title: MI503-3 uM-2

first: Denis

last: Wirtz

state: MD

address: 130 Croft Hall, Johns Hopkins University, 3400 N Charles Street

data_processing:
Transcript level counts were quantified from reads with salmon version 1.1.0 using human genome build h19. Quantification files generated by salmon were loaded into R/Bioconductor software.
We performed paired differential expression analysis that retain cell-line pairing using a multi-factor design using the tximport (v 1.14.2) and DESeq2 (v 1.26.0) packages. The only protein coding genes were used. Genes with FDR adjusted p-values below 0.05 and log fold change greater than 1 were called statistically significant.
Genome_build: human genome assembly Release 33 (GRCh38.p13)
Supplementary_files_format_and_content: text file containing gene-level counts

growth_protocol: MDA-MB-231 cells (WT, NTC, or shMLL1) were cultured at 37 C and 5% CO2. Mycoplasma testing was done every 6 months.

extract_protocol:
Total RNA was isolated and DNase I treated using Qiagen RNeasy Plus Mini Kit (Qiagen, Valencia, CA). The RNA integrity was checked by Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA) and samples with clean rRNA peaks (RIN>6) were used for library preparation.
RNA-Seq library was prepared according to KAPA mRNA HyperPrep kit with 200-300 bp insert size (Roche, Wilmington, MA) using 250 ng of total RNAs as input. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer (Thermo Fisher Scientific Inc, Waltham, MA). 150 bp PE (paired-end) reads were sequenced on Illumina HiSeq sequencer (Illumnia Inc., San Diego, CA).

treatment_protocol: Cells receiving drug treatment were incubated in media containing appropriate concentrations of MI-2-2 or MI-503 solublized in DMSO. Treatment time was 24 hours and control cells were trated with DMSO alone.

value: Breast adenocarcinoma cells

value: MI-503 at 3 μM for 24 hours

value: second


title: MI503-3 uM-1

status: Public on Mar 12 2024

type: SRA

city: Baltimore

country: USA

institute: Johns Hopkins University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: cell line

tag: treatment

tag: group


title: FCD2b_11

city: Brussels

first: Liesbeth

last: François

state: Brussels

address: Allée de la Recherche 60

country: Belgium

institute: UCB Pharma SA

data_processing:
The Decontamination Using Kmers (BBDuk) tool from the BBTools suite was used for adapter removal, quality trimming and removal of contaminant sequences (ribosomal or bacterial)60. A phred33 score of 20 was used to assess the quality of the read, with any read shorter than 31 nucleotides in length excluded from the downstream analysis. Reads were aligned directly to the human GRCh38 reference transcriptome (Gencode version 33)61 using Salmon v0.11.362. Transcript counts were summarized to the gene level and scaled using library size and average transcript length using the R package tximport63. Genes detected in less than 20% of the samples in any diagnosis cohort and with counts less than six across all samples were filtered out, resulting in 28,366 genes for downstream analysis. The gene counts were then normalized using the weighted trimmed mean of M-values method with the R package edgeR64. The normalized counts were then log2 transformed using the voom function from the R package limma65.
Assembly: GRCh38
Supplementary files format and content: Raw count matrix
Supplementary files format and content: Processed count matrix

source_name: Frontal

extract_protocol:
For RNA isolation, human tissue was homogenized in 700 µl Qiazol Lysis Reagent (Qiagen Benelux, Venlo, The Netherlands). Total RNA including the microRNA (miRNA) fraction was isolated using the miRNeasy Mini Kit (Qiagen Benelux, Venlo, The Netherlands) according to the manufacturer’s instructions. The concentration and purity of RNA was determined at 260/280 nm using a Nanodrop spectrophotometer (Ocean Optics, Dunedin, FL, USA) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA). Only samples with RNA integrity number (RIN) equal or greater than 6.0 were used for sequencing.
All library preparation and sequencing were performed by GenomeScan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) was used to process the samples. Sample preparation was performed according to the protocol NEBNext Ultra II Directional RNA Library prep Kit for Illumina (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of mRNA, cDNA synthesis was performed. Next, sequencing adapters were ligated to the cDNA fragments followed by polymerase chain reaction amplification. Clustering and DNA-sequencing was performed using the NovaSeq6000 (Illumina, Foster City, CA, USA) in accordance with manufacturers’ guidelines. All samples underwent paired-end sequencing of 150 nucleotides in length; the mean read depth per sample was 47 million reads.

tag: tissue

value: Frontal

tag: Sex

value: Male

tag: age

tag: disease state

tag: seisure frequency


title: MI503-1 uM-3

value: MI-503 at 1 μM for 24 hours


title: Hippocampus, Control rep1

first: Yongqing

last: Liu

state: MARYLAND

address: 725 N Wolfe Street, WBSB 216

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the mm10 reference genome using the kb-python program (version 0.25.0). The data was then imported into R and low quality nuclei and “empty droplets” were filtered out using the barcodeRanks from the DropletUtils package. The data was analyzed using the Seurat R package (version 4.0.1) as described previously. Briefly, data normalization was performed using SCTransform function. The uwot package (https://github.com/jlmelville/uwot) was used for UMAP dimensional reduction. Seurat FindMarkers function was used for the analysis of differential gene expression and plotted using ggplot2 and the tidyverse collection of R packages in RStudio.
Assembly: mm10
Supplementary files format and content: txt file with barcodes or genes for all samples
Supplementary files format and content: mtx file with matrix for all samples
Supplementary files format and content: Excel file with differential expressed genes between two groups

molecule: nuclear RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Mouse hippocampal tissues were rapidly dissected in ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH=7.8). The tissue was homogenized using a loose-fitting pestle in 1.5 ml of homogenization buffer supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1×EDTA-free protease inhibitor (Roche), and 60 U/mL RNasin Plus RNase Inhibitor (Promega, N2611). A 6% IGEPAL CA-630 solution was added to bring the homogenate to 0.3% IGEPAL CA-630, and the homogenate was further homogenized with five strokes of a tight-fitting pestle. The sample was filtered through a 50 μm filter, underlayed with solutions of 30% and 40% iodixanol (Sigma, D1556) in homogenization buffer, and centrifuged at 10,000 g for 20 min in a swinging bucket centrifuge at 4 °C. Nuclei were collected at the 30-40% interface, diluted with two volumes of homogenization buffer and concentrated by centrifugation for 10 min at 500 g at 4 °C. These nuclei can be used for snRNA sequencing.
10x Genomics Chromium single cell kit
snRNA-seq

value: Hippocampus

tag: genotype


title: MI503-3 uM-3


title: MI503-1 uM-1


title: MI503-1 uM-2


title: FCD2b_10


title: MI503-0.3 uM-3

value: MI-503 at 0.3 μM for 24 hours


title: TLE-HS_13

source_name: Temporal

value: Temporal

value: TLE-HS


title: MI503-0.3 uM-2


title: Hippocampus, Kat6a-cKO rep2


title: TLE-HS_12

value: Female


title: MI503-0.3 uM-1


title: MI22-30 uM-2

value: MI-2-2 at 30 μM for 24 hours


title: MI22-30 uM-3


title: TLE-HS_11


title: MI22-30 uM-1


title: MI22-10 uM-3

value: MI-2-2 at 10 μM for 24 hours


title: MI22-10 uM-2


title: TLE-HS_10


title: FCD2b_9


title: DMSO -3

value: DMSO for 24 hours (control)


title: Hippocampus, WT rep4

data_processing:
The raw sequencing data were aligned to the mouse preference genome (GRCm38, mm10) using STAR software (v2.5). Reads on each GENCODE annotated gene were counted using HTSeq, and then differential gene expression analysis was performed using DESeq2 R package.
Assembly: mm10
Supplementary files format and content: Excel file with fpkms for all genes for all samples
Supplementary files format and content: Excel file with differential expressed genes between two groups

extract_protocol:
Total RNA was isolated from mouse hippocampus tissues with Trizol reagents (Invitrogen) and any potential DNA contamination was removed by RNase-free DNase treatment (Promega, M6101).
NEBNextUltraII RNA Library Prep Kit

value: WT


title: Hippocampus, Kat6a+/- rep3


title: Hippocampus, Kat6a+/- rep1


title: Hippocampus, WT rep3


title: DMSO -2


title: Hippocampus, Kat6a+/- rep2


title: Hippocampus, Kat6a+/- rep4


title: ControlHippocampus_3

value: ControlHippocampus


title: DMSO -1


title: Hippocampus, WT rep2


title: shMLL-3

value: transduced with MLL1 shRNA

value: first


title: Hippocampus, WT rep1


title: shMLL-2

value: Breast adenocarcinoma cells


title: NTC-3

value: transduced with non-targeting scrambled shRNA control


title: FCD2b_8

source_name: Occipital

value: Occipital


title: NTC-2


title: NTC-1


title: WT-3

value: Untreated (not transduced)


title: liver, WT SHAM, rep4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

data_processing:
Reads were quality checked with fastqc and no urther preprocessing was needed
Reads were aligned to the mm10 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm10
Supplementary files format and content: matrix of raw counts for all samples

source_name: liver

extract_protocol:
RNA was obtained with the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s protocol
RNA was used to generate an Illumina sequencing library using the Illumina Stranded mRNA Ligation LP kit according to the manufacturer’s protocol

treatment_protocol: mice wer treated with tamoxifen for 5 days (1 mg in 1:8 ethanol:oil) to induce Hnf4a deletion in transgenic animals. Three days after the final injection mice were subjected to SHAM or CLP and liver were isolated after 8 hours and stored in RNAlater.

value: liver

value: SHAM


title: liver, WT SHAM, rep3


title: MI22-10 uM-1

value: second


title: WT-2


title: TLE-HS_8

value: Temporal


title: liver, WT SHAM, rep2


title: WT-1


title: FCD2b_7


title: CLDN1 mAb_m1

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

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

data_processing:
Reads were aligned to hg19 and mm10 chromosomes concurrently using HISAT2v2.1  to separate human and mouse reads.
Human reads were further processed and normalized using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DESeq2-normalized read counts for each sample

organism:
Homo sapiens
Mus musculus

source_name: Human liver chimeric mice

extract_protocol:
Non-tumorous liver tissue was lysed in TRI-reagent (Molecular Research Center), and RNA was purified using Direct-zol RNA MiniPrep (Zymo Research) according to the manufacturer’s instructions. RNA-Seq libraries were generated from 300 ng of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Fah-/-/Rag2-/-/Il2rg -/- (FRG) -NOD

value: non-tumorous liver

value: 38 weeks

tag: diet

value: CDA-HFD

value: CLDN1 mAb (500ug) i.p. 1/w for 8 weeks


title: liver, WT CLP, rep4

value: WT

value: CLP


title: CLDN1 mAb_m3


title: CLDN1 mAb_m2


title: liver, WT SHAM, rep1


title: shMLL-1

value: transduced with MLL1 shRNA


title: liver, WT CLP, rep3


title: FCD2b_6

value: Frontal

value: Male


title: CLDN1 mAb_m4


title: TLE-HS_9

value: TLE-HS


title: Control_m3

value: Vehicle Control (PBS)  i.p. 1/w for 8 weeks


title: Regular diet_m3

value: Regular diet

value: No treatment


title: Control_m2


title: ControlHippocampus_2

value: Hippocampus

value: ControlHippocampus


title: Control_m1


title: ControlCortex_10

value: ControlCortex


title: TSC_13

value: TSC


title: Regular diet_m1

value: Fah-/-/Rag2-/-/Il2rg -/- (FRG) -NOD

value: non-tumorous liver


title: Regular diet_m2

value: 38 weeks


title: TLE-HS_6

value: Temporal

value: Female


title: IP_X28.2

city: shanghai

first: li

last: peng

country: China

institute: PSC

library_source: genomic

data_processing:
We cleaned the paired-end reads by Trimimomatic. After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters.
Enriched peaks were identified by MACS (version 1.4) with default parameters.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files with RPM value

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark)  photoperiod at 23 °C.

extract_protocol: Lysates were clarified from sonicated nuclei and JMJ28-DNA complexes were isolated with antibody.

value: seedlings

value: 12-day-old seedlings

tag: antibody

value: Myc antibody


title: FCD2b_5

value: Frontal

value: Male


title: liver, KO SHAM, rep4

value: liver

value: Hnf4a KO

value: SHAM


title: IP_X28.1


title: TLE-HS_7

value: TLE-HS


title: liver, KO SHAM, rep3


title: IP_Col0.1

value: Col-0 WT


title: liver, WT CLP, rep2

value: WT

value: CLP


title: Input_Col0

value: input


title: Input_X28


title: liver, KO SHAM, rep2


title: jmj28-3_rep2

data_processing:
RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer’s instructions
Then clean reads were separately aligned to reference genome with orientation mode using TopHat
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method
RSEM was used to quantify gene abundances. R statistical package software EdgeR was utilized for differential expression analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel table with FPKM value

molecule: polyA RNA

extract_protocol: Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen)


title: jmj28-3_rep1


title: liver, WT CLP, rep1


title: ControlCortex_8

value: ControlCortex


title: Col-0_rep1


title: liver, KO SHAM, rep1


title: CLDN1 mAb_m6

data_processing:
Reads were aligned to mm10 using tophat2v2.0.14.
Mapped reads were further processed and normalized using the cufflinks software suite v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ciffnorm-normalized read counts for each sample

source_name: Liver

tag: tisse

value: non-tumorous liver

value: 32 weeks

value: CDA-HFD

value: 100mg/kg DEN once at w1, CLDN1 mAb (500ug) i.p. 1/w for 16 weeks

value: male


title: TLE-HS_4

value: Temporal


title: FCD2a_7


title: Col-0_rep2

value: seedlings

value: 12-day-old seedlings


title: liver, KO CLP, rep3

value: liver


title: liver, KO CLP, rep2

value: Hnf4a KO


title: IP_Col0.2

value: Myc antibody


title: TLE-HS_5

value: Male

value: TLE-HS


title: liver, KO CLP, rep1


title: CLDN1 mAb_m2


title: ControlCortex_7

value: Female


title: CLDN1 mAb_m3


title: MFM + HMOs, Colon, 4

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
FASTQ files were subject to quality control and adapter sequence trimming with FastQC (v0.11.9) and TrimGalore (v0.6.5).
Trimmed reads were aligned with STAR (v2.7.9a) against the mouse GRCm39_107 reference genome.
Aligned reads were processed with featureCounts (subread v2.0.1) to produce a gene-count matrix for all samples.
Assembly: GRCm39
Supplementary files format and content: Gene-count matrix for each tissue type (colon, ileum) containing per-sample counts annotated with ENSEMBL IDs and gene symbols.

source_name: Colon

growth_protocol: Fecal material inoculum

extract_protocol:
RNA was extracted using Trizol/BCP and Rneasy mini kit (QIAgen) and quantified using Qubit Flurometer
messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by the second strand of cDNA synthesis. This was followed by end repair, A-tailing, adapter ligation, size selection, amplification and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol:
Fecal material inoculum was prepared from infant feces who were consuming milk from secretor or non-secretor mothers or consuming infant formula. 10 mg of fecal material inoculum per mouse was transplanted on day 1 and day 7 via oral gavage
For one set of mice from each group, 15mg of pooled HMOs was gavaged daily for 14 days

value: Colon

value: MFM+HMOs


title: ControlCortex_9

value: Frontal

value: ControlCortex


title: liver, KO CLP, rep4

value: CLP


title: Vehicle Control_m6

value: non-tumorous liver

value: 32 weeks

value: CDA-HFD

value: 100mg/kg DEN once at w1, vehicle Control (PBS) i.p. 1/w for 16 weeks


title: Vehicle Control_m5

value: male


title: MFM + HMOs, Colon, 3


title: CLDN1 mAb_m5

value: 100mg/kg DEN once at w1, CLDN1 mAb (500ug) i.p. 1/w for 16 weeks


title: Vehicle Control_m3


title: Vehicle Control_m4


title: Vehicle Control_m2


title: CLDN1 mAb_m4


title: MFM + HMOs, Colon, 2


title: Vehicle Control_m1


title: ControlCortex_6


title: MFM + HMOs, Colon, 1


title: CLDN1 mAb_m1


title: ControlCortex_5


title: Regular diet_m4

value: Regular diet

value: No treatment


title: MFM, Colon, 4

value: MFM


title: TSC_12

value: Temporal

value: TSC


title: Regular diet_m2


title: Regular diet_m1


title: TSC_9

value: Male


title: FCD2b_4

value: Female


title: MFM, Colon, 3

value: Colon


title: TSC_11


title: K562 cells, SF3B1 K666N overexpression, 24 hours post-induction

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bases toward the interior of the sequenced fragment and were normalized to total reads aligned (RPKM). Bam files were then reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: K562 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 1 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.5-10 μg of chromatin was used for each IP. ChIP spike in normalization for the RNAPII ChIP assays was performed using Drosophila-specific chromatin and Drosophila-specific histone variant (H2Av) antibody. 50 ng of Drosophila S2 sheared crosslinked-chromatin was added to 10 μg of chromatin as spike-in control. RNAPII NTD antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.

treatment_protocol: Modified allele expression induced with doxycycline (1ug/ml) and maintained for 4 days

value: Immortalized epithelial cells


title: MFM, Colon, 2


title: FCD2b_3

value: Frontal


title: K562 cells, SF3B1 wild type overexpression, 24 hours post-induction 2

value: WT


title: K562 cells, SF3B1 K666R overexpression, 24 hours post-induction


title: TSC_10


title: K562 cells, U2AF1 S34F overexpression, 24 hours post induction

value: U2AF1 S34F


title: MFM, Colon, 1


title: K562 cells, SF3B1 wild type, si HTATSF1


title: Regular diet_m5

value: non-tumorous liver

value: 32 weeks


title: K562 cells, U2AF1 wild type overexpression, 24 hours post induction


title: K562 cells, SF3B1 wild type, si DDX46

value: WT_DDX46 knockdown


title: FCD2a_6


title: NSM + HMOs, Colon, 7

value: NSM+HMOs


title: K562 cells, SF3B1 K700E overexpression, 24 hours post-induction


title: K562 cells, SF3B1 K700E overexpression, 8 hours post-induction


title: Regular diet_m3

value: male


title: K562 cells, SF3B1 wild type, siControl

value: WT _control


title: TLE-HS_2

value: TLE-HS


title: TLE-HS_3


title: K562 cells, SF3B1 wild type overexpression, 8 hours post-induction


title: K562 cells, SF3B1K700E, 4 days, siPHF21A, ATAC-seq

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 (for human samples) and mus musculus (for murine samples) using Bowtie2 aligner
To create promoter nucleosome occupancy plots, the locations of the mapped ATAC-seq reads were extended to 150 bp to represent sequenced fragments, and the resulting Bam files were used in the NucleoATAC page to generate output files in the bigWig file format. For ATAC peak analysis in K562 cell data, Epic2 package was used to call differentially enriched domains in WT and SF3B1K700E, using default parameters. Differentially ATAC-seq peaks were determined as those with a |log2 fold change(L2FC)| > 0.58 and adjusted p value < 0.05, calculated with DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: K562 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. For the healthy volunteer and MDS patient samples, CD34 cells were isolated using FACS analysis. For the murine samples, cKit+Sca1+Lin- cells were isolated from bone marrow aspirates using FACS analysis

extract_protocol:
50,000 K562 cells or 5000 CD34+/murine HSC cells (flow sorted) were harvested, washed, and resuspended in PBS. Washed cells were resuspended in ATAC-seq resuspension buffer and  centrifuged at 500g for 5 min in a 4 °C. Cell pellets were then resuspended in 50 μl of ATAC resuspension buffer. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500g at 4 °C. Supernatant was carefully removed and nuclei were resuspended in transposition mix containing transposase enzyme by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 rpm.
DNA quality and size distribution were checked on Fragment Analyzer. 10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit

treatment_protocol: Modified allele expression induced with doxycycline (1ug/ml) and maintained for 4 days (in 562 cells). For the murine model, SF3B1 mutant (and WT counterparts) were treated with tamoxifen daily x 5 days at 5 weeks of age. Mice were euthanized at end of week 8 and bone marrow was harvested to isolate the HSC progenitors.

value: SF3B1 K700E


title: NSM + HMOs, Colon, 6


title: NSM + HMOs, Colon, 5


title: K562 cells, SF3B1K700E, 4 days, siING2, ATAC-seq


title: K562 cells, SF3B1K700E, 4 days, siHDAC2, ATAC-seq

value: SF3B1 WT


title: K562 cells, SF3B1 wild type overexpression, 24 hours post-induction 1


title: NSM, Colon, 6

value: NSM


title: K562 cells, SF3B1K700E, 4 days, siControl, ATAC-seq


title: NSM + HMOs, Colon, 4


title: NSM, Colon, 7


title: K562 cells, SF3B1 K700E, 4 days, Ser2P Pol II CTD

data_processing:
mNET-seq reads were trimmed with Cutadapt and the unique molecular identifiers (UMI) extracted using UMI_tools and aligned using star aligner to hg38 and duplicates removed using samtools --markdups option. Drosophila reads were aligned to dm6 and total aligned read numbers were used to scale bigwig files. Pol II position was determined from the end of R2 for genes with + orientation and start of R1 for genes with - orientation.
Assembly: hg38
Supplementary files format and content: bed files

extract_protocol:
mNET-seq was performed using ~25 million K562 cells per sample. All buffers contained protease inhibitor cocktail. Briefly, the nuclei were extracted by incubating cells in HLB+N buffer (10mM Tris HCl pH7.5, 10mM NaCl, 2.5mM MgCl2, 0.5% NP40) for 10 minutes on ice, followed bycentrifugation(400g, 5min) through a sucrose cushion (HLB+N+ 10%sucrose). Nuclei were then resuspended in 125μl NUN1 buffer (20mM Tris HCl pH8.0, 75mM NaCl, 0.5mM EDTA, 50% glycerol) followed by addition of 1.2ml of NUN2 (20mMHEPESpH 7.6, 300mM NaCl, 0.2mM EDTA, 7.5mM MgCl2, 1% NP40, 1M urea), vortexing, and incubating for 15min on ice. The chromatin was pelleted by centrifuging the nuclear lysate at 16000g for 10min at 4°C, followed by resuspension in 100μl of (2μl NEB MNase + 98 μl MNase buffer (50mM TrisHCl pH 7.9, 5mM CaCl2, 250mM NaCl)). The chromatin was incubated for 2minutes at 37º in a thermoshaker (14000 RPM), and the reaction was stopped by addition of EGTA to 12.5mM and incubation on ice for 10min. Samples were centrifuged at 16000g for 10min and the supernatants were diluted to 1ml with IP buffer (50mM Tris HCl pH 7.5, 140mM NaCl,.05% NP40)+2ul murine RNAse inhibitor (NEB).Immunoprecipitationwas carried out with anti-pan pol II CTD (Invitrogen, MA1-26249) or Ser2P pol II CTD (Activ Motif, 61984) coupled to protein A/G magnetic beads for 1.5hours at 4ºC. IPs were then washed eight times with wash buffer low salt wash buffer (50mM Tris HCl pH 7.5, 140mM NaCl,.05% NP40). After washing, on-bead phosphorylation was performed in a 25μl reaction with 5 units T4 PNK 3’phosphatase minus (NEB), 1μl murine RNAse inhibitor in 50mM Tris HCl pH 7.5, 100mM NaCl, 5mM MgCl2, 1mM DTT, 0.01% NP40 at 37º for 5min. in a Thermomixer (14000 RPM). The beads were immersed in Trizol, and subsequently, 0.5 ng of DNAse-treated Drosophila RNA spike-ins were added to each sample.
The RNA was extracted inTrizol(200μl) and libraries were generated with QIA miRNA seq kit


title: K562 cells, SF3B1 wild type, 4 days, Ser2P Pol II CTD


title: ControlCortex_4

value: ControlCortex


title: TLE-HS_1

value: Temporal

value: Male


title: FCD2b_2


title: ControlHippocampus_1

value: Hippocampus

value: ControlHippocampus


title: K562 cells, SF3B1 wild type, 4 days, pan Pol II, replicate 1

value: Immortalized epithelial cells

value: WT


title: K562 cells, SF3B1 K700E, 4 days, pan Pol II, replicate 2


title: FCD2b_1

value: Frontal

value: Female


title: NSM, Colon, 5

value: Colon


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, IP

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
The respective IP  BAM files were compared to each other while being simultaneously normalized for sequencing depth (using RPKM), and reformatting to the bigWig file format using deepTools BamCompare program. These were then normalized to input to generate log-normalized BigWig files
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. Ser5P RNAPII antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.


title: NSM, Colon, 4


title: K562 cells, SF3B1 wild type, 4 days, pan Pol II, replicate 2


title: FCD2a_5


title: K562 cells, SF3B1 K700E, 4 days, pan Pol II, replicate 1


title: K562 cells, SF3B1 SF3B1K700E, 4 days, replicate 2, IP (H3K36me3)

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
The respective IP  BAM files were compared to each other while being simultaneously normalized for sequencing depth (using RPKM), and reformatting to the bigWig file format using deepTools BamCompare program.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. H3K36me3 antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.

value: SF3B1 SF3B1K700E


title: FCD2a_4


title: SMM + HMOs, Colon, 7

value: SMM+HMOs


title: TSC_7

value: TSC


title: K562 cells, SF3B1 SF3B1K700E, 4 days, replicate 2, IP


title: SMM, Colon, 7

value: SMM


title: K562 cells, SF3B1 SF3B1K700E, 4 days, replicate 2, IP (CHD)

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
The respective IP  BAM files were compared to each other while being simultaneously normalized for sequencing depth (using RPKM) and drosophila reads, and reformatting to the bigWig file format using deepTools BamCompare program.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. CHD1 antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.


title: SMM + HMOs, Colon, 6


title: ControlCortex_3


title: TSC_6


title: CD34 cells, SF3B1-mutant MDS, replicate 7, Ser2PRNAPII CUT&RUN

data_processing:
library strategy: CUT&RUN
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligner
To create CUT&RUN-seq coverage plots, the locations of the mapped CUT&RUN-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to RPKM) and reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: K562 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. For the healthy volunteer and MDS patient samples, CD34 cells were isolated using FACS analysis

extract_protocol:
0.5 million K562 cells or 25,000 human CD34+ cells were harvested, washed, and bound to activated Concanavalin A-coated magnetic beads, then permeabilized with Wash buffer containing 0.05% Digitonin. The bead-cell slurry was incubated with 0.5 μl antibody in a antibody buffer at 4°C overnight on a nutator. After 3 washes in 1 ml Dig-wash, beads were resuspended in digitonin wash, mixed with pAG/MNase and incubated for 1 hr at room temperature. After two washes in Dig-wash, beads were resuspended in digitonin wash. Tubes were chilled to 0°C and 1 µl 100 mM CaCl2 was added while gently vortexing. Tubes were nutated at 4°C for 2 hours followed by addition of EGTA-STOP buffer. Beads were incubated at 37°C for 30 min, replaced on a magnet stand and the liquid was removed to a fresh tube and DNA was extracted.
DNA quality and size distribution were checked on Fragment Analyzer. 10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit

treatment_protocol: Modified allele expression induced with doxycycline (1ug/ml) and maintained for 4 days (in 562 cells)

value: hematopoeitic progenitor cells

value: SF3B1 K700E


title: SMM, Colon, 6


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, IP (CHD)

value: SF3B1 WT


title: SMM + HMOs, Colon, 5


title: SMM + HMOs, Colon, 4


title: K562 cells, SF3B1 SF3B1K700E, 4 days, replicate 2, IP (INTS-11)

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. INTS11 antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, IP (INTS-11)


title: CD34 cells, SF3B1-mutant MDS, replicate 6, Ser2PRNAPII CUT&RUN


title: TSC_4


title: CD34 cells, SF3B1-mutant MDS, replicate 4, Ser2PRNAPII CUT&RUN


title: CD34 cells, SF3B1-mutant MDS, replicate 5, Ser2PRNAPII CUT&RUN


title: TSC_5


title: CD34 cells, SF3B1-mutant MDS, replicate 1, Ser2PRNAPII CUT&RUN


title: TSC_8

source_name: Parietal

value: Parietal


title: SMM, Colon, 5


title: CD34 cells, healthy volunteer, replicate 5, Ser2PRNAPII CUT&RUN


title: GF, Colon, 6

value: Vehicle


title: CD34 cells, SF3B1-mutant MDS, replicate 3, Ser2PRNAPII CUT&RUN


title: CD34 cells, SF3B1-mutant MDS, replicate 2, Ser2PRNAPII CUT&RUN


title: TSC_3


title: FCD2a_3

value: Temporal

value: Male


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, IP (H3K36me3)


title: CD34 cells, healthy volunteer, replicate 4, Ser2PRNAPII CUT&RUN


title: SMM, Colon, 4


title: CD34 cells, healthy volunteer, replicate 2, Ser2PRNAPII CUT&RUN


title: ControlCortex_2

value: ControlCortex


title: CD34 cells, healthy volunteer, replicate 1, Ser2PRNAPII CUT&RUN


title: CD34 cells, healthy volunteer, replicate 3, Ser2PRNAPII CUT&RUN


title: GF, Colon, 5


title: ControlCortex_1


title: GF, Colon, 4


title: MFM + HMOs, Ileum, 4

source_name: Ileum

value: Ileum

value: MFM+HMOs


title: CD34 cells, SF3B1-mutant MDS, replicate 5, H3K4me3CUT&RUN


title: CD34 cells, SF3B1-mutant MDS, replicate 4, H3K4me3CUT&RUN


title: CD34 cells, SF3B1-mutant MDS, replicate 3, H3K4me3CUT&RUN


title: MFM + HMOs, Ileum, 3


title: CD34 cells, healthy volunteer, IgGCUT&RUN


title: CD34 cells, SF3B1-mutant MDS, replicate 2, H3K4me3CUT&RUN


title: CD34 cells, SF3B1-mutant MDS, replicate 1, H3K4me3CUT&RUN


title: FCD2a_1

value: Frontal


title: MFM + HMOs, Ileum, 2


title: CD34 cells, healthy volunteer, replicate 4, H3K4me3CUT&RUN


title: CD34 cells, healthy volunteer, replicate 5, H3K4me3CUT&RUN


title: MFM + HMOs, Ileum, 1


title: TSC_2

value: Female


title: CD34 cells, healthy volunteer, replicate 2, H3K4me3CUT&RUN


title: CD34 cells, healthy volunteer, replicate 3, H3K4me3CUT&RUN


title: K562 cells, SF3B1 K700E, 4 days, shScrambled, IgG CUT&RUN

value: Immortalized epithelial cells

value: IgG pulldown


title: MFM, Ileum, 3

value: MFM


title: CD34 cells, healthy volunteer, replicate 1, H3K4me3CUT&RUN


title: TSC_1

value: TSC


title: K562 cells, SF3B1 K700E, 4 days, shPHF21A, H3K4me3 CUT&RUN

value: PHF21A knockdown


title: K562 cells, SF3B1 K700E, 4 days, shING2, replicate2, H3K4me3 CUT&RUN

value: ING2 knockdown


title: NSM + HMOs, Ileum, 7

value: NSM+HMOs


title: FCD2a_2


title: MFM, Ileum, 2


title: K562 cells, SF3B1 K700E, 4 days, shHDAC2, replicate1, H3K4me3 CUT&RUN

value: SF3B1 K700E

value: HDAC2 knockdown


title: MFM, Ileum, 1


title: GSC4121, shLUCAT1 #1, hypoxia, rep2

city: CLEVELAND

first: Haidong

last: Huang

state: OH

address: 9500 EUCLID AVE RK-15

department: Cancer Biology

institute: Cleveland Clinic Foundation

data_processing:
Fastq files containing reads were quality-controlled with fastQC
The raw sequence reads from each replicate were aligned to the human genome GRCh38 with GENCODE annotation v30 using STAR aligner with quantMode mode to generate gene counts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw count for each sample

growth_protocol: GSC line 4121 was maintained in Neurobasal-A medium with B27 supplement, 20 ng/ml EGF and 20 ng/ml FGF, 1 mM L-Glutamine, 100 units/mL penicillin, and 100 μg/mL streptomycin) at 37 °C with 5% CO2.

extract_protocol:
Total RNAs were extracted with PureLink RNA Mini Kit.
RNA integrity and quantitation were determined using Agilent 2100 bioanalyzer. Oligo(dT) purified RNAs were used to construct stranded libraries, followed by quality control using Agilent 2100 bioanalyzer.

treatment_protocol: GSCs were transduced with shNT or shLUCAT1 lentivirus and incubated in 21% or 1% O2 for 24 hours.

value: glioma stem cell


title: GSC4121, shLUCAT1 #1, hypoxia, rep1


title: GSC4121, shLUCAT1 #2, hypoxia, rep2


title: GSC4121, shLUCAT1 #2, hypoxia, rep1


title: K562 cells, SF3B1 K700E, 4 days, shING2, replicate1, H3K4me3 CUT&RUN


title: K562 cells, SF3B1 K700E, 4 days, shScrambled, H3K4me3 CUT&RUN

value: shControl


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, IgG CUT&RUN

value: SF3B1 WT


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, H3K4me1 CUT&RUN


title: NSM + HMOs, Ileum, 6


title: GSC4121, shNT, hypoxia, rep2


title: NSM + HMOs, Ileum, 5


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, H3K4me1 CUT&RUN


title: GSC4121, shNT, hypoxia, rep1


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, H3K27ac CUT&RUN


title: NSM + HMOs, Ileum, 4


title: All_HUVEC_Cells

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

description: 10x Genomics

data_processing:
The Cell Ranger 7.1.0 pipeline (10X Genomics) was used to align reads to the GRCh38 reference genome and generate feature barcode matrix, filtering low-quality cells using default parameters.
The Monocle (v.3.1.2.9) platform was used for downstream analysis, combining read-depth normalized data across samples where applicable.
Assembly: GRCh38
Supplementary files format and content: 10X Cell Ranger output files in filtered feature-barcode matrix: "genes.tsv" contains gene information, "barcodes.tsv" contains cellular barcodes, and "matrix.mtx" contains a sparse matrix of UMIs. The prefix for each file designates the cellular treatment/condition.
Supplementary files format and content: Monocle cell data set file: "HUVEC_PRESSURE_COMBINED.RDS" contains monocle cell data sets for HUVEC pressure samples imported from 10Xoutput files, with no processing.
Supplementary files format and content: Monocle cell data set file: "HUVEC_PRESSURE_PROCESSED.RDS" contains monocle cell data sets for HUVEC pressure samples imported from 10Xoutput files following pre-processing, dimensionality reduction, and clustering steps.
Supplementary files format and content: Monocle cell data set file: "agmE8_11_ECHem.RDS" contains monocle cell data sets for previously published embryo data (GSE145886 and GSE171457) imported from 10Xoutput files following pre-processing, dimensionality reduction, clustering , and semi-supervised cell type classification (by Garnette), with removal of cell populations not classified as either endothelial or hematopoietic.

source_name: HUVEC

extract_protocol:
HUVECs were harvested from microfluidic devices by trypsinization, washed with PBS/0.04% ultrapure BSA, and resuspended in PBS/BSA for loading into the 10X Genomics Chromium Single Cell B Chip, and processed in the Chromium single cell controller.
The 10X Genomics Version 3.1 single cell 3’ kit with Feature Barcoding technology for Cell Surface Protein Sequencing was used to prepare single cell mRNA libraries for freshly isolated HUVECs was used according to manufacturer protocols with the Index Kit T Set A. Sequencing was performed for pooled libraries from each sample on an Illumina NextSeq 2000 using the 100 cycle, high output kit.

value: HUVEC

value: Endothelium


title: GSC4121, shNT, normoxia, rep2


title: NSM, Ileum, 7

value: Ileum

value: NSM


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, H3K27ac CUT&RUN


title: K562 cells, SF3B1 K700E, 4 days, shHDAC2, replicate2, H3K4me3 CUT&RUN


title: GSC4121, shNT, normoxia, rep1


title: NSM, Ileum, 6


title: K562 cells, SF3B1 K700E, 4 days, replicate 2, H3K27me3 CUT&RUN


title: RNA-seq: GM12878 Replicate 3

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were mapped using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon). The reads were mapped to 3 genomes: 1) the standard hg19 genome build (Genome Reference Consortium Human Build 37 (GRCh37)); 2) hg19 augmented with the B958 EBV (HHV4) genome (NC_007605.1); 3) hg19 augmented with the AG876 EBV (HHV4) genome (NC_009334.1).
Transcription abundance estimates generated by Salmon
Assembly: 3 assemblies: 1) hg19; 2) hg19 augmented with the B958 EBV (HHV4) genome (NC_007605.1); 3) hg19 augmented with the AG876 EBV (HHV4) genome (NC_009334.1).
Supplementary files format and content: quant.sf file generated by Salmon: tab-delimited txt file containing TPM results for reads aligned to the standard hg19 genome. Quantification is done on the transcript level.
Supplementary files format and content: quant.sf file generated by Salmon: tab-delimited txt file containing TPM results for reads aligned to the hg19 human genome augmented with the B958 EBV (HHV4) genome (NC_007605.1). Quantification is done on the transcript level.
Supplementary files format and content: quant.sf file generated by Salmon: tab-delimited txt file containing TPM results for reads aligned to the hg19 human genome augmented with the AG876 EBV (HHV4) genome (NC_009334.1). Quantification is done on the transcript level.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand.

growth_protocol: The AG876, Jiyoye, and GM12878 cell lines were grown in RPMI medium supplemented with 2 mM L-glutamine, 10% FBS, 1X antibiotic-antimycotic , and 0.2% Normocin at 200,000 – 500,000 viable cells/mL. Cells were incubated in flasks at 37C with 5% carbon dioxide in an upright position with vented.

extract_protocol:
Total RNA was extracted using Thermo Fisher's mirVana miRNA isolation kit according to the manufacturer's instructions.; quality and quantity determined by nanodrop and RNA TapeStation
Libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin according to the manufacturer's protocol.

tag: virus type

tag: virus strain


title: NSM, Ileum, 4


title: NSM, Ileum, 5


title: K562 cells, SF3B1 wild type, 4 days, replicate 2, H3K27me3 CUT&RUN


title: SMM + HMOs, Ileum, 7

value: SMM+HMOs


title: RNA-seq: GM12878 Replicate 2


title: RNA-seq: GM12878 Replicate 1


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, H3K27me3 CUT&RUN

value: Immortalized epithelial cells


title: RNA-seq: Jiyoye Replicate 3

source_name: Jiyoye

value: Jiyoye


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, H3K27me3 CUT&RUN


title: RNA-seq: Jiyoye Replicate 2


title: SMM + HMOs, Ileum, 5


title: RNA-seq: Jiyoye Replicate 1


title: SMM, Ileum, 7

value: SMM


title: K562 cells, SF3B1 wild type, 4 days,replicate 2, H3K4me3 CUT&RUN


title: SMM + HMOs, Ileum, 4


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, H3K4me3 CUT&RUN


title: RNA-seq: AG876 Replicate 3


title: SMM, Ileum, 6


title: liver, 39_8w-KO4

type: RNA

city: Paris

first: Fadila

last: Benhamed

address: 24 rue du Faubourg St Jacques

institute: Institut Cochin

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization were performed using TAC4.0 software (Thermofisher) with sst-RMA parameters.

label: Biotin

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Thermofisher). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Thermofischer). After purification according to Thermofisher protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled. After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Clariom S Mouse (Thermofischer) at 45°C for 17 hours

extract_protocol: Snap-frozen liver tissue was powdered, and approximately 15 mg of liver powder was used for RNA extraction using the SV Total RNA Isolation System (Promega, Madison, WI, USA; Z3101).

value: liver

value: OGTL KO


title: liver, 36_8w-KO1


title: liver, 38_8w-KO3


title: SMM + HMOs, Ileum, 6


title: K562 cells, SF3B1 K700E, 4 days, replicate 2, H3K4me3 CUT&RUN


title: liver, 40_8w-KO5


title: K562 cells, SF3B1 K700E, 4 days, shPHF21A, IP [RNAPIISer2PChIPseq_SF3B1K700E_shPHF21A_Input]

description: RNAPIISer2PChIPseq_SF3B1K700E_shPHF21A_IP_Input.bw

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
The respective IP and Input BAM files were compared to each other while being simultaneously normalized for sequencing depth (using RPKM), and reformatting to the bigWig file format using deepTools BamCompare program.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. CDK9 antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.

value: PHF21A knockdown


title: K562 cells, SF3B1 K700E, 4 days, shING2,Replicate2, Input [RNAPIISer2PChIPseq_SF3B1K700E_shING2-2_Input]

description: RNAPIISer2PChIPseq_SF3B1K700E_shING2-2_IP_Input.bw

value: ING2 knockdown


title: liver, 35_4w-KO5


title: liver, 33_4w-KO3


title: SMM, Ileum, 5


title: SPI1 ChIP-seq: Jiyoye Replicate 2

data_processing:
We performed quality control of raw sequencing reads using the ChIP-seq transcription factor Pipeline v2.2.0 from the ENCODE Project (https://www.encodeproject.org/pipelines/).
ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2. Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using the default parameters of MACS2 (p < 0.01).
The ENCODE blacklist region was removed upon establishing the final peak set.
Irreproducibility Discovery Rate (IDR) optimal peaks, generated from the ENCODE pipeline, were obtained for each cell type and used for downstream analyses.
EBV type 1-specific peaks, EBV type 2-specific peaks, and shared peaks were identified using bedtools commands on IDR optimal peaks
Assembly: hg19 (GRCh37)
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format. Peaks are filtered based on q-value and contain only those with a q-value < 0.01
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).

tag: chip antibody


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, H3K4me3 CUT&RUN

tag: cell type

value: SF3B1 K700E


title: SMM, Ileum, 4

tag: cell line


title: liver, 37_8w-KO2


title: liver, 34_4w-KO4


title: liver, 32_4w-KO2


title: K562 cells, SF3B1 K700E, 4 days, shING2, Replicate1, Input [RNAPIISer2PChIPseq_SF3B1K700E_shING2-1_Input]

description: RNAPIISer2PChIPseq_SF3B1K700E_shING2-1_IP_Input.bw

tag: treatment


title: liver, 31_4w-KO1


title: RNA-seq: AG876 Replicate 1


title: RNA-seq: AG876 Replicate 2


title: GF, Ileum, 6

value: Vehicle


title: K562 cells, SF3B1 K700E, 4 days, shHDAC2, Input [RNAPIISer2PChIPseq_SF3B1K700E_shHDAC2_Input]

description: RNAPIISer2PChIPseq_SF3B1K700E_shHDAC2-1_IP_Input.bw

value: HDAC2 knockdown


title: SPI1 ChIP-seq: AG876 Replicate 2


title: GF, Ileum, 5


title: SPI1 ChIP-seq: AG876 Replicate 1


title: liver, 30_8w-WT5

value: OGTL WT


title: K562 cells, SF3B1 K700E, 4 days, shPHF21A, IP [RNAPIISer2PChIPseq_SF3B1K700E_shPHF21A_IP]


title: GF, Ileum, 4


title: RBPJ ChIP-seq: GM12878 Replicate 2


title: RBPJ ChIP-seq: GM12878 Replicate 1


title: NSM + HMOs, Colon, 3

value: Colon

value: NSM+HMOs


title: NSM + HMOs, Colon, 2


title: K562 cells, SF3B1 K700E, 4 days, shING2, Replicate1, IP [RNAPIISer2PChIPseq_SF3B1K700E_shING2-1_IP]


title: RBPJ ChIP-seq: Jiyoye Replicate 2


title: K562 cells, SF3B1 K700E, 4 days, shING2,Replicate2, IP [RNAPIISer2PChIPseq_SF3B1K700E_shING2-2_IP]


title: NSM + HMOs, Colon, 1


title: K562 cells, SF3B1 K700E, 4 days, shHDAC2, Replicate2, IP [RNAPIISer2PChIPseq_SF3B1K700E_shHDAC2-2_IP]


title: RBPJ ChIP-seq: Jiyoye Replicate 1


title: liver, 26_8w-WT1


title: liver, 27_8w-WT2


title: NSM, Colon, 3


title: K562 cells, SF3B1 K700E, 4 days, shHDAC2, Replicate1, IP [RNAPIISer2PChIPseq_SF3B1K700E_shHDAC2-1_IP]


title: NSM, Colon, 2


title: K562 cells, SF3B1 K700E, 4 days, shScrambled, Input [RNAPIISer2PChIPseq_SF3B1K700E_shScrambled_Input]

description: RNAPIISer2PChIPseq_SF3B1K700E_shScrambled_IP_Input.bw

value: shControl


title: liver, 25_4w-WT5


title: liver, 29_8w-WT4


title: RBPJ ChIP-seq: AG876 Replicate 2


title: liver, 23_4w-WT3


title: liver, 24_4w-WT4


title: K562 cells, SF3B1 K700E, 4 days, shScrambled, IP [RNAPIISer2PChIPseq_SF3B1K700E_shScrambled_IP]


title: NSM, Colon, 1


title: RBPJ ChIP-seq: AG876 Replicate 1


title: K562 cells, SF3B1 K700E with shScrambled, Input [RNAPIISer2PChIPseq_K562_SF3B1K700E_shScrambled_Input]

description: RNAPIISer2PChIPseq_K562_SF3B1K700E_shScrambled_IP_Input.bw

value: shScrambled


title: liver, 21_4w-WT1


title: JUNB ChIP-seq: JIyoye Replicate 2

value: Active Motif 39549


title: K562 cells, SF3B1 wild type with shTATSF1, Input [RNAPIISer2PChIPseq_K562_WT_shHTATSF1_Input]

description: RNAPIISer2PChIPseq_K562_WT_shHTATSF1_IP_Input.bw

value: SF3B1 WT

value: HTATSF1 knockdown


title: E.coli, HM366, replicate2

city: New York

first: Ming-Ting

middle: Kessler

last: Tsai

state: NY

address: 408 E 69th Street Z1619

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The output data (fastq files) were submitted to BV-BRC web resources (https://github.com/BV-BRC) for analysis.
Read count matrix was generated using “RNA-seq analysis” service on BV-BRC with strain specific reference genome.
Count matrix from each individual strain were combined together as core_gene_count. (only keep common genes carried by all strains)
Assembly: Strain specific reference genome are avaliable on BV-BRC or Bioproject number: PRJNA725420 and. PRJNA1083051
Supplementary files format and content: tab-delimited text file includes raw counts for each samples, only 3166 core genes are listed.
Supplementary files format and content: tab-delimited text file includes raw counts for each samples, all genes are listed.

organism: Escherichia coli

growth_protocol: E. coli strains were grown in LB broth at 37°C, shake at 220 rpm until late log phase (OD600= 0.8-1).

extract_protocol:
RNA were harvested using Qiagen RNeasy Mini Kit with DNase treatment according to manufacturer’s protocols.
285-500 ng of total RNA with RIN values of 8.5-10 were underwent rRNA depletion and library preparation using Illumina Ribo-Zero Kit according to manufacturer’s instructions.

tag: culture media

value: LB broth

tag: condition

value: late log phase


title: JUNB ChIP-seq: JIyoye Replicate 1

value: Jiyoye


title: SMM + HMOs, Colon, 3

tag: tissue

value: SMM+HMOs


title: K562 cells, SF3B1 wild type with shDDX46, Input [RNAPIISer2PChIPseq_K562_WT_shDDX46_Input]

description: RNAPIISer2PChIPseq_K562_WT_shDDX46_IP_Input.bw

value: Immortalized epithelial cells

value: DD46 knockdown


title: K562 cells, SF3B1 wild type with shScrambled, Input [RNAPIISer2PChIPseq_K562_WT_shScrambled_Input]

description: RNAPIISer2PChIPseq_K562_WT_shScrambled_IP_Input.bw


title: E.coli, HM365, replicate1


title: JUNB ChIP-seq: AG876 Replicate 2


title: liver, 22_4w-WT2

value: liver

tag: age


title: E.coli, HM366, replicate1


title: JUNB ChIP-seq: AG876 Replicate 1


title: SMM + HMOs, Colon, 1


title: E.coli, HM356, replicate2


title: SMM, Colon, 2

value: SMM


title: SMM, Colon, 3


title: K562 cells, SF3B1 K700E with shScrambled, IP [RNAPIISer2PChIPseq_K562_SF3B1K700E_shScrambled_IP]

value: SF3B1 K700E


title: K562 cells, SF3B1 wild type with shTATSF1, IP [RNAPIISer2PChIPseq_K562_WT_shHTATSF1_IP]


title: E.coli, HM356, replicate1


title: EBNA2 ChIP-seq: GM12878 Replicate 1

value: Abcam ab90543


title: EBNA2 ChIP-seq: GM12878 Replicate 2


title: liver, 28_8w-WT3

value: OGTL WT


title: EBNA2 ChIP-seq: Jiyoye Replicate 2


title: SMM + HMOs, Colon, 2

value: Colon


title: K562 cells, SF3B1 wild type with shScrambled, IP [RNAPIISer2PChIPseq_K562_WT_shScrambled_IP]


title: E.coli, HM346, replicate2


title: EBNA2 ChIP-seq: Jiyoye Replicate 1


title: K562 cells, U2AF1 S34F, 4 days, replicate 1, Input [RNAPIISer2PChIPseq_K562_U2S34F_Input]

description: RNAPIISer2PChIPseq_K562_U2S34F_IP_Input.bw

value: U2AF1 S34F


title: GF, Colon, 1

value: Vehicle


title: E.coli, HM365, replicate2


title: EBNA2 ChIP-seq: AG876 Replicate 2


title: K562 cells, SF3B1 wild type with shDDX46, IP [RNAPIISer2PChIPseq_K562_WT_shDDX46_IP]


title: EBNA2 ChIP-seq: AG876 Replicate 1


title: K562 cells, U2AF1 wild type, 4 days, replicate 1, Input [RNAPIISer2PChIPseq_K562_U2WT_Input]

description: RNAPIISer2PChIPseq_K562_U2WT_IP_Input.bw

value: U2AF1 WT


title: SMM, Colon, 1


title: NSM + HMOs, Ileum, 3

value: Ileum

value: NSM+HMOs


title: K562 cells, SF3B1 K700E, 4 days, replicate 2, Input [RNAPIISer2PChIPseq_K562_SF3B1K700E_Input_Replicate2]

description: RNAPIISer2PChIPseq_K562_SF3B1K700E_IP_Input_Replicate2.bw


title: NSM + HMOs, Ileum, 2


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, Input [RNAPIISer2PChIPseq_K562_SF3B1K700E_Input_Replicate1]

description: RNAPIISer2PChIPseq_K562_SF3B1K700E_IP_Input_Replicate1.bw


title: E.coli, HM347, replicate2

value: LB broth


title: K562 cells, SF3B1 wild type, 4 days, replicate 2, Input [RNAPIISer2PChIPseq_K562_WT_Input_Replicate2]

description: RNAPIISer2PChIPseq_K562_WT_IP_Input_Replicate2.bw

value: SF3B1 WT


title: EBF1 ChIP-seq: AG876 Replicate 1

value: Santa Cruz sc-137065


title: NSM + HMOs, Ileum, 1


title: GF, Colon, 2


title: E.coli, HM347, replicate1

value: late log phase


title: GF, Colon, 3


title: Mu-4_Esophagus_3DP0_D-8_Control

city: Würzburg

first: Cindrilla

last: Chumduri

address: Am Hubland

department: Chair of Microbiology, Biozentrum

country: Germany

institute: Julius-Maximilians-Universität Würzburg

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data files were background corrected, quantile normalized, and further analyzed for differential gene expression using Rstudio (Rstudio. Inc.).

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Esophagus and Stomach epithelial 3D organoids were grown in defined media using the protocol described in the accompanying manuscript (Materials and Methods)

extract_protocol: Total RNA was isolated by the TRIzol Reagent, RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

tag: tissue type

tag: cell culture type

value: 3D Organoid


title: BATF ChIP-seq: Jiyoye Replicate 2

value: Jiyoye

value: Santa Cruz sc-100974


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, Input [RNAPIISer2PChIPseq_K562_WT_Input_Replicate1]

description: RNAPIISer2PChIPseq_K562_WT_IP_Input_Replicate1.bw

value: Immortalized epithelial cells

tag: genotype


title: Mu-2_Esophagus_3DP0_D-8_Control


title: NSM, Ileum, 2

extract_protocol:
RNA was extracted using Trizol/BCP and Rneasy mini kit (QIAgen) and quantified using Qubit Flurometer
messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by the second strand of cDNA synthesis. This was followed by 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.

tag: strain

value: NSM


title: K562 cells, SF3B1 K700E, 4 days, replicate 2, IP [RNAPIISer2PChIPseq_K562_SF3B1K700E_IP_Replicate2]

value: SF3B1 K700E


title: BATF ChIP-seq: Jiyoye Replicate 1


title: NSM, Ileum, 3


title: NSM, Ileum, 1


title: BATF ChIP-seq: AG876 Replicate 2


title: BATF ChIP-seq: AG876 Replicate 1


title: EBF1 ChIP-seq: AG876 Replicate 2


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, IP [RNAPIISer2PChIPseq_K562_SF3B1K700E_IP_Replicate1]


title: K562 cells, SF3B1 wild type, 4 days, replicate 2, IP [RNAPIISer2PChIPseq_K562_WT_IP_Replicate2]


title: E.coli, HM345, replicate1


title: SMM + HMOs, Ileum, 3

value: SMM+HMOs


title: Mu-2_Stomach_3DP0_D-8_Control


title: E.coli, HM345, replicate2


title: Mu-4_Stomach_3DP0_D-7_Control


title: Mu-1_Stomach_3DP0_D-8_Control


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, IP [RNAPIISer2PChIPseq_K562_WT_IP_Replicate1]


title: ATAC-seq: GM12878 Replicate 2

data_processing:
Quality control of raw sequencing reads was performed using the DNA Accessibility Pipeline v2.2.0 from the ENCODE Project.
ATAC-seq reads were aligned to the human genome (hg19) using Bowtie2 .
Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89)
Peaks were called using the default parameters of MACS2 (q < 0.01).
Irreproducibility Discovery Rate (IDR) optimal peaks, generated from the ENCODE pipeline, were obtained for each cell type and used for downstream analyses.
Assembly: hg19
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format. Peaks are filtered based on q-value and contain only those with a q-value < 0.01
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10

growth_protocol: The AG876, Jiyoye, GM12878, and MutuIII cell lines were grown in RPMI medium supplemented with 2 mM L-glutamine, 10% FBS, 1X antibiotic-antimycotic , and 0.2% Normocin at 200,000 – 500,000 viable cells/mL. Cells were incubated in flasks at 37C with 5% carbon dioxide in an upright position with vented.

extract_protocol:
Transposase Tn5 with sequencing adapter sequences was used to cut the accessible DNA as detailed in Buenrostro et al. 2015
The resulting accessible DNA sequences were isolated, and libraries were prepared from 50,000 cells from each cell line using the OMNI ATAC protocol as detailed in Corces et al 2017


title: Mu-1_Esophagus_3DP0_D-8_Control


title: E.coli, HM344, replicate2


title: SMM + HMOs, Ileum, 1

data_processing:
FASTQ files were subject to quality control and adapter sequence trimming with FastQC (v0.11.9) and TrimGalore (v0.6.5).
Trimmed reads were aligned with STAR (v2.7.9a) against the mouse GRCm39_107 reference genome.
Aligned reads were processed with featureCounts (subread v2.0.1) to produce a gene-count matrix for all samples.
Assembly: GRCm39
Supplementary files format and content: Gene-count matrix for each tissue type (colon, ileum) containing per-sample counts annotated with ENSEMBL IDs and gene symbols.


title: ATAC-seq: GM12878 Replicate 1


title: K562 cells, SF3B1 K700E, 8 days, replicate 2 [RNAseq_K562_SF3B1K700E_Replicate2_D8]

data_processing:
Sequence reads were trimmed for adaptors with Cutadapt
Trimmed sequence reads were mapped to hg38 using STAR aligner
Aligned bam files were used to determine gene expression and alterantive splicing changes
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1  ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using strand-speecific  Illumina-compatible cDNA libraries  (dUTP protocol)

treatment_protocol: Modified allele expression induced with doxycycline (1ug/ml)


title: SMM + HMOs, Ileum, 2


title: E.coli, HM346, replicate1


title: SPI1 ChIP-seq: Jiyoye Replicate 1


title: E.coli, HM344, replicate1


title: SMM, Ileum, 3

value: SMM


title: ATAC-seq: Jiyoye Replicate 2


title: SMM, Ileum, 2


title: E.coli, HM343, replicate2


title: K562 cells, SF3B1 K700E, 8 days, replicate 1 [RNAseq_K562_SF3B1K700E_Replicate1_D8]


title: K562 cells, SF3B1 wild type, 8 days, replicate 2 [RNAseq_K562_WT_Replicate2_D8]

value: WT


title: SMM, Ileum, 1


title: E.coli, HM343, replicate1


title: K562 cells, SF3B1 wild type, 8 days, replicate 1 [RNAseq_K562_WT_Replicate1_D8]


title: E.coli, HM342, replicate2


title: GF, Ileum, 3

value: Vehicle


title: E.coli, HM342, replicate1


title: K562 cells, SF3B1 K700E, 4 days, replicate 2 [RNAseq_K562_SF3B1K700E_Replicate2_D4]


title: 18-3_stimulated_3

city: Neuherberg

first: Sebastian

last: Schmidt

address: Ingolstädter Landstraße 1

department: Institute of Developmental Genetics

institute: Helmholtz Zentrum München

description:
18-3; Wnt stimulated; replicate 3
countmatrix.txt
22L001619

data_processing:
RNA-seq data were analyzed using a local Galaxy v 22.05 instance.
The quality of sequencing reads stored in FASTQ files was assessed using FastQC v0.72.
Paired-end reads were trimmed, and short reads (<20 bp) were removed using Trimmomatic v0.38.1.
RNA STAR Aligner v2.7.8a was used to align sequence reads to the human reference genome GRCh38.
Alignment summary statistics were reported using samtools idxstats v2.0.3.
Alignment quality was further assessed using RSeQC v1.1 and its provided annotation BED files for the human reference genome GRCh38.
The number of reads mapped to each gene was extracted from the STAR aligner BAM output file using featureCounts v1.6.4 and gene annotations (release 32) were obtained from GENCODE.
Gene counts were converted to a matrix using Count matrix v0.0.3.
Output results from FastQC, Trimmomatic, STAR aligner, samtools idxstats, featureCounts, and RSeQC were aggregated using MultiQC v1.9
Assembly: GRCh38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

growth_protocol: Neuronal precursor cells (NPCs) were cultivated at 37°C, 5% CO2, 21%O2 on Geltrex-coated plates (Thermo Fisher Scientific, A1413302) in maintenance medium (50% DMEM/F12-GlutaMAX (Life Technologies, 31331093), 50% Neurobasal (Life Technologies, 21103049) supplemented with 1% B27 minus vitamin A (Life Technologies, 12587010), 0.5% N2 (Life Technologies, 17502048), 10 µM SB431542 (Miltenyi Biotec, 130-106-275), 1 µM dorsomorphin (Tocris Bioscience, 3093/10), 4.44 nM FGF-8b (Miltenyi Biotec, 130-095-741), 150 µM ascorbic acid 2-phosphate (Sigma, A8960-5G), and 0.02% beta-mercaptoethanol (Life Technologies, 31350010)).

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, 74134) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA kit (Illumina) following manufacturar's protocols.

treatment_protocol: NPCs were stimulated for 48h with 3 µM CHIR99021 (Tocris Bioscience, 4423/10).

value: neuronal precursor cells

value: Wnt stimulated


title: GF, Ileum, 2

value: Ileum


title: 18-3_stimulated_2

description:
18-3; Wnt stimulated; replicate 2
countmatrix.txt
22L001618


title: K562 cells, SF3B1 K700E, 4 days, replicate 1 [RNAseq_K562_SF3B1K700E_Replicate1_D4]


title: E.coli, HM341, replicate2

value: LB broth


title: GF, Ileum, 1


title: K562 cells, SF3B1 wild type, 4 days, replicate 2 [RNAseq_K562_WT_Replicate2_D4]


title: 18-3_stimulated_1

description:
18-3; Wnt stimulated; replicate 1
countmatrix.txt
22L001617


title: SARS-CoV-2, Vehicle, 3

city: La Jolla

first: Judith

middle: Anne

last: Varner

state: CA

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

department: Pathology

institute: University of California, San Diego

description: Ribodepleted libraries were prepared and sequenced

data_processing:
Quality trimming of FASTQ files was performed using Trimmomatic (v0.36).
Paired-end reads were aligned to the mouse reference genome (GRCm39; annotation file, vM29) using STAR (v2.5.3a), followed by RSEM (v1.3.0) to quantify expression levels of transcripts.
The R BioConductor package DESeq2 was used to perform differential gene expression analysis from unnormalized counts. Lowly expressed genes – defined as those genes with mean <10 reads across all samples – were excluded prior to differential expression analysis.
Regularized log transformed (rlog) read counts were determined. Sample clustering was supervised or unsupervised (Pearson correlation) where indicated. Significance was defined by using an adjusted p-value cut-off of <0.05 after multiple testing correction.
Total differentially expressed genes or genes differentially expressed in multiple group comparisons were extracted for gene annotation and functional enrichment analysis using GSEA.
Assembly: GRCm39; annotation file, vM29
Supplementary files format and content: Mouse_SarsCov2_gene_counts.txt
Supplementary files format and content: Mouse_SarsCov2_gene_counts_clean.txt

source_name: lung

growth_protocol: 8-week-old K18-hACE2 C57Bl/6 male mice (Jackson Laboratories) were intranasally (i.n.) infected with 5000 Plaque Forming Units (PFU) of SARS-CoV-2/human/USA/WA-CDC-WA1/2020 (SARS2-WA, BEI Resources, NIAID, NIH, Bethesda, Maryland, USA).

extract_protocol:
Lungs were collected at day 5 p.i. from surviving mice (n=3 vehicle and n=4 IPI-549) and stored  in TRIzol (ThermoFisher Scientific, 15596018) for RNA-sequencing.
Ribo-depleted RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: Two days post-infection (p.i.), mice were treated with vehicle or 25mg/kg IPI-549 once daily by oral gavage (n=5 per study). Weight loss was monitored at day 0, 3, 4 and 5 p.i.

value: hACE2Tg C57/bl6

value: lung

tag: infection

tag: time of_drug_treatment

value: 3 days


title: E.coli, HM341, replicate1

value: late log phase


title: ATAC-seq: Jiyoye Replicate 1

value: Jiyoye


title: SARS-CoV-2, Vehicle, 2


title: E.coli, HM340, replicate2


title: 15-1_stimulated_2

description:
15-1; Wnt stimulated; replicate 2
countmatrix.txt
22L001615


title: 15-1_stimulated_3

description:
15-1; Wnt stimulated; replicate 3
countmatrix.txt
22L001616


title: K562 cells, SF3B1 K700E, 4 days, replicate 2 [DRIPseq_K562_SF3B1K700E_Replicate2]

data_processing:
library strategy: DRIP-seq
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligner
To create DRIP-seq coverage plots, the locations of the mapped DRIP-seq reads were extended to 150 bp to represent sequenced fragments, normalized (to RPKM) and reformatted in the bigWig file format.
Epic2 package was used to call differentially enriched domains in WT and SF3B1K700E, using default parameters. Differentially DRIP-seq peaks were determined as those with a |log2 fold change(L2FC)| > 0.58 and adjusted p value < 0.05, calculated with DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Digested DNA was purified by phenol/chloroform/isoamyl alcohol extraction, ethanol precipitation and quantified by Nanodrop. 4 μg of digested DNA was incubated with 10 μg of S9.6 antibody overnight at 4 °C on a rotator. DNA/antibody complexes were added for 2 hours at 4 °C to Agarose Protein-A/G beads. Immunoprecipitated DNA was eluted by incubating with an elution buffer containing proteinase K at 55 °C for 45 min on a rotator. The eluent was precipitated by phenol/chloroform/isoamylalcohol extraction and ethanol precipitation.
The pulled down material and input DNA were then sonicated, size-selected, and ligated to Illumina barcoded adaptors, using TruSeq ChIP Sample Preparation Kit or ThruPLEX® DNA-seq Kit

treatment_protocol:
Modified allele expression induced with doxycycline (1ug/ml)
Cells were harvested at 4 days after doxycycline induction


title: E.coli, HM340, replicate1


title: SARS-CoV-2, Vehicle, 1


title: ATAC-seq: AG876 Replicate 2


title: ATAC-seq: AG876 Replicate 1


title: E.coli, HM339, replicate2


title: SARS-CoV-2, IPI-549, 4


title: K562 cells, SF3B1 wild type, 4 days, replicate 2 [DRIPseq_K562_WT_Replicate2]


title: 4-5_stimulated_3

description:
4-5; Wnt stimulated; replicate 3
countmatrix.txt
22L001610


title: SARS-CoV-2, IPI-549, 3


title: E.coli, HM339, replicate1


title: K562 cells, SF3B1 wild type, 4 days, replicate 1 [DRIPseq_K562_WT_Replicate1]


title: 4-5_stimulated_2

description:
4-5; Wnt stimulated; replicate 2
countmatrix.txt
22L001609


title: SARS-CoV-2, IPI-549, 2


title: K562 cells, SF3B1 wild type, 4 days, replicate 1 [RNAseq_K562_WT_Replicate1_D4]


title: K562 cells, SF3B1 K700E, 4 days, replicate 1 [nascentSRSseq_K562_SF3B1K700E_Replicate1]

data_processing:
library strategy:  short read sequencing of nascent RNA (nSRS-seq)
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using STAR aligner
Aligned bam files were used to determine gene expression changes
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
All extraction steps were performed on ice, and all buffers contained 25 uM α-amanitin, 40 U/ml RNase inhibitor, and protease inhibitor. Chromatin fractions were isolated from the cellular pellets using a previously published protocol. Chromatin was immediately dissolved in PBS and TRIzol Reagent. RNA was purified from chromatin using the RNeasy Mini kit according to the manufacturer’s protocol, including the on-column DNase I digestion. For genome-wide nascent RNA-seq, samples were depleted three times of polyA(+) RNA using the Magnetic mRNA isolation kit, each time keeping the supernatant, then depleted of ribosomal RNA using oligo probe-based rRNA depletion
The isolated polyA, rRNA depleted RNA was then fragmented with a Bioruptor UCD-200, and the fragmented RNA was used to produce barcoded cDNA sequencing libraries using the SMARTer® Universal Low Input RNA Kit

treatment_protocol:
Modified allele expression induced with doxycycline (1ug/ml)
Cells (~20 million cells, per condition) were harvested at 4 days after doxycycline induction


title: 4-4_stimulated_3

description:
4-4; Wnt stimulated; replicate 3
countmatrix.txt
22L001607


title: E.coli, 541-15, replicate2


title: E.coli, HM337, replicate1


title: SARS-CoV-2, IPI-549, 1


title: K562 cells, SF3B1 wild type, 4 days, replicate 2 [nascentSRSseq_K562_WT_Replicate2]


title: 15-1_stimulated_1

description:
15-1; Wnt stimulated; replicate 1
countmatrix.txt
22L001614


title: K562 cells, SF3B1 K700E, 4 days, replicate 1 [DRIPseq_K562_SF3B1K700E_Replicate1]


title: E.coli, 541-15, replicate1


title: 4-4_stimulated_2

description:
4-4; Wnt stimulated; replicate 2
countmatrix.txt
22L001606


title: E.coli, GDAR2-2, replicate2


title: K562 cells, SF3B1 wild type, 4 days, replicate 1 [nascentSRSseq_K562_WT_Replicate1]


title: K562 cells, SF3B1 K700E, 4 days, replicate 2 [GROseq_K562_SF3B1K700E_Replicate2]

data_processing:
library strategy: GRO-seq or fastGRO-seq
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 (for coverage plot anslysis) and STAR (for splicing analysis) aligners
To create GRO-seq coverage plots, the locations of the mapped GRO-seq reads were extended to 150 bases toward the interior of the sequenced fragment and were normalized to total reads aligned (RPKM). Reads assigned to Watson and Crick strands using SAMtools (SAM flag 83/163 or 99/147) . Bam files were then normalized (to RPKM) and reformatted in the bigWig file format.
For splicing analysis, STAR-aligned bam files were used to determine splicing changes
Assembly: hg38
Supplementary files format and content: bigWig for all reads as well for reads aligning either to sense (forward) or anti-sense (reverse) strabds

extract_protocol:
Nuclear run-on RNA (NRO-RNA) was extracted with TRIzol LS reagent following the manufacturer’s instructions and ethanol precipitated. NRO-RNA was resuspended in water and concentration was determined. RNA was then chemically fragmented by mixing with RNA fragmentation buffer. Fragmented RNA was incubated in Biotinylation Solution. After ethanol precipitation, the biotinylated RNA was resuspended in water and biotinylated-RNA was separated with M280 Streptavidin Dynabeads. 100 ul/sample of beads were washed twice with 2 volumes of freshly prepared wash buffer and resuspended in 1 volume of wash buffer and added to the biotinylated-RNA. After 15 min in rotation at 4°C, beads were washed three times with wash buffer pre-warmed at 65°C and three times with a room temperature wash buffer. 4-S-UTP containing RNA was eluted and purified with RNA Clean and Purification kit with in-column DNaseq reaction to eliminate traces of genomic DNA.
The pulled down material and input DNA were then sonicated, size-selected, and ligated to Illumina barcoded adaptors, using TruSeq ChIP Sample Preparation Kit or ThruPLEX® DNA-seq Kit

treatment_protocol:
Modified allele expression induced with doxycycline (1ug/ml)
20 million cells from each replicate were used for each fGRO seq assay. Nuclei were extracted, thawed on ice just prior to the nuclear run-on. Nuclear run on buffer was added  and nuclei were incubated for 7 min at 30°C for the nuclear run-on.


title: HEPATOCYTES, Exe1, Input

city: xi'an

first: Xinpei

last: Wang

address: 169 Changle West Road

institute: Fourth Military Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <= 0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Isolated primary hepatocytes were fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris)
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme). 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: liver

value: hepatocytes

value: exercised

tag: antibody


title: 4-3_stimulated_3

description:
4-3; Wnt stimulated; replicate 3
countmatrix.txt
22L001604


title: HEPATOCYTES, Sed1

value: sedentary


title: HEPATOCYTES, Sed1, Input


title: E.coli, GDAR2-2, replicate1


title: HEPATOCYTES, Exe1


title: K562 cells, SF3B1 K700E, 4 days, replicate 1 [GROseq_K562_SF3B1K700E_Replicate1]

value: Immortalized epithelial cells


title: E.coli, HM337, replicate2


title: 4-3_stimulated_2

description:
4-3; Wnt stimulated; replicate 2
countmatrix.txt
22L001603


title: K562 cells, SF3B1 wild type, 4 days, replicate 2 [GROseq_K562_WT_Replicate2]


title: E.coli, 2A, replicate2


title: E.coli, 2A, replicate1


title: 4-3_stimulated_1

description:
4-3; Wnt stimulated; replicate 1
countmatrix.txt
22L001602


title: 4-5_stimulated_1

description:
4-5; Wnt stimulated; replicate 1
countmatrix.txt
22L001608


title: K562 cells, SF3B1 wild type, 4 days, replicate 1 [GROseq_K562_WT_Replicate1]


title: K562 cells, SF3B1 K700E, 4 days, replicate 2 [nascentSRSseq_K562_SF3B1K700E_Replicate2]


title: E.coli, K12, replicate2


title: 25-19_stimulated_3

description:
25-19; Wnt stimulated; replicate 3
countmatrix.txt
22L001589

value: EN1 ko


title: 25-19_stimulated_2

description:
25-19; Wnt stimulated; replicate 2
countmatrix.txt
22L001588


title: K562 cells, U2AF1 S34F, 4 days, replicate 2 [TTTLseq_K562_U2S34F_Replicate2]

data_processing:
library strategy: TT-TL-seq
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 (for coverage plot anslysis) and STAR (for splicing analysis) aligners
Trimmed reads were mapped to a combined hg38 and dm6 genome using Bowtie2. Bam files for uniquely mapped reads (SAM flag 83/163 or 99/147) were created, sorted and indexed using Samtools.
To calculate normalization factors, reads aligning to the dm6 genome were filtered and counted with Samtools. RPKM-normalized, Drosophila-scaled bigwig files and metaplot images were generated using deepTools 2.0.
To assess the TL-component in the TT-TL seq, unfiltered, trimmed reads were mapped to a combined hg38 and dm6 genome using HISAT-3N with default parameters and U-to-C mutation calls.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were harvested and washed in ice cold PBS and RNA extracted by Trizol and chloroform extraction, ethanol precipitation. Total RNA was resuspended and treated with DNase, then extracted with acidic phenol:chloroform:isoamyl alcohol and again ethanol precipitated. RNA was resuspended in water and concentration was determined. Up to 150 mg of RNA was transferred to a new tube and 5% (w/w) of Drosophila S2 spike-in RNA was added. RNA was then chemically fragmented by mixing with 2x RNA fragmentation buffer. Fragmented RNA was incubated in Biotinylation Solution (20 mM Tris pH 7.5, 2 mM EDTA pH 8.0, 40% dimethylformamide, 200 mg/ml EZ-link HPDP Biotin (Thermo Scientific, 21341)) for 2h in the dark at 25°C, 800 rpm. After chloroform: isoamyl alcohol (24:1) extraction followed by purification (Qiagen RNeasy Mini Kit, 74104), the biotinylated RNA was resuspended in water and biotinylated-RNA was isolated using Dynabeads MyOne Streptavidin C1 magnetic beads. s4U-biotinylated RNA was eluted from the beads by cleaving the HPDP Biotin in elution buffer and cleaned up using 1x RNAcleanXP beads. For time lapse chemistry, isolated s4U-enriched RNA was added to a mixture of 3M sodium acetate pH 5.2, EDTA, RNAse free water, and trifluoroethylamine. NaIO4 was then added dropwise, and the reaction mixture was incubated for 1 h at 45 °C. 1x volume of RNA clean beads were then added and purified. 2 μl of reducing master mix was added to each sample for a final volume of 20 μl, mixed, and incubated in thermocycler at 37C for 30 min. The mixture was then mixed with 1x RNAclean beads and RNA purified
Eluted RNA was quantified with Qubit High Sensitivity Assay kit and used to produce barcoded cDNA sequencing libraries using the SMARTer® Universal Low Input RNA Kit

treatment_protocol:
Modified allele expression induced with doxycycline (1ug/ml)
15 million cells fromeach replicate  were used for each TT-TL assay. About 15 million cells per sample was labeled with  s4U (by adding it to culture media at final concentration of 500 μM) for  5 minutes.

value: U2AF1 S34F


title: 4-4_stimulated_1

description:
4-4; Wnt stimulated; replicate 1
countmatrix.txt
22L001605

value: WT


title: im-scWAT, HY, D8

city: Tokyo

first: Juro

last: Sakai

address: 4-6-1, Komaba, Meguro-ku

department: Division of Metabolic Medicine

country: Japan

institute: Research Center for Advanced Science and Technology, The University of Tokyo

data_processing:
The libraries were sequenced on NovaSeq 6000 (Illumina).
Fastp were used to filter out low-quality reads and adapters from ATAC-seq reads in fastq files, and ATAC-seq reads passed quality filtering were aligned to the mouse mm9 genome by using bowtie2.
SAM files generated were converted to sorted bam files by using SAMtools, and PCR duplicates were removed using Picard.
Bigwig files were generated using deeptools bamCoverage after removing signals falling in regions blacklisted by mm9.
Peaks were called using MACS ver3 with a default setting.
Assembly: mm9
Supplementary files format and content: narrow peak files
Supplementary files format and content: bigwig files

source_name: im-scWAT cells

growth_protocol: im-scWAT cells were cultured in DMEM/Ham's F-12 medium supplemented with 10% fetal bovine serum and penicillin/streptomycin in a 5% CO2 atmosphere in a humidified incubator.

extract_protocol:
A nuclear suspension was prepared from im-scWAT cells using resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl2, pH 7.4).
Library was constructed using ATAC-Seq Kit (Active Motif) according to the manufacturer's instructions.

treatment_protocol: im-scWAT cells were culture to ~100% confluence and then treated with an induction medium containing 0.125 mM indomethacin, 2 μg/ml dexamethasone, 0.5mM 3-isobutyl-1-methylxanthine, 0.5 μM rosiglitazone, 5 µg/ml insulin, and 1 nM T3. After 2 days of induction, the cells were switched to a medium containing only insulin, T3, and rosiglitazone for another 6 days to support further differentiation and maturation into beige adipocytes.

value: im-scWAT cells

value: Jmjd1a HY/HY

value: after differentiation (D8)


title: E.coli, K12, replicate1

value: LB broth


title: im-scWAT, HY, D0

value: before differentiation (D0)


title: K562 cells,U2AF1 S34F, 4 days, replicate 1 [TTTLseq_K562_U2S34F_Replicate1]


title: im-scWAT, WT, D8

value: Jmjd1a +/+


title: 5-12_stimulated_3

description:
5-12; Wnt stimulated; replicate 3
countmatrix.txt
22L001586

value: neuronal precursor cells

value: Wnt stimulated


title: K562 cells, U2AF1 wild type, 4 days, replicate 2 [TTTLseq_K562_U2WT_Replicate2]

value: U2AF1 WT


title: im-scWAT, WT, D0


title: 5-12_stimulated_2

description:
5-12; Wnt stimulated; replicate 2
countmatrix.txt
22L001585


title: Mouse cells, SF3B1 Sf3b1K700E, replicate 2, Ser5P CTD

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. Either pan-Pol2 CTD, Ser5P CTD, or Ser2P CTD antibodies was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.

value: lineage -ve marrow cells


title: ATAC_MKO_DM_Rep3

city: Beijing

first: Yuting

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

institute: Peking University

data_processing:
Fastq files were aligned to the reference genome using bowtie262 with the setting of ‘-very-sensitive’. Duplicate reads were removed using PicardTools. Only uniquely mapped reads (MAPQ>30) were kept for the following processing. RPM-normalized coverage tracks were calculated by deepTools. Peaks were called using MACS2 with the settings ‘macs2 callpeak -q 0.01 –nomodel –extsize 147’.
Assembly: mm9
Supplementary files format and content: xlsx file includes FPKM values for each sample
Supplementary files format and content: txt file include positionS of identified narrow peakS by MACS2

source_name: skeletal muscle

extract_protocol:
Cells were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630)
A Nextera DNA Library Preparation kit (Illumina) was used to perform the transposition according to the manufacturer’s manual.

value: skeletal muscle

value: myocyte

value: MyoD knocout

value: myogenic differentiation for 24 h


title: Mouse cells, WT, Ser2P CTD


title: K562 cells, SF3B1 K700E, 4 days, replicate 2 [TTTLseq_K562_SF3B1K700E_Replicate2]

value: Immortalized epithelial cells

value: SF3B1 K700E


title: K562 cells, U2AF1 wild type, 4 days, replicate 1 [TTTLseq_K562_U2WT_Replicate1]


title: 5-12_stimulated_1

description:
5-12; Wnt stimulated; replicate 1
countmatrix.txt
22L001584

value: EN1 ko


title: Mouse cells, WT, replicate 2, Ser5P CTD

value: WT


title: ATAC_MKO_DM_Rep2


title: 5-6_stimulated_3

description:
5-6; Wnt stimulated; replicate 3
countmatrix.txt
22L001583


title: Mouse cells, SF3B1 Sf3b1K700E, replicate 1, Ser5P CTD


title: ATAC_MKO_DM_Rep1


title: K562 cells, SF3B1 K700E, 4 days, replicate 1 [TTTLseq_K562_SF3B1K700E_Replicate1]


title: K562 cells, SF3B1 wild type, 4 days, replicate 2 [TTTLseq_K562_WT_Replicate2]

value: SF3B1 WT


title: 5-6_stimulated_2

description:
5-6; Wnt stimulated; replicate 2
countmatrix.txt
22L001582


title: 5-6_stimulated_1

description:
5-6; Wnt stimulated; replicate 1
countmatrix.txt
22L001581


title: K562 cells, SF3B1 wild type, 4 days, replicate 1 [TTTLseq_K562_WT_Replicate1]


title: Mouse cells, SF3B1 Sf3b1K700E, Ser2P CTD


title: Mouse cells, SF3B1 Sf3b1K700E, panPol2 CTD


title: ATAC_MKO_GM_Rep3

value: myoblast


title: 18-3_unstimulated_3

description:
18-3; unstimulated; replicate 3
countmatrix.txt
22L001580

value: unstimulated


title: Mouse cells, WT, replicate 1, Ser5P CTD


title: K562 cells, SF3B1 K700E, 4 days, replicate 2 [RNAPIINTDChIPseq_K562_SF3B1K700E_Replicate2]

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bases toward the interior of the sequenced fragment and were normalized to total reads aligned (RPKM) and Drosophila reads. Bam files were then reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 1 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.5-10 μg of chromatin was used for each IP. ChIP spike in normalization for the RNAPII ChIP assays was performed using Drosophila-specific chromatin and Drosophila-specific histone variant (H2Av) antibody. 50 ng of Drosophila S2 sheared crosslinked-chromatin was added to 10 μg of chromatin as spike-in control. RNAPII NTD antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.


title: 25-19_stimulated_1

description:
25-19; Wnt stimulated; replicate 1
countmatrix.txt
22L001587


title: Mouse cells, WT, panPol2 CTD

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
The respective IP and Input BAM files were compared to each other while being simultaneously normalized for sequencing depth (using RPKM), and reformatting to the bigWig file format using deepTools BamCompare program.
Assembly: hg38
Supplementary files format and content: bigWig


title: K562 cells, SF3B1 K700E, 4 days, replicate 1 [RNAPIINTDChIPseq_K562_SF3B1K700E_Replicate1]


title: 18-3_unstimulated_2

description:
18-3; unstimulated; replicate 2
countmatrix.txt
22L001579


title: ATAC_MKO_GM_Rep1


title: ATAC_WT_DM_Rep3

value: wild type


title: K562 cells, SF3B1 wild type, 4 days, replicate 2 [RNAPIINTDChIPseq_K562_WT_Replicate2]