title: Small intestinal dendritic cells CCR7gfp SI LP DCs

status: Public on Jan 15 2025

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

country: Germany

institute: RWTH Aachen University Hospital

description: Library name: SI LP DCs

data_processing:
We obtain BCL raw data from the sequencer. FASTQ files were generated by 10X mkfastq function. Barcode, count matrix and feature files were generated by Cellranger pipeline v 1.7.0
Assembly: mm10
Supplementary files format and content: gz

molecule: cytoplasmic RNA

organism: Mus musculus

source_name: small intestine

extract_protocol:
SI LP cells were isolated from two CCR7gfp/+ mice and dendritic cells (DCs) were enriched using Magnisort Strptavidin Negative Selection (B220, CD19, CD3, CD64, IgA, Ly6G). DCs were identified as live, single cells, CD45+, MHCII+ CD11c+, CD64-. 36000 GFP- and 12000 GFP+ DCs were sorted into PBS (0.04% BSA) and set to 1200 cells/µl for subsequent library preparation.
Chromium Next GEM Chip K and the Next GEM Single Cell 5’ Kit were used for GEM generation and library was prepared using the Library Construction Kit according  to the Chromium Next GEM Single Cell 5-v2 User guide (10x Genomics; RevD steps 1, 2 and 5). In Step 5.5., 50 ng DNA with 14 total cycles were used. Sequencing was performed on a NextSeq 500 sequencing system (Illumina).

value: small intestine

value: dendritic cells


title: ChIA-PET from HCT116 (ENCLB476DBV)

status: Public on Jan 14 2025

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR309KYA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR309KYA
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2023-12-18
lab: Charles Lee
library encode accession: ENCLB476DBV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens HCT116 cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

tag: age

value: 48 year

tag: lab

value: Charles Lee

tag: source

value: Coriell

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS303KGS at ENCODE; https://www.encodeproject.org/ENCBS303KGS/


title: YNN1 replicate 1 60nM Pho4

status: Public on Jan 16 2025

city: State College

first: Shane

middle: Douglas

last: Stoeber

state: Pennsylvania

address: 406 South Frear Building

department: BMMB

institute: Penn State

description: Library name: YNN1 replicate 1 60nM Pho4 MNase-seq

library_source: other

data_processing:
Paired-end reads were aligned to the corresponding reference sequence (Widom 601 or YNN with or without factor binding site) with Bowtie2 on galaxy (https://usegalaxy.org/) in paired-end mode.
Unpaired and unmapped reads were removed using samtools view in galaxy (https://usegalaxy.org/).
Nucleosome coverage was calculated from the read counts normalized to total reads in BPM using bamCoverage. The minimum and maximum fragment length was set to 130 bp and 160 bp respectively unless otherwise stated to enrich reads for mono-nucleosome fragments. Files were outputted as a bedgraph and plotted to visualize nucleosome occupancy.
The dyad position for each sequence was calculated using bamCoverage –MNase in which only the three center bp of each fragment was used for analysis and were normalized to total reads in BPM. Files were outputted as a bedgraph and plotted to visualize dyad location.
Supplementary files format and content: All nucleosome coverage and dyad analysis are bedgraph

molecule: other

organism: synthetic construct

source_name: PCR generated DNA molecule

extract_protocol:
Nucleosome binding experiments were performed by incubating 60 nM nucleosome with 0 nM or 60 nM of TFs (Reb1, Cbf1, or Pho4) for 20 minutes at room temperature. Nucleosomes-TF binding was confirmed on a 5% acrylamide native gel. The incubated samples were then digested with 0.3 U, 1 U, 3 U, 10 U of MNase (New England Biolabs) for 8 minutes at 37 ⁰C and immediately quenched by adding quench buffer (0.1 % SDS, 20 mM EDTA pH8.0, 0.01 U proteinase K). Proteinase K digestion was carried out by incubating the quenched samples for 1 hour at 50 ⁰C. The final digested samples were analyzed by agarose gel electrophoresis with a 1.5% gel in 0.5x TAE buffer (20 mM Tris base, 10 mM acetic acid, 0.5 mM EDTA pH 8.0) (Figure S4). The digest DNA samples were then purified by agarose gel electrophoresis and then gel extraction with a Freeze 'N Squeeze DNA extraction kit (Bio-Rad).
After gel purification of the MNase digested samples, sequencing libraries were prepared using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina® (Catalog # E7645L) according to the manufacturer’s instructions. The sequencing libraries were sequenced on a NextSeq 2000 machine in 2 x 50 bp paired-end sequencing mode at the Genomics Research Incubator at The Pennsylvania State University.

tag: treatment

value: 1 unit micrococcal nuclease

value: 60nM Pho4


title: ChIA-PET from GM12878 (ENCLB903NQA)

description:
https://www.encodeproject.org/experiments/ENCSR355CTR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR355CTR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2023-12-18
lab: Charles Lee
library encode accession: ENCLB903NQA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens GM12878 cell line

value: female

value: unknown

value: ENCBS021YGS at ENCODE; https://www.encodeproject.org/ENCBS021YGS/


title: ChIA-PET from HCT116 (ENCLB837AMH)

description:
https://www.encodeproject.org/experiments/ENCSR635DLF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, CTCF tag and IAA treated
experiment encode accession: ENCSR635DLF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB837AMH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS827RZY at ENCODE; https://www.encodeproject.org/ENCBS827RZY/


title: ChIA-PET from GM12878 (ENCLB245KDA)

description:
https://www.encodeproject.org/experiments/ENCSR764VXA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR764VXA
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2023-12-18
lab: Charles Lee
library encode accession: ENCLB245KDA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: ENCBS781HHE at ENCODE; https://www.encodeproject.org/ENCBS781HHE/


title: ChIA-PET from HCT116 (ENCLB269MKV)

description:
https://www.encodeproject.org/experiments/ENCSR028AOM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR028AOM
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2023-12-18
lab: Charles Lee
library encode accession: ENCLB269MKV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: male

value: colorectal carcinoma

value: adult

value: ENCBS828MWC at ENCODE; https://www.encodeproject.org/ENCBS828MWC/


title: MG1655, control, 60min, rep2

status: Public on Jan 03 2025

city: Gdansk

first: Dariusz

last: Nowicki

state: pomorskie

address: Wita Stwosza 59

department: Bacterial Molecular Genetics

country: Poland

institute: University of Gdansk

library_source: transcriptomic

data_processing:
Galaxy platform v 23.0
Sequence trimming after FastQC v0.11.9 was performed using Trimmomatic v0.38.1 (adapter sequence: TruSeq2, paired-ended, for Illumina GAII). Reads were mapped to eschColi_K12 reference genome using HISAT2 (Forward (FR); Spliced alignment options:Penalty for canonical/non-canonical - 0/3, Penaulty function - Constant [f(x) = B] where constant term B=0
Rstudio R-4.3.1 environment was employed to DEGs (DESEq 1.40.2) analysis using BAM files from HISAT2
Assembly: GCA_000005845, Ensembl July 2023
Supplementary files format and content: .xlsx file includes raw count data and DEGs analysis (p ≤ 0.001 and log2FC ≥ 1.5) for each sample

molecule: total RNA

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Escherichia coli MG1655 cultured in fresh LB, aerobically with shaking at 37°C

extract_protocol:
RNA was harvested using RNase Mini Kit  (Qiagen) followed by additional pufification step with DNAse I (Qiagen). Samples where then validated using Bioanalyzer 2100
TruSeq total RNA stranded with NebNext Ribodepletion kit (bacteria)

treatment_protocol: CNMA (Sigma) was added to treated samples (OD=0.1) from 1M stock solution in DMSO to final concantration 0.94mM. Then, cultures were incubated in aerobic contitions by 30 and 60 min. Untreated bacteria were used as a control.

tag: strain

tag: time

tag: cell type

value: bacterial cell

tag: genotype

value: WT


title: MG1655, control, 30min, rep3


title: H3K27M_P2

status: Public on Feb 17 2025

city: Boston

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: fresh single whole cell RNA-seq: SmartSeq2

library_source: transcriptomic single cell

data_processing:
Illumina bcl2fastq 1.5 is used for demultiplexing
RNA-seq sequenced reads were mapped to hg19 using hisat2(2.1.0) with parameters --met 5 -k 10 --mp 1,1 --np 1 --score-min L,0,-0.1 --secondary --no-mixed --no-softclip --no-discordant --rdg 99999999,99999999 --rfg 99999999,99999999 --no-spliced-alignment --seed 12345
RNA-seq TPM were calculated using RSEM (v1.3.0) with parameters --estimate-rspd --paired-end -sam
Supplementary files: tab-delimited text files include TPM values for all cells passing QC (immune and tumor) separately for samples profiled by SmartSeq2 and/or 10X Genomics
tab-delimited text files for metadata for all cells passing QC (tumor and immune) separately for samples profiled by SmartSeq2 and/or 10X Genomics
Assembly: hg19
Supplementary files format and content: Tab-separated count matrix files and metadata files

molecule: polyA RNA

source_name: Human tissue H3-K27 mutated

extract_protocol:
Smart-seq2 protocol, 10X Genomics protocol
Smart-seq2: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol). Briefly: RNA was purified with Agencourt RNAClean. Oligo-dT primed reverse transcription (RT) was performed using Maxima H Minus reverse transcriptase (Life Technologies) and a template-switching oligonucleotide (TSO; Qiagen). For the reverse transcription step, Maxima RNaseH-minus RT (200 U/ml) was used as the RT enzyme at 2U/ml. The RT step was performed at 50 Celsius degree for 90 minutes followed by 85 Celsius degree for 5 minutes. In the PCR pre-amplification step, an ISPCR primer was used at 0.2 mM and PCR was performed for 21 cycles. ). PCR purification was performed using AMpure XP beads at 0.8X. Libraries were enriched with dual indexes using Illumina Nextera XT Library Prep kits
10X Genomics: The isolated single cells (T cells, Myeloid cells, or tumor cells) were loaded into separate channels of a Single Cell Chip A with reverse transcriptase reagent mixture and 50ul gel beads according to the manufacturer’s protocol.Chips were next loaded into the 10X Genomics Chromium Controller for single-cell partitioning, immediately followed by emulsion recovery from the chip and incubated in a Thermocycler for the RT reaction. cDNA isolation and library preparation were completed as per the manufacturer’s protocol. Isolated cDNA was amplified (13 cycles). cDNA was allocated for preparation of a gene expression library or TCR enrichment/library preparation with the Chromium Single Cell V(D)J TCR kit (10X Genomics)

value: 3 years old

tag: tissue

value: pediatric high grade glioma


title: MG1655, control, 30min, rep2


title: MG1655, control, 30min, rep1


title: MG1655, control, 60min, rep1


title: RNA-seq of mouse retina: WT-6m-3

status: Public on Dec 01 2024

city: Pittsburgh

first: Yuanyuan

last: Chen

state: PA

address: 1622 Locust Street,

department: Ophthalmology

institute: University of Pittsburgh

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program.
Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed. Goseq was uesd to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis
Assembly: mm9
Supplementary files format and content: Txt file including resm counts
Supplementary files format and content: Txt file including TMM normalized reads count per million

source_name: retina

growth_protocol: Animals were obtained from Jackson Labs

extract_protocol:
Total RNA was isolated using the Trizol kit. The integrity of the RNA samples were evaluated by Agilent Bioanalyzer to make sure RINs are higher than 6.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq poly(A) selected kit (KAPA Biosystems, Wilmington, MA)using 250 ng total RNAs for each sample.

value: retina

value: wildtype

value: 6 months


title: RNA-seq of mouse retina: WT-6m-2


title: RNA-seq of mouse retina: WT-6m-1


title: RNA-seq of mouse retina: WT-3m-2

value: 3 months


title: BR2020 Poly I:C Y1 Flu Day 7-9

status: Public on Apr 24 2025

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
The FASTQs were aligned to the Genome Reference Consortium Human (GRCh) version 38.91, using STAR v.2.4.2a and gene counts were generated using HTSeq-count (v0.4.1) (57, 58). Quality metrics were compiled from PICARD (v1.134FASTQC (v0.11.3) Samtools (v1.2)8, and HTSeq-count. Samples with high median covariance of coverage coverage (>0.6), low total read count (<1 million), and low percent alignment (<92%) were considered low quality and removed from further analysis. Read counts were TMM-normalized (59).
Assembly: GRCh38.91
Supplementary files format and content: gene count matrix

source_name: peripheral blood

growth_protocol: Peripheral blood was collected directly into control (unstimulated) TruCulture tubes or tubes pre-loaded with 0.4 µg/mL SEB, 1 ng/mL LPS, or 20 µg/mL poly I:C (Rules Based Medicine) for stimulation as previously described

extract_protocol:
We extracted RNA using the MagMAX RNA Isolation Kit (Thermo Fisher Scientific) then performed globin reduction with the GLOBINclear-Human Kit (Thermo Fisher Scientific)
We generated full-length cDNA from total RNA (0.5 ng). We amplified cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) and constructed sequencing libraries using the NexteraXT DNA Library prep kit (Illumina).
We pooled libraries, quantified concentration with a Qubit Fluorometer (Life Technologies), then sequenced on a NextSeq 2000 sequencer (Illumina) with 59-base paired-end reads on a NextSeq P2 flow cell (Illumina). We targeted a depth of 5 million reads per sample.

treatment_protocol: After 24 hours of incubation, samples were processed to supernatant and cellular fraction (including RBC).  Cellular fractions were mixed before adding 500 µL to 1.5 mL Tempus solution and stored at -20°C until RNA-seq was performed

value: peripheral blood

tag: stimulation

value: Poly I:C

tag: donor

tag: timepoint

value: Y1 Flu Day 7-9

tag: age cohort

tag: cmv status

value: Negative


title: RNA-seq of mouse retina: WT-3m-3

tag: age


title: RNA-seq of mouse retina: WT-1m-3

value: 1 month


title: RNA-seq of mouse retina: WT-1m-2


title: RNA-seq of mouse retina: WT-3m-1


title: RNA-seq of mouse retina: WT-1m-1


title: RNA-seq of mouse retina: P23H-6m-3


title: RNA-seq of mouse retina: P23H-6m-1


title: RNA-seq of mouse retina: P23H-3m-3


title: RNA-seq of mouse retina: P23H-3m-2


title: MG1655, control, 60min, rep3


title: RNA-seq of mouse retina: P23H-3m-1


title: GMCSF ADAR1 E861A/E861A sgGgnbp2 rep 3

status: Public on Nov 21 2024

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

description:
GMCSF ADAR1 E861A/E861A sgGgnbp2 rep 3
Sequenced at 150bp PE reads on the Illumina platform by Novogene (Singapore).

data_processing:
Sequenced reads (150 bp) were trimmed for adaptor sequence and low-quality reads using fastp (v 0.19.5) (44). Parameters: --trim_front1 10 --trim_front2 10. Reads mapping to rRNA were removed using Bbmap (parameters: bbsplit.sh minratio= 0.56 minhits = 1 maxindel = 16000) [BBMap – Bushnell B. – sourceforge.net/projects/bbmap/].
Trimmed and filtered reads were quantified using Salmon (v1.4.0) against gencode release M22. Gene level quantification was calculated in R using tximeta, with gene level summary using summarizeToGene with lengthScaledTPM.  Genes and transcripts were annotated in R using biomaRt (jul2019.archive.ensembl.org -  mm10.M22.ensembl97).
Differential expression was assessed using voom with sample weighting {Law, 2014}.
Genes with counts >= 10 and cpm > 1.0 in at least 3 samples were kept for further analysis.
Assembly: mm10
Supplementary files format and content: raw_counts_salmon

growth_protocol: HoxA9 immortalized myeloid cells were generated as previously described from ficoll depleted bone marrow isolated from adult mice (16). Cell lines were generated from at least two independent animals of the following genotypes Rosa26-CreERT2 Adar1fl/+, Rosa26-CreERT2 Adar1fl/E861A.

extract_protocol:
RNA was isolated from HoxA9 immortalized myeloid cells  (n=2 per genotype) at 0,2,4,7 days post tamoxifen treatment. RNA was ribosome depleted.
Post ribosome-depleted RNA was purified and subjected to indexing and library preparation using the Kapa Stranded RNA-seq Library Preparation Kit (Kapa Biosystems) and sequenced using the Illumina platform with 150-bp paired-end reads by Novogene (Novogene, Singapore) as previously described (43).

tag: strain background

value: adar1 WT

value: GMCSF

tag: rep


title: RNA-seq of mouse retina: P23H-1m-2


title: GMCSF ADAR1 E861A/E861A sgGgnbp2 rep 1

description:
GMCSF ADAR1 E861A/E861A sgGgnbp2 rep 1
Sequenced at 150bp PE reads on the Illumina platform by Novogene (Singapore).


title: GMCSF ADAR1 E861A/E861A sgGgnbp2 rep 2

description:
GMCSF ADAR1 E861A/E861A sgGgnbp2 rep 2
Sequenced at 150bp PE reads on the Illumina platform by Novogene (Singapore).


title: GMCSF ADAR1 +/ EV rep 3

description:
GMCSF ADAR1 +/ EV rep 3
Sequenced at 150bp PE reads on the Illumina platform by Novogene (Singapore).

value: EV


title: GMCSF ADAR1 +/ EV rep 2

description:
GMCSF ADAR1 +/ EV rep 2
Sequenced at 150bp PE reads on the Illumina platform by Novogene (Singapore).


title: GMCSF Day 7 Control rep 2

description: GMCSF Day 7 Control rep 2

data_processing:
Sequenced reads (150 bp) were trimmed for adaptor sequence and low-quality reads using fastp (v 0.19.5) (44). Parameters: --trim_front1 10 --trim_front2 10. Reads mapping to rRNA were removed using Bbmap (parameters: bbsplit.sh minratio= 0.56 minhits = 1 maxindel = 16000) [BBMap – Bushnell B. – sourceforge.net/projects/bbmap/].
Trimmed and filtered reads were quantified using Salmon (v1.4.0) against gencode release M22. Gene level quantification was calculated in R using tximeta, with gene level summary using summarizeToGene with lengthScaledTPM.  Genes and transcripts were annotated in R using biomaRt (jul2019.archive.ensembl.org -  mm10.M22.ensembl97).
Differential expression was assessed using voom with sample weighting {Law, 2014}.
Assembly: Genes with counts >= 10 and cpm > 1.0 in at least 3 samples were kept for further analysis.
Supplementary files format and content: csv file with gene level counts.

source_name: GMCSF Day 7 Control rep 2

tag: adar1 genotype

value: fl/+

tag: day


title: GMCSF ADAR1 +/ EV rep 1

description:
GMCSF ADAR1 +/ EV rep 1
Sequenced at 150bp PE reads on the Illumina platform by Novogene (Singapore).

tag: treatment


title: GMCSF Day 7 Control rep 1

description: GMCSF Day 7 Control rep 1

source_name: GMCSF Day 7 Control rep 1


title: GMCSF Day 2 Control rep 2

description: GMCSF Day 2 Control rep 2

source_name: GMCSF Day 2 Control rep 2


title: GMCSF Day 2 Control rep 1

description: GMCSF Day 2 Control rep 1

source_name: GMCSF Day 2 Control rep 1


title: GMCSF Day 0 Control rep 2

description: GMCSF Day 0 Control rep 2

source_name: GMCSF Day 0 Control rep 2


title: GMCSF Day 4 Control rep 2

description: GMCSF Day 4 Control rep 2

source_name: GMCSF Day 4 Control rep 2


title: GMCSF Day 4 ADAR E861A/E861A rep 2

description: GMCSF Day 4 ADAR E861A/E861A rep 2

source_name: GMCSF Day 4 ADAR E861A/E861A rep 2


title: RNA-seq of mouse retina: P23H-6m-2


title: GMCSF Day 7 ADAR E861A/E861A rep 2

description: GMCSF Day 7 ADAR E861A/E861A rep 2

source_name: GMCSF Day 7 ADAR E861A/E861A rep 2


title: GMCSF Day 4 ADAR E861A/E861A rep 1

description: GMCSF Day 4 ADAR E861A/E861A rep 1

source_name: GMCSF Day 4 ADAR E861A/E861A rep 1


title: GMCSF Day 0 ADAR E861A/E861A rep 2

description: GMCSF Day 0 ADAR E861A/E861A rep 2

source_name: GMCSF Day 0 ADAR E861A/E861A rep 2


title: GMCSF Day 2 ADAR E861A/E861A rep 1

description: GMCSF Day 2 ADAR E861A/E861A rep 1

source_name: GMCSF Day 2 ADAR E861A/E861A rep 1


title: GMCSF Day 7 ADAR E861A/E861A rep 1

description: GMCSF Day 7 ADAR E861A/E861A rep 1

source_name: GMCSF Day 7 ADAR E861A/E861A rep 1


title: GMCSF Day 2 ADAR E861A/E861A rep 2

description: GMCSF Day 2 ADAR E861A/E861A rep 2

source_name: GMCSF Day 2 ADAR E861A/E861A rep 2


title: GMCSF Day 0 ADAR E861A/E861A rep 1

description: GMCSF Day 0 ADAR E861A/E861A rep 1

source_name: GMCSF Day 0 ADAR E861A/E861A rep 1


title: sgGgnbp2_total_d3_rep3_CW_15

description: sgGgnbp2 frac: total d3 r3

data_processing:
Some samples had multiple fq files, these were concattenated to form single files. (CW17, CW18, CW35,CW53).
Sequenced reads (150 bp) were trimmed for adaptor sequence and low-quality reads using fastp (v 0.19.5) (44). Parameters: --trim_front1 10 --trim_front2 10. Reads mapping to rRNA were removed using Bbmap (parameters: bbsplit.sh minratio= 0.56 minhits = 1 maxindel = 16000) [BBMap – Bushnell B. – sourceforge.net/projects/bbmap/].
Trimmed and filtered reads were quantified using Salmon (v1.4.0) against gencode release M22. Gene level quantification was calculated in R using tximeta, with gene level summary using summarizeToGene with lengthScaledTPM.  Genes and transcripts were annotated in R using biomaRt (jul2019.archive.ensembl.org -  mm10.M22.ensembl97).
Differential expression was assessed using voom with sample weighting {Law, 2014}.
Genes with counts >= 10 and cpm > 1.0 in at least 3 samples were kept for further analysis.
Assembly: mm10
Supplementary files format and content: csv file with gene level counts.

source_name: GMCSF

growth_protocol: Fractionation was performed on three independent validated clones of sgControl, sgIfih1 and sgGgnbp2 Rosa26-CreERT2 Adar1fl/E861A immortalised myeloid cells. 12x 106 myeloid cells (either 1 day or 3 days in 200nM tamoxifen as described above) were treated with AEBSF (0.5mM) for 30 minutes in culture media to inhibit proteases prior to lysis.

extract_protocol:
2x106 cells were taken for total RNA extraction as previously described using Bioline RNA isolation kit. Remaining 10x106 cells were used for fractionation using the NE-PER kit (Thermo) following the manufacturer’s instructions with modifications for RNA extraction as follows. Briefly, cells were washed 2 x with PBS which was thoroughly removed on the second wash and the pellets were fractionated following instructions with 5 x protease, 1x phosphatase and 1 unit/100uL RNase inhibitor added to CERI and NER buffers. Prior to nuclear extraction, the nuclear pellet was gently washed 2 x with cold PBS to limit cross-over of cytoplasmic fraction. Fractions were prepared for RNA extraction. Liquid extraction protocol was followed from Bioline RNA isolation kit using 600uL of RLY buffer and 6uL of DTT for both the cytoplasmic and nuclear fractions.
For fractionation experiment, libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina due to a lack of availability of the Kapa kit (NEB #E7760, E7765).

value: ADAR/fl

tag: fraction

value: total

tag: replicate


title: RNA-seq of mouse retina: P23H-1m-3

source_name: retina


title: sgGgnbp2_cyto_d3_rep3_CW_51

description: sgGgnbp2 frac: cytoplasmic d3 r3

value: cytoplasmic


title: RNA-seq of mouse retina: P23H-1m-1


title: sgGgnbp2_total_d3_rep2_CW_14

description: sgGgnbp2 frac: total d3 r2


title: sgGgnbp2_nuclear_d3_rep2_CW_32

description: sgGgnbp2 frac: nuclear d3 r2

value: nuclear


title: sgGgnbp2_total_d3_rep1_CW_13

description: sgGgnbp2 frac: total d3 r1


title: sgGgnbp2_cyto_d3_rep1_CW_49

description: sgGgnbp2 frac: cytoplasmic d3 r1


title: sgGgnbp2_nuclear_d3_rep3_CW_33

description: sgGgnbp2 frac: nuclear d3 r3


title: sgGgnbp2_nuclear_d3_rep1_CW_31

description: sgGgnbp2 frac: nuclear d3 r1


title: sgGgnbp2_nuclear_d1_rep3_CW_24

description: sgGgnbp2 frac: nuclear d1 r3


title: GMCSF Day 4 Control rep 1

description: GMCSF Day 4 Control rep 1

source_name: GMCSF Day 4 Control rep 1


title: sgGgnbp2_cyto_d1_rep3_CW_42

description: sgGgnbp2 frac: cytoplasmic d1 r3


title: sgGgnbp2_total_d1_rep2_CW_5

description: sgGgnbp2 frac: total d1 r2


title: GMCSF Day 0 Control rep 1

description: GMCSF Day 0 Control rep 1

source_name: GMCSF Day 0 Control rep 1


title: sgGgnbp2_total_d1_rep3_CW_6

description: sgGgnbp2 frac: total d1 r3


title: sgGgnbp2_nuclear_d1_rep2_CW_23

description: sgGgnbp2 frac: nuclear d1 r2


title: sgGgnbp2_cyto_d1_rep2_CW_41

description: sgGgnbp2 frac: cytoplasmic d1 r2


title: sgGgnbp2_total_d1_rep1_CW_4

description: sgGgnbp2 frac: total d1 r1


title: sgGgnbp2_cyto_d1_rep1_CW_40

description: sgGgnbp2 frac: cytoplasmic d1 r1


title: sgMDA5_total_d3_rep3_CW_18

description: sgMDA5 frac: total d3 r3


title: sgGgnbp2_nuclear_d1_rep1_CW_22

description: sgGgnbp2 frac: nuclear d1 r1


title: sgMDA5_cyto_d3_rep3_CW_54

description: sgMDA5 frac: cytoplasmic d3 r3


title: sgMDA5_nuclear_d3_rep3_CW_36

description: sgMDA5 frac: nuclear d3 r3


title: sgMDA5_cyto_d3_rep2_CW_53

description: sgMDA5 frac: cytoplasmic d3 r2


title: sgMDA5_nuclear_d3_rep2_CW_35

description: sgMDA5 frac: nuclear d3 r2


title: sgMDA5_total_d3_rep2_CW_17

description: sgMDA5 frac: total d3 r2


title: sgMDA5_total_d3_rep1_CW_16

description: sgMDA5 frac: total d3 r1


title: sgMDA5_nuclear_d3_rep1_CW_34

description: sgMDA5 frac: nuclear d3 r1


title: sgMDA5_cyto_d3_rep1_CW_52

description: sgMDA5 frac: cytoplasmic d3 r1


title: sgGgnbp2_cyto_d3_rep2_CW_50

description: sgGgnbp2 frac: cytoplasmic d3 r2


title: sgMDA5_total_d1_rep3_CW_9

description: sgMDA5 frac: total d1 r3


title: sgMDA5_cyto_d1_rep3_CW_45

description: sgMDA5 frac: cytoplasmic d1 r3


title: sgMDA5_nuclear_d1_rep3_CW_27

description: sgMDA5 frac: nuclear d1 r3


title: sgMDA5_total_d1_rep2_CW_8

description: sgMDA5 frac: total d1 r2


title: sgMDA5_total_d1_rep1_CW_7

description: sgMDA5 frac: total d1 r1


title: sgMDA5_cyto_d1_rep1_CW_43

description: sgMDA5 frac: cytoplasmic d1 r1


title: sgMDA5_cyto_d1_rep2_CW_44

description: sgMDA5 frac: cytoplasmic d1 r2


title: sgMDA5_nuclear_d1_rep1_CW_25

description: sgMDA5 frac: nuclear d1 r1


title: sgCTRL_total_d3_rep3_CW_12

description: sgCTRL frac: total d3 r3

value: sgCTRL


title: sgCTRL_nuclear_d3_rep3_CW_30

description: sgCTRL frac: nuclear d3 r3


title: sgCTRL_cyto_d3_rep3_CW_48

description: sgCTRL frac: cytoplasmic d3 r3


title: sgCTRL_cyto_d3_rep2_CW_47

description: sgCTRL frac: cytoplasmic d3 r2


title: sgCTRL_nuclear_d3_rep2_CW_29

description: sgCTRL frac: nuclear d3 r2


title: sgCTRL_total_d3_rep1_CW_10

description: sgCTRL frac: total d3 r1


title: sgCTRL_total_d3_rep2_CW_11

description: sgCTRL frac: total d3 r2


title: sgCTRL_total_d1_rep3_CW_3

description: sgCTRL frac: total d1 r3


title: sgCTRL_nuclear_d3_rep1_CW_28

description: sgCTRL frac: nuclear d3 r1


title: sgCTRL_cyto_d1_rep3_CW_39

description: sgCTRL frac: cytoplasmic d1 r3


title: sgCTRL_cyto_d3_rep1_CW_46

description: sgCTRL frac: cytoplasmic d3 r1


title: sgCTRL_nuclear_d1_rep3_CW_21

description: sgCTRL frac: nuclear d1 r3


title: sgCTRL_total_d1_rep2_CW_2

description: sgCTRL frac: total d1 r2


title: sgCTRL_cyto_d1_rep1_CW_37

description: sgCTRL frac: cytoplasmic d1 r1


title: sgCTRL_nuclear_d1_rep2_CW_20

description: sgCTRL frac: nuclear d1 r2


title: sgCTRL_nuclear_d1_rep1_CW_19

description: sgCTRL frac: nuclear d1 r1


title: ADAR1 E861A/E861A sgIfih1 rep3

description: ADAR1 E861A/E861A sgIfih1 rep3

extract_protocol:
RNA was isolated from HoxA9 immortalized myeloid cells  (n=4 per genotype). RNA was ribosome depleted.
Post ribosome-depleted RNA was purified and subjected to indexing and library preparation using the Kapa Stranded RNA-seq Library Preparation Kit (Kapa Biosystems) and sequenced using the Illumina platform with 150-bp paired-end reads by Novogene (Novogene, Singapore) as previously described (43).
Sequenced at 150bp PE reads on the Illumina platform by Novogene (Singapore).

tag: sg


title: sgCTRL_total_d1_rep1_CW_1

description: sgCTRL frac: total d1 r1


title: sgMDA5_nuclear_d1_rep2_CW_26

description: sgMDA5 frac: nuclear d1 r2


title: ADAR1 E861A/E861A sgIfih1 rep4

description: ADAR1 E861A/E861A sgIfih1 rep4


title: ADAR1 E861A/E861A sgIfih1 rep2

description: ADAR1 E861A/E861A sgIfih1 rep2


title: ADAR1 E861A/E861A sgGgnbp2 rep3

description: ADAR1 E861A/E861A sgGgnbp2 rep3


title: ADAR1 E861A/E861A sgIfih1 rep1

description: ADAR1 E861A/E861A sgIfih1 rep1


title: ADAR1 E861A/E861A sgGgnbp2 rep2

description: ADAR1 E861A/E861A sgGgnbp2 rep2


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 E861A/E861A Day 7 rep 2 (165, S11)
165fl-E861ADay7Screen2_S11
E861A_D7_R2

data_processing:
Raw reads were mapped to sgRNA using CRISPRBetaBinomial package (CB2) (v 1.3.0).
Filtering step to remove sgRNA with less than 30 reads (filt.min30.n78837), CRISPR screen analysis was performed using MaGeCK (v5.9.3), with  replicates combined (ADAR.MLE.WT.only.filt30.gene_summary.txt , ADAR.MLE.E861A.only.filt30.gene_summary.txt)
For individual replicates, no filter was used and CRISPR screen analysis was performed using MaGeCK (v5.9.3), with  replicates combined ADAR.WT_R1.MLE.gene_summary.txt, ADAR.WT_R2.MLE.gene_summary.txt, ADAR.E861A_R1.MLE.gene_summary.txt, ADAR.E861A_R2.MLE.gene_summary.txt)
Assembly: mm10
Supplementary files format and content: CB2.count.txt CB2 raw counts
Library strategy: CRISPR screen

source_name: Hoxb8 imortalised GM-CSF cell line

extract_protocol:
Sequencing libraries were generated based on the PCR amplification of the integrated sgRNA constructs containing a barcode sequence for Illumina sequencing (protocol from Broad Institute; https://portals.broadinstitute.org/gpp/public/resources/protocols). Three time points (Day 0 (day of tamoxifen addition), 7, and 14) of the two cell lines (fl/+ and fl/E861A) were selected. To utilise the full amount of gDNA recovered from each 20 million-cell pellet, between 18 and 28 PCR reactions were performed. Each 100mL PCR reaction contained 10mg of gDNA, 10mL 10x ExTaq reaction buffer, 8mL 2.5 mM dNTP mixture, 0.75mL ExTaq polymerase, 0.5mL P5 primer mix (100mM), and, for each of the six samples, 10mL of a unique P7 index primer (5mM) in nuclease-free water. The PCR products were pooled together, and 5mL of each sample was loaded in a 3% agarose gel and run for 45 minutes at 120 V to  confirm the size of the band and check for the presence of contamination or degradation products. Pooled PCR products were then purified using AMPure XP magnetic beads to remove gDNA and PCR contaminants. In brief, 100mL of pooled PCR was mixed with 100mL of magnetic beads and incubated at room temperature for 5 minutes. Next, the tubes were placed on a magnetic plate for 5 minutes and the supernatant discarded. The beads were washed twice with 70% ethanol and the DNA eluted in 50 mL TE buffer. The purified pooled library was then quantified with Nanodrop spectrophotometer system, and 2mL of product was mixed with 2mL of nuclease-free water and 1.25mL of loading buffer and run on a 3% agarose gel for a final quality check. Finally, 50mL of the purified pooled library containing at least 3ng/mL of DNA was sent for sequencing by Illumina SE150 sequencing at Novogene (Singapore)
In total, 12 libraries were generated and sequenced on the Illumina platform using 150bp single end reads by Novogene (China).

tag: strain


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 E861A/E861A Day 14 rep 2 (165, S12)
165fl-E861ADay14Screen2_S12
E861A_D14_R2


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 E861A/E861A Day 7 rep 1 (165, S5)
165fl-E861ADay7Screen1_S5
E861A_D7_R1


title: ADAR1 E861A/E861A sgGgnbp2 rep1

description: ADAR1 E861A/E861A sgGgnbp2 rep1


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 E861A/E861A Day 0 rep 2 (165, S10)
165fl-E861ADay0Screen2_S10
E861A_D0_R2


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 E861A/E861A Day 14 rep 1 (165, S6)
165fl-E861ADay14Screen1_S6
E861A_D14_R1


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 fl/+ Day 7 rep 1 (167, S2)
167fl-POSDay7Screen1_S2
WT_D7_R1

value: WT


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 E861A/E861A Day 0 rep 1 (165, S4)
165fl-E861ADay0Screen1_S4
E861A_D0_R1


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 fl/+ Day 14 rep 2 (167, S9)
167fl-POSDay14Screen2_S9
WT_D14_R2


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 fl/+ Day 7 rep 2 (167, S8)
167fl-POSDay7Screen2_S8
WT_D7_R2


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 fl/+ Day 14 rep 1 (167, S3)
167fl-POSDay14Screen1_S3
WT_D14_R1


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 fl/+ Day 0 rep 2 (167, S3)
167fl-POSDay0Screen2_S7
WT_D0_R2


title: sgCTRL_cyto_d1_rep2_CW_38

description: sgCTRL frac: cytoplasmic d1 r2


description:
CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Adar1 fl/+ Day 0 rep 1 (167, S1)
167fl-POSDay0Screen1_S1
WT_D0_R1


title: mouse_3mth_FMC_ON2

status: Public on Oct 23 2024

city: Saint Louis

first: David

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

description:
F/M
10x Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
genome build: mm10-2020-A for mus musculus , GRCh38-2020-A for homo sapiens
single cell data were processed using Partek® Flow® (Version 10.0) https://www.partek.com/partek-flow/. Gene expression and TCR V(D)J data were overlaid by R scRepertoire package.
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by CPM (counts per million) normalization. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat3 integration method to produce batch-corrected data. PCA analysis followed by graph-based clustering using Louvain algorithm, and t-SNE/ UMAP generation employing Euclidean distance, were conducted on the first 20 principal components of the integrated expression data. Differential analyses were performed using gene specific analysis (GSA). Pathway analyses were performed using DAVID Bioinformatics platform.
Assembly: mm10-2020-A for mus musculus, GRCh38-2020-A for homo sapines
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: optic nerve

extract_protocol:
De-identified human PA samples (4 female sporadic PAs and 1 female NF1-PA; clinical information in Supplemental Table 3) were obtained under an approved Human Studies Protocol as dissociated frozen tumor single cells from the St. Louis Children’s Hospital Pediatric Tumor Bank. The frozen dissociated tumor single cells were thawed and resuspended in DMEM.The cells were then stained with 7-Aminoactinomycin D (7-AAD) (Fisher Scientific, A1310) for sorting using the MoFlo (Siteman Flow Cytometry Core at the Washington University in St Louis). Live cells were collected and submitted for single cell RNA sequencing (scRNA-seq).  Nf1-OPG optic nerves and meningeal duras were collected separately from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo. Live cells were collected and sent for scRNA sequencing with TCR V(D)J enrichment.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: optic nerve

value: 12 weeks

tag: Sex

value: mixed

tag: genotype


title: mouse_3mth_FMC_ON

description:
F/M
10x Genomics

tag: tissue


title: ApcKO_ISC

status: Public on Nov 15 2024

first: Ramesh

middle: A.

last: Shivdasani

address: 450 Brookline Ave. SM1060

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Bismark version 0.13.1 was used to align the data and generate Bedgraph files for visualization.
Assembly: mm10
Supplementary files format and content: The processed data is a Bedgraph file containing individual CpG methylation status.

source_name: Small intestine

extract_protocol:
Epithelium was isolated from the duodenum of adult mice using a 5mM EDTA chelation for 30 minutes at 4°C followed by disaggregation with 4x TrypLE Select for 30 minutes at 37°C. ISCs were isolated via flow cytometry. Cellular DNA was isolated and used for WGBS. The genomic DNA was extracted using the MasterPure DNA Purification kit (Epicenter MCD85201).
The WGBS libraries were prepared using the EpiGenome Methyl-Seq kit (Epicenter EGMK81312).

treatment_protocol: Treated with 5x 1mg Tamoxifen and primary duodenum ISCs were isolated 14dpi.

value: Small intestine

tag: cell type

value: Duodenum intestinal stem cell

value: Adult

value: 5x 1mg Tamoxifen

tag: time point

value: 14 dpi


title: mm202C-sgLuc_ChIP_H3K27me3_dTAG_500nM_24h_REP1_221026_ACAGTG_S5

status: Public on Sep 16 2024

first: Scott

last: Armstrong

address: 450 Brookline Ave

department: pediatric oncology

description: mouse leukemia

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the mouse (Gencode M24/mm10) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and ngs.plot (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
TSS- and other interval-associated signals were assessed using bedtools coverage (v2.28.0).
Assembly: Gencode M24/mm10
Supplementary files format and content: Broad TDF format for visualization in Integrated Genome Viewer

source_name: mouse leukemia

growth_protocol: IMDM with 20% FBS, 1% penicillin/streptomycin (Gibco), 6 mg/mL mIL3, 10 mg/mL mIL6, and 10 mg/mL mSCF (Stemcell Technologies) at 37°C and 5% CO2.

extract_protocol:
Cells were crosslinked using 1% methanol-free paraformaldehyde for 10 min at room temperature. Glycine (25 mM) was used to quench the reaction. Nuclei were extracted and chromatin was subjected to sonication using an E220 focused ultrasonicator (Covaris).
1-10 ng of DNA was used in preparation of Illumina-compatible libraries using a ThruPLEX DNA-Seq Kit (Takara) followed by sequencing using NextSeq550 (Illumina) to obtain 20-30e6 unique sequencing paired-end reads.

treatment_protocol: Cells were treated with 500 nM dTAG-13 or DMSO for 24 hours.

value: mouse leukemia

value: 500nM dTAG13

tag: timepoint

value: 24 hours

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog_number

tag: genetic background


title: DKC1 CLIP-seq rep3

status: Public on Oct 18 2024

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

description: Discover the pseudouridylation of the mammalian transcriptome

data_processing:
Raw data gained from Illumina HiSeqX10 with 150 bp paired end reads
Cutadapt (v2.8) was used to remove the adaptors of the paired-end reads with the following parameters: -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 15 -e 0.15. The paired-end reads without adaptors were further merged using FLASH software (v1.2.11) with following parameters: -z -m 10 -M 135 -x 0.25, and fastx_collapser software was used to collapse the reads with the default parameters. These filtered reads were subsequently mapped to the human reference genome (hg38) and transcriptome with STAR software with the following parameters: --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 30 --outFilterMismatchNmax 15 --outFilterMismatchNoverLmax 0.1  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --alignEndsProtrude 150 ConcordantPair --limitOutSJcollapsed 5000000 --readFilesCommand zcat.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using self-developed software; Scores represent Reads per million mapped reads (rpm).

source_name: HCT116-flag-DKC1 cells

growth_protocol: HCT116-flag-DKC1 cells were clutured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 95% air and 5% CO2.

extract_protocol:
RNA from the target regions (70-150 kD) was released from the membrane by digestion with proteinase K and recovered by phenol-chloroform extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells stably expressing DKC1-FLAG were plated on 15-cm plates and collected at approximately 70% confluence after 3 days. After washed by 5 ml of cold DPBS, the cells were crosslinked on ice with UV-C (254 nm) at 0.4 J/cm2 and transferred into 15 ml tubes by scraping with another 5ml of cold fresh DPBS.

tag: cell line


title: mm202C-sgLuc_ChIP_input_dTAG_500nM_24h_REP1_221026_GTGAAA_S14

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27me3_DMSO_24h_REP1_221026_CGATGT_S2

description: mouse leukemia

value: DMSO


title: mm202C-sgLuc_ChIP_input_DMSO_24h_REP1_221026_AGTCAA_S13

description: mouse leukemia


title: DKC1 CLIP-seq rep1


title: mm202C-sgLuc_ChIP_H3K27ac_dTAG_500nM_24h_REP1_221026_TGACCA_S4

description: mouse leukemia

value: Diagenode


title: mm202C-sgLuc_ChIP_H2aK119ub_dTAG_500nM_24h_REP1_221026_GCCAAT_S6

description: mouse leukemia

value: CST


title: mm202C-sgPcgf1_RNA_4-4_steadystate_REP3_240627_GTGGCC_S18

description: mm202C_sgPcgf1_4-4_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the mouse (Gencode M24/mm10) reference genome using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Assembly: Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Supplementary files format and content: M24/mm10
Supplementary files format and content: DESeq2 differential expression summary data (Excel .xlsx format)

source_name: leukemia cells

extract_protocol:
For RNA isolation from cell lines, 1x10^6 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions for cell line experiments.
1 ug RNA was used as the input quantity for library construction. Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).

value: leukemia cells

value: untreated

tag: guide rna


title: mm202C-sgPcgf1_RNA_4-4_steadystate_REP1_240627_GTCCGC_S16

tag: treatment


title: mm202C-sgLuc_RNA_steadystate_REP3_240522_GTGGCC_S12

description:
mm202C_sgBcorl1_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv
mm202C_sgBcor_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv
mm202C_sgKdm2b_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv
mm202C_sgPcgf1_4-4_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv

value: sgLuciferase


title: mm202C-sgLuc_ChIP_H2aK119ub_DMSO_24h_REP1_221026_TTAGGC_S3

description: mouse leukemia


title: mm202C-sgLuc_RNA_steadystate_REP2_240522_GTGAAA_S11


title: mm202C-sgLuc_ChIP_H3K27ac_DMSO_24h_REP1_221026_ATCACG_S1

description: mouse leukemia


title: mm202C-sgLuc_RNA_steadystate_REP1_240522_GTCCGC_S10


title: mm202C-sgKdm2b_RNA_steadystate_REP2_240522_CCGTCC_S8

description: mm202C_sgKdm2b_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv


title: mm202C-sgBcor_RNA_steadystate_REP1_240522_GATCAG_S1

description: mm202C_sgBcor_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv

value: sgBcor


title: mm202C-sgKdm2b_RNA_steadystate_REP3_240522_GTAGAG_S9


title: mm202C-sgKdm2b_RNA_steadystate_REP1_240522_ATGTCA_S7


title: mm202C-sgBcor_RNA_steadystate_REP3_240522_GGCTAC_S3


title: DKC1 CLIP-seq rep2


title: mm202C-sgBcorl1_RNA_steadystate_REP2_240522_AGTCAA_S5

description: mm202C_sgBcorl1_vs_mm202C_sgLuc_diffexp_sorted_rmdup.csv


title: mm202C-sgBcorl1_RNA_steadystate_REP1_240522_CTTGTA_S4


title: mm202C-sgLuc_ChIP_MLL1_dTAG_500nM_24h_REP1_221027_CTTGTA_S9

description: mouse leukemia

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the mouse (Gencode M24/mm10) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
TSS- and other interval-associated signals were assessed using bedtools coverage (v2.28.0).
Assembly: Gencode M24/mm10
Supplementary files format and content: Genome-wide signal pileup files for visualization in IGV in TDF format
Supplementary files format and content: Bedrools coverage output for signal at TSS-associated intervals (-1kb to +3kb for each annotated protein-coding transcription start site), summarixed in Excel spreadsheet format

value: Bethyl


title: mm202C-sgLuc_ChIP_RNAPol2_pS2_DMSO_96h_REP1_240304_ACAGTG_S3

description: mouse leukemia

value: 96 hours

value: RNA Pol2_pSer2


title: mm202C-sgLuc_ChIP_input_DMSO_24h_REP1_221027_ATTCCT S21

description: mouse leukemia


title: mm202C-sgLuc_ChIP_MLL1_DMSO_24h_REP1_221027_CAGATC_S4

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_DMSO_96h_REP1_240304_GTGGCC_S19

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_dTAG_500nM_96h_REP1_240304_GTTTCG_S20

description: mouse leukemia


title: mm202C_ChIP_RNAPol2_pS2_dTAG_500nM_1h_REP1_240522_TTAGGC_S1

description: mouse leukemia

value: 1 hour


title: mm202C-sgPcgf1_RNA_4-4_steadystate_REP2_240627_GTGAAA_S17


title: mm202C_ChIP_MLL1_dTAG_500nM_1h_REP1_240523_ACAGTG_S3

description: mouse leukemia


title: mm202C_ChIP_RNAPol2_pS2_DMSO_4h_REP1_240612_TTAGGC_S3

description: mouse leukemia

value: 4 hours


title: mm202C_ChIP_RNAPol2_dTAG_500nM_1h_REP1_240522_TGACCA_S2

description: mouse leukemia

value: RNA Pol2


title: mm202C_ChIP_MLL1_DMSO_48h_REP1_240523_ACTGAT_S11

description: mouse leukemia

value: 48 hours


title: mm202C_ChIP_RNAPol2_DMSO_48h_REP1_240523_TGACCA_S10

description: mouse leukemia


title: mm202C_ChIP_input_VTP_2uM_96h_REP1_210629_ACTTGA_S8

description: mouse leukemia


title: mm202C-sgBcorl1_RNA_steadystate_REP3_240522_AGTTCC_S6


title: mm202C_ChIP_input_dTAG_500nM_1h_REP1_240523_GTTTCG_S16

description: mouse leukemia

value: 500nM dTAG13


title: mm202C_ChIP_MLL1_dTAG_500nM_16h_REP1_240612_CTTGTA_S12

description: mouse leukemia

value: 16 hours


title: mm202C_ChIP_input_DMSO_4h_REP1_240612_AGTCAA_S13

description: mouse leukemia


title: mm202C_ChIP_MLL1_DMSO_4h_REP1_240612_TGACCA_S4

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_dTAG_500nM_24h_REP1_221027_ATCACG S22

description: mouse leukemia

value: 24 hours


title: mm202C_ChIP_H3K79me2_dTAG_500nM_96h_REP1_240522_ATTCCT_S5

description: mouse leukemia

value: Abcam


title: mm202C_ChIP_H3K79me2_dTAG_500nM_48h_REP1_240523_CAGATC_S4

description: mouse leukemia


title: mm202C_ChIP_RNAPol2_pS2_dTAG_500nM_16h_REP1_240612_GGCTAC_S11

description: mouse leukemia


title: mm202C_ChIP_H3K79me2_dTAG_4h_REP1_240509_CGATGT_S2

description: mouse leukemia


title: mm202C_ChIP_input_dTAG_500nM_48h_REP1_240523_CGTACG_S17

description: mouse leukemia


title: mm202C_ChIP_input_dTAG_500nM_16h_REP1_240612_ATGTCA_S15

description: mouse leukemia


title: mm202C_ChIP_MLL1_dTAG_500nM_48h_REP1_240523_TAGCTT_S6

description: mouse leukemia


title: mm202C-sgBcor_RNA_steadystate_REP2_240522_TAGCTT_S2


title: mm202C_ChIP_H3K79me2_dTAG_16h_REP1_240509_CTTGTA_S8

description: mouse leukemia


title: mm202C_ChIP_H3K4me3_VTP_2uM_96h_REP1_210629_TGACCA_S4

description: mouse leukemia


title: mm202C_ChIP_input_dTAG_24h_REP1_240509_GATCAG_S17

description: mouse leukemia


title: mm202C_ChIP_H3K79me2_DMSO_48h_REP1_240523_CTTGTA_S8

description: mouse leukemia

value: DMSO


title: mm202C_ChIP_H3K79me2_dTAG_24h_REP1_240509_ATTCCT_S11

description: mouse leukemia


title: mm202C_ChIP_input_DMSO_96h_REP1_210629_CAGATC_S7

description: mouse leukemia


title: mm202C_ChIP_H3K27ac_dTAG_4h_REP1_240509_ATCACG_S1

description: mouse leukemia

value: Diagenode


title: mm202C_ChIP_H3K27ac_dTAG_500nM_1h_REP1_240523_ATCACG_S1

description: mouse leukemia

value: leukemia cells


title: mm202C_ChIP_H3K27ac_dTAG_16h_REP1_240509_GGCTAC_S7

description: mouse leukemia


title: mm202C_ChIP_input_DMSO_48h_REP1_240523_GAGTGG_S18

description: mouse leukemia


title: mm202C_ChIP_EP300_dTAG_500nM_16h_REP1_240612_TAGCTT_S10

description: mouse leukemia

value: LifeTech


title: mm202C_ChIP_H3K79me2_dTAG_500nM_1h_REP1_240523_CGATGT_S2

description: mouse leukemia


title: mm202C_ChIP_CBP_DMSO_4h_REP1_240612_ATCACG_S1

description: mouse leukemia

value: Cbp


title: mm202C_ChIP_EP300_DMSO_4h_REP1_240612_CGATGT_S2

description: mouse leukemia


title: mm202C_ChIP_input_dTAG_500nM_48h_REP1_240522_CGTACG_S6

description: mouse leukemia


title: mm202C_ChIP_H3K27ac_dTAG_24h_REP1_240509_CCGTCC_S10

description: mouse leukemia


title: mm202C_ChIP_input_dTAG_4h_REP1_240509_TGACCA_S16

description: mouse leukemia


title: mm202C_ChIP_H3K4me3_DMSO_96h_REP1_210629_TTAGGC_S3

description: mouse leukemia


title: mm202C-H9C_SLAM_DMSO_4h_REP1_2020R1x2_GCCACA_S7

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
SLAMseq FASTQ files were analyzed using the Slamdunk pipeline, described elsewhere.
Differential SLAMseq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using Slamdunk converted counts.
Assembly: Gencode M24/mm10
Supplementary files format and content: DESeq2 differential gene expression summary and per-gene expression count (in regularized log scale) using Slamdunk pipeline output (comma-separated value .csv format)
Library strategy: SLAM-seq

molecule: nuclear RNA

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions (Qiagen).
The QuantSeq 3’ mRNA-Seq Library Preparation kit (Lexogen) was used to prepare SLAM-seq libraries and. Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina) and approximately 25 million 75 base-pair, single-end reads per sample.

treatment_protocol: SLAM-seq was performed using the Lexogen SLAM-Seq Metabolic Labeling kit (Lexogen). NUP98-r leukemia cells were plated at 5e5 cells/mL in the appropriate culture medium and were pre-treated either with 0.1% DMSO or with dTAG-13 (500nM) for 1 hour. Subsequently, nascent transcripts were labeled by adding 4SU (Lexogen) at a final concentration of 100mM to the culture media for 3 hours. The same concentration of dTAG was maintained in the culture media such that the total time for protein degradation was 4 hours.

tag: genomic background


title: mm202A-J1AC_SLAM_dTAG13_500nM_4h_REP3_2020R1x2_CTCATA_S12


title: mm202C-H9C_SLAM_dTAG13_500nM_4h_REP3_2020R1x2_GACATC_S12


title: mm202C-H9C_SLAM_DMSO_4h_REP2_2020R1x2_ATTGGT_S8


title: mm202A-J1AC_SLAM_dTAG13_500nM_4h_REP1_2020R1x2_GGCCAA_S10


title: mm202A-J1AC_SLAM_DMSO_4h_REP3_2020R1x2_AGACCA_S9


title: mm202A-J1AC_SLAM_DMSO_4h_REP2_2020R1x2_CGCGGA_S8


title: mm202C-H9C_SLAM_dTAG13_500nM_4h_REP1_2020R1x2_CGTCGC_S10


title: mm202C-H9C_SLAM_dTAG13_500nM_4h_REP2_2020R1x2_CGATCT_S11


title: mm202C-H9C_SLAM_DMSO_4h_REP3_200928_ATGGCG_S9


title: mm202A-J1AC_SLAM_dTAG13_500nM_4h_REP2_2020R1x2_CCGACC_S11


title: mm202C-sgPCGF1_ChIP_MLL1_VTP_2uM_96h_REP1_221114_CGTACG_S20

description: mouse leukemia

value: 4 days


title: mm202C_ChIP_CBP_dTAG_500nM_16h_REP1_240612_GATCAG_S9

description: mouse leukemia


title: mm202C_ChIP_H3K27ac_dTAG_500nM_48h_REP1_240522_GCCAAT_S3

description: mouse leukemia


title: mm202A-J1AC_SLAM_DMSO_4h_REP1_2020R1x2_CCTGCT_S7


title: mm202C-sgPCGF1_ChIP_RNF2_VTP_2uM_96h_REP1_221111_ATTCCT_S16

description: mouse leukemia

value: CST


title: mm202C-sgPCGF1_ChIP_RNF2_dTAG13_500nM_96h_REP1_230113_CTTGTA_S12

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_KDM2B_VTP_2uM_96h_REP1_221111_GAGTGG_S14

description: mouse leukemia

value: Millipore


title: mm202C-sgPCGF1_ChIP_MLL1_DMSO_96h_REP1_221114_CCGTCC_S15

description: mouse leukemia

value: Bethyl


title: mm202C-sgPCGF1_ChIP_RNF2_DMSO_96h_REP1_221111_GTTTCG_S12

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_RNF2_DMSO_96h_REP1_230113_GATCAG_S9

description: mouse leukemia


title: mm202C_ChIP_H3K27ac_DMSO_48h_REP1_240523_GGCTAC_S7

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_MLL1_dTAG13_500nM_96h_REP1_230112_GTTTCG_S20

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_KDM2B_DMSO_96h_REP1_230113_ACTTGA_S8

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_input_VTP_2uM_96h_REP1_221111_GCCAAT_S20

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_MLL1_DMSO_96h_REP1_230112_ATGTCA_S15

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_input_dTAG13_500nM_96h_REP1_230113_ATTCCT_S16

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_input_DMSO_96h_REP1_230113_ACTGAT_S15

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_input_DMSO_96h_REP1_230112_ACTGAT_S23

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_input_DMSO_96h_REP1_221111_ACAGTG_S19

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_KDM2B_DMSO_96h_REP1_221111_GTGAAA_S10

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_input_dTAG13_500nM_96h_REP1_230112_ATTCCT_S24

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_HA_VTP_2uM_96h_REP1_221114_GTTTCG_S19

description: mouse leukemia

value: HA


title: mm202C-sgPCGF1_ChIP_input_DMSO_96h_REP1_221114_ACTGAT_S23

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_input_VTP_2uM_96h_REP1_221114_ATTCCT_S24

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_HA_dTAG13_500nM_96h_REP1_230112_GTGGCC_S19

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27me3_VTP_2uM_96h_REP1_221114_GTGAAA_S17

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_HA_DMSO_96h_REP1_221114_ATGTCA_S14

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_KDM2B_dTAG13_500nM_96h_REP1_230113_GGCTAC_S11

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27me3_DMSO_96h_REP1_221114_AGTCAA_S12

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_HA_DMSO_96h_REP1_230112_AGTTCC_S14

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27me3_DMSO_96h_REP1_230112_CTTGTA_S12

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27me3_dTAG13_500nM_96h_REP1_230112_GTCCGC_S17

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27ac_VTP_2uM_96h_REP1_221114_GTCCGC_S16

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27ac_DMSO_96h_REP1_221114_CTTGTA_S11

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H2aK119ub_dTAG13_500nM_96h_REP1_230112_GTGAAA_S18

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27ac_DMSO_96h_REP1_230112_GGCTAC_S11

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H3K27ac_dTAG13_500nM_96h_REP1_230112_CCGTCC_S16

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H2aK119ub_VTP_2uM_96h_REP1_221114_GTGGCC_S18

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_H2aK119ub_DMSO_96h_REP1_221114_AGTTCC_S13

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_BCOR_VTP_2uM_96h_REP1_221111_CGTACG_S13

description: mouse leukemia

value: Bcor

value: VWR


title: mm202C-sgPCGF1_ChIP_H2aK119ub_DMSO_96h_REP1_230112_AGTCAA_S13

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_BCOR_DMSO_96h_REP1_221111_GTCCGC_S9

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_BCOR_dTAG13_500nM_96h_REP1_230113_TAGCTT_S10

description: mouse leukemia


title: mm202C-sgPCGF1_ChIP_BCOR_DMSO_96h_REP1_230113_CAGATC_S7

description: mouse leukemia


title: mm202C-sgLuc_ChIP_RNF2_VTP_2uM_96h_REP1_221111_CCGTCC_S8

description: mouse leukemia

value: sgLuciferase


title: mm202C-sgLuc_ChIP_RNF2_dTAG13_500nM_96h_REP1_230113_GCCAAT_S6

description: mouse leukemia

value: 500nM dTAG13


title: mm202C-sgLuc_ChIP_RNF2_DMSO_96h_REP1_230113_TTAGGC_S3

description: mouse leukemia


title: mm202C-sgLuc_ChIP_RNF2_DMSO_96h_REP1_221111_CTTGTA_S4

description: mouse leukemia


title: mm202C-sgLuc_ChIP_RNF2_DMSO_24h_REP1_221027_ACTTGA_S5

description: mouse leukemia


title: mm202C-sgLuc_ChIP_RNF2_dTAG_500nM_24h_REP1_221027_AGTCAA_S10

description: mouse leukemia


title: mm202C-sgLuc_ChIP_MLL1_dTAG13_500nM_96h_REP1_230112_TAGCTT_S10

description: mouse leukemia


title: mm202C-sgLuc_ChIP_MLL1_VTP_2uM_96h_REP1_221114_GGCTAC_S10

description: mouse leukemia


title: mm202C-sgLuc_ChIP_MLL1_DMSO_96h_REP1_221114_ACAGTG_S5

description: mouse leukemia


title: mm202C-sgLuc_ChIP_KDM2B_VTP_2uM_96h_REP1_221111_AGTTCC_S6

description: mouse leukemia


title: mm202C-sgLuc_ChIP_KDM2B_dTAG_500nM_24h_REP1_221027_GGCTAC_S8

description: mouse leukemia


title: mm202C-sgLuc_ChIP_MLL1_DMSO_96h_REP1_230112_ACAGTG_S5

description: mouse leukemia


title: mm202C-sgLuc_ChIP_KDM2B_DMSO_96h_REP1_230113_CGATGT_S2

description: mouse leukemia


title: mm202C-sgLuc_ChIP_KDM2B_DMSO_96h_REP1_221111_ACTTGA_S2

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_VTP_2uM_96h_REP1_221114_GAGTGG_S22

description: mouse leukemia


title: mm202C-sgLuc_ChIP_KDM2B_dTAG13_500nM_96h_REP1_230113_ACAGTG_S5

description: mouse leukemia


title: mm202C-sgLuc_ChIP_KDM2B_DMSO_24h_REP1_221027_GCCAAT_S3

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_VTP_2uM_96h_REP1_221111_CGATGT_S18

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_dTAG_500nM_24h_REP1_221027_ATCACG_S22

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_dTAG13_500nM_96h_REP1_230113_GAGTGG_S14

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_dTAG13_500nM_96h_REP1_230112_GAGTGG_S22

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_DMSO_96h_REP1_230113_CGTACG_S13

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_DMSO_96h_REP1_230112_CGTACG_S21

description: mouse leukemia


title: mm202C-sgLuc_ChIP_HA_VTP_2uM_96h_REP1_221114_GATCAG_S9

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_DMSO_96h_REP1_221111_ATCACG_S17

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_DMSO_96h_REP1_221114_TAGCTT_S21

description: mouse leukemia


title: mm202C-sgLuc_ChIP_HA_dTAG13_500nM_96h_REP1_230112_GATCAG_S9

description: mouse leukemia


title: mm202C-sgLuc_ChIP_HA_DMSO_96h_REP1_230112_TGACCA_S4

description: mouse leukemia


title: mm202C-sgLuc_ChIP_HA_DMSO_96h_REP1_221114_TGACCA_S4

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27me3_VTP_2uM_96h_REP1_221114_CAGATC_S7

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27me3_DMSO_96h_REP1_221114_CGATGT_S2

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27ac_dTAG13_500nM_96h_REP1_230112_GCCAAT_S6

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27me3_dTAG13_500nM_96h_REP1_230112_CAGATC_S7

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27ac_DMSO_96h_REP1_230112_ATCACG_S1

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27ac_DMSO_96h_REP1_221114_ATCACG_S1

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H2aK119ub_VTP_2uM_96h_REP1_221114_ACTTGA_S8

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H2aK119ub_DMSO_96h_REP1_230112_TTAGGC_S3

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H2aK119ub_dTAG13_500nM_96h_REP1_230112_ACTTGA_S8

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H2aK119ub_DMSO_96h_REP1_221114_TTAGGC_S3

description: mouse leukemia


title: mm202C-sgLuc_ChIP_BCOR_VTP_2uM_96h_REP1_221111_AGTCAA_S5

description: mouse leukemia


title: mm202C-sgLuc_ChIP_BCOR_dTAG13_500nM_96h_REP1_230113_TGACCA_S4

description: mouse leukemia


title: mm202C-sgLuc_ChIP_BCOR_DMSO_24h_REP1_221027_TGACCA_S1

description: mouse leukemia


title: mm202C-sgLuc_ChIP_BCOR_dTAG_500nM_24h_REP1_221027_GATCAG_S6

description: mouse leukemia


title: mm202C-sgLuc_ChIP_BCOR_DMSO_96h_REP1_230113_ATCACG_S1

description: mouse leukemia


title: mm202C_ChIP_RNF2_dTAG_500nM_4d_REP1_220706_CCGTCC_S14

description: mouse leukemia


title: mm202C-sgLuc_ChIP_BCOR_DMSO_96h_REP1_221111_GATCAG_S1

description: mouse leukemia


title: mm202C_ChIP_RNF2_VTP_2uM_4d_REP1_220523_AGTTCC_S14

description: mouse leukemia


title: mm202C-sgLuc_ChIP_input_DMSO_24h_REP1_221027_ATTCCT_S21

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27me3_DMSO_96h_REP1_230112_CGATGT_S2

description: mouse leukemia


title: mm202C_ChIP_RNF2_DMSO_4d_REP1_220523_CAGATC_S7

description: mouse leukemia


title: mm202C-sgLuc_ChIP_H3K27ac_VTP_2uM_96h_REP1_221114_GCCAAT_S6

description: mouse leukemia


title: mm202C_ChIP_KDM2B_VTP_2uM_4d_REP1_220523_AGTCAA_S13

description: mouse leukemia


title: mm202C_ChIP_KDM2B_DMSO_4d_REP1_220706_GCCAAT_S6

description: mouse leukemia


title: mm202C_ChIP_input_VTP_2uM_4d_REP1_220523_GTGAAA_S18

description: mouse leukemia


title: mm202C_ChIP_KDM2B_DMSO_4d_REP1_220523_GCCAAT_S6

description: mouse leukemia


title: mm202C_ChIP_input_DMSO_4d_REP1_220523_CCGTCC_S16

description: mouse leukemia


title: mm202C_ChIP_input_DMSO_4d_REP1_220523_ATGTCA_S15

description: mouse leukemia


title: mm202C_ChIP_input_DMSO_4d_REP1_220706_GTCCGC_S15

description: mouse leukemia


title: mm202C_ChIP_H3K27me3_VTP_2uM_4d_REP1_220523_GATCAG_S9

description: mouse leukemia


title: Armstrong003_PR1046_Pcgf1_dTAG2

data_processing:
FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the hg38 reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl).
For promoter reads, annotated transcription start sites were obtained from human (GRCh38.99) GTFs from Ensembl. After removing transcripts with {immunoglobulin, Mt, Mt_tRNA, rRNA} biotypes, PRO-seq signal in each sample was calculated in the window from the annotated TSS to +150 nt downstream, using a custom script, make_heatmap.pl.
For differential expression analysis, reads were summed within the TSS to TES window for each active gene. DEseq2, using the Wald test, was used to determine statistically significant differentially expressed genes. Unless otherwise noted, the default size factors determined by DEseq2 were used.
Pausing indices were generated by summing in the window from TSS to +150 for each active gene, and from +250 downstream of the TSS to the TES, using the refined annotations described above. The ratio of promoter proximal signal (TSS to +150) over gene body signal (+250 to TES) is the Pausing Index.
Assembly: Gencode M24/mm10
Supplementary files format and content: DESeq2 differential gene expression summaries in tab-delimited text (.txt) format
Library strategy: PRO-seq

extract_protocol:
10 million cells were harvested and washed once with ice cold PBS (Gibco). To obtain single-cell suspensions, cell pellets were resuspended in 250mL wash buffer (10 mM Tris-Cl, pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10 % (v/v) Glycerol, supplemented freshly with 0.5 mM DTT, 0.2mL/mL RNase inhibitor and protease inhibitor). 10mL of permealization buffer (10 mM Tris-Cl, pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.1 % (v/v), Igepal CA-630, 0.05 % (v/v) Tween-20, 10 % (v/v) Glycerol, supplemented freshly with 0.5mM DTT, 0.2mL/mL RNase inhibitor and protease inhibitor) was added dropwise and cells were incubated on ice for 5 min. Following centrifugation of the permeabilized cells, cells were washed in 10mL wash buffer and then resuspended in freezing buffer (50 mM Tris-Cl, pH 8.0, 40 % (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, supplemented freshly with 0.5 mM DTT and 1mL/mL RNase inhibitor). Cells were counted and permeabilization was visualized using trypan blue. At least 5e6 permeabilized cells were snap-frozen in 500ul freezing buffer in liquid nitrogen and stored at -80 C.
1 million permeabilized cells were used for nuclear run-on, with 50,000 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run on assays and library preparation were performed essentially as described in Reimer et al. (Reimer et al., 2021)with modifications noted: 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 40uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/uL SuperaseIN (Thermo), 1% sarkosyl). Run-on reactions were performed at 37°C. Adenylated 3’ adapter was prepared using the 5’ DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturers instructions with 15% PEG-8000 final) and incubated at 16°C overnight. 180uL of betaine blocking buffer (1.42g of betaine brought to 10mL with binding buffer supplemented to 0.6 uM blocking oligo (TCCGACGATCCCACGTTCCCGTGG/3InvdT/)) was mixed with ligations and incubated 5 min at 65°C and 2 min on ice prior to addition of streptavidin beads. After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and blocking oligo wash (0.25X T4 RNA ligase buffer (NEB), 0.3uM blocking oligo) solutions and resuspended in 5’ adapter mix (10 pmol 5’ adapter, 30 pmol blocking oligo, water). 5’ adapter ligation was per Reimer but with 15% PEG-8000 final. Eluted cDNA was amplified 5-cycles (NEBNext Ultra II Q5 master mix (NEB) with Illumina TruSeq PCR primers RP-1 and RPI-X) following the manufacturer's suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Pooled libraries were sequenced using the Illumina NovaSeq platform.

treatment_protocol: NUP98-r leukemia cells were plated at 5e5 cells/mL in the appropriate culture medium and were treated either with 0.1% DMSO or with dTAG-13 (500nM) for 1 hour.

value: 60 minutes


title: mm202C_ChIP_H3K27me3_dTAG_500nM_4d_REP1_220706_TAGCTT_S9

description: mouse leukemia


title: Armstrong003_PR1045_Pcgf1_dTAG1


title: Armstrong003_PR1044_Pcgf1_DMSO2


title: mm202C_ChIP_H3K27me3_DMSO_4d_REP1_220706_CGATGT_S2

description: mouse leukemia


title: Armstrong003_PR1042_LUC_dTAG2


title: Armstrong003_PR1043_Pcgf1_DMSO1


title: mm202C_ChIP_H3K27ac_VTP_2uM_4d_REP1_220523_ACTTGA_S8

description: mouse leukemia


title: mm202C_ChIP_H3K27ac_dTAG_500nM_4d_REP1_220706_GATCAG_S8

description: mouse leukemia


title: Armstrong003_PR1041_LUC_dTAG1


title: mm202C_ChIP_H3K27me3_DMSO_4d_REP1_220523_CGATGT_S2

description: mouse leukemia


title: mm202C_ChIP_KDM2B_dTAG_500nM_4d_REP1_220706_ATGTCA_S13

description: mouse leukemia


title: Armstrong003_PR1040_LUC_DMSO2


title: mm202C_ChIP_RNF2_DMSO_4d_REP1_220706_CAGATC_S7

description: mouse leukemia


title: mm202C_ChIP_input_VTP_2uM_4d_REP1_220523_GTCCGC_S17

description: mouse leukemia


title: mm202C_ChIP_H2aK119ub_dTAG_500nM_4d_REP1_220706_GGCTAC_S10

description: mouse leukemia


title: mm202C_ChIP_H2aK119ub_DMSO_4d_REP1_220706_TTAGGC_S3

description: mouse leukemia


title: Armstrong003_PR1039_LUC_DMSO1


title: mm202C_ChIP_BCOR_dTAG_500nM_4d_REP1_220706_CTTGTA_S11

description: mouse leukemia


title: mm202C_ChIP_H3K27ac_DMSO_4d_REP1_220706_ATCACG_S1

description: mouse leukemia


title: mm202C_ChIP_BCOR_VTP_2uM_4d_REP1_220523_GGCTAC_S11

description: mouse leukemia


title: mm202C_ChIP_H2aK119ub_DMSO_4d_REP1_220523_TTAGGC_S3

description: mouse leukemia


title: mm202C_ChIP_BCOR_DMSO_4d_REP1_220706_TGACCA_S4

description: mouse leukemia


title: mm202C_ChIP_BCOR_DMSO_4d_REP1_220523_TGACCA_S4

description: mouse leukemia


title: mm202C_CRISPR_Epi_14d_VTP_REP3_S14

data_processing:
FASTQ files were processed and trimmed to retrieve sgRNA target sequences followed by alignment to the reference sgRNA library file.
Sequencing read counts were summarized at the gene level per sample and used as input to run differential analysis using the DESeq2 package.
The log2 fold-change values were used as “Gene Score” for the final visualization. Genome-wide screening data were analyzed using MAGeCK Flute pipeline as described (Li et al. 2015).
Assembly: Gencode M24/mm10
Supplementary files format and content: MaGeCK Flute gene-level summary files in tab-delimited text (.txt) format
Library strategy: CRISPR-seq

source_name: NUP98-HOXA9 murine leukemia cells

extract_protocol:
DNA was extracted from cell pellets at the indicated timepoint using the phenol:chloroform extraction method.
We used a modified two-step PCR version of the protocol published by Doench et al. 2016. After an initial “enrichment” PCR, whereby the integrated sgRNA cassettes were amplified from gDNA, a second PCR was performed to append Illumina sequencing adapters on the 5′- and 3′-ends of the amplicon, as well as a random nucleotide stagger and unique demultiplexing barcode on the 5′-end.

treatment_protocol: A chromatin-focused CRISPR-Cas9 genetic screen (Soto-Feliciano et al., 2023) was performed in immortalized NUP98-HOXA9 mouse LSK cells that were derived from single cell clones selected for CRISPR editing efficiency, as previously described (Heikamp et al., 2022). The library was a gift from Y. Soto-Feliciano (MIT) and was generated as previously described (Soto-Feliciano et al., 2023). For transduction of NUP98-HOXA9 mouse leukemia cells, viral supernatant produced by transfection of HEK-293T cells was titered in a pilot experiment to achieve a multiplicity of infection (MOI) of ∼0.3, to ensure that most cells received a single sgRNA integration event. At 72 hours after infection, viral transduction efficiency was quantified by the percentage of RFP+ cells as determined by flow cytometry on an LSR Fortessa (BD Biosciences). Subsequently, cells were selected with 2.5 μg/mL puromycin (Gibco) for 3 days. A baseline (Day 0) timepoint was obtained by harvesting 2 million puromycin-selected, RFP+ cells in duplicate, and the remaining cells were cultured with either DMSO- or 200 nM VTP50469–containing media (IC50 concentration). Cells were maintained under these conditions for 14 days to allow 12 cumulative population doublings (TF/final). To achieve a minimum representation of 1,000× coverage, each passage of the cells was optimized to maintain at least 5e6 cells. For each timepoint, at least 10 million cells were harvested and pelleted in triplicate, except for the day 0 timepoint which was harvested in duplicate. Timepoints were harvested and sequenced at Day 0, at the midpoint of the screen (7 days), and at the end of the screen (14 days).

tag: crispr library

value: 14 days

value: NUP98-HOXA9 murine leukemia cells


title: mm202C_CRISPR_Epi_14d_VTP_REP2_S13


title: mm202C_ChIP_H2aK119ub_VTP_2uM_4d_REP1_220523_TAGCTT_S10

description: mouse leukemia


title: mm202C_CRISPR_Epi_7d_VTP_REP3_S11

value: 7 days


title: mm202C_CRISPR_Epi_7d_VTP_REP1_S9


title: mm202C_CRISPR_Epi_7d_VTP_REP2_S10


title: mm202C_CRISPR_Epi_14d_DMSO_REP2_S7

value: DMSO


title: mm202C_CRISPR_Epi_14d_DMSO_REP1_S6


title: mm202C_CRISPR_Epi_7d_DMSO_REP2_S4


title: mm202C_CRISPR_Epi_7d_DMSO_REP3_S5


title: mm202C_ChIP_H3K27ac_DMSO_4d_REP1_220523_ATCACG_S1

description: mouse leukemia

value: Diagenode

value: leukemia cells


title: mm202C_CRISPR_Epi_7d_DMSO_REP1_S3


title: mm202C_CRISPR_Epi_0d_REP1_S1

value: 0 days


title: Epas1 EC-WT mouse 2

status: Public on Aug 27 2024

city: London

first: Paul

last: Evans

address: Charterhouse square

country: United Kingdom

institute: QMUL

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode and UMI. Read 2 was assigned 60 base pairs and used to map to the Mouse GRCm38 reference genome with BWA-MEM 0.7.15. Briefly, mapping and generation of count tables was automated using MapAndGO. Unsupervised clustering and differential expression analysis was performed with the Seurat R toolkit
Assembly: mm10 (GRCm38)
Supplementary files format and content: *.TranscriptCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. TranscriptCounts files show the estimated original transcript counts, based on the fact that you are randomly sampling from a small fraction of the original pool of molecules.
Supplementary files format and content: *.BarcodeCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. BarcodeCounts files show the number of UMI-corrected read counts.
Supplementary files format and content: *.ReadCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. ReadCounts files shows the number of raw read counts.

source_name: aorta

extract_protocol:
Mice were given intraperitoneal injections of 100 μl pentobarbital. The mouse chest was dissected, revealing the heart. The vasculature was perfused with 10 ml phosphate buffered saline (PBS) containing 2% heparin. The aorta was dissected and cleaned and the adipose and connective tissue surrounding the aorta were removed. To digest the aorta, (which included the aortic arch, ascending, descending, thoracic, and abdominal portions) the sample was placed in a 35mm dish containing 125 U/mL collagenase type XI, 60 U/mL hyaluronidase type 1-s, 60 U/mL DNase I, 450 U/mL collagenase type I and 0.5 mg/ml elastase in 2.5 ml of PBS, at 37ºC for 1h. After the first 10 mins of incubation, the adventitia was removed using forceps. Following the incubation, single cell suspensions from the digested aorta were prepared by pipetting the solution through a 40 μm cell strainer. Cells were washed and resuspended in FACS buffer (PBS with 1% BSA) and stained with CD31-AF488 and CD45-APC antibodies and TOPRO3. Alive, CD45-, CD31+ cells were sorted using a BDFACSMelody cell sorter (BD Biosciences) into single wells of 384-well plates containing reverse transcription primers, deoxyribonucleotide triphosphates, External RNA Controls Consortium (ERCC) RNA Spike-Ins, and mineral oil.
scRNA-seq libraries were generated using the SORT-seq protocol (Muraro et al., 2016) a partially robotized method based on the CEL-Seq2 protocol (Hashimshony et al., 2016). Single cells were lysed at 65°C for 5 min, and second-strand mixers and reverse transcriptase were added to the wells using the Nanodrop II liquid handling platform (GC Biotech). The mRNA of each cell was reserve-transcribed, double-stranded complementary DNAs (cDNAs) from single cells were pooled, and in vitro transcription was performed for linear amplification, resulting in amplified RNA. The Illumina sequencing libraries were prepared using TruSeq small RNA primers (Illumina), and the DNA libraries were then sequenced paired-end at 75–base pair read length using the Illumina NextSeq 500 by Single Cell Discoveries (Utrecht, The Netherlands). The RNA yield of the amplified RNA and the quality and concentration of the final cDNA libraries were assessed by Bioanalyzer (Agilent).

value: aorta

value: endothelial cells (CD45-, CD31+ cells)

value: Epas1fl/fl, Cdh5+/+


title: mm202C_CRISPR_Epi_0d_REP2_S2


title: Epas1 EC-KO mouse 2

value: Epas1fl/fl, Cdh5Cre/+


title: Epas1 EC-KO mouse 1


title: HEK293, pThr4, Ssu72, rep1

status: Public on Aug 01 2024

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
After initial assessment of read quality, pSer2 and  RPRD1B (HA-tag) ChIP-Seq data was mapped onto human reference genome, hg38, with Bowtie2 v. 2.5.0 aligner for paired-end reads using default parameters. pThr4 single-end ChIP-Seq reads were mapped onto human reference genome, hg19, using BWA v.0.7.17.
Coverage tracks in .bigwig format were generated from filtered .bam files (mapq > 20).
TSS/TES profiling was done using plotProfile on matrices generated with 50-bp bins using the computeMatrix function from the deeptools v.2.2.3
After alignment, MACS2 v.2.2.7.1 in Galaxy (parameters: --broad; --broad-cutoff of q < 0.1 for pThr4 and HA-RPRD1B; pSer2 -default) was used to call peaks for IP-samples against Input.
Assembly: hg19 (pThr4), hg38 (pSer2, HA-RPRD1B)
Supplementary files format and content: bigWig, broadPeak

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, for HA-tagged RPRD1B, HEK293 cells were double crosslinked with 2mM DSG for 15 min followed by secondary fixation with 1% formaldehyde for 10 min at room temperature. Single crosslinking was used for RPB1 ChIP using 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of HA antibody (cat: C29F4), pThr4 antibody (Active Motif, cat: 61361), or pSer2 antibody (Sigma, SKU: MABE953) was pre-mixed in a 50μl volume of Dynabeads protein A or protein G (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0.
The extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina HiSeq 3000 or NovaSeq X Plus system.

treatment_protocol: To prepare samples for pThr4 ChIP, we treated HEK293 cell lysate with Ssu72/symplekin complex at 4°C for 30 minutes before binding to the 6D7 antibody. To generate T4A and T4WT CTD samples for pSer2 immunoprecipitation, transient transfection of 12 μg of either plasmid was performed using PEI. Following transfection, 2.5 μg of alpha amanitin was added to cells for 48 hours. Finally, to prepare HA-RPRD1B samples, HEK293 were transfected with HA-RPRD1B using PEI (1:7 plasmid to reagent ratio) to overexpress the protein of interest.

value: Human embryonic kidney

value: pThr4 (ActiveMotif, #61361)


title: mm202C_CRISPR_Epi_14d_VTP_REP1_S12


title: pLHiC-G1-OHT

status: Public on Jul 15 2024

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

description: pLHiC-seq

data_processing:
Basecalls were performed using bcl2fastq v1.1.0 (Illumina) and the quality of the generated FASTQ files was analysed with FastQC.
For pLHi-C, pLHiChIP and spLHiChIP sequencing reads, the program HiC-Pro v2.11.4 was used to trim linker sequences, align to hg19, filter by DpnII restriction fragments and carry out qualtiy controls. HiC-Pro was also used to generate valid pairs outputs (bedpe files). For pLHi-C, the program HiC-Pro was further used to build contact maps and to transform those into HIC format (hic files).
For spLHiChIP, a spike-in (mouse; mm10) normalization was done. The number of spike-in normalized reads per sample was calculated by dividing the number of reads mapping exclusively to hg19 by the number of reads mapping exclusively to mm10 and multiplying this number with the smallest number of reads mapping to mm10 of all samples. For spLHiChIP and pLHiChIP valid pairs, DNA loops were called using the program hichipper v0.7.7.
Assembly: hg19 (GRCh37) and mm10
Supplementary files format and content: For pLHi-C, the provided processed files are hic files for display and further analysis of contact maps. For pLHiChIP and spLHiChIP sequencing experiments, the provided processed files are bedpe files used to describe pairs of genomic regions.

source_name: SH-EP NMYC-ER

growth_protocol: Human neuroblastoma derived SH-EP cells expressing an exogenous and 4-OHT inducible NMYC allele (SH-EP-NMYC-ER), were grown in RPMI-1640 medium supplemented with with 10% horse serum and 1% penicillin/ streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For phosphorylated linker Hi-C (pLHi-C), phosphorylated linker HiChIP (pLHiChIP) and spike-in phosphorylated linker HiChIP (spLHiChIP), cells were cross-linked with 1% formaldehyde for 5 min and stopped by adding 125 mM glycine for 10 min at room temperature. Nuclei were isolated and a one-step in situ digestion and dephosphorylation took place by using DpnII and rSAP enzymes. During the nuclei isolation step, only for the spLHiChIP samples, murine NHO2A cells were added as exogenous control (spike-in) at a 1:20 cell ratio. Next, biotinylated oligos with 5’ end phosphate were used with T4 ligase for the ligation step.
Chromatin fragmentation was performed using the Covaris Focused Ultrasonicator M220 for 30 min per ml lysate. Samples were de-crosslinked overnight and Protein and RNA were digested with proteinase K and RNase A. DNA was isolated using ChIP DNA Clean & Concentrator (Zymo Research). Biotin pull-down was performed with MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to manufacturer’s instructions.
Only for pLHiChIP and spLHiChIP samples, the chromatin fragmentation was followed by an immunoprecipitation of the target protein. To this end, Dynabeads Protein A and Protein G were pre-incubated overnight with 10-15 µg antibody in the presence of 5 mg/ml BSA. Next, chromatin was added to the pre-incubated beads for at least 6h at 4°C with rotation. Beads were then washed with different TRIS buffers containing distinct salt-concentrations, EDTA and detergents, followed by wahsing with only TE-buffer.
The immunoprecipitated chromatin of the pLHiChIP and spLHiChIP samples was eluted with 100mM NaHCO3 and 1% SDS for 15 min. Eluted samples were de-crosslinked overnight. DNA was isolated using ChIP DNA Clean & Concentrator (Zymo Research). Biotin pull-down was performed with MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to manufacturer’s instructions.
Library preparation was the same for all samples and was done on beads using the NEBNext ChIP-Sequencing Library Prep Master Mix Set for Illumina (NEB) according to manufacturer's instrcutions. The only deviation from the instructions was an additional washing step between each module using a Tris-buffer with 0.5 mM EDTA, 1 M NaCl and 0.05% Tween followed by a washing step with only TE buffer. Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq500 or NextSeq2000 platform (Illumina).
pLHi-C sequencing (Illumina NextSeq500) and (s)pLHiChIP sequencing (Illumina NextSeq500 or NextSeq2000)

treatment_protocol:
The indcution of NMYC in the SH-EP-NMYC-ER cells was achieved by adding 4-OHT (200 nM) for 4 hours. The expression of an shRNA targeting TF3C5 in the SHEP-NMYCER cells was induced with 1 µg/ml doxycycline for 48 hours. Where indicated, SH-EP-NMYC-ER cells were treated with MLN8237 (1 µM) or DRB (100 µM) for 2 hours.
For spike-in phosphorylated linker HiChIP (spLHiChIP) samples, an exogenous control (spike-in) was used. For that purpose, murine NHO2A cells were added at a 1:20 cell ratio to the samples during the nuclei isolation step.

value: SH-EP NMYC-ER

value: Neuroblastoma

tag: cell cycle_synchronization

value: G1-phase synchronized

tag: dox-treatment (shrna-tf3c5)

value: not applicable

tag: 4-oht treatment_(nmyc_expresion)

value: induced (NMYC expression)

tag: treatment with_inhibitor

tag: spike-in


title: Epas1 EC-WT mouse 1

tag: tissue

tag: cell type

tag: genotype


title: HEK293, pThr4, Ssu72, rep2

tag: chip antibody


title: 19521X7_tp53mut_control

status: Public on Jul 09 2024

city: Salt Lake City

first: Rodney

last: Stewart

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

institute: University of Utah

description: NovaSeq Reagent Kit v1.5_150x150 bp sequencing (100 M read-pairs)

data_processing:
The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a
Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text file containing gene id, log2FC, padj, and raw counts.

organism: Danio rerio

source_name: brain

growth_protocol: Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.

extract_protocol:
Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit (Qiagen 217084). Homogenization was performed with a 20-25.5 gauge needle 10 times. Samples were Dnase treated.
Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold (Illumina 20020598).

treatment_protocol: Brains were frozen at -80C in RNA stabilization solution (QIAGEN).

value: brain

tag: tumor status

value: control

tag: age

value: 1 year

value: tp53 mutant


title: pLHiC-G1

description: pLHiC-seq

value: uninduced (no NMYC expression)


title: 19521X3_tp53mut_tumor

value: tumor

value: 4 wpf


title: 19521X9_tp53mut_control


title: 19521X6_tp53het_tumor

value: 7 wpf

value: tp53 heterozygote


title: 19521X2_tp53mut_tumor

value: 8 wpf


title: 19521X1_tp53mut_tumor


title: adultSN, OMM12_96_3

status: Public on Jun 10 2024

city: Turin

first: Chiara

last: Cicconetti

state: (TO)

address: Via Nizza, 52

department: Dept. of Life Sciences and Systems Biol

country: Italy

institute: University of Turin

data_processing:
After quality controls with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), raw reads were aligned to the mouse reference genome (UCSC mm10/GRCm38) using STAR 2.7.1a (Dobin et al., 2013) (with parameters –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04). Gene expression levels were quantified with featureCounts v1.6.3 (Liao et al., 2014) (options: -t exon -g gene_name) using GENCODE M23 annotation. Multi-mapped reads were excluded from quantification. Gene expression counts were next analysed using the edgeR package (Robinson et al., 2010). After low expressed genes filtration (1 count per million (CPM) in less than 3 samples), normalisation factors were calculated using the trimmed-mean of M-values (TMM) method (implemented in the calcNormFactors function).
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file of normalized read counts per gene/samples.

source_name: Sciatic nerves

growth_protocol: Neonatal (P8-14) and young adult (63-76 days old) germ-free (GF), gnotobiotic (colonized with Oligo-Mouse Microbiota12, OMM12) and SPF C57BL6/JZtm (complex microbiota) mice were obtained from the Central Animal Facility (Hannover Medical School, Hannover, Germany). Breeding and maintenance of GF and gnotobiotic mice was performed in plastic film isolators (Metall+Plastik GmbH, Radolfzell-Stahringen, Germany) located in a room with a controlled environment (20–22 °C, 50–55 % humidity) and 12-hour light/dark cycles. GF and gnotobiotic mice received pelleted 50 kGy gamma-irradiated feed (V1124-927, Ssniff Spezialdiäten GmbH, Germany) and autoclaved water ad libitum. SPF mice were housed in individually ventilated cages (XJ Edge, Allentown) in a room with a controlled environment (20–22 °C, 50–55 % humidity) and 12 h light/dark cycles. SPF mice received pelleted 50 kGy gamma-irradiated feed (1314 breeding diet for mice and rats, Altromin) and chlorinated water ad libitum. Routine microbiological monitoring according to FELASA recommendations (Mähler et al., 2014) and recommendations for maintaining gnotobiotic colonies (Nicklas et a., 2015) did not reveal any evidence of infection with common murine pathogens in SPF animals or contaminants in GF and gnotobiotic animals.   In total, this study included tissue sampling from 42 adult and 41 neonatal animals. The animals were sacrificed by decapitation (adults ones after inducing anaesthesia in CO2 atmosphere). All procedures were performed in accordance with the German Animal Welfare Legislation and the principles of the Basel Declaration and recommendations of Directive 2010/63/EU, they were approved by the local Institutional Animal Care and Research Advisory Committee and registered with the animal care committee of Lower-Saxony, Germany.

extract_protocol:
Neonatal and adult DRG and sciatic nerve total RNA was isolated using TRIzol reagent (Life Technology) and processed according to manufacturer's instructions.
Neonatal and adult DRG and sciatic nerve total RNA was isolated using TRIzol reagent (Life Technology) and processed according to manufacturer's instructions. Quality of the extracted RNAs was assessed using the RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Sequencing of pooled dorsal root ganglia and peripheral nerves collected from young adult CGM, GF and OMM12 mice was performed on the Illumina NextSeq 500 platform. Sequencing of pooled dorsal root ganglia and peripheral nerves collected from neonatal CGM, GF and OMM12 mice was performed on the Illumina NextSeq 1000 platform.

value: Sciatic nerves

tag: strain

tag: condition

value: Oligo-mouse microbiota

tag: developmental stage

value: young adult (63-76 days old)


title: mm202C_CRISPR_Epi_14d_DMSO_REP3_S8

tag: timepoint

value: 14 days

tag: treatment

value: DMSO

tag: genetic background

value: NUP98-HOXA9 murine leukemia cells


title: adultSN, OMM12_96_2


title: adultSN, GF_96_6

value: Germ free


title: adultSN, GF_96_5


title: adultSN, OMM12_96_1


title: adultSN, GF_96_4


title: HEK293, pThr4, Ssu72, rep3

tag: cell line

value: Human embryonic kidney

value: pThr4 (ActiveMotif, #61361)


title: adultSN, CGM_96_8

value: Complex microbiota


title: adultSN, CGM_96_9


title: adultDRG, OMM12_96_28

source_name: Dorsal root ganglia

value: Dorsal root ganglia


title: adultDRG, OMM12_96_26


title: 19521X8_tp53mut_control

value: brain

value: control

value: 1 year

value: tp53 mutant


title: 19521X5_tp53het_tumor

value: tumor

value: 7 wpf

value: tp53 heterozygote


title: adultDRG, OMM12_96_27

value: Oligo-mouse microbiota


title: adultSN, CGM_96_7

value: Sciatic nerves

value: young adult (63-76 days old)


title: adultDRG, CGM_96_34


title: adultDRG, GF_96_31


title: adultDRG, GF_96_29


title: adultDRG, CGM_96_32


title: Xbp1s, repeat2, CUT&Tag_seq

status: Public on May 28 2024

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

data_processing:
The raw reads were further filtered by Cutadapt (version: cutadapt-4.7).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using Bowtie2 (Version 2.5.1).
Sequence tags were aligned to the genome and then subsequently analyzed by MACS2 (version 2.2.9.1) to detect genomic regions enriched for multiple overlapping DNA fragments (peaks).
Assembly: mm10
Supplementary files format and content: bigwig

source_name: colon

extract_protocol:
Cultured-ILC2s were sorted by FACSMelody.
CUT&Tag libraries was generated and indexed using Hyperactive Universal CUT&Tag Assay Kit for Illumina and then TurePrep Index Kit for Illumina.

value: colon

value: immune cell


title: 19521X4_tp53het_tumor


title: Xbp1s, repeat1, CUT&Tag_seq


title: adultDRG, GF_96_30

value: Germ free


title: adultDRG, CGM_96_33