title: U87MG cells, IDH1 WT expression, tumor collected 27 days after cell injection, sample 7

city: San Diego

first: Christal

last: Sohl

address: 5500 Campanile Rd.

department: Chemistry and Biochemistry

institute: San Diego State University

data_processing:
Methylation calls were produced using Bismark and imported into the MethylKit R package (v. 1.28.0). CpGs with more than ten reads were included in the downstream analysis. Filtered counts were normalized and CpG dinucleotides were merged (destrand = FALSE). Most variable CpGs across tumors were calculated as having a standard deviation > 0.90. Samples were visualized using PCA and hierarchical clustering using the Ward method.
For HT1080* tumors, to perform pairwise comparisons in methylation levels, samples of interest were merged into one object containing common CpGs. Pearson correlation was used to assess concordance between D2HG amount in the tumors and DNA methylation levels of CpG sites. Differential methylation analysis was performed using Fisher’s exact test and differentially methylated CpGs were selected based on q < 0.05 and percent methylation difference > 20%.
For U87MG tumors, CpGs were first filtered to include the most variable sites (CpGs with standard deviation > 10) and differential methylation analysis was performed as described, with a notable exception that CpGs were selected based on q < 0.05 and methylation difference > 10%.
Feature annotation was done using ChIPseeker (v. 1.38.0) R package. Genomic annotation for hg38 were retrieved using the TxDb.Hsapiens.UCSC.hg38.knownGene R package.GREAT analysis software tool (with default parameters) was applied to determine enriched GO terms near the differentially methylated CpGs. The entire filtered CpG sites used for differential methylation analysis was used as the genomic background for GREAT analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text (TXT) format. Bismark genome-wide cytosine methylation report for each sample. Columns include chromosome, CpG position, strand, methylated count, unmethylated count, CpG context, and trinucleotide context.

source_name: tumor

growth_protocol: 2×106 U87MG IDH1-WT, IDH1 R132H, or IDH1 R132Q cells suspended in Matrigel and PBS (1:1) or 2 × 106 HT1080 (+/-) IDH1 WT, IDH1 R132H, or IDH1 R132Q cells suspended in PBS were implanted subcutaneously into the left flanks of 6–8-week-old female athymic Nu/Nu mice. Vehicle controls (1:1 Matrigel/PBS or PBS alone) were injected subcutaneously into the corresponding right flanks. Twice weekly, mice were weighed, and tumor volume was measured with a Vernier caliper. Mice were sacrificed once tumors reached 20 mm in length or 120 days of growth.

extract_protocol:
100–200 mg of tumor tissue from 22 U87MG and HT1080 xenografts tumors was weighed and then shipped in dry ice for RRBS analysis at Active Motif (Carlsbad, CA). There, tissues were subjected to proteinase K digest solution (0.5% SDS, 0.5mg/ml proteinase K, 100 mM EDTA, in TE pH 8) by allowing the samples to rotate overnight at 55⁰C. For library preparation and sequencing, 100 ng of gDNA was digested with TaqaI at 65 ⁰C for 2 h followed by MspI treatment at 37⁰C overnight.
Following enzymatic digestion, samples were used for library generation using the Ovation RRBS Methyl-Seq System following the manufacturer’s instructions. The digested DNA was randomly ligated, and, following fragment end repair, bisulfite was converted using the EpiTect Fast DNA Bisulfite Kit following the Qiagen protocol. After conversion and clean-up, samples were amplified, resuming the Ovation RRBS Methyl-Seq System protocol for library amplification and purification. Libraries were measured using the Agilent 2200 TapeStation System and quantified using the KAPA Library Quant Kit ABI Prism qPCR Mix. Libraries were sequenced on a NovaSeq 6000 at SE75.

value: tumor

value: human glioma

value: IDH1 WT

value: injection with human cells stably overexpressing IDH1 form


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 23

status: Public on Apr 11 2025

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: IDH1 R132Q

tag: treatment


title: U87MG cells, IDH1 WT expression, tumor collected 27 days after cell injection, sample 21


title: Brain_PFC_DNA [BBN_8965]

type: genomic

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

country: United Kingdom

institute: University of Exeter Medical School

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using the BeadArray Scanner (iScan) under standard settings

data_processing:
wateRmelon package in R environment (3.5.2)
Beta value

label: Bisulfite conversion

organism: Homo sapiens

source_name: Prefrontal Cortex

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from PFC tissue using the All-prep universal kit (Qiagen)

value: Prefrontal Cortex

tag: brain bank

value: Bristol

tag: post-mortem delay

tag: braak stage

tag: age

tag: Sex

value: F

tag: ad diagnosis

value: AD


title: ER-Hoxb8 PMN-MDSC PAO1 WT 3

city: Paris

first: Maelys

last: BORN-BONY

address: 16 rue Henri Huchard

country: France

institute: INSERM

description: Library name: D1765T69

library_source: transcriptomic

data_processing:
Sequencing was performed on the NovaSeq 6000 (Illumina), targeting between 15 and 20 M reads per sample and using paired-end 2 x 100 bp.  Analysis of the raw data was performed using R script and subsequent analysis and visualization were done using the Phantasus online tool
Assembly: Mm10
Supplementary files format and content: tab delimited text files which includes annotaion and raw counts for each sample

molecule: total RNA

source_name: ER-Hoxb8 PMN-MDSC

extract_protocol:
SINGLE CELL RNA PURIFICATION KIT Norgen 51800
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara)

value: ER-Hoxb8 PMN-MDSC

value: PAO1 WT


title: Brain_PFC_DNA [BBN_8961]


title: Brain_PFC_DNA [BBN001.28402]

value: Edinburgh

value: M

value: Ctl


title: Brain_PFC_DNA [BBN_9189]


title: ER-Hoxb8 PMN-MDSC PAO1 WT 2

description: Library name: D1765T67


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 9


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 19


title: Brain_PFC_DNA [BBN006.32578]


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 24

value: IDH1 R132H


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 10


title: Brain_PFC_DNA [BBN001.26500]


title: Brain_PFC_DNA [BBN_4214]


title: U87MG cells, IDH1 WT expression, tumor collected 27 days after cell injection, sample 26


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 4


title: Brain_PFC_DNA [BBN001.35109]


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 27


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 1


title: Brain_PFC_DNA [BBN001.30142]


title: Brain_PFC_DNA [BBN_8846]


title: HT1080 cells (+/-), IDH1 WT expression, tumor collected 89 days after cell injection, sample 44

value: human fibrosarcoma


title: HT1080 cells (+/-), IDH1 WT expression, tumor collected 33 days after cell injection, sample 32


title: HT1080 cells (+/-), IDH1 R132Q expression, tumor collected 33 days after cell injection, sample 49


title: HT1080 cells (+/-), IDH1 R132Q expression, tumor collected 54 days after cell injection, sample 46


title: HT1080 cells (+/-), IDH1 R132Q expression, tumor collected 54 days after cell injection, sample 31


title: Brain_PFC_DNA [BBN006.28766]


title: Brain_PFC_DNA [BBN001.35381]


title: HT1080 cells (+/-), IDH1 R132Q expression, tumor collected 33 days after cell injection, sample 28


title: Brain_PFC_DNA [BBN_25739]


title: HT1080 cells (+/-), IDH1 R132H expression, tumor collected 50 days after cell injection, sample 54


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 20


title: HT1080 cells (+/-), IDH1 R132H expression, tumor collected 33 days after cell injection, sample 30


title: Brain_PFC_DNA [BBN_9122]


title: HT1080 cells (+/-), IDH1 R132Q expression, tumor collected 40 days after cell injection, sample 43


title: Brain_PFC_DNA [BBN006.32924]


data_processing:
The quality of the raw RNAseq data was evaluated using FASTQC v0.12.1.
Based on the FASTQC reports, potential adapter contamination and low-quality sequences were identified and trimmed using Cutdapt v4.8.Cutadapt parameters were set for paired-end reads, with a quality cutoff of 20 and a minimum filter length of 20.
The genome index was constructed using the hg38 reference genome assembly obtained from the National Center for Biotechnology Information (NCBI) with the Spliced Transcripts Alignment to a Reference (STAR) aligner version v2.7.11b. Quality-filtered reads were aligned to this genome index using STAR. The aligned reads were sorted by read name using sambamba v1.01 to prepare them for counting. featureCounts v2.0.6 was utilized to count the number of reads per annotated gene.
The raw gene counts underwent normalization using DESeq2 for subsequent analyses. DESeq2 was also used to identify differentially expressed genes (DEGs) in the mutants when compared to the WT. Significant DEGs are defined as genes exhibiting an adjusted p-value (FDR) below 0.05.
Pathway analysis was performed to identify significantly enriched gene sets from the Kyoto Encyclopedia of Genes and Genomes (KEGG), as well as the Gene Ontology (GO) databases covering biological processes, molecular functions, and cellular components using ClusterProfiler v4.10.1. Significantly enriched, upregulated, and downregulated pathway alterations in the mutants when compared to the wild type are determined by an adjusted p-value (FDR) below 0.05.
Assembly: hg38
Supplementary files format and content: Excel file includes DEseq2 results (mean, fold change, p-values) for each sample group comparison and normalized counts by sample.

extract_protocol:
RNA samples were extracted from 22 tumor tissues using QIAzol Lysis Reagent. 100–200 mg of the tumor tissue was placed in gentle MACS M tubes. 500 µL of QIAzol Lysis Reagent was added to the tissue, and the samples were dissociated mechanically using a gentle MACS Dissociator following manufacturer's protocol
Libraries were generated using the Illumina Ribo-Zero Plus rRNA Depletion Kit with IDT for Illumina RNA UD Indexes following manufacturer's protocol. Generated libraries were multiplexed and sequenced with 150 base pair (bp) Paired End (PE150) to a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000. Samples were finally demultiplexed using bcl2fastq v2.20 Conversion Software


title: Brain_PFC_DNA [BBN_24563]


title: U87MG cells, IDH1 WT expression, tumor collected 27 days after cell injection, sample 21


title: Brain_PFC_DNA [BBN003.28342]

value: Newcastle


title: Brain_PFC_DNA [BBN003.26893]


title: U87MG cells, IDH1 WT expression, tumor collected 27 days after cell injection, sample 7

value: tumor


title: Brain_PFC_DNA [BBN_9113]


title: Brain_PFC_DNA [BBN_19608]


value: human glioma


title: Brain_PFC_DNA [BBN_2624]


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 23


title: Brain_PFC_DNA [BBN_13407]


title: Brain_PFC_DNA [BBN001.29521]


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 9


title: Brain_PFC_DNA [BBN006.32514]


title: Brain_PFC_DNA [BBN_8857]


title: Brain_PFC_DNA [BBN003.28692]


title: Brain_PFC_DNA [BBN001.26722]


title: Brain_PFC_DNA [BBN_7517]


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 24


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 10


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 4


title: HT1080 cells (+/-), IDH1 WT expression, tumor collected 89 days after cell injection, sample 44

value: IDH1 WT


title: Brain_PFC_DNA [BBN_9423]


title: Brain_PFC_DNA [BBN005.29822]

value: Manchester


title: Brain_PFC_DNA [BBN_24561]


title: Brain_PFC_DNA [BBN001.26309]


title: Brain_PFC_DNA [BBN_9413]


title: Brain_PFC_DNA [BBN001.30147]


title: Brain_PFC_DNA [BBN001.30208]


value: IDH1 R132Q

value: injection with human cells stably overexpressing IDH1 form


title: HT1080 cells (+/-), IDH1 R132H expression, tumor collected 36 days after cell injection, sample 55


title: U87MG cells, IDH1 R132Q expression, tumor collected 27 days after cell injection, sample 19


title: Brain_PFC_DNA [BBN_9435]

value: Prefrontal Cortex

value: Bristol


title: Brain_PFC_DNA [BBN006.29018]

value: F


title: U87MG cells, IDH1 R132H expression, tumor collected 27 days after cell injection, sample 1


title: Brain_PFC_DNA [BBN_7539]

value: AD


title: RS25_950_Distal Colon

city: Beltsville

first: Allen

last: Smith

state: MD

address: 10300 Baltimore Ave, BARC-East, 307C

institute: USDA ARS

data_processing:
CLC Genomics Workbench v.24
Assembly: mm10
Supplementary files format and content: compressed tab delimited text with gene counts for each sample

source_name: Distal Colon

extract_protocol:
RNA was extracted from tissues using Zymo Tri-Reagent and Invitrogen PureLink RNA isolation kits followed by further purification using Zymo RNA Clean and Concentrate kits.
Libraries were prepared using Illumina Stranded mRNA Prep, Ligation kit with IDT for Illumina Unique Dual Indexes following manufacturer’s recommendations, except that half reaction volumes were used. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were pooled in equimolar amounts for multiplexed sequencing, and the pool quantified using the Invitrogen Collibri Quantification qPCR kit.

value: Distal Colon

tag: strain


title: Brain_PFC_DNA [BBN003.32261]


title: HT1080 cells (+/-), IDH1 WT expression, tumor collected 33 days after cell injection, sample 32


title: Brain_PFC_DNA [BBN_9419]


title: Brain_PFC_DNA [BBN_7125]


title: RS25_948_Distal Colon


title: RS25_949_Distal Colon


title: Brain_PFC_DNA [BBN_24526]

value: Edinburgh


title: Brain_PFC_DNA [BBN006.34151]


title: Brain_PFC_DNA [BBN005.32843]


title: RS25_947_Distal Colon


title: RS25_940_Distal Colon


title: Brain_PFC_DNA [BBN001.28771]

value: M


title: RS25_946_Distal Colon


title: RS25_939_Distal Colon


title: Brain_PFC_DNA [BBN_7569]


title: RS25_938_Distal Colon


title: Brain_PFC_DNA [BBN_9392]

value: Ctl


title: HC11_rep2

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description: Library name: HC11_rep2

data_processing:
Data were analyzed using VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. From this paper: https://link.springer.com/article/10.1186/s12859-018-2139-9 Instructions on this site: https://bitbucket.org/cfce/viper/src/master/
Raw reads were mapped or aligned to the reference organism using STAR software.
Assembly: mm9
Supplementary files format and content: txt file contains RPKM for each sample

molecule: polyA RNA

growth_protocol: Mammary epithelial BC44 cells (a kind gift of Marie-Anne Deugnier, Institute Curie, Paris, France) were cultured in RPMI1640 + L-Glut (Fisher, 11973466), supplemented with 10% FBS (Gibco, cat# 10270-106) and 5ug/ml insulin (Sigma-Aldrich, cat. #I9278). HC11 mammary epithelial cells were also cultured in RPMI1640 + L-Glut with 10% FBS and 5ug/ml insulin, with the addition of 10ng/ml EGF (Peprotech, cat. #AF-100-15-B). C57MG cells were grown in DMEM GlutaMAX with 10% FBS and 10 µg/ml insulin. Cells were dissociated with 0.05% trypsin and split 1:10 every 3 days. 6x10e5 cells were plated on a 10 cm dish. Cells were harvested 2 days later.

extract_protocol:
RNA isolation was performed via a combination protocol using Trizol and Phasemaker tubes (#15608948), then Qiagen RNeasy Mini Kit (#74104) with On-Column DNAse digestion (RNase-free DNase set #79254)
1μg of RNA was used as starting material for poly-A enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). Next, RNA-Seq libraries were generated according to the manufacturers’ protocols using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) (New England BioLabs). Distribution of the size of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) was used for library quantification using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to manufacturer’s instructions.

value: mammary epithelial

value: untreated, grown on plastic


title: Brain_PFC_DNA [BBN_9359]


title: HC11_rep1

description: Library name: HC11_rep1


title: BC44_rep2

description: Library name: BC44_rep2


title: Brain_PFC_DNA [BBN001.28799]


title: C57MG_rep1

description: Library name: C57MG_rep1


title: RS25_936_Distal Colon


title: RS25_930_Distal Colon


title: BC44_rep1

description: Library name: BC44_rep1


title: Brain_PFC_DNA [BBN006.32544]


title: RS25_929_Distal Colon


title: Ovaries - flam {-515; +2086} Tomato

city: Cambridge

first: Azad

last: Alizada

state: Cambridgeshire

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

data_processing:
Adapters were trimmed.
size selection was performed to retain only 18-29 nucleotide reads.
small RNA pipeline sRNAPipe (Pogorelcnik et al., 2018)
Assembly: release 6.03
Supplementary files format and content: .txt read counts at piRNA clusters

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Total RNA extraction with TRIzolTM (Invitrogen) Polyacrylamide gel size selection of 18-30 nucleotides
Library preparation using illumina TruSeq small RNA kit, Specific treatment anti 2S

treatment_protocol: Ovary dissections

value: ovaries


title: Brain_PFC_DNA [BBN_25060]


title: C57MG_rep2

description: Library name: C57MG_rep2


title: C2 CAF co-cultured with SCC070 cells biol rep 2

city: Kalyani

first: Sandeep

last: Singh

state: West Bengal

address: NSS TB Hospital, Block A

department: Biomedical Genomics

country: India

institute: BRIC-National Institute of Biomedical Genomics

description: Library name: SS5-H

data_processing:
quality assesment was performed using Agilent Bioanalyser-2100 with Agilent nano Kit (Agilent Technologies)
Raw data QC was performed through FastQC, and the RNA sequence data was aligned to hg19 primary assembly using STAR aligner (version 2.6.0) with GRCh37.87 (Ensembl) transcript model
HTSeq (version 0.11.0) was used to generate count data
Assembly: GRCh37
Supplementary files format and content: COUNT files with raw counts for all the samples

source_name: oral cavity

growth_protocol: KV07 CAF is cultured in DMEM:F12 (1:1) Media supplimented with  1X Antibiotic-antimycotic, 1% fetal bovine serum, 0.1% ITS, and 3% Sodium bicarbonate. SCC070 cells were cultured over KV07 CAFs in same media in a 37°C humidified chamber with 5% C02.

extract_protocol:
CD+ CAFs and CD90- cancer cells were sorted using FACS and total RNA was extracted using RNA- Easy plus kit (Cat#74034, Qiagen) as per the manufacturer’s instructions
The library was prepared by TruSeq Stranded Total RNA Library prep kit, following manufactures protocol

treatment_protocol: KV07 CAF is treated with 10 ng/mL TGF-beta prior to co-culture.

value: oral cavity

value: Fibroblast

value: TGF-beta


title: C2 CAF co-cultured with SCC070 cells biol rep 1

description: Library name: SS5-G


title: RS25_937_Distal Colon


title: Ovaries - flam {-515; +432} Tomato


title: Brain_PFC_DNA [BBN001.26719]


title: Ovaries - flam{-515; +30} Tomato

value: flam{-515; +30} Tomato


title: RS25_928_Distal Colon


title: C1 CAF co-cultured with SCC070 cells biol rep 2

description: Library name: SS5-F


title: RS25_927_Distal Colon


title: Brain_PFC_DNA [BBN006.30850]


title: Brain_PFC_DNA [BBN_2612]

value: Newcastle


title: C1 CAF co-cultured with SCC070 cells biol rep 1

description: Library name: SS5-E


title: RS25_926_Distal Colon


title: SCC070 cells co-cultured with C2 CAF biol rep 2

description: Library name: SS5-D

value: Epithelial


title: SCC070 cells co-cultured with C2 CAF biol rep 1

description: Library name: SS5-C


title: Brain_PFC_DNA [BBN005.28597]

value: Prefrontal Cortex

value: Manchester


title: SCC070 cells co-cultured with C1 CAF biol rep 2

description: Library name: SS5-B


title: RS25_924_Distal Colon


title: SCC070 cells co-cultured with C1 CAF biol rep 1

description: Library name: SS5-A


title: RS25_925_Distal Colon


title: Brain_PFC_DNA [BBN_3442]


title: HeLa-MCUKO-Rep2

city: Seattle

first: Yasemin

last: Sancak

state: WA

address: 1959 NE Pacific Street K526

department: Pharmacology

institute: University of Washington

description:
Library name: HeLa-MCUKO-2
Column name HeLa-MCUKO-2

data_processing:
The reads were trimmed and mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner (v.2.5.2b).
Hit counts for genes and exons were calculated with featureCounts (Subread package, v.1.5.2).
DESeq2 was used for analysis of differential gene expression.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: csv file contains normalized counts for each sample.

source_name: Cervix

growth_protocol: Cell lines were grown in a standard tissue culture incubator at 37°C with 5% CO2,   cultured in DMEM supplemented with 10% FBS, 2 mM GlutaMAX , and 100 IU/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
total RNA was isolated using an RNeasy kit (Qiagen, 74106)
Samples underwent mRNA enrichment, mRNA fragmentation, and random priming. Genewiz performed first and second strand cDNA synthesis followed by end repair, 5’ phosphorylation, and dA-Tailing.cDNA was sequenced, following adaptor ligation and enrichment by PCR.

value: Cervix

value: HeLa

value: epithelial cell

value: MCU KO


title: Brain_PFC_DNA [BBN_7530]

value: F

value: AD


title: HeLa-WT-Rep3

description:
Library name: HeLa-WT-3
Column name HeLa-WT-3

value: WT


title: RS25_922_Distal Colon

value: Distal Colon


title: HeLa-WT-Rep1

description:
Library name: HeLa-WT-1
Column name HeLa-WT-1


title: HeLa-WT-Rep2

description:
Library name: HeLa-WT-2
Column name HeLa-WT-2


title: Brain_PFC_DNA [BBN_8958]

value: Bristol

value: M


title: HeLa-MCUKO-Rep1

description:
Library name: HeLa-MCUKO-1
Column name HeLa-MCUKO-1


title: RS25_899_Distal Colon


title: Set6_HTA10_Myc_rep2

city: Shanghai

first: Xiang

last: Li

state: Shanghai

address: Songhu Road 2005

country: China

institute: Fudan University

description: Library name: Set6_HTA10_Myc_rep2

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The filtered reads were mapped to Arabidopsis thaliana genome (TAIR10) using Bowtie2 .
SAMtools was used to remove the PCR duplicates and the low mapped quality reads and to obtain high mapping quality reads.
The enrichment levels (Reads Per Kilobase per Million mapped reads, RPKM) of ChIP-seq were calculated using bamCoverage tool of deepTools and the corresponding enrichment peaks were obtained by comparing the differences between IP and Input groups using MACS2 software, with a threshold set at q < 0.05 (broad-cutoff).
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana seedlings were grown on MS medium under 16-h light/8-h dark conditions at 22°C for 14 days.

extract_protocol:
Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
the libraries were prepared using the VAHTS Universal DNA Library Prep Kit (ND607; Vazyme, Nanjing, China) and sequenced on an Illumina NovaSeq 6000 instrument via NEO-BIO (Shanghai, China).

value: seedlings

value: keep in 22°C


title: Set6_HTA10_Myc_rep1

description: Library name: Set6_HTA10_Myc_rep1


title: RS25_921_Distal Colon


title: HeLa-MCUKO-Rep3

description:
Library name: HeLa-MCUKO-3
Column name HeLa-MCUKO-3


title: Brain_PFC_DNA [BBN_9378]


title: Set6_HTA10_Input_rep1

description: Library name: Set6_HTA10_Input_rep1


title: Brain_PFC_DNA [BBN005.29874]

value: Ctl


title: Brain_PFC_DNA [BBN_7574]

value: Newcastle


title: Brain_PFC_DNA [BBN_9268]


title: Set6_h2a_Myc_rep2

description: Library name: Set6_h2a_Myc_rep2

value: mutant h2a


title: RS25_923_Distal Colon


title: Set6_h2a_Myc_rep1

description: Library name: Set6_h2a_Myc_rep1


title: Set6_HTA10_Input_rep2

description: Library name: Set6_HTA10_Input_rep2


title: RS25_898_Distal Colon


title: Set6_h2a_Input_rep2

description: Library name: Set6_h2a_Input_rep2


title: RS25_900_Distal Colon


title: Brain_PFC_DNA [BBN003.28355]

value: Prefrontal Cortex


title: Set6_h2a_Input_rep1

description: Library name: Set6_h2a_Input_rep1


title: RS25_897_Distal Colon


title: Brain_PFC_DNA [BBN_9188]


title: Set4_Col_for_h2aw_rep3

description: Library name: Set4_Col_for_h2aw_rep3

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
trimmed reads were mapped to the Arabidopsis reference genome (TAIR10) using HISAT2 v2.2.1, excluding reads from chloroplast and mitochondrial genomes.
SAMtools (v.1.13) was used to remove  the low mapped quality reads and to obtain high mapping quality reads.The bamCoverage tool of deepTools v3.5.3 software was used to normalize high-quality reads and convert bam files to bigWig format. Genomic track files were visualized using the genome browser IGV v2.11.1
Read counts for gene exons were obtained from bam files using featureCounts v2.0.1, followed by differential expression analysis using R package DESeq2 v1.36.0. The threshold for identifying differentially expressed genes was set as follows: | log2 (Fold change) | ≥ log2 (2) and P-adj ≤ 0.01.
The R toolkit clusterProfiler v4.4.4 was used to perform GO enrichment analysis. The screening threshold was set to a p-value of ≤ 0.01, and the top 20 enriched biological processes were selected for display. Transcriptome-related heatmaps were generated using R package ComplexHeatmap v2.12.1
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was extracted from 200 mg 14-d-old seedlings grown under LD conditions using the RNAprep pure Plant Kit (DP432; Tiangen Biotech, Beijing, China).
Sequencing libraries were prepared with the KAPA stranded mRNA-Seq Kit for the Illumina® Platform (KR0960-v.5.17; Kapa Biosystems, Wilmington, MA, USA), and sequencing was performed on an Illumina NovaSeq 6000 instrument via NEO-BIO (Shanghai, China).


title: Brain_PFC_DNA [BBN003.28567]


title: RS25_896_Distal Colon


title: Set4_h2aw_rep3

description: Library name: Set4_h2aw_rep3

value: mutant h2a.w


title: RS25_895_Distal Colon


title: Set4_h2aw_rep1

description: Library name: Set4_h2aw_rep1


title: Brain_PFC_DNA [BBN_7602]


title: RS25_894_Distal Colon


title: Set5_h2az_rep3

description: Library name: Set5_h2az_rep3

value: mutant h2a.z


title: Brain_PFC_DNA [BBN003.32849]


title: Set4_Col_for_h2aw_rep2

description: Library name: Set4_Col_for_h2aw_rep2


title: RS25_893_Distal Colon


title: Brain_PFC_DNA [BBN_19597]

value: Edinburgh


title: Set5_h2az_rep1

description: Library name: Set5_h2az_rep1


title: Set5_h2a_rep3

description: Library name: Set5_h2a_rep3


title: Set4_Col_for_h2aw_rep1

description: Library name: Set4_Col_for_h2aw_rep1


title: Set5_h2a_rep2

description: Library name: Set5_h2a_rep2


title: Set5_h2az_rep2

description: Library name: Set5_h2az_rep2


title: Brain_PFC_DNA [BBN_8960]


title: Set5_h2a_rep1

description: Library name: Set5_h2a_rep1


title: RS25_891_Distal Colon


title: Brain_PFC_DNA [BBN_9421]


title: Set5_Col_for_h2a_h2az_rep2

description: Library name: Set5_Col_for_h2a_h2az_rep2


title: RS25_890_Distal Colon


title: Set5_Col_for_h2a_h2az_rep3

description: Library name: Set5_Col_for_h2a_h2az_rep3


title: Set5_Col_for_h2a_h2az_rep1

description: Library name: Set5_Col_for_h2a_h2az_rep1


title: Set4_h2aw_rep2

description: Library name: Set4_h2aw_rep2


title: Brain_PFC_DNA [BBN_9341]


title: RS25_889_Distal Colon


title: Brain_PFC_DNA [BBN_7557]


title: RS25_888_Distal Colon


title: Brain_PFC_DNA [BBN_7465]


title: Set3_h2az_H2A_rep1

description: Library name: Set3_h2az_H2A_rep1

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The ChIP-seq filtered reads were mapped to Arabidopsis thaliana genome (TAIR10) using Bowtie2.
SAMtools was used to remove PCR duplicates and low mapping quality reads to obtain high quality reads.
The enrichment levels (Reads Per Kilobase per Million mapped reads, RPKM) of ChIP-seq were calculated using bamCoverage tool of deepTools and the corresponding enrichment peaks were obtained by comparing the differences between IP and Input groups using MACS2 software, with a threshold set at q < 0.05 (broad-cutoff).
BEDTOOLS was used to select intersections among the peaks of H2A and its variants.
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol:
Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
For sequencing of H2A, H2A.Z, and H2A.W, the libraries were prepared using the VAHTS Universal DNA Library Prep Kit (ND607; Vazyme, Nanjing, China) and sequenced on an Illumina NovaSeq 6000 instrument via NEO-BIO (Shanghai, China).


title: Set3_h2az_Input_rep1

description: Library name: Set3_h2az_Input_rep1


title: RS25_892_Distal Colon


title: RS25_887_Distal Colon


title: Set3_h2aw_Input_rep2

description: Library name: Set3_h2aw_Input_rep2


title: RS25_886_Distal Colon


title: Set3_h2aw_H2A_rep2

description: Library name: Set3_h2aw_H2A_rep2


title: Set3_h2az_H2A_rep2

description: Library name: Set3_h2az_H2A_rep2


title: Brain_PFC_DNA [BBN_9219]


title: Set3_h2aw_Input_rep1

description: Library name: Set3_h2aw_Input_rep1


title: RS25_885_Distal Colon


title: Brain_PFC_DNA [BBN006.27017]


title: Set3_Col_Input_rep1

description: Library name: Set3_Col_Input_rep1


title: Set3_Col_Input_rep2

description: Library name: Set3_Col_Input_rep2


title: Set3_h2aw_H2A_rep1

description: Library name: Set3_h2aw_H2A_rep1


title: Brain_PFC_DNA [BBN_14416]

value: Manchester


title: Set3_Col_H3K9me2_rep2

description: Library name: Set3_Col_H3K9me2_rep2


title: Set3_Col_H3K9me2_rep1

description: Library name: Set3_Col_H3K9me2_rep1


title: Brain_PFC_DNA [BBN006.29614]


title: Set3_Col_H3K36me3_rep2

description: Library name: Set3_Col_H3K36me3_rep2


title: Set3_Col_H3K36me3_rep1

description: Library name: Set3_Col_H3K36me3_rep1


title: RS25_883_Distal Colon


title: RS25_884_Distal Colon


title: Brain_PFC_DNA [BBN_7570]


title: Set3_h2az_Input_rep2

description: Library name: Set3_h2az_Input_rep2


title: Brain_PFC_DNA [BBN_4219]


title: Set3_Col_H2A_rep1

description: Library name: Set3_Col_H2A_rep1


title: Brain_PFC_DNA [BBN_8770]


title: RS25_882_Distal Colon


title: Set2_h2aw_Input_rep2

description: Library name: Set2_h2aw_Input_rep2


title: Set2_h2aw_H3_rep2

description: Library name: Set2_h2aw_H3_rep2


title: Set2_h2aw_Input_rep1

description: Library name: Set2_h2aw_Input_rep1


title: RS25_881_Distal Colon


title: RS25_950_Cecum

source_name: Cecum

value: Cecum


title: Set2_h2aw_H3_rep1

description: Library name: Set2_h2aw_H3_rep1


title: Brain_PFC_DNA [BBN_12609]

value: Queen Sqaure

value: F


title: Brain_PFC_DNA [BBN_7419]

value: AD


title: Set2_h2aw_H2AZ_rep1

description: Library name: Set2_h2aw_H2AZ_rep1


title: RS25_949_Cecum


title: Set2_Col_Input_rep1

description: Library name: Set2_Col_Input_rep1


title: RS25_948_Cecum


title: HT1080 cells (+/-), IDH1 R132Q expression, tumor collected 54 days after cell injection, sample 46

value: tumor

value: human fibrosarcoma

value: IDH1 R132Q

value: injection with human cells stably overexpressing IDH1 form


title: Set2_Col_H3_rep1

description: Library name: Set2_Col_H3_rep1

value: keep in 22°C


title: Set2_Col_H3_rep2

description: Library name: Set2_Col_H3_rep2


title: RS25_947_Cecum


title: Set2_Col_H2AW_rep2

description: Library name: Set2_Col_H2AW_rep2


title: Brain_PFC_DNA [BBN_7519]

value: M

value: Ctl


title: Brain_PFC_DNA [BBN_7511]

value: Newcastle


title: RS25_946_Cecum


title: Set3_Col_H2A_rep2

description: Library name: Set3_Col_H2A_rep2


title: Brain_PFC_DNA [BBN_8872]

value: Prefrontal Cortex

value: Bristol


title: Set2_Col_H2AW_rep1

description: Library name: Set2_Col_H2AW_rep1


title: Set2_Col_H2AZ_rep2

description: Library name: Set2_Col_H2AZ_rep2


title: Set2_Col_H2AZ_rep1

description: Library name: Set2_Col_H2AZ_rep1


title: Set1_h2az_Input_rep2

description: Library name: Set1_h2az_Input_rep2

value: mutant h2a.z


title: RS25_940_Cecum


title: Set1_h2az_H3_rep2

description: Library name: Set1_h2az_H3_rep2


title: RS25_939_Cecum


title: Set2_h2aw_H2AZ_rep2

description: Library name: Set2_h2aw_H2AZ_rep2

value: mutant h2a.w


title: Brain_PFC_DNA [BBN_15810]

value: Edinburgh


title: Set1_h2az_Input_rep1

description: Library name: Set1_h2az_Input_rep1


title: RS25_938_Cecum

value: Cecum


title: Brain_PFC_DNA [BBN005.29468]

value: Manchester


title: Set1_h2az_H3_rep1

description: Library name: Set1_h2az_H3_rep1


title: Brain_PFC_DNA [BBN_10591]


title: RS25_937_Cecum


title: Set2_Col_Input_rep2

description: Library name: Set2_Col_Input_rep2


title: Brain_PFC_DNA [BBN_9371]

value: F


title: RS25_936_Cecum


title: Set1_h2a_Input_rep2

description: Library name: Set1_h2a_Input_rep2

value: mutant h2a


title: Set1_h2az_H2AW_rep1

description: Library name: Set1_h2az_H2AW_rep1


title: Brain_PFC_DNA [BBN003.32218]

value: AD


title: Brain_PFC_DNA [BBN_7494]


title: RS25_930_Cecum


title: Set1_h2a_H3_rep2

description: Library name: Set1_h2a_H3_rep2


title: Set1_h2a_H3_rep1

description: Library name: Set1_h2a_H3_rep1


title: Set1_h2a_H2AW_rep2

description: Library name: Set1_h2a_H2AW_rep2


title: Set1_h2a_Input_rep1

description: Library name: Set1_h2a_Input_rep1


title: Brain_PFC_DNA [BBN006.31488]


title: RS25_929_Cecum


title: Set1_h2a_H2AZ_rep2

description: Library name: Set1_h2a_H2AZ_rep2


title: Set1_h2a_H2AZ_rep1

description: Library name: Set1_h2a_H2AZ_rep1


title: Set1_h2az_H2AW_rep2

description: Library name: Set1_h2az_H2AW_rep2


title: Brain_PFC_DNA [BBN_24322]


title: Brain_PFC_DNA [BBN_9354]


title: Set1_Col_Input_rep2

description: Library name: Set1_Col_Input_rep2


title: Set1_Col_Input_rep1

description: Library name: Set1_Col_Input_rep1


title: RS25_927_Cecum


title: RS25_928_Cecum


title: Brain_PFC_DNA [BBN_9430]


title: RS25_926_Cecum


title: Set1_Col_H2AW_rep2

description: Library name: Set1_Col_H2AW_rep2


title: Set1_Col_H3_rep2

description: Library name: Set1_Col_H3_rep2


title: Set1_Col_H3_rep1

description: Library name: Set1_Col_H3_rep1


title: Set1_Col_H2AW_rep1

description: Library name: Set1_Col_H2AW_rep1


title: RS25_925_Cecum


title: RS25_924_Cecum


title: Brain_PFC_DNA [BBN_8651]


title: Set1_h2a_H2AW_rep1

description: Library name: Set1_h2a_H2AW_rep1


title: RS25_923_Cecum


title: AAV-Ctnnd2, PFC, biol rep 4

city: Beijing

first: Feng

last: Yang

address: 119 South Fourth Ring Road West, Fengtai District

institute: Beijing Tiantan Hospital, Capital Medical University

data_processing:
The clustering of the index-coded samples was performed on a cBotCluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Raw data (raw reads) of fastq format were firstly processed through fastp software
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach
Assembly: ensembl_97_rattus_norvegicus_rnor_6_0_toplevel
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

organism: Rattus norvegicus

extract_protocol:
RNA was harvested using Trizol from tissue,1000ng of total RNA was used for the construction of sequencing libraries
mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out usingdivalent cations under elevated temperature in First Strand SynthesisReaction Buffer(5X). First strand cDNA was synthesized using randomhexamer primer and M-MuLV Reverse Transcriptase(RNase H-).Second strand cDNA synthesis was subsequently performed usingDNA Polymerase I and RNase H. Remaining overhangs were convertedinto blunt ends via exonuclease/polymerase activities. After adenylationof 3’ ends of DNA fragments, Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNA fragmentsof preferentially 370~420 bp in length, the library fragments werepurified with AMPure XP system. Then PCR was performed withPhusion High-Fidelity DNA polymerase, Universal PCR primers andIndex (X) Primer. At last, PCR products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer2100 system

value: CdCS


title: Brain_PFC_DNA [BBN003.32278]


title: AAV-Ctnnd2, PFC, biol rep 2


title: AAV-Ctnnd2, PFC, biol rep 3


title: T47DS_shGRHL2_R5020_24h_rep3

description: Library name: T47DS_shGRHL2_R5020_24h_3

data_processing:
Quality control on FASTQ files was performed using MultiQC, followed by removal of overrepresented sequences by read trimming with Trimmomatic  using a list of selected adapters. Trimmed reads were then mapped to the human reference genome (version GRCh38.p14) using HISAT. Mapping quality was inspected using SAMtools stats and visualized using MultiQC. HTSeq count179 was then used to create a count matrix. Further differential gene expression analysis was performed using DESeq2  in R studio.
Assembly: hg38
Supplementary files format and content: txt file contains raw counts for each sample

growth_protocol: T47DS human epithelial breast cancer cells were cultured in DMEM + GlutaMAX supplemented with 10% FBS. Cells were split 1:5–1:10 twice a week and routinely tested for mycoplasma.

extract_protocol:
RNA isolation was performed using the RNeasy mini kit (Qiagen, #74104), including on-column DNAse digestion (Qiagen, RNase-free DNase set #79254) according to manufacturer’s instructions.
1μg of RNA was used as starting material for poly-A enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). Next, RNA-Seq libraries were generated according to the manufacturers’ protocols using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) (New England BioLabs). Distribution of the size of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) was used for library quantification using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to manufacturer’s instructions.

treatment_protocol: T47DS cells were plated in 6-well plates containing DMEM + GlutaMAX supplemented with 5% Charcoal Stripped Fetal Bovine Serum. For 24hr induction of progesterone signaling, the medium was refreshed 24 hrs after plating and cells were treated for another 24hr with either 1nM R5020 or EtOH (as a control) added to the culture medium. For 4hr induction of progesterone signaling the medium was refreshed 44hr after plating and cells were treated for another 4 hr with either 1nM R5020 or EtOH (as a control). All cells were then harvested and further processed simultaneously.

value: Epithelial breast cancer

value: GRHL2 knockdown


title: RS25_922_Cecum


title: Brain_PFC_DNA [BBN_8997]


title: AAV-Ctnnd2, PFC, biol rep 1


title: Brain_PFC_DNA [BBN003.28560]


title: T47DS_shGRHL2_control_rep3

description: Library name: T47DS_shGRHL2_control_3

value: No treatment


title: T47DS_WT_R5020_24h_rep3

description: Library name: T47DS_WT_R5020_24h_3

value: WT


title: Brain_PFC_DNA [BBN_8868]

value: M


title: AAV, PFC, biol rep 3

value: AAV


title: AAV, PFC, biol rep 4

value: Prefrontal Cortex


title: RS25_900_Cecum


title: Brain_PFC_DNA [BBN001.29136]

value: Ctl


title: AAV, PFC, biol rep 2


title: Set1_Col_H2AZ_rep1

description: Library name: Set1_Col_H2AZ_rep1

value: keep in 22°C


title: T47DS_WT_control_rep3

description: Library name: T47DS_WT_control_3


title: Set1_Col_H2AZ_rep2

description: Library name: Set1_Col_H2AZ_rep2


title: Brain_PFC_DNA [BBN_19206]

value: Newcastle


title: Brain_PFC_DNA [BBN_7110]


title: RS25_898_Cecum


title: T47DS_shGRHL2_R5020_24h_rep2

description: Library name: T47DS_shGRHL2_R5020_24h_2


title: RS25_897_Cecum


title: AAV, PFC, biol rep 1


title: Brain_PFC_DNA [BBN_3447]


title: Brain_PFC_DNA [BBN_9342]

value: Bristol


title: CdCS, PFC, biol rep 4


title: CdCS, PFC, biol rep 3


title: RS25_896_Cecum

value: Cecum


title: T47DS_WT_R5020_24h_rep2

description: Library name: T47DS_WT_R5020_24h_2


title: RS25_921_Cecum


title: Brain_PFC_DNA [BBN_8819]


title: RS25_899_Cecum


title: CdCS, PFC, biol rep 2


title: RS25_894_Cecum


title: T47DS_WT_R5020_4h_rep2

description: Library name: T47DS_WT_R5020_4h_2


title: Brain_PFC_DNA [BBN_7623]


title: T47DS_WT_R5020_4h_rep3

description: Library name: T47DS_WT_R5020_4h_3


title: T47DS_WT_control_rep2

description: Library name: T47DS_WT_control_2


title: CdCS, PFC, biol rep 1


title: RS25_893_Cecum


title: WT, PFC, biol rep 4


title: RS25_892_Cecum


title: T47DS_shGRHL2_R5020_24h_rep1

description: Library name: T47DS_shGRHL2_R5020_24h_1


title: Brain_PFC_DNA [BBN_11763]

value: Queen Sqaure


title: RS25_891_Cecum


title: WT, PFC, biol rep 3


title: Brain_PFC_DNA [BBN_24254]


title: T47DS_shGRHL2_control_rep2

description: Library name: T47DS_shGRHL2_control_2


title: RS25_890_Cecum


title: WT, PFC, biol rep 2


title: RS25_895_Cecum


title: T47DS_shGRHL2_control_rep1

description: Library name: T47DS_shGRHL2_control_1


title: T47DS_WT_R5020_24h_rep1

description: Library name: T47DS_WT_R5020_24h_1


title: WT, PFC, biol rep 1


title: Brain_PFC_DNA [BBN006.35477]

value: F


title: T47DS_WT_R5020_4h_rep1

description: Library name: T47DS_WT_R5020_4h_1


title: RS25_889_Cecum


title: AAV-Ctnnd2, HPC, biol rep 4

source_name: Hippocampus

value: Hippocampus


title: RS25_888_Cecum


title: T47DS_WT_control_rep1

description: Library name: T47DS_WT_control_1


title: AAV-Ctnnd2, HPC, biol rep 3


title: Brain_PFC_DNA [BBN006.31516]


title: Brain_PFC_DNA [BBN_9005]

value: AD


title: RS25_887_Cecum


title: Brain_PFC_DNA [BBN003.29753]


title: AAV-Ctnnd2, HPC, biol rep 2

value: CdCS


title: 2323-Tumor, replicate 2, scRNAseq

city: Aurora

first: Xiying

last: Fan

state: CO

department: Dermatology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin tumor

extract_protocol:
Control skin and skin tumors were excised from mice, minced, and dissociated with a 0.5% collagenase IV (Worthington, LS004188) at 37 °C for 2h. Cells were spun down for 5min at 300g and strained through a 70μm strainer before counting and downstream analysis. Next, cells were stained with CD45-APC (Life technologies, MCD4505) for 30min on ice and then washed with PBS. Live/dead exclusion was performed using 0.1mg/mL DAPI (4’,6-diamidino-2’phenylindole dihydrochloride). Then, single cell suspension was used to sort for CD45+ /DAPI- immune cells on a Beckman Coulter XDP100 cell sorter at the University of Colorado Cancer Center Flow Cytometry Shared Resource.
The sorted CD45+ cells from two 2323 tumors and two C57 control skins were loaded into a Chromium Single Cell 3’ Solution Capture System (10X Genomics). The processed libraries were sequenced on Illumina Novaseq6000 at the Genomics Shared Resource at University of Colorado Anschutz Medical Campus.

value: skin tumor

value: 2323 cell line

value: immune cells


title: RS25_885_Cecum


title: Brain_PFC_DNA [BBN001.26718]

value: Edinburgh


title: C57, replicate 1, scRNAseq

institute: University of Colorado Anschutz Medical Campus

description: 10x Genomics

source_name: normal skin

value: normal skin


title: AAV, HPC, biol rep 4

value: AAV


title: Brain_PFC_DNA [BBN_7591]

value: Prefrontal Cortex


title: AAV-Ctnnd2, HPC, biol rep 1


title: RS25_883_Cecum


title: Brain_PFC_DNA [BBN003.26947]

value: Ctl


title: C57, replicate 2, scRNAseq

description: 10x Genomics


title: Brain_PFC_DNA [BBN_9303]

value: M


title: Brain_PFC_DNA [BBN_9123]


title: [ED1]

city: Kolkata

first: A

last: G

address: B.T. Road

institute: INSTITUTE

data_processing:
Prepared libraries were sequenced on Illumina Hiseq X
Functional annotation was obtained from JGI. Ensembl gene IDs were mapped to JGI gene IDs.
GO annotation in JGI covers 1411 (39.60%) genes.
Assembly: Bacillus coagulans ASM75628v1, INSDC Assembly GCA_000756285.1, Sep 2014

organism: Heyndrickxia coagulans

source_name: Bacteria

extract_protocol:
Both the samples of control and treatment were stabilized by RNAprotect Bacteria Reagent 2×100 ml. Two tubes of required volume of bacterial culture and double volume of RNAprotect Bacteria Reagent were mixed by vortexing for few seconds (individual tubes for treatment and control). Then the mixtures were incubated for 5 min at room temperature (15-25˚C) and centrifuged for few min at ×g. After that, the supernatants were discarded;the pellets were kept in a freezer.  The RNA was expected to remain intact in a deep freezer for up to one month. On-column  enzyme digestion was performed to digest and remove genomic DNA. Concentrations of RNA were measured with the NanoDrop, while RNA quality was assessed. Samples included in the present analysis had a RIN score greater than 6.
For library preparation, “Microbe express kit” was used for mRNA capture by oligo mag beads, followed by mRNA fragmentation. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA where Uracil is added instead of Thymine and adds dAMP to the 3′ ends of the resulting dscDNA. In Adapter ligation, where dsDNA adapters with 3′ dTMP overhangs are ligated to library insert fragments followed by library amplification, to amplify library fragments carrying appropriate adapter sequences at both ends using high-fidelity, low-bias PCR.

value: Capsule

value: 18 hours

value: Treatment with nanoparticle


title: AAV, HPC, biol rep 2


title: Brain_PFC_DNA [BBN003.35201]

value: Newcastle


title: AAV, HPC, biol rep 3


title: RS25_882_Cecum

value: Cecum


title: AAV, HPC, biol rep 1

value: Hippocampus


title: Brain_PFC_DNA [BBN003.31464]

value: F


title: RS25_881_Cecum


title: RS25_884_Cecum


title: SpCas9 – IRF3 sgRNA

city: Salt Lake City

first: Justin

middle: G

last: English

state: UT

address: 15 N Medical Drive East RM 4100

department: Biochemistry

institute: University of Utah

description: Library name: Sample 37

library_source: other

data_processing:
Basecalling of raw nanopore trace files was performed after sequencing with Guppy or during sequencing with MinKNOW software. In both cases, the ‘super accuracy’ basecalling algorithm was utilized. Default software read quality thresholds were maintained throughout.
Basecalled reads in fastq format were processed into bins by our ConSeqUMI according to unique 5’ and 3’ sequence tags. Each bin was exported as a single fastq file containing all basecalled reads belonging to the bin.
ConSeqUMI was then used to derive a consensus sequence for each individual bin based on constituent sequences therein.
Assembly: GRCh38/hg38 (Ded. 2013)
Supplementary files format and content: FASTA files contain consensus sequences generated by ConSeqUMI

molecule: other

source_name: Kidney

growth_protocol: 293 cells were maintained in DMEM supplemented with 10% FBS and 200 ug/mL Geneticin.

extract_protocol:
Target amplicons were purified after polymerase chain reactions using gel extraction or column purification.
Sequencing libraries were prepared using Native Ligation kits and protocols developed by Oxford Nanopore Technologies according to their instructions.

value: Kidney

value: Epithelial

value: Infected with AAV2 carrying an sgRNA expression cassette for the targeting of human IRF3 exon 2


title: Brain_PFC_DNA [BBN001.30916]


title: CdCS, HPC, biol rep 4

value: CdCS


title: DC2-P6

first: Haidong

last: Tang

address: Shuangqing Road

institute: Tsinghua University

data_processing:
Raw reads were obtained and quality control was performed using FastQC. Low-quality bases, TSO sequences, polyA sequences, and adapter sequences were removed. The cleaned sequences were aligned to the mm10 reference genome using STAR (version 2.7.9a). Normalization and expression level verification across samples were conducted using Seurat (version 4.0.5).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Tumor

extract_protocol:
Single-cell transcriptome amplification followed the SMART-SEQ2 protocol with minor modifications. Briefly, single cells were sorted into 2.55 ul cell lysis buffer containing RNase inhibitor (40 U/ul), Triton X-100 (10%), barcode primer (5 uM), and dNTP mix (10 mM). Reverse transcription was performed using a 25-nt oligo(dT) primer anchored with an 8-nt cell-specific barcode and 8-nt unique molecular identifiers (UMIs). After first-strand synthesis, second-strand cDNA was synthesized, followed by amplification through PCR.
The amplified cDNA was pooled and further amplified using biotinylated pre-indexted primers. Approximately 300 ng cDNA was sheared to ~300 bp using a Covaris S2, and the 3’ end was captured using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher). Libraries were constructed from the enriched cDNA fragments attached to the C1 beads using KAPA Hyper Prep Kits (KK8505) and NEB U-shape adaptor for ligation.

value: Tumor


title: CdCS, HPC, biol rep 3


title: RS25_886_Cecum


title: 2323-Tumor, replicate 1, scRNAseq

description: 10x Genomics

value: skin tumor

value: 2323 cell line

value: immune cells


title: DC1-P5


title: Dex + KLA, rep 2

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Low quality nucleotides and adapter sequences were removed from raw reads using trimmomatic PE (v. 0.36; PE, LEADING:3, TRAILING:3, MINLEN:36).
Abundant sequences (sequencing adapters, mitochondrial and ribosomal sequences) were removed, and remaining reads were mapped to human genome hg38 with bwa mem aligner (v.0.7.17).
Transcript-level count matrix (counts.HEPG2_RNAseq.txt) was produced using analyzeRepeats function (analyzeRepeats.pl rna hg38 -raw) in homer (v4.10).
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing transcript refSeq ID, transcript information (chromosome, start, end, strand, length, copies, annotations), and raw counts for each sample.

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Monarch ® Total RNA Miniprep Kit based on the manufacturers protocol.
RNA-seq libraries were prepared using NEBNext Ultra II DNA library kit for illumina platform following manufacturers protocol.

treatment_protocol: HepG2 cells were pretreated with growth media containing charcoal stipped serum for 24 hours followed by Dex (50nM), KLA (100ng/ul) or combined treatment for 24 hours. DMSO (0.1%) was used as vehicle control.

value: Hepatoma derived cell line

value: WT

value: DexKLA

tag: time

value: 24 hours


title: Dex + KLA, rep 3


title: Brain_PFC_DNA [BBN_4240]

data_processing:
wateRmelon package in R environment (3.5.2)
Beta value

extract_protocol: genomic DNA was extracted from PFC tissue using the All-prep universal kit (Qiagen)

value: Prefrontal Cortex

value: Bristol

value: Ctl


title: CdCS, HPC, biol rep 2

value: Hippocampus


title: Dex + KLA, rep 1


title: CdCS, HPC, biol rep 1


title: [EA1]

extract_protocol:
Both the samples of control and treatment were stabilized by RNAprotect Bacteria Reagent 2×100 ml. Two tubes of required volume of bacterial culture and double volume of RNAprotect Bacteria Reagent were mixed by vortexing for few seconds (individual tubes for treatment and control). Then the mixtures were incubated for 5 min at room temperature (15-25˚C) and centrifuged for few min at ×g. After that, the supernatants were discarded;the pellets were kept in a freezer. The RNA was expected to remain intact in a deep freezer for up to one month. On-column enzyme digestion was performed to digest and remove genomic DNA. Concentrations of RNA were measured with the NanoDrop, while RNA quality was assessed. Samples included in the present analysis had a RIN score greater than 6.
For library preparation, “Microbe express kit” was used for mRNA capture by oligo mag beads, followed by mRNA fragmentation. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA where Uracil is added instead of Thymine and adds dAMP to the 3′ ends of the resulting dscDNA. In Adapter ligation, where dsDNA adapters with 3′ dTMP overhangs are ligated to library insert fragments followed by library amplification, to amplify library fragments carrying appropriate adapter sequences at both ends using high-fidelity, low-bias PCR.

value: Capsule

value: 18 hours


title: DC1-P3


title: Brain_PFC_DNA [BBN_24668]

value: Edinburgh

value: F

value: AD


title: DC1-P4

value: Tumor


title: KLA 100ng/µl, rep 3

value: KLA


title: Brain_PFC_DNA [BBN_7306]

value: Newcastle


title: DC2-P2


title: KLA 100ng/µl, rep 2


title: Brain_PFC_DNA [BBN_9134]

value: M


title: WT, HPC, biol rep 3


title: KLA 100ng/µl, rep 1

value: Hepatoma derived cell line


title: DC2-P1


title: AZD1775 rep3 [A-3]

data_processing:
Pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Bone marrow-derived dendritic cells

extract_protocol:
RNA was harvested using TRIzol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Hyper Prep Kits following manufacturer's protocols.

value: Bone marrow-derived dendritic cells


title: Brain_PFC_DNA [BBN_22226]


title: WT, HPC, biol rep 2

value: WT


title: Brain_PFC_DNA [BBN003.32222]


title: WT, HPC, biol rep 1


title: Brain_PFC_DNA [BBN_2602]


title: Dex 50nM, rep 3

value: Dex

value: 24 hours


title: AZD1775 rep2 [A-2]


title: AZD1775 rep1 [A-1]


title: Brain_PFC_DNA [BBN005.31442]

value: Prefrontal Cortex

value: Manchester


title: Dex 50nM, rep 1


title: SerRS overexpression 3

city: Toronto

first: Haissi

last: Cui

address: 80 St George St

department: Chemistry

country: Canada

institute: University of Toronto

data_processing:
Ribosomal footprints were analyzed as described by Ingolia et al. with these modifications: Trimgalore was used to trim off adapters and clip the first nucleotide off the 5’ end. Reads were then mapped to ribosomal RNA using bowtie2 (39) and unmapped reads were further mapped to the human transcriptome (v19) with STAR aligner (33).
Expected read length distribution was tested with the R package RiboProfiling. To center ribosomes and obtain a list of genes with P-sites in their 3’ UTR, we used functionalities within Ribowaltz (40) and a custom python script by Scott Adamson, UConn, and Jax Laboratories.
Observed/expected ratios were calculated using a custom script by Scott Adamson. Obs/exp indicates the number of observed codons in the A-site of the ribosome vs the calculated hypothetical expected number of observations. If ribosome pausing occurs, obs/exp > 1.
Assembly: hg19
Supplementary files format and content: Excel file
Library strategy: Ribo-Seq

growth_protocol: Two 10 cm dishes of cells were used for each biological replicate, and three biological replicates were prepared for each cell line (MDA-MB-231-empty vector, MDA-MB-231-SARS).

extract_protocol:
Ribosome profiling libraries were generated as previously described by Ingolia et al with some minor modifications. Cell homogenization was performed in 1 ml lysis buffer (20mM Tris-Cl, pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml CHX, 1% (v/v) TritonX-100, 50 units/ml Turbo DNaseI). RNase I-treated lysates were overlaid on top of a sucrose cushion in 5 ml Beckman Ultraclear tubes and centrifuged in an SW55Ti rotor for 4 hours at 4ºC at 46,700 rpm. Pellets were resuspended and RNA was extracted using the miRNeasy kit (Qiagen) according to manufacturer’s instructions.
26-34 nucleotide RNA fragments were purified by electrophoresis on a 15% denaturing gel. Linker addition, cDNA generation (first-strand synthesis was performed at 50°C for 1 h), circularization, rRNA depletion, and amplification of cDNAs with indexing primers were performed.
Library quality and concentration were assessed using high sensitivity D1000 screen tape on the Agilent tape station, Qubit 2.0 Fluorometer, and qPCR. All libraries were pooled and run on HiSeq4000 (SR75).

value: Breast Cancer

value: SerRS overexpression


title: SerRS overexpression 2


title: SerRS overexpression 1


title: Vehicle rep3 [D-3]

value: DMSO


title: WT, HPC, biol rep 4

value: Hippocampus


title: Vehicle rep2 [D-2]


title: DMSO 0.1% (vehicle control), rep 3


title: Brain_PFC_DNA [BBN_9429]

value: Bristol

value: Ctl


title: DMSO 0.1% (vehicle control), rep 2


title: Brain_PFC_DNA [BBN006.35513]

value: AD


title: ctrl 2

value: control


title: ctrl 3


title: Vehicle rep1 [D-1]


title: SSX2_Pten_3

city: Heidelberg

first: Ana

last: Banito

address: Im Neuenheimer Feld 581

country: Germany

institute: KiTZ, DKFZ

data_processing:
Sequencing was carried out on Illumina’s NovaSeq 6000 S1 or S4 flow cell with paired-end 50 bp reads, yielding an average of approximately 20 million reads per sample
Sequencing reads were aligned to the mouse reference genome (GRCm38mm10) by DKFZ’s Omics IT and Data Management Core Facility (ODCF) using the One Touch Pipeline (OTP)264 / RNAseq workflow pipeline, version 1.3.0 (STAR Version 2.5.3a, Merging/duplication marking program: Sambamba Version 0.6.5. SAMtools program: Version 1.6.), resulting in raw counts, RPKM, and TPM values.
Assembly: GRCm38mm10
Supplementary files format and content: TPM counts for all samples.txt

extract_protocol:
DNA and RNA were extracted from the same tumor tissue piece, approximately 20-30 mg in weight, using Qiagen’s DNA/RNA AllPrep kit (80204) following the manufacturer’s protocol.
Only samples with RNA integrity scores (RIN) exceeding 7 proceeded to library preparation using the TruSeq Stranded total mRNA protocol, starting with 50 μl of undegraded RNA at concentrations ranging from 50 to 80 ng/μl per sample.

value: Tumor

value: EPO P30

value: SS18-SSX1; sgPten


title: Human GBM 3, Visium

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Rnger pipeline to generate FSATQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barodes
Supplementary files format and content: features.tsv.gz: kist of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligend_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_potitions_list.csv.gz: list of spatial barcode and the coordinates specifying spots
Library strategy: Spatial Transcriptome

source_name: brain

extract_protocol:
Tissues were Formalin-Fixed Paraffin-Embedded, and 5µm sections were cut with microtome
Spatial transcriptome sequencing librarys were prepared with 10xGenomics Visium CytAssist Spatial Gene Expression Reagent Kits according to manufacture's construction

value: brain


title: Brain_PFC_DNA [BBN001.26307]

first: Katie

last: Lunnon

institute: University of Exeter Medical School

value: Edinburgh

value: F


title: Dex 50nM, rep 2

value: Hepatoma derived cell line

value: WT

value: Dex

value: 24 hours


title: SSX2_Pten_2


title: ctrl 1

value: Breast Cancer


title: SSX2_Pten_1_SamF

source_name: SAM from Tumor fragments

value: SAM from Tumor fragments


title: Human GBM 2, Visium

description: FFPE Spatial transcriptome sequencing


title: Brain_PFC_DNA [BBN006.33738]

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: Brain_PFC_DNA [BBN_24312]

value: Bristol

value: M


title: KO -2

city: Chicago

first: Hai

last: Wang

state: IL

address: 303E Chicago Avenue

department: Department of Pathology

institute: Northwestern University

data_processing:
The quality of DNA reads was evaluated using FastQC. Adapters were trimmed and reads of poor quality or those aligning to ribosomal RNA sequences were filtered.The cleaned reads were aligned to the Mus musculus Ensembl release 110  using HISAT2.
Assembly: Mus musculus Ensembl release 110
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Primary iTregs

growth_protocol: Treg cells were cultured in a T cell medium made of complete RPMI 1640 medium containing 10% FBS, 1% penicillin/streptomycin, 50 μM β-mercaptoethanol (Gibco), and 1% L-glutamine (Gibco) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted with a RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen#74106)
RNA libraries were prepared using SMARTER mRNA-Seq Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: Splenic CD4 T cells were cultured in Treg polarization condition for 2 days in the presence of 4-hydroxytamoxifen

value: Primary iTregs

value: KO

value: Treg in vitro induction


title: Brain_PFC_DNA [BBN_19630]

city: Exeter

address: RILD Level 4, Barrack Road

value: Ctl


title: Brain_PFC_DNA [BBN_9295]

value: AD


title: SSX2_Pten_1_CL3D

source_name: Cell line 3D

value: Cell line 3D

value: EPO P30

value: SS18-SSX1; sgPten


title: KO -1


title: Brain_PFC_DNA [BBN_9422]

value: F


title: WT -2

value: WT


title: SSX2_Pten_1_CL2D

source_name: Cell 2D

value: Cell 2D


title: WT -3


title: Brain_PFC_DNA [BBN_12400]

value: Queen Sqaure


title: FL_NUP98-NSD1/WT1ko_leukemic cells Input

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Input

data_processing:
Reads were first evaluated for their quality using FastQC (v0.11.8).
Reads were trimmed for adaptor sequences using Trim Galore! (v0.6.6) and aligned to the GRCh38/hg38 using Bowtie2 (v2.1.0).
Picard (v2.2.4) was used to remove duplicated reads (http://broadinstitute.github.io/picard/).
Binary alignment map (BAM) files were generated with samtools v1.9, and were used in downstream analysis.
Significant peaks were identified on bam files with MACS2 (v2.1.1.2) using input as control (q-value < 0.01).
Peaks in ENCODE blacklisted regions were removed.
Coverage tracks were generated from Bam files using deepTools (v3.2.1) bamCoverage with parameters –normalizeUsingRPKM --binsize 10 --extendReads=200.
Assembly: hg38 (GRCh38)
Supplementary files format and content: BAM file containing aligned sequencing reads
Supplementary files format and content: Bed file containing MACS2 called peaks

source_name: Human fetal liver derived CD34+ HSPC

growth_protocol: Cell were cultured in in X-VIVO 10 medium, supplemented with 1% BSA and FLT3L, G-CSF, SCF, TPO and IL-6.

extract_protocol:
For each condition, approximately 1 × 10⁷ NUP98-NSD1/WT1ko leukemic cells were crosslinked, followed by ChIP using PRDM16 or H3K27ac antibodies. The immunoprecipitated DNA was then purified using SPRIselect beads, followed by library preparation, including end repair, adapter ligation, and PCR amplification. Quality control was performed to assess fragment size and concentration before the samples were subjected to next-generation sequencing.
Library construction was performed using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: No treatment.

value: Human fetal liver derived CD34+ HSPC

value: Human NUP98-NSD1/WT1ko leukemic cells


title: Brain_PFC_DNA [BBN_9183]

value: Prefrontal Cortex


title: Brain_PFC_DNA [BBN_8719]

value: Bristol


title: KO -3


title: DMSO 0.1% (vehicle control), rep 1

value: Hepatoma derived cell line

value: DMSO

value: 24 hours


title: SSX1_Pten_neo_5_CL2D

value: EPO P0 (Neonatal)


title: FL_NUP98-NSD1/WT1ko_leukemic cells H3K27ac

description: Library name: H3K27ac


title: Brain_PFC_DNA [BBN_9016]

value: M


title: SSX1_Pten_neo_5

value: Tumor


title: Brain_PFC_DNA [BBN_19364]

value: Edinburgh

value: Ctl


title: FL_NUP98-NSD1/WT1ko_leukemic cells PRDM16

description: Library name: PRDM16


title: NCL

first: Hong

last: Zhou

address: 650 Xinsongjiang Road

department: Clinical Insititute of immunology

institute: Shanghai general hospital

data_processing:
Agilent 2100 bioanalyzer to construct the library then QC by Agilent High Sencitive DNA Kit. The reads were mapping to the miRNA database. DEG between ASO and CRO group was anlyzed.
Assembly: mm9
Supplementary files format and content: Agilent 2100 bioanalyzer to construct the library then QC by Agilent High Sencitive DNA Kit. The reads were mapping to the miRNA database. DEG between ASO and CRO group was anlyzed.

source_name: spleen

growth_protocol: 1640 culuted medium

extract_protocol:
Trizoll
illumina TruSeq small RNA Sample Kit

treatment_protocol: activated by anti-CD3/28

value: spleen

value: CD4+ T cells

value: wild type


title: SSX2_Pten_1_SamC

source_name: SAM from Single cells

value: SAM from Single cells

value: EPO P30

value: SS18-SSX1; sgPten


title: Brain_PFC_DNA [BBN_11560]

value: Queen Sqaure

value: F

value: AD


title: Nucleus_R2

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

description: Illumina TruSeq

data_processing:
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed using the CLC workbench with quality score limit set to 0.05 and 25 nt minimal read length
Trimmed sequences were mapped to the GRCh38 human reference genome using the CLC workbench with the following parameters: Mismatch cost: 2. Insertion cost: 3. Deletion cost: 3. Length fraction: 0.8. Similarity fraction: 0.8. Max. hits for a read: 10. Strand specific: both.
Normalized expression values (e.g. RPKM) were calculated based on the read counts obtained from the CLC genomics workbench analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, including gene identifiers and coordinates, read counts and RPKM values for each sample.

source_name: blood

growth_protocol: AEC II cells were cultured on ThinCert™ transwells in SAGM medium (Lonza), supplemented with 2% FCS. Primary macrophages were cultured in X-Vivo-15 medium (Lonza), supplemented with 5 % FCS.  THP1 cells were cultivated in RPMI Glutamax medium, supplemented with 5 % FCS. All cells were cultured at 37 °C with humidified 5% CO2 atmosphere.

extract_protocol:
RNA was extracted with Trizol reagent and DNaseI-treated, using established protocols. PolyA RNA was selected using magnetic beads.
Libraries were generated using the TruSeq Stranded mRNA Kit (Illumina) or the QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen), as indicated.

treatment_protocol:
Blood-derived monocytes (CD14 MACS purification) were differentiated into macrophages using 15 ng / ml recombinant GM-CSF or M-CSF for 7 days. THP1 cells were differentiated with PMA (20 nM) for two days.
Upon differentiation / attachment, cells were treated with different immune-stimuli at the following concentrations: Flagellin: 1 µg / ml. LPS: 100 ng / ml. Pam3csk4: 200 ng / ml. IFNalpha: 100 ng / ml.
For inhibitor experiments, cells were pre-treated with for 2 hours as follows, prior to further stimulations: - (DMSO only as solvent control). BAY 11-7082: 5 or 10 µM. Ruxolitinib: 1 or 5 µM, BX795: 1 or 5 µM

value: blood

value: blood-derivedmacrophage

tag: source

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

value: LPS

value: 4 h


title: CRO2

data_processing:
Agilent 2100 bioanalyzer to construct the library then QC by Agilent High Sencitive DNA Kit. The reads were mapping to the miRNA database. DEG between ASO and CRO group was anlyzed.
Assembly: mm9
Supplementary files format and content: ASO_vs_CRO.DESeq.DE_results.xlsx
Supplementary files format and content: DEG_count.xlsx

treatment_protocol: transfected by ASO or CRO

value: naive CD4+ T cells

value: transfected by CRO


title: Cytoplasm_R2

description: Illumina TruSeq


title: SSX1_Pten_neo_4

value: Tumor

value: EPO P0 (Neonatal)


title: CRO1

value: spleen

value: CD4+ T cells

value: wild type


title: SSX1_Pten_neo_3

value: SS18-SSX1; sgPten


title: SSX2_Pten_1

value: EPO P30


title: SSX1_Pten_neo_1


title: Cytoplasm_R1

description: Illumina TruSeq


title: SSX1_Pten_neo_2


title: SSX1_Pten_neo_6


title: ASO2

value: transfected by ASO


title: Brain_PFC_DNA [BBN_9205]

value: Prefrontal Cortex

value: Bristol

value: F

value: AD


title: Input1


title: RNAseq of Daphnia magna young rep1

city: Johnson City

first: Lev

middle: Y

last: Yampolsky

state: Tennessee

address: 811 Lazywood Dr

department: Biological sciences

institute: East Tennessee State University

data_processing:
alignment: STAR
indexing and read counts: samtools
Assembly: Xnb3, PRJNA624896
Supplementary files format and content: YOrOnByGene_RPKM.csv :: rows=genes; columns=samples; content: RPKM
Supplementary files format and content: YOrOnByGene_reads.csv :: rows=genes; columns=samples; content: reads count

organism: Daphnia magna

source_name: whole body, somatic

growth_protocol: individually housed in 20 mL of ADaM medium, 20 C, fed 100,000 cells of Scenedesmus acutus per mL per day

extract_protocol:
Qiagen Rneasy
NEBNext Ultra II Directional RNA Library prep

treatment_protocol: no treatments other than age

value: female

value: whole body, somatic

value: young


title: SSX1_neo_3


title: WT -1

value: Primary iTregs

value: WT

value: Treg in vitro induction


title: Brain_PFC_DNA [BBN_8879]


title: ASO1

value: naive CD4+ T cells


title: Exp5_Ctrl-CRISPRi2_LPS_R3

description: Lexogen Quantseq

value: blood

value: monocytic

value: ATTC TIB-202; PMA-differentiated

value: LPS

value: 8 h


title: SSX1_neo_2

value: Tumor

value: EPO P0 (Neonatal)


title: Nucleus_R1

description: Illumina TruSeq

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: 4 h


title: Brain_PFC_DNA [BBN006.28893]

value: Prefrontal Cortex

value: Bristol

value: M

value: Ctl


title: Exp5_Ctrl-CRISPRi1_LPS_R2

description: Lexogen Quantseq


title: SSX1_neo_1


title: Brain_PFC_DNA [BBN005.32822]

value: Manchester

value: F


title: RNAseq of Daphnia magna young rep 3

value: female

value: whole body, somatic

value: young


title: Brain_PFC_DNA [BBN006.35895]

value: AD


title: Exp5_AC022816.1-gRNA1_LPS_R1

description: Lexogen Quantseq

value: blood

value: monocytic

value: ATTC TIB-202; PMA-differentiated

value: LPS


title: RNAseq of Daphnia magna young rep2


title: RNAseq of Daphnia magna old, non-reproducing rep 1

value: old, non-reproducing


title: Brain_PFC_DNA [BBN007.29605]

value: Queen Sqaure


title: Brain_PFC_DNA [BBN006.35953]


title: SSX1_1

value: Tumor

value: EPO P30


title: Exp5_AC022816.1-gRNA1_LPS_R2

description: Lexogen Quantseq

value: 8 h


title: Exp5_AC022816.1-gRNA2_LPS_R3

description: Lexogen Quantseq


title: Exp5_Ctrl-CRISPRi1_LPS_R1

description: Lexogen Quantseq


title: RNAseq of Daphnia magna old, non-reproducing rep 2


title: Smarcb1_p53_4

value: sgSmarcb1; sgp53


title: Brain_PFC_DNA [BBN001.30047]

value: Prefrontal Cortex

value: Edinburgh

value: M

value: Ctl


title: RNAseq of Daphnia magna young rep 4

value: female

value: whole body, somatic


title: Smarcb1_p53_3


title: Brain_PFC_DNA [BBN_4205]

value: Bristol


title: RNAseq of Daphnia magna old, reproducing rep 1

value: old, reproducing


title: Exp4_LINC01215-gRNA2_LPS_R3

description: Lexogen Quantseq

value: blood

value: monocytic


title: Brain_PFC_DNA [BBN_9076]

value: F

value: AD


title: Smarcb1_p53_2


title: RNAseq of Daphnia magna old, reproducing rep 2


title: Smarcb1_p53_1


title: Brain_PFC_DNA [BBN007.26827]

value: Queen Sqaure


title: Exp4_Ctrl-CRISPRi2_LPS_R3

description: Lexogen Quantseq

value: ATTC TIB-202; PMA-differentiated

value: LPS


title: RNAseq of Daphnia magna old, reproducing rep 3


title: Pax-Foxo_P53_CL3D

value: Cell line 3D

value: EPO P30

value: PAX3-FOXO1; sgp53


title: Brain_PFC_DNA [BBN003.28372]

value: Prefrontal Cortex

value: Newcastle


title: Exp4_Ctrl-CRISPRi1_LPS_R2

description: Lexogen Quantseq

value: 8 h


title: Brain_PFC_DNA [BBN_9377]

value: M


title: RNAseq of Daphnia magna old, non-reproducing rep 3

value: female

value: whole body, somatic

value: old, non-reproducing


title: Pax-Foxo_P53_CL2D

source_name: Cell line 2D

value: Cell line 2D


title: Pax-Foxo_P53_5_CL2D


title: RNAseq of Daphnia magna old, reproducing rep 4

value: old, reproducing


title: Brain_PFC_DNA [BBN_9315]

value: Bristol

value: F


title: Exp4_Ctrl-CRISPRi1_LPS_R1

description: Lexogen Quantseq

value: blood

value: monocytic


title: Exp4_LINC01215-gRNA1_LPS_R1

description: Lexogen Quantseq

value: ATTC TIB-202; PMA-differentiated

value: LPS


title: Brain_PFC_DNA [BBN_7541]

value: AD


title: RNAseq of Daphnia magna old, non-reproducing rep 4


title: Exp3_LINC00158-gRNA2_LPS_R3

description: Lexogen Quantseq


title: Pax-Foxo_P53_5

value: Tumor

value: EPO P30

value: PAX3-FOXO1; sgp53


title: 985-6, homozygote KI, left lung, E18.5

city: Bunkyo-ku

first: Ayako

last: Kashimada

state: Tokyo

address: Yushima 1-5-45

department: Pediatrics and Developmental Biology

institute: Institute of Science Tokyo

description: Library name: 985-6_HOMO_E18.A

data_processing:
Quality control was performed on the raw reads by BGI using the filtering software SOAPnuke v1.5.2. Clean reads were mapped to the reference genome by HISAT2 v2.0.4/BOWTIE2v.
Assembly: Mus musculus, NCBI, GCF_000001635.27_GRCm39
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Lung

extract_protocol:
Lungs  from E18.5 WT/heterozygote KI/ homozygote KI C57BL/6 mice were harvested, and the left lungs were flash frozen. Total RNA was isolated at BGI (Hong Kong) according to company’s protocol. RNA-sequencing was carried at BGI (Hong Kong) according to company’s protocol. Total RNA was qualified and quantified using Agilent RNA 6,000 Nano Kit and Agilent 2,100 bioanalyzer.
Library preparation for RNA-Seq was carried at BGI(Hong Kong) as follows.Enriching mRNA involves using oligo dT beads to isolate mRNA with poly A tails from total RNA samples. The mRNA is then fragmented and converted into first strand cDNA using random primers. The second strand cDNA is synthesized using dUTP instead of dTTP. The cDNA undergoes end-repair, 3' adenylation, and adaptor ligation. After PCR amplification and library quality control, the library is circularized and amplified to form DNA nanoballs (DNBs), which are then sequenced using the DNBSEQ Sequencing platform (BGI Genomics, China) at PE100 read-length

value: Lung

value: homozygote knockin

value: fresh frozen


title: Exp3_Ctrl-CRISPRi2_LPS_R3

description: Lexogen Quantseq

value: 8 h


title: Pax-Foxo_P53_4


title: 985-5, heterozygote KI, left lung, E18.5

description: Library name: 985-5_HET_E18.5A

value: Heterozygote knockin


title: Brain_PFC_DNA [BBN_8978]

value: Prefrontal Cortex

value: M


title: Brain_PFC_DNA [BBN_14795]

value: Newcastle


title: Exp4_LINC01215-gRNA1_LPS_R2

description: Lexogen Quantseq


title: Exp3_LINC00158-gRNA1_LPS_R2

description: Lexogen Quantseq


title: Pax-Foxo_P53_2


title: Brain_PFC_DNA [BBN_9198]

value: Bristol

value: F


title: Exp3_Ctrl-CRISPRi1_LPS_R2

description: Lexogen Quantseq

value: blood

value: monocytic


title: 985-3, heterozygote KI, left lung, E18.5

description: Library name: 985-3_HET_E18.5A


title: 985-4, homozygote KI, left lung, E18.5

description: Library name: 985-4_HOMO_E18.A


title: Brain_PFC_DNA [BBN001.29522]

value: Edinburgh


title: Pax-Foxo_P53_1


title: Exp3_LINC00158-gRNA1_LPS_R1

description: Lexogen Quantseq

value: ATTC TIB-202; PMA-differentiated

value: LPS


title: Brain_PFC_DNA [BBN_9031]

value: AD


title: Exp3_Ctrl-CRISPRi1_LPS_R1

description: Lexogen Quantseq


title: Pax-Foxo_1_CL3D

value: Cell line 3D

value: EPO P30


title: Pax-Foxo_1

value: Tumor


title: Brain_PFC_DNA [BBN_9408]

value: Ctl


title: 985-1, heterozygote KI, left lung, E18.5

description: Library name: 985-1_HET_E18.5A

value: Lung

value: fresh frozen


title: Exp2_AC010980.1-gRNA2_LPS_R3

description: Lexogen Quantseq

value: 8 h


title: 983-5, wild-type, left lung, E18.5

description: Library name: 983-5_WT_E18.5A

value: WT


title: p53_5


title: Brain_PFC_DNA [BBN005.32560]

value: Prefrontal Cortex

value: Manchester

value: M


title: p53_4


title: Pax-Foxo_P53_3

value: PAX3-FOXO1; sgp53


title: Brain_PFC_DNA [BBN_9003]

value: Bristol


title: 983-3, wild-type, left lung, E18.5

description: Library name: 983-3_WT_E18.5A


title: Exp2_AC010980.1-gRNA1_LPS_R2

description: Lexogen Quantseq

value: blood

value: monocytic


title: 983-1, wild-type, left lung, E18.5

description: Library name: 983-1_WT_E18.5A


title: p53_2


title: Brain_PFC_DNA [BBN_24895]


title: p53_3


title: Exp2_Ctrl-CRISPRi1_LPS_R2

description: Lexogen Quantseq

value: ATTC TIB-202; PMA-differentiated

value: LPS


title: ntrc_adult_3

city: Sevilla

first: Fernando

last: Rodríguez-Marín

state: Sevilla

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Library name: Sample3

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Assembly: tair10
Supplementary files format and content: comma-delimited text files include FPKM values for each sample

source_name: Young rosette leaves

extract_protocol:
RNA extraction was performed using Sure Prep kit (Fisher), following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Stranded Total RNA with Ribo-Zero kit (Illumina) and Illumina Stranded mRNA prep ligation kit (Illumina) were used for the construction of cDNA libraries for adult and seedling samples, respectively.

value: Young rosette leaves

value: ntrc mutant

value: Eight weeks in short-day photoperiod at 125 µE m−2 s−1 grown in soil


title: ntrc_adult_2

description: Library name: Sample2


title: Brain_PFC_DNA [BBN007.35762]

value: Queen Sqaure

value: F

value: Ctl


title: Brain_PFC_DNA [BBN006.29470]


title: 985-2, homozygote KI, left lung, E18.5

description: Library name: 985-2_HOMO_E18.A

value: Lung

value: homozygote knockin

value: fresh frozen


title: p53_1

value: Tumor

value: EPO P30


title: ntrc_adult_1

description: Library name: Sample1


title: Exp2_Ctrl-CRISPRi1_LPS_R1

description: Lexogen Quantseq

value: 8 h


title: Brain_PFC_DNA [BBN_7196]

value: Prefrontal Cortex

value: Newcastle


title: NTRK_p53_neo_6

value: EPO P0 (Neonatal)

value: ETV6-NTRK3; sgp53


title: Exp1_Ctrl-CRISPRi3_LPS_R3

description: Lexogen Quantseq

value: blood

value: monocytic

value: ATTC TIB-202; PMA-differentiated

value: LPS


title: Exp1_LINC01268-gRNA3_LPS_R3

description: Lexogen Quantseq


title: SARS-CoV-2 genomes – patient 3

description: Library name: Sample 41

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Viral genomes

value: Viral genomes


title: Brain_PFC_DNA [BBN_9505]

value: Edinburgh

value: M

value: AD


title: SARS-CoV-2 genomes – patient 4

description: Library name: Sample 42


title: NTRK_p53_neo_4

source_name: Tumor


title: Brain_PFC_DNA [BBN_3463]

value: Manchester

value: Ctl


title: Exp2_Ctrl-CRISPRi2_LPS_R3

description: Lexogen Quantseq


title: SARS-CoV-2 genomes – patient 2

description: Library name: Sample 40


title: NTRK_p53_neo_3

value: Tumor


title: Brain_PFC_DNA [BBN_7545]

value: F


title: Exp2_AC010980.1-gRNA1_LPS_R1

description: Lexogen Quantseq

value: 8 h


title: SARS-CoV-2 genomes – patient 1, replicate 2

description: Library name: Sample 39


title: Exp1_Ctrl-CRISPRi3_Ctrl_R3

description: Lexogen Quantseq

value: control


title: Brain_PFC_DNA [BBN_3454]

value: Prefrontal Cortex


title: Exp1_Ctrl-CRISPRi2_LPS_R2

description: Lexogen Quantseq


title: Brain_PFC_DNA [BBN005.30104]


title: Exp1_Ctrl-CRISPRi2_Ctrl_R2

description: Lexogen Quantseq


title: Exp1_LINC01268-gRNA2_LPS_R2

description: Lexogen Quantseq


title: SARS-CoV-2 genomes – patient 1, replicate 1

description: Library name: Sample 38


title: NTRK_p53_neo_1

value: EPO P0 (Neonatal)


title: NTRK_p53_neo_2

value: ETV6-NTRK3; sgp53


title: NTRK_p53_neo_5


title: 2609

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
IDAT files were obtained and processed using the R package sesame, version 1.16.1 (SEnsible Step-wise Analysis of DNA MEthylation BeadChips)(Zhou et al., 2018) to generate normalized beta values. Probe intensities underwent background correction using the p-value with the out-of-band array hybridization approach, followed by a normal-exponential out-of-band approach. Dye bias correction was performed by aligning green and red to the midpoint using the dyeBiasCorrTypeINorm method in sesame. Probes targeting the X and Y chromosomes were excluded. Clustering analysis was performed with R packages Rtsne and umap based on the 2,000 or 10,000 most variably methylated probes, with perplexity values set to 5 for tSNE and 15 for umap clustering.
Average Beta values

source_name: ASPS

label_protocol: Illumina protocol

extract_protocol: A minimum of 500ng of genomic DNA extracted from frozen tissue was submitted per sample. DNA quality was ensured by digital gel electrophoresis (Agilent, G2939BA).

tag: gender

value: f

tag: location

value: Cranial vault

tag: type of gemm


title: NTRK_p53_6

tag: tissue

value: EPO P30


title: Exp1_LINC01268-gRNA1_LPS_R1

description: Lexogen Quantseq

value: blood

tag: cell line

value: monocytic

value: ATTC TIB-202; PMA-differentiated

value: LPS


title: 2602

value: m


title: Brain_PFC_DNA [BBN003.28367]

value: Newcastle

value: M

value: AD


title: Exp1_Ctrl-CRISPRi1_LPS_R1

description: Lexogen Quantseq

tag: cell type


title: Brain_PFC_DNA [BBN_19605]

value: Edinburgh

value: Ctl


title: 2608


title: NTRK_p53_4

value: Tumor

tag: genotype


title: Brain_PFC_DNA [BBN_7485]

value: Prefrontal Cortex

value: F


title: Exp1_Ctrl-CRISPRi1_Ctrl_R1

description: Lexogen Quantseq

tag: treatment

value: control

value: 8 h


title: 2607

value: f

value: Cranial vault


title: LPS_BX795_5µM_R2

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

value: 5 M BX795 + LPS

value: 4 h


title: Brain_PFC_DNA [BBN_7310]

tag: brain bank

value: Newcastle

value: M


title: NTRK_p53_2

value: EPO P30

value: ETV6-NTRK3; sgp53


title: 2604

value: m


title: 3006

source_name: Synovial Sarcoma

value: Soft tissue


title: LPS_BX795_1µM_R2

description: Lexogen Quantseq

value: 1 M BX795 + LPS


title: Brain_PFC_DNA [BBN_9332]

value: Prefrontal Cortex

value: Bristol

tag: post-mortem delay

value: F

value: AD


title: LPS_RUXO_5µM_R2

description: Lexogen Quantseq

value: blood

value: 5 M Ruxolitinib + LPS


title: LPS_RUXO_1µM_R2

description: Lexogen Quantseq

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: 1 M Ruxolitinib + LPS


title: 1467


title: Brain_PFC_DNA [BBN003.32233]

tag: braak stage


title: NTRK_p53_1

value: Tumor


title: NTRK_p53_5


title: Brain_PFC_DNA [BBN001.35156]

value: Edinburgh

tag: age

value: Ctl


title: 1388


title: LPS_BAY_5µM_R2

description: Lexogen Quantseq

value: WT

value: 4 h


title: Brain_PFC_DNA [BBN003.28631]

value: Newcastle

tag: Sex


title: 2166

value: f

value: Soft tissue


title: Nf1_p53_5_CL2D

value: Cell line 2D

value: EPO P30

value: sgNf1; sgp53


title: LPS_BAY_10µM_R2

description: Lexogen Quantseq


title: Nf1_p53_4


title: LPS_R2

description: Lexogen Quantseq

value: LPS


title: Brain_PFC_DNA [BBN_12527]

value: Prefrontal Cortex

value: Queen Sqaure

value: NK

value: F

tag: ad diagnosis


title: Nf1_p53_3


title: NTRK_p53_3

value: ETV6-NTRK3; sgp53


title: Brain_PFC_DNA [BBN_24324]

value: Bristol

value: M

value: AD


title: Ctrl_R2

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

value: control


title: Brain_PFC_DNA [BBN001.32929]

value: Edinburgh


title: NTRK_p53_1_CL_2D

value: Cell line 2D

value: EPO P30


title: ASP_TFE_P53_3_CL2D

value: f

value: Thigh

value: EPO-GEMM

value: 2D cell line


title: ASP_TFE_p53_Neo_1

description: 206448030020 _R06C02


title: LPS_BX795_5µM_R1

description: Lexogen Quantseq

value: 5 M BX795 + LPS

value: 4 h


title: Nf1_p53_1

value: Tumor

value: sgNf1; sgp53


title: Brain_PFC_DNA [BBN003.29202]

value: Prefrontal Cortex

value: Newcastle

value: M

value: Ctl


title: p53_5

description: 206448030020 _R05C02

source_name: UPS (P53)

value: m


title: 1929

value: Soft tissue


title: LPS_RUXO_5µM_R1

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

value: 5 M Ruxolitinib + LPS


title: Neo_Kras_p53_3

value: EPO P0 (Neonatal)

value: KRASG12V; sgp53


title: Brain_PFC_DNA [BBN_7540]

source_name: Prefrontal Cortex

value: F

value: AD


title: Brain_PFC_DNA [BBN001.35215]

value: Edinburgh


title: Pax-Foxo_P53_5_CL2D

source_name: aRMS (Pax3-Foxo1)

value: Thigh

value: EPO-GEMM

value: 2D cell line


title: Nf1_p53_5

value: Tumor

value: EPO P30

value: sgNf1; sgp53


title: Neo_Kras_p53_1


title: Smarcb1_p53_4

description: 206448030020 _R03C02

source_name: MRT (SMARCB1_P53)

value: m


title: LPS_BAY_10µM_R1

description: Lexogen Quantseq

value: blood

value: 4 h


title: Pax-Foxo_P53_5

description: 206448030020 _R02C02


title: Brain_PFC_DNA [BBN_9367]

value: Prefrontal Cortex

value: Bristol

value: M


title: Neo_Kras_p53_2

value: EPO P0 (Neonatal)


title: LPS_RUXO_1µM_R1

description: Lexogen Quantseq

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

value: 1 M Ruxolitinib + LPS


title: LPS_BX795_1µM_R1

description: Lexogen Quantseq

value: 1 M BX795 + LPS


title: Pax-Foxo_P53_4

description: 206448030020 _R01C02

value: f

value: Thigh

value: EPO-GEMM


title: Brain_PFC_DNA [BBN_9263]

value: AD


title: LPS_BAY_5µM_R1

description: Lexogen Quantseq


title: Nf1_p53_2

value: Tumor

value: EPO P30

value: sgNf1; sgp53


title: Muscle_5

source_name: Normal muscle

value: Normal muscle

value: no EPO


title: Brain_PFC_DNA [BBN_7422]

value: Prefrontal Cortex

value: Newcastle

value: Ctl


title: Brain_PFC_DNA [BBN_15259]

value: Edinburgh

value: F


title: Pax-Foxo_P53_3

description: 206448030020 _R06C01

value: m


title: LPS_R1

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

value: LPS

value: 4 h


title: Ctrl_R1

description: Lexogen Quantseq

value: control


title: Brain_PFC_DNA [BBN_19207]


title: p53_4

description: 206448030020 _R04C02

value: Thigh

value: EPO-GEMM


title: ASP_TFE_P53_4

description: 206448030020 _R05C01


title: Muscle_3

value: Normal muscle


title: Brain_PFC_DNA [BBN_9405]

value: Bristol

value: M

value: AD


title: Muscle_6

value: no EPO


title: ASP_TFE_P53_3

description: 206448030020 _R04C01

value: f


title: Brain_PFC_DNA [BBN_9262]

value: Prefrontal Cortex


title: Muscle_2


title: Muscle_1


title: 12h_Ctrl_R2

description: Lexogen Quantseq


title: Brain_PFC_DNA [BBN_9389]

value: F

value: Ctl


title: ASP_TFE_P53_2

description: 206448030020 _R03C01


title: ASP_TFE_P53_1

description: 206448030020 _R02C01


title: 6h_LPS_R2

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: 6 h


title: Muscle_4

value: WT


title: Brain_PFC_DNA [BBN_9151]


title: 10h_LPS_R2

description: Lexogen Quantseq

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: LPS


title: SSX1_neo_3

value: m

value: Thigh


title: Kras_p53_4

value: Tumor

value: EPO P30

value: KRASG12V; sgp53


title: 12h_LPS_R2

description: Lexogen Quantseq


title: Brain_PFC_DNA [BBN001.29135]

value: Edinburgh

value: M

value: AD


title: Kras_p53_5


title: SSX1_neo_2

value: f

value: EPO-GEMM


title: Kras_p53_3


title: Brain_PFC_DNA [BBN_3476]

value: Prefrontal Cortex

value: Manchester

value: F

value: Ctl


title: SSX1_neo_1


title: NTRK_1

description: 206448030020 _R01C01

source_name: Fusion-dominated IFS (ETV6-NTRK3_P53)


title: 4h_IFNalpha_R2

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: WT

value: IFNalpha

value: 4 h


title: Kras_p53_2

value: Tumor


title: 4h_Pam3csk4_R2

description: Lexogen Quantseq

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days


title: Brain_PFC_DNA [BBN_22622]

value: Bristol


title: 8h_LPS_R2

description: Lexogen Quantseq

value: LPS

value: 8 h


title: Kras_p53_6

value: EPO P30

value: KRASG12V; sgp53


title: Brain_PFC_DNA [BBN_4204]

value: M

value: AD


title: 4h_LPS_R2

description: Lexogen Quantseq


title: Brain_PFC_DNA [BBN_7214]

value: Prefrontal Cortex

value: Newcastle


title: Pax-Foxo_1_SAM_fragments

value: F

value: Thigh

value: EPO-GEMM

value: SAM primary fragments


title: Brain_PFC_DNA [BBN007.30022]

value: Queen Sqaure

value: Ctl


title: 2h_IFNalpha_R2

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: WT

value: IFNalpha

value: 2 h


title: Pax-Foxo_1_3D

value: 3D cell line


title: Kras_p53_1

value: Tumor

value: EPO P30

value: KRASG12V; sgp53


title: Pax-Foxo_1_SAM_cells

value: SAM primary cells


title: Kras_Bcor_4


title: 2h_Pam3csk4_R2

description: Lexogen Quantseq

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days


title: Brain_PFC_DNA [BBN003.28369]

value: Prefrontal Cortex

value: Newcastle

value: M


title: Kras_Bcor_2


title: Pax-Foxo_1

value: F

value: Thigh

value: EPO-GEMM


title: 2h_LPS_R2

description: Lexogen Quantseq

value: blood

value: LPS


title: SS18-SSX2_Pten_1_3D


title: 1h_LPS_R2

description: Lexogen Quantseq

value: blood-derivedmacrophage

value: WT

value: 1 h


title: Brain_PFC_DNA [BBN_24325]

value: Bristol

value: Ctl


title: 0.5h_LPS_R2

description: Lexogen Quantseq


title: Kras_Bcor_1

value: Tumor

value: EPO P30


title: Brain_PFC_DNA [BBN_24528]

value: Edinburgh


title: SS18-SSX2_Pten_1_2D

value: 2D cell line


title: Kras

value: KRASG12V, sgCrtl


title: 0.5h_Ctrl_R2

description: Lexogen Quantseq

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: control


title: Brain_PFC_DNA [BBN_4229]

value: Prefrontal Cortex

value: F


title: SS18-SSX2_Pten_1_SAM_fragments

value: Thigh

value: EPO-GEMM

value: SAM primary fragments


title: ASP_TFE_P53_4

value: ASPSCR1-TFE3, sgp53


title: Brain_PFC_DNA [BBN_7535]

value: Newcastle

value: M

value: AD


title: 12h_Ctrl_R1

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: WT


title: ASP_TFE_P53_3_CL2D

value: Cell line 2D

value: EPO P30


title: 12h_LPS_R1

description: Lexogen Quantseq

value: LPS


title: Kras_Bcor_3

value: Tumor

value: KRASG12V; sgp53


title: Brain_PFC_DNA [BBN_7462]

value: Prefrontal Cortex


title: SS18-SSX2_Pten_1

value: F


title: Brain_PFC_DNA [BBN003.33724]

value: Ctl


title: Nf1_p53_5_3D

source_name: MPNST (Nf1_P53)

value: Thigh

value: EPO-GEMM

value: 3D cell line


title: AAV genomes – hSyn promoter

description: Library name: Sample 36

data_processing:
Basecalling of raw nanopore trace files was performed after sequencing with Guppy or during sequencing with MinKNOW software. In both cases, the ‘super accuracy’ basecalling algorithm was utilized. Default software read quality thresholds were maintained throughout.
Basecalled reads in fastq format were processed into bins by our ConSeqUMI according to unique 5’ and 3’ sequence tags. Each bin was exported as a single fastq file containing all basecalled reads belonging to the bin.
ConSeqUMI was then used to derive a consensus sequence for each individual bin based on constituent sequences therein.
Assembly: GRCh38/hg38 (Ded. 2013)
Supplementary files format and content: FASTA files contain consensus sequences generated by ConSeqUMI

organism: mixed DNA library

source_name: Input

extract_protocol:
Target amplicons were purified after polymerase chain reactions using gel extraction or column purification.
Sequencing libraries were prepared using Native Ligation kits and protocols developed by Oxford Nanopore Technologies according to their instructions.

value: Input


title: ASP_TFE_P53_3

value: ASPSCR1-TFE3, sgp53


title: SS18-SSX2_Pten_1_SAM_cells

value: SAM primary cells


title: 6h_LPS_R1

description: Lexogen Quantseq

source_name: blood

value: blood

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: 6 h


title: ASP_TFE_neo_P53_1

value: EPO P0 (Neonatal)


title: Nf1_p53_5_2D

value: 2D cell line