title: si-NEXN+PDGF-BB, rep1

description:
Library name: sample 4
1_genes_fpkm_expression.txt


title: 48558_C045-

status: Public on May 16 2025

type: SRA

city: Duarte

first: Eric

middle: Gunnar

last: Carlson

state: CA

address: 1500 E. Duarte Rd.

department: Population Sciences

country: USA

institute: Irell & Manella Graduate School of Biological Sciences

description:
Library name: Sample 29
column name in raw_counts_All_samples.csv: 48558_C045_neg.bam.count; row names: ENSEMBL_SYMBOL

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed to remove sequencing adapters using Trimmomatic
The processed reads were mapped back to the human genome (hg19) using TOPHAT2 software
HTSeq (37) and RSeQC (38) software packages were applied to generate the count matrices and strand information, respectively, using default parameters
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: human peri-epithelial breast fibroblast

growth_protocol: Peri-epithelial mammary fibroblasts were maintained in M87A supplemented with 5% fetabl bovine serum in an incubator with 5% CO2 at 37° C

extract_protocol:
RNA extraction from the sorted cells was performed using a Quick-RNA Microprep kit with Zymo-Spin IC columns (Zymo Research, catalog no. R1050)
RNA-seq libraries were prepared using KAPA RNA mRNA HyperPrep Kit (KAPABiosystems, catalog no. KR1352) according to the manufacturer’s protocol

treatment_protocol: Fibroblasts were sorted into CD105+ and CD105- subtypes using an ARIAIII FACS instrument

tag: publication sample_name

tag: cell type

value: human peri-epithelial breast fibroblast

tag: cd105 expression

value: negative


title: 48557_122_pos

description:
Library name: Sample 28
column name in raw_counts_All_samples.csv: 48557_122_pos.bam.count; row names: ENSEMBL_SYMBOL

value: positive


title: 48556_122-

description:
Library name: Sample 27
column name in raw_counts_All_samples.csv: 48556_122_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48553_112_pos

description:
Library name: Sample 24
column name in raw_counts_All_samples.csv: 48553_112_pos.bam.count; row names: ENSEMBL_SYMBOL


title: NC+PDGF-BB, rep1

city: Guangzhou

first: Hanyan

last: Yang

address: Zhujiang Hospital, Southern Medical University, Haizhu District, Guangzhou City, Guangdong Province

country: China

institute: Southern Medical University

description:
Library name: sample 1
1_genes_fpkm_expression.txt

data_processing:
Step 1: Use Fastp software (https://github.com/OpenGene/fastp) to filter out reads with adapter contamination, low quality, and undetermined bases, and verify sequence quality.
Step 2: Employ HISAT2 (https://ccb.jhu.edu/software/hisat2) for read mapping to the Homo sapiens GRCh38 reference genome.
Step 3: Use StringTie (https://ccb.jhu.edu/software/stringtie) to assemble the mapped reads and merge transcriptomes across samples to reconstruct a comprehensive transcriptome, which was further refined using gffcompare (https://github.com/gpertea/gffcompare/).
Step 4: Estimate expression levels with StringTie, calculating FPKM values for mRNAs.
Step 5: Conduct differential expression analysis with edgeR, identifying mRNAs with a |log2(FC)|>1 (fold change > 2 or < 0.5) and a P - value < 0.05 from parametric F - tests.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

molecule: total RNA

source_name: human aortic isolated SMCs (HASMCs)

growth_protocol: Primary human aortic smooth muscle cells (HASMCs) were sourced from iCell Bioscience Inc. (catalog number: HUM-iCell-c010) and cultured in proprietary low-serum medium (PriMed-iCell-004) in strict adherence to the manufacturer's guidelines. These cells were meticulously cultivated under controlled conditions in a humidified incubator at a temperature of 37°C, with an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted and purified using TRIzol Reagent (Invitrogen, 15596026). Its quantity and purity were measured with a NanoDrop ND - 1000. RNA integrity was ensured with a RIN score above 7.0, assessed by Bioanalyzer 2100 and agarose gel electrophoresis. Poly(A) RNA was selected from total RNA using Dynabeads Oligo (dT) 25 - 61005.
The selected poly(A) RNA fragments were reverse - transcribed into cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649). Then, it was converted into U - labeled second - stranded DNAs. An A - base was added to the ends for adapter ligation. Indexed adapters were ligated to the A - tailed DNA, and products were size - selected with AMPureXP beads. After UDG enzyme (NEB, cat.m0280) treatment, the products were amplified by PCR. The final cDNA library had an average insert size of 300±50 bp.

treatment_protocol: HASMCs were pre-transfected with NC or si-NEXN. and then followed by PDGF-BB stimulation for 24h.

value: human aortic isolated SMCs (HASMCs)

tag: treatment

value: Pre - transfect with NC, then stimulate with PDGF - BB for 24 h


title: 48555_C094_pos

description:
Library name: Sample 26
column name in raw_counts_All_samples.csv: 48555_C094_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48554_C094-

description:
Library name: Sample 25
column name in raw_counts_All_samples.csv: 48554_C094_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48550_117-

description:
Library name: Sample 21
column name in raw_counts_All_samples.csv: 48550_117_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48551_117_pos

description:
Library name: Sample 22
column name in raw_counts_All_samples.csv: 48551_117_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48552_112-

description:
Library name: Sample 23
column name in raw_counts_All_samples.csv: 48552_112_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48548_169-

description:
Library name: Sample 19
column name in raw_counts_All_samples.csv: 48548_169_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48549_169_pos

description:
Library name: Sample 20
column name in raw_counts_All_samples.csv: 48549_169_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48547_C023_pos

description:
Library name: Sample 18
column name in raw_counts_All_samples.csv: 48547_C023_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48546_C023-

description:
Library name: Sample 17
column name in raw_counts_All_samples.csv: 48546_C023_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48545_C147_pos

description:
Library name: Sample 16
column name in raw_counts_All_samples.csv: 48545_C147_pos.bam.count; row names: ENSEMBL_SYMBOL


title: Bbs5_12 wks_mut_B6

city: London

first: Naila

last: Haq

state: London

address: Room HB4.2E, 2nd Floor, Hodgkin Building, Guy's Campus, London Bridge,

country: United Kingdom

institute: King's College London

description: Library name: Sample 5

data_processing:
TopHat and Bowtie
SAMtools
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw conts for each samples
Supplementary files format and content: tab-delimited text files include RPKM for each samples
Supplementary files format and content: excel files for analyses

organism: Mus musculus

source_name: Hypothalamic tissue

growth_protocol: No growth protocol

extract_protocol:
Core hypothalamic tissues of 12 weeks old Bbs5 male (3 knockouts and 2 controls littermates) mice were isolated using brain tissue slicer and micro-puncher (Integra-Miltex).
Sample libraries were prepared with the NEBNext® UltraTM Directional RNA Library Prep for Illumina® kit (New England Biolabs, Inc.).

treatment_protocol: no treatment protocol

tag: tissue

value: Hypothalamic tissue

value: neuronal

tag: genotype

value: Bbs5_12 wks_mut(B6)

value: no treatment


title: 48544_C147-

description:
Library name: Sample 15
column name in raw_counts_All_samples.csv: 48544_C147_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48543_C051_pos

description:
Library name: Sample 14
column name in raw_counts_All_samples.csv: 48543_C051_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48541_C073_pos

description:
Library name: Sample 12
column name in raw_counts_All_samples.csv: 48541_C073_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48542_C051-

description:
Library name: Sample 13
column name in raw_counts_All_samples.csv: 48542_C051_neg.bam.count; row names: ENSEMBL_SYMBOL


title: si-NEXN+PDGF-BB, rep2

description:
Library name: sample 5
1_genes_fpkm_expression.txt

value: Pre - transfect with si-NEXN, then stimulate with PDGF - BB for 24 h


title: 48540_C073-

description:
Library name: Sample 11
column name in raw_counts_All_samples.csv: 48540_C073_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48537_C145_pos

description:
Library name: Sample 8
column name in raw_counts_All_samples.csv: 48537_C145_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48538_051L-

description:
Library name: Sample 9
column name in raw_counts_All_samples.csv: 48538_051L_neg.bam.count; row names: ENSEMBL_SYMBOL


title: NC+PDGF-BB, rep2

description:
Library name: sample 2
1_genes_fpkm_expression.txt


title: 48539_051L_pos

description:
Library name: Sample 10
column name in raw_counts_All_samples.csv: 48539_051L_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48536_C145-

description:
Library name: Sample 7
column name in raw_counts_All_samples.csv: 48536_C145_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48559_C045_pos

description:
Library name: Sample 30
column name in raw_counts_All_samples.csv: 48559_C045_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48534_C078-

description:
Library name: Sample 5
column name in raw_counts_All_samples.csv: 48534_C078_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48535_C078_pos

description:
Library name: Sample 6
column name in raw_counts_All_samples.csv: 48535_C078_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48530_160-

description:
Library name: Sample 1
column name in raw_counts_All_samples.csv: 48530_160_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48532_240-

description:
Library name: Sample 3
column name in raw_counts_All_samples.csv: 48532_240_neg.bam.count; row names: ENSEMBL_SYMBOL


title: 48533_240_pos

description:
Library name: Sample 4
column name in raw_counts_All_samples.csv: 48533_240_pos.bam.count; row names: ENSEMBL_SYMBOL


title: 48531_160_pos

description:
Library name: Sample 2
column name in raw_counts_All_samples.csv: 48531_160_pos.bam.count; row names: ENSEMBL_SYMBOL


title: WCM929_Z1, RRBS

city: Boston

first: Kei

last: Mizuno

state: MASSACHUSETTS

address: 450 Brookline Avenue

institute: Dana-Farber Cancer institute

description: Library name: Sample98

library_source: genomic

data_processing:
Raw sequencing data were processed using the Bismark pipeline, which encompassed quality control, alignment with the GRCh37 reference genome, and methylation calling.
Assembly: GRCh37
Supplementary files format and content: mincov0.txt file

molecule: genomic DNA

source_name: Bladder

extract_protocol:
Reduced representation bisulfite sequencing was performed according to the manufacturer’s protocol.
Library preparation for reduced representation bisulfite sequencing samples was performed according to the manufacturer’s protocol

value: Bladder

tag: disease state

value: advanced prostate cancer


title: WCM90_Z21, eRRBS

description: Library name: Sample97

source_name: Liver

value: Liver


title: WCM90_Z1, eRRBS

description: Library name: Sample96


title: Multiome_snATAC-seq

city: Chicago

first: Mazhar

last: Adli

state: IL

address: 303 E. Superior St

department: Department of Obstetrics & Gynecology

institute: Northwestern University

description:
Library name: HGSOC_Epithelial-Enriched_Tumor_snATAC-seq
10X Genomics

library_source: genomic single cell

data_processing:
FASTQ files were demultiplexed using 10X Genomics' Cellranger
FASTQ files were aligned to GRCh38 using 10X Genomics' Cellranger-arc v. 2.0.2 using default settings
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: High grade serous ovarian cancer

extract_protocol:
The fresh tissues were washed with cold PBS and first mechanically disrupted to generate small pieces. Then, they were subjected to enzymatic digestion with the Tissue Dissociation Kit (Miltenyi Biotec, 130-095-929) following the manufacturer’s instructions. Enzymatic digestion was carried out for 2 hours at 37° C with shaking at 350 rpm. The digested samples were then filtered through 70 micron cell strainers and subjected to the red-blood cell lysis using RBC lysis buffer (eBioScience, 00-4333-57). Cells were counted and subjected to the tumor cell enrichment. For the tumor cell enrichment, we used the tumor cell isolation kit (Miltenyi Biotec, 130-108-339) following the manufacturer’s instructions.
The isolated nuclei were immediately used for transposition, followed by GEM generation and barcoding, cleanup and library pre-amplification PCR following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide (10X Genomics, Rev E). The pre-amplified samples were used to generate ATAC library construction and cDNA amplification for Gene Expression library construction.

value: High grade serous ovarian cancer


title: WCM90_1, eRRBS

description: Library name: Sample93

source_name: LN

value: LN


title: WCM90_2, eRRBS

description: Library name: Sample94


title: WCM90_3, eRRBS

description: Library name: Sample95

source_name: Bone

value: Bone


title: WCM677_4, eRRBS

description: Library name: Sample91


title: WCM677_5, eRRBS

description: Library name: Sample92

source_name: Lung

value: Lung


title: WCM677_2, eRRBS

description: Library name: Sample89

source_name: Peritoneum

value: Peritoneum


title: WCM677_3, eRRBS

description: Library name: Sample90


title: WCM677_1, eRRBS

description: Library name: Sample88


title: WCM63_Z7, RRBS

description: Library name: Sample85

source_name: Diaphragm

value: Diaphragm


title: WCM63_Z8, RRBS

description: Library name: Sample86


title: WCM63_Z6, RRBS

description: Library name: Sample84


title: WCM63_Z9, RRBS

description: Library name: Sample87


title: WCM63_Z5, RRBS

description: Library name: Sample83


title: WCM63_Z4, RRBS

description: Library name: Sample82


title: WCM59_Z2, eRRBS

description: Library name: Sample79


title: WCM63_Z11, RRBS

description: Library name: Sample80


title: WCM493_Z1, RRBS

description: Library name: Sample78

source_name: Brain

value: Brain


title: WCM3672_Z1, RRBS

description: Library name: Sample76


title: WCM3574_Z4, RRBS

description: Library name: Sample75


title: Multiome_snRNA-seq

description:
Library name: HGSOC_Epithelial-Enriched_Tumor_snRNA-seq
10X Genomics

library_source: transcriptomic single cell

molecule: nuclear RNA


title: WCM3672_Z2, RRBS

description: Library name: Sample77


title: WCM63_Z3, RRBS

description: Library name: Sample81


title: WCM3574_Z3, RRBS

description: Library name: Sample74


title: WCM2939_Z4, RRBS

description: Library name: Sample70


title: WCM3574_Z1, RRBS

description: Library name: Sample72


title: WCM2939_Z2, RRBS

description: Library name: Sample68


title: WCM2848_X1, RRBS

description: Library name: Sample67

source_name: Prostate

value: Prostate


title: WCM2939_Z6, RRBS

description: Library name: Sample71


title: WCM2596_Z1, RRBS

description: Library name: Sample64


title: WCM2549_Z6, RRBS

description: Library name: Sample62


title: WCM3574_Z2, RRBS

description: Library name: Sample73

source_name: Kidney

value: Kidney


title: WCM258_Z2, RRBS

description: Library name: Sample63


title: WCM2549_Z5, RRBS

description: Library name: Sample61


title: WCM2549_Z4, RRBS

description: Library name: Sample60

source_name: Adrenal gland

value: Adrenal gland


title: WCM2698_Z1, RRBS

description: Library name: Sample65


title: WCM2738_Z1, RRBS

description: Library name: Sample66


title: WCM2939_Z3, RRBS

description: Library name: Sample69


title: WCM2549_Z3, RRBS

description: Library name: Sample59


title: WCM2549_Z2, RRBS

description: Library name: Sample58


title: WCM2549_Z1, RRBS

description: Library name: Sample57


title: WCM2343_Z1, RRBS

description: Library name: Sample55


title: WCM2524_Z1, RRBS

description: Library name: Sample56

source_name: Dura mater

value: Dura mater


title: WCM2086_Z1, RRBS

description: Library name: Sample54


title: WCM191_Z8, RRBS

description: Library name: Sample53


title: WCM159_3, eRRBS

description: Library name: Sample51


title: WCM159_Z6, eRRBS

description: Library name: Sample52


title: WCM159_2, eRRBS

description: Library name: Sample50


title: WCM1358_Z4, RRBS

description: Library name: Sample48


title: WCM159_1, eRRBS

description: Library name: Sample49


title: WCM1358_Z3, RRBS

description: Library name: Sample47


title: WCM1358_Z2, RRBS

description: Library name: Sample46


title: WCM1358_Z1, RRBS

description: Library name: Sample45


title: WCM1089_Z3, RRBS

description: Library name: Sample43


title: WCM1089_Z2, RRBS

description: Library name: Sample42


title: WCM12_Z13, eRRBS

description: Library name: Sample44


title: WCM1089_Z1, RRBS

description: Library name: Sample41


title: WCM1070_Z7, RRBS

description: Library name: Sample39


title: WCM1070_Z4, RRBS

description: Library name: Sample36


title: WCM1070_Z5, RRBS

description: Library name: Sample37


title: WCM1024_Z1, RRBS

description: Library name: Sample35


title: WCM0_PM2, eRRBS

description: Library name: Sample34

source_name: Pelvic mass

value: Pelvic mass


title: WCM0_LM1A, eRRBS

description: Library name: Sample33


title: WCM0_3, eRRBS

description: Library name: Sample31


title: WCM0_4, eRRBS

description: Library name: Sample32


title: WCM0_2, eRRBS

description: Library name: Sample30


title: WCM0_1, eRRBS

description: Library name: Sample29


title: DFCI53_Z1, RRBS

description: Library name: Sample26


title: DFCI53_Z2, RRBS

description: Library name: Sample27


title: WCM1070_Z6, RRBS

description: Library name: Sample38


title: DFCI46_Z5, RRBS

description: Library name: Sample25


title: DFCI46_Z4, RRBS

description: Library name: Sample24


title: DFCI53_Z3, RRBS

description: Library name: Sample28


title: DFCI46_Z3, RRBS

description: Library name: Sample23


title: DFCI46_Z1, RRBS

description: Library name: Sample21


title: DFCI46_Z2, RRBS

description: Library name: Sample22


title: DFCI24_Z2, RRBS

description: Library name: Sample19


title: DFCI24_Z3, RRBS

description: Library name: Sample20


title: DFCI23_Z3, RRBS

description: Library name: Sample17


title: DFCI23_Z2, RRBS

description: Library name: Sample16


title: DFCI24_Z1, RRBS

description: Library name: Sample18


title: DFCI23_Z1, RRBS

description: Library name: Sample15


title: WCM1070_Z8, RRBS

description: Library name: Sample40


title: DFCI20_Z3, RRBS

description: Library name: Sample14


title: DFCI20_Z2, RRBS

description: Library name: Sample13


title: DFCI19_Z1, RRBS

description: Library name: Sample11


title: CA0090_Z6, RRBS

description: Library name: Sample9


title: CA0090_Z5, RRBS

description: Library name: Sample8


title: CA0090_Z3, RRBS

description: Library name: Sample6


title: CA0090_Z4, RRBS

description: Library name: Sample7


title: CA0046_Z3, eRRBS

description: Library name: Sample3


title: CA0046_Z2, eRRBS

description: Library name: Sample2


title: WCM90_Z21, H3K27me3, ChIP-seq

description: Library name: Sample266

data_processing:
We used Bowtie2 to map the reads to GRCh37, and extracted uniquely mapped reads.
The data were processed using the MACS2 pipeline for peak calling. We used the “-f BAM” flag with a genome size of 2.7e9 and the standard FDR threshold of 0.01. For H3K27me3 data, the flag “--broad” was used.
Assembly: GRCh37
Supplementary files format and content: bigwig

extract_protocol:
ChIP-seq was performed according to the manufacturer’s protocol.
Library preparation for ChIP-seq samples was performed according to the manufacturer’s protocol


title: CA0090_Z2, RRBS

description: Library name: Sample5


title: WCM90_Z21, H3K27ac, ChIP-seq

description: Library name: Sample265


title: CA0046_Z1, eRRBS

description: Library name: Sample1


title: WCM677_3, H3K27me3, ChIP-seq

description: Library name: Sample264


title: WCM677_3, H3K27ac, ChIP-seq

description: Library name: Sample263


title: WCM677_1, H3K27ac, ChIP-seq

description: Library name: Sample261


title: WCM677_1, H3K27me3, ChIP-seq

description: Library name: Sample262


title: WCM159_Z6, H3K27me3, ChIP-seq

description: Library name: Sample260


title: WCM159_Z6, H3K27ac, ChIP-seq

description: Library name: Sample259


title: WCM159_2, H3K27ac, ChIP-seq

description: Library name: Sample257


title: WCM159_1, H3K27me3, ChIP-seq

description: Library name: Sample256


title: WCM159_2, H3K27me3, ChIP-seq

description: Library name: Sample258


title: WCM12_Z13, H3K27me3, ChIP-seq

description: Library name: Sample254


title: WCM12_Z13, H3K27ac, ChIP-seq

description: Library name: Sample253


title: DFCI16_Z1, RRBS

description: Library name: Sample10


title: WCM0_4, H3K27me3, ChIP-seq

description: Library name: Sample252


title: DFCI20_Z1, RRBS

description: Library name: Sample12

source_name: Pleura

value: Pleura


title: WCM159_1, H3K27ac, ChIP-seq

description: Library name: Sample255


title: WCM0_3, H3K27ac, ChIP-seq

description: Library name: Sample249


title: WCM0_4, H3K27ac, ChIP-seq

description: Library name: Sample251


title: WCM0_2, H3K27ac, ChIP-seq

description: Library name: Sample247


title: WCM0_2, H3K27me3, ChIP-seq

description: Library name: Sample248


title: WCM63_Z9, H3K27me3, CUT&Tag

description: Library name: Sample246

data_processing:
We used Bowtie2 to map the reads to GRCh37, and extracted uniquely mapped reads.
the data were processed using the MACS2 pipeline for peak calling. We used the “-f BAMPE” flag with a genome size of 2.7e9 and the standard FDR threshold of 0.01. For H3K27me3 data, the flag “--broad” was used.
Assembly: GRCh37
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed according to the manufacturer’s protocol.
Library preparation for CUT&Tag samples was performed according to the manufacturer’s protocol


title: CA0090_Z1, RRBS

description: Library name: Sample4


title: WCM63_Z9, H3K27ac, CUT&Tag

description: Library name: Sample245


title: WCM63_Z8, H3K27me3, CUT&Tag

description: Library name: Sample244


title: WCM63_Z8, H3K27ac, CUT&Tag

description: Library name: Sample243


title: WCM63_Z7, H3K27ac, CUT&Tag

description: Library name: Sample241


title: WCM63_Z7, H3K27me3, CUT&Tag

description: Library name: Sample242


title: WCM63_Z6, H3K27me3, CUT&Tag

description: Library name: Sample240


title: WCM63_Z6, H3K27ac, CUT&Tag

description: Library name: Sample239


title: WCM63_Z4, H3K27me3, CUT&Tag

description: Library name: Sample236


title: WCM63_Z5, H3K27me3, CUT&Tag

description: Library name: Sample238


title: WCM63_Z4, H3K27ac, CUT&Tag

description: Library name: Sample235


title: WCM63_Z3, H3K27me3, CUT&Tag

description: Library name: Sample234


title: WCM63_Z11, H3K27me3, CUT&Tag

description: Library name: Sample232


title: WCM63_Z11, H3K27ac, CUT&Tag

description: Library name: Sample231


title: WCM0_3, H3K27me3, ChIP-seq

description: Library name: Sample250


title: WCM63_Z3, H3K27ac, CUT&Tag

description: Library name: Sample233


title: WCM493_Z1, H3K27ac, CUT&Tag

description: Library name: Sample229


title: WCM493_Z1, H3K27me3, CUT&Tag

description: Library name: Sample230


title: WCM2848_X1, H3K27me3, CUT&Tag

description: Library name: Sample228


title: WCM2549_Z6, H3K27ac, CUT&Tag

description: Library name: Sample226


title: WCM2549_Z5, H3K27me3, CUT&Tag

description: Library name: Sample225


title: WCM2549_Z4, H3K27me3, CUT&Tag

description: Library name: Sample223


title: WCM2549_Z3, H3K27me3, CUT&Tag

description: Library name: Sample221


title: WCM2549_Z5, H3K27ac, CUT&Tag

description: Library name: Sample224


title: WCM2549_Z4, H3K27ac, CUT&Tag

description: Library name: Sample222


title: WCM2549_Z3, H3K27ac, CUT&Tag

description: Library name: Sample220


title: WCM2549_Z1, H3K27ac, CUT&Tag

description: Library name: Sample216


title: WCM2549_Z1, H3K27me3, CUT&Tag

description: Library name: Sample217


title: WCM1358_Z3, H3K27ac, CUT&Tag

description: Library name: Sample214


title: WCM1358_Z3, H3K27me3, CUT&Tag

description: Library name: Sample215


title: WCM63_Z5, H3K27ac, CUT&Tag

description: Library name: Sample237


title: WCM1358_Z2, H3K27me3, CUT&Tag

description: Library name: Sample213


title: WCM1070_Z8, H3K27me3, CUT&Tag

description: Library name: Sample211


title: WCM1070_Z8, H3K27ac, CUT&Tag

description: Library name: Sample210


title: WCM1070_Z7, H3K27me3, CUT&Tag

description: Library name: Sample209


title: WCM1070_Z6, H3K27me3, CUT&Tag

description: Library name: Sample207


title: WCM1070_Z6, H3K27ac, CUT&Tag

description: Library name: Sample206


title: WCM2549_Z6, H3K27me3, CUT&Tag

description: Library name: Sample227


title: WCM1070_Z4, H3K27me3, CUT&Tag

description: Library name: Sample203


title: WCM1070_Z5, H3K27me3, CUT&Tag

description: Library name: Sample205


title: WCM1070_Z4, H3K27ac, CUT&Tag

description: Library name: Sample202


title: WCM1070_Z7, H3K27ac, CUT&Tag

description: Library name: Sample208


title: DFCI24_Z3, H3K27ac, CUT&Tag

description: Library name: Sample201


title: DFCI24_Z2, H3K27ac, CUT&Tag

description: Library name: Sample199


title: WCM2549_Z2, H3K27ac, CUT&Tag

description: Library name: Sample218


title: WCM929_Z1, RNA-seq

description: Library name: Sample196

data_processing:
The raw sequencing data were processed using the STAR aligner for mapping to the human reference genome (GRCh37).
RSEM was used for quantification of gene expression.
Assembly: GRCh37
Supplementary files format and content: txt file

extract_protocol:
RNA-seq was performed according to the manufacturer’s protocol.
Library preparation for RNA-seq samples was performed according to the manufacturer’s protocol


title: DFCI23_Z3, H3K27ac, CUT&Tag

description: Library name: Sample197


title: WCM90_3, RNA-seq

description: Library name: Sample193


title: WCM90_Z1, RNA-seq

description: Library name: Sample194


title: DFCI23_Z3, H3K27me3, CUT&Tag

description: Library name: Sample198


title: WCM90_1, RNA-seq

description: Library name: Sample191


title: WCM90_2, RNA-seq

description: Library name: Sample192


title: WCM90_Z21, RNA-seq

description: Library name: Sample195


title: DFCI24_Z2, H3K27me3, CUT&Tag

description: Library name: Sample200


title: WCM2549_Z2, H3K27me3, CUT&Tag

description: Library name: Sample219


title: WCM677_4, RNA-seq

description: Library name: Sample189


title: WCM1358_Z2, H3K27ac, CUT&Tag

description: Library name: Sample212


title: WCM677_5, RNA-seq

description: Library name: Sample190


title: WCM677_3, RNA-seq

description: Library name: Sample188


title: WCM677_1, RNA-seq

description: Library name: Sample186


title: WCM677_2, RNA-seq

description: Library name: Sample187


title: WCM1070_Z5, H3K27ac, CUT&Tag

description: Library name: Sample204


title: WCM63_Z7, RNA-seq

description: Library name: Sample183


title: WCM63_Z6, RNA-seq

description: Library name: Sample182


title: WCM63_Z4, RNA-seq

description: Library name: Sample180


title: WCM63_Z5, RNA-seq

description: Library name: Sample181


title: WCM63_Z3, RNA-seq

description: Library name: Sample179


title: WCM63_Z11, RNA-seq

description: Library name: Sample178


title: WCM59_Z2, RNA-seq

description: Library name: Sample177


title: WCM3672_Z1, RNA-seq

description: Library name: Sample174


title: WCM3672_Z2, RNA-seq

description: Library name: Sample175


title: WCM3574_Z2, RNA-seq

description: Library name: Sample171


title: WCM3574_Z3, RNA-seq

description: Library name: Sample172


title: WCM3574_Z4, RNA-seq

description: Library name: Sample173


title: WCM2939_Z6, RNA-seq

description: Library name: Sample169


title: WCM2939_Z4, RNA-seq

description: Library name: Sample168


title: WCM2738_Z1, RNA-seq

description: Library name: Sample164


title: WCM2848_X1, RNA-seq

description: Library name: Sample165


title: WCM2939_Z2, RNA-seq

description: Library name: Sample166


title: WCM2939_Z3, RNA-seq

description: Library name: Sample167


title: WCM258_Z2, RNA-seq

description: Library name: Sample161


title: WCM2549_Z6, RNA-seq

description: Library name: Sample160


title: WCM2698_Z1, RNA-seq

description: Library name: Sample163


title: WCM2549_Z4, RNA-seq

description: Library name: Sample158


title: WCM63_Z9, RNA-seq

description: Library name: Sample185


title: WCM63_Z8, RNA-seq

description: Library name: Sample184


title: WCM2549_Z1, RNA-seq

description: Library name: Sample155


title: WCM2549_Z3, RNA-seq

description: Library name: Sample157


title: WCM2549_Z2, RNA-seq

description: Library name: Sample156


title: WCM2343_Z1, RNA-seq

description: Library name: Sample153


title: WCM2549_Z5, RNA-seq

description: Library name: Sample159


title: WCM493_Z1, RNA-seq

description: Library name: Sample176


title: WCM2524_Z1, RNA-seq

description: Library name: Sample154


title: WCM191_Z8, RNA-seq

description: Library name: Sample151


title: WCM2086_Z1, RNA-seq

description: Library name: Sample152


title: WCM3574_Z1, RNA-seq

description: Library name: Sample170


title: WCM159_3, RNA-seq

description: Library name: Sample149


title: WCM159_Z6, RNA-seq

description: Library name: Sample150


title: WCM1358_Z2, RNA-seq

description: Library name: Sample144


title: WCM159_1, RNA-seq

description: Library name: Sample147


title: WCM1358_Z1, RNA-seq

description: Library name: Sample143


title: WCM1358_Z3, RNA-seq

description: Library name: Sample145


title: WCM2596_Z1, RNA-seq

description: Library name: Sample162


title: WCM159_2, RNA-seq

description: Library name: Sample148


title: WCM1089_Z3, RNA-seq

description: Library name: Sample141


title: WCM12_Z13, RNA-seq

description: Library name: Sample142


title: WCM1070_Z6, RNA-seq

description: Library name: Sample136


title: WCM1070_Z7, RNA-seq

description: Library name: Sample137


title: WCM1089_Z2, RNA-seq

description: Library name: Sample140


title: WCM1070_Z5, RNA-seq

description: Library name: Sample135


title: WCM1070_Z8, RNA-seq

description: Library name: Sample138


title: WCM0_PM2, RNA-seq

description: Library name: Sample132


title: WCM1024_Z1, RNA-seq

description: Library name: Sample133


title: WCM0_LM1A, RNA-seq

description: Library name: Sample131


title: WCM0_4, RNA-seq

description: Library name: Sample130


title: WCM0_3, RNA-seq

description: Library name: Sample129


title: WCM0_2, RNA-seq

description: Library name: Sample128


title: WCM0_1, RNA-seq

description: Library name: Sample127


title: WCM1358_Z4, RNA-seq

description: Library name: Sample146


title: DFCI53_Z1, RNA-seq

description: Library name: Sample124


title: DFCI53_Z3, RNA-seq

description: Library name: Sample126


title: DFCI46_Z4, RNA-seq

description: Library name: Sample122


title: DFCI23_Z3, RNA-seq

description: Library name: Sample115


title: DFCI23_Z2, RNA-seq

description: Library name: Sample114


title: DFCI46_Z1, RNA-seq

description: Library name: Sample119


title: DFCI24_Z2, RNA-seq

description: Library name: Sample117


title: WCM1089_Z1, RNA-seq

description: Library name: Sample139


title: DFCI24_Z1, RNA-seq

description: Library name: Sample116


title: DFCI23_Z1, RNA-seq

description: Library name: Sample113


title: WCM1070_Z4, RNA-seq

description: Library name: Sample134


title: DFCI20_Z1, RNA-seq

description: Library name: Sample110


title: DFCI24_Z3, RNA-seq

description: Library name: Sample118


title: DFCI16_Z1, RNA-seq

description: Library name: Sample108


title: DFCI20_Z3, RNA-seq

description: Library name: Sample112


title: CA0090_Z6, RNA-seq

description: Library name: Sample107


title: DFCI20_Z2, RNA-seq

description: Library name: Sample111


title: DFCI19_Z1, RNA-seq

description: Library name: Sample109


title: CA0090_Z5, RNA-seq

description: Library name: Sample106


title: CA0090_Z4, RNA-seq

description: Library name: Sample105


title: CA0090_Z3, RNA-seq

description: Library name: Sample104


title: CA0090_Z1, RNA-seq

description: Library name: Sample102


title: DFCI46_Z5, RNA-seq

description: Library name: Sample123


title: DFCI53_Z2, RNA-seq

description: Library name: Sample125


title: DFCI46_Z3, RNA-seq

description: Library name: Sample121


title: CA0046_Z3, RNA-seq

description: Library name: Sample101


title: DFCI46_Z2, RNA-seq

description: Library name: Sample120


title: CA0046_Z1, RNA-seq

description: Library name: Sample99


title: KIAA1549:BRAF r4

first: April

last: Apfelbaum

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-farber Cancer Institute

description:
Library name: sample 39
KB4

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 with 2 x 150bp read length. Reads were mapped to a reference genome (GRCh38) from multiple databases (NCBI/UCSC/Ensembl) using Hisat2 v2.0.5. featureCounts v1.5.0-p3was used to count reads and an FPKM (Fragments per Kilobase of transcript per Million mapped reads) value was calculated per gene. Differentially expressed genes for individual comparisons were determined using the DESeq2 package in R, with the resulting P values adjusted using Benjamini and Hochberg’s approach.
Assembly: hg38
Supplementary files format and content: CSV file with raw counts for all samples
Supplementary files format and content: DE analysis results in the paper supplemental files

source_name: immortalized human neural stem cells  (H9)

growth_protocol: H9 Neural stem cells (N7800-100) were immortalized and cultured as cultured as adherent culture on geltrex-coated plates in Tumor Stem Media.

extract_protocol:
RNA was extracted from cells using the TRI reagent protocol. A total of 1 µg of RNA material was used per sample for RNA preparation. The mRNA was purified by poly-T magnetic beads, followed by fragmentation and conversation to cDNA.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.


title: KIAA1549:BRAF r3

description:
Library name: sample 38
KB3

value: immortalized human neural stem cells  (H9)


title: KIAA1549:BRAF r5

description:
Library name: sample 40
KB5


title: KIAA1549:BRAF r2

description:
Library name: sample 37
KB2


title: BRAF V600E r5

description:
Library name: sample 35
V600E5


title: KIAA1549:BRAF r1

description:
Library name: sample 36
KB1


title: BRAF V600E r4

description:
Library name: sample 34
V600E4


title: BRAF V600E r3

description:
Library name: sample 33
V600E3


title: FGFR1-ITD r4

description:
Library name: sample 29
ITD4


title: FGFR1-ITD r5

description:
Library name: sample 30
ITD5


title: BRAF V600E r2

description:
Library name: sample 32
V600E2


title: FGFR1-ITD r3

description:
Library name: sample 28
ITD3


title: FGFR1-ITD r2

description:
Library name: sample 27
ITD2


title: FGFR1-ITD r1

description:
Library name: sample 26
ITD1


title: FGFR1:TACC1 r3

description:
Library name: sample 23
TACC3


title: FGFR1:TACC1 r2

description:
Library name: sample 22
TACC2


title: FGFR1:TACC1 r1

description:
Library name: sample 21
TACC1


title: FGFR1:TACC1 r4

description:
Library name: sample 24
TACC4


title: FGFR1 N546K + PTPN11 E69K r4

description:
Library name: sample 19
F_P4


title: FGFR1 N546K + PTPN11 E69K r3

description:
Library name: sample 18
F_P3


title: FGFR1 N546K + PTPN11 E69K r2

description:
Library name: sample 17
F_P2


title: FGFR1 N546K + PTPN11 E69K r1

description:
Library name: sample 16
F_P1


title: FGFR1 N546K r3

description:
Library name: sample 13
FGFR3


title: FGFR1 N546K r5

description:
Library name: sample 15
FGFR5


title: CA0046_Z2, RNA-seq

description: Library name: Sample100


title: FGFR1 N546K r2

description:
Library name: sample 12
FGFR2


title: FGFR1 N546K r1

description:
Library name: sample 11
FGFR1


title: FGFR1 N546K r4

description:
Library name: sample 14
FGFR4


title: PTPN11 E69K alone r5

description:
Library name: sample 10
PTP5


title: BRAF V600E r1

description:
Library name: sample 31
V600E1


title: PTPN11 E69K alone r4

description:
Library name: sample 9
PTP4


title: PTPN11 E69K alone r1

description:
Library name: sample 6
PTP1


title: Vector control r5

description:
Library name: sample 5
GFP5


title: PTPN11 E69K alone r3

description:
Library name: sample 8
PTP3


title: FGFR1:TACC1 r5

description:
Library name: sample 25
TACC5


title: Vector control r2

description:
Library name: sample 2
GFP2


title: Vector control r3

description:
Library name: sample 3
GFP3


title: Vector control r4

description:
Library name: sample 4
GFP4


title: rs1173771_ref_lowBP_iVSMC cells_region capture Micro-C

city: Tucson

first: Yong

last: Liu

state: AZ

address: The University of Arizona

department: Physiology

institute: University of Arizona

description: Library name: huiEV771CMC_3

data_processing:
Dovetail Micro-C data analysis pipeline was used to generate .hic file for visualization with JuiceBox and .cool file for differential chromatin interaction analysis. Briefly, the sequencing reads were trimmed and cleaned to remove adaptor and low-quality reads with Trim Galore. The cleaned paired sequence reads were aligned to human hg38 genome with bwa. The parse, sort, dedup, and split function of pairtools were sequentially used to record valid ligation event, sort the pairsam file, remove PCR duplicates, and generate .pairs and .bam files, respectively. The .bam file was sorted and indexed with samtools sort and samtools index, respectively. A QC report was generated by a Python file provided by the pipeline. The contact map file (.hic) was generated by juicer too pre with the generated mapped.pairs file. The compressed mapped.pair (by gbgzip) was used to generate .cool file at 1kb or 5kb resolution by cooler cload_pairix. HiCompare39 was used to statistically compare chromatin interactions between cells with different genotypes.
Assembly: hg38
Supplementary files format and content: hic contact map file

growth_protocol: human iPSC cell line 039B were cultured on dishes coated with Matrigel using mTeSR plus medium

extract_protocol:
Using Dovetail Micro-C Kit following the manufacturer’s User Guide.
Dovetail Micro-C kit was used following manufacturer’s User Guide to create Micro-C libraries. Region capture Micro-C libraries were then generated with reagents from Dovetail targeted enrichment panels. Indexed Micro-C libraries were pooled together to perform region capture Micro-C. The probe panel targeting human chr5: 32,443,700-33,470,100 (hg38) was designed and synthesized by Twist Bioscience. The panel of 80bp probes covers the rs1173771 LD region and promoters of adjacent protein coding genes. The libraries were sequenced using the Illumina NovaSeq sequencers.

treatment_protocol: To induce endothelial lineage differentiation, mesoderm cells were cultured in StemPro-34 SFM medium (STEMCELL Technologies) supplemented with 200 ng/ml VEGF (PeproTech) and 2 µM forskolin (Abcam) for 2 days. On day 6, endothelial cells were purified using CD144 (VE-Cadherin) magnetic beads (Miltenyi Biotec). The purified CD144-positive cells were cultured in StemPro-34 SFM medium with 50 ng/ml VEGF for an additional 6 days before harvest. For VSMC induction, mesoderm cells (on day 4) were cultured in N2B27 medium supplemented with 10 ng/ml PDGF-BB (PeproTech) and 2 ng/ml Activin A (PeproTech) for 2 days. Contractile VSMCs were subsequently induced by culturing in N2B27 medium containing 2 ng/ml Activin A and 2 µg/ml Heparin (STEMCELL Technologies) for 6 days. On day 12, VSMCs were enriched by depleting CD144-positive cells using CD144 magnetic beads. The purified VSMCs were replated and cultured in N2B27 medium supplemented with 2 ng/ml Activin A, 2 µg/ml Heparin, and 1 µM PD0325901 (a MEK inhibitor; Selleck Chemicals) for an additional 6 days before harvest.

tag: cell line

value: iPSC derived vascular smooth muscle cells

value: rs1173771 LD with homozygous ref or lowBP alleles


title: rs1173771_alt_highBP_iVSMC cells_region capture Micro-C

description: Library name: huiEV771CMC_4

value: rs1173771 LD with homozygous alt or highBP alleles


title: FGFR1 N546K + PTPN11 E69K r5

description:
Library name: sample 20
F_P5


title: rs1173771_alt_highBP_iEC cells_region capture Micro-C

description: Library name: huiEV771CMC_2

value: iPSC derived endothelial cells


title: rs1173771_ref_lowBP_iEC cells_region capture Micro-C

description: Library name: huiEV771CMC_1


title: Ahr knocked-out T cells, donor 3, restimulated four times

city: Besançon

first: Valentine

last: De Castro

state: Franche-Comté

address: 8 rue du Dr JFX Girod

country: France

institute: Université de Franche-Comté

data_processing:
Demultiplexing of the sequences was performed using bcl-convert (v4.1.5, Illumina, San Diego, CA, USA). Quality of the sequences and potential contamination were assessed using FastQC (v. 0.11.9), FastQ Screen (v0.15.1) and MultiQC (v1.14).
Sequence reads were trimmed for adaptor sequence/low-quality using trimmomatic v0.39 (with parameters keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:33).
The trimmed sequences were mapped to the indexed human reference genome (GRCh38) using STAR v2.7.8a
read Counts were performed using the function featureCounts of Subread v2.0.3
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count for all samples
Supplementary files format and content: tab-delimited text files includes raw count for each sample

source_name: T cells

growth_protocol: T cells were maintained in RPMI supplemented with 10% human serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C and in presence of IL-2

extract_protocol:
RNA was extracted using Macherey Nagel extraction kit.
Libraries were prepared using Illumina’s Stranded mRNA Prep Ligation kit following manufacturer’s instructions.

value: T cells

value: Ahr KO


title: Control T cells, donor 3, restimulated four times

value: WT


title: Control T cells, donor 3, restimulated once


title: Ahr knocked-out T cells, donor 3, restimulated once


title: Ahr knocked-out T cells, donor 2, restimulated four times


title: Ahr knocked-out T cells, donor 2, restimulated once


title: Control T cells, donor 2, restimulated four times


title: Control T cells, donor 1, restimulated four times


title: Ahr knocked-out T cells, donor 1, restimulated four times


title: Ahr knocked-out T cells, donor 1, restimulated once


title: Control T cells, donor 2, restimulated once


title: PTPN11 E69K alone r2

description:
Library name: sample 7
PTP2


title: Control T cells, donor 1, restimulated once


title: Vector control r1

description:
Library name: sample 1
GFP1


title: TLseq, HEL-RM cells, biological rep 3, dox24h s4U 2h

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

institute: Yale University

data_processing:
Bulk RNAseq (primary murine MKP/ERP): After quality control (FastQC version 0.11.5), reads generated from each sample were aligned to the mouse genome (GRCm38.p3) with STAR (version 2.5.3a,–quantMode GeneCounts), using the Gencode M15 transcript annotation as a transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR Bioconductor package, using a double threshold on the log2 fold change (absolute value >0.5) and corresponding statistical significance (P < 0.05).
Bulk RNAseq (HEL, 6133, CAOM cells): After quality control (FastQC version 0.11.9,  https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ), reads generated from each sample were deduplicated with FastUniq (version 1.1, FastUniq download | SourceForge.net) and aligned to the mouse genome (GRCm39) or the human genome (GRCh38) with STAR (version 2.7.10a, - quantMode GeneCounts), using the Gencode M31 (mouse) and 37 (human) gene annotation, respectively. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR (version 4.2.0) package in Bioconductor (https://bioconductor.org/). Differentially expressed genes were identified with the “glmQLFTest” function, using a double threshold on gene expression changes and associated statistical significance (absolute log2 fold change > 0.75, FDR < 0.05).
eCLIP and m6A eCLIP: Initial peak calling was performed with PureCLIP(Krakau, Richard, and Marsico 2017) (version 1.3.1, https://github.com/skrakau/PureCLIP). Nucleotides with a Hidden state of 3 (enriched + crosslink) were considered potential crosslink nucleotides. The regions of the initial crosslinked nucleotides were extended by 7 nucleotides upstream and downstream, resulting in 15 nucleotide long regions. Overlapping regions on the same strand were merged with the merge Bedtools function. Read coverage on each region for each replicate was quantified with Bedtools coverage. Only regions with a minimum count of 10 among all the replicates in at least 1 condition were considered as regions with sufficient signal. Additionally, for m6A eCLIP, only regions containing at least one A were considered. Read counts for each region were normalized and differential analysis was performed in the same manner as RNA-seq. To identify high-confidence CLIP regions for eCLIP, only regions enriched over both input and control conditions were considered; for m6A eCLIP, only the regions enriched over input were considered (p-value <0.05 and log2 fold enrichment >1).
TimeLapse-seq: Reads were trimmed and aligned with HISAT-3N to the human hg38 genome as described in the TimeLapse preprocessing pipeline (Schofield et al. 2018). After T-to-C mutation calling, bakR and DESeq2 were used to calculate differences in kinetic parameters and gene expression levels across RBM15 overexpression, RM overexpression, and parental control conditions(Love, Huber, and Anders 2014; Vock and Simon 2023). Library size factors were estimated using DESeq2. The cB output file of the TimeLapse preprocessing pipeline was used as a count table in bakR to model transcript-specific changes in RNA degradation and synthesis rates. bakR was run using the hybrid model with all read filtering parameters set to default.
Assembly: 6133 and CAOM experiments: GRCm39. Primary MKP/ERP experiments: GRCh38.p3. HEL cell experiments: GRCh38.
Supplementary files format and content: eCLIP and meCLIP files.bed: bed files indicating peak coverage in CLIP experiments
Supplementary files format and content: HEL_RNAseq_counts.xlsx, 6133_CAOM_METTL3i_RNAseq.xlsx, MKP_WT_1_ReadsPerGene.out.tab, MKP_WT_2_ReadsPerGene.out.tab, ERP_WT_1_ReadsPerGene.out.tab, ERP_WT_2_ReadsPerGene.out.tab: gene counts for indicated RNAseq experiments
Supplementary files format and content: TL-seq: bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos).

source_name: cell line

growth_protocol: HEL cells: RPMI 1640 with 10% tetracycline-negative FBS 1% L-glutamine 1% penicillin-streptomycin, 5μg/mL blasticidin. HEL-RBM15, HEL-RM, and HEL-MKL1 cells were additionally cultured with 375μg/mL hygromycin. 6133 and CAOM cells: RPMI 1640 with 10% FBS, 1% L-glutamine, 1% penicillin-streptomycin, 100ng/mL murine stem cell factor and 10ng/mL murine interleukin 3.

extract_protocol:
HEL cell RNAseq: QIAGEN RNeasy Mini Kit. 6133 and CAOM cell RNAseq: ThermoFisher SCIENTIFIC TRIzol. TL-seq: ThermoFisher SCIENTIFIC TRIzol. eCLIP-seq: Zymo Research RNA Clean & Concentrator-5 kit m6A eCLIP-seq: QIAGEN RNeasy Mini kit with DNAse treatment. ERP/MKP RNAseq: QIAGEN RNeasy Mini Kit.
eCLIP-seq: HEL cells expressing FLAG-tagged RBM15 or RM or empty vector control were UV-crosslinked twice at 2000mJ/cm2 using a Stratalinker at 254nm. Cells were sonicated for a total of 60 seconds in lysis buffer and treated with RNAse 1 (ThermoFisher SCIENTIFIC cat# AM2295) for 3 minutes at 37ºC. Protein-RNA complexes were immunoprecipitated using Dynabeads (ThermoFisher SCIENTIFIC cat# 10004D) and 12ug anti-FLAG antibody (Sigma Aldrich, cat# F1804). Libraries were prepared as described (Biancon et al., 2022). m6A eCLIP-seq: mRNA was isolated from 75ug total RNA by oligo-dT beads (ThermoFisher Dynabeads™ mRNA Purification Kit, cat#61006) and eluted in 5μL DNase-RNase free water. RNA was fragmented using 2 μL of RNA fragmentation reagent (ThermoFisher, cat# AM8740) at 75ºC for 6 minutes and RNA integrity and fragment size wasnassessed using an Agilent TapeStation. mRNA was incubated with 2μL of ribonuclease inhibitor (SuperaseIn) and 5ug anti-m6A antibody (202 011, Synaptic Systems) for 2 hours, rotating, at 4ºC. Each sample was then UV-crosslinked and immunoprecipitated using Dynabeads as for eCLIP-seq. HEL cell and 6133/CAOM RNA-seq: RNA underwent poly-A selection, reverse transcription, and library preparation using the KAPA mRNA HyperPrep kit. TimeLapse-seq: Total RNA was isolated and extracted with phenol-chloroform. Following precipitation in isopropanol supplemented with 1mM DTT and 20µg of glycogen, RNA pellets were washed twice with fresh 75% EtOH. Dried RNA pellets were resuspended in DEPC-treated water and treated with Turbo DNase to deplete genomic DNA. After purification with one equivalent volume of Agencourt RNAClean XP beads, 5µg of eluted RNA were processed for TimeLapse chemistry using meta-chloroperoxybenzoic acid as the oxidant(Schofield et al. 2018). For each sample, 10ng of TimeLapse-treated RNA input were used to prepare sequencing libraries from the Clontech SMARTer Stranded Total RNA-Seq kit (Pico Input) with ribosomal cDNA depletion. ERP/MKP RNAseq: RT with SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and library construction with Nextera XT DNA Sample Preparation kit.

treatment_protocol: Dox induction: 10ng/mL for 24hr. TL-seq: 100uM 4-thiouridine for 2 hours. METTL3 inhibitor: 1uM STM3675 for 48hr.

value: cell line

value: HEL

value: human erythroleukemia

value: RM

value: dox 24h, s4U 2h


title: TLseq, HEL-RM cells, biological rep 2, dox24h s4U 2h


title: TLseq, HEL-RM cells, biological rep 1, dox24h s4U 2h


title: TLseq, HEL-RBM15 cells, biological rep 3, dox24h s4U 2h


title: cKO4

city: Hang Zhou

first: Yan

last: Wei

state: Zhejiang

address: 2318 Yuhang Tang Road

department: Medicine

institute: Hangzhou Normal University

description: Library name: Sample 7

data_processing:
Indexing of the reference genome was constructed using HISAT2v2.0.5 and paired-end clean reads were aligned to the reference genome using HISAT2v2.0.5 and featureCounts (1.5.0-p3) were used to calculate reads mapped to each gene. For samples with biological replicates, differential expression analysis between the two comparison combinations was performed using DESeq2 software (1.20.0).
Assembly: mm10
Supplementary files format and content: table-delimited text file inclueds raw counts for each sample
Supplementary files format and content: txt file include FPKM values for each sample

source_name: motor cortex

growth_protocol: Brain tissue sampling was performed after behavioral testing 3 months after GA100 virus injection in P0 WT and CKO mice

extract_protocol:
RNA was extracted from tissues using standard extraction methods, and RNA samples were subjected to strict quality control by Agilent 2100 bioanalyzer to precisely detect RNA integrity.
The first strand cDNA was synthesized in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primers, followed by RNA strand degradation with RNaseH, and the second strand cDNA was synthesized from dNTPs in DNA polymerase I system. The purified double-stranded cDNA was end-repaired, A-tailed and ligated with sequencing adapters, and the cDNA of about 250 – 300 bp was screened with AMPure XP beads, amplified by PCR and the PCR product was purified again using AMPure XP beads to finally obtain the library.

treatment_protocol: P0 WT and CKO mice were injected with GA100 virus into the left and right lateral ventricles.

value: motor cortex

value: CKO

value: P0 injected GA100 virus

tag: batch


title: cKO3

description: Library name: Sample 6


title: TLseq, HEL-RBM15 cells, biological rep 2, dox24h s4U 2h


title: cKO2

description: Library name: Sample 5


title: TLseq, HEL-RBM15 cells, biological rep 1, dox24h s4U 2h


title: left atrium, tac, biological replicate 7

type: RNA

city: Barcelona

first: Eduard

last: Guasch

state: Catalonia

address: Rosselló 149

country: Spain

institute: Hospital Clinic Barcelona, IDIBAPS

hyb_protocol: After fragmentation and terminal labeling, the ss-cDNAs were hybridized for 17 h at 45 °C un a on a GeneChip Rat Clariom S array plate (Thermo Fisher) .

scan_protocol: Automated GeneTitan System (Thermo Fisher), which included a hybridization oven, Fluidic Station and Scanner

data_processing: The data were analyzed with Transcriptomic Analysis Console v4.03 (Thermo Fisher) via SST-RMA normalization and R v3.6 (R Foundation for Statistical Computing, Vienna, Austria) (CHP files provided here). For initial analyses, the atrial factor (right, left) was considered a repeated measurement.

label: biotin

organism: Rattus norvegicus

source_name: left atrium from a TAC animal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol f(Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted from LA and RA samples by using TRIzol (Invitrogen, CA, USA) and the mirVana miRNA Isolation Kit (Invitrogen) following the manufacturer’s protocol.

value: atrial tissue

tag: atrial side

value: left

tag: experimental group

value: TAC

tag: Sex

value: male


title: right atrium, tac, biological replicate 7

source_name: right atrium from a TAC animal

value: right


title: TLseq, HEL-RBM15 cells, dox 24h

value: dox 24h


title: right atrium, sham, biological replicate 6

source_name: right atrium from a sham animal

value: sham


title: cKO1

description: Library name: Sample 4


title: right atrium, sham, biological replicate 5


title: left atrium, sham, biological replicate 6

source_name: left atrium from a sham animal


title: left atrium, tac, biological replicate 5


title: right atrium, tac, biological replicate 6


title: left atrium, tac, biological replicate 6


title: TLseq, HEL-RM cells, dox 24h


title: TLseq, HEL-parental cells, biological rep 3, dox24h s4U 2h


title: Ctrl3

description: Library name: Sample 3


title: Ctrl1

description: Library name: Sample 1


title: Ctrl2

description: Library name: Sample 2


title: TLseq, HEL-parental cells, biological rep 2, dox24h s4U 2h


title: right atrium, tac, biological replicate 5


title: TLseq, HEL-parental cells, biological rep 1, dox24h s4U 2h


title: left atrium, tac, biological replicate 3


title: left atrium, sham, biological replicate 4


title: left atrium, sham, biological replicate 5


title: right atrium, sham, biological replicate 4


title: right atrium, tac, biological replicate 4


title: right atrium, tac, biological replicate 2


title: left atrium, tac, biological replicate 2


title: left atrium, tac, biological replicate 4


title: m6A eCLIPseq, HEL-RM cells, rep 2, dox 24h, pre-IP RNA

value: 10ng/mL dox 24h


title: right atrium, tac, biological replicate 3


title: m6A eCLIPseq, HEL-RM cells, rep 1, dox 24h, pre-IP RNA


title: TLseq, HEL-parental cells, dox 24h


title: 15 week,  perisynaptic, SBMA, rep 3

city: IRVINE

first: Anastasia

last: Gromova

email: agromova@uci.edu, agromova@gmail.com

address: 419 South Circle View Drive

department: Pathology

institute: UC Irvine

description: Library name: AH112_p

data_processing:
Reads were aligned to mm10 using STARv2.6.1 and counts matrix was generated using featureCounts
Assembly: mm10
Supplementary files format and content: csv file with raw gene-level counts for all samples

source_name: skeletal muscle

extract_protocol:
RNA was extracted using Qiagen miRNeasy Kit with on-column DNA digestion
Libaries were generated using KAPA Stranded mRNA-Seq kit with mRNA capture beads

value: skeletal muscle

tag: tissue subtype

value: perisynaptic diaphragm

tag: age


title: 15 week,  perisynaptic, control, rep 2

description: Library name: AH117_p


title: 15 week, extrasynaptic, control, rep 2

description: Library name: AH117_e

value: extrasynaptic diaphragm


title: m6A eCLIPseq, HEL-RM cells, technical rep 3, dox 24h

value: cell line

value: HEL

value: human erythroleukemia


title: 15 week,  perisynaptic, SBMA, rep 2

description: Library name: AH111_p


title: 15 week, extrasynaptic, SBMA, rep 2

description: Library name: AH111_e


title: m6A eCLIPseq, HEL-RM cells, biological rep 1, dox 24h

value: RM


title: left atrium, sham, biological replicate 3


title: m6A eCLIPseq, HEL-RM cells, biological rep 2, dox 24h


title: m6A eCLIPseq, HEL-RBM15 cells, rep 2, dox 24h, pre-IP RNA


title: left atrium, tac, biological replicate 1


title: left atrium, sham, biological replicate 1


title: 15 week,  perisynaptic, SBMA, rep 1

description: Library name: AH110_p


title: right atrium, sham, biological replicate 3


title: right atrium, sham, biological replicate 1


title: right atrium, tac, biological replicate 1


title: left atrium, sham, biological replicate 2


title: right atrium, sham, biological replicate 2


title: right atrium, moderate exercise, biological replicate 9

source_name: right atrium myocardium, moderate exercise

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: exercise group

value: moderate


title: left atrium, moderate exercise, biological replicate 8

source_name: left atrium myocardium, moderate exercise


title: right atrium, moderate exercise, biological replicate 7


title: left atrium, moderate exercise, biological replicate 9


title: m6A eCLIPseq, HEL-RBM15 cells, rep 1, dox 24h, pre-IP RNA


title: right atrium, moderate exercise, biological replicate 8


title: left atrium, moderate exercise, biological replicate 7


title: 15 week, extrasynaptic, SBMA, rep 3

description: Library name: AH112_e


title: 15 week, extrasynaptic, SBMA, rep 1

description: Library name: AH110_e


title: left atrium, intense exercise, biological replicate 9

source_name: left atrium myocardium, intense exercise

value: intense


title: m6A eCLIPseq, HEL-RBM15 cells, biological rep 3, dox 24h


title: right atrium, intense exercise, biological replicate 7

source_name: right atrium myocardium, intense exercise

value: atrial tissue


title: 15 week,  perisynaptic, control, rep 1

description: Library name: AH109_p


title: m6A eCLIPseq, HEL-RBM15 cells, technical rep 3a, dox 24h


title: m6A eCLIPseq, HEL-RBM15 cells, biological rep 1, dox 24h


title: right atrium, intense exercise, biological replicate 8


title: left atrium, intense exercise, biological replicate 7

value: left


title: 15 week, extrasynaptic, control, rep 1

description: Library name: AH109_e


title: 15 week, extrasynaptic, SBMA, rep 4

description: Library name: AH119_e


title: m6A eCLIPseq, HEL-parental cells, biological rep 2, dox 24h


title: right atrium, intense exercise, biological replicate 6


title: left atrium, intense exercise, biological replicate 8


title: 26 week,  perisynaptic, SBMA, rep 4

description: Library name: AH098_p


title: 15 week,  perisynaptic, SBMA, rep 4

description: Library name: AH119_p


title: m6A eCLIPseq, HEL-parental cells, biological rep 1, dox 24h


title: 26 week, extrasynaptic, SBMA, rep 4

description: Library name: AH098_e


title: m6A eCLIPseq, HEL-RBM15 cells, biological rep 2, dox 24h


title: right atrium, moderate exercise, biological replicate 6


title: left atrium, sedentary, biological replicate 4

source_name: left atrium myocardium, sedentary

value: sedentary


title: right atrium, sedentary, biological replicate 5

source_name: right atrium myocardium, sedentary

value: male


title: right atrium, intense exercise, biological replicate 4

value: right


title: left atrium, moderate exercise, biological replicate 6


title: left atrium, intense exercise, biological replicate 4


title: left atrium, sedentary, biological replicate 2


title: left atrium, intense exercise, biological replicate 5


title: eCLIPseq, HEL-RBM15 cells, biological rep 2, dox 24h


title: right atrium, sedentary, biological replicate 3


title: right atrium, moderate exercise, biological replicate 4


title: 26 week,  perisynaptic, control, rep 4

description: Library name: AH097_p


title: m6A eCLIPseq, HEL-parental cells, technical rep 1a, dox 24h


title: right atrium, sedentary, biological replicate 4


title: left atrium, sedentary, biological replicate 3


title: 26 week, extrasynaptic, SBMA, rep 3

description: Library name: AH096_e


title: eCLIPseq, HEL-RBM15 cells, biological rep 1, dox 24h, pre-IP RNA


title: eCLIPseq, HEL-RM cells, biological rep 1, dox 24h, pre-IP RNA


title: 26 week, extrasynaptic, control, rep 4

description: Library name: AH097_e


title: eCLIPseq, HEL-RM cells, biological rep 2, dox 24h


title: 26 week,  perisynaptic, control, rep 3

description: Library name: AH095_p


title: eCLIPseq, HEL-RBM15 cells, biological rep 3, dox 24h


title: 26 week,  perisynaptic, SBMA, rep 3

description: Library name: AH096_p


title: left atrium, moderate exercise, biological replicate 1


title: right atrium, sedentary, biological replicate 2


title: left atrium, intense exercise, biological replicate 3


title: 26 week,  perisynaptic, SBMA, rep 2

description: Library name: AH082_p


title: left atrium, moderate exercise, biological replicate 4


title: left atrium, sedentary, biological replicate 1


title: left atrium, moderate exercise, biological replicate 2


title: left atrium, moderate exercise, biological replicate 3


title: right atrium, sedentary, biological replicate 1


title: eCLIPseq, HEL-RBM15 cells, biological rep 1, dox 24h


title: eCLIPseq, HEL-parental cells, biological rep 2, dox 24h


title: 26 week, extrasynaptic, SBMA, rep 2

description: Library name: AH082_e


title: right atrium, intense exercise, biological replicate 2


title: right atrium, moderate exercise, biological replicate 3


title: left atrium, intense exercise, biological replicate 1


title: 15 week, extrasynaptic, control, rep 3

description: Library name: AH118_e


title: right atrium, moderate exercise, biological replicate 2


title: eCLIPseq, HEL-parental cells, biological rep 1, dox 24h


title: 26 week, extrasynaptic, control, rep 3

description: Library name: AH095_e


city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt

data_processing:
The full protocol is described in the corresponding manuscript. In short, reads overlapping the SB-genome junction were selected, SB-sequences were trimmed off (using an adapted version of cutadapt) and reads were mapped to the genome (mm10 or an in silico version of mm10 including the hopping launch pad at -116 kb), filtering for mapq >=10. All putative integrations are lifted over to mm10.
Assembly: mm10
Supplementary files format and content: The processed data file reports all putative integrations mapped in a pool or clone (supported by at least one mapping read, filtering in the manuscript can be more strict). Columns: chr = chromosome; start, end = integration location; seq = dinucleotide at integration site (expected for SB: TA); strand = strand of integration (orientation); read_count = total read count, mapq = total mapping quality (of all reads); read_count_1/mapq_1 = forward mapping reads (3' ITR); read_count_2/mapq_2 = reverse mapping reads (5' ITR); all other columns specify and annotate the sequenced sample. There is one processed data file per founder cell line (pool-based experiments) and one for the isolated clones.

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) Sox2 mCherry+/eGFP+ were cultured in Serum+Lif+2i condition. Briefly, cells were cultured on gelatin-coated (0.1%) culture plates in Glasgow minimum essential medium (Sigma-Aldrich, G5154) supplemented with 15% fetal bovine serum (Thermo Fisher Scientific, 10270-106), 1% L-glutamine (Thermo Fisher Scientific, 25030024), 1% sodium pyruvate (Thermo Fisher Scientific, 11360-70), 1% MEM non-essential amino acids (Thermo Fisher Scientific, 11140-50), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15070063), 100 µM ß-mercaptoethanol, 10 x 4 U leukemia inhibitory factor (LIF; esg1107, Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress) in 5% CO2 at 37°C. Cells were passaged every 2 days.

extract_protocol:
Sorted pools and clones were expanded and crude lysates were obtained from a full 96 well plate by lysing with 50 µL DirectPCR Lysis Reagent (102-T, Viagen Biotec) supplemented with 100 µg/mL proteinase K, and incubating 2.5 h at 55 °C and 45 min at 85 °C. For unsorted control cell pools, gDNA was extracted after expansion using the ISOLATE II Genomic DNA Kit (BIO-52067, Bioline).
SBt integrations were mapped by amplifying and sequencing the ITR-genome junction using a tagmentation-based approach. The procedure was similar to {Schep, 2021, 33848455}, but using the following SB-ITR specific primers: MEP009 (5′ ITR, reverse) or LD027 (3′ ITR, forward) for the linear enrichment and MEP011 (5′ ITR, reverse) or MEP034 (3′ ITR, forward) for PCR.Input for one tagmentation reaction was either 100ng gDNA or 3 µL crude lysate. The 72 °C extension times of all PCRs were increased to 1 min. In addition, the composition of the linear enrichment PCR was changed to 10 μL of tagmented DNA, 2 μL of 1 μM primer, 4 μL dNTPs (10mM), 8 μL 5x Phusion® HF Buffer (NEB), 0.5 μL Phusion® HS Flex polymerase (2 U/μL - NEB), in a final volume of 40 μL. For all clones and some experiments with sorted pools (proof-of-principle experiment, third replicate of the reporter hopping) we halved this reaction to a final volume of 20 µL. For the unsorted control pools, 10 separate tagmentation reactions and library preparations were performed, usually using one set of sequencing indices. Libraries were sequenced with 150 bp paired-end reads using either an Illumina MiSeq system (reagent kit v2) or  Illumina NextSeq 550 system (mid-output kit) including 10% of PhiX spike-in.  Primers are described in the corresponding manuscript.

treatment_protocol: SB hopping was induced by transfecting 2.5 to 5 million cells with the bicistronic plasmid (pME07) encoding SB transposase SB100x and the human nerve growth factor receptor (LNGFR), using Lipofectamine 2000 (Invitrogen, 11668019) and 5 µg of plasmid per million cells. After 30 hours, transfected cells were enriched using MACS MS columns (130-042-201, Miltenyi Biotec) and LNGFR MicroBeads (130-091-330, Miltenyi Biotec) according to the manufacturer’s protocol. One week after transfection, 0.2 million SB-transposase-transfected cells were set apart as an unsorted pool and the remaining cells were FACS sorted into pools (of up to 1000 cells) based on reporter expression. Clones were obtained by sorting single cells from previously obtained pools, or sorted directly from the full pool of SB-transposase-transfected cells.

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: Sox2::mCherry deleted

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: eCLIPseq, HEL-RM cells, biological rep 3, dox 24h

tag: cell type

value: 10ng/mL dox 24h


title: 15 week,  perisynaptic, control, rep 3

description: Library name: AH118_p

value: skeletal muscle

value: perisynaptic diaphragm


title: RNAseq, HEL-RBM15 cells, biological rep 1, no dox

value: cell line

value: HEL


title: right atrium, moderate exercise, biological replicate 1


title: right atrium, intense exercise, biological replicate 3


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool3 rep1 Fw
Sox2P-reporter +715 kb, population P6 pool3 rep1
mapped_integrations_+715kb_Sox2P_pools.txt

value: WT


title: eCLIPseq, HEL-RM cells, biological rep 1, dox 24h

value: human erythroleukemia

value: RM

tag: treatment


title: left atrium, intense exercise, biological replicate 2

tag: tissue

value: atrial tissue

value: intense


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt

tag: genotype


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool4 rep1 Fw
Sox2P-reporter +715 kb, population P5 pool4 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: RNAseq, HEL-parental cells, biological rep 2, no dox


title: right atrium, intense exercise, biological replicate 1


title: 26 week, extrasynaptic, SBMA, rep 1

description: Library name: AH079_e

value: extrasynaptic diaphragm


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool1 rep1 Fw
Sox2P-reporter +715 kb, population P5 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: RNAseq, HEL-parental cells, biological rep 1, no dox


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool4 rep1 Fw
Sox2P-reporter +715 kb, population P6 pool4 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool5 rep1 Fw
Sox2P-reporter +715 kb, population P6 pool5 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: 26 week, extrasynaptic, control, rep 2

description: Library name: AH081_e

value: male


title: 26 week,  perisynaptic, control, rep 1

description: Library name: AH080_p


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool2 rep1 Fw
Sox2P-reporter +715 kb, population P6 pool2 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: RNAseq, CAOM cells, biological rep 3, 1uM STM3675 48h

value: CAOM

value: murine AMKL


title: RNAseq, HEL-RBM15 cells, biological rep 2, dox 24h


description:
Library name: E2716 Sox2P-reporter +715 kb, population P2 pool1 rep1 Fw
Sox2P-reporter +715 kb, population P2 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool5 rep1 Fw
Sox2P-reporter +715 kb, population P5 pool5 rep1
mapped_integrations_+715kb_Sox2P_pools.txt

value: sorted pool


title: RNAseq, HEL-parental cells, biological rep 2, dox 24h

value: 10ng/mL dox 24h


description:
Library name: E2716 Sox2P-reporter +715 kb, population P4 pool1 rep1 Fw
Sox2P-reporter +715 kb, population P4 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P3 pool1 rep1 Fw
Sox2P-reporter +715 kb, population P3 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: 26 week,  perisynaptic, control, rep 2

description: Library name: AH081_p

value: skeletal muscle


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool3 rep1 Fw
Sox2P-reporter +715 kb, population P5 pool3 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P1 pool1 rep1 Fw
Sox2P-reporter +715 kb, population P1 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: RNAseq, HEL-parental cells, biological rep 1, dox 24h


title: 26 week,  perisynaptic, SBMA, rep 1

description: Library name: AH079_p

value: perisynaptic diaphragm


title: RNAseq, HEL-RBM15 cells, biological rep 2, no dox

value: cell line


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool1 rep1 Fw
Sox2P-reporter +715 kb, population P6 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool2 rep1 Fw
Sox2P-reporter +715 kb, population P5 pool2 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: 26 week, extrasynaptic, control, rep 1

description: Library name: AH080_e


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool4 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool4 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt

value: Sox2::mCherry deleted


title: RNAseq, HEL-RBM15 cells, biological rep 1, dox 24h

value: HEL


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool3 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool3 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, CAOM cells, biological rep 2, 1uM STM3675 48h


title: RNAseq, CAOM cells, biological rep 3, DMSO

value: DMSO


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool5 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool5 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool5 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool5 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool1 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, HEL-MKL1 cells, biological rep 1, no dox

value: human erythroleukemia


title: RNAseq, CAOM cells, biological rep 2, DMSO

value: RM


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool4 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool4 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, CAOM cells, biological rep 1, 1uM STM3675 48h


title: RNAseq, HEL-MKL1 cells, biological rep 2, no dox


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool2 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, HEL-MKL1 cells, biological rep 2, dox 24h


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool2 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, CAOM cells, biological rep 1, DMSO


title: RNAseq, 6133 cells, biological rep 6, 1uM STM3675 48h


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, 6133 cells, biological rep 5, 1uM STM3675 48h


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool3 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool3 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, HEL-RM cells, biological rep 2, no dox


title: RNAseq, HEL-RM cells, biological rep 1, no dox


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool1 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, 6133 cells, biological rep 4, 1uM STM3675 48h


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool2 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, HEL-RM cells, biological rep 2, dox 24h


title: RNAseq, HEL-MKL1 cells, biological rep 1, dox 24h


title: RNAseq, HEL-RM cells, biological rep 1, dox 24h


description:
Library name: E2716 Sox2P-reporter -116 kb, unsorted control pool rep4 Rv
Sox2P-reporter -116 kb, unsorted control pool rep4
mapped_integrations_-116kb_Sox2P_pools.txt

value: WT

value: control pool


description:
Library name: E2716 Sox2P-reporter +715 kb, unsorted control pool rep1 Rv
Sox2P-reporter +715 kb, unsorted control pool rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: RNAseq, 6133 cells, biological rep 3, 1uM STM3675 48h


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: aortic dissectionl-2+

city: Tianjin

first: Meng

last: Wang

state: --- Select One ---

address: No. 261, Taierzhuang South Road, Jinnan District, Tianjin

institute: Tianjin chest hospital

data_processing:
Sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2
The read length was 2×150 bp. Clean reads were aligned to the Human genome hg38 using STAR.StringTie
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.
Assembly: Human genome hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: aorta

extract_protocol:
Total RNA was isolated from each sample using the RNAmini kit ( Qiagen, Germany).
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)

value: aorta


title: aortic dissection-4+


description:
Library name: E2716 Sox2P-reporter -116 kb, unsorted control pool rep4 Fw
Sox2P-reporter -116 kb, unsorted control pool rep4
mapped_integrations_-116kb_Sox2P_pools.txt


title: aortic dissection-6


description:
Library name: E2716 Sox2P-reporter +715 kb, unsorted control pool rep1 Fw
Sox2P-reporter +715 kb, unsorted control pool rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: RNAseq, 6133 cells, biological rep 3, DMSO


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: RNAseq, 6133 cells, biological rep 1, 1uM STM3675 48h


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool5 rep1 Rv
Sox2P-reporter +715 kb, population P6 pool5 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: RNAseq, 6133 cells, biological rep 1, DMSO


title: control-6


title: FGFR1_TACC1

description: 10X genomics

data_processing:
The CellRanger (v6.1.2) pipeline was used to map the sequencing data to the mouse genome (mm10). We then used the Seurat library (4.3.0) to convert the expression data to Seurat objects and perform quality control. First, we filtered for genes that appeared in at least 3 cells. Consistent with our expectation from mouse models, the fraction of reads that corresponded to mitochondrial RNA was very low (0.32% +/- 0.29%), thus we did not need to filter out cells by mitochondrial content. We filtered out indexes with fewer than 8000 reads to ensure we picked up cells that have one unique index.
Assembly: mm10
Supplementary files format and content: .h5 matrix files

source_name: mouse neural stem cells  from CD1 mice

growth_protocol: Mouse neural stem cells (mNSC) obtained from the subventricular zone of CD1 mice23 were cultured as neurospheres in ultra-low adherence vessels (Corning, NY, USA) in tumor stem media (TSM) (500 mL Neurobasal-A (#10888-022), 500 mL DMEM/F12 (#11330-032), 10 mL HEPES Buffer Solution 1M (#15630-080), 10 mL MEM sodium pyruvate solution 100 mM (#11360-070), 10 mL MEM Non-essential amino acid solution 10 mM (#11140-050), 10 mL GlutaMAX solution (#35050-061), 10 mL Penicillin/Streptomycin (#15140122) and 1X B-27 Supplement Minus Vitamin A (from 50X) (#12587-010) from Invitrogen (MA, USA). When indicated, TSM media was supplemented with 12 ng/mL human-EGF (#78006), 12 ng/mL human-bFGF (#78006) and 2 ug/mL heparin solution 0.2% (#07980) from Stemcell Technologies (Vancouver, Canada). Neurospheres were dissociated using Accutase (#00-4555-56, Invitrogen) every 3-4 days and reseeded as single cells suspension with a density of 80-100,000 cells/mL in ULA flasks/plates.

extract_protocol:
10,000 cells were loaded on the 10X controller for each sample
Single-cell RNA-seq was performed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) kit as per manufacturer’s instructions. Uniquely indexed libraries were pooled in an equimolar ratio and sequenced on a NovaSeq 6000 S2 flowcell targeting 4 billion reads.

tag: strain

value: mouse neural stem cells  from CD1 mice


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool3 rep1 Rv
Sox2P-reporter +715 kb, population P6 pool3 rep1
mapped_integrations_+715kb_Sox2P_pools.txt

tag: cell line


title: aortic dissection-5


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool2 rep1 Rv
Sox2P-reporter +715 kb, population P6 pool2 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool1 rep1 Rv
Sox2P-reporter +715 kb, population P6 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: aortic dissection-4


title: FGFR1_ITD

description: 10X genomics


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool5 rep1 Rv
Sox2P-reporter +715 kb, population P5 pool5 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: aortic dissection-3


title: RNAseq, 6133 cells, biological rep 2, 1uM STM3675 48h

value: murine AMKL


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool4 rep1 Rv
Sox2P-reporter +715 kb, population P5 pool4 rep1
mapped_integrations_+715kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: aortic dissectionl-2


title: FGFR1_PTPN11

description: 10X genomics


title: aortic dissectionl-1


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool1 rep1 Rv
Sox2P-reporter +715 kb, population P5 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt

value: mESC


description:
Library name: E2716 Sox2P-reporter +715 kb, population P6 pool4 rep1 Rv
Sox2P-reporter +715 kb, population P6 pool4 rep1
mapped_integrations_+715kb_Sox2P_pools.txt

value: sorted pool


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool2 rep1 Rv
Sox2P-reporter +715 kb, population P5 pool2 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P3 pool1 rep1 Rv
Sox2P-reporter +715 kb, population P3 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: FGFR1_N546K_LACZ

description: 10X genomics


title: RNAseq, 6133 cells, biological rep 2, DMSO


title: control-5


title: KIAA1549:BRAF r2

data_processing:
Sequenced reads were aligned to the UCSC mm10 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)54. Differential expression analysis was performed using the R package DESeq2 v1.22.155. RNAseq analysis was performed using the VIPER snakemake pipeline56.
Assembly: mm10
Supplementary files format and content: CSV file with raw counts for all samples
Supplementary files format and content: DE analysis results in the paper supplemental files

source_name: mouse neural stem cells from CD1 mice

extract_protocol:
Bulk RNA was extracted from mNSC cells using the Qiagen RNeasy kit (74104).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 150bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: mouse neural stem cells from CD1 mice


description:
Library name: E2716 Sox2P-reporter +715 kb, population P1 pool1 rep1 Rv
Sox2P-reporter +715 kb, population P1 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, unsorted control pool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P4 pool1 rep1 Rv
Sox2P-reporter +715 kb, population P4 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter +715 kb, population P2 pool1 rep1 Rv
Sox2P-reporter +715 kb, population P2 pool1 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


title: control-4


title: KIAA1549:BRAF r1


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool4 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool4 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: control-3


description:
Library name: E2716 Sox2P-reporter +715 kb, population P5 pool3 rep1 Rv
Sox2P-reporter +715 kb, population P5 pool3 rep1
mapped_integrations_+715kb_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool5 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool5 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool3 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool3 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: BRAF V600E r3


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool1 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: control-2


title: BRAF V600E r2


title: control-1


title: KIAA1549:BRAF r3


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool2 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_L pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: BRAF V600E r1


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool4 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool4 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool2 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: FGFR1-ITD r3


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool3 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool3 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: HepG2 small RNA rep2

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

description:
ZA4
mutation.hepG2.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.6)
PCR duplicates were removed with the BBMap tool (https://sourceforge.net/projects/bbmap/).
Random barcodes at reads end were trimmed, and low-quality reads were removed using the cutadapt tool again
Then the remaining reads were aligned to the human genome (hg38) using  bowtie2 (version 2.5.1) allowing a maximum of three mismatches.
Read count extraction and differential expression levels of exons and genes were analyzed using RADAR (0.2.4) followed by DEseq2 (1.36.0).
Cleaned reads that failed to align to the human genome were applied using Kraken2 with its standard database, which contains bacterial, archaeal, viral, and human sequences. Based on the aligned results from Kraken2, we normalized the data by calculating the reads per million (RPM). Then we performed student t-test (two tailed) to calculate the p value for the differential expression.
We identified microbial species in cfRNA samples using kraken2 (version 2.1.3)52, setting a threshold whereby the median reads of the specie must exceed 10 in at least one group (CRC or non-cancer). Following species identification, we extracted their sequences from the kraken2 reference genome. To construct a new, streamlined reference, we limited each microbial species to a maximum of ten reference genomes, minimizing redundancy Subsequently, we aligned the reads that failed to align to the human genome to this curated microbiome reference genome using bowtie2. The alignments generated by bowtie2 were applied in the calculation of the microbiome mapping ratio. Variant identification within these sequences is then achieved through the precise analysis of base composition at each genomic position, employing bam-readcount tool (https://github.com/genome/bam-readcount). The generated bam-readcount output results were parsed and analyzed to calculate the misincorporation ratio.
Assembly: hg38 (GRCh38.107)
Assembly: Kraken 2 standard database
Supplementary files format and content: abundance.host.csv|containing the abundance (raw reads), fold change, p value of various human transcirpts from cfRNA.
Supplementary files format and content: abundance.microbiome.csv|containing the RPM, fold change, p value of various microbial abundance from cfRNA.
Supplementary files format and content: mutation.microbiome.csv |containing the p value, fold change, and mutation ratio at modified sites in microbiome-dervied cfRNA.
Supplementary files format and content: mutation.host.rRNA.csv |containing the p value, fold change, and mutation ratio at human rRNA from cfRNA.
Supplementary files format and content: mutation.host.tRNA.csv |containing the p value, fold change, and mutation ratio at human tRNA from cfRNA.
Supplementary files format and content: mutation.hepG2.csv |containing mutation ratio of human tRNA from HepG2.
Library strategy: LIME-seq

source_name: Blood

extract_protocol:
cfRNAs were isolated from 600 μl plasma using QIAamp ccfDNA/RNA Kit (Qiagen, Cat. 55184) according to the manufacturer's protocol. In brief, 180 μl RPL buffer was added into 600 μl plasma, followed by vortexing for 5 s. After leaving at room temperature for 3 mins, 100 μl RPP buffer is added. Then close EP tube cap and immediately mix vigorously by vortexing 10 s for 2 times, which is important to disperse the solid. Incubate the EP tube on ice for 3 min. After the standard steps of washing and concentration following the manufacturer's protocol, the purified cfRNA was finally eluted in 14 µl of RNase-free water.
Plasma cell-free RNA (cfRNA) or small RNA from HepG2 (<200 nt) were fragmented to lengths of ~35-55 nucleotides using the 10X RNA Fragmentation Reagent (AM8740, Invitrogen), which was used as 15X with heating at 70 °C for 14 mins. Purify the fragmented RNA using the Oligo Clean & Concentrator kit (Zymo Research) with a final elution volume of 10 μl. The subsequent 3′-end repair involved the preparation of a mixture of fragmented RNA, 2 μl of 10× T4 Polynucleotide Kinase Reaction Buffer (B0201S, NEB), 2 μl of T4 PNK, 1 μl SUPERase•In RNase Inhibitor and a proper volume of RNase-free water. Mix the 20 μl reaction mixture very well and incubate at 37°C for 1 hour. 3’-end-repaired RNA fragments were purified by Oligo Clean & Concentrator kit and eluted in 10 μl of RNase-free water. For 3′-adapter ligation, RNA fragments were denatured with 1ul of 10 μM RNA 3′-linker (5′rApp-NNNNN AGATCGGAAGAGCGTCGTG-3SpC3) by heating at 70°C for 2 minutes and then immediately moved onto ice. Then a mixture of 2.5 μl of 10× T4 RNA Ligase Reaction Buffer (NEB), 7.5 μl of 50% PEG8000, 1 μl SUPERase•In, and 2 μl T4 RNA ligase 2 truncated KQ (NEB) was prepared, followed by mixing well and incubating at 25°C for 2 hrs and then at 16°C for 10 hrs. The excessive adapters were removed by adding 2 μl of 5′-deadenylase (NEB) with an incubation at 30 °C for 45 mins, followed by adding 1.0 μl of RecJf (NEB) with an incubation at 37 °C for 45 mins. The 3’-ligated RNA was then purified by RNA Clean & Concentrator (Zymo Research) and eluted in 10 μl of RNase-free water.  Reverse transcription was initiated by mixing the 3’-ligated RNA with 1 ul of 2.0 μM RT primer (5′-ACACGACGCTCTTCCGATCT-3′) and heating at 65°C for 2 minutes. Then move the samples onto ice immediately. A mixture of 2 μl of 10× AMV Reverse Transcriptase Reaction Buffer (NEB), 2 μl of 10 mM dNTPs, 1 μl RNaseOUT (Thermo Fisher Scientific), 2 μl HIV Recombinant Reverse Transcriptase (Worthington) and a proper volume of RNase-free water was prepared, to give a final volume of 20 μl for a one-hour incubation at 37°C. Upon the completion of RT, 1.0 μl volume of RNase H (NEB, M0297L) was added to the reaction mixture, followed by incubation at 37 °C for 20 min and 70 °C for 5 min. The produced cDNAs after RT were purified by Oligo Clean & Concentrator (Zymo Research) and eluted in 10 μl of RNase-free water. A mixture of eluted cDNA and 2.0 μl of 10 μM cDNA 3′-linker (5′Phos-NNNNNAGATCGGAAGAGCACACGTCTG-3SpC3) was denatured at 75 °C for 2 min and then moved onto ice immediately. 3-μl of 10× T4 RNA Ligase Reaction Buffer (NEB), 15 μl of 50% PEG8000, 3 μl of 10 mM ATP, and 1.0 μl of T4 RNA ligase 1 (high concentration, NEB) were added to the cDNA–adapter mixture and mixed very well. Incubate the ligation reaction mixture at 25 °C for 12 h. The libraries were amplified using universal and indexed primers from NEBNext Multiplex Oligos for Illumina (NEB). All libraries were sequenced on an Illumina NovaSeq 6000 or NovaSeqX with SE100 bp mode. The LIME-seq method enables high mutation ratio detection across multiple RNA modifications, including m1A, m3C, m1G, m22G, m3U, etc., with an enhanced read-through at these methylation sites. Such performance has been facilitated by the robust HIV RT enzyme, and it effectively uncovered methylation fraction information at methylated sites

value: Blood

tag: disease state

tag: fraction

value: small RNA


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_L pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: FGFR1-ITD r1


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool1 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt