title: Penicillium oxalicum, ∆PoxCxrE, Glucose, 24 h, rep1


title: AsPC-1 cells, Palbociclib, 24 h, rep3

status: Public on Nov 12 2025

type: SRA

city: Göttingen

first: Maj-Britt

last: Paulsohn

address: Justus-von-Liebig-Weg 11

department: Department of Molecular Oncology

country: Germany

institute: University Medical Center Göttingen

description:
Library name: Palbociclib_3
Palbo.3

library_source: transcriptomic

data_processing:
Galaxy environment provided by the GWDG (Gesellschaft für wissenschafltiche Datenverarbeitung mbH Göttingen, https://galaxy.gwdg.de/)
Sequences were trimmed for 11 nucleotides (Trim, version 0.0.2).
Alignment was performed on GRCh38 using HISAT2 (version 2.0.5.2).
Read counts were acquired via featureCounts (version 1.6.3+galaxy2).
DeSeq2 (version 2.11.40.6+galaxy1) was used to perform differential gene expression analysis and to obtain normalized counts.
Assembly: CRCh38
Supplementary files format and content: tab-delimited file contains normalized count data

molecule: total RNA

organism: Homo sapiens

growth_protocol: AsPC-1 cells were maintained in RPMI 1640 supplemented with 10% FCS, 50 U/mL Penicillin, 50 μg/mL Streptomycin and 2 mM Glutamin. AsPC-1 RRID: CVCL_0152

extract_protocol:
Total RNA was extracted from cells using TRIzol®. 200 µL Chloroform was added per 1000 µL TRIzol. For phase separation, samples were centrifuged, and the aqueous phase was used to precipitate the RNA with 800 µL isopropanol. Two washing steps with 75 % ethanol were performed before the RNA was resuspended in nuclease-free water. 400 ng RNA was used for sequencing.
mRNA library preparation (poly A enrichment) and reverse transcription into cDNA followed by QC at Novogene

treatment_protocol: AsPC-1 cells were seeded. Next day, treatment was applied as follows: DMSO, Palbociclib (5 µM), MRTX1133 (0.5 µM), or the combination (Palbociclib + MRTX1133). After 24 h of treatment RNA was harvested.

tag: cell line

tag: cell type

value: pancreatic cancer cells

tag: treatment

value: Palbociclib (5 µM)

tag: time


title: FF3_4

city: Santa Monica

first: Lucy

middle: K

last: Bicks

state: CA

address: 1033 3rd street, apartment 106, apartment 106

department: Neurology

country: USA

institute: UCLA School of Medicine

description: RNA-seq, 100-base-pair paired end reads on an Illumina HiSeq 4000

data_processing:
The reads were mapped to the human genome (hg38) with Gencode v25 annotations using STAR (v.2.5.2b) and gene expression was quantified using rsem (v1.3.0)
Genes that were expressed at very low levels (less that 10 reads in 30% of samples from a given day) were removed from the analysis
Samples with standardized sample network connectivity Z scores below –2 in each mutation were defined as outliers and removed
To control for technical variation due to the sequencing and library prep we calculated the principal components of the Picard sequencing metrics (http://broadinstitute.github.io/picard/) using the CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics, and MarkDuplicates modules and included them in our model
To infer genetic ancestry, we called SNPs from the aligned reads using the GATK (v3.3) Haplotype caller. Sites with more than 5% missing samples, with rare minor allele frequency (less than 0.05) and Hardy–Weinberg disequilibrium (less than 1 × 10–6) were removed using plink (v1.09). We then used the remaining high-quality SNPs to run MDS together with HapMap3.3 (hg38). The first two MDS values, referred to as genetic ancestry PC1/2, were then included in our model.
Assembly: (hg38) with Gencode v25
Supplementary files format and content: counts

source_name: cortical organoid

extract_protocol:
ribosomal RNA depleted (RiboZero Gold, Illumina)
Truseq stranded RNA RiboZero Gold (Illumina)

tag: tissue

value: cortical organoid

tag: source tissue

value: fibroblast

tag: genotype

value: Control

tag: differentiation day

tag: differentiation


title: Penicillium oxalicum, ∆PoxCxrE,  Avicel, 24 h, rep3

city: Nanning

first: Di

last: Tian

address: DaXue east road

country: China

institute: College of Life Science and Technology,GuangXi university

data_processing:
Data filtering: The raw data was filtered by software SOAPnuke v1.5.2 to generate clean data,clean reads were obtained and stored in FASTQ format
Reference genome mapping: The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) .The expression level of genes was calculated by RSEM (v1.2.8)
Differential Gene Expression: The differentially expressed genes (DEGs) were calculated by DESeq2 tool with |Log2 fold change| ≥ 1 and q-value ≤ 0.05 as thresholds
Assembly: P. oxalicum HP7-1 genome (accession number JRVD00000000)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Penicillium oxalicum

source_name: Mycelium

extract_protocol:
RNA was extracted with Trizol,  the purity of RNA (OD260/280) was detected by Nanodrop2000. The integrity of RNA were accurately detected by Agilent 2100,the detection indicators include: RIN value, 28S/18S, whether the map baseline is raised, 5S peak, and electrophoresis to detect whether the RNA sample is diffuse or has a genome DNA contamination.
After the sample is qualified, the library is constructed. The main process is as follows: 1) mRNA enrichment for total RNA by mRNA enrichment method: Enrich mRNA with polyA tail using magnetic beads with Oligo dT. 2) Fragment the RNA obtained by interrupting the buffer, perform reverse transcription with random N6 primers, and synthesize the double-stranded cDNA to form double-stranded DNA. 3) Fill in the end of the synthesized double-stranded DNA and phosphorylate the 5' end, form a sticky end with a protruding "A" at the 3' end, and then connect a bubbling linker with a protruding "T" at the 3' end. 4) The ligation product is amplified by PCR with specific primers. 5) The PCR product is thermally denatured into single-stranded DNA, and then a single-stranded circular DNA library is obtained by circularizing the single-stranded DNA with a bridge primer.

value: Mycelium

value: PoxCxrE knockout in Wild type

value: Cultivated in medium containing Avicel


title: AsPC-1 cells, Palbociclib, 24 h, rep2

description:
Library name: Palbociclib_2
Palbo.2


title: FF3_3


title: Pool-2-GTGAAACG


title: FF2_1


title: Pool-1-GCCAATAT


title: AsPC-1 cells, DMSO, 24 h, rep3

description:
Library name: DMSO_3
DMSO.3

value: DMSO


title: Penicillium oxalicum, ∆PoxCxrE,  Avicel, 24 h, rep2


title: AsPC-1 cells, Palbociclib, 24 h, rep1

description:
Library name: Palbociclib_1
Palbo.1


title: Penicillium oxalicum, ∆PoxCxrE,  Avicel, 24 h, rep1


title: FF2_7


title: Penicillium oxalicum, ∆PoxKu70,  Avicel, 24 h, rep1

value: Wild type


title: FF2_50


title: Candida albicans mss2Δ rep3 on solid

city: Taipei

first: Ching-Hsuan

last: Lin

state: Taiwan

address: National Taiwan University, 1 Roosevelt Rd. Sec. 4

department: Department of Biochemical Science and Technology

country: Taiwan

institute: National Taiwan University

description:
Library name: Sample 12
Column name in Raw_Count_All_Samples.txt: Solid_mss2_3

data_processing:
Read counts were normalized, and differentially expressed (DE) genes were identified using the DESeq2 package from R Bioconductor. Volcano plots and heat maps were created in R-studio with the appropriate packages, following normalization of read counts.
data visualization, including volcano plots and heatmaps, was carried out in RStudio using appropriate R packages.
Assembly: Candida albicans SC5314 reference sequence
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Candida albicans SC5314

source_name: Candida albicans

growth_protocol: Hyphae grown in RPMI 1640 liquid medium or on RPMI 1640 agar plate at 30°C.

extract_protocol:
Total RNA was extracted using the MasterPure™ Yeast RNA Purification Kit (Epicentre, Madison, WI, USA). To eliminate genomic DNA contamination, the RNA samples were treated with DNase I (Thermo Fisher Scientific, Waltham, MA, USA). RNA quality and concentration were confirmed using a BioAnalyzer for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested after 24 hours and washed 3 times with sterile water.

value: Candida albicans

value: mss2 mutant

value: RPMI1640 solid agar

tag: batch

value: 24 hours


title: FF2_52


title: Candida albicans mss2Δ rep2 on solid

description:
Library name: Sample 11
Column name in Raw_Count_All_Samples.txt: Solid_mss2_2


title: Penicillium oxalicum, ∆PoxCxrE, Glucose, 24 h, rep2

value: Cultivated in medium containing glucose


title: FF4_58


title: FF2_51


title: AsPC-1 cells, DMSO, 24 h, rep2

description:
Library name: DMSO_2
DMSO.2


title: FF4_7


title: 51T-2D cells, Palbociclib+Sotorasib, day7, rep3

description:
Library name: Palbociclib+Sotorasib_D7_3
PS7.3

growth_protocol: 51T-2D cells (KFO5002 patient TM047) were maintained in RPMI 1640 supplemented with 10 % FCS and 2mM Glutamine. Cell line published in DOI: 10.1002/1878-0261.13725.

treatment_protocol: 51T-2D cells were seeded. Next day, treatment was applied for 48 h on day 1 as follows: DMSO, Palbociclib (5 µM), Sotorasib (2.5 µM) or combination (Palbociclib + Sotorasib)). On day3 samples were harvested. Furthermore, treated cells were reseeded and kept in regular cultivation medium for an additonal four days of recovery phase (day7). On day7 RNA was harvested, too.

value: Palbociclib (5 µM) + Sotorasib (2.5 µM); + 4 days cultivation in normal medium

value: 48h + 4 days / day7


title: FF4_3


title: AsPC-1 cells, DMSO, 24 h, rep1

description:
Library name: DMSO_1
DMSO.1

value: pancreatic cancer cells


title: FF4_8


title: FF4_45


title: Candida albicans mss2Δ rep2 in liquid

description:
Library name: Sample 8
Column name in Raw_Count_All_Samples.txt: Liquid_mss2_2

value: RPMI1640 liquid medium


title: 51T-2D cells, Palbociclib+Sotorasib, day7, rep2

description:
Library name: Palbociclib+Sotorasib_D7_2
PS7.2


title: FF4_64

value: cortical organoid


title: 51T-2D cells, Palbociclib+Sotorasib, day7, rep1

description:
Library name: Palbociclib+Sotorasib_D7_1
PS7.1


title: FF4_76

value: fibroblast


title: FF4_99


title: FF4_19


title: Candida albicans mss2Δ rep1 in liquid

description:
Library name: Sample 7
Column name in Raw_Count_All_Samples.txt: Liquid_mss2_1


title: FF4_82


title: 51T-2D cells, Sotorasib, day7, rep2

description:
Library name: Sotorasib_D7_2
Soto7.2

value: Sotorasib (2.5 µM); + 4 days cultivation in normal medium


title: FF4_65


title: Candida albicans WT rep3 on solid

description:
Library name: Sample 6
Column name in Raw_Count_All_Samples.txt: Solid_WT_3

value: wild-type


title: Candida albicans WT rep2 on solid

description:
Library name: Sample 5
Column name in Raw_Count_All_Samples.txt: Solid_WT_2


title: FF4_44


title: FF4_24


title: Candida albicans WT rep1 on solid

description:
Library name: Sample 4
Column name in Raw_Count_All_Samples.txt: Solid_WT_1


title: 51T-2D cells, Sotorasib, day7, rep1

description:
Library name: Sotorasib_D7_1
Soto7.1


title: Candida albicans mss2Δ rep1 on solid

description:
Library name: Sample 10
Column name in Raw_Count_All_Samples.txt: Solid_mss2_1


title: FF4_100


title: Candida albicans WT rep3 in liquid

description:
Library name: Sample 3
Column name in Raw_Count_All_Samples.txt: Liquid_WT_3


title: 51T-2D cells, Palbociclib, day7, rep3

description:
Library name: Palbociclib_D7_3
Palbo7.2

value: Palbociclib (5 µM); + 4 days cultivation in normal medium


title: 51T-2D cells, Palbociclib, day7, rep2

description:
Library name: Palbociclib_D7_2
Palbo7.1


title: FF4_27


title: Candida albicans mss2Δ rep3 in liquid

description:
Library name: Sample 9
Column name in Raw_Count_All_Samples.txt: Liquid_mss2_3


title: Candida albicans WT rep2 in liquid

description:
Library name: Sample 2
Column name in Raw_Count_All_Samples.txt: Liquid_WT_2


title: 51T-2D cells, DMSO, day7, rep3

description:
Library name: DMSO_D7_3
DMSO7.3

value: DMSO; + 4 days cultivation in normal medium


title: FF4_49


title: FF4_26


title: 51T-2D cells, Sotorasib, day7, rep3

description:
Library name: Sotorasib_D7_3
Soto7.3


title: FF3_193_redo


title: FF3_192


title: Nsun7ko_smallRNA_rep3

city: Shanghai

first: Jing

last: Li

address: Haike Road 230

department: School of Life Science and Technology

institute: ShanghaiTech University

description:
Library name: Sample 18
Column name in WT_Nsun7ko_smallRNA_sites.csv: Nsun7-/-_rep3

library_source: other

data_processing:
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome with Hisat2 and then transcriptome with Bowtie2. Pileup was performed using samtools API pysam, and m5C sites were called from the pileup files.
Assembly: GRCm39
Supplementary files format and content: csv files include m5C modification sites

molecule: other

organism: Mus musculus

source_name: testis

growth_protocol: adult WT and Nsun7 KO mice

extract_protocol:
Total RNA from testes were extracted using TRIZol.  mRNA can be captured through beads conjugated with oligo-dT. Large or small RNA was extracted using RNA Clean & Concentrator-5 (Zymo).
100ng-1μg RNA was treated with UBS-2 buffer. For mRNA UBS-seq library preparation, the Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal) was used. For large RNA UBS-seq library preparation, the converted RNA were firstly fragmented in the presence of MgCl2 and VAHTS Small RNA Library Prep Kit for Illumina V2 (Vazyme) was used. For small RNA UBS-seq library preparation, VAHTS Small RNA Library Prep Kit for Illumina V2 (Vazyme) was used.

value: testis

value: Nsun7 Knockout


title: FF3_193


title: 51T-2D cells, DMSO, day7, rep1

description:
Library name: DMSO_D7_1
DMSO7.1


title: FF4_69


title: FF3_194


title: Nsun7ko_smallRNA_rep2

description:
Library name: Sample 17
Column name in WT_Nsun7ko_smallRNA_sites.csv: Nsun7-/-_rep2


title: Nsun7ko_smallRNA_rep1

description:
Library name: Sample 16
Column name in WT_Nsun7ko_smallRNA_sites.csv: Nsun7-/-_rep1


title: FF3_187

description: RNA-seq, 100-base-pair paired end reads on an Illumina HiSeq 4000


title: 51T-2D cells, Palbociclib+Sotorasib, day3, rep2

description:
Library name: Palbociclib+Sotorasib_D3_2
PS3.2

value: Palbociclib (5 µM) + Sotorasib (2.5 µM)

value: 48h / day3


title: FF3_190


title: WT_smallRNA_rep3

description:
Library name: Sample 15
Column name in WT_Nsun7ko_smallRNA_sites.csv: WT_rep3

value: WT


title: FF4_56


title: FF4_6


title: Stroke brain circadian rhapsody sample tags

city: Madrid

first: María

middle: Ángeles

last: Moro

address: C. de Melchor Fernández Almagro, 3

department: Cardiovascular Risk Factors and Brain Health

country: Spain

institute: CNIC

description: Library name: tags

library_source: transcriptomic single cell

data_processing:
Rhapsody processing pipeline
Assembly: GRCm39
Supplementary files format and content: Seurat r object containing the raw counts and metadata

molecule: polyA RNA

source_name: brain and blood

growth_protocol: All experiments were performed on 7–16-week-old C57BL/6 male mice. Chow and water were available ad libitum.

extract_protocol:
For the generation of single-cell whole-transcriptomes we used a BD Rhapsody system according to manufacture instructions. 60,000 sorted live cells were loaded into a Rhapsody Single Cell Analysis System cartridge. Cell capture and cDNA synthesis were performed according to manufacturer’s instructions; cells were isolated into nanowells by gravity, then cells lysed and mRNA, AbSeq oligos and Sample tags oligos were released and captured by beads present in the nanowells.
Two separated indexed libraries were prepared for whole transcriptome analysis and Sample Tag demultiplexing following manufacturer’s instructions. The average size of the libraries was calculated using the 2100 Bioanalyzer (Agilent) and the concentration was determined using the Qubit fluorometer (Thermofisher). Finally, libraries were combined and sequenced together in a paired end run (60x42) using a NextSeq 2000 system (Illumina) and a P2 flowcell. Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).

treatment_protocol: For the generation of single-cell whole-transcriptomes, brain cell solution was sorted in BD FACS Aria Fusion sorter as DAPI-CD11b+Ly6G+ cells and loaded into a BD Rhapsody cartridge

value: brain and blood

value: Leukocyte

tag: Sex

value: male

tag: library type

value: Rhapsody tags


title: FF3_189_redo


title: Candida albicans WT rep1 in liquid

description:
Library name: Sample 1
Column name in Raw_Count_All_Samples.txt: Liquid_WT_1

value: Candida albicans

value: 24 hours


title: Stroke brain circadian rhapsody transcriptome

description: Library name: cDNA

value: mRNA


title: 51T-2D cells, Sotorasib, day3, rep3

description:
Library name: Sotorasib_D3_3
Soto3.3

value: pancreatic cancer cells

value: Sotorasib (2.5 µM)


title: WT_smallRNA_rep1

description:
Library name: Sample 13
Column name in WT_Nsun7ko_smallRNA_sites.csv: WT_rep1


title: FF3_188

value: cortical organoid

value: fibroblast


title: 51T-2D cells, Sotorasib, day3, rep2

description:
Library name: Sotorasib_D3_2
Soto3.2


title: 51T-2D cells, DMSO, day7, rep2

description:
Library name: DMSO_D7_2
DMSO7.2

value: DMSO; + 4 days cultivation in normal medium

value: 48h + 4 days / day7


title: TAa8_PlusDox_HSATIIKD_Rep2

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

description:
Library name: TA_a8_S8_R1_001.fastq.gz
Column name in count file TAa8_PlusDox_HSATIIKD_Rep2_Kallisto48_GencodeR45

data_processing:
Reads trimmed for low quality/adapter sequences with Cut-Adapt
Transcripts were quantified using Kallisto 0.48.0
Differential isoform usage and splicing analysis was done with IsoformSwitchAnalyzeR 2.4.0
Assembly: GRCH38 p14 genome, Gencode R45 annotation
Supplementary files format and content: tsv format containing kallisto abundance estimates

source_name: MB135 iDUX4ca

growth_protocol: Myoblasts were cultured in F-10 media supplemented with 20% Fetal bovine serum (FBS), 1% pen/strep, 10ng/mL rhFGF Basic, 1uM dexamethasone, and 3ug/mL puromycin

extract_protocol:
RNA extracted using Takara NucleoSpin RNA kit
TruSeq Stranded mRNA

treatment_protocol: Plus Dox samples were pulsed for 4 hours with 2ug/mL doxycycline and then treated with gapmer transfected using RNAiMax per manufacturer protocol

value: MB135 iDUX4ca

value: Myoblast line with dox inducible DUX4 transgene

value: HSATII Gapmer, Plus Dox


title: FF3_191


title: FF3_75

value: Control


title: 51T-2D cells, Palbociclib+Sotorasib, day3, rep3

description:
Library name: Palbociclib+Sotorasib_D3_3
PS3.3

value: Palbociclib (5 µM) + Sotorasib (2.5 µM)

value: 48h / day3


title: 51T-2D cells, Sotorasib, day3, rep1

description:
Library name: Sotorasib_D3_1
Soto3.1


title: FF3_77


title: TAa7_PlusDox_HSATIIKD_Rep1

description:
Library name: TA_a7_S7_R1_001.fastq.gz
Column name in count file TAa7_PlusDox_HSATIIKD_Rep1_Kallisto48_GencodeR45


title: Nsun7ko_largeRNA_rep3

description:
Library name: Sample 12
Column name in WT_Nsun7ko_largeRNA_sites.csv: Nsun7-/-_rep3

value: testis

value: Nsun7 Knockout


title: 51T-2D cells, Palbociclib, day3, rep3

description:
Library name: Palbociclib_D3_3
Palbo3.3

value: Palbociclib (5 µM)


title: TAa6_PlusDox_CtrlKD_Rep2

description:
Library name: TA_a6_S6_R1_001.fastq.gz
Column name in count file TAa6_PlusDox_CtrlKD_Rep2_Kallisto48_GencodeR45

value: Control Gapmer, Plus Dox


title: FF3_76


title: 51T-2D cells, Palbociclib+Sotorasib, day3, rep1

description:
Library name: Palbociclib+Sotorasib_D3_1
PS3.1


title: FF3_189


title: 51T-2D cells, Palbociclib, day3, rep2

description:
Library name: Palbociclib_D3_2
Palbo3.2


title: FF3_77_redo


title: TAa5_PlusDox_CtrlKD_Rep1

description:
Library name: TA_a5_S5_R1_001.fastq.gz
Column name in count file TAa5_PlusDox_CtrlKD_Rep1_Kallisto48_GencodeR45


title: WT_smallRNA_rep2

description:
Library name: Sample 14
Column name in WT_Nsun7ko_smallRNA_sites.csv: WT_rep2

value: WT


title: 51T-2D cells, Palbociclib, day3, rep1

description:
Library name: Palbociclib_D3_1
Palbo3.1

value: pancreatic cancer cells


title: WT_largeRNA_rep3

description:
Library name: Sample 9
Column name in WT_Nsun7ko_largeRNA_sites.csv: WT_rep3


title: FF5_57


title: 51T-2D cells, DMSO, day3, rep3

description:
Library name: DMSO_D3_3
DMSO3.3

value: DMSO


title: WT_largeRNA_rep1

description:
Library name: Sample 7
Column name in WT_Nsun7ko_largeRNA_sites.csv: WT_rep1


title: TAa3_NoDox_HSATIIKD_Rep1

description:
Library name: TA_a3_S3_R1_001.fastq.gz
Column name in count file TAa3_NoDox_HSATIIKD_Rep1_Kallisto48_GencodeR45

value: HSATII Gapmer, No Dox


title: FF5_62

value: cortical organoid

value: fibroblast


title: 51T-2D cells, DMSO, day3, rep2

description:
Library name: DMSO_D3_2
DMSO3.2


title: TAa2_NoDox_CtrlKD_Rep2

description:
Library name: TA_a2_S2_R1_001.fastq.gz
Column name in count file TAa2_NoDox_CtrlKD_Rep2_Kallisto48_GencodeR45

value: Control Gapmer, No Dox


title: Nsun7ko_largeRNA_rep2

description:
Library name: Sample 11
Column name in WT_Nsun7ko_largeRNA_sites.csv: Nsun7-/-_rep2


title: Nsun7ko_mRNA_rep3

description:
Library name: Sample 6
Column name in WT_Nsun7ko_mRNA_sites.csv: Nsun7-/-_rep3


title: FF5_58

description: RNA-seq, 100-base-pair paired end reads on an Illumina HiSeq 4000


title: 51T-2D cells, DMSO, day3, rep1

description:
Library name: DMSO_D3_1
DMSO3.1


title: TAa1_NoDox_CtrlKD_Rep1

description:
Library name: TA_a1_S1_R1_001.fastq.gz
Column name in count file TAa1_NoDox_CtrlKD_Rep1_Kallisto48_GencodeR45

value: MB135 iDUX4ca


title: Nsun7ko_largeRNA_rep1

description:
Library name: Sample 10
Column name in WT_Nsun7ko_largeRNA_sites.csv: Nsun7-/-_rep1


title: Nsun7ko_mRNA_rep2

description:
Library name: Sample 5
Column name in WT_Nsun7ko_mRNA_sites.csv: Nsun7-/-_rep2


title: MDAMB231_DMSO

city: Montréal

first: Robin

last: Minati

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: Library name: MDAMB231_DMSO

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 37 (based on Ensembl 103)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: TNBC cell line

value: DMSO for 96h

tag: strand

value: forward


title: FF5_64

value: Control


title: FF5_66


title: Nsun7ko_mRNA_rep1

description:
Library name: Sample 4
Column name in WT_Nsun7ko_mRNA_sites.csv: Nsun7-/-_rep1


title: Primary colon cancer, subject 722, sample ID 29, long-read, PacBio

city: St. Louis

first: Christopher

last: Maher

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

description:
circRNA-RCA RNA
Pacific Biosciences long-read
P_722_PacBio
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz

data_processing:
STAR v2.7.3a for short-read RNA-Seq alignment
CIRCexplorer2 v2.3.8 for short-read circRNA detection
LoRDEC v0.9 for long-read correction
isoCirc v1.0.6 and CIRI-long v1.0.3 for long-read circRNA detection
featureCounts v1.6.0 for short-read linear gene quantification
Assembly: Gene annotations were combined from Gencode v23, RefSeq downloaded from the UCSC Genome Browser, and the Broad long noncoding RNA (lncRNA) catalog (see supplementary file hg38_annotation.gtf.gz in Accession GSE221240)
Supplementary files format and content: For short-read cell lines, tab-delimited text files include 1) Raw counts for each sample for circRNAs; 2) TPM values for each sample for circRNAs.
Supplementary files format and content: For long-read, tab-delimited text files include 1) Raw counts for each sample for circRNAs detected by isoCirc; 2) Raw counts for each sample for circRNAs detected by CIRI-long.

source_name: Primary colon cancer

growth_protocol: For cell lines, HCT116 and HT29 cells were grown in McCoy’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. SW480 and SW620 cells were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Sigma, St. Louis, MO) and 1% penicillin/streptomycin. LoVo cells were grown in DMEM/F12 (Invitrogen) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin.

extract_protocol:
For cell line short-read samples, total RNA inputs of 1μg were used to generate libraries using the Illumina (San Diego, CA) TruSeq Stranded Total RNA with Ribo-Zero Fold.  For long-read samples, the RNA of the cells lines HCT116, HT29, and LoVo was isolated using the Macherey-Nagel NucleoSpin RNA, Mini kit (MACHEREY-NAGEL, Düren, Germany). The RNA of patient trio samples was isolated using the Invitrogen TRIzol protocol (ThermoFisher Scientific, Waltham, MA) with DNase treatment (ZYMO RESEARCH, Irvine, CA).
For cell line short-read samples, 200ng aliquots of each library were pooled and used as input for cDNA-Capture. The IDT xGen Exome Research Panel v2 including 415,115 exon probes was used for exome capture. For long-read samples, the published protocol in Xin et al. (https://www.nature.com/articles/s41467-020-20459-8) was used for circRNA enrichment and rolling circle amplification for long-read sequencing with the following exceptions. We used the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (#E7400X, New England BioLabs, Ipswich, MA) to remove the rRNA. Per the manufacturer’s protocol, multiple reactions were set up to accommodate a 25µg total RNA input. The rRNA depleted RNA was concentrated using RNAClean XP beads (2.0X) (#A63987, Beckman Coulter, Brea, CA) and eluting in 17μL of nuclease-free water. The RNase R treated sample was the purified using RNAClean XP beads (1.8X) and eluted in 10µL of nuclease-free water. The reverse transcription reaction was incubated for 5 minutes at 25°C, 1 hour at 42°C, and 10 minutes at 65°C. Precipitated circDNA was used as input for a 250μL rolling circle amplification reaction, per the TempliPhi 100 Amplification Kit protocol (#25-6400-10, GE Healthcare, Chicago, IL). The amplified sample was then purified using AMPure XP beads (1.8X) and eluted in 42µL of nuclease-free water. The purified sample was digested to remove branched structures by adding 5μL of 10X NEBuffer2 and 2.5µL of T7 Endonuclease I (#M0302L, New England BioLabs, Ipswich, MA) and incubating for 1 hour at 37°C. The digested sample was then size selected using two round of AMPure XP beads (0.5X). The sample was eluted with 36μL of 10mm Tris (pH 8.0).  For samples sequenced using the Nanopore platform, a 2µg input of cDNA was used with Oxford Nanopore’s Ligation Sequencing Kit (#SQK-LSK110, Oxford, United Kindom) to prepare a sequence ready library. The library was run on one flow cell on the GridION instrument. For samples sequenced using the PacBio platform, a 500ng input of cDNA was used to generate the long read sequencing library following the Iso-seq protocol (Pacific Biosciences, Menlo Park, CA). The library was run on a single SMRT cell on the Sequel II.
cDNA-Cap RNA-Seq for cell line short-read samples; Oxford Nanopore long-read RNA-seq for two HCT116 cell line samples; PacBio long-read RNA-seq for other cell line and patient samples.

value: Primary colon cancer


title: TAa4_NoDox_HSATIIKD_Rep2

description:
Library name: TA_a4_S4_R1_001.fastq.gz
Column name in count file TAa4_NoDox_HSATIIKD_Rep2_Kallisto48_GencodeR45

value: Myoblast line with dox inducible DUX4 transgene


title: WT_largeRNA_rep2

description:
Library name: Sample 8
Column name in WT_Nsun7ko_largeRNA_sites.csv: WT_rep2

value: testis


title: WT_mRNA_rep3

description:
Library name: Sample 3
Column name in WT_Nsun7ko_mRNA_sites.csv: WT_rep3


title: MDAMB231_Abema

description: Library name: MDAMB231_Abema

value: 100nM Abemaciclib for 96h


title: FF5_67


title: Normal colon mucosa, subject 722, sample ID 30, long-read, PacBio

description:
circRNA-RCA RNA
Pacific Biosciences long-read
N_722_PacBio
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz

source_name: Normal colon mucosa

value: Normal colon mucosa


title: WT_mRNA_rep2

description:
Library name: Sample 2
Column name in WT_Nsun7ko_mRNA_sites.csv: WT_rep2

value: WT


title: CAMA1_DMSO_3

description: Library name: CAMA1_DMSO_3

value: HR+ BC cell line


title: LoVo cell line, long-read, PacBio

description:
circRNA-RCA RNA
Pacific Biosciences long-read
LoVo_PacBio
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz

source_name: LoVo

value: LoVo

value: Humancolon cancercell line


title: CAMA1_DMSO_2

description: Library name: CAMA1_DMSO_2


title: WT_mRNA_rep1

description:
Library name: Sample 1
Column name in WT_Nsun7ko_mRNA_sites.csv: WT_rep1


title: CAMA1_DMSO_1

description: Library name: CAMA1_DMSO_1


title: HT29 cell line, long-read, PacBio

description:
circRNA-RCA RNA
Pacific Biosciences long-read
HT29_PacBio
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz


title: FF5_65

value: cortical organoid


title: Sp5GOF_Flag_2

city: Frederick

first: Terry

middle: P

last: Yamaguchi

state: Maryland (MD)

address: Building 560,  1050 Boyles St

department: Cancer and Developmental Biology

institute: NIH/NCI

description:
Library name: Sample 18
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

library_source: genomic

data_processing:
Adaptor sequences were trimmed using Cutadapt with the resulting reads aligned to the mm10 reference mouse genome using BWA.
Alignments with a MAPQ score of ≤ 5 were filtered out and PCR duplicates were removed using Picard's MarkDuplicates tool. Peak calling was performed using MACS2 and annotated using ChIPseeker.
Visualization and normalized bigWig tracks were generated using deepTools.
Motif analysis was carried out using Genomatix Genome Analysis software, based on Matrix library 8.4, ElDorado database version 08-2011, search mode: TF matrices and both the genomic and promoter background for calculating enrichment statistics.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

growth_protocol: ES cells were differentiated in serum free N2B27 media and treated with bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3. 1ug/mL DOX was added Day2 to Day3 for dox-inducible expression of flag-tagged Sp5.

extract_protocol:
genomic DNA
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing. All the samples have percent of Q30 bases above 94%. All the samples have yields between 42 and 67 million pass filter reads. Samples were trimmed for adapters using Cutadapt before the alignment. The trimmed reads were aligned with mm10 reference using Bowtie2 alignment. Overall alignment percentage for the samples is 96%. Unique alignment is above 68%. There are 1.67 to 7.82% unmapped reads. Library complexity is measured by uniquely aligned reads using picard’s markduplicate utility. All the samples have library complexity with percent non-duplicated reads ranging from 30 to 84%

value: Mouse Embryonic stem cell

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR, 1ug/mL Dox, and 12ng/ml bFGF from Day2 to day3

tag: chip antibody

value: anti-Flag antibody


title: FF5_63

value: fibroblast


title: Liver metastasis, subject 722, sample ID 37, long-read, PacBio

description:
circRNA-RCA RNA
Pacific Biosciences long-read
M_722_PacBio
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz

source_name: Liver metastasis

value: Liver metastasis


title: HCT116 cell line, long-read, PacBio

description:
circRNA-RCA RNA
Pacific Biosciences long-read
HCT116_PacBio
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz


title: CAMA1_Abema_3

description: Library name: CAMA1_Abema_3

value: 50nM Abemaciclib for 96h

value: forward


title: Sp5GOF_Flag_1

description:
Library name: Sample 17
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.


title: FF5_61

description: RNA-seq, 100-base-pair paired end reads on an Illumina HiSeq 4000

value: Control


title: Atest3

first: Hai

last: Tang

address: 507 Zhengmin Road, Yangpu District, Shanghai, China

institute: Shanghai Pulmonary Hospital affiliated to Tongji University

description: Library name: Sample6

data_processing:
cutadapt (v1.9.3)
Raw data quality control was performed first using the Q30 value.
Use cutadapt software (v1.9.3) to remove adapters, remove low-quality reads, and obtain high-quality clean reads.
The clean reads were aligned to the rat reference genome (rn6) using hisat2 software. Then, under the guidance of the Ensembl gtf gene annotation file, the cuffdiff software was used to obtain the gene-level mRNA FPKM value as the mRNA expression profile.
Assembly: oryCun2
Supplementary files format and content: Gene Expression Profiling_PEG.xlsx

organism: Oryctolagus cuniculus

source_name: subcutaneous tissue

growth_protocol: animal room

extract_protocol:
Total RNA was extracted from tissue with TRIzol reagent (TaKaRa), which was used to remove the rRNAs by Ribo-Zero rRNA Removal Kits (Illumina) following the manufacturer’s instructions.
RNA libraries were constructed by using rRNA-depleted RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions.Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc.).

value: subcutaneous tissue


title: FF5_59


title: CAMA1_Abema_2

description: Library name: CAMA1_Abema_2


title: FF5_60


title: CAMA1_Abema_1

description: Library name: CAMA1_Abema_1


title: Atest2

description: Library name: Sample5


title: Endogenous FlagSp5_Flag_2

description:
Library name: Sample 15
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3


title: FF5_68


title: FF5_54


title: Atest1

description: Library name: Sample4


title: Endogenous FlagSp5_Flag_1

description:
Library name: Sample 14
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day4


title: Donor J DP 2

city: Muenster

first: Markus

last: Fehrholz

address: Mendelstr. 17

institute: Monasterium Laboratory GmbH

data_processing:
Sequencing was performed on a NovaSeq 6000 using 2x100 bp read length with an output of appr. 50 M clusters (10 Gb) per sample.
Demultiplexing: Illumina bcl2fastq v2.20; adapter trimming: Skewer v0.2.2; Pico v2 SMART adapter trimming: Cutadapt v1.12.
Quality trimming of the reads was not performed. The quality of the FASTQ files was analyzed with FastQC v0.11.9.
Trimmed raw reads were aligned to a GRCh38.105 reference using STAR (version 2.7.10a). Only samples with a mapping rate > 50% and a phred score > 30 were included in the analysis.
Normalized counts were created using DESeq2 v1.28.1 in R v4.0.2.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: hair follicle

extract_protocol:
Total RNA was isolated from hair follicle tissue collected via laser capture microdissection using the PicoPure™ RNA-Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol.
Library preparation was performed using the SMART-Seq® stranded total RNA kit (Takara Bio, USA) according to the manufacturer's protocol with a maximal input of 7 µL.

value: hair follicle

tag: compartment

value: DP

value: female

value: untreated


title: Acontrol3

description: Library name: Sample3


title: WT_input_3

description:
Library name: Sample 13
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: input


title: Donor I CTS 2

value: CTS

value: male


title: FF5_52

value: cortical organoid


title: Donor J DC 2

value: DC


title: Acontrol2

description: Library name: Sample2


title: FF5_50

value: fibroblast


title: Sp5_8DKO_TLE_2

description:
Library name: Sample 12
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: Mouse Embryonic stem cell

value: Sp5_8 DKO

value: anti-TLE antibody


title: FF5_55

value: Control


title: Acontrol1

description: Library name: Sample1

value: subcutaneous tissue


title: Sp5_8DKO_TLE_1

description:
Library name: Sample 11
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3


title: Donor I bORS 2

value: bORS


title: Donor I DP 2

value: hair follicle


title: Sp5GOF_input_1

description:
Library name: Sample 16
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR, 1ug/mL Dox, and 12ng/ml bFGF from Day2 to day3


title: N913_Post_F_NR_1

city: Ramat Gan

first: Nissan

last: Yissachar

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

description: Library name: N913

data_processing:
RNAseq fastq files from 24 samples from 8 patients were aligned to the M. musculus reference genome mm10 using STAR (version 2.7.10a) (26). The resulting BAM files were sorted and indexed using Samtools. Read counts per gene were performed using htseq-count (27) (version 0.12.4). Differential gene expression analysis was performed using the DESeq2 (1.36.0) R/bioconductor package.
Assembly: mm10
Supplementary files format and content: DGE-post_vs_pre.xlsx
Supplementary files format and content: DGE-R_vs_NR.xlsx

source_name: colon

extract_protocol:
Colon tissue fragments (~3 mm) were placed in RNAlater overnight at 4°C, and then the samples were stored at -80°C. For RNA extraction, tissues were homogenized using a bead beater, and RNA was extracted with the Qiagen RNeasy Micro kit (Qiagen).
The Illumina TruSeq stranded mRNA library prep kit (Illumina) was used for library generation, and next-generation sequencing was performed at the Bar-Ilan University scientific equipment center using the Illumina NextSeq platform (NextSeq 500 High Output v2 kit).

value: colon

value: WT

tag: patientid

tag: group

value: Post

tag: responder

value: NR

value: F


title: Sp5_8DKO_input_2

description:
Library name: Sample 10
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

tag: cell line

tag: cell type

value: input


title: Donor F bORS 2

value: female

tag: treatment

value: untreated


title: FF5_53

tag: tissue

value: cortical organoid

value: fibroblast


title: N912_Pre_F_NR_1

description: Library name: N912

value: Pre


title: FF5_49

tag: source tissue

value: Control


title: Donor F sbORS 2

value: sbORS


title: WT_TLE_1

description:
Library name: Sample 8
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: Mouse Embryonic stem cell

tag: genotype

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3

value: anti-TLE antibody


title: N911_CTRL_F__1

description: Library name: N911

value: CTRL


title: FF5_56

tag: differentiation day


title: Donor F IRS 2

value: hair follicle

value: IRS


title: N910_Pre_F_NR_15

description: Library name: N910

value: colon

value: WT


title: FF3_61_redo

tag: differentiation


title: WT_input_2

description:
Library name: Sample 7
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.


title: Donor F HM2 2


title: N909_CTRL_F__14

description: Library name: N909

value: F


title: N908_Post_F_R_5

description: Library name: N908

value: Post

value: R


title: Donor F gHM 2

value: gHM

value: female

value: untreated


title: Sp5_8DKO_TCF7_2

description:
Library name: Sample 6
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: Sp5_8 DKO

value: anti-TCF7 antibody


title: Donor F DP 2

value: DP


title: FF3_59

value: cortical organoid

value: fibroblast

value: Control


title: WT_TLE_2

description:
Library name: Sample 9
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: Mouse Embryonic stem cell

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3

value: anti-TLE antibody


title: FF3_62


title: Sp5_8DKO_TCF7_1

description:
Library name: Sample 5
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.


title: WT_TCF7_2

description:
Library name: Sample 3
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.


title: FF3_60


title: Donor F IRS 1

value: hair follicle

value: IRS


title: N907_CTRL_F__5

description: Library name: N907

value: colon

value: WT

value: CTRL

value: F


title: N905_Post_F_NR_15

description: Library name: N905

value: Post

value: NR


title: WT_TCF7_1

description:
Library name: Sample 2
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.


title: Donor F DC 1

value: DC

value: female

value: untreated


title: N906_CTRL_F__4

description: Library name: N906


title: FF3_178

value: cortical organoid


title: N904_CTRL_F__15

description: Library name: N904


title: Donor C CTS 5

value: CTS

value: male


title: FF3_176

value: fibroblast


title: WT_Input_1

description:
Library name: Sample 1
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: Mouse Embryonic stem cell

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3

value: input


title: N903_Post_F_NR_14

description: Library name: N903


title: Donor C sbORS 5

value: hair follicle

value: sbORS


title: CML shOxr1 GFP+ BC, 5

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
Reads in FASTQ format were evaluated using FastQC (version 0.11.7), trimmed with cutadapt (version 1.14), aligned to the mouse genome (mm10) with Burrows Wheeler Aligner (BWA, version 0.7.12)
Processed BAM files were cleaned, sorted, and marked for duplicates with Picard Tools (version 1.85) and further filtered using the TruSeq_Exome_TargetedRegions_v1.2.bed file. Variants were detected using bcftools mpileup4 with minimum base quality and maximum depth parameters set to 20 and 1000, respectively; VCF files were filtered for quality and depth of 20 and 10, annotated with SnpEff (version 4.3), and analyzed for mutational patterns with the MutationalPatterns package in RStudio.
Assembly: mm10
Supplementary files format and content: vcf files
Library strategy: Whole Exome Sequencing

source_name: Bone marrow

growth_protocol: GFP- or GFP+ bone marrow cells (BMCs) from secondary transplant CML mice, transduced with either shOxr1 or shControl, were collected using a FACSARIA 4-Laser Sorter. For comparison, BMCs from age-matched wild-type control mice were also collected.

extract_protocol:
Genomic DNA (gDNA) was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Cat# 69504)
Libraries were constructed with 100 ng of QC-passed gDNA using the Illumina TruSeq Exome Library Prep Kit, hybridized to exome oligo probes with unique barcoding, validated with Qubit and Bioanalyzer, and sequenced on an Illumina NovaSeq NGS System to generate paired-end 150 bp reads.

treatment_protocol: Mice were treated with imatinib and subjected to 2-3 cycles of alum injection

value: Bone marrow

value: GFP+ BMCs

value: IM+alum injection


title: FF3_175


title: FF3_61

value: Control


title: CML shOxr1 GFP+ BC, 4


title: Donor C IRS 5

value: IRS


title: FF3_177_redo


title: FF3_177


title: Sp5_8DKO_input_1

description:
Library name: Sample 4
ChIP-seq samples were pooled and sequenced on NovaSeq Xplus 1.5B using TruSeq® ChIP SMP Prep and single-end sequencing.

value: Sp5_8 DKO


title: N902_Pre_F_NR_14

description: Library name: N902

value: colon

value: WT

value: Pre

value: NR

value: F


title: N901_Post_M_R_9

description: Library name: N901

value: Post

value: R

value: M


title: N900_Pre_M_R_9

description: Library name: N900


title: Donor C HM2 5

value: male

value: untreated


title: FF3_174

description: RNA-seq, 100-base-pair paired end reads on an Illumina HiSeq 4000

value: cortical organoid

value: fibroblast


title: CML shOxr1 GFP+ BC, 3

value: Bone marrow

value: GFP+ BMCs


title: Donor A sbORS 1

value: hair follicle

value: sbORS

value: female


title: Donor C gHM 5

value: gHM


title: CML shOxr1 GFP+ BC, 1

value: IM+alum injection


title: CML shOxr1 GFP+ BC, 2


title: N898_Post_M_NR_8

description: Library name: N898

value: colon

value: WT


title: Donor E CTS 2

value: CTS


title: N899_CTRL_M__9

description: Library name: N899

value: CTRL


title: FF3_173_redo


title: CML shOxr1 GFP+ CP, 2


title: N897_Pre_M_NR_8

description: Library name: N897

value: Pre

value: NR


title: Donor E bORS 2

value: bORS


title: FF3_171


title: FF3_172


title: CML shOxr1 GFP+ CP, 1


title: Donor E sbORS 2

value: untreated


title: N896_CTRL_M__8

description: Library name: N896

value: M


title: CML shControl GFP+ CP, 3


title: Donor E IRS 2

value: IRS


title: FF3_173

value: cortical organoid

value: fibroblast


title: N895_Post_M_R_6

description: Library name: N895

value: Post

value: R


title: CML shControl GFP+ CP, 2

value: Bone marrow

value: GFP+ BMCs


title: FF3_169


title: Donor E HM2 2

value: hair follicle

value: female


title: CML shControl GFP+ CP, 1

value: IM+alum injection


title: N893_CTRL_M__6

description: Library name: N893

value: colon

value: WT


title: Donor E gHM 2

value: gHM


title: FF3_169_redo


title: N894_Pre_M_R_6

description: Library name: N894

value: Pre


title: wt-50wks, control, 3

value: BMCs

value: alum injection


title: N892_Pre_F_R_5

description: Library name: N892

value: F


title: Donor E DP 2

value: DP

value: untreated


title: FF3_170

value: cortical organoid

value: fibroblast


title: wt-50wks, control, 2


title: Donor E DC 2

value: DC


title: N891_Post_F_R_4

description: Library name: N891

value: Post

value: R


title: FF3_168


title: wt-50wks, control, 1

value: Bone marrow


title: Donor E bORS 1

value: hair follicle

value: bORS

value: female


title: N890_Pre_F_R_4

description: Library name: N890

value: colon

value: WT


title: Donor D CTS 4

value: CTS


title: 10-G-T_S10

description:
Library name: Sample 4
ChIP libraries were prepared and sequenced in two separate NextSeq runs using V2 chemistry. Samples were generated using the Illumina TruSeq ChIP sample preparation kit.

growth_protocol: ES cells were differentiated in serum free N2B27 media and treated with bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3.

extract_protocol:
genomic DNA
Single end ChIP libraries were prepared and sequenced in two separate NextSeq runs using V2 chemistry. Samples were generated using the Illumina TruSeq ChIP sample preparation kit. Each sample included duplicates, with sequencing yielding 15 to 55 million pass-filter reads per replicate and over 90% of bases achieving a base call quality of Q30 or higher.

value: Mouse Embryonic stem cell

value: Wild type

tag: antibody

value: Goat IgG and anti-T/Brachyury antibodies (AB-108-C, AF2085, R&D systems, Inc respectively)


title: FF3_202


title: FF3_200


title: CML shOxr1 GFP-, 2

value: GFP- BMCs

value: IM+alum injection


title: Donor D bORS 4

tag: Sex

value: untreated


title: 9-G-T_S9

description:
Library name: Sample 3
ChIP libraries were prepared and sequenced in two separate NextSeq runs using V2 chemistry. Samples were generated using the Illumina TruSeq ChIP sample preparation kit.

value: bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3


title: CML shOxr1 GFP-, 1


title: Donor D sbORS 4

value: sbORS


title: 8-G-IgG_S8

description:
Library name: Sample 2
ChIP libraries were prepared and sequenced in two separate NextSeq runs using V2 chemistry. Samples were generated using the Illumina TruSeq ChIP sample preparation kit.


title: FF3_201

value: cortical organoid

value: fibroblast


title: FF3_167


title: CML shControl GFP-, 3

value: Bone marrow


title: Donor D IRS 4

value: hair follicle

value: IRS


title: 7-G-IgG_S7

description:
Library name: Sample 1
ChIP libraries were prepared and sequenced in two separate NextSeq runs using V2 chemistry. Samples were generated using the Illumina TruSeq ChIP sample preparation kit.


title: CML shControl GFP-, 2


title: FF3_186


title: FF3_185_redo


title: FF3_183


title: CML shControl GFP-, 1


title: FF3_185


title: Donor D HM2 4

value: female


title: CML mice in remission, IM+Embelin, 1

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR
Gene counting was performed using htseq-count version 0.6 1p1
Differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited file with read counts per gene

source_name: Bone marrow cells

growth_protocol: GFP+Lin− bone marrow cells from secondary recipients of BCR-ABL-transduced CML mice were sorted with FACSARIA 4-Laser Sorter

extract_protocol:
RNA was isolated from the transplanted mBMCs using the RNeasy plus micro kit (Qiagen 74034). RNA quality was determined using an Agilent Bioanalyzer 2100 (Agilent Research Laboratories, Santa Clara, CA).
Libraries were prepared with the TruSeq Stranded mRNA kit (Illumina Inc, San Diego, CA) and validated.

treatment_protocol: Secondary transplants were treated with IM, IM+YM155, or IM+Embelin, respectively.

value: Bone marrow cells

value: Lin-GFP+ cells

value: Imatinib + Embelin


title: CML shOxr1 GFP-, 3


title: CML mice in remission, IM+Embelin, 2


title: CML mice in remissin, IM+YM155, 2

value: Imatinib + YM155


title: wt-30wks, control, 2

value: BMCs

value: alum injection


title: Donor D gHM 4

value: gHM


title: wt-30wks, control, 3


title: CML mice in remissin, IM+YM155, 1


title: FF3_184


title: CML mice in remission, IM, 2

value: Imatinib


title: wt-30wks, control, 1


title: Donor D DC 3

value: DC

value: untreated


title: FF3_182


title: FF3_201_redo


title: FF3_179


title: Donor A gHM 2


title: CML mice in remission, IM, 1


title: RNAseq_SV_HFD_6

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Raw reads were trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Bowtie (v.2.2.3) was used to identify reads that align to known possible contaminants, which were then discarded.
Reads were then aligned to strain specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.6.1). Alignment was done using manual two-pass alignment: After first alignment the splice junctions were collected and used on the second pass alignment with ‘–sjdbFileChrStartEnd’ parameter along with the 2nd pass index generated with the splice junctions. STAR parameters were as follows: --outFilterMultimapNmax 100 –outFilterMismatchNmax 33 –seedSearchStartLmax 12 –alignSJoverhangMin 15 –outFilterMatchNminOverLread 0 –outFilterScoreMinOverLread 0.3 –outFilterType BySJout).
Assembly: mm10
Supplementary files format and content: Raw counts: Read counts for genes were generated using STARs ‘-quantMode GeneCounts’ option. Gene IDs are ENSEMBL IDs from Gencode M25 annotation.
Supplementary files format and content: VST normalized counts: Normalized counts for samples passing PcaGrid outlier detection were generated using DESeq2 (v1.34.0) for blind VST normalization and batch corrected for cell type composition batch effects using limma::removeBatchEffect.

source_name: eWAT

extract_protocol:
Total RNA was extracted from mouse eWAT tissue using the miRNeasy Mini Kit and QIAzol Lysis Reagent from QIAGEN, according to the manufacturer's protocol. The RNA was treated with RNase-Free DNase (QIAGEN) to remove any DNA. The RNA quality was assessed with an Agilent Bioanalyzer and the RNA 6000 Nano kit, with all samples showing a RIN score of 7 or higher.
Ribosomal RNA was first removed with the NEBNext rRNA Depletion Kit (New England BioLabs). The libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs), according to the manufacturer's guidelines. The yield of the libraries was assessed using the Qubit DNA High Sensitivity assay (Invitrogen), and quality control was conducted with the Agilent Bioanalyzer using the DNA 1000 kit (Agilent). Finally, the indexed libraries were pooled and sequenced on the NextSeq 500 platform (Illumina) with 75 bp single-end reads.

value: eWAT

tag: strain

value: HFD


title: Donor D DP 4

value: DP


title: Donor D DC 4


title: CTRL_CTRL_ctrl

description: Library name: 461165_CTRL

data_processing:
The QIIME pipeline (version qiime2-2022.11) was used on 16S rRNA gene raw sequences from microbial communities.
Assembly: green genes database
Supplementary files format and content: 16S-level7.csv
Library strategy: 16S rRNA-seq

organism: feces metagenome

source_name: Feces

extract_protocol:
DNA was extracted using the PureLink™ Microbiome DNA Purification Kit (Invitrogen).
16S libraries for Illumina sequencing were prepared using a two-step PCR protocol. In the first PCR, primers containing tails were used to amplify the V4 region of the 16S rRNA gene. The Access Array primers for Illumina (Fluidigm) were used in the second PCR to add the adaptor and index sequences to each sample. After the second PCR, the reactions were cleaned using Kapa Pure beads (Roche) to remove unincorporated primers and any primer-dimer produced. The concentration of each library was measured by Qubit (Life Technologies) using the Denovix ds DNA HS assay (Deonvix) and then the samples were combined in equal amounts to a single pool. The pooled sample was run on the Tapestation (Agilent) using a DNA 1000 screentape to determine the size of the pooled libraries. The pooled library was then loaded on the Illumina Miseq and sequenced using a Miseq V2 Kit (500 cycles) to generate 2 3 250 paired-end reads. The data were de-multiplexed using Basespace, the Illumina cloud software to generate two FASTQ files per sample.

value: Feces

tag: biology sample

value: human fecal sample

value: CTRL

value: ctrl


title: Donor A HM2 2

value: hair follicle

value: female


title: FF3_181_redo

source_name: cortical organoid

extract_protocol:
ribosomal RNA depleted (RiboZero Gold, Illumina)
Truseq stranded RNA RiboZero Gold (Illumina)

value: cortical organoid

value: fibroblast


title: Donor A DP 2


title: 659B_NR_pre

description: Library name: 461165_659B

value: NR

value: pre


title: FF3_180


title: Donor A DC 2


title: FF3_181


title: 659V2_NR_post

description: Library name: 461165_659V2

value: post


title: RNAseq_SV_HFD_3


title: 641B_NR_pre

description: Library name: 461165_641B


title: 641V2_NR_post

description: Library name: 461165_641V2


title: RNAseq_SV_HFD_2


title: Donor B bORS 6

value: bORS

value: male


title: FF5_47

value: Control


title: 631V2_NR_post

description: Library name: 461165_631V2


title: 631B_NR_pre

description: Library name: 461165_631B


title: RNAseq_SV_HFD_5

value: eWAT


title: 608V2_NR_post

description: Library name: 461165_608V2


title: RNAseq_SV_HFD_4

value: HFD


title: FF5_39


title: Donor B CTS 6

value: CTS

value: untreated


title: RNAseq_SV_HFD_1


title: Donor B IRS 6

value: IRS


title: RNAseq_B6_HFD_7


title: 608B_NR_pre

description: Library name: 461165_608B

value: Feces

value: human fecal sample


title: FF5_41


title: Donor B gHM 6

value: hair follicle

value: gHM


title: 608Bp_NR_pre

description: Library name: 461165_608Bp


title: RNAseq_B6_HFD_6


title: FF5_40

value: cortical organoid


title: Donor B DP 6

value: DP


title: RNAseq_B6_HFD_5


title: 608V2p_NR_post

description: Library name: 461165_608V2p

value: NR


title: RNAseq_B6_HFD_4


title: FF5_38

value: fibroblast


title: Donor B DC 6

value: DC


title: FF5_48


title: FF5_44


title: 605V2_R_post

description: Library name: 461165_605V2

value: R

value: post


title: Donor B sbORS 6

value: sbORS

value: male


title: 605B_R_pre

description: Library name: 461165_605B

value: pre


title: 603V2_R_post

description: Library name: 461165_603V2


title: Donor B HM2 5


title: FF5_42

value: Control


title: Donor J CTS 2

value: CTS

value: female

value: untreated


title: 603B_R_pre

description: Library name: 461165_603B

value: Feces

value: human fecal sample


title: Donor J IRS 0

value: hair follicle

value: IRS


title: FF5_43

value: cortical organoid


title: FF5_46


title: RNAseq_B6_HFD_2

value: eWAT

value: HFD


title: RNAseq_B6_HFD_3


title: Donor J HM2 0


title: 602V2_R_post

description: Library name: 461165_602V2


title: FF5_45

value: fibroblast


title: RNAseq_SV_Chow_5

value: Chow


title: Donor J gHM 0

value: gHM


title: 602B_R_pre

description: Library name: 461165_602B

value: R


title: RNAseq_SV_Chow_4


title: FF5_37


title: RNAseq_SV_Chow_3


title: Donor I CTS 3

value: male


title: 600V2p_R_post

description: Library name: 461165_600V2p

value: post


title: FF5_35

value: Control


title: Donor I bORS 3

value: bORS


title: FF5_33


title: RNAseq_SV_Chow_2


title: FF5_36


title: RNAseq_B6_HFD_1


title: RNAseq_SV_Chow_1


title: RNAseq_B6_Chow_6


title: Donor I DP 3

value: DP


title: 600Bp_R_pre

description: Library name: 461165_600Bp

value: pre


title: M

first: Lei

last: Zhao

state: Shanghai

address: 500 Zhennan Road

institute: Tongji University

description: Library name: M_P

data_processing:
The raw sequencing data were processed using Cell Ranger software (version 6.1.1) to generate gene expression matrices based on the mm10 genome assembly. The pre-processed mouse reference genome (mm10) was downloaded from the 10x Genomics website. The gene expression matrices were imported into R for downstream analysis using the Read10X function in Seurat (version 4.1.1). Cells with fewer than 200 genes or more than 15% mitochondrial gene content were excluded from further analysis.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: periosteal

extract_protocol:
The periosteal tissue was dissociated using a mixed enzyme solution prepared according to the manufacturer’s protocol (Majorbio Bio-Pharm Technology Co. Ltd., Shanghai, China). The solution contained 2 mg/ml type II collagenase, 0.5 mg/ml dispase, 50 U/ml DNase. After preheating the mixed enzyme solution at 37°C for 30 minutes, periosteal tissue was incubated with the enzyme mixture in a water bath at 37°C. The digestion process was repeated four times, each for 15 minutes. After each digestion, the suspension was filtered through a 40 μm mesh and neutralized with an equal volume of complete medium (α-MEM containing 10% fetal bovine serum and 1% penicillin-streptomycin). The remaining tissue was subjected to a second round of digestion. At the end of the four digestions, the cell suspension was centrifuged at 300 g for 5 minutes. The pellet was resuspended in 1 mL of 1× erythrocyte lysis buffer for 5 minutes, washed with 10 mL of ice-cold PBS, and centrifuged again at 300 g for 5 minutes. The final cell pellet was resuspended in 50 μL of PBS. Viability was assessed using the AO/PI staining method and an automated cell counter, with cell viability confirmed to be >80%. The concentration of the cell suspension was adjusted to approximately 1000 cells/μL.
Library preparation and sequencing were conducted by Majorbio Bio-Pharm Technology Co. Single-cell suspensions were loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single-cell gel bead emulsions, following the manufacturer’s guidelines (Chromium Single Cell 3ʹ v3.1). The Chromium Single-Cell 3' Gel Bead and Library V3 Kit was used for cDNA synthesis and amplification, and sequencing was carried out on an Illumina NovaSeq 6000 platform.

value: periosteal

tag: age

value: 9 month old


title: FF3_48

data_processing:
The reads were mapped to the human genome (hg38) with Gencode v25 annotations using STAR (v.2.5.2b) and gene expression was quantified using rsem (v1.3.0)
Genes that were expressed at very low levels (less that 10 reads in 30% of samples from a given day) were removed from the analysis
Samples with standardized sample network connectivity Z scores below –2 in each mutation were defined as outliers and removed
To control for technical variation due to the sequencing and library prep we calculated the principal components of the Picard sequencing metrics (http://broadinstitute.github.io/picard/) using the CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics, and MarkDuplicates modules and included them in our model
To infer genetic ancestry, we called SNPs from the aligned reads using the GATK (v3.3) Haplotype caller. Sites with more than 5% missing samples, with rare minor allele frequency (less than 0.05) and Hardy–Weinberg disequilibrium (less than 1 × 10–6) were removed using plink (v1.09). We then used the remaining high-quality SNPs to run MDS together with HapMap3.3 (hg38). The first two MDS values, referred to as genetic ancestry PC1/2, were then included in our model.
Assembly: (hg38) with Gencode v25
Supplementary files format and content: counts


title: Y

description: Library name: Y_P

value: 3 month old


title: RNAseq_B6_Chow_5


title: Donor I DC 3

value: hair follicle

tag: compartment

value: DC

value: untreated


title: FF5_20

value: cortical organoid


title: Donor I HM2 2


title: FF5_34

value: fibroblast


title: Donor J DP 0

value: female


title: RNAseq_B6_Chow_3

value: eWAT

value: Chow


title: 600V2_R_post

description: Library name: 461165_600V2

value: Feces

value: human fecal sample

value: R


title: Mouse 4mg/kg paclitaxel injection rep4

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: Library name: Sample 8

data_processing:
Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to curated Mus musculus tRNA reference genome.
The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA mutation and deletion rate  were detected based on aligned reads using samtools sort (http://www.htslib.org/, Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify charging as well as coverage of aligned reads.
Assembly: GRCm39
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: .sam.tsv files with mutation, deletion, coverage for each gene position per sample
Library strategy: MSR-Seq

source_name: Neurons

extract_protocol:
Total RNA was extracted from cells using Tri-zol extraction.
MSR-seq (PMID 35513407)

treatment_protocol: Male C57BL/6 mice were injected with 4mg/kg paclitaxel injection or vehicle control. One day after injection, mice were sacrificed and DRGs were harvested.

value: Neurons

value: dorsal root ganglion

value: Male

value: 4mg/kg paclitaxel


title: Donor H IRS 0

value: IRS

value: male


title: RNAseq_B6_Chow_2


title: FF3_49

value: Control


title: Donor I sbORS 3

value: hair follicle

value: sbORS


title: Mouse 4mg/kg paclitaxel injection rep3

description: Library name: Sample 7


title: Mouse 4mg/kg paclitaxel injection rep2

description: Library name: Sample 6


title: Donor H gHM 0

value: gHM

value: untreated


title: Donor H HM2 0


title: FF3_47_redo

value: cortical organoid

value: fibroblast


title: Mouse 4mg/kg paclitaxel injection rep1

description: Library name: Sample 5


title: Donor H DP 0

value: DP


title: FF3_50


title: O

description: Library name: O_P

value: periosteal

value: 18 month old


title: H3K27ac_SV_HFD_1

data_processing:
Reads were then trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Alignment was done using to strain-specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.6.1) with ‘--alignIntronMax 1 --alignEndsType "EndToEnd"’.
Reads were filtered for true pairs and MAPQ>20 with Samtools (v1.9) and duplicates were removed using Picard (v2.8.13) MarkDuplicates.
Peaks were called with MACS2 (v2.2.7.1) using ‘-g mm -B --call-summits --keep-dup auto -q 0.05’.
Assembly: mm10
Supplementary files format and content: Sample-wise peaks: H3K27ac summits were widened to peaks with Bedtools (v2.27.1) using ‘slop -b 75’. Peaks were shifted to mm10 coordinates using g2gtools. ENCODE blacklisted regions were removed from the regions.
Supplementary files format and content: BigWigs: BAM files shifted to mm10 coordinates were downsampled after and merged by group using Samtools. BigWigs were generated using Deeptools (v3.4.2) bamCoverage with '--normalizeUsing CPM --outFileFormat bigwig --binSize 10'.

extract_protocol:
Frozen tissue was Dounce homogenized and fixed with 20 strokes using the loose pestle A followed by 20 strokes with the tight pestle B in Cell Lysis Buffer (5 mM PIPES pH 8, 85 mM KCl, 1% Igepal, 1× protease inhibitor) containing 0.5% formaldehyde. The mixture was rotated for 8 minutes at room temperature. The cross-linking reaction was quenched by adding 150 mM glycine for 5 minutes at room temperature. Samples were washed twice with ice-cold Cell Lysis Buffer supplemented with 1× protease inhibitors. The pellet was suspended in 300 µl of SDS Lysis Buffer (50 mM Tris-Cl, 0.5% SDS, 10 mM EDTA, 1× protease inhibitor) and incubated on ice for 1 hour. Chromatin was sheared using a Bioruptor Plus sonicator (Diagenode) for 35 cycles at a high setting (30s ON, 30s OFF per cycle), allowing the sonicator to cool down for 5 minutes after every 10 cycles. Triton-X-100 was added to a final concentration of 1% along with 1× protease inhibitors. Samples were centrifuged at 13,000 rpm for 20 minutes, and the supernatant was collected for immunoprecipitation.
ChIP and library preparation were performed using the recently described ChIPmentation protocol (Gustafsson C et al. BMC Genomics. 2019;20(1):59) with minor modifications. For ChIP, 2 µg of rabbit polyclonal anti-CTCF antibody, 5µl of rabbit monoclonal anti-TCF4/TCF7L2 antibody or 2 µg of Anti-Histone H3 (acetyl K27) antibody was added to 50 µl Protein G-coupled Dynabeads (Thermo Fisher Scientific) in 1 × PBS with 0.5% bovine serum albumin (BSA) and rotated at 40 rpm for 4 h at 4°C. Dynabeads were washed three times with PBS with 0.5% BSA and then mixed with 190 µl chromatin samples in 1.5 ml tubes. The samples were rotated at 40 rpm overnight at 4°C. Chromatin was washed with 150 µl of low-salt buffer (50 mM Tris/HCl, 150 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and 1 mM EDTA), high-salt buffer (50 mM Tris/HCl, 500 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and 1 mM EDTA) and LiCl buffer (10 mM Tris/HCl, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, and 1 mM EDTA), followed by two washes with TE buffer (10 mM Tris/HCl and 1 mM EDTA) and two washes with ice-cold Tris/HCl pH 8. Chromatin was resuspended in 30 µl of 2 × TD buffer and 1 µl of transposase (Nextera, Illumina) for tagmentation. Samples were incubated at 37°C for 10 min followed by two washes with low-salt buffer. Bead bound tagmented chromatin was diluted in 23 µl of water and 25 µl of 2 × Ultra II Q5 Master Mix (New England BioLabs, M0544S) and 1 µl of both amplification primers (Buenrostro et al, 2013; 0.125 µM final concentration) were added. The libraries were incubated as follows: 72 °C 5 min (adapter extension); 95 °C 5 min (reverse cross-linking); followed by 11 cycles of 98 °C 10s, 63 °C 30s and 72 °C 3 min. After PCR amplification, double-sided purification was performed using SPRIselect beads (Beckman Coulter). To prepare input controls, 2 μl of 50 mM MgCl2 was added to 10 μl sonicated lysate to neutralize the EDTA in the SDS lysis buffer. Tagmentation and amplification was done as described above.

value: eWAT

tag: chip antibody

value: HFD


title: FF3_52


title: Mouse vehicle control rep4

description: Library name: Sample 4

value: Neurons

value: dorsal root ganglion

value: Vehicle Control


title: H3K27ac_B6_HFD_3


title: Donor G bORS 3

value: bORS

value: female


title: RNAseq_B6_Chow_4

value: Chow


title: H3K27ac_SV_HFD_2


title: FF5_19

value: Control


title: H3K27ac_B6_HFD_1


title: FF3_51


title: Mouse vehicle control rep2

description: Library name: Sample 2

value: Male


title: Donor G sbORS 3

value: hair follicle

value: sbORS


title: RNAseq_B6_Chow_1


title: Mouse vehicle control rep1

description: Library name: Sample 1


title: Donor G DP 3

value: untreated


title: FF3_46

value: cortical organoid

value: fibroblast


title: FF5_18


title: H3K27ac_SV_Chow_1


title: IL16-/-ApoE-/-3

city: Gui'an

first: Hailong

last: Ou

state: Guizhou

address: No.6 Ankang Avenue

institute: Guizhou Medical University

description: Sample 6

data_processing:
Cutadapt was used to filter out unqualified sequences (sequencing adapters, low-quality sequences, etc.) from the raw data
Hisat2 was used for reference genome alignment
StringTie was ued to reconstruct transcripts and calculate the expressions of all genes in each sample
Assembly: Ensembl_v101
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: aorta

extract_protocol:
RNA was extracted and purified using TRIzol (Thermo Fisher, 15596018). A concentration>50ng/µL, RIN value>7.0, and total RNA>1µg are sufficient for downstream experiments. Use oligo (dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) to specifically capture mRNA containing PolyA (polyadenylation) through two rounds of purification. The captured mRNA was fragmented using the NEBNextR Magnesium RNA Fragmentation Module (cat. E6150S, USA) under high temperature conditions at 94 ℃ for 5-7 minutes.
cDNA was synthesized using Invitrogen SuperScriptTM II Reverse Transcriptase (cat. 1896649, CA, USA), and E Escherichia coli DNA polymerase I (NEB, cat. m0209, USA) and RNase H (NEB, cat. m0297, USA) were subjected to double stranded synthesis. The double stranded DNA was digested using UDG enzyme (NEB, cat. m0280, MA, US), and a library with fragment size of 300bp ± 50bp was formed by PCR (chain specific library)

value: aorta


title: FF5_17

first: Lucy

last: Bicks

address: 1033 3rd street, apartment 106, apartment 106

institute: UCLA School of Medicine


title: H3K27ac_B6_Chow_2


title: IL16-/-ApoE-/-2

description: Sample 5


title: Donor G DC 3

value: DC


title: Donor G CTS 3

value: CTS


title: IL16-/-ApoE-/-1

description: Sample 4


title: Mouse vehicle control rep3

description: Library name: Sample 3


title: H3K27ac_B6_Chow_1

value: eWAT


title: Donor F IRS 3

value: IRS


title: 6PGDKO

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
6PGD-KO-iT-CD45 : Oligo 310
10X Genomics

data_processing:
The demultiplexing, bardoded processing,  gene count and aggregation were make with CellRanger v6.1.2
The downstream data analyses were done using Seurat.
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files.

source_name: Tumor

growth_protocol: AT3 cell line was cultured in DMEM containing 10% FBA, 1X nonessential amino acids, 1X Pen/Strep and incubated in 7% CO2 at 37 C.

extract_protocol:
CD45+ cells were sorted from tumors and single cell libraries were generated using the 10X Genomics platform.  First, Feature Barcode conjugated molecules were bound to cell surface proteins.  Then live-CD11b+ cells were isolated using the SONY MA900 cell sorter (Sony Biotechnology).  Single-cell suspensions were pooled together and assessed with AOPI stain using a Cellometer K2 automated cell counter (Nexcelom), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells were loaded into the Chromium Controller (10X Genomics) where they were partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription was performed, and the resulting cDNA is amplified.
Amplified cDNA is separated into full-length and Feature Barcode fractions using SPRISelect beads (Beckman Coulter).  The full-length amplified cDNA was used to generate libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  Feature barcode derived cDNA was PCR amplified to incorporate Illumina adapter sequences and unique sample indexes.  The resulting libraries were evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies) and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina.  They were then pooled, denatured, and diluted to 300 pM with 1% PhiX control library added.  The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

value: Tumor

value: Immune cell


title: FF5_13


title: Apo-/-2

description: Sample 2


title: WT

description:
WT-iT-CD45 : Oligo 309
10X Genomics

value: WT


title: Donor F HM2 3

value: female


title: H3K27ac_SV_Chow_2

value: Chow


title: Donor F gHM 3

value: gHM


title: SW620 cell line, short-read

description:
cDNA-Capture RNA
SW620_Illumina_TruSeq
WUSTL_cell_lines_Illumina_TruSeq_circRNA_count.csv.gz
WUSTL_cell_lines_Illumina_TruSeq_circRNA_tpm.csv.gz

value: Humancolon cancercell line


title: FF3_47

value: Control


title: FF5_11


title: Apo-/-1

description: Sample 1


title: SW480 cell line, short-read

description:
cDNA-Capture RNA
SW480_Illumina_TruSeq
WUSTL_cell_lines_Illumina_TruSeq_circRNA_count.csv.gz
WUSTL_cell_lines_Illumina_TruSeq_circRNA_tpm.csv.gz


title: FF5_12


title: FF3_39


title: Donor F DC 3

value: hair follicle


title: Scr Neuron 3

city: New York

first: Richard

address: 1150 St Nicholas Ave

institute: Columbia University

data_processing:
Adaptor and low quality reads were removed by Trim Galore 0.6.10
Reads were mapped to mm10 using bismark 0.24.2
differentially methylated cytosines were called by methylkit 3.19
Assembly: mm10
Supplementary files format and content: tab delimited text file containing coordinates, methylation difference, and q value for differentially methylated cytosines

source_name: Brain

extract_protocol:
genomic DNA was extracted from bulk liver tissue or sorted neuronal nuclei using Qiagen DNeasy Blood and Tissue Kit
Library was prepared using Zymo Pico Methyl-Seq Prep Kit according to manufacturer instructions

value: Brain

value: Neuron

value: LSL-dC-T


title: Donor C CTS 6

value: male

value: untreated


title: LoVo cell line, short-read

description:
cDNA-Capture RNA
LoVo_Illumina_TruSeq
WUSTL_cell_lines_Illumina_TruSeq_circRNA_count.csv.gz
WUSTL_cell_lines_Illumina_TruSeq_circRNA_tpm.csv.gz

extract_protocol:
For cell line short-read samples, total RNA inputs of 1μg were used to generate libraries using the Illumina (San Diego, CA) TruSeq Stranded Total RNA with Ribo-Zero Fold.  For long-read samples, the RNA of the cells lines HCT116, HT29, and LoVo was isolated using the Macherey-Nagel NucleoSpin RNA, Mini kit (MACHEREY-NAGEL, Düren, Germany). The RNA of patient trio samples was isolated using the Invitrogen TRIzol protocol (ThermoFisher Scientific, Waltham, MA) with DNase treatment (ZYMO RESEARCH, Irvine, CA).
For cell line short-read samples, 200ng aliquots of each library were pooled and used as input for cDNA-Capture. The IDT xGen Exome Research Panel v2 including 415,115 exon probes was used for exome capture. For long-read samples, the published protocol in Xin et al. (https://www.nature.com/articles/s41467-020-20459-8) was used for circRNA enrichment and rolling circle amplification for long-read sequencing with the following exceptions. We used the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (#E7400X, New England BioLabs, Ipswich, MA) to remove the rRNA. Per the manufacturer’s protocol, multiple reactions were set up to accommodate a 25µg total RNA input. The rRNA depleted RNA was concentrated using RNAClean XP beads (2.0X) (#A63987, Beckman Coulter, Brea, CA) and eluting in 17μL of nuclease-free water. The RNase R treated sample was the purified using RNAClean XP beads (1.8X) and eluted in 10µL of nuclease-free water. The reverse transcription reaction was incubated for 5 minutes at 25°C, 1 hour at 42°C, and 10 minutes at 65°C. Precipitated circDNA was used as input for a 250μL rolling circle amplification reaction, per the TempliPhi 100 Amplification Kit protocol (#25-6400-10, GE Healthcare, Chicago, IL). The amplified sample was then purified using AMPure XP beads (1.8X) and eluted in 42µL of nuclease-free water. The purified sample was digested to remove branched structures by adding 5μL of 10X NEBuffer2 and 2.5µL of T7 Endonuclease I (#M0302L, New England BioLabs, Ipswich, MA) and incubating for 1 hour at 37°C. The digested sample was then size selected using two round of AMPure XP beads (0.5X). The sample was eluted with 36μL of 10mm Tris (pH 8.0).  For samples sequenced using the Nanopore platform, a 2µg input of cDNA was used with Oxford Nanopore’s Ligation Sequencing Kit (#SQK-LSK110, Oxford, United Kindom) to prepare a sequence ready library. The library was run on one flow cell on the GridION instrument. For samples sequenced using the PacBio platform, a 500ng input of cDNA was used to generate the long read sequencing library following the Iso-seq protocol (Pacific Biosciences, Menlo Park, CA). The library was run on a single SMRT cell on the Sequel II.
cDNA-Cap RNA-Seq for cell line short-read samples; Oxford Nanopore long-read RNA-seq for two HCT116 cell line samples; PacBio long-read RNA-seq for other cell line and patient samples.

value: LoVo


title: Donor F sbORS 3

value: sbORS


title: Scr Neuron 2


title: Apo-/-3

description: Sample 3

value: aorta


title: FF3_45

value: cortical organoid

value: fibroblast


title: FF5_16


title: HCT116 cell line, short-read

description:
cDNA-Capture RNA
HCT116_Illumina_TruSeq
WUSTL_cell_lines_Illumina_TruSeq_circRNA_count.csv.gz
WUSTL_cell_lines_Illumina_TruSeq_circRNA_tpm.csv.gz


title: FF3_44


title: HT29 cell line, short-read

description:
cDNA-Capture RNA
HT29_Illumina_TruSeq
WUSTL_cell_lines_Illumina_TruSeq_circRNA_count.csv.gz
WUSTL_cell_lines_Illumina_TruSeq_circRNA_tpm.csv.gz


title: Donor C bORS 6

value: bORS


title: Mecp2 Pool Neuron 3


title: FF3_42


title: Scr Neuron 1


title: Sp8exp8

description:
Library name: Sample 4
The libraries were prepared according to standard Illumina's TruSeq Chip protocol before being sequenced on the Illumina Genome Analyzer IIx

data_processing:
Base calling was performed with the RTA 1.9.35.0 software
Raw Fastq reads were aligned to the mouse mm10 build using Bowtie aligner with default parameters.  Library complexity was measured by uniquely aligned reads using Picard’s markduplicate utility
Peak calling between the replicate samples for Sp5 and the replicate samples for the Input control was carried out using MACS2 algorithm. Peaks were called using the following parameters in MACS2: significance threshold q<0.1, bandwidth=300bp, model fold = [5,50].
HOMER was used to annotate the peaks to the nearest genomic features on the mm10 reference genome. The distance to TSS information and the gene start and end co-ordinates were used to determine if a peak was either upstream of the gene, within the gene-body or downstream of the gene.
Motif analysis was carried out using Genomatix Genome Analysis software, based on Matrix library 8.4, ElDorado database version 08-2011, search mode: TF matrices and both the genomic and promoter background for calculating enrichment statistics.
Assembly: mm10
Supplementary files format and content: BigWig

growth_protocol: ES cells were maintained in 15%serum/DMEM supplemented with 1unit per ml culutre medum and grown on primary MEFs (derived from FVB mouse stain). ES colonies were dissacociated with TypLE and MEFs were stripped away. ES cells were then plated at 2.5x10^6 per 100mm petri dish for suspension growth and embryoid body formation. Flag-Sp8 expression was initiated on day 2 of embryoid body formation, for a total of 24 hrs.

extract_protocol:
genomic DNA
Cells were fixed for 15mins in 1% formaldehyde, quenched with glycine. Cells were lysed to extract nuclei which were then sonicated to obtain sheared genomic DNA ~100-300bp in size for sequencing. The libraries were prepared according to standard Illumina's TruSeq Chip protocol. The ChIP DNA is blunt-ended and phosphorylated. A single 'A' nucleotide is added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products are purified and size-selected. The size-selected DNA is purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantitated by qPCR before cluster generation and sequencing.

treatment_protocol: After 2 days of embryoid body formation cells were treated with Doxycycline to induce Flag-Sp8 expression for 24 hrs

value: Mouse embryonic stem cell

value: M2 (Sigma, catalog# F3165, lot# SLBF1225). Used 4ug of antibody per ChIP


title: FF5_10


title: Donor C IRS 6

value: IRS


title: FF5_14


title: Mecp2 Pool Neuron 2


title: Mecp2 Pool Neuron 1


title: Donor C HM2 6


title: Donor F DP 3

value: DP

value: female


title: Sp8exp7

description:
Library name: Sample 3
The libraries were prepared according to standard Illumina's TruSeq Chip protocol before being sequenced on the Illumina Genome Analyzer IIx

value: After 2 days of embryoid body formation cells were treated with Doxycycline to induce Flag-Sp8 expression for 24 hrs


title: Input_exp_8

description:
Library name: Sample 2
The libraries were prepared according to standard Illumina's TruSeq Chip protocol before being sequenced on the Illumina Genome Analyzer IIx

value: input


title: FF3_40

value: Control


title: Input_exp_7

description:
Library name: Sample 1
The libraries were prepared according to standard Illumina's TruSeq Chip protocol before being sequenced on the Illumina Genome Analyzer IIx


title: Donor C gHM 6

value: hair follicle

value: gHM


title: FF3_41


title: Scr Liver 2

source_name: Liver

value: Liver

value: LSL-dC-D


title: FF3_43


title: Donor C sbORS 6

value: sbORS

value: male

value: untreated


title: Scr Liver 1


title: Donor C DP 6


title: CAMA1_shRB1#2_Abema_n4

description: Library name: CAMA1_shRB1#2_Abema_n4

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 33 (based on Ensembl 99)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: HR+ BC cell line

value: 50nM Abemaciclib for 96h

tag: strand

value: forward


title: CAMA1_shRB1#2_Abema_n3

description: Library name: CAMA1_shRB1#2_Abema_n3


title: FF5_9

value: cortical organoid

value: fibroblast


title: Pcsk9 Liver 2


title: CAMA1_shRB1#2_Abema_n1

description: Library name: CAMA1_shRB1#2_Abema_n1


title: Donor E CTS 3

extract_protocol:
Total RNA was isolated from hair follicle tissue collected via laser capture microdissection using the PicoPure™ RNA-Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol.
Library preparation was performed using the SMART-Seq® stranded total RNA kit (Takara Bio, USA) according to the manufacturer's protocol with a maximal input of 7 µL.

value: CTS


title: Pcsk9 Liver 3


title: Pcsk9 Liver 1


title: Donor C DC 6

value: DC


title: FF3_37


title: CAMA1_shRB1#2_Abema_n2

description: Library name: CAMA1_shRB1#2_Abema_n2


title: Donor E IRS 3

value: IRS

value: female


title: FF3_38

value: Control


title: FF3_39_redo


title: Donor E HM2 3

value: hair follicle


title: Donor E sbORS 3


title: CAMA1_shRB1#2_DMSO_n3

description: Library name: CAMA1_shRB1#2_DMSO_n3

value: DMSO for 96h


title: Scr Liver 3

value: Liver


title: CAMA1_shRB1#2_DMSO_n4

description: Library name: CAMA1_shRB1#2_DMSO_n4


title: AML12 dCas9-Dnmt3a Pcsk9 sgRNAs Input

data_processing:
Adapters and low quality reads were removed using Trim Galore 0.6.4
Reads were mapped to mm10 using Bowtie2 2.3.5.1 using default parameters
Peaks were called using Macs2 2.1.2
Assembly: mm10
Supplementary files format and content: narrowPeak files for ChIP samples over Input were generated with Macs2 using default settings

growth_protocol: Mecp2-Luciferase fibroblasts were cultured in DMEM supplemented with 10% CCS and antibiotics in 37C with 5% CO2, AML12 were cultured in DMEM with 10% CCS with antibiotics and 1% Insulin-Transferrin-Selenium

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature, quenched and lysed. Chromatin was sonicated using a Covaris M220 ultrasonicator
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit using NEB Multiplex Oligos for Illumina Set 1 Primers. 10 ng DNA was used as starting material. 10 cycles of enrichment were used for amplification.

value: Hepatocyte


title: AML12 dCas9-Dnmt3a Scr sgRNA Input


title: Donor E gHM 3

value: gHM


title: CAMA1_shRB1#2_DMSO_n2

description: Library name: CAMA1_shRB1#2_DMSO_n2


title: FF5_15


title: FF3_18


title: FF3_17


title: AML12 Mock Input


title: Donor E DP 3

value: DP


title: Donor E DC 3

value: untreated


title: CAMA1_shRB1#2_DMSO_n1

description: Library name: CAMA1_shRB1#2_DMSO_n1

value: HR+ BC cell line


title: FF3_19


title: Donor D CTS 6


title: CAMA1_shRB1#1_Abema_n3

description: Library name: CAMA1_shRB1#1_Abema_n3

value: 50nM Abemaciclib for 96h


title: AML12 dCas9-Dnmt3a Pcsk9 sgRNAs

value: Cas9 (Active Motif 8C1-F10)


title: FF3_20

value: cortical organoid


title: CAMA1_shRB1#1_Abema_n4

description: Library name: CAMA1_shRB1#1_Abema_n4

value: forward


title: Pool-4-ACAGTGAT

value: fibroblast


title: CAMA1_shRB1#1_DMSO_n4

description: Library name: CAMA1_shRB1#1_DMSO_n4


title: Fibroblast dCas9-Tet1 Mecp2 Pool sgRNAs Input

source_name: Mecp2-Luciferase Fibroblast

value: Mecp2-Luciferase Fibroblast

value: Fibroblast


title: AML12 dCas9-Dnmt3a alone Input


title: FF3_19_redo


title: Donor D bORS 6

value: bORS

value: female


title: Pool-1-ATCACGAT


title: AML12 dCas9-Dnmt3a alone

description: dC-D


title: Donor D sbORS 6

value: hair follicle

value: sbORS


title: Donor D gHM 6


title: CAMA1_shRB1#1_Abema_n2

description: Library name: CAMA1_shRB1#1_Abema_n2


title: CAMA1_shRB1#1_Abema_n1

description: Library name: CAMA1_shRB1#1_Abema_n1


title: AML12 Mock

description: Mock-D


title: Donor D IRS 6

value: IRS


title: Nor_GFP_3

city: Seoul

first: Mi-Kyung

last: Oh

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences

country: South Korea

institute: Seoul National University

description: Library name: NG_3

data_processing:
cutadapt
miRDeep2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of raw counts of all samples

source_name: WJ-MSCs

extract_protocol:
Trizol
The RNA isolated from each sample was used to construct sequencing libraries with the SMARTer smRNA-Seq Kit for Illumina, following the manufacturer's protocol. Briefly, Input RNA is first polyadenylated in order to provide a priming sequence for an oligo-(dT) primer. cDNA synthesis is primed by the 3’ smRNA dT Primer, which incorporates an adapter sequence at the 5’ end of each first-strand cDNA molecule. When the MMLV-derived PrimeScript™ Reverse Transcriptase (RT) reaches the 5’ end of each RNA template, it adds nontemplated nucleotides which are bound by the SMART smRNA Oligo-enhanced with locked nucleic acid (LNA) technology for greater sensitivity. In the template-switching step, PrimeScript RT uses the SMART smRNA Oligo as a template for the addition of a second adapter sequence to the 3’ end of each first-strand cDNA molecule. In the next step, full-length Illumina adapters (including index sequences for sample multiplexing) are added during PCR amplification. The Forward PCR Primer binds to the sequence added by the SMART smRNA Oligo, while the Reverse PCR Primer binds to the sequence added by the 3’ smRNA dT Primer. Resulting library cDNA molecules include sequences required for clustering on an Illumina flow cell.

value: WJ-MSCs

value: Normoxia+GFP transfection


title: Donor D HM2 6

data_processing:
Sequencing was performed on a NovaSeq 6000 using 2x100 bp read length with an output of appr. 50 M clusters (10 Gb) per sample.
Demultiplexing: Illumina bcl2fastq v2.20; adapter trimming: Skewer v0.2.2; Pico v2 SMART adapter trimming: Cutadapt v1.12.
Quality trimming of the reads was not performed. The quality of the FASTQ files was analyzed with FastQC v0.11.9.
Trimmed raw reads were aligned to a GRCh38.105 reference using STAR (version 2.7.10a). Only samples with a mapping rate > 50% and a phred score > 30 were included in the analysis.
Normalized counts were created using DESeq2 v1.28.1 in R v4.0.2.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: Pool-3-CCGTCCCG

city: Santa Monica


title: CAMA1_shCTL_Abema_n4

description: Library name: CAMA1_shCTL_Abema_n4

value: ShCTL


title: Fibroblast dCas9-Tet1 Mecp2 Pool sgRNAs

description: dC-T-Pool


title: AML12 dCas9-Dnmt3a Scr sgRNA

description: dC-D-Scr

value: Hepatocyte


title: CAMA1_shRB1#1_DMSO_n3

description: Library name: CAMA1_shRB1#1_DMSO_n3

value: HR+ BC cell line

value: DMSO for 96h


title: Donor A HM2 3

value: untreated


title: Fibroblast dCas9-Tet1 Scr sgRNA Input


title: CAMA1_shRB1#1_DMSO_n2

description: Library name: CAMA1_shRB1#1_DMSO_n2


title: Fibroblast dCas9-Tet1 alone Input


title: CAMA1_shRB1#1_DMSO_n1

description: Library name: CAMA1_shRB1#1_DMSO_n1


title: Donor D DP 6

value: DP


title: Donor A gHM 3

value: gHM


title: Nor_GFP_2

description: Library name: NG_2


title: Nor_GFP_1

description: Library name: NG_1


title: Fibroblast Mock Input


title: Donor A DC 3

value: DC


title: Hyp_BMI_2

description: Library name: HB_2

value: Hypoxia+BMI1 transfection


title: CAMA1_shCTL_Abema_n1

description: Library name: CAMA1_shCTL_Abema_n1

value: 50nM Abemaciclib for 96h

value: forward


title: CAMA1_shCTL_DMSO_n4

description: Library name: CAMA1_shCTL_DMSO_n4


title: CAMA1_shCTL_Abema_n3

description: Library name: CAMA1_shCTL_Abema_n3


title: Scr_3

data_processing:
low quality reads were filtered using fastQC
reads comparing Pcsk9 vs Scr samples were mapped to either mm39 using Hisat2 v2.0.5, reads comparing Mecp2 Pool to Scr samples were mapped to mm10 using STAR 2.5.0a
normalized read count data was obtained using featureCounts v1.5.0-p3
Assembly: mm39, mm10
Supplementary files format and content: tab-delimited text file contains normalized counts data for Pcsk9 vs Scr samples
Supplementary files format and content: tab-delimited text file contains normalized counts data for Mecp2 Pool vs Scr samples

growth_protocol: Mecp2-Luciferase fibroblasts were cultured in DMEM supplemented with 10% CCS and antibiotics in 37C with 5% CO2

extract_protocol:
RNA was extracted using Zymo Direct-zol RNA miniprep kit
mRNA was purified from total RNA using poly-T beads and fragmented, then reverse transcribed into cDNA. Adapters were then ligated and PCR amplified with specified indices before sequencing

value: Mecp2-Luciferase Fibroblast

value: Fibroblast

value: Scr sgRNA


title: Hyp_BMI_3

description: Library name: HB_3


title: Fibroblast dCas9-Tet1 Scr sgRNA

description: dC-T-Scr

value: Cas9 (Active Motif 8C1-F10)


title: Fibroblast Mock

description: Mock-T


title: Fibroblast dCas9-Tet1 alone

description: dC-T


title: CAMA1_shCTL_Abema_n2

description: Library name: CAMA1_shCTL_Abema_n2


title: Donor B CTS 7

value: hair follicle

value: CTS

value: male


title: DNV_205_8

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Library name: DNV_205_8

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (TrimGalore), then mapped to mRatBN7.2.112 whole genome using STAR 2.7.3a with default parameters. Count matrices were generated using featureCounts v2.0.3 (-B -C -t exon -p --countReadPairs -s 2) and DESeq2 1.44 used to calculate normalized counts and perform differential expression analysis.
Assembly: mRatBN7.2.112
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text files includes DESeq2 normalized counts for all samples
Supplementary files format and content: tab-delimited text files includes differential gene expression analysis output from DESeq2

organism: Rattus norvegicus

source_name: Skeletal muscle (diaphragm)

extract_protocol:
Total RNA was extracted from the diaphragm using TRIzol (Life Technologies, Carlsbad, CA). RNA integrity was analyzed using Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).
Approximately ~1 ug of sample total RNA was used for cDNA library preparation performed according to the Illumina mRNA stranded poly-A tail enrichment Kit manufacturer’s instructions (Illumina, San Diego, CA). RNA sequencing was carried out using the Illumina NextSeq 2000 (NextSeq 2x100pb, 8.4-13.9 million paired-end reads depth).

value: Wistar

value: Skeletal muscle (diaphragm)

value: WT

value: Unilateral diaphragm denervation 12 h + MuRF1 inhibitor (MyoMed-205)


title: Donor B sbORS 7

value: sbORS

value: untreated


title: Donor A IRS 3

value: IRS

value: female


title: CAMA1_shCTL_DMSO_n2

description: Library name: CAMA1_shCTL_DMSO_n2

value: HR+ BC cell line

value: ShCTL

value: DMSO for 96h


title: CAMA1_shCTL_DMSO_n3

description: Library name: CAMA1_shCTL_DMSO_n3

value: forward


title: Donor B IRS 7


title: Scr_2

value: Mecp2-Luciferase Fibroblast

value: Fibroblast

value: Scr sgRNA


title: Hyp_BMI_1

description: Library name: HB_1

value: WJ-MSCs

value: Hypoxia+BMI1 transfection


title: Donor B bORS 7

value: hair follicle

value: bORS

value: male


title: DNV_205_7

description: Library name: DNV_205_7

value: Wistar

value: Skeletal muscle (diaphragm)

value: WT

value: Unilateral diaphragm denervation 12 h + MuRF1 inhibitor (MyoMed-205)


title: Mecp2 Pool 3

value: Mecp2 Pool sgRNAs


title: CAMA1_WT_Abema_n4

description: Library name: CAMA1_WT_Abema_n4

value: HR+ BC cell line

value: 50nM Abemaciclib for 96h


title: DNV_205_6

description: Library name: DNV_205_6


title: DNV_205_5

description: Library name: DNV_205_5


title: Mecp2 Pool 2


title: CAMA1_shCTL_DMSO_n1

description: Library name: CAMA1_shCTL_DMSO_n1

value: ShCTL

value: DMSO for 96h