TX BX_1125792_03

description:
TX
_


title: TX BX_1124885_03

description:
TX
_


title: Vehicle, 24hours, rep3

data_processing:
Fastq files were processed using Ceto pipeline created by Dr. Elizabeth Bartom
Assembly: RNA sequence reads were aligned to reference genome using STAR (v 2.7.5). Gene expression was quantified using HTSeq and differential gene expression profiles were generated using DESeq2.
Filtered counts tables were normalized using VST.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: prostate

growth_protocol: PC-3 cells were grown in F12K (Gibco) medium supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (10,000U/ml, Life Technologies) and cultured with 5% CO2 in a humidified incubator at 37 °C.

extract_protocol:
Cells were collected using trypsinization and washed with ice-cold PBS and centrifuged at 1500 rpm for 5 minutes. Total RNA was extracted from cell pellet using Qiagen RNeasy Plus kit. Total RNA examples were checked for quality on Agilent Bioanalyzer 2100 and quantity with Qubit fluorometer. 1.3 ug of total RNA was used for the construction of sequencing libraries
The NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare sequencing libraries. The Kit procedure was performed without modifications. This procedure includes rRNA depletion, remaining RNA purification and fragmentation, cDNA synthesis, end preparation, Illumina adapter ligation, library PCR amplification and validation.

treatment_protocol: Cells were plated at 70% confluence, allowed to adhere to plate and acclimate overnight. Then treated with HYDRAC or negative control (vehicle/DMSO or polymer with scrambled targeting sequence) at 5 uM for 24 hours.

value: prostate

value: epithelial


title: polar_1

description:
Library name: Sample 2
Cells cultured ex vivo from the nasal mucosa of the first patient


title: Vehicle, 24hours, rep2


title: humanDLPFC_Control_4

city: Madison

first: anthony

middle: shawn

last: abrantes

state: WI

address: 402 Paunack st apt 1

department: genetic medicine

institute: unc-chapel hill

data_processing:
SMRTLink (v8.0.0)
removed primers using Lima (v2.0.0).
clustered using IsoSeq3
aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
SQANTI3 QC filtering
Assembly: GRCh38.p13
Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts

source_name: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)

extract_protocol:
The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.

value: Control

tag: batch


title: liver, WT, ZT18, rep1, RNA-seq

description:
matrix column name: SM4483
mx_rawCounts_wt_zt.txt

source_name: liver

value: male


title: liver, WT, ZT14, rep3, RNA-seq

description:
matrix column name: SM4479
mx_rawCounts_wt_zt.txt


title: liver, WT, ZT18, rep2, RNA-seq

description:
matrix column name: SM4484
mx_rawCounts_wt_zt.txt


title: ct_1

description:
Library name: Sample 1
Cells cultured ex vivo from the nasal mucosa of the first patient

value: control


title: liver, WT, ZT14, rep2, RNA-seq

description:
matrix column name: SM4478
mx_rawCounts_wt_zt.txt

value: WT


title: HYDRAC, 24hours, rep3

value: 5 uM


title: humanDLPFC_Control_5

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)


title: humanDLPFC_Control_3


title: HYDRAC, 24hours, rep2


title: ct_2

description:
Library name: Sample 4
Cells cultured ex vivo from the nasal mucosa of the second patient


title: humanDLPFC_Schizophrenia_5

value: Schizophrenia


title: TX BX_1124759_03

city: La Jolla

first: SUNIL

last: KURIAN

address: 10666 N Torrey Pines Rd

institute: Scripps Health

description:
TX
_


title: subAR BX_1124371_03

description:
subAR
_

value: Subclinical acute rejection


title: liver, WT, ZT10, rep3, RNA-seq

description:
matrix column name: SM4467
mx_rawCounts_wt_zt.txt

value: liver


title: TX BX_1124720_03

description:
TX
_


title: subAR BX_1124979_03

description:
subAR
_


title: TX BX_1127503_03

description:
TX
_


title: HYDRAC, 24hours, rep1


title: subAR BX_1124267_03

description:
subAR
_


title: humanDLPFC_Schizophrenia_4


title: subAR BX_1124254_03

description:
subAR
_


title: liver, WT, ZT10, rep2, RNA-seq

description:
matrix column name: SM4466
mx_rawCounts_wt_zt.txt


title: Vehicle, 24hours, rep1


title: liver, WT, ZT14, rep1, RNA-seq

description:
matrix column name: SM4477
mx_rawCounts_wt_zt.txt


title: P-shR, 24hours, rep3


title: P-shR, 24hours, rep2


title: P-shR, 24hours, rep1


title: humanDLPFC_Schizophrenia_3


title: liver, WT, ZT6, rep3, RNA-seq

description:
matrix column name: SM4464
mx_rawCounts_wt_zt.txt


title: liver, WT, ZT6, rep2, RNA-seq

description:
matrix column name: SM4463
mx_rawCounts_wt_zt.txt


title: humanDLPFC_Control_2


title: humanDLPFC_Control_1


title: TX BX_1124364_03

description:
TX
_


title: WT T3 S6

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

institute: Glasgow University

data_processing:
Raw sequencing data was pre-processed using the University of Glasgow high performance computing clusters for which quality control was performed by FastQC (0.11.9) and the reads were trimmed by fastp (0.23.2). Trimmed reads were aligned to human reference genome hg38 using STAR (2.7.10a) and assigned by the feature counting tool featureCount (2.0.1). Differentially expressed genes between experimental conditions were obtained by DESeq2 (1.36.0) in R.
Assembly: human reference genome GRCh38/hg38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: JURL-MK1 (WT)

growth_protocol: The nilotinib resistant JURL-MK1 (C3) cell line and the parental JURL-MK1 (WT) cell line were grown in RPMI 1640 (Sigma) supplemented with 10% fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine and 1% (v/v) penicillin-streptomycin.

extract_protocol:
The cells were pelleted by centrifugation in culture media, washed and then pelleted again in phosphate buffered saline pH 7.4, and total cellular RNA extracted from a minimum of 1 x106 cells in TRIzoLTM Reagent (ThermoFisher). The concentration of the RNA was measured using the Nanodrop 2000, and the quality and RIN value was determined using the Agilent Bioanalyser RNA Nano kit (Agilent).
RNA-seq libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) with single indexing following the manufacturers’ instructions. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: The nilotinib resistant JURL-MK1 cell line (C3) was cultured as above with the addition of 1µM NIL to maintain resistance prior to its use in experiments. Prior to RNA extraction for this study, nilotinib resistant JURL-MK1 cells were grown in the absence of nilotinib for 72 hrs.

value: JURL-MK1 (WT)

value: leukaemia

value: CML

value: M


title: TX BX_1124253_03

description:
TX
_


title: liver, WT, ZT6, rep1, RNA-seq

description:
matrix column name: SM4462
mx_rawCounts_wt_zt.txt


title: WT T2 S5


title: WT T1 S4


title: subAR BX_1124251_03

description:
subAR
_


title: liver, WT, ZT2, rep3, RNA-seq

description:
matrix column name: SM4461
mx_rawCounts_wt_zt.txt


title: H19,Time3

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

address: 2125 Delaware Ave. Suite B

institute: RealSeq Biosciences

description: Library name: H19_3

data_processing:
First, sequencing reads were trimmed of the adapter sequence using cutadapt (Martin, 2011). Trimming statistics revealed excluded dimers in a range of 5.41% – 21.76%, nevertheless, their average proportions were comparable in individual sampling times: 13.40%, 12.55%, 11.79% for T1-T3 respectively. The final average reads passing the filters were 8,133,803 per sample. Next, the per-base sequence quality was checked. This test indicated high-quality scores (above 30) for all positions in reads up to 91 bases. An additional part of the data quality control (FastQC) focused on the distribution of the read length. The data showed a comparable trend in distribution among the individual samples, with the majority of read lengths being around 21 nucleotides. Reads were then sequentially aligned using either bowtie or bowtie2 (Langmead and Salzberg, 2012) to vector the contaminants (UniVec), rRNAs, tRNAs (with the addition of the -CCA tail) identified using tRNAScan-SE (Chan et al., 2021), miRNAs from miRbase (Kozomara et al., 2019), snRNAs/snoRNAs from Ensembl (Dyer et al., 2025), piRNAs from piRbase (Wang et al., 2022), processed mRNA transcripts (mRNA/protein coding) from Ensembl (Dyer et al., 2025), and lastly to the genome. The counts associated with these features were then quantified using a custom Python script, choosing the feature annotation with the largest degree of overlap. Multimapping ncRNA reads with more than one highest-scoring alignment were randomly selected, while multimapping protein-coding reads were not included in the downstream analysis. For tRNA mapping reads, a read was assigned as either a ‘5p’, ‘3p’, or as an ‘internal’ feature based on where it mapped in the parent transcript. For ‘5p’ features, it must map within 10 bp of the 5’ end, ‘3p’ features must map within 10 bp of the 3’ end, and an ‘internal’ feature does not map within 10 bp of either the 5’ or 3’ end of the parent transcript. Furthermore, the Median Absolute Deviation Analysis (MAD) method was used for the identification of samples with extreme deviations in count distributions for individual experimental groups. The MAD method computed a modified Z-score for each sample, resulting in eleven samples with normal values and one T1 sample as a potential outlier (|Z| > 3). Additional analysis included mapping statistics: (i) the percentage of mapped reads were in the range 89.04% - 97.68% among individual samples, with an average of 3,747,657 reads; (ii) for the distribution of RNA biotypes and the number of detected transcripts, see section 3.2. In general, the data presented in this study were mostly analyzed and/or visualized by Principal Component Analyses (PCA), Differential Expression Analyses using DESeq2 (Love et al., 2014) with the following settings: log2FC (Fold Change) cutoff = 1; adjusted p-value cutoff = 0.05, and boxplots showing the normalized count values across different experimental conditions for selected transcripts (see Results section).
Assembly: GRCh38/hg38
Supplementary files format and content: readcounts.csv contains raw counts for annotated RNA transcripts.

source_name: Blood

growth_protocol: The personal and exposure characteristics obtained from the questionnaires are summarized in Table 1. Participants of this pilot study were firefighters (mean age 45) with long-time occupational exposure history (14-30 years, starting at the age of 19-22 years). At the time of sampling, all subjects were active firefighters, with mostly 5 – 10 fire interventions during the last year. Additional inhalation exposure from smoking at the time of the study was reported by one of these participants.

extract_protocol:
The total RNA was extracted from 2.5 ml of whole blood samples by using a PAXgene Blood miRNA Kit (PreAnalytiX, Qiagen, Switzerland). The RNA quantity and concentration were measured with a Qubit 4.0 Fluorometer using a High-Sensitivity RNA kit, the Qubit® RNA HS (High Sensitivity) Assay Kit (both ThermoFisher Scientific, Wilmington, DE, USA). The RNA quality and fragmentation were assessed with a Fragment Analyzer using an SS RNA kit (both Agilent Technologies, Santa Clara, CA, USA). The mean RNA integrity number (RIN) for all samples was 7.6 (range: 4-9.6), with individual RINs of 8.6, 7.1, and 7 for sampling times T1 to T3, respectively. The following analysis steps were performed to identify a broad spectrum of individual RNAs, including mRNA, rRNA, tRNA, miRNA, snRNA, snoRNA, lncRNA, piRNA, other sRNAs, and unannotated and unmapped RNAs.
RiboMarker® RNA Fragmentomics Library Preparation Kit #400-00012 (RealSeq Biosciences, Santa Cruz, USA) was used for preparing all individual libraries from 50 ng of the total RNA according to the manufacturer’s protocol. Briefly, the two-day workflow involved: (i) RNA pretreatment [with RNA Clean & Concentrator-5 #R1015 (Zymo Research, Irvine, CA, USA)], adapter ligation, and blocking on the first day, followed by (ii) circularization, dimer removal, reverse transcription, PCR amplification, and size selection with SPRI beads on the second day. The RNA libraries concentration was measured with the 1× dsDNA HS kit (ThermoFisher Scientific) on the Qubit 4.0 fluorometer, and the quality was checked using the Fragment Analyzer with the HS NGS Fragment Kit (Agilent Technologies). The libraries had estimated profiles with the main peak of fragment length between 147-162bp.

value: Blood

tag: time


title: liver, WT, ZT2, rep2, RNA-seq

description:
matrix column name: SM4460
mx_rawCounts_wt_zt.txt

tag: strain


title: liver, WT, ZT10, rep1, RNA-seq

description:
matrix column name: SM4465
mx_rawCounts_wt_zt.txt


title: TX BX_1124085_03

description:
TX
_

value: Well Functioning Transplant


title: TX BX_1124246_03

description:
TX
_


title: H17,Time3

description: Library name: H17_3


title: C3 T3 S3

source_name: JURL-MK1 (C3) nilotinib resistant

value: JURL-MK1 (C3) nilotinib resistant


title: liver, WT, ZT2, rep1, RNA-seq

description:
matrix column name: SM4459
mx_rawCounts_wt_zt.txt


title: TX BX_1123947_03

description:
TX
_


title: C3 T2 S2


title: H10,Time3

description: Library name: H10_3


title: humanDLPFC_Schizophrenia_2


title: cAR BX_1123830_03

description:
cAR
_

value: Clinical acute rejection


title: H9,Time3

description: Library name: H9_3


title: liver, dKO, ZT10, BRG1, ChIP

data_processing:
Reads were aligned using BWA (v0.7.17).
Duplicates were flagged by MarkDuplicates (Picard tools). Filtering steps were applied to exclude reads with low mapping quality (MAPQ<30), reads/mates that were unmapped, reads failing platform and those not classified as primary alignments and duplicates (samtools view -q 30 -F 1804 -f 2).
Peaks were called using MACS2 (BAMPE format), with broad settings and a q-value cutoff of 0.05. Input samples (IPs) were used as a control in peak calling and all IPs in one experiment were pooled. Reads in peaks were quantified and normalized via DiffBind (v3.0.15) with default settings except filter=0. Overlapping TF binding sites was performed using Intervene software.
DeepTools was used for generation of bigwig tracks with RPGC normalization. Bigwig files from replicates were merged using WiggleTools for heatmaps. SparK was used for visualization of bigwig tracks.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak (consensus peak of WT samples)

extract_protocol:
For all ChIPs 2-3 biological replicates for each condition were pooled by weighing a total of ~220-250mg of snap-frozen liver tissue. Which was homogenized in 10mL PBS containing 2mM DSG (ProteoChem, 79642-50-5) using IKA T10 standard ULTRA TURRAX on level 4 for 15 sec followed by dounce homogenization in a 15mL douncer for 20 strokes with a tight pestle. The samples were incubated for 40 min at RT under rotation and centrifuged for 5 min at 900g. Supernatant was discarded, and the pellet was resuspended in 10mL PBS, centrifuged for 5 min at 900g, and supernatant was discarded. The pellet was resuspended in 10mL PBS containing 1% formaldehyde (Thermo Scientific, 28908) and incubated at RT for 5 min under rotation. 1mL 1.25M glycine was added, and samples were incubated for 5 min at RT under rotation to stop the crosslinking. The samples were dounce homogenized in a douncer for 20 strokes with a tight pestle and filtered through a 70µM pluriStrainer (pluriSelect, 43-50070). The samples were centrifuged at 900g for 5min at 4 °C and supernatant was discarded. Pellet was resuspended in 10mL PBS with 1mM phenylmethylsulfonyl fluoride (PMSF) (Sigma, 11359061001). The samples were centrifuged at 900g for 5min at 4 °C and supernatant was removed. The pellet was resuspended in 10mL cell wash buffer 1 (10mM Tris-HCl pH 8, 10mM EDTA, 0.5mM egtazic acid (EGTA), 0.25% Triton X-100) containing 1mM PMSF, centrifuged, and supernatant was discarded. Hereafter the pellet was resuspended in 10mL cell wash buffer 2 (10mM Tris-HCl pH 8, 1mM EDTA, 0.5mM EGTA, 200mM NaCl) containing 1mM PMSF. The samples were centrifuged, and supernatant was discarded. The pellet was resuspended in 1mL of ChIP buffer (50mM Trish-HCl pH 8, 1mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% deoxycholic Na, 0.1% SDS) with 1:200 PIC.
25µL Pierce ChIP-grade Protein A/G Magnetic Beads (Thermo Scientific, 26162) were prepared for each sample. The total volume of beads needed was aliquoted to a new tube and placed in a magnetic rack for 5 min. Supernatant was removed. Beads were washed twice by resuspending in 600µL ChIP buffer, placing the tube in a magnetic rack, turning 20x180°, leaving it for 2 min, and discarding supernatant. After the second wash the beads were resuspended in the initial volume of ChIP buffer (25µL per sample). 25µL of the prepared beads were added to each sample and they were incubated under rotation for 30 min at 4 °C. This preclearing gets rid of chromatin fragments that bind unspecifically to the beads, meaning that they bind to the beads without the presence of antibody. After incubation, the samples were placed in a magnetic rack, incubated for 5 min, and the supernatant was transferred to a new tube. 1% of the volume was transferred to a new tube and saved as an input. 5µL drosophila spike-in chromatin (active motif, 53083) and 2µL spike-in antibody (active motif, 61686) was added. The spike-in can be used to normalize for efficiency of immunoprecipitation after sequencing. However, this normalization method was not used in this report. 10µL of BRG1 antibody (Abcam, ab110641) was added to the samples, followed by ON incubation under rotation at 4 °C.
50µL of beads, prepared as described above, was added to each sample, and the samples were incubated for 1 hour under rotation at 4 °C. The samples were placed in a magnetic rack for 2 min and supernatant was discarded. Beads were subsequently washed by resuspending in different wash buffers, listed below, by placing the tube in a magnetic rack, turning 20x180°, incubating for 2 min, and discarding the supernatant. The washing buffers are: ChIP wash 1 (20mM Tris pH 8, 150mM NaCl, 2mM EDTA, 0.1% deoxycholic Na, 1% Triton X-100), ChIP wash 2 (20mM Tris pH 8, 500mM NaCl, 2mM EDTA, 0.1% deoxycholic Na, 1% Triton X-100), ChIP wash 3 (10mM Tris pH 8, 250mM LiCl, 1mM EDTA, 0.7% deoxycholic Na, 1% Igepal CA-630), and twice with TE buffer (10mM Tris-HCl pH 8, 1mM EDTA). After the final wash in TE buffer the supernatant was discarded and 150µL of elution buffer (1% SDS, 100mM NaHCO3) was added to the beads. The samples were incubated in a thermomixer at 65 °C at 1000 rpm for 30 min. The tubes were placed in a magnetic rack and incubated for 5 min. The supernatant was transferred to a new tube and the beads was resuspended with 150µL elution buffer and incubated in the thermomixer again. The tubes were transferred to a magnetic rack and the supernatant was pooled with supernatant from first elution and the beads were discarded. Elution buffer was added to the input samples for a final volume of 300µL. 12µL 5M NaCl was added to all samples, including inputs, and the samples were incubated at 65 °C ON to reverse DNA-protein crosslinking. 6µL 0.5M EDTA, 12µL 1M Tris-HCl pH 6.5, and 1µL 10mg/mL RNase A (Thermo Scientific, EN0531) was added to the samples. The samples were incubated at 37 °C for 30 min. 5µL 20 g/L proteinase K (Invitrogen, 25530049) was added and the samples was incubated at 56 °C for one hour.
The DNA was purified using MinElute PCR purification kit. 7 volumes of buffer PB was added to the samples. 700µL of the sample was loaded onto the column, centrifuged at 16000g, and flowthrough was discarded. This process was repeated until the entire sample was passed through the column. The column was washed twice with buffer PE. Flowthrough was discarded and the column was centrifuged an additional time to get rid of excess ethanol, possible leftover ethanol around the O-ring was removed with a pipette. The column was transferred to a clean DNA LoBind tube (Eppendorf). 12µL of buffer EB was loaded to the center of the membrane, the samples were incubated for 1 min and centrifuged for 1 min. DNA concentrations of the samples was determined using Qubit.
ChIP samples were generated using NEBNext® reagents and kits for Illumina® Sequencing following manufacturer’s instrcutions. Samples were sequenced on an Illumina NovaSeq 6000 instrument.

value: Smarca2 -/- Smarca4 fl/fl

value: AAV-TBG-CRE

value: BRG1 antibody (Abcam, ab110641)


title: liver, dKO, ZT10, Input

value: male