title: SC35 IP rep2, Day8

data_processing:
(Sample 1-8) For both IP datasets in Day8, all reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using STAR, and uniquely mapped reads were retained for calculating gene counts by FeatureCounts with two parameters separately: “-t exon -C -J” (for exon reads and exon–exon junction reads) and “-t gene -C -J” (for all exon and intron reads).
The splicing efficiency(SE) metric was computed as the fraction of exon counts over intron + exon (total) counts, and the transcripts with SE ≤1.00 and SE > 0.99 were considered as mature transcripts.
For both Input datasets, all reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.83) using STAR, and uniquely mapped reads were retained for calculating gene counts by FeatureCounts with default parameter.
The protein-bound transcripts were identified by DESeq2 with P-value < 0.05 and fold change (IP versus Input) > 1.2. All genes with TPM ≥ 1 in both Input samples were considered.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: (Sample 1-6) For RIP-seq on day 8 of erythroid differentiation: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml SCF ,10^-6 M Hydrocortisone and 3 U/ml human EPO for 8 days.

extract_protocol:
About 2×107 CD34+ cells were conducted and RNA-protein complexes were isolated by SC35 antibody on Protein A beads according to the protocol. Then the RNA was purified for subsquential processes.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: wild-type; NSPC; Aph; lamhtgts; chr14; theta collection; rep1

status: Public on Mar 03 2026

type: SRA

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

country: Germany

institute: German Cancer Research Center

description: Library name: wt-aph-lamhtgts-chr14-LC212-rep1

library_source: genomic

data_processing:
*library strategy: linear amplification (LAM)-High-throughput Genome-wide Translocation Sequencing (HTGTS)
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sigularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: GRO-seq: bigwig files for plus and minus strands.
Supplementary files format and content: LAM-HTGTS: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Repli-seq: log2 smoothed ratio file for early and late fractions.

molecule: genomic DNA

organism: Mus musculus

source_name: Primary NSPC

growth_protocol: Mouse neural progenitor cells and primary neural stem/progenitor cells were cultured in NBBG medium (NeralBasalA, 2% B27 supplement without RA, 0.5 mM Glutamax, 10ng/ml human EGF, 10ng/ml mouse FGFb). Neural progenitor cells were then collected for nucleofection (LAM-HTGTS), GRO-seq, or Repli-seq experiments. For Aph treated cells, these cells were treated with 0.5 uM Aph for 72 hours and 0.25 uM for 24 hours. For PolQ inhibition, cells were incubated with 5uM ART558 for 72 hours then with 2.5 uM for 24 hours.

extract_protocol:
Genomic DNA for LAM-HTGTS: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. RNA were removed by treating samples with RNAseA prior phenol/chlroform extraction. Genomic DNA for Repli-seq: cells were lyzed in proteinase K digestion buffer, fragmented by a Covaris fragmentation device to 200 bp, and nacent DNA were pulldowned by using an BrdU-specific antiboty.
We follow the published protocol, as indicated below, to construct the libraries. Repli-seq: https://www.nature.com/articles/nprot.2017.148 LAM-HTGTS: https://www.nature.com/articles/nprot.2016.043

treatment_protocol: Cells were treated with indicated concentration of aphidicolin or the veichle control DMSO for the indicated period.

tag: cell type

value: Primary NSPC

tag: genotype

value: Wild-type

tag: treatment

value: APH


title: d2 TT-TSS-seq R2

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: d2 TT-TSS-seq R2

library_source: transcriptomic

data_processing:
TT-TSS-seq and Poly(A)-TSS-seq read demultiplexing was performed using Ultraplex with parameters “--phredquality 15 --min_length 0”. Adaptor trimming was performed using Cutadapt with parameters “--minimum-length 20”. Bowtie 2 was used for pre-mapping to ribosomal and small RNAs. Genome mapping was performed using STAR, for mouse samples with Ensembl GRCm38 (mm10) release-89 annotation. Umitools was used for deduplication. BEDTools was used to identify the 5’-most nucleotide (tag) and for genome-wide comparative analyses.
RNA-seq and TT-chem-seq time course analysis read processing using nf-core/rnaseq (3.13.2). Adaptor and quality trimming were performed using Trim Galore! (minimum trimmed read threshold: 10,000). Genome mapping was performed using STAR with Ensembl GRCm38 (mm10) release-89 annotation (minimum uniquely mapped read threshold: 5%). Transcript assembly was performed using StringTie.
Assembly: GRCm38 (mm10)
Supplementary files format and content: processed files are higher bigwig or bedgraphs

molecule: total RNA

growth_protocol: mESCs (HM-1) cells that had been passaged at least twice post-thawing were used for differentiation. The protocol for spinal cord motor neuron differentiation was adapted. Cells were lifted and resuspended in N2B27 (49% DMEM/F12-/- (Gibco), 49% Neurobasal (Gibco), 1X N2 (Gibco), 1X B27 (Gibco), 0.05 mM 2-Mercaptoethanol (Gibco), 2mM L-Glutamine (Gibco)) with bFGF (10 ng/ml, Bio-Techne, 3139-FB-025) before 85,000 cells were plated on Geltrex- (or Matrigel-) coated 6-well plates in N2B27 with bFGF (10 ng/ml). 48 hours later the media was changed to N2B27 with bFGF (10ng/ml), CHIR99021 (5μM, Axon MedChem, 1386), SB 431542 (10uM, Cambridge Bioscience S0400) and DMH1 (2uM, Cambridge Bioscience, 16679). 20 hours later the media was changed to N2B27 with 100 nM RA (Sigma Aldrich, R2625) and 100 nM SAG (Merck, 566660). After this, the media was replaced every 24 hours for up to 7 days of total differentiation. Treatment with 10 µg/ml notch inhibitor DBZ (Tocris 4889) occurred from day 5 onwards.

extract_protocol:
RNA was extracted from mESCs and NIH/3T3 fibroblasts by the standard TRIzol extraction procedure (Thermo Fisher). rDNase (Qiagen) digestion was carried out, and purification was performed by spin column (Qiagen) or by phenol: chloroform extraction and ethanol precipitation.  4SU labelling was carried out as detailed previously, with a few modifications. Cell culture media was removed, filtered, and 1 mM 4SU (Glentham Life Sciences) was added. The cells were returned to the incubator and labelled with 4SU for 15 minutes before medium aspiration and TRIzol addition. 1/5 volume of chloroform was added, followed by isopropanol precipitation. The pellet was then washed with 85% ethanol, dried, and resuspended. RNA integrity was checked for a selection of samples using Bioanalyzer (Agilent Technologies). 4SU incorporation was assessed using a slot blot. RNA clean-up was performed by phenol/chloroform/isoamyl alcohol, and precipitation by isopropanol. The pellet was washed with 85% ethanol, dried, and resuspended.
The TT-TSS-seq and Poly(A)-TSS-seq methods were previously described in detail. In short, total RNA was dephosphorylated with quickCIP (NEB, 1.2 U/µg RNA. RNA was extracted using phenol/chloroform/isoamyl alcohol. RNA was treated with mRNA decapping enzyme (NEB, 0.7 U/µg RNA) followed by purification by phenol/chloroform/isoamyl alcohol. RNA and the 5’ adaptor ligation was performed T4 RNA ligase I (30 U). RNAClean XP (1.8X ratio, Beckman Coulter) was used to remove unligated adaptors, according to the manufacturer’s instructions. Poly(A)+ RNA was enriched using Dynabeads Oligo(dT)25 (Thermo Fisher), or 4SU+ RNA was purified as detailed in the TT-chem-seq protocol. RNA was fragmented, and 3’ ends were fixed by quickCIP treatment (NEB, 30 U). Pre-adenylated 3’ adaptor (2 µM) were denatured and ligation was carried out by T4 Rnl2tr (NEB,200 U). Reverse transcription was carried out by SuperScript III (2 µl, Invitrogen). AMPure XP beads (Agencourt, Beckman Coulter) were used to clean up the cDNA. cDNA pre-amplification was performed with i5_s and i7_s (300 nM each) primers and Phusion HF PCR Mastermix (Thermo Fisher). 6 PCR cycles were carried. ProNex beads (Promega) with a 1:2.95 ratio to sample were used to remove sequences less than 55 nt (including primer dimers). Final amplification was carried out with NEBNext i50 and i70 primers (500 nM each) and Phusion HF PCR Mastermix, for 8 cycles. Amplification was checked by using Novex 6% TBE (Tris/Borate/EDTA) gel and staining with SYBR Green.For RNA-seq, libraries were prepared using NEB ultra II, with poly(A)+ purification, according to the manufacturer's protocol. Sequencing was performed on NovaSeq 6000 (Illumina) using 100 bp paired-end reads.  For TTchem-seq, at least 10 ng of eluted RNA was used for library preparation with NEBNext Ultra II Directional Poly(A) mRNA, according to the manufacturer’s protocol for fragmented RNA. Libraries were sequenced using NovaSeq 6000 (Illumina) as 100 bp paired-end reads.

tag: cell line

value: mESC

value: WT

value: day 2


title: DON - Rep3

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

description:
Library name: RS2156.S13
RS2156.S13

data_processing:
BaseCalls were converted and demultiplexed using Illumina bcl2fastq software to generate raw fastq files.
The analysis pipeline was executed with Nextflow v22.12.0-edge (Di Tommaso et al., 2017) and processed using nf-core/rnaseq v3.12.0 (doi: https://doi.org/10.5281/zenodo.7998767) of the nf-core collection of workflows (Ewels et al., 2020). The parameter "--extra_trimgalore_args '--clip_R1 1 --clip_R2 1' " were used in complement to default nfcore pipeline parameters.
Rattus norvegicus genome reference mRatBN7.2 (GCA_015227675.2) and GTF annotation file were used as reference sequences for nf-core/rnaseq pipeline.
Biostatistics treatments were performed under R v4.2.2 (R Core Team, 2022), edgeR package (Robinson et al., 2010) and Bioconductor packages (Huber et al. 2015). Briefly, raw count table was filtered to eliminate undetected genes using filterByExpr function with min.count=10 parameters. Normalization factors were calculated using TMM method. Then the common, trended and tagwise negative binomial dispersions were estimated with the robust mode of estimateDisp function. Normalized log2 CPM (counts per million reads) were exported to generate the normalized data file which is provided as 'processed data file'.
Assembly: mRatBN7.2 / GCA_015227675.2
Supplementary files format and content: Matrix table (tab separated tsv file) with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table (semicolon separated csv file) with log2CPM values for every gene and every sample

organism: Rattus norvegicus

growth_protocol: IEC-6 cells were seeded in 60mm dishes at a density of 1,10e6 cells per well.

extract_protocol:
Cells were then collected in Extract-All (Eurobio Scientific)
RNAseq libraries were constructed from 1000 ng of total RNA at the GeT‐TRiX facility (GénoToul, Génopole Toulouse Midi-Pyrénées) using Illumina® Stranded mRNA Prep kit (Illumina, San Diego, CA, USA) following the manufacturer's instructions. Briefly, mRNAs were captures, then fragmented, converted to double stranded cDNAs and sequencing adaptors were ligated. Libraries were amplified with ten cycles of PCR.

treatment_protocol: Treatment of IEC-6 cells with vehicule, deoxynivalenol (3 and 10µM) acrylamide (6mM) during 4 hours before ARN extraction

value: DON

tag: serial


title: d7DBZ TT-TSS-seq R1

description: Library name: d7DBZ TT-TSS-seq R1

value: day 7 DBZ


title: ACRYLAMIDE - Rep3

description:
Library name: RS2156.S12
RS2156.S12

value: ACRYLAMIDE


title: TAL1 rep2, Day8

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

country: China

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

data_processing:
(Sample 9-16) For analysis, the raw reads were trimmed low quality reads and adapter sequence using Trimmomatic with “ILLUMINACLIP: ~/adapters/NexteraPE-PE.fa:2:30:10:1:true SLIDINGWINDOW:4:15 MINLEN:50”.
Then trimmed reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using STAR, and uniquely mapped reads were retained.
For peak calling, parameters used were MACS2 callpeak with “-t bam_file -p 1e-5 -keep-dup all”. These peaks were annotated by HOMER and the enrichment of RNA binding sites on the genomic region was calculated by HOMER 'annotatePeaks.pl'.
Assembly: GRCh38
Supplementary files format and content: peak text file, bw file
Library strategy: CUT&Tag

organism: Homo sapiens

source_name: HSPC

growth_protocol: (Sample 9-16) For CUT&Tag on day 8 of erythroid differentiation: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml SCF ,10^-6 M Hydrocortisone and 3 U/ml human EPO for 8 days.

extract_protocol:
1 × 105 HSPC cells were harvested freshly. The cells were enriched by ConA Beads and antibody. Then the beads were washed for 3 times using antibody buffer and then incubated with proteinA/G-Tn5 transposome for 1 h and washed for 3 times by ChiTaq buffer. Cells were resuspended in 50 µL Tagmentation buffer (10 mM MgCl2 in ChiTaq Buffer) and incubated at 37 °C for 1 h. The incubation was stopped by adding 10 µL 10% SDS at 55 °C for 10 min. The DNA fragments were extracted by Tagment DNA extract beads and amplified using 5× AmpliMix. Then the DNA was re-extracted by DNA clean beads for sequencing.
cDNA libraries were prepared as described (Nat Commun. 2019 Apr 29;10(1):1930) and sequenced with Novaseq-PE250 platform.

value: HSPC


title: d2 TT-TSS-seq R1

description: Library name: d2 TT-TSS-seq R1


title: CONTROL - Rep4

description:
Library name: RS2156.S11
RS2156.S11

value: CONTROL


title: d0 TT-TSS-seq R2

description: Library name: d0 TT-TSS-seq R2

value: day 0


title: TAL1 rep1, Day8


title: GSCs, shControl-2, Day4

city: Boston

first: Hayk

last: Mnatsakanyan

state: MA

address: 149 13th Street Charlestown

department: Neurology

country: USA

institute: Massachusetts General Hospital

description: Library name: scr2

data_processing:
Subread alignment (Subjunc)
ENTREZ annotation
FeatureCount was used for quantifying the number of reads
R DESeq2 package for differential gene expression
Assembly: GRCh38
Supplementary files format and content: txt processed_data file contains raw counts data

extract_protocol:
Quick-RNA Miniprep (Zymo)
NEBNext Ultra II RNA Library Prep Kit for Illumina/NEBNext Poly(A) mRNA Magnetic Isolation Module

value: Glioma stem cells


title: d7 TT-TSS-seq R1

description: Library name: d7 TT-TSS-seq R1

value: day 7


title: GSCs, shControl-1, Day4

description: Library name: scr1


title: d6 TT-TSS-seq R2

description: Library name: d6 TT-TSS-seq R2

value: day 6


title: H2122_AR30_rep1

type: RNA

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

country: Japan

institute: Kindai Universty Hospital

description: gene expression data from H2122 AR30

hyb_protocol: Following fragmentation, 2.3 mg of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, human. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 7G, affymetrix.

data_processing: The data were analyzed with Transcriptome Analysis Console using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Restitance clone of sotorasib-sensitive KRASG12C-mutant NSCLC cell lines NCI-H2122 AR30

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Gene Chip WT PLUS Reagent kit, Affymetrix).

growth_protocol: The KRASG12C-mutant NSCLC cell lines NCI-H2122 were obtained from American Type Culture Collection (Manassas, VA). H2122 cells were cultured under a humidified atmosphere of 5% CO2 at 37°C in RPMI 1640 (Sigma-Aldrich, St. Louis, MO) supplemented with 10% FBS and 1% penicillin-streptomycin.

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

tag: tissue

value: Lung


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr6; theta collection; rep2

description: Library name: wt-aph-lamhtgts-ipolq-LC229-rep2

value: ATR558 plus aphidicolin


title: Pol II rep2, Day8


title: d5 TT-TSS-seq R2

description: Library name: d5 TT-TSS-seq R2

value: day 5


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr6; theta collection; rep1

description: Library name: wt-aph-lamhtgts-ipolq-LC228-rep1

value: Primary NSPC

value: Wild-type


title: REH_sgCTRL#1 (Hi-C)

city: New York

first: Yohana

middle: E

last: Ghebrechristos

state: NY

address: 550 1st Ave.

department: Pathology

institute: NYU Grossman School of Medicine

data_processing:
Reads were processed using the HiC-Bench pipeline, where trimmed reads were aligned to GRCh37 using bowtie2 v2.3.5.1.  After filtering deduplicated reads were then used to generate HIC tracks provided with juicer v1.5.
Assembly: hg19
Supplementary files format and content: HIC file

source_name: B-cell acute lymphoblastic leukemia

growth_protocol: Primary B-ALL samples and healthy bone marrow samples were thawed and immediately processed for sorting. REH and SEM cell lines were grown in RPMI1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin under 5% CO2 at 37°C.

extract_protocol: Immediately after sorting, cells were washed with PBS. Nuclei were extracted with cold lysis buffer and Tagmented with Illumina Tagment DNA Enzyme and Buffer Large kit (20034198). For RNA-seq, cells for RNA extraction were pelleted in Eppendorf tube, and resuspended with 350μl of Buffer RLT Plus containing 10ul of b-Mercaptoethanol (b-ME) per 1ml. For Hi-C, cells were crosslinked in a DNA low-bind Eppendorf tube at a final concentration of 2% formaldehyde and incubated at RT for 10 min on a tube revolver. Samples were then frozen in liquid nitrogen and stored in -80°C for future processing.

treatment_protocol: Primary B-ALL and healthy bone marrow cell pellets were re-suspended in 300 uL of PBS with 2% FCS per 2 x 106 cells, supplemented with DAPI (0.5 ug/mL) for live/dead staining. Cell sorting was performed using the SY3200™ highly automated parallel sorting (HAPS) cell sorter (Sony). After sorting, cells were washed with PBS and split for RNA-seq, Hi-C and ATAC-seq.

value: B-cell acute lymphoblastic leukemia

value: REH

value: ERG WT


title: RIP input rep2, Day0

growth_protocol: (Sample 7-8) For RIP-seq on day 0 of erythroid differentiation: CD34+ were cultured in IMDM supplemented with 30% fetal bovine serum, 1% BSA, 100 µM 2-ME, 2 ng/ml recombinant human IL-3, 100 ng/ml recombinant human SCF for 3 days.


title: wild-type; NSPC; Aph; lamhtgts; chr14; theta collection; rep4

description: Library name: wt-aph-lamhtgts-chr14-LC215-rep4

value: APH


title: H2122_AR14_rep1

description: gene expression data from H2122 AR14

source_name: Restitance clone of sotorasib-sensitive KRASG12C-mutant NSCLC cell lines NCI-H2122 AR14


title: REH_sgERG#6 (Hi-C)

value: ERG KO


title: wild-type; NSPC; Aph; lamhtgts; chr6; theta collection; rep3

description: Library name: wt-aph-lamhtgts-chr6-LC226-rep3


title: H2122_AR14_rep2

description: gene expression data from H2122 AR14


title: ACRYLAMIDE - Rep2

description:
Library name: RS2156.S16
RS2156.S16

value: ACRYLAMIDE


title: RIP input rep1, Day0

value: HSPC


title: d7DBZ Poly(A)-TSS-seq R2

description: Library name: d7DBZ Poly(A)-TSS-seq R2

value: mESC

value: WT

value: day 7 DBZ


title: wild-type; NSPC; Aph; lamhtgts; chr6; theta collection; rep2

description: Library name: wt-aph-lamhtgts-chr6-LC225-rep2


title: d5 TT-TSS-seq R1

description: Library name: d5 TT-TSS-seq R1


title: RIP input rep2, Day8


title: wild-type; NSPC; Aph; lamhtgts; chr14; theta collection; rep2

description: Library name: wt-aph-lamhtgts-chr14-LC213-rep2


title: ProB003 (Hi-C)

source_name: Healthy bone marrow

value: Healthy bone marrow

value: Healthy BM

value: Pro-B


title: DON_ACRYLAMIDE - Rep1

description:
Library name: RS2156.S14
RS2156.S14


title: RIP input rep1, Day8


title: ACRYLAMIDE - Rep4

description:
Library name: RS2156.S5
RS2156.S5


title: ProB002 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr8; theta collection; rep2

description: Library name: x4p53-ipolq-lamhtgts-chr8-LC184-rep2

value: ES cell derived NPC


title: CONTROL - Rep1

description:
Library name: RS2156.S15
RS2156.S15

value: CONTROL


title: d3 TT-TSS-seq R1

description: Library name: d3 TT-TSS-seq R1

value: day 3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr8; theta collection; rep1

description: Library name: x4p53-ipolq-lamhtgts-chr8-LC183-rep1


title: DON - Rep2

description:
Library name: RS2156.S9
RS2156.S9

value: DON


title: ProB001 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr8; theta collection; rep3

description: Library name: x4p53-dmso-lamhtgts-chr8-LC173-rep3

value: DMSO


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr6; theta collection; rep4

description: Library name: wt-aph-lamhtgts-ipolq-LC231-rep4

value: Primary NSPC

value: Wild-type

value: ATR558 plus aphidicolin


title: SC35 IP rep1, Day8


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr6; theta collection; rep3

description: Library name: wt-aph-lamhtgts-ipolq-LC230-rep3


title: ACRYLAMIDE - Rep1

description:
Library name: RS2156.S1
RS2156.S1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr8; theta collection; rep1

description: Library name: x4p53-dmso-lamhtgts-chr8-LC171-rep1


title: PreB002 (Hi-C)

value: Pre-B


title: SON IP rep2, Day8


title: SON IP rep1, Day8


title: d0 TT-TSS-seq R1

description: Library name: d0 TT-TSS-seq R1

value: day 0


title: DON_ACRYLAMIDE - Rep4

description:
Library name: RS2156.S10
RS2156.S10


title: Immune Cells from CT2A bearing Glut5 KO mouse

city: Chicago

first: Shashwat

last: Tripathi

state: Illinois

address: 302 e Huron St

department: Neurosurgery

institute: Northwestern

description: Library name: KO

library_source: transcriptomic single cell

data_processing:
The multiplexed libraries were pooled and sequenced on Illumina HiSeq 4000 sequencer with paired-end 50 kits using the following read length: 28 bp Read1 for cell barcode and UMI and 91 bp Read2 for transcript.
Raw sequencing files were aligned to mm10 reference using Cell Ranger (v3.1.0).
Assembly: mm10
Supplementary files format and content: Features, Matrix and barcode files are included for every sample

source_name: Brain

extract_protocol:
CT-2A tumor cells were implanted intracranially, and the resulting tumor was removed after 14 days and digested into single-cell suspension using the adult brain dissociation kit (Miltenyi) according to the manufacturers instructions. CD45+ cells were isolated via magnetic bead isolation (Miltenyi) and submitted to the Northwestern University NUseq facility core for single cell library preparation and sequencing.
AOPI fluorescent staining was used to determine cell number and viability Nexcelom Cellometer Auto2000 with. Sixteen thousand cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip K (10X Genomics, PN-1000127), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10X Genomics, PN-1000283) according to the manufacturer’s manual.

value: Brain

value: Immune Cells

value: Glut5 KO


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr8; theta collection; rep3

description: Library name: x4p53-aph-lamhtgts-ipolq-chr8-LC248-rep3


title: d7DBZ Poly(A)-TSS-seq R1

description: Library name: d7DBZ Poly(A)-TSS-seq R1

value: mESC

value: WT

value: day 7 DBZ


title: DON - Rep4

description:
Library name: RS2156.S8
RS2156.S8


title: d4 Poly(A)-TSS-seq R1

description: Library name: d4 Poly(A)-TSS-seq R1

value: day 4


title: PHL002 (Hi-C)

value: B-cell acute lymphoblastic leukemia

value: Primary B-ALL

value: BCR-ABL1 Like


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr8; theta collection; rep2

description: Library name: x4p53-aph-lamhtgts-ipolq-chr8-LC247-rep2

value: ES cell derived NPC


title: PreB001 (Hi-C)

value: Healthy bone marrow

value: Healthy BM


title: REH_sgERG#1 (Hi-C)

value: REH

value: ERG KO


title: d3 Poly(A)-TSS-seq R1

description: Library name: d3 Poly(A)-TSS-seq R1

value: day 3


title: d3 Poly(A)-TSS-seq R2

description: Library name: d3 Poly(A)-TSS-seq R2


title: Hypoxia_KO_5

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez Ramirez

state: CA

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

data_processing:
Data was processed using the systempipeR workflow.
RNA reads were aligned to the GRCm39 genome assembly using hisat2.
Differential gene expression was calculated using EdgeR.
Assembly: GRCm39 release 104
Supplementary files format and content: BEC_RPKM_countDFeByg.csv
Supplementary files format and content: BEC_countDFeByg.csv

extract_protocol:
Isolatedbrain endothelial cells were harvested from animals and homogenized in TRIzol solution for RNAseq analysis according to the manufacturer’s instructions.
Following isolation, RNA quality was assessed using an Agilent Tapestation 4200. Only samples with with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the Illumina Stranded mRNA Prep according to the manufacturer’s insturctions.

treatment_protocol: Hypoxic conditions consisted of 12% O2,  for seven days and normoxic conditions consisted of 21% O2.


title: CONTROL - Rep3

description:
Library name: RS2156.S6
RS2156.S6

value: CONTROL


title: wild-type; NSPC; Aph; lamhtgts; chr6; theta collection; rep1

description: Library name: wt-aph-lamhtgts-chr6-LC224-rep1

value: Primary NSPC

value: Wild-type

value: APH


title: d7 Poly(A)-TSS-seq R2

description: Library name: d7 Poly(A)-TSS-seq R2

value: mESC

value: day 7


title: PHL001 (Hi-C)


title: DON_ACRYLAMIDE - Rep3

description:
Library name: RS2156.S7
RS2156.S7


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr8; theta collection; rep3

description: Library name: x4p53-ipolq-lamhtgts-chr8-LC185-rep3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr8; theta collection; rep3

description: Library name: x4p53-aph-lamhtgts-chr8-LC176-rep3


title: d7 Poly(A)-TSS-seq R1

description: Library name: d7 Poly(A)-TSS-seq R1

value: WT


title: iAMP21001 (Hi-C)


title: DON - Rep1

description:
Library name: RS2156.S4
RS2156.S4

value: DON


title: d6 Poly(A)-TSS-seq R2

description: Library name: d6 Poly(A)-TSS-seq R2

value: day 6


title: d6 Poly(A)-TSS-seq R1

description: Library name: d6 Poly(A)-TSS-seq R1


title: DON_ACRYLAMIDE - Rep2

description:
Library name: RS2156.S3
RS2156.S3


title: d5 Poly(A)-TSS-seq R2

description: Library name: d5 Poly(A)-TSS-seq R2

value: day 5


title: CONTROL - Rep2

description:
Library name: RS2156.S2
RS2156.S2


title: PreB003 (Hi-C)

value: Pre-B


title: Hypoxia_KO_3

value: Brain


title: d4 Poly(A)-TSS-seq R2

description: Library name: d4 Poly(A)-TSS-seq R2

value: day 4


title: d0 Poly(A)-TSS-seq R2

description: Library name: d0 Poly(A)-TSS-seq R2

value: day 0


title: d0 Poly(A)-TSS-seq R1

description: Library name: d0 Poly(A)-TSS-seq R1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr8; theta collection; rep2

description: Library name: x4p53-dmso-lamhtgts-chr8-LC172-rep2

value: ES cell derived NPC

value: DMSO


title: Hypoxia_KO_2


title: Hypoxia_KO_1


title: OTH004 (Hi-C)

value: B-cell acute lymphoblastic leukemia

value: Primary B-ALL

value: Other


title: Hypoxia_Flox_5

value: Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a


title: d5 Poly(A)-TSS-seq R1

description: Library name: d5 Poly(A)-TSS-seq R1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr6; theta collection; rep2

description: Library name: x4p53-ipolq-lamhtgts-chr6-LC195-rep2


title: Immune Cells from CT2A bearing wildtype mouse

description: Library name: WT

value: Immune Cells

value: Wildtype


title: PH003 (Hi-C)


title: Hypoxia_KO_4


title: OTH001 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr8; theta collection; rep1

description: Library name: x4p53-aph-lamhtgts-ipolq-chr8-LC186-rep1

value: ATR558 plus aphidicolin


title: d2 Poly(A)-TSS-seq R2

description: Library name: d2 Poly(A)-TSS-seq R2

value: mESC

value: WT

value: day 2


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr6; theta collection; rep1

description: Library name: x4p53-ipolq-lamhtgts-chr6-LC194-rep1


title: Hypoxia_Flox_3


title: KMT2Ar005 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; theta collection; rep2

description: Library name: x4p53-dmso-lamhtgts-chr6-LC192-rep2


title: PH002 (Hi-C)


title: ASH2L gRNA TSS1 R2

description: Library name: ASH2L gRNA TSS1 R2

data_processing:
ChIP-seq of ASH2L and H3K4me3 were processed using the nf-core chipseq pipeline revision: 2.0.0 against a composite mouse (GRCm38) and Drosophila (BDGP6-46) genome. Transcript annotations were derived from the mouse Ensembl release 102. Peak-calling was conducted using MACS2 against matched input controls (--macs_gsize 2467481108 , --macs_fdr 0.05), considering the ENCODE mm10 blacklist to remove false positives. Bigwig files representing genome-wide coverage were created directly from the BAM files and scaled based on the Drosophila spike-in.  A per-sample scale factor was derived by dividing the smallest observed spike-in read count across all samples by the equivalent count from the sample in question. The Bioconductor packages DiffBind and DESeq2 were used to test for differential binding between H3K4me3 conditions.  Consensus peaks (i.e. a reduced set of all peaks found consistently in the 3 replicates of each group) were resized to each have a width of 2kb centred around their summits. Next, the Control (input) read counts were subtracted for each site in each sample before normalisation using the spike-in reads via a “background” approach.  Essentially, the spike-in genome was divided into “background” bins of sufficient size (15000bp) so as to not show differential enrichment between samples. Counts over these bins were then used to generate per-sample scale-factors and passed to DESeq2 for significance testing of pairwise comparisons, thresholding for significance at FDR<0.05.  A post filter (minimum peak signal to >=300, fold-change>1.25) was used to remove weak peaks after manual inspection.
Assembly: GRCm38
Supplementary files format and content: Bigwig

growth_protocol: The chromatin immunoprecipitation (ChIP) protocol was adapted from.1.6 million HM-1 in 2i/LIF media and 2.5 million NIH/3T3 cells were plated in 15-cm plates, and 48 hours later the cells were fixed for 10 minutes at 37°C with a 1% formaldehyde solution in PBS, before the reaction was quenched with 250 mM glycine. Cells were washed twice in cold PBS before being collected using a cell scraper in 3 ml of cold PBS containing 1x protease inhibitor cocktail (Roche).

extract_protocol:
Following centrifugation the cell pellet was lysed in 5 ml of lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% Triton-X-100, 1x protease inhibitor cocktail, 1 mM PMSF), then washed in 5 ml of buffer (5 mM HEPES pH 8.0, 85 mM KCl, 1x protease inhibitor cocktail, 1 mM PMSF), before being resuspended in buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA, 1x Protease inhibitor cocktail, 1 mM PMSF) and snap-frozen on dry ice. Once the samples were thawed, sonication was carried out with 5 cycles of 30 seconds on/off (Bioruptor Plus (Diagenode), low intensity setting). Following centrifugation, 10% of the sample was removed for input. The input sample was treated with proteinase K (NEB) overnight at 65°C and purified using Zymo ChIP and concentrate, and used to check for sonication efficiency. The remaining sample was precleared with a 1:1 mix of protein-A and protein-G Dynabeads (pre-equilibrated in PBS 0.1% BSA) for 1 hour at 4°C. The pre-cleared sample was then mixed with the antibody overnight at 4°C, before 1:1 mix of protein-A and protein-G Dynabeads (pre-equilibrated in PBS 0.1% BSA) were added for 2 hours. The beads were then washed 3 times in FA/SDS solution (50 mM HEPES KOH pH 7.5, 150 mM NaCl, 1% Triton-X-100, 0.1% Na deoxycholate, 1x Protease inhibitor cocktail, 1 mM PMSF) with the last wash being performed for 10 minutes at 4°C. The beads were then washed once in WB buffer (10 mM Tris-HCl pH 8, 0.25 M LiCl, 1 mM EDTA, 0.5% NP40, 0.5% Na-deoxycholate), once in TE (Tris/EDTA) buffer pH 8.0, before being eluted in elution buffer (25 mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% SDS) at 65°C for 25 minutes. The samples were treated with RNase (NEB) for 30 minutes at 37°C before being reverse crosslinked overnight with Proteinase K at 65°C, and finally purified with Zymo ChIP clean and concentrate.
For ChIP-seq, libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina accordingly.

value: gRNA TSS1


title: Normoxia_KO_6


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr6; theta collection; rep3

description: Library name: x4p53-aph-lamhtgts-ipolq-chr6-LC198-rep3


title: PH001 (Hi-C)


title: KMT2Ar003 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr8; theta collection; rep2

description: Library name: x4p53-aph-lamhtgts-chr8-LC175-rep2

value: APH


title: d2 Poly(A)-TSS-seq R1

description: Library name: d2 Poly(A)-TSS-seq R1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr8; theta collection; rep1

description: Library name: x4p53-aph-lamhtgts-chr8-LC174-rep1


title: OTH003 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr6; theta collection; rep3

description: Library name: x4p53-ipolq-lamhtgts-chr6-LC196-rep3


title: ASH2L gRNA TSS2 R3

description: Library name: ASH2L gRNA TSS2 R3

value: gRNA TSS2


title: Hypoxia_Flox_4

value: Brain


title: KMT2Ar001 (Hi-C)


title: ASH2L gRNA TSS2 R2

description: Library name: ASH2L gRNA TSS2 R2


title: OTH002 (Hi-C)


title: Normoxia_KO_2


title: ASH2L control R2

description: Library name: ASH2L control R2

value: control


title: Hypoxia_Flox_2


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr6; theta collection; rep1

description: Library name: x4p53-aph-lamhtgts-chr6-LC193-rep1

value: ES cell derived NPC


title: ASH2L control R1

description: Library name: ASH2L control R1


title: ASH2L gRNA TSS2 R1

description: Library name: ASH2L gRNA TSS2 R1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; theta collection; rep1

description: Library name: x4p53-dmso-lamhtgts-chr6-LC191-rep1

value: DMSO


title: ImmatureB002 (Hi-C)

value: Healthy bone marrow

value: Healthy BM

value: Immature-B


title: Normoxia_KO_1


title: ASH2L gRNA TSS1 R3

description: Library name: ASH2L gRNA TSS1 R3


title: KMT2Ar004 (Hi-C)

value: B-cell acute lymphoblastic leukemia

value: Primary B-ALL


title: ASH2L control R3

description: Library name: ASH2L control R3


title: Normoxia_Flox_4

value: Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a


title: ASH2L gRNA TSS1 R1

description: Library name: ASH2L gRNA TSS1 R1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr6; theta collection; rep2

description: Library name: x4p53-aph-lamhtgts-ipolq-chr6-LC197-rep2

value: ATR558 plus aphidicolin


title: input ASH2L gRNA TSS1 mESC

description: Library name: input ASH2L gRNA TSS1 mESC

value: mESC


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr12; theta collection; rep1

description: Library name: x4p53-ipolq-lamhtgts-chr12-LC204-rep1


title: HD001 (Hi-C)

value: Hyperdiploid


title: KMT2Ar002 (Hi-C)


title: input ASH2L gRNA TSS2  mESC

description: Library name: input ASH2L gRNA TSS2  mESC


title: input ASH2L control mESC

description: Library name: input ASH2L control mESC


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr12; theta collection; rep2

description: Library name: x4p53-dmso-lamhtgts-chr12-LC201-rep2


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr6; theta collection; rep1

description: Library name: x4p53-aph-lamhtgts-ipolq-chr6-LC190-rep1


title: Normoxia_KO_4


title: Normoxia_Flox_1


title: Rats, diabetic,rep3

city: Hefei

first: xiaomin

last: nie

address: 17 Lujiang Road

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

description: Library name: s3

data_processing:
Raw reads obtained from sequencing machines contained adapters or low-quality bases, which could impact subsequent assembly and analysis. Therefore, to obtain high-quality clean reads, the data were filtered via fastp (version 0.18.0). The filtering parameters were as follows: 1) removal of reads containing adapters; 2) removal of reads with more than 10% unknown nucleotides (N); and 3) removal of low-quality reads containing more than 50% low-quality bases (Q value ≤ 20). Short reads were aligned to the ribosomal RNA (rRNA) database via Bowtie2 (version 2.2.8). Reads mapped to rRNA were subsequently removed, and the remaining clean reads were used for assembly and gene abundance calculation. An index of the reference genome was created, and paired-end clean reads were mapped to the reference genome via HISAT2 (version 2.4) with "-rna-strandness RF" and other parameters set to defaults. The mapped reads of each sample were assembled via StringTie v1.3.1 via a reference-based approach. For each transcription region, a Fragments Per Kilobase of transcript per Million mapped reads (FPKM) value was calculated to quantify expression abundance and variations via RSEM software.
Assembly: mRatBN7.2 (rn7)
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: csv files include raw counts for each Sample

source_name: central amygdala

extract_protocol:
Total RNA was extracted via a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed via an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and confirmed via RNase-free agarose gel electrophoresis. Following RNA extraction, eukaryotic mRNA was enriched via oligo (dT) beads.
The enriched mRNA was then fragmented into short fragments via fragmentation buffer and reverse transcribed into cDNA via the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end-repaired, a base was added, and the fragments were ligated to Illumina sequencing adapters. The ligation reaction mixture was purified via AMPure XP beads (1.0X). Ligated fragments underwent size selection through agarose gel electrophoresis and were then amplified via polymerase chain reaction (PCR). The resulting cDNA library was sequenced via an Illumina NovaSeq 6000 system by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: central amygdala

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

tag: sample group

value: diabetic


title: ETV004 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr12; theta collection; rep3

description: Library name: x4p53-aph-lamhtgts-ipolq-chr12-LC189-rep3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr12; theta collection; rep3

description: Library name: x4p53-ipolq-lamhtgts-chr12-LC206-rep3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; ART558; lamhtgts; chr12; theta collection; rep2

description: Library name: x4p53-ipolq-lamhtgts-chr12-LC205-rep2


title: ETV003 (Hi-C)


title: ImmatureB001 (Hi-C)


title: Normoxia_KO_5

value: Brain


title: Normoxia_Flox_2


title: ImmatureB003 (Hi-C)


title: ETV005 (Hi-C)


title: H3k4me3 gRNA TSS2 R3 3T3

description: Library name: H3k4me3 gRNA TSS2 R3 3T3

value: gRNA TSS2


title: Rats, control,rep3

description: Library name: c6

value: control


title: Normoxia_Flox_3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr12; theta collection; rep1

description: Library name: x4p53-dmso-lamhtgts-chr12-LC199-rep1

value: ES cell derived NPC

value: DMSO


title: H3k4me3 gRNA TSS2 R2 3T3

description: Library name: H3k4me3 gRNA TSS2 R2 3T3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr12; theta collection; rep2

description: Library name: x4p53-aph-lamhtgts-ipolq-chr12-LC188-rep2


title: Rats, diabetic,rep2

description: Library name: s4


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr12; theta collection; rep2

description: Library name: x4p53-aph-lamhtgts-chr12-LC203-rep2

value: APH


title: H3k4me3 gRNA TSS2 R1 3T3

description: Library name: H3k4me3 gRNA TSS2 R1 3T3


title: ETV002 (Hi-C)


title: CLP003 (Hi-C)

value: Healthy bone marrow

value: Healthy BM

value: Common lymphoid progenitor


title: Rats, diabetic,rep1

description: Library name: s5


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr12; theta collection; rep1

description: Library name: x4p53-aph-lamhtgts-chr12-LC202-rep1


title: Rats, control,rep2

description: Library name: c4


title: ETV001 (Hi-C)

value: B-cell acute lymphoblastic leukemia

value: Primary B-ALL


title: H3k4me3 gRNA TSS1 R2 3T3

description: Library name: H3k4me3 gRNA TSS1 R2 3T3

value: gRNA TSS1


title: SEM_sgCTRL#2 (RNA-seq)

data_processing:
Reads were processed using the Seq-N-Slide pipeline, where trimmed reads were aligned to GRCh37 and genes annotated with the corresponding GTF file using STAR version 2.7.3a.DEseq2 was used for differential gene expression analysis and TPM counts generation. An excel files containing TPM counts are provided.
Assembly: hg19
Supplementary files format and content: TPM counts file

molecule: polyA RNA

value: SEM B-ALL

value: ERG WT


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr14; rep3

description: Library name: Nrg3-parental-APH-lamhtgts-chr14-LC177-rep3


title: Rats, control,rep1

description: Library name: c5

value: central amygdala

value: Sprague-Dawley


title: RBNS_noEDTA_ZC3H4_2400nM_rep2

city: Milano

first: Gaurav

last: Mandana

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology

description:
Library name: RBNS_53
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt

data_processing:
All libraries were sequenced in paired-end mode, but only Read 1 (R1) was used for downstream analysis, according to standard RBNS protocols; Read 2 (R2) was discarded.
Reads were adapter-trimmed (adapter sequence: TGGAAT), demultiplexed by barcode, and trimmed to a fixed length of 40 nt before k-mer analysis. K-mer counting was performed using the pipeline described by Lambert et al. (2014) PMID: 24837674, with the following parameters: naive counting mode (ks=3–10), homopolymeric k-mers excluded, stream-based and position-specific models disabled.
All downstream analyses were performed with a custom script, starting from the k-mer count tables generated by the RBNS pipeline. Only 9-mers were selected for further analysis. Counts were normalized to total reads per library, and enrichment was computed relative to the 0 nM (no-protein) control. Only 9-mers with enrichment >1 over 0 nM were retained to reduce background. These filtered 9-mers were re-normalized, and final RBNS R-values were calculated relative to the input library. 9-mers with R-values greater than two standard deviations above the mean were considered enriched.
Assembly: No genome assembly used.
Supplementary files format and content: The processed data files consist of raw 9-mer count tables, generated as described in Lambert et al., 2014 (PMID: 24837674). Each row represents a unique 9-mer sequence, and each column indicates the raw (unnormalized) count for that 9-mer in the corresponding experimental condition. Column headers indicate either the input or the concentration of recombinant ZC3H4 protein used in each library. Tables are provided as tab-delimited text files.

organism: synthetic construct

source_name: Not applicable; experiment uses in-vitro transcribed RNA

extract_protocol:
RNAs with a random region of 40nt were prepared by in vitro transcription and incubated with an increasing concentration of the three zinc fingers motif or ZC3H4-WDR82 omplex (0, 5, 20, 80, 320, 1200, 2400 and 6000 nM). Complexes were eluted from the beads by incubation in 50 μL elution buffer (10 mM Tris-HCl pH 7.0, 1mM EDTA, 1% SDS) at 70°C for 10 min. in agitation at 1200 rpm in a Thermomixer. RNA was extracted using the Trizol LS Reagent following the manufacturet's instruction
The extracted RNA was reverse transcribed into cDNA. Illumina sequencing libraries were generated by amplifying the resulting cDNA via PCR with Phusion DNA Polymerase (NEB M0530L). Primers containing Illumina adapters and a single index were used for this amplification.


title: H3k4me3 gRNA TSS1 R3 3T3

description: Library name: H3k4me3 gRNA TSS1 R3 3T3


title: H3k4me3 gRNA TSS1 R1 3T3

description: Library name: H3k4me3 gRNA TSS1 R1 3T3


title: SEM_sgERG#6 (RNA-seq)

value: ERG KO


title: CLP002 (Hi-C)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; lamhtgts; chr12; theta collection; rep1

description: Library name: x4p53-aph-lamhtgts-ipolq-chr12-LC187-rep1

value: ATR558 plus aphidicolin


title: H3k4me3 control R2 3T3

description: Library name: H3k4me3 control R2 3T3


title: H3k4me3 control R3 3T3

description: Library name: H3k4me3 control R3 3T3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr14; rep2

description: Library name: Nrg3-parental-APH-lamhtgts-chr14-LC170-rep2


title: RBNS_noEDTA_ZC3H4_1200nM_rep2

description:
Library name: RBNS_52
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt

value: Not applicable; experiment uses in-vitro transcribed RNA


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr14; rep4

description: Library name: Nrg3-parental-DMSO-lamhtgts-chr14-LC167-rep4


title: SEM_sgERG#4 (RNA-seq)


title: SEM_sgCTRL#1 (RNA-seq)


title: SEM_sgERG#1 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr14; rep3

description: Library name: Nrg3-parental-DMSO-lamhtgts-chr14-LC166-rep3


title: H3k4me3 control R1 3T3

description: Library name: H3k4me3 control R1 3T3

value: control


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr14; rep2

description: Library name: Nrg3-parental-DMSO-lamhtgts-chr14-LC165-rep2

value: ES cell derived NPC


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr14; rep1

description: Library name: Nrg3-parental-DMSO-lamhtgts-chr14-LC164-rep1

value: DMSO


title: RBNS_noEDTA_ZC3H4_5nM_rep2

description:
Library name: RBNS_48
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt


title: RBNS_noEDTA_ZC3H4_6000nM_rep2

description:
Library name: RBNS_54
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt


title: RBNS_noEDTA_ZC3H4_80nM_rep2

description:
Library name: RBNS_50
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt


title: H3k4me3 gRNA TSS2 R3 mESC

description: Library name: H3k4me3 gRNA TSS2 R3 mESC

value: mESC

value: gRNA TSS2


title: REH_sgCTRL#2 (RNA-seq)

value: REH B-ALL


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; lamhtgts; chr14; rep1

description: Library name: Nrg3-parental-APH-lamhtgts-chr14-LC169-rep1

value: APH


title: input control 3T3

description: Library name: input control 3T3


title: input gRNA TSS1 3T3

description: Library name: input gRNA TSS1 3T3


title: input gRNA TSS2  3T3

description: Library name: input gRNA TSS2  3T3


title: RBNS_noEDTA_ZC3H4_320nM_rep2

description:
Library name: RBNS_51
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; Aph; lamhtgts; chr14; rep3

description: Library name: Nrg3-pe-del2-APH-lamhtgts-chr14-LC178-rep3


title: RBNS_noEDTA_ZC3H4_6000nM_rep1

description:
Library name: RBNS_46
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: H3k4me3 gRNA TSS2 R1 mESC

description: Library name: H3k4me3 gRNA TSS2 R1 mESC


title: REH_sgERG#4 (RNA-seq)

value: B-cell acute lymphoblastic leukemia


title: H3k4me3 gRNA TSS2 R2 mESC

description: Library name: H3k4me3 gRNA TSS2 R2 mESC


title: H3k4me3 gRNA TSS1 R3 mESC

description: Library name: H3k4me3 gRNA TSS1 R3 mESC


title: REH_sgERG#6 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; Aph; lamhtgts; chr14; rep1

description: Library name: Nrg3-pe-del2-APH-lamhtgts-chr14-LC162-rep1


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; Aph; lamhtgts; chr14; rep2

description: Library name: Nrg3-pe-del2-APH-lamhtgts-chr14-LC163-rep2


title: REH_sgERG#1 (RNA-seq)


title: H3k4me3 gRNA TSS1 R2 mESC

description: Library name: H3k4me3 gRNA TSS1 R2 mESC


title: REH_sgCTRL#1 (RNA-seq)


title: RBNS_noEDTA_ZC3H4_20nM_rep2

description:
Library name: RBNS_49
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; Aph; lamhtgts; chr14; rep4

description: Library name: Nrg3-pe-del2-APH-lamhtgts-chr14-LC179-rep4


title: RBNS_noEDTA_ZC3H4_0nM_rep2

description:
Library name: RBNS_47
RBNS_noEDTA_ZC3H4_9mer_counts_rep2.txt


title: RBNS_noEDTA_ZC3H4_1200nM_rep1

description:
Library name: RBNS_44
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; lamhtgts; chr14; rep3

description: Library name: Nrg3-pe-del2-DMSO-lamhtgts-chr14-LC158-rep3


title: RBNS_noEDTA_ZC3H4_2400nM_rep1

description:
Library name: RBNS_45
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: RBNS_noEDTA_ZC3H4_320nM_rep1

description:
Library name: RBNS_43
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; lamhtgts; chr14; rep4

description: Library name: Nrg3-pe-del2-DMSO-lamhtgts-chr14-LC161-rep4


title: RBNS_noEDTA_ZC3H4_80nM_rep1

description:
Library name: RBNS_42
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: iAMP21002 (RNA-seq)


title: H3k4me3 gRNA TSS1 R1 mESC

description: Library name: H3k4me3 gRNA TSS1 R1 mESC


title: iAMP21001 (RNA-seq)


title: ProB003 (RNA-seq)

value: Healthy bone marrow

value: Healthy BM

value: Pro-B


title: H3k4me3 control R3 mESC

description: Library name: H3k4me3 control R3 mESC


title: ProB004 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; Aph; lamhtgts; chr14; rep4

description: Library name: Nrg3-pe-del1-APH-lamhtgts-chr14-LC181-rep4


title: ProB002 (RNA-seq)


title: input gRNA TSS1 mESC

description: Library name: input gRNA TSS1 mESC

value: gRNA TSS1


title: PreB004 (RNA-seq)

value: Pre-B


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; lamhtgts; chr14; rep2

description: Library name: Nrg3-pe-del2-DMSO-lamhtgts-chr14-LC157-rep2


title: RBNS_noEDTA_ZC3H4_0nM_rep1

description:
Library name: RBNS_39
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: POMC cells from PTKO;Ai9 mice, biol rep 2

city: Chengdu

first: Qin

last: Tang

state: Select...

address: 37 Guoxue Xiang, Wuhou District, Chengdu, Sichuan Province, China

institute: West China Hospital of Sichuan University

description:
Library name: Sample 4
ko-3

data_processing:
After the library construction was completed, initial quantification was performed using Qubit 4.0, followed by detection of the insert size distribution of the library using the Agilent 2100. Once the insert size met the expected criteria, the effective concentration of the library (with an effective concentration higher than 3 nM) was accurately quantified using the qRT-PCR method to ensure library quality.
Assembly: GRCm38.94
Supplementary files format and content: FPKM values for each Sample

source_name: Hypothalamus

extract_protocol:
The collected cells were subjected to RNA extraction using a specialized reagent provided by Shi-Bio Technology (Wuhan, China), with 1-1.5 μg of total RNA used for constructing the sequencing library.
The sequencing library was constructed using a modified high-activity Tn5 transposase to simultaneously fragment the DNA and add adapters to both ends of the cDNA.

value: Hypothalamus

value: KO

value: High-fat diet for 16 weeks


title: RBNS_ZC3H4_WDR82_80nM_rep2

description:
Library name: RBNS_36
RBNS_ZC3H4_WDR82_9mer_counts_rep2.txt

value: Not applicable; experiment uses in-vitro transcribed RNA


title: H3k4me3 control R1 mESC

description: Library name: H3k4me3 control R1 mESC

value: control


title: PreB001 (RNA-seq)


title: POMC cells from PTKO;Ai9 mice, biol rep 1

description:
Library name: Sample 3
ko-2


title: H3k4me3 control R2 mESC

description: Library name: H3k4me3 control R2 mESC


title: RBNS_ZC3H4_WDR82_20nM_rep2

description:
Library name: RBNS_35
RBNS_ZC3H4_WDR82_9mer_counts_rep2.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; lamhtgts; chr14; rep1

description: Library name: Nrg3-pe-del2-DMSO-lamhtgts-chr14-LC156-rep1

value: ES cell derived NPC


title: input gRNA TSS2  mESC

description: Library name: input gRNA TSS2  mESC


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; lamhtgts; chr14; rep2

description: Library name: Nrg3-pe-del1-DMSO-lamhtgts-chr14-LC154-rep2

value: DMSO


title: ProB001 (RNA-seq)


title: RBNS_ZC3H4_WDR82_1200nM_rep2

description:
Library name: RBNS_38
RBNS_ZC3H4_WDR82_9mer_counts_rep2.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; Aph; lamhtgts; chr14; rep3

description: Library name: Nrg3-pe-del1-APH-lamhtgts-chr14-LC180-rep3


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; Aph; lamhtgts; chr14; rep2

description: Library name: Nrg3-pe-del1-APH-lamhtgts-chr14-LC160-rep2


title: POMC cells from Pomc-cre;Ai9 mice, biol rep 1

description:
Library name: Sample 1
Ctrl-2

value: WT


title: PreB003 (RNA-seq)


title: input control mESC

description: Library name: input control mESC

value: mESC


title: RBNS_ZC3H4_WDR82_0nM_rep2

description:
Library name: RBNS_33
RBNS_ZC3H4_WDR82_9mer_counts_rep2.txt


title: RBNS_ZC3H4_WDR82_320nM_rep2

description:
Library name: RBNS_37
RBNS_ZC3H4_WDR82_9mer_counts_rep2.txt


title: PHL003 (RNA-seq)

value: Primary B-ALL

value: BCR-ABL1 Like


title: RBNS_noEDTA_ZC3H4_5nM_rep1

description:
Library name: RBNS_40
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: RBNS_noEDTA_ZC3H4_20nM_rep1

description:
Library name: RBNS_41
RBNS_noEDTA_ZC3H4_9mer_counts_rep1.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; rep7

description: Library name: Ctnna2-parental-DMSO-lamhtgts-chr6-VI059-rep7


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; lamhtgts; chr14; rep3

description: Library name: Nrg3-pe-del1-DMSO-lamhtgts-chr14-LC155-rep3


title: POMC cells from Pomc-cre;Ai9 mice, biol rep 2

description:
Library name: Sample 2
Ctrl-3


title: PreB002 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; rep6

description: Library name: Ctnna2-parental-DMSO-lamhtgts-chr6-VI053-rep6


title: RBNS_ZC3H4_WDR82_320nM_rep1

description:
Library name: RBNS_31
RBNS_ZC3H4_WDR82_9mer_counts_rep1.txt


title: RBNS_ZC3H4_WDR82_5nM_rep2

description:
Library name: RBNS_34
RBNS_ZC3H4_WDR82_9mer_counts_rep2.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; rep5

description: Library name: Ctnna2-parental-DMSO-lamhtgts-chr6-VI047-rep5


title: PHL002 (RNA-seq)

value: B-cell acute lymphoblastic leukemia


title: SFTPC, SARS-CoV-2 Infected, rep3

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: si3

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 algorithm
gene count measurements were obtained using FeatureCounts using refseq annotation
Assembly: mm9
Supplementary files format and content: Tab-delimited text file with columns: 1) GeneID, 2) Chr; 3) transcript start position; 4) transcript end position; 5) Strand; 6) Length of transcript; 7) read counts

extract_protocol:
Total RNA from organs of infected or control mice was isolated using Quick-RNA miniprep kit (Zymo Research)
Total RNA samples  were used for sequencing library preparation according to Illumina stranded mRNA sample preparation guide. Each library was bar-coded and then pooled for sequencing run with 100bp paired-end sequencing protocol.

treatment_protocol: Ten to twelve-week-old male and female mice were used for experiments. To induce hACE2 expression, 6–8-week-old adult mice were treated with 5mg tamoxifen (TAM) in 100ml of corn oil containing 10% ethanol by oral gavage for 4 consecutive days. Mice were used for experiments one month after TAM treatment. For SARS-CoV-2 infection, mice were infected with 1x105 PFU SARS-CoV-2 WA1/2020 in 50µl either intratracheally or intranasally, and RNA were harvested on day 5.

value: SftpcCreERT2 (Jax 028054) crossed with R26-LSL-hACE2 mice

value: lung

value: Mice were infected with 1x105 PFU SARS-CoV-2 WA1/2020 in 50µl either intratracheally or intranasally, and RNA were harvested on day 5.


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; lamhtgts; chr14; rep1

description: Library name: Nrg3-pe-del1-DMSO-lamhtgts-chr14-LC153-rep1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; rep4

description: Library name: Ctnna2-parental-DMSO-lamhtgts-chr6-VI035-rep4


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; Aph; lamhtgts; chr14; rep1

description: Library name: Nrg3-pe-del1-APH-lamhtgts-chr14-LC159-rep1

value: APH


title: RBNS_ZC3H4_WDR82_20nM_rep1

description:
Library name: RBNS_29
RBNS_ZC3H4_WDR82_9mer_counts_rep1.txt


title: SFTPC, Naive, rep3

description: Library name: sn4

value: no infection


title: PHL001 (RNA-seq)


title: RBNS_ZC3H4_WDR82_5nM_rep1

description:
Library name: RBNS_28
RBNS_ZC3H4_WDR82_9mer_counts_rep1.txt


title: RBNS_ZC3H4_WDR82_1200nM_rep1

description:
Library name: RBNS_32
RBNS_ZC3H4_WDR82_9mer_counts_rep1.txt


title: SFTPC, Naive, rep2

description: Library name: sn3


title: PH003 (RNA-seq)


title: SFTPC, Naive, rep1

description: Library name: sn2


title: RBNS_ZC3H4_WDR82_80nM_rep1

description:
Library name: RBNS_30
RBNS_ZC3H4_WDR82_9mer_counts_rep1.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; rep1

description: Library name: Ctnna2-parental-DMSO-lamhtgts-chr6-LC024-rep1


title: PH001 (RNA-seq)


title: CC10, Naïve, rep1

description: Library name: cn2

value: CC10CreER mice (Jax 016225) crossed with R26-LSL-hACE2 mice


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; rep2

description: Library name: Ctnna2-parental-DMSO-lamhtgts-chr6-VI020-rep2


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; Aph; lamhtgts; chr6; rep3

description: Library name: Ctnna2-pe-del2-APH-lamhtgts-chr6-VI066-rep3


title: SFTPC, SARS-CoV-2 Infected, rep2

description: Library name: si2


title: CC10, Naïve, rep3

description: Library name: cn4


title: RBNS_ZC3H4_20nM_rep2

description:
Library name: RBNS_23
RBNS_ZC3H4_9mer_counts_rep2.txt


title: CC10, SARS-CoV-2 Infected, rep3

description: Library name: ci3


title: SFTPC, SARS-CoV-2 Infected, rep1

description: Library name: si1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; lamhtgts; chr6; rep3

description: Library name: Ctnna2-parental-DMSO-lamhtgts-chr6-PW055-rep3


title: RBNS_ZC3H4_80nM_rep2

description:
Library name: RBNS_24
RBNS_ZC3H4_9mer_counts_rep2.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; lamhtgts; chr6; rep3

description: Library name: Ctnna2-pe-del2-DMSO-lamhtgts-chr6-VI065-rep3


title: PH002 (RNA-seq)


title: RBNS_ZC3H4_1200nM_rep2

description:
Library name: RBNS_26
RBNS_ZC3H4_9mer_counts_rep2.txt


title: OTH003 (RNA-seq)

value: Other


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; Aph; lamhtgts; chr6; rep2

description: Library name: Ctnna2-pe-del2-APH-lamhtgts-chr6-VI058-rep2


title: OTH001 (RNA-seq)


title: RBNS_ZC3H4_0nM_rep2

description:
Library name: RBNS_21
RBNS_ZC3H4_9mer_counts_rep2.txt


title: KMT2Ar005 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; lamhtgts; chr6; rep2

description: Library name: Ctnna2-pe-del2-DMSO-lamhtgts-chr6-VI057-rep2


title: CC10, SARS-CoV-2 Infected, rep1

description: Library name: ci1


title: CC10, Naïve, rep2

description: Library name: cn3


title: OTH004 (RNA-seq)


title: KMT2Ar002 (RNA-seq)


title: RBNS_ZC3H4_1200nM_rep1

description:
Library name: RBNS_20
RBNS_ZC3H4_9mer_counts_rep1.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; Aph; lamhtgts; chr6; rep1

description: Library name: Ctnna2-pe-del2-APH-lamhtgts-chr6-VI034-rep1


title: KMT2Ar001 (RNA-seq)


title: KMT2Ar004 (RNA-seq)


title: Tuberous Sclerosis Mice Renal Cystadenomas (biol rep 3)

first: Uchenna

last: Unachukwu

state: New York

address: 630 West 168th Street, P&S 7-430

department: Anesthesiology

institute: Columbia University Medical Center

description:
Library name: DU03
10x Genomics

data_processing:
Cell Ranger (v6.1.2; 10x genomics) was used to demultiplex, generate FASTQ files, align reads to the GRCm38 (mouse), filter both cell- and unique molecular identifier (UMI) barcodes, and count gene expression per cell.
Assembly: GRCm38 (mouse)
Supplementary files format and content: Tar archive file containing the main outputs from a cellranger count analysis

source_name: Renal Cystadenoma

extract_protocol:
Excised renal tissues/tumors were rinsed twice with ice-cold phosphate-buffered saline (PBS), minced with fine, sterile razors, and incubated in digestion buffer (2 mg/ml collagenase I + 10ug/ml DNase I + elastase (0.075 U/ml) + 10mM EDTA dissolved in DMEM), at 37°C in a shaker at 300 rpm for 45 mins and then again for 30mins after vigorously trituration. Samples were centrifuged at 200 x g for 3 minutes at room temperature, and pellets were resuspended in 1x red blood cell lysis buffer for 10 minutes at room temperature. Lysis buffer is neutralized by mixing an equal volume of cell sorting media (PBS + 0.5% FBS) to the suspension, followed by centrifugation for 3 min at 200 x g at 4°C. Tissue pellets were resuspended in cell sorting media and passed sequentially through 100µm, 70µm, and 40µm cell strainers. After counting, cells were incubated with sytox green viability dye (1:1000 (v/v)) for 10 minutes in the dark at 4°C prior to cell sorting by flow cytometry using a BD FACS Aria II cell sorter (Becton Dickinson). Sytox Green (-) fractions per sample with cell viability of >85% were adjusted to 1000 cells/µl concentration before sequencing.
Cell suspensions were sequenced using the 10x Genomics 3’ Single Cell Gene Expression (GEX) workflow. Gel bead partitioning and cellular barcoding were done in the 10x Genomics Chromium Single Cell Controller, and library construction was performed using Illumina Single Cell 3’ v3 chemistry according to the Chromium Single Cell 3' GEM library & gel bead kit protocol (version 3; 10x Genomics). Single-cell transcriptome libraries were pooled and sequenced on a NovaSeq6000 System (Illumina).

treatment_protocol: 8-month-old wildtype B6129SF2/J mice renal tissues (JAX #101045; N=3 female mice, 1 tissue per mouse) versus 8-month-old  tuberous sclerosis Tsc2+/- mice renal adenocarcinomas (JAX #004686; (N=4 female mice, 3-7 tumors per mouse)  (JAX: The Jackson Laboratories, Bar Harbor, ME)

value: Renal Cystadenoma

value: Renal Cystadenoma Cells

value: Tsc2 heterozygote


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; Aph; lamhtgts; chr6; rep4

description: Library name: Ctnna2-pe-del1-APH-lamhtgts-chr6-VI064-rep4

value: ES cell derived NPC


title: OTH002 (RNA-seq)


title: KMT2Ar003 (RNA-seq)


title: RBNS_ZC3H4_320nM_rep2

description:
Library name: RBNS_25
RBNS_ZC3H4_9mer_counts_rep2.txt

value: Not applicable; experiment uses in-vitro transcribed RNA


title: CC10, SARS-CoV-2 Infected, rep2

description: Library name: ci2


title: RBNS_ZC3H4_20nM_rep1

description:
Library name: RBNS_17
RBNS_ZC3H4_9mer_counts_rep1.txt


title: RBNS_ZC3H4_5nM_rep2

description:
Library name: RBNS_22
RBNS_ZC3H4_9mer_counts_rep2.txt


title: ImmatureB001 (RNA-seq)

value: Healthy bone marrow

value: Healthy BM

value: Immature-B


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; Aph; lamhtgts; chr6; rep1

description: Library name: Ctnna2-pe-del1-APH-lamhtgts-chr6-VI033-rep1


title: Tuberous Sclerosis Mice Renal Cystadenomas (biol rep 1)

description:
Library name: DU002
10x Genomics


title: Tuberous Sclerosis Mice Renal Cystadenomas (biol rep 4)

description:
Library name: DU04
10x Genomics


title: RBNS_ZC3H4_0nM_rep1

description:
Library name: RBNS_15
RBNS_ZC3H4_9mer_counts_rep1.txt


title: Wildtype Mice Renal Cortical Tissue (biol rep 2)

description:
Library name: DU01
10x Genomics

source_name: Renal Cortex

value: Renal Cortex

value: Renal Cortical Cells

value: Wildtype


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; lamhtgts; chr6; rep1

description: Library name: Ctnna2-pe-del2-DMSO-lamhtgts-chr6-LC025-rep1

value: DMSO


title: ETV007 (RNA-seq)

value: B-cell acute lymphoblastic leukemia

value: Primary B-ALL


title: RBNS_ZC3H4_320nM_rep1

description:
Library name: RBNS_19
RBNS_ZC3H4_9mer_counts_rep1.txt


title: ImmatureB004 (RNA-seq)


title: ETV006 (RNA-seq)


title: RBNS_ZC3H4_WDR82_1200nM_rep3

description:
Library name: RBNS_13
RBNS_ZC3H4_WDR82_9mer_counts_rep3.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; lamhtgts; chr6; rep2

description: Library name: Ctnna2-pe-del1-DMSO-lamhtgts-chr6-VI045-rep2


title: Tuberous Sclerosis Mice Renal Cystadenomas (biol rep 2)

description:
Library name: JU001
10x Genomics


title: Wildtype Mice Renal Cortical Tissue (biol rep 3)

description:
Library name: DU02
10x Genomics


title: RBNS_ZC3H4_WDR82_320nM_rep3

description:
Library name: RBNS_12
RBNS_ZC3H4_WDR82_9mer_counts_rep3.txt


title: shCdkn2a_shSlc39a9 #2_treated with anti-PD1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: PD1_1250

data_processing:
SCIPIO cell bar codes were replaced with Illumina cell bar codes using the method cellRanger software uses to identify cell barcodes. Then using mm10(gtf, fasta) and cellRanger(7.0.1)  software, fastq files were processed to make matrix,feature for each sample.
Assembly: Mouse MM10
Supplementary files format and content: Matrix(gene expression), feature(genes), barcodes(cell bar codes) are text files

source_name: Melanoma

growth_protocol: Yumm5.2 murine melanoma cells (ATCC, catalog no. CRL-3367, RRID: CVCL_JK43) were cultured in DMEM and Ham's F-12 (50/50) media (Corning, catalog no. 10-092-CV), supplemented with nonessential amino acids (Corning, catalog no. 25-025-Cl), 10% fetal bovine serum (FBS; BioWest, catalog no. S1620), and 1% Penicillin/Streptomycin (Gibco, catalog no. 15-140-122). Cells were maintained at 37°C in a humidified incubator with 5% CO₂. Three hundred fifty thousand cells were implanted subcutaneously in the right flank of C57BL/6 mice. Once palpable mice were randomized and assigned to corresponding treatment (anti-PD1 or IgG , three times a week, i.p). The antibodies used were: anti-mouse PD-1 (Leinco Technologies, catalog no. P362) or placebo IgG2a (Leinco Technologies, catalog no. I-1177).

extract_protocol:
To obtain a single-cell suspension, dissected tumors were enzymatically and mechanically disrupted. First, the tumors were mechanically minced using surgical disposable scalpels (Surgical Design, catalog no. SCALPEL 12B) into pieces smaller than 5 mm in diameter on a 6 cm plate (Falcon, catalog no. 353002). Next, 2 mL of enzymatic cocktail [8 mg of collagenase IV (Gibco, catalog no. 17104-019), 800 µL of dispase (Stem Cell Technologies, catalog no. 07913), and 25 µg of DNase (Sigma Aldrich, catalog no. D4263-5VL) diluted in FBS-free MEM (Corning, catalog no. 10-009-CV)] was added to the minced tumors. The mixture was incubated for 20 minutes at 37°C in a non-CO₂ incubator. Minced tumor pieces were then further disrupted by smashing them between two fully frosted cytology slides (Fisherbrand, catalog no. 1255015). The resulting single-cell suspension was filtered through a 70 µm strainer (Fisherbrand, catalog no. 22-363-548) and resuspended in 5 mL of FBS-free media. The cells were centrifuged at 350 g for 5 minutes at 4°C and resuspended in 1x RBC lysis buffer (BD, catalog no. 555899). The RBC lysis reaction was incubated for 2–5 minutes at room temperature, after which the reaction was stopped by adding 5 mL of FBS-free media. The cells were then centrifuged at 350 g for 5 minutes at 4°C, resuspended in DPBS, and were ready for subsequent procedures.
Libraries were prepared using the single-cell RNA-Seq Benchtop kit (catalog no. 001-100) following the manufacturer’s instructions

value: Melanoma

value: 200ug anti-PD1


title: shCdkn2a_shSlc39a9 #2_treated with IgG

description: Library name: IgG_1250

treatment_protocol: Once palpable mice were randomized and assigned to corresponding treatment (anti-PD1 or IgG , three times a week, i.p). The antibodies used were: anti-mouse PD-1 (Leinco Technologies, catalog no. P362) or placebo IgG2a (Leinco Technologies, catalog no. I-1177).

value: 200ug IgG


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; Aph; lamhtgts; chr6; rep3

description: Library name: Ctnna2-pe-del1-APH-lamhtgts-chr6-VI052-rep3

data_processing:
*library strategy: linear amplification (LAM)-High-throughput Genome-wide Translocation Sequencing (HTGTS)
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sigularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: GRO-seq: bigwig files for plus and minus strands.
Supplementary files format and content: LAM-HTGTS: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Repli-seq: log2 smoothed ratio file for early and late fractions.

value: APH


title: ImmatureB003 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; lamhtgts; chr6; rep1

description: Library name: Ctnna2-pe-del1-DMSO-lamhtgts-chr6-LC026-rep1


title: ETV004 (RNA-seq)


title: shCdkn2a_shSlc39a9 #1_treated with IgG

description: Library name: IgG_1246


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; late; rep2

description:
Library name: Ctnna2-pe-del2-repliseq-late-rep2
18_4_rep2_log2smooth_50000.bedgraph

data_processing:
*library strategy: Repli-seq
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sigularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: GRO-seq: bigwig files for plus and minus strands.
Supplementary files format and content: LAM-HTGTS: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Repli-seq: log2 smoothed ratio file for early and late fractions.

value: solution control (DMSO)


title: RBNS_ZC3H4_5nM_rep1

description:
Library name: RBNS_16
RBNS_ZC3H4_9mer_counts_rep1.txt


title: Wildtype Mice Renal Cortical Tissue (biol rep 1)

description:
Library name: DU001
10x Genomics


title: RBNS_ZC3H4_80nM_rep1

description:
Library name: RBNS_18
RBNS_ZC3H4_9mer_counts_rep1.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; Aph; lamhtgts; chr6; rep2

description: Library name: Ctnna2-pe-del1-APH-lamhtgts-chr6-VI046-rep2


title: HD001 (RNA-seq)

value: Hyperdiploid


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; late; rep1

description:
Library name: Ctnna2-pe-del2-repliseq-late-rep1
18_4_rep1_log2smooth_50000.bedgraph

value: ES cell derived NPC


title: RBNS_ZC3H4_WDR82_20nM_rep3

description:
Library name: RBNS_10
RBNS_ZC3H4_WDR82_9mer_counts_rep3.txt

value: Not applicable; experiment uses in-vitro transcribed RNA


title: ETV002 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; lamhtgts; chr6; rep4

description: Library name: Ctnna2-pe-del1-DMSO-lamhtgts-chr6-VI063-rep4


title: RBNS_INPUT_rep1

description:
Library name: RBNS_14
RBNS_ZC3H4_9mer_counts_rep1.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; lamhtgts; chr6; rep3

description: Library name: Ctnna2-pe-del1-DMSO-lamhtgts-chr6-VI051-rep3


title: shCdkn2a_shControl_treated with IgG

description: Library name: IgG_1333


title: ETV005 (RNA-seq)


title: ETV003 (RNA-seq)


title: RBNS_ZC3H4_WDR82_0nM_rep3

description:
Library name: RBNS_8
RBNS_ZC3H4_WDR82_9mer_counts_rep3.txt


title: CLP004 (RNA-seq)

value: Healthy bone marrow

value: Common lymphoid progenitor


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; early; rep1

description:
Library name: Ctnna2-pe-del2-repliseq-early-rep1
18_4_rep1_log2smooth_50000.bedgraph


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; late; rep2

description:
Library name: Ctnna2-pe-del1-repliseq-late-rep2
38_3_rep2_log2smooth_50000.bedgraph


title: RBNS_ZC3H4_320nM_rep3

description:
Library name: RBNS_6
RBNS_ZC3H4_9mer_counts_rep3.txt


title: CLP002 (RNA-seq)

value: Healthy BM


title: RBNS_ZC3H4_80nM_rep3

description:
Library name: RBNS_5
RBNS_ZC3H4_9mer_counts_rep3.txt


title: shCdkn2a_shSlc39a9 #1_treated with anti-PD1

description: Library name: PD1_1246


title: RBNS_ZC3H4_WDR82_5nM_rep3

description:
Library name: RBNS_9
RBNS_ZC3H4_WDR82_9mer_counts_rep3.txt


title: RBNS_ZC3H4_WDR82_80nM_rep3

description:
Library name: RBNS_11
RBNS_ZC3H4_WDR82_9mer_counts_rep3.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; early; rep2

description:
Library name: Ctnna2-pe-del1-repliseq-early-rep2
38_3_rep2_log2smooth_50000.bedgraph


title: Heart, AAV9-cTnT-EGFP, P10, TNC_13

city: Hangzhou

first: Xinjian

last: Wang

address: No. 866, yuhangtang Road, Xihu District

department: School of Medicine

institute: Zhejiang University

data_processing:
Raw sequence reads were obtained and de-multiplexed using the bcl2fastq script (v2.20). The RAVED pipeline was used to analyze RNA-Sequencing data. Adapter sequences in raw reads were removed using Trimmomatic (v.0.32), and overall QC metrics were obtained using FastQC (v.0.11.7). Trimmed reads for each sample were aligned to the mouse reference genome mm10 using STAR (v.2.7.1). Subsequently, Bamtools (v.2.3.0) was used to summarize the number of mapped reads, including junction-spanning reads. To compute the number of bases assigned to various classes of RNA, the Picard Tools (v.1.96) RnaSeqMetrics function was used, according to an mm10 refFlat file obtained from UCSC Genome Table Browser. Genome Table HTSeq (v.0.11.2) was used to quantify gene-level read counts, using provided mm10 mouse transcriptome files. Differential expression analysis was conducted using DESeq2 (v.1.22.2) under a negative binomial distribution model. This analysis filtered out genes with total read counts less than 10 before differential analysis and disabled the default option for independent filtering of differential expression results. Corresponding P-values were adjusted to q-values using the Benjamini-Hochberg method.
Assembly: mm10
Supplementary files format and content: Differential expressed genes between AAV9-cTnT-Cre-T2A-EGFP injection (Tsg101-KO, TCK) samples and AAV9-cTnT-EGFP injection (Control, Ctrl or TNC) samples.

source_name: Heart

growth_protocol: All mice housed in a certificated specific-pathogen-free (SPF) grade facility, with a temperature of 20-22°C and a light/dark cycle of 12 hours. They had free access to food and water.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104), following the manufacturer’s instructions.
To construct the RNA-sequencing libraries, 1 μg of purified RNA was used with the VAHTS Universal V10 RNA-seq Library Prep Kit (Vazyme), following the manufacturer’s instructions.

treatment_protocol: Postnatal-day-0 (P0) Tsg101F/F mice were injected with 2×1010 vg/g AAV9-cTnT-Cre-T2A-EGFP at P0 (called after TCK), with controls receiving an equivalent dose of AAV9-cTnT-EGFP (called after TNC). Hearts were harvest at P10.

value: Heart


title: Heart, AAV9-cTnT-EGFP, P10, TNC_11


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; early; rep2

description:
Library name: Ctnna2-pe-del2-repliseq-early-rep2
18_4_rep2_log2smooth_50000.bedgraph

extract_protocol:
Genomic DNA for LAM-HTGTS: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. RNA were removed by treating samples with RNAseA prior phenol/chlroform extraction. Genomic DNA for Repli-seq: cells were lyzed in proteinase K digestion buffer, fragmented by a Covaris fragmentation device to 200 bp, and nacent DNA were pulldowned by using an BrdU-specific antiboty.
We follow the published protocol, as indicated below, to construct the libraries. Repli-seq: https://www.nature.com/articles/nprot.2017.148 LAM-HTGTS: https://www.nature.com/articles/nprot.2016.043


title: ETV001 (RNA-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; early; rep1

description:
Library name: Ctnna2-pe-del1-repliseq-early-rep1
38_3_rep1_log2smooth_50000.bedgraph


title: RBNS_ZC3H4_1200nM_rep3

description:
Library name: RBNS_7
RBNS_ZC3H4_9mer_counts_rep3.txt


title: Heart, AAV9-cTnT-EGFP, P10, TNC_16


title: shCdkn2a_shControl_treated with anti-PD1

description: Library name: PD1_1333


title: SEM_ERG#3 (ChIP-seq)

data_processing:
Reads were processed using the Seq-N-Slide pipeline, where trimmed reads were aligned to GRCh37 using bowtie v2.3.4.1. Sambamba v0.6.8 was used to deduplicate aligned reads. Macs2 v2.1.2 was used for peak calling and bedtools v2.27.1 was used to generate bigwig files provided.
Assembly: hg19
Supplementary files format and content: bigwig

value: SEM B-ALL

value: WT

tag: chip antibody

value: ERG


title: CLP003 (RNA-seq)


title: Heart, AAV9-cTnT-Cre-T2A-EGFP, P10, TCK_6


title: RBNS_ZC3H4_0nM_rep3

description:
Library name: RBNS_2
RBNS_ZC3H4_9mer_counts_rep3.txt


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; late; rep1

description:
Library name: DMSO-repliseq-late-rep1
dmso_rep1_log2smooth_50000.bedgraph


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; late; rep2

description:
Library name: DMSO-repliseq-late-rep2
dmso_rep2_log2smooth_50000.bedgraph


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; late; rep1

description:
Library name: Ctnna2-pe-del1-repliseq-late-rep1
38_3_rep1_log2smooth_50000.bedgraph


title: RBNS_ZC3H4_20nM_rep3

description:
Library name: RBNS_4
RBNS_ZC3H4_9mer_counts_rep3.txt


title: Heart, AAV9-cTnT-Cre-T2A-EGFP, P10, TCK_5


title: Heart, AAV9-cTnT-EGFP, P10, TNC_12


title: RBNS_INPUT_rep3

description:
Library name: RBNS_1
RBNS_ZC3H4_9mer_counts_rep3.txt


title: RBNS_ZC3H4_5nM_rep3

description:
Library name: RBNS_3
RBNS_ZC3H4_9mer_counts_rep3.txt


title: SEM_ERG#1 (ChIP-seq)

value: B-cell acute lymphoblastic leukemia


title: SEM_CTCF#2 (ChIP-seq)

value: CTCF


title: SIA2-ADAR,rep2

city: Shanghai

first: Zhibo

last: Shao

institute: Fudan University Shanghai Cancer Center

description: Library name: T47D_SIA2_2

data_processing:
Raw reads were trimmed by fastp(v0.23.4) to obtain clean reads. Then clean reads were mapped by STAR (v2.7.11a) to hg38, and gene counts were generated through featureCounts (v2.0.6) with parameters "-t exon  -p  --countReadPairs"
Assembly: hg38
Supplementary files format and content: txt

source_name: cell line

extract_protocol:
The total RNA samples were treated with VAHTS mRNA Capture Beads (Vazyme) to enrich polyA+ RNA before constructing the RNA-seq libraries.
RNA-seq libraries were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme) following the manufacturer’s instructions. Briefly, polyA+ RNA samples were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer

value: Breast

value: Human breast cancer cells


title: SEM_INPUT  (ChIP-seq)


title: Heart, AAV9-cTnT-EGFP, P10, TNC_10


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; GRO-seq, rep2

first: Pei-Chi

institute: German Cancer Research Center

description: Library name: Nrg3-pe-del2-groseq-rep2

data_processing:
GRO-seq: a sigularity pacakge https://github.com/brainbreaks/GROseq
Assembly: mm10
Supplementary files format and content: GRO-seq: bigwig files for plus and minus strands.
Library strategy: GRO-Seq

molecule: nuclear RNA

extract_protocol:
Nascent RNA for GRO-seq: nuclei were lysed in TriZol reagents. RNA were extraced as manufacture instruction.
We follow the published protocol, as indicated below, to construct the libraries. GRO-seq:https://www.sciencedirect.com/science/article/pii/S0092867415017031?via%3Dihub


title: SIA1-ADAR,rep2

description: Library name: T47D_SIA1_2


title: CLP001 (RNA-seq)

value: Primary B-ALL


title: Heart, AAV9-cTnT-Cre-T2A-EGFP, P10, TCK_1


title: Heart, Corn oil, P10, Ctrl_13

data_processing:
Raw sequence reads were obtained and de-multiplexed using the bcl2fastq script (v2.20). The RAVED pipeline was used to analyze RNA-Sequencing data. Adapter sequences in raw reads were removed using Trimmomatic (v.0.32), and overall QC metrics were obtained using FastQC (v.0.11.7). Trimmed reads for each sample were aligned to the mouse reference genome mm10 using STAR (v.2.7.1). Subsequently, Bamtools (v.2.3.0) was used to summarize the number of mapped reads, including junction-spanning reads. To compute the number of bases assigned to various classes of RNA, the Picard Tools (v.1.96) RnaSeqMetrics function was used, according to an mm10 refFlat file obtained from UCSC Genome Table Browser. Genome Table HTSeq (v.0.11.2) was used to quantify gene-level read counts, using provided mm10 mouse transcriptome files. Differential expression analysis was conducted using DESeq2 (v.1.22.2) under a negative binomial distribution model. This analysis filtered out genes with total read counts less than 10 before differential analysis and disabled the default option for independent filtering of differential expression results. Corresponding P-values were adjusted to q-values using the Benjamini-Hochberg method.
Assembly: mm10
Supplementary files format and content: Differential expressed genes between Tamoxifen treatment (Chmp4b-KO, cKO) samples and Corn oil treatment (Control, Ctrl) samples.

treatment_protocol: postnatal-day-0 (P0) MCM; Chmp4bF/F mice received subcutaneous injections of 0.1 mg/g tamoxifen for two consecutive days. As a control, MCM; Chmp4bF/F mice were injected with corn oil.  Hearts were harvest at P10.

value: MCM; Chmp4bF/F

value: Corn oil


title: REH_ERG#3 (ChIP-seq)

value: REH B-ALL


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; GRO-seq, rep2

description: Library name: Nrg3-pe-del1-groseq-rep2

value: ES cell derived NPC

value: solution control (DMSO)


title: REH_INPUT (ChIP-seq)


title: NC-ADAR,rep2

description: Library name: T47D_NC_2


title: Heart, Corn oil, P10, Ctrl_9


title: Heart, Corn oil, P10, Ctrl_8


title: REH_ERG#1 (ChIP-seq)


title: Heart, Corn oil, P10, Ctrl_6


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; GRO-seq, rep1

description: Library name: Ctnna2-pe-del2-groseq-rep1


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C2; DMSO; GRO-seq, rep2

description: Library name: Ctnna2-pe-del2-groseq-rep2


title: NC-ADAR,rep1

description: Library name: T47D_NC_1


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; early; rep1

description:
Library name: DMSO-repliseq-early-rep1
dmso_rep1_log2smooth_50000.bedgraph


title: SEM_ERG#2 (ChIP-seq)


title: Heart, AAV9-cTnT-Cre-T2A-EGFP, P10, TCK_3


title: SIA2-ADAR,rep1

description: Library name: T47D_SIA2_1


title: REH_CTCF#2 (ChIP-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; early; rep2

description:
Library name: DMSO-repliseq-early-rep2
dmso_rep2_log2smooth_50000.bedgraph


title: STAT1-KO,SIA2-ADAR,rep2

description: Library name: STAT1KO_SIA2_2


title: Heart, AAV9-cTnT-Cre-T2A-EGFP, P10, TCK_4


title: SEM_CTCF#1 (ChIP-seq)


title: REH_CTCF#1 (ChIP-seq)


title: REH_sgCTRL#2 (ChIP-seq)

value: ERG WT


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; GRO-seq, rep1

description: Library name: Nrg3-pe-del2-groseq-rep1


title: STAT1-KO,SIA2-ADAR,rep1

description: Library name: STAT1KO_SIA2_1


title: SIA1-ADAR,rep1

description: Library name: T47D_SIA1_1


title: Heart, Tamoxifen, P10, cKO_7

value: Tamoxifen


title: STAT1-KO,SIA1-ADAR,rep2

description: Library name: STAT1KO_SIA1_2


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; GRO-seq, rep2

description: Library name: Ctnna2-pe-del1-groseq-rep2


title: REH_sgCTRL#1 (ChIP-seq)


title: Xrcc4-/-::p53-/-; ESC-NPC; Ctnna2 pe-del C1; DMSO; GRO-seq, rep1

description: Library name: Ctnna2-pe-del1-groseq-rep1


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; GRO-seq, rep1

description: Library name: Nrg3-pe-del1-groseq-rep1


title: REH_ERG#2 (ChIP-seq)


title: STAT1-KO,SIA1-ADAR,rep1

description: Library name: STAT1KO_SIA1_1


title: NC-ADAR,rep3

description: Library name: T47D_NC_3


title: STAT1-KO,NC-ADAR,rep3

description: Library name: STAT1KO_NC_3


title: Heart, Tamoxifen, P10, cKO_3


title: Heart, Corn oil, P10, Ctrl_4


title: REH_sgERG#4 (ChIP-seq)

value: ERG KO


title: EtOH4W_KO3

city: Bethesda, MD

first: Frank

last: Gonzalez

address: Bldg. 37 National Institutes of Health

department: Center for Cancer Research

institute: National Institutes of Health, National Cancer Institute

description: Library name: 19_EtOH4W_KO3

data_processing:
For RNA-seq data analysis, reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic 0.36 software before alignment with the reference genome (Mouse-mm10) and the annotated transcripts using STAR 2.5.1.
The mapping statistics were calculated using Picard 1.84 software.
Library complexity was measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility.
The gene expression quantification analysis was performed for all samples using STAR/RSEM 1.2.22 tools.
Differential gene expression was assessed with DESeq2 with the parameters P-adj 0.05 and log2 fold 1 (for 2-fold differentially expressed genes).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Liver

extract_protocol:
Using Rneasy Plus Mini Kit (#74136, Qiagen)
Illumina TruSeq Stranded mRNA Library Prep (#20020596, Illumina)

value: Liver

value: Cre+

value: hepatocyte Cebpa knockout mice (KO) were acclimated to a liquid control diet for 5 days first, followed by a 5% (vol/vol) ethanol liquid diet feeding for 4 weeks.

tag: replicate

value: Rep 1


title: STAT1-KO,NC-ADAR,rep1

description: Library name: STAT1KO_NC_1


title: C2C12, untreated, 12h, trial 3

city: Ottawa

first: Neena

last: Lala-Tabbert

state: Ontario

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Insitute

data_processing:
The quality of the FASTQ sequencing data was assessed using FastQX v.0.11.9.
Adapters were trimmed using Trim Galore v.0.5.0
Reads were aligned to the mouse reference genome (release m27, GRCm39) using the STAR aligner, v2.6.0c.
The STAR alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2.
Two-condition differential expression was performed with the R package DESeq2 v.1.22.2.
Assembly: mouse reference genome (release m27, GRCm39)
Supplementary files format and content: Tab-delimited text file that includes FPKM for each samples and log2Fold Change between Treated and Untreated samples

growth_protocol: C2C12 myoblasts were grown in DMEM containing 10% FBS and supplemented with non-essential amino acids. Cells were incubated at 37C in 5% CO2.

extract_protocol:
Total RNA from untreated (control) and 10ng/ml TWEAK-treated C2C12 myotubes was extracted using RNAzol® RT (R4533, Millipore Sigma) according to manufacturer’s protocol.
The mRNA library was prepared using poly (A)-tailed enchriched mRNA (NEBNext)

treatment_protocol: C2C12 myoblasts were grown to 80-90% confluency in 15cm plates and then switched to DMEM containing 2% HS. Cells were differentiated for three days and myotubes were left untreated or treated with 10ng/ml TWEAK for 12 hours.

value: cell line

value: myoblast

value: untreated


title: EtOH4W_KO2

description: Library name: 18_EtOH4W_KO2


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; GRO-seq, rep2

city: Heidelberg

last: Wei

address: Im Neuenheim Feld 280

description: Library name: DMSO-groseq-rep2


title: Heart, Tamoxifen, P10, cKO_5

value: Heart


title: ImmatureB (ATAC-seq)

data_processing:
Reads were processed using the Seq-N-Slide pipeline, where trimmed reads were aligned to GRCh37 using bowtie v2.3.4.1.Macs2 v2.1.2 was used for peak calling and bedtools v2.27.1 was used to generate bigwig files provided.
Assembly: hg19
Supplementary files format and content: bigwig

value: Healthy bone marrow

value: Immature-B


title: DHODH_KDR_2_1

city: Houston

first: Arun

last: Sreekumar

address: One Baylor Plaza

department: Molecular and Cell Biology

institute: Baylor College of Medicine

description: Library name: Sample 11

data_processing:
Fastq files were run through fastqc for primary qc
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (parameter- Default settings)
Trimmed sequence reads were mapped to GRCh38 using HISAT2
Read count extraction and normalization were performed using Feature Counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Feature counts

growth_protocol: 2B-MDA-PCa was cultured in BRFF-HPC1 media (AthenaES, Baltimore, MD) with 20% FBS (FBS, Hyclone Labs, Thermo Scientific, Rockford, IL) and 0.1% penicillin-streptomycin (Hyclone Labs, Thermo Scientific, Rockford, IL). MDA-PCa-2a cells were cultured in plates or flasks pre-coated with a fibronectin solution (AthenaES, Baltimore, MD).

extract_protocol:
RNA extraction was performed using the Aurum™ Total RNA Mini Kit (Bio-Rad).
Libraries were prepared using ABclonal mRNA-seq Library Prep Kit for Illumina (poly-A selection). RNA integrity and quantification was confirmed on the AATI Fragment Analyzer and quantitative PCR. Quality assessment and sequencing were performed by Novogene Corporation, Sacramento. Sequencing was performed using Illumina NovaSeq X Plus (PE150).


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; DMSO; GRO-seq, rep1

description: Library name: DMSO-groseq-rep1


title: REH_sgERG#6 (ChIP-seq)

extract_protocol: Immediately after sorting, cells were washed with PBS. Nuclei were extracted with cold lysis buffer and Tagmented with Illumina Tagment DNA Enzyme and Buffer Large kit (20034198). For RNA-seq, cells for RNA extraction were pelleted in Eppendorf tube, and resuspended with 350μl of Buffer RLT Plus containing 10ul of b-Mercaptoethanol (b-ME) per 1ml. For Hi-C, cells were crosslinked in a DNA low-bind Eppendorf tube at a final concentration of 2% formaldehyde and incubated at RT for 10 min on a tube revolver. Samples were then frozen in liquid nitrogen and stored in -80°C for future processing.

value: B-cell acute lymphoblastic leukemia


title: EtOH4W_KO4

description: Library name: 20_EtOH4W_KO4


title: KMT2r005 (ATAC-seq)

value: Primary B-ALL


title: C2C12, treated, 12h, trial 2

value: 10ng/ml TWEAK


title: EtOH4W_WT3

description: Library name: 15_EtOH4W_WT3

value: Cre-

value: hepatocyte Cebpa flox/flox (WT) mice were acclimated to a liquid control diet for 5 days first, followed by a 5% (vol/vol) ethanol liquid diet feeding for 4 weeks.


title: DHODH_KD2_3_1

description: Library name: Sample 9


title: KMT2r004 (ATAC-seq)


title: DHODH_KDR_3_1

description: Library name: Sample 12


title: EtOH4W_KO1

description: Library name: 17_EtOH4W_KO1


title: C2C12, treated, 12h, trial 3


title: Heart, Tamoxifen, P10, cKO_1

value: MCM; Chmp4bF/F

value: Tamoxifen


title: C2C12, untreated, 12h, trial 1


title: C2C12, untreated, 12h, trial 2


title: PreB (ATAC-seq)

value: Pre-B


title: EtOH4W_WT4

description: Library name: 16_EtOH4W_WT4

value: Liver


title: ETV007 (ATAC-seq)


title: DHODH_KD2_2_1

description: Library name: Sample 8


title: DHODH_KD2_1_1

description: Library name: Sample 7


title: RAW264.7 cells, Kdm7a gRNA (KO), M2 macrophage stimulated with Il-4, 10, 13 and Tgf-β1 for 48 hours., rep-2

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

description: Library name: Sample17

data_processing:
The fastq data was processed by Trim_galore, Star mapping, and Rsem.
Assembly: mm10
Supplementary files format and content: Raw count all sample.txt containts all raw count data from 18 samples.

growth_protocol: RAW264.7 cells were cultured in Dulbecco-modified eagle’s medium (DMEM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), and penicillin/streptomycin (P/S).

extract_protocol:
Total RNA was extracetd using Rneasy Mini kit folloing manufacturer's instructions.
poly(A) RNA was isolated and library was prepared using NEBNext Ultra II RNA Library Prep Kit for Ilumina following manufacturer's instructions.

treatment_protocol: RAW264.7 cells were polarized by expose to 2 ng/ml mouse IFN-γ and 0.1 µg/ml LPS (M1) or 20 ng/ml IL-4, IL-10, and IL-13 (from mouse) and 2 ng/ml human TGF-β1 (M2) during 48 hours.

value: Kdm7a KO_M2

value: Kdm7a Knockout

value: M2 macrophage stimulation


title: DHODH_KDR_1_1

description: Library name: Sample 10


title: GW4064-2

first: Senlin

last: Zhao

address: 270 Dong An Road

department: Colorectal Surgery

institute: Cancer Hospital, Fudan University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: GW4064 treatment group

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: subcutaneous xenograft

value: CRC cells

value: WT


title: ETV005 (ATAC-seq)

first: Yohana

institute: NYU Grossman School of Medicine


title: ETV006 (ATAC-seq)


title: KMT2r001 (ATAC-seq)


title: GW4064-1


title: C2C12, treated, 12h, trial 1

value: cell line

value: myoblast


title: DHODH_KD1_1_1

description: Library name: Sample 4


title: RAW264.7 cells, Kdm7a gRNA (KO), M2 macrophage stimulated with Il-4, 10, 13 and Tgf-β1 for 48 hours., rep-1

description: Library name: Sample16


title: EtOH4W_WT1

description: Library name: 13_EtOH4W_WT1

value: Rep 1


title: CON3

source_name: Control group

value: CON


title: SEP3wt_rep2_R1

city: Berlin

first: Kerstin

last: Kaufmann

address: Philippstr. 11-13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt-Universitaet zu Berlin

description:
X56
SEP3wt_peaks.narrowPeak

data_processing:
Read were timmed with Trimmomatic v0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
Trimmed reads were mapped to the Arabidopsis genome using bowtie2 v2.2.5 with default parameters
Peak calling was done using MACS2 (version 2.2.7.1) comparing IP vs mock with defaults parameters except: -g 101274395
Wiggle tracks were generated by DeepTools with the command “bamCoverage” with parameters -bs 10 --skipNonCoveredRegions
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for mock samples)

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were growing at 22°C under the long-day condition (daily cycles of 16 hours with light and 8 hours in dark).

extract_protocol:
~1g inflorescence were collected as starting material. Then, tissue fixation and nuclei isolation were done according to the published protocol (Kaufmann, K., Muiño, J.M., Østerås, M., Farinelli, L., Krajewski, P., and Angenent, G.C. (2010a). Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5: 457–472.). Native SEP3 antibody and Dynabeads protein A (Thermo Fisher) were used for immunoprecipitation.
ChIP-seq library preparation was done with the ThruPlex DNA-Seq kit following the kit manual.

value: inflorescence

value: floral cells


title: CON2


title: EtOH4W_WT2

description: Library name: 14_EtOH4W_WT2

value: Cre-

value: hepatocyte Cebpa flox/flox (WT) mice were acclimated to a liquid control diet for 5 days first, followed by a 5% (vol/vol) ethanol liquid diet feeding for 4 weeks.


title: DHODH_NT_3_1

description: Library name: Sample 3


title: STAT1-KO,NC-ADAR,rep2

description: Library name: STAT1KO_NC_2

value: Breast

value: Human breast cancer cells


title: DHODH_KD1_3_1

description: Library name: Sample 6


title: Heart, Tamoxifen, P10, cKO_6

value: Heart

value: MCM; Chmp4bF/F

value: Tamoxifen


title: RAW264.7 cells, Kdm7a gRNA (KO), M2 macrophage stimulated with Il-4, 10, 13 and Tgf-β1 for 48 hours., rep-3

description: Library name: Sample18

value: Kdm7a KO_M2

value: Kdm7a Knockout

value: M2 macrophage stimulation


title: REH_sgERG#1 (ChIP-seq)

last: Ghebrechristos

address: 550 1st Ave.

value: B-cell acute lymphoblastic leukemia

value: REH B-ALL

value: ERG KO