title: MC3T3-E1 cells, shRcor2-20, 7d, sample 2

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
The raw reads were subjected to quality control using FastQC
The reads were aligned to mm9 version of UCSC mouse genome using TopHat version 2.0.9 for 64bit Linux x86 (Kim et al. 2013) with default parameters that have been optimized for mammalian genomes.
After exploratory section the samples were subjected to differential expression analysis using R package DESeq2. Shortly, gene expressions were adjusted with over dispersion estimates obtained from the DESeq model fit and differences between sample group expression means and their statistical significance was estimated by t-testing.
Assembly: mm9
Supplementary files format and content: Tab-separated file of read counts count_matrix.txt

growth_protocol: Mouse MC3T3-E1 osteoblastic cell line (CRL-2593, ATCC, USA) was maintained in aMEM medium supplemented with 10% fetal bovine serum (FBS) and 100 U/ml penicillin-streptomycin

extract_protocol:
Cells were harvested at 80% confluence representing proliferative stage, as well as at confluency and after 24 hours, 14 days and 21 days of osteogenic differentiation in OM. At indicated timepoints, the cells were washed once with PBS, lysed and RNA extracted by RNeasy mini kit (Qiagen)
RNA-seq was performed on the Illumina2000 platform as 100 bp reads

treatment_protocol: Osteogenic differentiation was induced by osteogenic medium (OM) composed of growth medium supplemented with 5 mM Na-β-glycerophosphate, 50 µg/ml ascorbic acid and 10 nM dexamethasone

value: preosteoblast

value: RCOR2 knockdown


title: DDX54_KD_LLC1_1

status: Public on Mar 19 2025

type: SRA

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

description:
Library name: DDX54_KD_LLC1_1
Bulk RNA-seq

library_source: transcriptomic

data_processing:
Trimmomatic - STAR - HTSeq
Assembly: mm10
Supplementary files format and content: tsv file format

molecule: polyA RNA

organism: Mus musculus

source_name: Lung cancer cell line

growth_protocol: We culture LLC1 cells in 10% FBS DMEM culture media.

extract_protocol: We extract mRNA using iNtron extraction kit.

treatment_protocol: We knocked down Ddx54 gene in LLC1 using shRNA

tag: cell line

value: Lung cancer cell line

tag: genotype

value: DDX54 KD


title: MC3T3-E1 cells, shRcor2-20, 7d, sample 1

molecule: total RNA

tag: cell type

tag: time


title: MC3T3-E1 cells, shRcor2-18, 7d, sample 1


title: MC3T3-E1 cells, shRcor2-18, 7d, sample 2


title: MC3T3-E1 cells, shRcor2-18, 24h, sample 1


title: MC3T3-E1 cells, shScramble, 7d, sample 2

value: WT


title: MC3T3-E1 cells, shRcor2-18, 24h, sample 2


title: MC3T3-E1 cells, shRcor2-20, 24h, sample 2


title: MC3T3-E1 cells, shScramble, 7d, sample 1


title: MC3T3-E1 cells, shRcor2-20, 24h, sample 1


title: MC3T3-E1 cells, shScramble, 24h, sample 1


title: C3,ChIP,IgG,rep1

city: Beer Sheva

first: Adam

last: Zaretsky

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gutrion University of the Negev

library_source: genomic

data_processing:
Raw fastq files from both experiments were analyzed with nf-core/chipseq pipeline (v2.0) . In brief, reads were trimmed with TrimGalore!  and align to the hg38 reference genome using BWA algorithm . The peak calling step was performed with MACS2 software , followed by the identification of the consensus and condition-specific peak sets. Peak annotation and enrichment analysis were performed with clusterProfiler R package. Publicly available Lamin B ChIP-seq human brain data  was used to annotate LAD regions. Heterochromatin regions in SK-N-SH cells, defined using H3K27me3 and H3K9me3 peaks were downloaded from The Human Heterochromatin Chromatin Database (HHCDB). The significance of the overlap between peak sets used as a measure for REST occurrence at LAD or heterochromatin regions was calculated with regioneR package  with ‘randomizeRegions’ argument in permTest() function, aiming to preserve the size of tested regions for permutations (N = 3000).
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
ChIP–qPCR analysis ChIP-seq sample preparation was carried out as previously described49. Briefly, SHSY-5Y cells WT and SIRT6 KO, or WT and SIRT KO transfected with Flag-REST, K494A, K494M, K494Q were cultured up to 80% of confluence. In the case of ChIP negative controls cells were transfected with an empty vector (CMV-Flag). Cells were cross-linked with 1% formaldehyde for 10 minutes and blocked with 0.125M Glycine for 5 minutes. Cross-linked cells were scrapped on RIPA buffer (150mM NaCl, 1% NP-40, 0.5% Sodium deoxycholate, 0.1% SDS, 50mM Tris pH 8, 5mM EDTA, 0.5mM PMSF, 50mM NaF/0.2mM Sodium orthovanadate, 5uM trichostatin A), and chromatin was sonicated with a needle sonicator (VibraCell VCX130, Sonics, CT, USA) during 25 minutes, 30/30 seconds on/off cycles at 40% of amplitude. One milligram of the sonicated chromatin was incubated overnight with previously blocked SureBeads™ Protein G Magnetic Beads or Anti-FLAG® M2 Magnetic Beads. The beads were then washed 4 times with RIPA buffer, 4 times with LiCl buffer (500mM LiCl, 100mM Tris-HCl pH 8.5, 1% NP-40, 1% sodium deoxycholate), and 2 times with TE buffer (10mM Tris-HCl pH 8, 1mM EDTA). Chromatin was eluted from beads using elution buffer (70mM Tris-HCl pH 8, 1mM EDTA, 1.5% SDS) and cross-linking was reversed by adding 200mM NaCl, 1U of Proteinase K, and incubating the eluted chromatin at 65C for 5 hours. The obtained DNA was further purified using the Nucleo Spin Gel and PCR Clean-Up kit. For qPCR analysis of specific REST binding regions in the genome, we used the set of primers listed in the key resources table. qPCR was performed according to the method described. We used 1uL of Input and ChIP samples per qPCR reaction.
ChIP DNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and the DNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). ChIP-Seq library preparation and sequencing reactions were conducted at GENEWIZ, Inc/Azenta US, Inc. (South Plainfield, NJ, USA). NEB Next Ultra II DNA Library Preparation kit was used following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). Briefly, the ChIP DNA was end repaired and adapters were ligated after adenylation of the 3’ends. Adapter-ligated DNA was size selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as real time PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was performed using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the Novaseq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina instrument was converted into fastq files and demultiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

tag: chip-antibody

value: Rabbit IgG (Part No. PP64B)

value: Neuroblastoma

value: SIRT6 KO

tag: treatment

value: No treatment


title: MC3T3-E1 cells, shRcor2-20, 0h, sample 1


title: MC3T3-E1 cells, shRcor2-20, 0h, sample 2


title: MC3T3-E1 cells, shScramble, 24h, sample 2


title: MC3T3-E1 cells, shRcor2-18, 0h, sample 2


title: MC3T3-E1 cells, shRcor2-18, 0h, sample 1


title: WT_Ddx54_LLC1_1

description:
Library name: WT_Ddx54_LLC1_1
Bulk RNA-seq

value: WT DDX54


title: MC3T3-E1 cells, shScramble, 0h, sample 1


title: MC3T3-E1 cells, shScramble, 0h, sample 2


title: maternal peripheral blood, E01354.V2

type: genomic

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

country: India

institute: National institute of Biomedical Genomics

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using GenomeStudio using standard recommended Illumina scanner setting

data_processing: Control normalization and Background subtraction performed using the Methylation module of GenomeStudio (Illumina) software version 2011.1

label: Cy5 and Cy3

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using QIAamp blood midi kit (Qiagen) according to manufacturer’s protocol

tag: individual id

tag: Sex

value: Female

tag: tissue

value: peripheral blood

tag: pregnancy

value: Term

tag: sampling time

value: Sampled during 18-20 weeks of gestation


title: maternal peripheral blood, E04489.V5

value: Sampled at delivery


title: maternal peripheral blood, E06436.V5


title: maternal peripheral blood, E04391.V5

value: Preterm


title: maternal peripheral blood, E02132.V5


title: maternal peripheral blood, E02032.V1

value: Sampled during 11-14 weeks of gestation


title: maternal peripheral blood, E05391.V5


title: maternal peripheral blood, E01354.V5


title: maternal peripheral blood, E00946.V2


title: maternal peripheral blood, E00946.V1


title: maternal peripheral blood, E02336.V3

value: Sampled during 26-28 weeks of gestation


title: maternal peripheral blood, E01417.V5


title: maternal peripheral blood, E06698.V5


title: maternal peripheral blood, E00946.V5


title: maternal peripheral blood, E02336.V1


title: maternal peripheral blood, E02336.V5


title: maternal peripheral blood, E06228.V5


title: maternal peripheral blood, E01354.V1


title: maternal peripheral blood, E04534.V5


title: maternal peripheral blood, E06332.V5


title: maternal peripheral blood, E00206.V5


title: maternal peripheral blood, E00946.V3


title: maternal peripheral blood, E02032.V3


title: maternal peripheral blood, E04725.V5


title: maternal peripheral blood, E06643.V5


title: maternal peripheral blood, E02032.V2


title: maternal peripheral blood, E02336.V2


title: maternal peripheral blood, E05895.V5


title: maternal peripheral blood, E02032.V5


title: maternal peripheral blood, E01354.V3


title: maternal peripheral blood, E01417.V2


title: maternal peripheral blood, E00937.V5


title: E00191.V3

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC Beadchip using standard Illumina protocol

data_processing: GenomeStudio software (Illumina) version 2011.1.

source_name: genomic DNA from maternal peripheral blood

tag: sample type

tag: disease state

tag: timepoint


title: maternal peripheral blood, E00858.V2


title: maternal peripheral blood, E00471.V1


title: maternal peripheral blood, E01041.V5


title: maternal peripheral blood, E01417.V1


title: maternal peripheral blood, E01417.V3


title: maternal peripheral blood, E00858.V5


title: E00191.V1


title: E00073.V3


title: maternal peripheral blood, E01041.V3


title: E00435.V3


title: maternal peripheral blood, E00858.V1


title: maternal peripheral blood, E00585.V2


title: E00073.V2


title: E00435.V2


title: maternal peripheral blood, E00937.V2


title: maternal peripheral blood, E00937.V1


title: E00472.V3


title: maternal peripheral blood, E00937.V3


title: E00191.V2


title: E00472.V1


title: E00918.V3


title: E00918.V2


title: E00435.V1


title: E00073.V1


title: maternal peripheral blood, E00471.V2


title: E00666.V3


title: maternal peripheral blood, E00325.V2


title: E01709.V3


title: E01709.V2


title: E01709.V1


title: maternal peripheral blood, E00858.V3


title: maternal peripheral blood, E00585.V1


title: E01532.V1


title: E01532.V2


title: E03907.V3


title: E01532.V3


title: E03907.V2


title: maternal peripheral blood, E01041.V2


title: maternal peripheral blood, E00471.V3


title: E03857.V3


title: E03857.V1


title: E03857.V2


title: maternal peripheral blood, E00340.V5


title: maternal peripheral blood, E00340.V3


title: E03907.V1


title: E04263.V3


title: maternal peripheral blood, E00585.V3


title: E04263.V2


title: maternal peripheral blood, E00340.V2


title: maternal peripheral blood, E00471.V5


title: E04263.V1


title: E04146.V3


title: E04146.V2


title: E04146.V1


title: E00666.V1


title: E05613.V2


title: maternal peripheral blood, E00340.V1


title: E00666.V2


title: maternal peripheral blood, E01041.V1


title: E05613.V1


title: E05224.V3


title: E05613.V3


title: E05224.V1


title: E00472.V2


title: E06021.V3


title: maternal peripheral blood, E00325.V3


title: E06021.V2


title: E06021.V1


title: E05550.V3


title: E05550.V1


title: E05224.V2


title: E05783.V3


title: E05783.V2


title: E05783.V1


title: maternal peripheral blood, E00325.V1


title: maternal peripheral blood, E00585.V5


title: E06450.V2


title: E05550.V2


title: E00918.V1


title: E05765.V2


title: E06450.V1


title: E06454.V3


title: E06653.V1


title: E06653.V2


title: E06653.V3


title: E06454.V1


title: E06864.V3


title: E06784.V1


title: E06626.V2


title: E06864.V2


title: E06812.V1


title: E06864.V1


title: E06784.V3


title: E05765.V3


title: E06626.V1


title: E06454.V2


title: E06812.V2


title: E06829.V1


title: E06829.V3


title: E06829.V2


title: maternal peripheral blood, E00325.V5


title: E07044.V3


title: E07044.V2


title: E06812.V3


title: E06784.V2


title: E07044.V1


title: E06979.V3


title: E06979.V1


title: E04316.V3


title: E04316.V1


title: E05071.V2


title: E04391.V1


title: E04391.V3


title: E04391.V2


title: E00164.V3


title: E05071.V3


title: E00206.V3


title: E05071.V1


title: E00164.V1


title: E00206.V2


title: E06626.V3


title: E04725.V1


title: E04725.V3


title: E04725.V2


title: E00164.V2


title: E00206.V1


title: E02131.V3


title: E02131.V1


title: E06979.V2


title: E02132.V3


title: E02132.V2


title: E02132.V1


title: E04316.V2


title: E04707.V3


title: E04707.V2


title: E04707.V1


title: E04489.V2


title: E04489.V1


title: E04682.V3


title: E04489.V3


title: E04682.V2


title: E05502.V3


title: E05502.V1


title: E05391.V3


title: E04534.V2


title: E05502.V2


title: E05895.V3


title: E06370.V3


title: E02131.V2


title: E06370.V1


title: E05391.V2


title: E05895.V1


title: E05895.V2


title: E06289.V3


title: E06289.V1


title: E06289.V2


title: E06228.V3


title: E06228.V2


title: E05391.V1


title: E05765.V1


title: E04682.V1


title: E04534.V1


title: E04534.V3


title: E06228.V1


title: E06511.V2


title: E06511.V1


title: E06370.V2


title: E06511.V3


title: E06332.V3


title: E06332.V1


title: E06332.V2


title: E06695.V2


title: E06695.V3


title: E06785.V3


title: E06436.V2


title: E06436.V3


title: E06436.V1


title: E06785.V1


title: E06643.V3


title: E06643.V2


title: E06643.V1


title: E06902.V3


title: E06902.V1


title: E06902.V2


title: E06698.V2


title: E06698.V1


title: E06695.V1


title: E06785.V2


title: E06698.V3


title: E06450.V3


title: 1769-V1 genomic DNA from maternal peripheral blood

tag: time point


title: 1845-V5 genomic DNA from maternal peripheral blood


title: 1656-V5 genomic DNA from maternal peripheral blood


title: 1769-V5 genomic DNA from maternal peripheral blood


title: 0251-V1 genomic DNA from maternal peripheral blood


title: 0328-V1 genomic DNA from maternal peripheral blood


title: 1769-V2 genomic DNA from maternal peripheral blood


title: 1845-V1 genomic DNA from maternal peripheral blood


title: 0876-V2 genomic DNA from maternal peripheral blood


title: 0328-V3 genomic DNA from maternal peripheral blood


title: 1563-V1 genomic DNA from maternal peripheral blood


title: 0876-V5 genomic DNA from maternal peripheral blood


title: 1656-V2 genomic DNA from maternal peripheral blood


title: 1563-V3 genomic DNA from maternal peripheral blood


title: 1563-V5 genomic DNA from maternal peripheral blood


title: 0876-V3 genomic DNA from maternal peripheral blood


title: 0251-V3 genomic DNA from maternal peripheral blood


title: 0251-V2 genomic DNA from maternal peripheral blood


title: 1769-V3 genomic DNA from maternal peripheral blood


title: 0876-V1 genomic DNA from maternal peripheral blood


title: 1563-V2 genomic DNA from maternal peripheral blood


title: 1845-V3 genomic DNA from maternal peripheral blood


title: 1656-V3 genomic DNA from maternal peripheral blood


title: 0251-V5 genomic DNA from maternal peripheral blood


title: 1656-V1 genomic DNA from maternal peripheral blood


title: 1845-V2 genomic DNA from maternal peripheral blood


title: 0328-V5 genomic DNA from maternal peripheral blood


title: 0682-V5 genomic DNA from maternal peripheral blood


title: 0328-V2 genomic DNA from maternal peripheral blood


title: 0682-V1 genomic DNA from maternal peripheral blood


title: 1441-V2 genomic DNA from maternal peripheral blood


title: 0682-V2 genomic DNA from maternal peripheral blood


title: 0682-V3 genomic DNA from maternal peripheral blood


title: 1441-V1 genomic DNA from maternal peripheral blood


title: 1213-V2 genomic DNA from maternal peripheral blood


title: 1441-V5 genomic DNA from maternal peripheral blood


title: 1213-V1 genomic DNA from maternal peripheral blood


title: 1213-V5 genomic DNA from maternal peripheral blood


title: 0375-V1 genomic DNA from maternal peripheral blood


title: 0828-V3 genomic DNA from maternal peripheral blood


title: 1213-V3 genomic DNA from maternal peripheral blood


title: 0978-V1 genomic DNA from maternal peripheral blood


title: 0375-V3 genomic DNA from maternal peripheral blood


title: 0285-V5 genomic DNA from maternal peripheral blood


title: 0978-V2 genomic DNA from maternal peripheral blood


title: 0464-V3 genomic DNA from maternal peripheral blood


title: 0464-V1 genomic DNA from maternal peripheral blood


title: 0828-V2 genomic DNA from maternal peripheral blood


title: 0375-V2 genomic DNA from maternal peripheral blood


title: 0978-V3 genomic DNA from maternal peripheral blood


title: 0285-V3 genomic DNA from maternal peripheral blood


title: 0375-V5 genomic DNA from maternal peripheral blood


title: 0828-V5 genomic DNA from maternal peripheral blood


title: 0828-V1 genomic DNA from maternal peripheral blood


title: 0285-V2 genomic DNA from maternal peripheral blood


title: 0203-V2 genomic DNA from maternal peripheral blood


title: 0464-V5 genomic DNA from maternal peripheral blood


title: 0464-V2 genomic DNA from maternal peripheral blood


title: 0203-V5 genomic DNA from maternal peripheral blood


title: 0107-V5 genomic DNA from maternal peripheral blood


title: 0107-V3 genomic DNA from maternal peripheral blood


title: 0107-V2 genomic DNA from maternal peripheral blood


title: 0029-V5 genomic DNA from maternal peripheral blood


title: 0203-V3 genomic DNA from maternal peripheral blood


title: 0029-V3 genomic DNA from maternal peripheral blood


title: 0029-V2 genomic DNA from maternal peripheral blood


title: 3501-V2 genomic DNA from maternal peripheral blood


title: 0107-V1 genomic DNA from maternal peripheral blood


title: 1441-V3 genomic DNA from maternal peripheral blood


title: 4293-V3 genomic DNA from maternal peripheral blood


title: 4293-V2 genomic DNA from maternal peripheral blood


title: 0285-V1 genomic DNA from maternal peripheral blood


title: 3640-V3 genomic DNA from maternal peripheral blood


title: 4293-V1 genomic DNA from maternal peripheral blood


title: 4006-V5 genomic DNA from maternal peripheral blood


title: 4006-V1 genomic DNA from maternal peripheral blood


title: 4293-V5 genomic DNA from maternal peripheral blood


title: 4006-V3 genomic DNA from maternal peripheral blood


title: 4006-V2 genomic DNA from maternal peripheral blood


title: 3248-V3 genomic DNA from maternal peripheral blood


title: 3501-V1 genomic DNA from maternal peripheral blood


title: 3501-V3 genomic DNA from maternal peripheral blood


title: 3248-V2 genomic DNA from maternal peripheral blood


title: 3248-V5 genomic DNA from maternal peripheral blood


title: 3501-V5 genomic DNA from maternal peripheral blood


title: 3138-V3 genomic DNA from maternal peripheral blood


title: 3640-V1 genomic DNA from maternal peripheral blood


title: 0029-V1 genomic DNA from maternal peripheral blood


title: 3640-V2 genomic DNA from maternal peripheral blood


title: 3138-V5 genomic DNA from maternal peripheral blood


title: 0978-V5 genomic DNA from maternal peripheral blood


title: 0203-V1 genomic DNA from maternal peripheral blood


title: 3248-V1 genomic DNA from maternal peripheral blood


title: 1031-V3 genomic DNA from maternal peripheral blood


title: 1423-V3 genomic DNA from maternal peripheral blood


title: 1537-V5 genomic DNA from maternal peripheral blood


title: 3138-V1 genomic DNA from maternal peripheral blood


title: 1537-V1 genomic DNA from maternal peripheral blood


title: 1537-V3 genomic DNA from maternal peripheral blood


title: 1537-V2 genomic DNA from maternal peripheral blood


title: 1423-V1 genomic DNA from maternal peripheral blood


title: 3138-V2 genomic DNA from maternal peripheral blood


title: 1378-V3 genomic DNA from maternal peripheral blood


title: 1031-V5 genomic DNA from maternal peripheral blood


title: 1031-V1 genomic DNA from maternal peripheral blood


title: 1423-V2 genomic DNA from maternal peripheral blood


title: 1031-V2 genomic DNA from maternal peripheral blood


title: 1378-V1 genomic DNA from maternal peripheral blood


title: 1423-V5 genomic DNA from maternal peripheral blood


title: 1378-V5 genomic DNA from maternal peripheral blood


title: 3640-V5 genomic DNA from maternal peripheral blood


title: nucleus pulposus progenitor cell-derived exosomes_4

city: Chongqing

first: Wenkai

last: Wang

state: Chongqing

address: Gaotanyan main street

country: China

institute: Army Medical University

description:
Library name: Sample 8
NPPC_Exos_4

data_processing:
ACGT101-miR (LC Sciences, Houston, Texas, USA); CASAVA 1.8
Assembly: miRBase
Supplementary files format and content: txt files include normalized (norm) and raw expression data for each samples

organism: Rattus norvegicus

source_name: intervertebral disc

extract_protocol:
Total RNAs were isolated using the Total Exosome RNA Isolation Kit (Thermo Scientific) and miRNA sequencing was conducted by LC-Bio Technology Co., Ltd. (Hangzhou, China). The quality and quantity of total RNA were assessed using a Bioanalyzer 2100 (Agilent) with an RIN number >7.0.
Small RNA libraries were prepared from approximately 1 μg of total RNA according to the TruSeq Small RNA Sample Prep Kits (Illumina) protocol.

value: intervertebral disc

value: nucleus pulposus progenitor cells


title: nucleus pulposus progenitor cell-derived exosomes_3

description:
Library name: Sample 7
NPPC_Exos_3


title: nucleus pulposus progenitor cell-derived exosomes_2

description:
Library name: Sample 6
NPPC_Exos_2


title: nucleus pulposus progenitor cell-derived exosomes_1

description:
Library name: Sample 5
NPPC_Exos_1


title: nucleus pulposus cell-derived exosomes_4

description:
Library name: Sample 4
N_Exos_4

value: nucleus pulposus cells


title: 1085-V5 genomic DNA from maternal peripheral blood


title: 1131-V5 genomic DNA from maternal peripheral blood


title: nucleus pulposus cell-derived exosomes_3

description:
Library name: Sample 3
N_Exos_3


title: nucleus pulposus cell-derived exosomes_2

description:
Library name: Sample 2
N_Exos_2


title: 1378-V2 genomic DNA from maternal peripheral blood


title: 1085-V3 genomic DNA from maternal peripheral blood


title: 0952-V5 genomic DNA from maternal peripheral blood


title: nucleus pulposus cell-derived exosomes_1

description:
Library name: Sample 1
N_Exos_1


title: 1085-V1 genomic DNA from maternal peripheral blood


title: SH-mNeonGreen_rep2

city: Edinburgh

first: Paul

last: Ross

address: Hugh Robson Building. George Square

country: United Kingdom

institute: University of Edinburgh

description:
Library name: Sample 17
Column name in all_samples_gene_count_matrix.csv: SH-mNeonGreen_rep2

data_processing:
Low quality reads and adapters were removed using Cutadapt
Reads were mapped to the reference human genome using HISAT2
Gene level read count matrix generated using StringTie
Data normalized and lowly expressed genes filtered out using edgeR
Linear modelling and empirical Bayes moderation to assess differential expression (Limma using voom method)
Assembly: GRCh38 (hg38)
Supplementary files format and content: all_samples_gene_count_matrix.csv

growth_protocol: HEK293A, HepG2, SH-SY5Y, and COS7 cells (American Type Culture Collection [ATCC]) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 4.5 g/L D-glucose supplemented with 10 % heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, and 1× MEM nonessential amino acids solution (Thermo Fisher Scientific). Cells were subcultured every 2-3 days and seeded at 2×106 cells in T175 vented flasks (Greiner Bio-One). Cells were grown in a humidified incubator at 37 °C and 5 % CO2.

extract_protocol:
RNA was extracted from  transfected cells by homogenization in Qiazol (79306; Qiagen) following the manufacturer’s instructions. RNA was reconstituted in 25 µL nuclease-free water, and concentrations were measured using a Nanodrop 2000 (ThermoFisher Scientific). RNA quality was assessed using an Agilent TapeStation 4200 (Agilent Technologies)
Illumina TruSeq Stranded mRNA using standard manufacturer protocol

treatment_protocol: For HEK293A and HepG2 cells were cultured to 80-90 % confluency before the day of transfection, trypsinized (TrypLE™ Express, Life Technologies), and seeded into 96- well plates (Greiner Bio-One) coated with poly-L-ornithine (Sigma Aldrich) and fibronectin (Sigma Aldrich) at 8×103 cells per well. Cells were transfected using Lipofectamine 2000 (Life Technologies) following the manufacturer’s protocol with 100 ng plasmid mixed with Opti-MEM (ThermoFisher Scientific) per well. SH-SY5Y cells were transfected using the Lonza 4D-NucleofectorTM system, according to the recommendations of the supplier.

value: NeonGreen plasmid transfection


title: SH-mNeonGreen-EXACT1_rep2

description:
Library name: Sample 14
Column name in all_samples_gene_count_matrix.csv: SH-mNeonGreen-EXACT1_rep2

value: NeonGreen + EXACT1 plasmid transfection


title: SH-mNeonGreen_rep1

description:
Library name: Sample 16
Column name in all_samples_gene_count_matrix.csv: SH-mNeonGreen_rep1

value: Neuroblastoma


title: SH-mNeonGreen-EXACT1_rep3

description:
Library name: Sample 15
Column name in all_samples_gene_count_matrix.csv: SH-mNeonGreen-EXACT1_rep3


title: Hep-mNeonGreen_rep1

description:
Library name: Sample 10
Column name in all_samples_gene_count_matrix.csv: Hep-mNeonGreen_rep1

value: Hepatocellular carcinoma


title: SH-mNeonGreen_rep3

description:
Library name: Sample 18
Column name in all_samples_gene_count_matrix.csv: SH-mNeonGreen_rep3


title: Hep-mNeonGreen-EXACT1_rep3

description:
Library name: Sample 9
Column name in all_samples_gene_count_matrix.csv: Hep-mNeonGreen-EXACT1_rep3


title: Hep-mNeonGreen_rep2

description:
Library name: Sample 11
Column name in all_samples_gene_count_matrix.csv: Hep-mNeonGreen_rep2


title: Hep-mNeonGreen-EXACT1_rep2

description:
Library name: Sample 8
Column name in all_samples_gene_count_matrix.csv: Hep-mNeonGreen-EXACT1_rep2


title: SH-mNeonGreen-EXACT1_rep1

description:
Library name: Sample 13
Column name in all_samples_gene_count_matrix.csv: SH-mNeonGreen-EXACT1_rep1


title: Hep-mNeonGreen_rep3

description:
Library name: Sample 12
Column name in all_samples_gene_count_matrix.csv: Hep-mNeonGreen_rep3


title: 1131-V2 genomic DNA from maternal peripheral blood


title: HEK-mNeonGreen_rep3

description:
Library name: Sample 6
Column name inall_samples_gene_count_matrix.csv: HEK-mNeonGreen_rep3

value: Embryonic kidney


title: HEK-mNeonGreen_rep2

description:
Library name: Sample 5
Column name in all_samples_gene_count_matrix.csv: HEK-mNeonGreen_rep2


title: HEK-mNeonGreen_rep1

description:
Library name: Sample 4
Column name in all_samples_gene_count_matrix.csv: HEK-mNeonGreen_rep1


title: HEK-mNeonGreen-EXACT1_rep3

description:
Library name: Sample 3
Column name in all_samples_gene_count_matrix.csv: HEK-mNeonGreen-EXACT1_rep3


title: HEK-mNeonGreen-EXACT1_rep2

description:
Library name: Sample 2
Column name in all_samples_gene_count_matrix.csv: HEK-mNeonGreen-EXACT1_rep2


title: HGC27 cells, OASL_3

city: Changsha

first: Fen

state: Hunan

address: 138 Tongzipo Road

institute: The Third Xiangya Hospital, Central South University

description:
Library name: Sample 6
Column name in gene_count_matrix.txt: OE15

data_processing:
Libraries were deeply sequenced on the Illumina Novaseq 6000 according to the activity and expected data volume.
The raw RNA-Seq sequence reads were trimmed using Trimmomatic (version 0.39) to remove low-quality reads and adapters.
Assembly: Trimmed data were first evaluated by the software “FastQC” (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with the default parameter and then aligned with Hisat2 (version 2.1.0) against the human (hg38) genome guided by GENCODE gene annotation (version 34) with the default parameter.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: RPMI-1640 mediu mcontaining 10% fetal bovine serum

extract_protocol:
Total RNA was isolated using RNAiso Plus (Total RNA extraction reagent, Thermo Fisher Scientific) according to the manufacturer’s instructions and quantified by the NanoDrop 2000 spectrophotometer.
TruSeq Stranded Total Sample Preparation Kit (Illumina, 20020596) was used for sequencing library construction.

value: gastric epithelial cells

value: TRAF1 overexpressing

value: subculture


title: HGC27 cells, OASL_1

description:
Library name: Sample 4
Column name in gene_count_matrix.txt: OE13


title: HGC27 cells, OASL_2

description:
Library name: Sample 5
Column name in gene_count_matrix.txt: OE14


title: HGC27 cells, Control_3

description:
Library name: Sample 3
Column name in gene_count_matrix.txt: NC15

value: WT


title: 0952-V2 genomic DNA from maternal peripheral blood

value: Female

value: peripheral blood

value: Sampled during 18-20 weeks of gestation


title: 0952-V3 genomic DNA from maternal peripheral blood

value: Preterm


title: HGC27 cells, Control_1

description:
Library name: Sample 1
Column name in gene_count_matrix.txt: NC13


title: HEK-mNeonGreen-EXACT1_rep1

description:
Library name: Sample 1
Column name in all_samples_gene_count_matrix.csv: HEK-mNeonGreen-EXACT1_rep1


title: 1085-V2 genomic DNA from maternal peripheral blood


title: POD5

city: Palo Alto

first: Takaya

last: Ishii

state: California

address: 3165 PORTER DRIVE

country: USA

institute: Stanford University

description:
Library name: D5
10x Genomics

library_source: transcriptomic single cell

data_processing:
The row reads were mapped to human reference genome version GRCh38 and unique molecular identifiers (UMIs) counts for each gene in each cell by CellRanger Arch v2.0.0. (10x Genomics)
Assembly: GRCh38
Supplementary files format and content: tab-separated values files, matrix files

molecule: nuclear RNA

source_name: brain

extract_protocol:
Nuclei were extracted from frozen brain tissues.Frozen tissue was homogenized in a chilled lysis buffer using a Dounce homogenizer, followed by differential centrifugation with iodixanol gradient separation to isolate the nuclei. The nuclei pellet was then carefully collected, resuspended, and subjected to additional washes and centrifugation steps. The final nuclei were resuspended in PBS/1% BSA, snap-frozen, and stored
10,000 nuclei were applied for library preparation using Chromium Next GEM Single Cell Multiome Reagent Kit (10x Genomics) following the manufacturer’s protocol

value: brain


title: POD7

description:
Library name: D7
10x Genomics


title: POD9

description:
Library name: D9
10x Genomics


title: 0952-V1 genomic DNA from maternal peripheral blood

value: Sampled during 11-14 weeks of gestation


title: POD6

description:
Library name: D6
10x Genomics


title: POD4

description:
Library name: D4
10x Genomics


title: POD3

description:
Library name: D3
10x Genomics


title: POD1

description:
Library name: D1
10x Genomics


title: POD2

description:
Library name: D2
10x Genomics


title: 1131-V3 genomic DNA from maternal peripheral blood

value: Term

value: Sampled during 26-28 weeks of gestation


title: non-POD9

description:
Library name: N9
10x Genomics


title: 0345-V1 genomic DNA from maternal peripheral blood


title: non-POD8

description:
Library name: N8
10x Genomics


title: non-POD7

description:
Library name: N7
10x Genomics


title: POD8

description:
Library name: D8
10x Genomics


title: non-POD1

description:
Library name: N1
10x Genomics


title: non-POD2

description:
Library name: N2
10x Genomics


title: non-POD3

description:
Library name: N3
10x Genomics


title: non-POD4

description:
Library name: N4
10x Genomics


title: KO

city: hangzhou

first: Yunyi

last: Gao

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388

institute: Zhejiang university

description: Library name: Sample22

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
Illumina sequencing reads were treated with fastp (version 0.23.2)  for adaptor removal and quality trimming.
The remaining reads were mapped to  human transcriptome using BWA-MEM with default parameters.
SAMtools(version 1.9) were used to select high-quality alignments, remove PCR duplications, and extract the reads mapping of every nucleotide in the transcriptome
Mismatch rate was calculated using in-house scripts. RPKM was calculated using in-house scripts following the definition of RPKM.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include the mismatch rate for m3C for each sample. Comma-Separated Values files include the RPKM values for each each.

extract_protocol:
Total RNA was isolated from cell lines by Trizol(Invitrogen).tRNA was purified by 7M 10% denaturing polyacrylamide TBE-urea gel. polyA+ RNA was purified using Dynabeads Oligo(dT)25 (Invitrogen).
polyA+ RNA RNA fragments or tRNAs were converted to cDNA with high-processive reverse transcriptases SuperScript IV (Invitrogen) and sequenced (Input), or precipitated by m3C antibody before cDNA synthesis (IP), and the use of demethylase treatment improves the confidence of detection (Dm).

value: Human embryonic kidney

value: METTL8 KO


title: 0735-V2 genomic DNA from maternal peripheral blood


title: 0733-V3 genomic DNA from maternal peripheral blood


title: 0345-V3 genomic DNA from maternal peripheral blood


title: 0735-V1 genomic DNA from maternal peripheral blood


title: 0735-V3 genomic DNA from maternal peripheral blood


title: 0733-V2 genomic DNA from maternal peripheral blood


title: CTL

description: Library name: Sample21


title: tRNA_m3C_Dm-mix

description: Library name: Sample20


title: HGC27 cells, Control_2

description:
Library name: Sample 2
Column name in gene_count_matrix.txt: NC14


title: tRNA_m3C_Input-mix

description: Library name: Sample18


title: 0345-V5 genomic DNA from maternal peripheral blood

value: Sampled at delivery


title: m3C_Dm1

description: Library name: Sample11


title: m3C_Dm2

description: Library name: Sample12


title: m3C_IP2

description: Library name: Sample10


title: 1131-V1 genomic DNA from maternal peripheral blood


title: 0735-V5 genomic DNA from maternal peripheral blood


title: 0733-V1 genomic DNA from maternal peripheral blood


title: m3C_Input2

description: Library name: Sample8


title: m3C_IP1

description: Library name: Sample9


title: 0345-V2 genomic DNA from maternal peripheral blood


title: tRNA_m3C_Dm1

description: Library name: Sample5


title: m3C_Input1

description: Library name: Sample7


title: tRNA_m3C_Dm2

description: Library name: Sample6


title: tRNA_m3C_IP2

description: Library name: Sample4


title: tRNA_m3C_IP1

description: Library name: Sample3


title: tRNA_m3C_Input2

description: Library name: Sample2


title: NBB_AD34_HIP

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Library name: NBB_AD34_HIP

data_processing:
Seurat v4.0.3 with default parameters was used to perform sctransform (SCT) normalization, integration and Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction. The FindClusters function was used for cell clustering. To improve clustering, all samples were analyzed in an integrated analysis, based on canonical correlation analysis (CCA).
Assembly: GRCH38
Supplementary files format and content: h5ad file - AnnData file containing count and annotation results for all samples

source_name: Brain

extract_protocol:
FACS sorting of PU.1+ nuclei from postmortem samples. Single-nuclei RNA-Seq of FACSsorted nuclei suspensions was performed on Chromium instrument (10X genomics) following the user guide manual (Reagent Kit 3’ v3.1).
Each sample, containing approximately 10,000 nuclei at a final dilution of ~1,000 cells/μl was loaded onto the cartridge following the manual. The individual transcriptomes of encapsulated cells were barcoded during RT step and resulting cDNA purified with DynaBeads followed by amplification per manual guidelines. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to the sequencing adapters and indexed by PCR. The indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher). Sequencing depth was ~200 million reads per sample on average. FASQ files were processed using SEQC pipeline 36 for quality control, mapping to GRCH38 reference genome, and log2 transformation of the data with the default SEQC parameters to obtain the gene-cell count matrix.

value: Brain

value: primary

value: Microglia

value: Alzheimer's Disease


title: NBB_C11_AG

description: Library name: NBB_C11_AG

value: Normal


title: NBB_AD52_HIP

description: Library name: NBB_AD52_HIP


title: NBB_AD53_HIP

description: Library name: NBB_AD53_HIP


title: tRNA_m3C_IP-mix

description: Library name: Sample19

value: WT


title: NBB_AD52_SPG

description: Library name: NBB_AD52_SPG


title: 02MV4-11-LDB1

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description:
Library name: Sample 2
CUT&Tag DNA

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS3 (v3.0.2)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).


title: MV4-11-LDB1

description:
Library name: Sample 1
CUT&Tag DNA


title: 0733-V5 genomic DNA from maternal peripheral blood

value: Female


title: Hep-mNeonGreen-EXACT1_rep1

description:
Library name: Sample 7
Column name in all_samples_gene_count_matrix.csv: Hep-mNeonGreen-EXACT1_rep1

value: Hepatocellular carcinoma

value: NeonGreen + EXACT1 plasmid transfection


title: tRNA_m3C_Input1

description: Library name: Sample1


title: HCT116 cells(IgG-3)

city: shanghai

first: shihui

last: shen

state: Shanghai

address: 500 Dongchuan Road

institute: East China Normal University

description: Library name: IgG-3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and discarded reads left with < 20 bp. ChlP-seg reads were aligned to the UcsC hg38 genome using Bowtie version 2.2.9. Only uniquely mapping reads with at most two mismatches were retained.
To create ChlP-seg coverage plots, the locations of the mapped ChlP-seg reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million.rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.6 with the significance cut-off q-value <=0.01
BigWig files were generated using the genomicRanges R package. Score represents thenormalized coverage of DNA fragments at a given genomic coordinate. narrowPeak fileswere generated using MACS v2.2.6 with default settings
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Collect HCT116 live cells (cell viability over 90%) and prepare DNA libraries using the Vazyme Hyperactive Universal CUT&Tag kit (TD904, Vazyme).
CHIP-seq libraries were prepared for sequencing using standard lllumina protocols

value: Human colon cancer cells


title: RA109 IFN

city: Durham

first: George

middle: Alexander

last: Truskey

state: NC

address: 101 Science Drive Room 1427 Room 1427

department: Biomedical Engineering

institute: Duke University

description:
Library name: R109-IFN-V
column name in Counts.txt: R109-IFN-V

data_processing:
RNA-seq data was processed using the TrimGalore toolkit (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) which employs Cutadapt  to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.
Only reads that were 20nt or longer after trimming were kept for further analysis.
Assembly: Reads were mapped to the GRCh38v93 version of the human genome and transcriptome (http://www.ensembl.org) using the STAR RNA-seq alignment tool (http://www-huber.embl.de/users/anders/HTSeq/ )
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: vastus lateralis

growth_protocol: Myobundles were cultured in human growth media (hGM) containing low-glucose (1 g/L glucose) DMEM  supplemented with 8% fetal bovine serum (Hyclone), 0.4 µg/mL Dexamethasone, 10 ng/mL EGF, 50 µg/mL Fetuin, 0.1% Gentamycin, 0.1% Amphotericin B, 1.5 mg/mL 6-aminocaproic acid (ACA) on a rocker (0.33 Hz) at 37°C. On day 4, the media was switched to differentiation media  consisting of LG-DMEM supplemented with 1X N-2 supplement (ThermoFisher Scientific), 0.1% gentamycin, 0.1% amphotericin B, and 2 mg/mL of ACA.

extract_protocol:
RNA was extracted using the Aurum Total RNA Mini Kit from BioRAD.
RNA libraries were built by the Duke Sequencing and Genomics Technologies Core Facility using stranded mRNA kit (Roche: 07962207001, Indianapolis, IN, USA)
RNA libraries were sequenced as 50 pair-ended base pairs with a NovaSeq 6000 S-Prime

treatment_protocol: Beginning on day 7 of differentiation, myobundles made with myoblasts from RA donors or healthy age-matched controles were treated with 5 ng/mL IFN-γ with or without 5 ng/ml IL-6 in differentiation mediafor 7 days after which RNA sequencing was perfimend .

value: vastus lateralis

value: primary cells

value: skeletal muscle myotube

value: Rheumatoid arthritis

value: Interferon-g


title: RA109 IFN_IL-6

description:
Library name: R109-IFN_IL6-X
column name in Counts.txt: R109-IFN_IL6-X


title: HCT116 cells,NRF2-3 (CHIP)

description: Library name: NRF2-3, CHIP

value: NRF2 CHIP antibody  (Abcam, #ab137550)


title: HCT116 cells,NRF2-1 (CHIP)

description: Library name: NRF2-1, CHIP


title: HCT116 cells(IgG-2)

description: Library name: IgG-2


title: HCT116 cells(IgG-1)

description: Library name: IgG-1


title: RA109  IL-6

description:
Library name: R109-IL6-W
column name in Counts.txt: R109-IL6-W


title: RA106 Untreated (NT)

description:
Library name: R106-NT-Q
column name in Counts.txt: R106-NT-Q

value: untreated


title: RA104 IFN_IL-6

description:
Library name: R104-IFN_IL6-P
column name in Counts.txt: R104-IFN_IL6-P


title: non-POD6

description:
Library name: N6
10x Genomics

value: brain


title: RA106 IFN_IL-6

description:
Library name: R106-IFN_IL6-T
column name in Counts.txt: R106-IFN_IL6-T


title: RA106  IL-6

description:
Library name: R106-IL6-S
column name in Counts.txt: R106-IL6-S


title: RA106 IFN

description:
Library name: R106-IFN-R
column name in Counts.txt: R106-IFN-R


title: HCT116 cells,NRF2-2 (CHIP)

description: Library name: NRF2-2, CHIP


title: RA104  IL-6

description:
Library name: R104-IL6-O
column name in Counts.txt: R104-IL6-O


title: RA109 Untreated (NT)

description:
Library name: R109-NT-U
column name in Counts.txt: R109-NT-U


title: RA104 IFN

description:
Library name: R104-IFN-N
column name in Counts.txt: R104-IFN-N


title: non-POD5

description:
Library name: N5
10x Genomics


title: RA104 Untreated (NT)

description:
Library name: R104-NT-M
column name in Counts.txt: R104-NT-M


title: C111  IL-6

description:
Library name: C111-IL6-K
column name in Counts.txt: C111-IL6-K


title: C111 IFN

description:
Library name: C111-IFN-J
column name in Counts.txt: C111-IFN-J


title: C109 IFN_IL-6

description:
Library name: C109-IFN_IL6-H
column name in Counts.txt: C109-IFN_IL6-H


title: C109  IL-6

description:
Library name: C109-IL6-G
column name in Counts.txt:C109-IL6-G


title: C109 IFN

description:
Library name: C109-IFN-F
column name in Counts.txt: C109-IFN-F


title: C109 Untreated (NT)

description:
Library name: C109-NT-E
column name in Counts.txt: C109-NT-E


title: C107 IFN_IL-6

description:
Library name: C107-IFN_IL6-D
column name in Counts.txt: C107-IFN_IL6-D


title: C111 Untreated (NT)

description:
Library name: C111-NT-I
column name in Counts.txt: C111-NT-I


title: C107 IFN

description:
Library name: C107-IFN-B
column name in Counts.txt: C107-IFN-B


title: C107 Untreated (NT)

description:
Library name: C107-NT-A
column name in Counts.txt: C107-NT-A


title: C107  IL-6

description:
Library name: C107-IL6-C
column name in Counts.txt: C107-IL6-C


title: EC2

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: No. 251, Yaojiayuan Road, Chaoyang District

institute: Beijing Obstetrics and Gynecology Hospital, Capital Medical University

description: Library name: Sample 5

data_processing:
CLC Genomics workbench v11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each samples

source_name: Human endometrial epithelium

extract_protocol:
Total RNA was isolated using Trizol reagent (RNA Extraction Kit, AG11701, Accurate Biology Co.,Ltd)，1.4μg of total RNA was used for the construction of sequencing  libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Human endometrial epithelium

value: Human endometrial epithelial cells

value: endometrial epithelial primary cells


title: EC1

description: Library name: Sample 4


title: Ctrl2

description: Library name: Sample 2


title: Ctrl3

description: Library name: Sample 3


title: Hashed_eGBOs_1mo

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

description: Library name: Hashed Brain Organoids

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed using the 10X Cell Ranger software version 6.1.1
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dissociated whole brain organoids

growth_protocol: Brain organoids were generated using the same protocol as described Lancaster et al. Nature Protocols 2014, with the exception that mTESR1 (Stem Cell Technologies) was used during embryoid body formation. After 1 month of in vitro differentiation, brain organoid were dissociated into cells and injected into the brain of seven-week-old female athymic nude mice.

extract_protocol:
Approximately ten organoids per condition were pooled and dissociated in TrypLE for 15min with gentle agitation every 5min. Single cell solutions were resuspended in 200µL of cell staining buffer (BioLegend, 420201) plus 1µg of TotalSeq-A hashtag antibodies (BioLegend, 399907) and incubated for 30min on ice. After three washes in 1mL of cell staining buffer, cells were resuspended in DMEM at a concentration of 1000cells/µL and pooled together. Recovered tumors were dissociated using the Brain Tumor Dissociation Kit (Miltenyi Biotec, 130-095-942). Myelin was removed using Myelin
For library preparations, the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics) was used following the provided protocol. The library was sequenced with a NovaSeq 6000 System (Illumina) at the recommended 26x98bp.

treatment_protocol: Genetically engineered H1 hPSCs cell lines were generated by the Genome Engineering & Stem Cell Center at Washington University School of Medicine in St. Louis. Briefly, H1 hPSCs were transfected with Cas9 recombinant protein and synthetic single guide RNA to introduce a C>T mutation within the telomerase reverse transcriptase (TERT) gene promoter. The H1 TERT mutant cell line was then further to modified, by the same procedure, to introduce either a point mutation targeting the TP53 gene or knockouts mutations in the PTEN and NF1 genes.

value: Dissociated whole brain organoids

value: H1 hESC


title: Txp3mo_MES_eGBO

description: Library name: Transplanted MES Brain Organoids

source_name: Dissociated tumor

value: Dissociated tumor

value: Dissociated brain organoid cells were injected into the brain of seven-week-old female athymic nude mice and recovered after 3 months. Tumors were dissociated using the Brain Tumor Dissociation Kit (Miltenyi Biotec, 130-095-942). Myelin was removed using Myelin Removal Beads II (Miltenyi Biotec, 130-096-731). Mouse cells were removed using the Mouse Cell Depletion Kit (Miltenyi Biotec, 130-104-694).


title: Txp3mo_PRO_eGBO

description: Library name: Transplanted PRO Brain Organoids


title: Txp3mo_WT_eGBO

description: Library name: Transplanted WT Brain Organoids


title: 22_NCIH510_sgBRD4_2_Hypoxia_rep2

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: S22

data_processing:
Preprocessing was performed using CETO Toolbox (48). Sequence quality was assessed using FastQC v 0.11.2 (49), and quality trimming was done using Trimmomatic (50) with parameters TRAILING:30 MINLEN:20. RNA-seq reads were aligned to the GRCh38 genome using STAR v.2.5.2 (51) and only uniquely mapped reads with a two-mismatch threshold were considered for downstream analysis and quantified to the gene level using HTSeq (52).
Output BAM files were converted into bigWig track files to display coverage throughout the genome (in rpm). Gene count tables were constructed following Ensembl GRCh38.p13, release 98 (45).
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Lung carcinoma

growth_protocol: NCI-H510 cells were cultured in rectangular flask (Corning, #430639).

extract_protocol:
Total RNAs were extracted using the RNeasy mini kit from Qiagen (Qiagen, #74106) according to the procedure. mRNAs were enriched using the NEBNext poly(A) mRNA magnetic isolation module (NEB, #E7490L).
Libraries were prepared using the NEBNext Ultra II Directional RNA library preparation kit (NEB, #E7760L) and sequenced on the NovaSeq 6000 (29).

treatment_protocol: To deplete both BRD4 and BRDT, 250nM dBET6 was added to the sgCtrl cells 3h prior to hypoxia induction. To carry out hypoxia induction, normoxia plates were kept in normal incubator while hypoxia plates were moved to the hypoxia station. 6 hours later, all plates were transferred to the cold room and cell pellets were collected. 20% of the cell pellets were saved for western blot and 80% for RNA extraction.

value: Lung carcinoma

value: epithelial

value: BRD4 knockdown

tag: treatment 1

value: Hypoxia 6h


title: 20_NCIH510_sgCtrl_dBET6_Hypoxia_rep2

description: Library name: S20

value: WT

tag: treatment 2

value: dBET6 250nM


title: Ctrl1

description: Library name: Sample 1

tag: cell line


title: 24_NCIH510_sgBRDT_2_Hypoxia_rep2

description: Library name: S24

tag: genotype

value: BRDT knockdown


title: 23_NCIH510_sgBRDT_1_Hypoxia_rep2

description: Library name: S23

tag: cell type


title: C111 IFN_IL-6

description:
Library name: C111-IFN_IL6-L
column name in Counts.txt: C111-IFN_IL6-L

value: vastus lateralis

value: primary cells

value: skeletal muscle myotube


title: 18_NCIH510_sgBRDT_2_Normoxia_rep2

description: Library name: S18

value: Normoxia


title: 19_NCIH510_sgCtrl_Hypoxia_rep2

description: Library name: S19


title: 17_NCIH510_sgBRDT_1_Normoxia_rep2

description: Library name: S17


title: 16_NCIH510_sgBRD4_2_Normoxia_rep2

description: Library name: S16


title: 15_NCIH510_sgBRD4_1_Normoxia_rep2

description: Library name: S15


title: 14_NCIH510_sgCtrl_dBET6_Normoxia_rep2

description: Library name: S14


title: 13_NCIH510_sgCtrl_Normoxia_rep2

description: Library name: S13


title: EC3

description: Library name: Sample 6

value: Human endometrial epithelium

value: Human endometrial epithelial cells


title: 11_NCIH510_sgBRDT_1_Hypoxia_rep1

description: Library name: S11


title: 10_NCIH510_sgBRD4_2_Hypoxia_rep1

description: Library name: S10


title: 09_NCIH510_sgBRD4_1_Hypoxia_rep1

description: Library name: S09


title: 06_NCIH510_sgBRDT_2_Normoxia_rep1

description: Library name: S06


title: 08_NCIH510_sgCtrl_dBET6_Hypoxia_rep1

description: Library name: S08


title: 07_NCIH510_sgCtrl_Hypoxia_rep1

description: Library name: S07


title: 21_NCIH510_sgBRD4_1_Hypoxia_rep2

description: Library name: S21


title: 04_NCIH510_sgBRD4_2_Normoxia_rep1

description: Library name: S04


title: 01_NCIH510_sgCtrl_Normoxia_rep1

description: Library name: S01


title: 02_NCIH510_sgCtrl_dBET6_Normoxia_rep1

description: Library name: S02


title: 03_NCIH510_sgBRD4_1_Normoxia_rep1

description: Library name: S03


title: ChIP_H510_K4me3

description: Library name: S07

data_processing:
ChIP-seq reads in the NCI-H510 cells were at least 30 M/sample and were aligned to hg19 following procedures previously described (29). ChIP-seq reads in DLD-1 were aligned to hg38 with bowtie v1.2. Sequence quality was assessed using FastQC v 0.11.2 (49), and quality trimming was done using Trimmomatic (50) with parametersTRAILING:30 MINLEN:20.
Assembly: DLD-1 hg38
Assembly: NCI-H510 hg19
Supplementary files format and content: bigWig

growth_protocol: cell lines were in RPMI (ThermoFisher, #A1049101). Both media were supplemented with 10% FBS (Sigma-Aldrich, #F2442), 1% PS (Gibco, #15140122), and 1% Glutmax (Gibco, #35050061). Cells were cultured in an incubator at 37°C with supply of 5% CO2.

extract_protocol:
ChIP-seq experiments were carried out as previously described (29). Briefly, cells in a 15cm plate were crosslinked by 15ml 1% PFA (ThermoFisher, #28908) in PBS with shaking for 10 minutes at room temperature. 2ml of 2.5M Gylcine was added to quench the reaction and continue shaking for 5 minutes. Crosslinked cells were then scraped and collected. Covaris E200 was used for chromatin sonication with following settings: 10% duty factor, 200 cycles per burst, and 140 peak intensity power, 10 minute. For NCI-H510 cells, antibodies wer added, then incubated with the lysate over night at 4°C with rotation for immunoprecipitation. Protein G-coupled Dynabeads (Invitrogen, #10004D) were used to pull down the immune complexes. Protease K (Roche, #3115828001) was used during reverse crosslink (65°C, 1200rpm, overnight). DNA was then purified through QIAquick PCR Purification Kit (Qiagen, #28106).
Libraries were prepared by using the KAPA HTP library preparation kit (Roche, #07961901001) and sequenced on the Illumina NovaSeq 6000.

tag: antibody

value: H3K4me3 (Active Motif 39159)


title: ChIP_DLD1_Vector_48hDox_3hAux_Pol2CST

description: Library name: S12

source_name: Colorectal cancer

value: Colorectal cancer

value: Vector

value: Pol2 (CST)

value: Dox 48h, Auxin 3h


title: ChIP_H510_K4me1

description: Library name: S06

value: Lung carcinoma

value: epithelial

value: H3K4me1 (Abcam 8895)


title: ChIP_DLD1_BRD4-FL_48hDox_3hAux_Pol2CST

description: Library name: S13


title: ChIP_H510_BRDT_dBET6_hg19

description: Library name: S09

value: WT

value: BRDT-HA


title: ChIP_DLD1_Vector_48hDox_3hH2O_Pol2CST

description: Library name: S11

value: Dox 48h


title: ChIP_DLD1_BRDT-C_48hDox_3hAux_Pol2CST

description: Library name: S15

value: BRDT-C


title: ChIP_H510_BRDT_DMSO_hg19

description: Library name: S10

value: DMSO


title: ChIP_H510_input

description: Library name: S08


title: ChIP_H510_Pol2

description: Library name: S01

value: Rpb1 (Cell Signaling Technology, #D8L4Y)


title: ChIP_H510_BRD4

description: Library name: S02

value: BRD4 (Bethyl lab, #A700-004)


title: ChIP_H510_CDK9

description: Library name: S03

value: CDK9 (Cell Signaling Technology, #2316)


title: ChIP_H510_K27Ac

description: Library name: S04

value: H3K27ac (Cell Signaling Technology, #8173)


title: after_4

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.1.1.
Gene-level expression raw read counts for each gene were calculated with featureCounts in the subread-2.0.0 package (option: -M -O --fraction).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Raw Count values for each sample

source_name: Whole blood

extract_protocol:
Total RNA was isolated using the PAXgene™ Blood RNA System.
Sequencing libraries were constructed with the TruSeq stranded mRNA Library Prep kit (Illumina).

value: Whole blood

value: after the night shift


title: 12_NCIH510_sgBRDT_2_Hypoxia_rep1

description: Library name: S12

value: BRDT knockdown

value: Hypoxia 6h


title: before_4

value: before the night shift


title: after_3


title: after_2


title: 05_NCIH510_sgBRDT_1_Normoxia_rep1

description: Library name: S05

value: Lung carcinoma

value: Normoxia


title: before_3


title: ChIP_DLD1_BRDT-FL_48hDox_3hAux_Pol2CST

description: Library name: S14

value: Colorectal cancer

value: epithelial

value: BRDT-FL

value: Pol2 (CST)

value: Dox 48h, Auxin 3h


title: before_2


title: before_1


title: after_1


title: GPCR2_K10_High

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

library_source: other

data_processing:
library strategy: CRISPR-Flow
A custom snakemake was used to process raw data files, https://github.com/khavarilab/crispr-flow
UMIs were couted using "umi_tools count --per-contig --method unique"
Further enrichment statistics were generated from the counts files using MageCK.
Assembly: Custom
Supplementary files format and content: The counts file contains estimates of UMI numbers from umi_tools, and the guides files contain the sequences of the Cas9 CRISPR guides.

molecule: other

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were infected with CRISPR libraries against GPCRs and controls.

extract_protocol:
Total genomic DNA was extracted using the SPRI beads (Beckman Coulter, B23317).
Genomic DNA was extracted and amplified by specific primers via PrimeStar(Takara, #R045A) to add the index sequence for further sequencing.

treatment_protocol: The differentiatiated keratinocytes were seeded at confluent density with 1.2mM Calcium, then sorted with a KRT10 antibody (Novus, NBP2-47825AF647) by FACS into low, medium and high expression. Genomic DNA was harvested for gRNA library amplification.

value: Primary keratinocytes

tag: replicate

value: Biological replicate 2

value: CRISPR flow high KRT10 sorted differentiated cells, GPCR guide library


title: GPCR2_K10_Low

tag: treatment

value: CRISPR flow low KRT10 sorted differentiated cells, GPCR guide library


title: ChIP_H510_K27me3

description: Library name: S05

value: WT

value: H3K27me3 (Cell Signalling 9733)


title: GPCR1_K10_Low

value: Biological replicate 1


title: GPCR1_d3

value: CRISPR flow unsorted control of differentiated cells, GPCR guide library


title: ADC_patient3

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

description: 10X Genomics

data_processing:
Illumina BCL files were demultiplexed and converted to FASTQ files using ‘cellranger mkfastq’ function in Cell Ranger software (v.7.0.1) (10x Genomics).
The resulting FASTQ files were used to perform alignment to GRCh38 genome, filtering, and UMI counting, as well as to produce gene-barcode matrices using cellranger count.
The subsequent data analysis was performed using the R package Seurat (v.4.0.4).
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Cervix tissue

extract_protocol:
Cellular suspensions were loaded onto a chromium controller (10x Genomics) to generate nanoliter-sized gel bead-in-emulsions (GEMs) containing single cells, reagents, and a single gel bead containing barcoded oligonucleotides.
Barcoded sequencing libraries were prepared using Chromium Next GEM Single Cell 3’ v3.1 Dual Index (10X Genomics), according to the manufacturer’s protocol.

value: Cervix tissue

tag: disease

value: ADC

value: female


title: PC9C

city: Harbin

first: Yan

last: Yu

state: Heilongjiang

address: Haping Road No 150

department: Department of Medical Oncology

institute: Harbin Medical University Cancer Hospital

description: NC group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to gossypium hirsutum using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes differential expression RNA used to draw heat maps of gene expression
Supplementary files format and content: tab-delimited text file includes gene expression for each sample

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: NC


title: GPCR1_K10_High


title: GPCR1_K10_Med

value: CRISPR flow medium KRT10 sorted differentiated cells, GPCR guide library


title: PC9SH1A

description: SHRBM10 group, replicate biosample1


title: PC9SH3A

description: SHRBM10 group, replicate biosample3


title: PC9SH2A

description: SHRBM10 group, replicate biosample2


title: ADS_patient1

description: 10X Genomics

value: ADS

tag: Sex


title: PC9A

description: NC group, replicate biosample 1


title: ADC_patient2

description: 10X Genomics

tag: tissue


title: SCC_patient10

description: 10X Genomics

value: SCC


title: SCC_patient12

description: 10X Genomics


title: SCC_patient11

description: 10X Genomics


title: SCC_patient8

description: 10X Genomics


title: GPCR2_d3


title: SCC_patient7

description: 10X Genomics


title: GPCR2_K10_Med


title: SCC_patient9

description: 10X Genomics


title: SCC_patient6

description: 10X Genomics


title: SCC_patient2

description: 10X Genomics


title: SCC_patient5

description: 10X Genomics


title: GPCR2_d0

value: CRISPR flow unsorted control of progenitor cells, GPCR guide library


title: SCC_patient1

description: 10X Genomics


title: GPCR1_d0


title: PC9B

description: NC group, replicate biosample 2


title: ADC_patient1

description: 10X Genomics


title: DMSO-3

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments per kilobase per million (FPKM) estimation was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq (a Python framework to work with high-throughput sequencing data), and differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MV4-11 cell line

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: MV4-11 cell lines were cultured with DMSO, Mitoxantrone (20 nM), or Gilteritinib(25 nM) , or combination(Mitoxantrone20nM plus Gilteritinib 20nM) for  24 h, followed by RNA-seq

value: MV4-11 cell line

value: Acute myeloid leukemia cells

value: Wild-type

value: DMSO


title: DMSO-1


title: Drug-combination-3

value: Mitoxantrone+Gilteritinib


title: DMSO-2


title: Drug-combination-2


title: Drug-combination-1


title: Gilteritinib-2

value: Gilteritinib


title: Gilteritinib-1


title: Gilteritinib-3


title: Mitoxantrone-2

value: Mitoxantrone


title: Mitoxantrone-1


title: SCC_patient4

description: 10X Genomics


title: Mitoxantrone-3


title: SCC_patient3

description: 10X Genomics


title: EU_shSETX_67_OHT

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

description:
EU_shSETX_OHT_average.bw
Summary_TPM_DESeq2.xlsx

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
reads alignment with STAR v. 2.7.5c
Assembly: hg38
Supplementary files format and content: Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Supplementary files format and content: BigWig files were generated using the bamCoverage function of deeptools v. 3.5.1 with the spike-in reads used as scaleFacor. WiggleTools was used to create average bigWigs per condition.
Library strategy: EU-Seq

extract_protocol:
RNA was then extracted and purified using the Quick-RNATM Miniprep Kit (Zymo Research, cat. #R1.fastq.gz055) according to the manufacturer’s instructions. Nascent RNA was biotinylated and purified starting from 50 μg of total RNA. EU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) (kind gift from Thanos Halazonetis) using the Click-IT chemistry as shown below: 50 μg of RNA (40 μg of human EU-labelled RNA and 10 μg of murine EU-labelled RNA) were mixed with the same volume of 2X Click-IT reaction cocktail (171 mM Tris-HCl pH 8, 8 mM CuSO4, 200 mM sodium-L-ascorbate, 0,1 mM biotin–azide) and incubated for 30 minutes at RT with gentle shaking. RNA was precipitated and the EU-labelled RNA was then isolated using 50 μl of Dynabeads MyOne streptavidin C1 (Invitrogen, Cat. No. 65001) each sample, that were washed before use two times with Binding and Washing Buffer 1X (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.5% Tween-20), followed by two washes with solution A (0.1 M NaOH, 0.05 M NaCl) and two washes with solution B (0.1 M NaCl). After washing, the beads were resuspended to twice the original volume with Binding and Washing Buffer 2X. RNase OUT (1:100, Invitrogen, Cat. No. 10777-019) was added to RNA and then samples were heated at 70°C for 5 minutes and placed back on ice to remove secondary structures. Then EU-labelled RNA was mixed with an equal volume of washed beads (100 µL) and incubated for 30 minutes on a rotating wheel at room temperature. The RNA-beads complex was then washed three times with Binding and Washing Buffer 1X and once with RNase free-water. Finally, the EU-labelled RNA was eluted by incubating the streptavidin beads with 55 μl of 2% β -mercaptoethanol (Calbiochem, Cat. No. 444203) in 10 mM Tris-HCl pH. 8 for 1 h at room temperature. 5 μl of each sample were used for Qubit quantification (RNA HS assay kit; Thermofisher, Cat. No. Q32852). TruSeq Stranded Total RNA Gold (Illumina, Cat. No. 20020598)
TruSeq Stranded Total RNA Gold (Illumina, Cat. No. 20020598)

value: SETX silencing and MycER activation


title: EU_shSETX_64

description:
EU_shSETX_average.bw
Summary_TPM_DESeq2.xlsx

value: SETX silencing


title: EU_shSETX_64_OHT


title: EU_shSETX_66


title: EU_shNT_OHT_rep1

description:
EU_shNT_OHT_average.bw
Summary_TPM_DESeq2.xlsx

value: mock silencing and MycER activation


title: EU_shSETX_66_OHT


title: EU_shNT_OHT_rep2


title: EU_shNT_rep3

description:
EU_shNT_average.bw
Summary_TPM_DESeq2.xlsx

value: mock silencing


title: EU_shNT_OHT_rep3


title: EU_shNT_rep1


title: DRIP_shSETX_66_OHT_RNAseH

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
reads were aligned using the BWA v.0.6.2 tool with default settings
Assembly: hg38
Supplementary files format and content: Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Supplementary files format and content: BigWig files were generated using the bamCoverage function of deeptools v. 3.5.1 with the spike-in reads used as scaleFacor. WiggleTools was used to create average bigWigs per condition.
Library strategy: DRIP-seq

extract_protocol:
Cells were resuspended in 1X TE buffer (Tris HCl pH 7.6 10 mM, EDTA pH 8 1 mM) and lysed O/N at 37°C with 0.5% SDS and 62.5 μg/mlProteinase K in 1X TE buffer. Chromatin was then precipited with isopropanolo and sodio acetato, washed with ethanol and resuspeded in 1X TE for 4h at 30°C. O/N digestion was performed with restriction enzymes cocktail. (Sanz, L. A. & Chédin, F. High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing. Nature Protocols 14, 1734-1755, doi:10.1038/s41596-019-0159-1 (2019))
According to Sanz, L. A. & Chédin, F. High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing. Nature Protocols 14, 1734-1755, doi:10.1038/s41596-019-0159-1 (2019)
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers

value: S9.6 antibody (Kerafast, cat. No. ENH001)

value: SETX silencing,MycER activation and treatment with RNAseH


title: DRIP_shNT_OHT_RNAseH

value: mock silencing,MycER activation and treatment with RNAseH


title: EU_shNT_rep2


title: DRIP_shNT_RNAseH

value: mock silencing and treatment with RNAseH


title: DRIP_shSETX_67_OHT

description:
DRIP_shSETX_OHT_average.bw
Summary_TPM_DESeq2.xlsx


title: DRIP_shSETX_64_OHT_RNAseH


title: DRIP_shSETX_64_OHT


title: DRIP_shSETX_66

description:
DRIP_shSETX_average.bw
Summary_TPM_DESeq2.xlsx


title: EU_shSETX_67


title: DRIP_shNT_OHT_rep3

description:
DRIP_shNT_OHT_average.bw
Summary_TPM_DESeq2.xlsx


title: DRIP_shSETX_64


title: DRIP_shSETX_66_OHT


title: DRIP_shNT_rep1

description:
DRIP_shNT_average.bw
Summary_TPM_DESeq2.xlsx


title: BLISS_shSETX_67_OHT

data_processing:
Data were analysed according to the sBLISS-seq protocol (Bouwman, B.A.M., Agostini, F., Garnerone, S. et al. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 15, 3894–3941 (2020). https://doi.org/10.1038/s41596-020-0397-2)
Assembly: hg38
Supplementary files format and content: Bed files with "_union" result from the union of all regions between the same condition
Supplementary files format and content: BLISS_shNT_OHT_union.bed file, specifically, is obtained merging the regions identified in our new file BLISS_shNT_OHT_R1.fastq.gz and some 2 samples (GSM7549772 GSM7549773) from GSE236553.
Library strategy: sBLISS-seq

extract_protocol:
Cells were fixed with 2%PFA and processed according to the publised sBLISS protocol (Bouwman, B.A.M., Agostini, F., Garnerone, S. et al. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 15, 3894–3941 (2020). https://doi.org/10.1038/s41596-020-0397-2)
sBLISS-seq (Bouwman, B.A.M., Agostini, F., Garnerone, S. et al. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 15, 3894–3941 (2020). https://doi.org/10.1038/s41596-020-0397-2)


title: DRIP_shNT_rep3


title: BLISS_shSETX_66_OHT


title: BLISS_shSETX_67


title: Human Umbilical Vein Endothelial Cells, Experiment knock down CAVIN3, Replicate 2

city: Shanghai

first: Yingji

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

data_processing:
The Salmon v1.9.0 was used to calculate counts and transcript per million reads (TPM) of each gene.
DESeq2 v1.34.0 was applied to identify differentially expressed genes. GO analyses based on the RNA-Seq data was conducted with clusterProfiler v4.12.3.
Assembly: GRCh38
Supplementary files format and content: csv text file includes raw counts for each Sample

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs (Accession number: PCS-100-013; ATCC) were cultured in DMEM/Low Glucose medium supplemented with 10% fetal bovine serum (FBS; Invitrogen, Carlsbad, CA, USA), penicillin (100U/mL; Invitrogen) and streptomycin (100 U/mL; Invitrogen). Cells were maintained at 37°C with 21% O2 and 5% CO2. HUVECs were transfected with indicated siRNAs using Lipofectamine 3000 (Invitrogen). Scramble siRNA and siRNAs targeting CAVIN3 were purchased from GenePharma (Shanghai, China). Scramble siRNA and siRNAs targeting TUBB6 were purchased from RiboBio (Guangzhou, China) .

extract_protocol:
Total RNA was isolated from cell lysates using TRIzol reagent (Invitrogen). The concentration and purity of RNA were measured with a Nano-Drop ND-1000 spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA) and the Agilent 2100 Bioanalyzer system (Agilent BioTek; Winooski, VT, USA).
RNA with high quality was sent for library construction. The RNA-Seq library was further sequenced with Illumina Novaseq 6000 platform (Illumina) to generate 150 base pair (bp) reads. Quality control and raw sequencing data filtration were achieved with the Fastp v0.23.2 and sortmerna v4.3.4 software. The STAR v2.7.10 software was then applied to align clean reads to the human genome GRCh38.

value: Human Umbilical Vein Endothelial Cells

value: Experiment knock down CAVIN3


title: Human Umbilical Vein Endothelial Cells, Experiment knock down CAVIN3, Replicate 3


title: BLISS_shSETX_66


title: Human Umbilical Vein Endothelial Cells, Experiment knock down TUBB6, Replicate 3

value: Experiment knock down TUBB6


title: BLISS_shNT_OHT

description: BLISS_shNT_OHT_union.bed (the processed file for the new sample plus the old samples GSM7549772 GSM7549773 from GSE236553; see the Data table on the Series record)


title: Human Umbilical Vein Endothelial Cells, Experiment knock down TUBB6, Replicate 2


title: Human Umbilical Vein Endothelial Cells, Control, Replicate 1

value: Control


title: BLISS_shNT


title: DRIP_shSETX_67


title: pbmc, HS group [LSK_0038109145]

city: Chengdu

first: Juan

last: Wu

state: Sichuan

address: No. 37 Guo Xue Alley, Wuhou District

department: Anesthesiology

institute: West China Hospital of Sichuan University

description: 10x Genomics

data_processing:
CellRanger software (version 7.0.0, 10X Genomics) was used to analyze the sequencing data, and gene expression information for each cell was obtained.
Assembly: Ensembl V105
Supplementary files format and content: Tab-separated values and Matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells were isolated by density gradient centrifugation using Ficoll Hypaque density solution. Cells were used only if >80% were viable based on trypan blue staining, in which case they were subjected to single-cell RNA sequencing.
An appropriate volume of peripheral blood mononuclear cells was loaded onto a 10X Genomics Chromium instrument to capture 8000 single cells according to the manufacturer’s instructions for the 10X Genomics Chromium Single-Cell 5’ kit (version 2). Subsequent cDNA amplification and library construction were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150 bp) at LC-Bio Technology (Hangzhou, China) at a minimum depth of 20,000 reads per cell.

value: PBMC

tag: group

value: Heatstroke


title: pbmc, HC group [ZTS]

description: 10x Genomics

value: Healthy control


title: Human Umbilical Vein Endothelial Cells, Control, Replicate 2


title: Human Umbilical Vein Endothelial Cells, Experiment knock down CAVIN3, Replicate 1


title: Human Umbilical Vein Endothelial Cells, Experiment knock down TUBB6, Replicate 1


title: CBL HET C404Y 71 NT 2

data_processing:
Samples with high quality reads (Phred score >= 30) were aligned to  Homo sapiens (assembly GRCh38.p14) using STAR aligner
Gene quantification was performed using feature counts from the Subread package in R
Gene expression levels were normalized and log2 transformed using the Trimmed Mean of M-values (TMM) method and differential expression analysis was performed using the edgeR package in R
Assembly: GRCh38.p14
Supplementary files format and content: Excel where each column contains Normalized gene counts for a given sample. The first column contains gene id

source_name: huIPSC

extract_protocol:
Phase separation in cells lysed in 1 mL TRIzol Reagent (ThermoFisher Scientific) was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the miRNeasy Mini Kit (Qiagen) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol with 350 µL input, or using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher Scientific) on the KingFisher Flex Magnetic Particle Processor (ThermoFisher Scientific) according to the manufacturer’s protocol with 350 µL input. Samples were eluted in 30 µL RNase-free water
PolyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, Illumina), with 8 cycles of PCR.

value: huIPSC

value: macrophages

value: CBL HET C404Y 71 NT


title: pbmc, HC group [DP]

description: 10x Genomics


title: DRIP_shNT_rep2


title: DRIP_shNT_OHT_rep1


title: CBL HET C404Y 71 NT 1


title: CBL HET C404Y 89 NT 3

value: CBL HET C404Y 89 NT


title: Human Umbilical Vein Endothelial Cells, Control, Replicate 3


title: pbmc, HS group [LCY003751621]

description: 10x Genomics


title: CBL WT 93 NT 2

value: CBL WT 93 NT


title: CBL WT 93 NT 3


title: CBL HET C404Y 89 NT 1


title: CBL HET C404Y 71 NT 3


title: CBL HET C404Y 89 NT 2


title: DRIP_shNT_OHT_rep2

value: mock silencing and MycER activation


title: CBL WT 93 NT 1


title: CBL WT 91 NT 1

value: CBL WT 91 NT


title: CBL WT 91 NT 3


title: CBL WT 91 NT 2


title: con-YZ240410-5

city: Shang Hai Shi

first: Bowen

last: Zhu

state: Shang Hai Shi

address: Pu Dong Xin Qu Hua Tuo Lu 88Hao, Gao Ke Yuan18-604

institute: Interdisciplinary Research Center on Biology and Chemistry

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to the Homo sapiens genome (GRCh38) using bismark (v0.24.1) with default parameters. Uniquely mapped read pairs were extracted using samtools (v1.17) Methylation level was extracted by bismark.
After extracting the methylation data using bismark to obtain the raw data, we found that there were many invalid site data with all values of 0 or NA in the data, so we used two conditions to screen for valid methylation sites: 1. Since we designed five pairs of PCR primers to be amplified and then sequenced, only the CpG sites located within these five sequences could be valid sites. 2. Methylation ratio screening, we considered that only sites with a methylation rate greater than 0 in 70% of the population were valid sites, and the final results of the screening can be found in the file I uploaded, 'methylation_whole_1.csv'.
Assembly: GRCh38
Supplementary files format and content: csv table with methylation site at row and samples at column; the proportion of methylation at the specific locus for each sample.

source_name: Blood

extract_protocol:
Genomic DNA was extracted and purified using MagPure Uninversal DNA Kit B (Magen, catalog: D6310-03B) and RNase A (ABclonal, Catalog: RM29870)
Converted DNA libraries were prepared using Bisulfite Conversion Kit(Singlera, catalog: EP110192) and PCR

value: Blood

value: M

tag: age


title: con-YZ240410-9


title: con-YZ240410-6


title: con-YZ240410-8


title: con-YZ240410-59


title: con-YZ240410-7


title: pbmc, Sepsis group [HR]

description: 10x Genomics

value: Sepsis


title: con-YZ240410-56


title: pbmc, Sepsis group [CB]

description: 10x Genomics


title: con-YZ240410-57


title: con-YZ240410-60


title: con-YZ240410-55


title: con-YZ240410-52


title: con-YZ240410-58


title: con-YZ240410-54


title: con-YZ240410-53


title: con-YZ240410-51


title: con-YZ240410-49


title: con-YZ240410-4

value: F


title: con-YZ240410-48


title: con-YZ240410-46


title: con-YZ240410-47


title: con-YZ240410-50


title: con-YZ240410-45


title: con-YZ240410-44


title: con-YZ240410-3


title: con-YZ240410-40


title: con-YZ240410-41


title: con-YZ240410-42


title: con-YZ240410-43


title: con-YZ240410-32


title: con-YZ240410-39


title: con-YZ240410-38


title: con-YZ240410-35


title: con-YZ240410-31


title: con-YZ240410-2


title: con-YZ240410-26


title: con-YZ240410-29


title: con-YZ240410-36


title: con-YZ240410-27


title: con-YZ240410-33


title: con-YZ240410-34


title: con-YZ240410-25


title: con-YZ240410-28


title: con-YZ240410-22


title: con-YZ240410-23


title: con-YZ240410-19


title: con-YZ240410-20


title: con-YZ240410-1


title: con-YZ240410-18


title: con-YZ240410-21


title: con-YZ240410-17


title: con-YZ240410-15


title: con-YZ240410-13


title: con-YZ240410-11


title: con-YZ240410-16


title: con-YZ240410-14


title: con-YZ240410-10


title: con-timepie-YJP-re


title: con-CHY


title: con-YQC


title: con-YZ240410-24


title: con-XK20240313-LN


title: con-YZ240410-30


title: con-XK20240313-17


title: con-XK20240313-77


title: con-SZK240204-2-LN


title: con-SZK240204-1-LN


title: con-231212-5-xp


title: con-231212-4-xp


title: con-231212-2-xp


title: con-231211-1-xp


title: con-PN-9


title: con-YZ240410-37


title: con-PN-8


title: con-PN-7


title: con-PN-15


title: con-PN-14


title: con-PN-12


title: con-PN-11


title: con-CZ0506MM-8


title: con-CZ0506MM-9


title: con-CZ0506MM-7


title: con-CZ0506MM-6


title: con-CZ0506MM-5


title: con-CZ0506MM-4


title: con-CZ0506MM-30


title: con-CZ0506MM-31


title: con-231212-3-xp


title: con-CZ0506MM-2


title: con-CZ0506MM-24


title: con-CZ0506MM-28


title: con-CZ0506MM-27


title: con-CZ0506MM-17


title: con-PN-6


title: con-CZ0506MM-29


title: con-CZ0506MM-26


title: con-CZ0506MM-25


title: con-CZ0506MM-1


title: con-CZ0506MM-21


title: con-CZ0506MM-14


title: con-CZ0506MM-12


title: con-CZ0506MM-22


title: con-CZ0506MM-16


title: con-CZ0506MM-11


title: con-CZ0506MG-6


title: con-PN-13


title: con-CZ0506MG-8


title: con-CZ0506MM-13


title: con-CZ0506MG-5


title: con-CZ0506MG-4


title: con-CZ0506MG-29


title: con-CZ0506MG-30


title: con-CZ0506MG-26


title: con-CZ0506MG-25


title: con-CZ0506MG-23


title: con-CZ0506MG-21


title: con-CZ0506MG-1


title: con-CZ0506MG-18


title: con-CZ0506MG-19


title: con-CZ0506MG-13


title: con-CZ0506MG-15


title: con-CZ0506MG-14


title: con-CZ0506MG-16


title: con-CZ0506MG-10


title: con-CZ0506MG-11


title: con-YY230411-7


title: con-CZ0506MG-17


title: con-YY230411-4


title: con-YY230411-8


title: con-YY230411-33


title: con-CZ0506MG-28


title: con-YY230411-5


title: con-YY230411-9


title: con-YY230411-2


title: con-YY230411-6


title: con-YY230411-26


title: con-YY230411-28


title: con-YY230411-24


title: con-CZ0506MG-24


title: con-YY230411-25


title: con-YY230411-22


title: con-YY230411-21


title: con-CZ0506MG-12


title: con-YY230411-20


title: con-YY230411-27


title: con-YY230411-18


title: con-YY230411-31


title: con-YY230411-19


title: con-YY230411-12


title: con-YY230411-11


title: con-YY230411-10


title: con-YY230409-6


title: con-YY230409-9


title: con-YY230409-5


title: con-YY230409-7


title: con-YY230409-8


title: con-YY230409-38


title: con-YY230409-36


title: con-YY230409-3


title: con-YY230409-42


title: con-YY230409-4


title: con-YY230409-34


title: con-YY230409-37


title: con-YY230411-23


title: con-YY230409-35


title: con-YY230409-41


title: con-YY230409-32


title: con-YY230409-30


title: con-YY230409-24


title: con-YY230409-26


title: con-YY230409-27


title: con-YY230409-25


title: con-YY230409-29


title: con-YY230409-2


title: con-YY230409-22


title: con-YY230409-21


title: con-YY230409-20


title: con-YY230409-19


title: con-YY230409-18


title: con-YY230409-1


title: con-YY230409-17


title: con-YY230409-16


title: con-YY230409-12


title: con-YY230409-15


title: con-YY230409-11


title: con-YY230409-10


title: con-YY230409-33


title: con-CZ20231019-9


title: con-YY230409-14


title: con-YY230409-13


title: con-CZ20231019-3


title: con-CZ20231019-8


title: con-CZ20231019-14


title: con-YY230409-23


title: con-CZ20231019-13


title: con-CZ20231019-11


title: con-YY230316-40


title: con-YY230316-38


title: con-YY230316-39


title: con-YY230316-37


title: con-YY230316-36


title: con-YY230316-35


title: con-YY230408-37


title: con-YY230408-36


title: con-YY230316-32


title: con-YY230316-29


title: con-YY230316-26


title: con-YY230316-31


title: con-YY230316-28


title: con-YY230316-22


title: con-YY230316-21


title: con-YY230316-25


title: con-YY230316-19


title: con-CZ20231019-2


title: con-YY230316-20


title: con-YY230316-14


title: con-YY230316-17


title: con-YY230316-18


title: con-YY230316-16


title: con-YY230316-13


title: con-YY230316-12


title: con-YY230316-15


title: con-YY230314-9


title: con-YY230314-7


title: con-YY230314-8


title: con-YY230314-6


title: con-YY230314-3


title: con-YY230314-2


title: con-YY230314-29


title: con-YY230314-28


title: con-YY230314-26


title: con-YY230314-24


title: con-YY230314-27


title: con-YY230314-23


title: con-YY230314-22


title: con-YY230314-18


title: con-YY230314-19


title: con-YY230314-16


title: con-YY230314-14


title: con-YY230314-12


title: con-YY230314-15


title: con-YY230314-13


title: con-YY230314-11


title: con-YY230314-5


title: con-YY230411-3


title: con-YY230413-5


title: con-YY230409-40


title: con-YY230408-1


title: con-YY230314-30


title: con-YY230406-3


title: con-YY230406-2


title: con-YY230406-1


title: con-YY230406-14


title: con-YY230314-25


title: con-YY230314-20


title: con-YY230316-41


title: con-YY230314-17


title: con-YY230318-37


title: con-YY230318-41


title: con-YY230318-36


title: con-YY230318-39


title: con-YY230318-34


title: con-YY230411-1


title: con-YY230318-32


title: con-YY230318-26


title: con-YY230318-27


title: con-YY230318-30


title: con-YY230318-29


title: con-YY230318-24


title: con-YY230318-23


title: con-YY230316-8


title: con-YY230316-6


title: con-YY230316-4


title: con-YY230316-3


title: con-YY230316-11


title: con-YY230316-1


title: con-YY230316-9


title: con-YY230406-12


title: con-YY230328-33


title: con-YY230316-2


title: con-YY230316-10


title: con-YY230328-32


title: con-YY230318-33


title: con-YY230328-29


title: con-YY230328-30


title: con-YY230328-26


title: con-YY230328-17


title: con-YY230328-10


title: con-YY230318-25


title: con-YY230323-1


title: con-YY230321-31-2


title: con-YY230321-28-2


title: con-YY230318-9


title: con-YY230321-39


title: con-YY230321-33-2


title: con-YY230318-8


title: con-YY230318-7


title: con-YY230318-5


title: con-YY230318-4


title: con-YY230318-22


title: con-YY230318-6


title: con-YY230318-2


title: con-YY230318-3


title: con-YY230318-20


title: con-YY230328-20


title: con-YY230318-21


title: con-YY230318-16


title: con-YY230328-12


title: con-YY230318-18


title: con-YY230318-17


title: con-YY230321-40


title: con-YY230318-12


title: con-YY230318-11


title: con-YY230323-31


title: con-YY230323-30


title: con-YY230318-15


title: con-YY230323-38


title: con-YY230323-29


title: con-YY230323-24


title: con-CZ20231019-7


title: con-YY230321-7


title: con-YY230321-33


title: con-YY230323-12


title: con-YY230321-31


title: con-YY230321-2


title: con-YY230321-28


title: con-YY230321-22


title: con-YY230321-1


title: con-YY230321-27


title: con-YY230318-19


title: con-YY230321-14


title: con-YY230321-21


title: con-YY230321-18


title: con-YY230323-6


title: con-6-48


title: con-6-43


title: con-YY230318-10


title: con-6-40


title: con-6-46


title: con-6-47


title: con-6-32


title: con-6-31


title: WT cells, biol rep 3

city: Toronto

first: Delphine

last: Dufour

state: Ontario

address: 124 Edward Street

country: Canada

institute: Faculty of Dentistry, University of Toronto

data_processing:
The Illumina bcl2fastq Conversion software was used for demultiplexing and to convert the base call files generated by the Illumina sequencing into FASTAQ files.
Quality of the raw data was assessed with FastQC (v0.11.9).
Removal of sequencing adapters and low-quality ends was performed using Trim Galore (v0.5.0) and the QC checks were repeated with FastQC to ensure that high-quality data was retained.
The reads were then aligned to S. Mutans UA159 complete genome (NC_004350.2) downloaded from NCBI using STAR aligner (v2.6.0c).
Assembly: NC_004350.2
Supplementary files format and content: htseq files include read counts for each sample

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans UA159

growth_protocol: S. mutans UA159 WT and DpnII R-M mutant cells were grown in THYE broth at 37C with 5% CO2 for 20 hours.

extract_protocol:
RNA  was harvested using the RiboPure-Bacteria purification kit. 0.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit following manufacturer's protocols.

value: Streptococcus mutans UA159

value: WT


title: con-6-24


title: con-6-28


title: con-YY230323-17


title: WT cells, biol rep 2


title: con-4-4-45


title: con-6-27


title: con-4-4-42


title: DpnII R-M mutant cells, biol rep 3


title: DpnII R-M mutant cells, biol rep 2


title: con-4-4-40


title: con-4-4-41


title: DpnII R-M mutant cells, biol rep 1


title: con-4-4-38


title: con-4-4-39


title: SMPAT_dcp2∆pab1-AID+NAA_Replicate_2

city: Bethesda

first: Poonam

last: Poonia

state: MD

address: 6 Center Drive, Bldg 6, Room 240

department: NICHD

institute: NIH

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with HISAT2 (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For SMPAT-Seq: Sequencing reads from the Sequel instrument come in the form of continuous reads around a “rolling circle.” The insert is read over multiple passes in each direction. These insert passes are referred to as subreads. Multiple passes gives circular consensus sequences (CCS; also referred to as HiFi). CCS reads were demultiplexed to individual samples using the program “lima” (v2.6 or above) using the appropriate sample barcodes utilized during library construction. Samtools was used to convert demultiplexed sample CCS reads to fastq format for further processing and alignment. CCS read IDs are assigned to transcripts through the use of PacBio minimap2 to align reads to Ensembl Saccharomyces cerevisiae.R64-1-1 release 109. To determine and assign a poly(A) tail length to a CCS ID, reads are evaluated in either direction for a poly(A) stretch abutting the adapter utilized in library construction. A one base mismatch is tolerated for the adapter sequence pattern matching.
Assembly: sacCer3 and Saccharomyces cerevisiae.R64-1-1 release 109
Supplementary files format and content: Processed data (.txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For RNA-sequencing, with spike-in normalization, processed file is a matrix with 6 columns providing: systemmatic gene name (Gene_ID), chromosome (Chr), start and end coordinates of genes (Start and End), strand information (Strand), length of the gene in basepairs (length) and multiple columns with read counts for different samples. For CAGE-sequencing the file contains three columns providing: Chromosome (Chr), Position of detected TSS (pos), strand information (strand) and 14 columns with read counts for different samples. For SMPAT-Seq, report.txt file contains multiple columns providing: Gene name (#Gene), Counts for each gene (Counts), mean poly(A) tail lengths (MeanPolyA), Standard error (STDERR), Minimum poly(A) tail length (Min), Quartile1 (Q1), median poly(A) tail lengths (Median), Quartile 3rd (Q3), Maximun poly(A) tail lengths (Max) and ListOfValues.
Library strategy: SMPAT-seq

organism: Saccharomyces cerevisiae

source_name: W303 PRY1 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 dcp2∆::HIS3 lys2:: PADH1-OsTIR1-7myc-TADH1 pab1-AID (71-114)-9myc::hphNT1)

growth_protocol: Yeast cells were cultured in YPD at 30°C for one division and thereafter NAA was added to a final concentration of 1mM and growth was continued for 6h.

extract_protocol: SM-PAT sequencing was conducted on the same total RNA samples described above that were subjected to RNA-Seq and Ribo-Seq. SM-PAT libraries were constructed from  total RNA for each sample as previously described in "Single-Molecule Poly(A) Tail Sequencing (SM-PATseq) Using the PacBio Platform. Iben et al., 2024, Methods Mol Biol, 2723, 285-301.

value: Yeast whole cells

value: 1mM 1-Napthaleneacetic acid (NAA)


title: con-4-4-37


title: con-4-4-36


title: SMPAT_dcp2∆pab1-AID+NAA_Replicate_1


title: SMPAT_dcp2∆+NAA_Replicate_1

source_name: W303 PMY3 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 dcp2∆::HIS3 lys2::PADH1-OsTIR1-7myc-TADH1)


title: SMPAT_dcp2∆+NAA_Replicate_2


title: con-4-1


title: con-4-4-35


title: con-3-30-15


title: SMPAT_dcp2∆+NAA_Replicate_3


title: WT cells, biol rep 1


title: SMPAT_pab1-AID+NAA_Replicate_3

source_name: W303 PMY2 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::PADH1-OsTIR1-7myc-TADH1 pab1-AID (71-114)-9myc::hphNT1)


title: SMPAT_pab1-AID+NAA_Replicate_2


title: con-3-30-14


title: con-3-30-13