title: RNA_CBMS1_scRR1_WholeS_079


title: RNA_CBMS1_scRR1_WholeS_078

status: Public on Aug 26 2025

type: SRA

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

country: Japan

institute: Mie University

library_source: transcriptomic single cell

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: mm10
Supplementary files format and content: txt, bedGraph

molecule: total RNA

organism: Mus musculus

extract_protocol:
Single cells were collected into 0.2 ml PCR tubes by cell sorter or manually picked and lysed in RamDA-seq lysis buffer (TOYOBO, #RMD-101) containing 2 mg/ml Dynabeads™ MyOne™ Carboxylic Acid (Invitrogen, #65011). Genomic DNA was trapped on the beads, while RNA was released into the lysis buffer. The isolated DNA on magnetic beads was subjected to whole-genome amplification (WGA) and Next-Generation Sequencing (NGS) library preparation, as described in scRepli-seq (Takahashi et al., Nat Genet 2019). The DNA-seq (scRepli-seq) data was used to assess genome-wide DNA copy numbers, karyotype G1-phase cells, and analyze the replication state of S-phase cells. In parallel, the RNA isolated in the supernatant was subjected to scRamDA-seq (Hayashi et al., Nat Commun 2018) using the GenNext®RamDA-seq™ Single Cell Kit (TOYOBO, #RMD-101) according to the manufacturer’s instructions with modifications.
Sample and library preparation for scRR-seq-DNA (scRepli-seq): Genomic DNA was subjected to WGA with a SeqPlex kit (Sigma, SEQXE) in a 30-µl reaction volume, per the manufacturer’s instructions. Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads (1.7× reaction volume), and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The gDNA was then purified with Agencourt AMPure XP SPRI beads (2.0× reaction volume) and eluted in 20 µl of 1/10× Elution Buffer (Qiagen). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu). We could easily distinguish single cells from zero or two cells by quantification of DNA with MultiNA, which provided reassurance that the gDNA was indeed derived from single cells. Then NGS libraries were constructed using the NGS LTP Library Preparation Kit (KAPA, KK8232) with a SeqCap adapter kit A/B (Roche, 07141530001/07141548001) or NEXTflex DNA barcode (Bio Scientific, NOVA), or the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England BioLabs , #E7645) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, Set 2) (New England BioLabs , #E7600S, #E7780S ) or NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, Set 2, Set 3, Set 4) (New England BioLabs , #E7355L, E7500L, E7710L, E7730L). Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).  Library preparation for scRR-seq-RNA scRamDA-seq NGS libraries were generated by using the Nextera® XT Library Prep Kit 24 Samples (illumina, #15032350, #15032352) with Nextera® XT Index Kit v2 Set A 96 indexes-samples (Illumina, #15052163) according to the manufacturer’s instructions with modifications. Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).

tag: cell line

tag: cell type

value: embryonic stem cell


title: VEZF1-2A

city: 重庆

first: Yang

middle: jia

last: yao

address: Medical College Road

department: Key Laboratory of Molecular Biology for Infectious Diseases

country: China

institute: Chongqing Medical University

library_source: genomic

data_processing:
Illumina Hiseq
fastp (version 0.23.1, Shifu Chen 2018)
Assembly: GRCh38_release101
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include bigWig values for each sample

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
RNA was harvested using Rneasy mini plus kit
RNA libraries for ChIP-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: we used lentivirus-encoded sgRNA to eliminate endogenous VEZF1 in HepG2 cells followed by re-expression of VEZF1WT or VEZF12A.RNA-seq was performed.

tag: chip antibody

value: VEZF1(Santa #sc-365560)


title: RNA_RPE1_scRR1_Lot2_WholeS_064

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: hg38, hg19
Supplementary files format and content: txt, bedGraph


title: bulkATAC_D4_CD4_Naive

city: New Delhi

first: Veena

middle: S.

last: Patil

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description:
Library name: bATAC_D4_N
aggregated .bw file for 10 donors
N_out.bw

data_processing:
Raw demultiplexed FASTQ files (n = 20; 10 donors, 2 cell types – CD4-Naïve TN and CD4-TEMRA-E) were quality filtered, and adaptor trimmed using trim_galore, and trimmed reads were mapped to the GRCh38 (hg38) human reference sequence using Bowtie2.
Publicly available pipelines from snakemake and nfcore were followed to analyze ATAC-Seq data.
De-duplicated reads (using picard markduplicates) were filtered for reads mapping to ENCODE blacklisted region, mitochondrial genome and low-quality reads (bedtools and samtools).
Reads passing all quality checks were called for peaks using MACS2 narrowPeak caller. BAM files for each cell type across 10 donors were merged using samtools.
Assembly: GRCh38 (hg38)
Supplementary files format and content: N_out.bw and E_out.bw. bigWig files for each cell type is the aggregated file from 10 donors.

source_name: PBMC

growth_protocol: CD4-Naive and CD4-TEMRA-E were isolated from PBMCs using flow cytometry (FACS). The FACS sorted cells were used for nuclei isolation using Omni ATAC-Seq protocol by Corces et.al., 2017.

extract_protocol:
Cells sorted in collection media (1:1 FBS:PBS) were counted, and 55,000 cells were taken in LoBind 0.6 mL microcentrifuge tubes (Eppendorf) and washed with 0.5 mL chilled PBS. Cell pellet was resuspended in 50 uL chilled freshly-made lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL-CA630, 0.1% Tween-20, 0.01% Digitonin, 1X Protease Inhibtor, 20 mM NaBu) supplemented with 1 U/uL recombinant RNase Inhibtor. After 5 minutes of lysis on ice, 0.2 mL of wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) supplemented with 1 U/uL recombinant RNase Inhibitor, was added. Pelleted nuclei were transposed using Tn5 transposase from Illumina, in a 50 uL reaction mix supplemented with 1X PBS, 0.1% Tween-20 and 0.01% Digitonin, at 37°C for 30 minutes.
Tagmented DNA was purified using Zymo DNA Clean and Concentrator-5 kit followed by amplification using barcoded Nextera XT primers with KAPA Hi-Fi HotStart Ready Mix. After the initial 5 cycles of amplification, cycle threshold determination (CTD) was performed using SYBR and ROX. Based on the CTD the additional cycles (CTD-2 cycle) were performed on the amplified DNA. Final libraries were purified and size-selected using double sided purification by Ampure XP beads (0.5X / 1.8X).
Pooled libraries were sequenced using NovaSeq 6000 (Illumina) for 150-bp paired-end sequencing.

treatment_protocol: No particular treatment was done to the PBMCs. PBMCs were immuno stained and sorted using FACS.

tag: tissue

value: PBMC

tag: attribute


title: RNA_RPE1_scRR1_Lot2_WholeS_058


title: bulkATAC_D5_CD4_Naive

description:
Library name: bATAC_D5_N
aggregated .bw file for 10 donors
N_out.bw


title: VEZF1-WT


title: RNA_CBMS1_scRR1_WholeS_077


title: bulkATAC_D3_CD4_Naive

description:
Library name: bATAC_D3_N
aggregated .bw file for 10 donors
N_out.bw


title: RNA_RPE1_scRR1_Lot2_WholeS_054


title: bulkATAC_D2_CD4_Naive

description:
Library name: bATAC_D2_N
aggregated .bw file for 10 donors
N_out.bw


title: RNA_CBMS1_scRR1_WholeS_076


title: RNA_RPE1_scRR1_Lot2_WholeS_051


title: RNA_CBMS1_scRR1_WholeS_075


title: bulkATAC_D1_CD4_Naive

description:
Library name: bATAC_D1_N
aggregated .bw file for 10 donors
N_out.bw


title: RNA_CBMS1_scRR1_WholeS_074


title: MT-3

city: Hubei

first: Cai

middle: Xia

last: Yang

address: Jingzhou

institute: Yangtze University

library_source: transcriptomic

data_processing:
Illumina high-throughput sequencing results were converted into original sequencing sequences after sequence base recognition by bcl2fastq2 software (Raw reads)
Clean Data were mapped to the reference genome using HISAT2. HISAT2 is a specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again--rna-strandness RF --dta–t–p 4.
Gene expression quantification uses the featureCounts tool in the subread software to analyze the gene expression levels in the data, and then calculates the FPKM for each gene based on the length of the gene.
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

organism: Sus scrofa

source_name: immature sertoli cells

extract_protocol:
RNA was harvested using Trizol reagent.Illumina NovaSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: immature sertoli cells

value: Sertoli cell

tag: genotype


title: MT-2


title: RNA_RPE1_scRR1_Lot2_WholeS_048


title: shddx3x2-Input

city: Guangzhou

first: Dian

last: Meijuan

address: NANFANG HOSPITAL SOUTHERN MEDICAL UNIVERSITY

institute: the sourthern medical university

data_processing:
Differential analysis of transcriptome and proteome sequencing data was conducted using DESeq2. Expression pattern plots for differential genes and proteins were generated using quadrant plots. GO enrichment analysis was performed separately for differential genes, differential proteins, and the intersection of differential genes and proteins using the clusterProfiler package in R.
Assembly: GRCh38.p13
Supplementary files format and content: DEGs-input-FC1.5-up
Supplementary files format and content: DEGs-input-FC1.5-down

source_name: lung

extract_protocol: Total RNA was extracted using RNAiso plus (Takara) following the manufacture’s protocol

value: lung

value: epithelial cell

value: DDX3X knockdown


title: RNA_RPE1_scRR1_Lot2_WholeS_049


title: RNA_CBMS1_scRR1_WholeS_073


title: shddx3x1-Input


title: MT-1


title: RNA_RPE1_scRR1_Lot2_WholeS_044


title: Control-3


title: RNA_CBMS1_scRR1_WholeS_072


title: RNA_CBMS1_scRR1_WholeS_071


title: Control-1


title: RNA_RPE1_scRR1_Lot2_WholeS_045


title: shNS2-Input

value: WT


title: RNA_RPE1_scRR1_Lot2_WholeS_004


title: RNA_RPE1_scRR1_Lot2_WholeS_043


title: RNA_CBMS1_scRR1_WholeS_070


title: shNS1-Input


title: Wild type non-fed replicate 3

city: New York

first: Laura

middle: B.

last: Duvall

state: NY

address: 1212 Amsterdam Ave

country: USA

institute: Columbia University

description:
Library name: LVP-NF-3
Column name in TPM_values_LVP_NF.csv: LVP-NF-3

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Assembly: AaegL5.0
Supplementary files format and content: csv files include raw TPM for each sample

organism: Aedes aegypti

source_name: Hindgut

growth_protocol: Mosquitoes were maintained and reared at 28°C, 70 – 80% relative humidity with a 12 h light: 12 h dark schedule.

extract_protocol:
80-100 hindgut were dissected into ice cold 1x PBS with 0.025% Triton from cold-anesthetized females. RNA was extracted using TriZol and RNEasy kit (Qiagen).
Sequencing libraries were constructed by Azenta (MA) using NEBNext Ultra II Kit for Illumina using manufacturer’s instructions

value: Hindgut

value: insect cells

value: wild type


title: shddx3x-MeRIPrep2

data_processing:
For MeRIP-seq analysis: Paired-end reads were sequenced on the Illumina NovaSeq 6000 platform with a 150bp read length. Quality control was initiated by calculating Q30 scores. Subsequently, adapter trimming was performed using Cutadapt (v 1.14), and low-quality reads were removed with Trimmomatic (v 0.36). Quality checks were conducted using FastQC (v 0.11.5) software. To eliminate mitochondrial, ribosomal RNA, and tRNA sequences, Bowtie2 (v 2.2.9) was employed. Clean reads were then aligned to Homo sapiens transcripts (GENCODE Release 36, GRCh38.p13) using Bowtie2 (v 2.2.9) with the parameters (–local -x). Methylated sites on peaks were identified using MACS2 (v 2.2.7.1) peak-calling software, using corresponding input samples as controls. Differentially methylated sites were determined with the BEDTools map function in the R language. For peak annotation, the R package ChIPseeker (v 1.38.0) was utilized. The distribution of m6A peaks on mRNA features was visualized using the R package Guitar (v 2.18.0). Enriched motifs within m6A peaks were identified with HOMER.
Assembly: GRCh38.p13
Supplementary files format and content: Quality control was initiated by calculating Q30 scores.

source_name: cell line

extract_protocol:
In brief, m6A RNA immunoprecipitation (IP) was carried out utilizing a GenSeq™ m6A RNA IP Kit (GenSeq).
Both the input and m6A IP samples were prepared for NGS. The library was constructed using a NEBNext® Ultra II Directional RNA Library Prep Kit (NEB). The library's quality was assessed using a BioAnalyzer 2100 system (Agilent).

value: cell line

value: lung cancer

tag: treatment

tag: rip antibody


title: RNA_CBMS1_scRR1_WholeS_069


title: RNA_CBMS1_scRR1_WholeS_066


title: Wild type non-fed replicate 2

description:
Library name: LVP-NF-2
Column name in TPM_values_LVP_NF.csv: LVP-NF-2


title: shddx3x-MeRIP rep1


title: RNA_RPE1_scRR1_Lot2_WholeS_031


title: RNA_RPE1_scRR1_Lot2_WholeS_037


title: RNA_CBMS1_scRR3_WholeS_063


title: Wild type non-fed replicate 1

description:
Library name: LVP-NF-1
Column name in TPM_values_LVP_NF.csv: LVP-NF-1


title: shNS-MeRIP rep2

value: shNS


title: RNA_RPE1_scRR1_Lot2_WholeS_028


title: cwh8_BioRep4

city: Hanover

first: Daniel

middle: John

last: Gutzmann

state: NH

address: Vail Building 208, Geisel School of Medicine at Dartmouth

department: Microbiology and Immunology

institute: Dartmouth College

description:
Library name: Sample 17
Experiment 2

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3)
Read mapping was performed with STAR (v2.7.10) for experiment 1 and Kalisto for experiments 2 and 3.
Feature quantification was performed using RSEM (v1.3.3) for experiment 1 and Kallisto for experiments 2 and 3.
Read counts loaded into R and were normalized using edgeR’s (v1.14.5) Trimmed Mean of M values (TMM) algorithm.
Experiment 1: Subsequent values were then converted to counts per million (cpm). Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups. The file “AllQuantified Genes.tsv” contains the results of the qlfTest for all genes in addition to the normalized counts per million. Experiment 2/3: Differential expression was performed using DEseq2 against groups.
Assembly: ASM18296v3
Supplementary files format and content: Tab-separated values file contains raw counts for each sample
Supplementary files format and content: Tab-separated values file contains the results of the qlfTest for all genes in addition to the normalized counts per million

organism: Candida albicans

source_name: SC5314 derived

growth_protocol: Three biological replicates of SN152+, msn4, and cas5 were grown in YPD, 16 hours and 30°C, 225 RPM to generate a preinoculum. This preinoculum was diluted into 75 mL of YPD (0.1 OD600). Cultures were harvested after they had reached an early stationary phase (10 OD600), which is when farnesol levels peak (13), washed in ice-cold RNasefree H20, and frozen at -80°C.  For the second and third RNA seq experiments, cells were grown in mRPMI 1640 at 30°C, 225 RPM to generate a preinoculum. This preinoculum was diluted into 30 mL of mRPMI 1640 (0.1 OD600). Cultures were harvested after  6 hours post innoculation, washed in ice-cold RNasefree H20, and frozen at -80°C.

extract_protocol:
Total RNA was extracted using the hot-phenol method  and further cleaned up using the RNeasy mini kit (Qiagen). RNA quality was assessed by gel, spectrophotometric analysis (Spectramax Plus 384, Molecular Devices), and bioanalyzer analysis (Agilent). RNA samples sent for sequencing had a RIN > 8 and absorbance 260/280 of >2.0. RNA was quantified for sequencing by Quibit (Thermofischer Scientific). Samples were treated with DNase (RNAse free); Invitrogen.
Illumina’s Stranded mRNA prep with 10bp IDT for Illumina indices

value: SC5314 derived


title: RNA_CBMS1_scRR1_WholeS_065


title: shNS-MeRIP rep1


title: MAY1375_BioRep_2-1

description:
Library name: Sample 18
Experiment 2


title: cwh8_BioRep3

description:
Library name: Sample 16
Experiment 2


title: RNA_RPE1_scRR1_Lot2_WholeS_035


title: RNA_RPE1_scRR1_Lot2_WholeS_026


title: RNA_CBMS1_scRR3_WholeS_060


title: shddx3x-Input rep1

value: none (input)


title: shNS-Input rep2


title: shddx3x-Input rep2


title: Control-2


title: cwh8_BioRep2

description:
Library name: Sample 15
Experiment 2


title: RNA_CBMS1_scRR3_WholeS_061

value: embryonic stem cell


title: shNS-Input rep1


title: RNA_RPE1_scRR1_Lot2_WholeS_020


title: RNA_CBMS1_scRR3_WholeS_057


title: cwh8_BioRep1

description:
Library name: Sample 14
Experiment 2


title: RNA_CBMS1_scRR3_WholeS_055


title: MAY1375_BioRep_1-4

description:
Library name: Sample 13
Experiment 2


title: RNA_CBMS1_scRR3_WholeS_053


title: CD34_Diff_Day16_PROseq

city: Beijing,haidian

first: Shicong

last: Zhu

state: Beijing

address: Yi heyuan street, 5th.

department: School of life science and technology

institute: Peking university

description: Ex vivo cultured day 16 primary CD34 cells from cord blood PRO-seq

data_processing:
Reads adapters were removed by Trim_galore ( v0.6.6)
For RNA-seq, Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the hg19 genome using Hisat2 (v2.0.5) ,and then featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
For Cut&Tag data, Index of the reference genome was built using bowtie2 (v 2.4.5) and paired-end clean reads were aligned to the hg19 genome using bowtie2 (v 2.4.5) ,and then MACS2 (v 2.2.6) was used to call peaks.
For PRO-seq data analysis, Cutadapt (version 4.1) was used to remove adapter (parmaters: -q 20). Because of the short read length, only the Reads1 was used for next analysis. Clean reads were aligned to the hg19 genome using bowtie (version 1.3.0) with -m 2 parameters. Samtools (version 1.17) was used for align quality filter and separate the strand.
Assembly: hg19
Supplementary files format and content: RNA-seq results in excel format
Supplementary files format and content: Cut&Tag results in bigwig format
Supplementary files format and content: PRO-seq results in bigwig format
Library strategy: PRO-seq

source_name: Cord Blood

growth_protocol: The base medium contained IMDM (Gibco, Waltham, MA, USA), 5% human AB serum (Wokavi Biotech, Beijing, China), 10% FBS (Gibco), 10 ng/mL heparin (Sigma, St. Louis, MO, USA), 10 μg/mL insulin (Sigma), 2 mM L-Glutamine (Gibco), 3 IU/mL erythropoietin (Amgen, Thousand Oaks, CA, USA), and 300 μg/mL holo-Transferrin (Sigma). Phase-I medium was supplemented with 50 ng/mL Human Recombinant SCF (Stem Cell Technologies, Vancouver, BC, Canada) and 10 ng/mL Human Recombinant IL-3 (Stem Cell Technologies). Phase-II medium was supplemented with 50 ng/mL Human Recombinant SCF only. Cells were cultured in Phase-I medium for 8 days and then transferred to Phase-II medium for 6-8 days. K562 cell lines were cultured in 1640 medium supplemented with 10%FBS. All mouse and human cell lines were cultured in a 90% (v/v) humidified atmosphere with 5% (v/v) CO2 at 37 °C.

extract_protocol:
CD34+ cells were purified from human cord blood (Cord Blood Bank of Beijing) using the MACS MicroBead kit (Miltenyi Biotec, Bergisch Gladbach, Germany).
The CUT&Tag assay was performed as previously described48 and followed the manufacturer’s instructions for the kit (Vazyme, Nanjing, China). Briefly, 100,000 cells were freshly collected and captured using Concanavalin A (ConA) beads at room temperature. The cell/ConA beads complex was permeabilized and incubated with the primary antibody (at 1:100 dilution) overnight at 4 °C. The secondary antibody was added to the solution and incubated at room temperature for 1 h. The secondary antibody was washed off prior to adding pA/G-Tn5 to the cell suspension and then incubated at room temperature for 1 h. The adapters were then inserted into the Tn5-tagged genome using the TruPrep Tagment Buffer L (TTBL). The genomic DNA was extracted with DNA beads, and the tagged DNA fragments were amplified using the Next-Generation Sequencing (NGS) adapters with 16 cycles of PCR. The adaptor dimer was removed from the PCR products with DNA Clean Beads (Vazyme, Nanjing, China). The library was quantified before sequencing.
20 millions Day 4 or Day 16 ex vivo-cultured permeabilized CD34 cell nuclei were added to a 2 × Nuclear Run-On (NRO) reaction mixture and incubated for 3 min at 37 °C. Nascent RNA was extracted and fragmented by base hydrolysis in 0.2 N NaOH on ice for 10 min and neutralized by adding a 1× volume of 1 M Tris-HCl pH 6.8. Fragmented nascent RNA was subjected to buffer exchange and purified using streptavidin beads and ligated with reverse 3’ RNA adapter VRA3 (5'p-GAUCGUCGGACUGUAGAACUCUGAAC-/3’inverted dT/), and the products were enriched by a second round of streptavidin enrichment. Then, for 5’ end repair, the RNA products were treated with RppH (Thermo Fisher) and polynucleotide kinase (PNK, NEB). The 5’ repaired RNA was ligated to the reverse 5’ RNA adaptor VRA5 (5'-CUGAACAAGCAGAAGACGGCAUACGA-3') before the third round of streptavidin bead enrichment. RNA was reverse-transcribed using RT primer (5’AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3’). The cDNA product was amplified for 18 cycles, and the library larger than 150 bp (insert > 70 bp) was purified from the PAGE gel. The library was quantified before NGS.

value: Cord Blood

value: primary CD34 cell from cord blood


title: RNA_CBMS1_scRR3_WholeS_052


title: RNA_RPE1_scRR1_Lot2_WholeS_002


title: MAY1375_BioRep_1-2

description:
Library name: Sample 11
Experiment 2


title: MAY1375_BioRep_1-1

description:
Library name: Sample 10
Experiment 2


title: RNA_CBMS1_scRR3_WholeS_050


title: RNA_CBMS1_scRR3_WholeS_048


title: K562_KO_MED26_CUTTag

description: MED26 knock out K562 cell line CUT&Tag antibody-MED26

data_processing:
Reads adapters were removed by Trim_galore ( v0.6.6)
For RNA-seq, Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the hg19 genome using Hisat2 (v2.0.5) ,and then featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
For Cut&Tag data, Index of the reference genome was built using bowtie2 (v 2.4.5) and paired-end clean reads were aligned to the hg19 genome using bowtie2 (v 2.4.5) ,and then MACS2 (v 2.2.6) was used to call peaks.
For PRO-seq data analysis, Cutadapt (version 4.1) was used to remove adapter (parmaters: -q 20). Because of the short read length, only the Reads1 was used for next analysis. Clean reads were aligned to the hg19 genome using bowtie (version 1.3.0) with -m 2 parameters. Samtools (version 1.17) was used for align quality filter and separate the strand.
Assembly: hg19
Supplementary files format and content: RNA-seq results in excel format
Supplementary files format and content: Cut&Tag results in bigwig format
Supplementary files format and content: PRO-seq results in bigwig format
Library strategy: CUT&Tag

source_name: Blood

value: Blood

value: K562 cell line


title: MAY1375_BioRep_1-3

description:
Library name: Sample 12
Experiment 2


title: K562_WT_PAF1_CUTTag

description: Wild type K562 cell line CUT&Tag antibody-PAF1


title: RNA_RPE1_scRR1_Lot2_WholeS_024


title: RNA_RPE1_scRR1_Lot2_WholeS_016


title: K562_WT_MED26_CUTTag

description: Wild type K562 cell line CUT&Tag antibody-MED26


title: RNA_RPE1_scRR1_Lot1_WholeS_007


title: RNA_CBMS1_scRR3_WholeS_047


title: RNA_RPE1_scRR1_Lot1_WholeS_008


title: msn4_BioRep_1

description: Library name: Sample 7

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3)
Read mapping was performed with STAR (v2.7.10)
Feature quantification was performed using RSEM (v1.3.3)
Read counts loaded into R and were normalized using edgeR’s (v1.14.5) Trimmed Mean of M values (TMM) algorithm.
Subsequent values were then converted to counts per million (cpm). Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups. The file “AllQuantified Genes.tsv” contains the results of the qlfTest for all genes in addition to the normalized counts per million.
Assembly: ASM18296v3
Supplementary files format and content: Tab-separated values file contains raw rsem counts for each sample
Supplementary files format and content: Tab-separated values file contains the results of the qlfTest for all genes in addition to the normalized counts per million

source_name: SN152 derived

growth_protocol: Three biological replicates of SN152+, msn4, and cas5 were grown  in YPD, 16 hours and 30°C, 225 RPM to generate a preinoculum. This preinoculum was diluted into 75 mL of YPD (0.1 OD600). Cultures were harvested after they had reached an early stationary phase (10 OD600), which is when farnesol levels peak (13), washed in ice-cold RNasefree H20, and frozen at -80°C.

value: SN152 derived

value: msn4 (msn4::ST13-C.d.HIS1/msn4::ST13-C.m.LEU2, leu2/leu2, ura3/URA3, his1/his1, arg4/arg4, iro1/IRO1, MTLa/ MTLalpha)


title: RNA_RPE1_scRR1_Lot1_WholeS_005


title: msn4_BioRep_2

description: Library name: Sample 8


title: RNA_RPE1_scRR1_Lot1_WholeS_006


title: msn4_BioRep_3

description: Library name: Sample 9


title: RNA_CBMS1_scRR3_WholeS_046


title: CD34_Diff_Day16_Rpb1_Rep1

description: Enriched genomic DNA

data_processing:
Reads adapters were removed by Trim_galore ( v0.6.6).
For RNA-seq, Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the hg19 genome using Hisat2 (v2.0.5), and then featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
For Cut&Tag data, Index of the reference genome was built using bowtie2 (v 2.4.5) and paired-end clean reads were aligned to the hg19 genome using bowtie2 (v 2.4.5), and then MACS2 (v 2.2.6) was used to call peaks.
Assembly: hg19
Supplementary files format and content: RNA-seq results in tab-delimited text format.
Supplementary files format and content: Cut&Tag results in bigwig format.
Library strategy: CUT&Tag

source_name: Primary CD34 cell from cord blood

growth_protocol: The two-phase erythroid differentiation protocol was modified from the previous study. The base medium contained IMDM (Gibco, Waltham, MA, USA), 5% human AB serum (Wokavi Biotech, Beijing, China), 10% FBS (Gibco), 10 ng/mL heparin (Sigma, St. Louis, MO, USA), 10 μg/mL insulin (Sigma), 2 mM L-Glutamine (Gibco), 3 IU/mL erythropoietin (Amgen, Thousand Oaks, CA, USA), and 300 μg/mL holo-Transferrin (Sigma). Phase-I medium was supplemented with 50 ng/mL Human Recombinant SCF (Stem Cell Technologies, Vancouver, BC, Canada) and 10 ng/mL Human Recombinant IL-3 (Stem Cell Technologies). Phase-II medium was supplemented with 50 ng/mL Human Recombinant SCF only. Cells were cultured in Phase-I medium for 8 days and then transferred to Phase-II medium for 6-8 days. K562 cell lines were cultured in 1640 medium supplemented with 10%FBS. All mouse and human cell lines were cultured in a 90% (v/v) humidified atmosphere with 5% (v/v) CO2 at 37 °C.

extract_protocol:
CD34+ cells were purified from human cord blood (Cord Blood Bank of Beijing) using the MACS MicroBead kit (Miltenyi Biotec, Bergisch Gladbach, Germany).
The CUT&Tag assay was performed as previously described and followed the manufacturer’s instructions for the kit (Vazyme, Nanjing, China). Briefly, 100,000 cells were freshly collected and captured using Concanavalin A (ConA) beads at room temperature. The cell/ConA beads complex was permeabilized and incubated with the primary antibody (at 1:100 dilution) overnight at 4 °C. The secondary antibody was added to the solution and incubated at room temperature for 1 h. The secondary antibody was washed off prior to adding pA/G-Tn5 to the cell suspension and then incubated at room temperature for 1 h. The adapters were then inserted into the Tn5-tagged genome using the TruPrep Tagment Buffer L (TTBL). The genomic DNA was extracted with DNA beads, and the tagged DNA fragments were amplified using the Next-Generation Sequencing (NGS) adapters with 16 cycles of PCR. The adaptor dimer was removed from the PCR products with DNA Clean Beads (Vazyme, Nanjing, China). The library was quantified before sequencing.

value: Primary CD34 cell from cord blood

tag: time point

value: Diff Day16

tag: antibody


title: RNA_CBMS1_scRR3_WholeS_045


title: RNA_RPE1_scRR1_Lot1_WholeS_003


title: CD34_Diff_Day16_MED26_Rep1

description: Enriched genomic DNA

value: WT


title: RNA_RPE1_scRR1_Lot1_WholeS_016


title: CD34_Diff_Day4_PROseq

description: Ex vivo cultured day 4 primary CD34 cells from cord blood PRO-seq


title: cas5_BioRep_3

description: Library name: Sample 6

value: cas5 (cas5::ST13-C.d.HIS1/cas5::ST13-C.m.LEU2, leu2/leu2, ura3/URA3, his1/his1, arg4/arg4, iro1/IRO1, MTLa/ MTLalpha)


title: RNA_RPE1_scRR1_Lot2_WholeS_011


title: K562_KO_PAF1_CUTTag

description: MED26 knock out K562 cell line CUT&Tag antibody-PAF1


title: cas5_BioRep_2

description: Library name: Sample 5


title: RNA_CBMS1_scRR3_WholeS_038


title: RNA_CBMS1_scRR3_WholeS_040


title: CD34_Diff_Day16_NC_Rep1

description: Enriched genomic DNA

value: NC


title: RNA_RPE1_scRR1_Lot1_WholeS_015


title: RNA_CBMS1_scRR3_WholeS_037


title: cas5_BioRep_1

description: Library name: Sample 4


title: RNA_CBMS1_scRR3_WholeS_036


title: RNA_RPE1_scRR1_Lot1_WholeS_014


title: SN152+_BioRep_3

description: Library name: Sample 3

value: SN152+ (Arg-, His+, Leu+)


title: SN152+_BioRep_1

description: Library name: Sample 1


title: CD34_Diff_Day4_MED1_Rep1

description: Enriched genomic DNA

value: Diff Day4


title: DNA_RPE1_scRR3_G0_003

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: hg38
Supplementary files format and content: txt
Library strategy: scRepli-seq

extract_protocol:
For samples subjected to scRR-seq protocol, single cells were individually collected into 0.2 ml PCR tubes by cell sorter or manually picked and lysed in RamDA-seq lysis buffer (TOYOBO, #RMD-101) containing 2 mg/ml Dynabeads™ MyOne™ Carboxylic Acid (Invitrogen, #65011). Genomic DNA was trapped on the beads, while RNA was released into the lysis buffer. The isolated DNA on magnetic beads was subjected to whole-genome amplification (WGA) and Next-Generation Sequencing (NGS) library preparation, as described in scRepli-seq (Takahashi et al., Nat Genet 2019). The DNA-seq (scRepli-seq) data was used to assess genome-wide DNA copy numbers, karyotype G1-phase cells, and analyze the replication state of S-phase cells. In parallel, the isolated RNA in the supernatant was subjected to scRamDA-seq (Hayashi et al., Nat Commun 2018) using the GenNext®RamDA-seq™ Single Cell Kit (TOYOBO, #RMD-101) according to the manufacturer’s instructions with modifications. For samples subjected to scRamDA-seq protocol, single cells were individually collected into 0.2 ml PCR tubes by cell sorter or manually picked and lysed in RamDA-seq lysis buffer (TOYOBO, #RMD-101). Then, the samples were directly subjected to scRamDA-seq (Hayashi et al., Nat Commun 2018) using the GenNext®RamDA-seq™ Single Cell Kit (TOYOBO, #RMD-101) according to the manufacturer’s instructions with modifications.
Sample and library preparation for scRR-seq-DNA (scRepli-seq): Genomic DNA was subjected to WGA with a SeqPlex kit (Sigma, SEQXE) in a 30-µl reaction volume, per the manufacturer’s instructions. Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads (1.7× reaction volume), and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The gDNA was then purified with Agencourt AMPure XP SPRI beads (2.0× reaction volume) and eluted in 20 µl of 1/10× Elution Buffer (Qiagen). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu). We could easily distinguish single cells from zero or two cells by quantification of DNA with MultiNA, which provided reassurance that the gDNA was indeed derived from single cells. Then NGS libraries were constructed using the NGS LTP Library Preparation Kit (KAPA, KK8232) with a SeqCap adapter kit A/B (Roche, 07141530001/07141548001) or NEXTflex DNA barcode (Bio Scientific, NOVA), or the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England BioLabs , #E7645) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, Set 2) (New England BioLabs , #E7600S, #E7780S ) or NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, Set 2, Set 3, Set 4) (New England BioLabs , #E7355L, E7500L, E7710L, E7730L). Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).  Library preparation for scRR-seq-RNA scRamDA-seq NGS libraries were generated by using the Nextera® XT Library Prep Kit 24 Samples (illumina, #15032350, #15032352) with Nextera® XT Index Kit v2 Set A 96 indexes-samples (Illumina, #15052163) according to the manufacturer’s instructions with modifications. Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).


title: CD34_Diff_Day4_Rpb1_Rep1

description: Enriched genomic DNA


title: SN152+_BioRep_2

description: Library name: Sample 2


title: CD34_Diff_Day4_MED26_Rep1

description: Enriched genomic DNA


title: RNA_CBMS1_scRR3_WholeS_032


title: RNA_RPE1_scRR1_Lot1_WholeS_013


title: CD34_Diff_Day4_H3K27ac_Rep1

description: Enriched genomic DNA


title: RNA_CBMS1_scRR3_WholeS_029


title: CD34_Diff_Day16_MED1_Rep1

description: Enriched genomic DNA


title: DNA_RPE1_scRR3_MidS_Lot2_009


title: RNA_CBMS1_scRR3_WholeS_030


title: iPSC-derived smooth muscle cells 5

city: Munich

first: Rainer

last: Malik

address: Feodor-Lynen-Str. 17

department: Institute for Stroke and Dementia Research

country: Germany

institute: Klinikum der Universität München

description: Library name: iSMC_5

data_processing:
Bwa-mem2 (2.2) was used for aligning the reads with the human genome of reference GRCh38. Normalization was performed using edgeR (4.4.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw gene counts for each sample

source_name: iPSC-derived smooth muscle cells

growth_protocol: endothelial and mural cells were differentiated from iPSCs and grown as described in detail in our publication 'A fully iPSC-derived 3D model of the human blood-brain barrier for exploring neurovascular disease mechanisms and therapeutic interventions'.

extract_protocol:
RNA was extracted from cell pellets using Trizol (Qiagen, Cat# 79306) and purified using the RNeasy mini kit (Qiagen, Cat# 74106) following manufacturer’s instructions. Total RNA concentration was determined using a NanoDrop spectrophotometer. RNA was stored at -80ºC.
Library construction was done as previously described by BGI (Chen et al. 2018, SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data) using 400ng of RNA of each cell type.

value: iPSC-derived smooth muscle cells


title: DNA_RPE1_scRR3_G0_015


title: K562_MED26_KO_Rep2

data_processing:
Reads adapters were removed by Trim_galore ( v0.6.6).
For RNA-seq, Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the hg19 genome using Hisat2 (v2.0.5), and then featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
For Cut&Tag data, Index of the reference genome was built using bowtie2 (v 2.4.5) and paired-end clean reads were aligned to the hg19 genome using bowtie2 (v 2.4.5), and then MACS2 (v 2.2.6) was used to call peaks.
Assembly: hg19
Supplementary files format and content: RNA-seq results in tab-delimited text format.
Supplementary files format and content: Cut&Tag results in bigwig format.


title: iPSC-derived smooth muscle cells 3

description: Library name: iSMC_3


title: iPSC-derived smooth muscle cells 4

description: Library name: iSMC_4


title: DNA_RPE1_scRR3_MidS_Lot2_008


title: CD34_Diff_Day4_NC_Rep1

description: Enriched genomic DNA


title: iPSC-derived smooth muscle cells 2

description: Library name: iSMC_2


title: RNA_CBMS1_scRR3_WholeS_024


title: K562_MED26_KO_Rep1


title: iPSC-derived smooth muscle cells 1

description: Library name: iSMC_1


title: DNA_RPE1_scRR3_MidS_Lot2_007


title: K562_WT_Rep2


title: DNA_RPE1_scRR3_MidS_Lot2_016


title: iPSC-derived pericytes 4

description: Library name: iPE_4

source_name: iPSC-derived pericytes

value: iPSC-derived pericytes


title: RNA_CBMS1_scRR3_WholeS_023


title: K562_WT_Rep1


title: DNA_RPE1_scRR3_MidS_Lot2_015


title: RNA_CBMS1_scRR3_WholeS_022


title: RNA_CBMS1_scRR3_WholeS_021


title: RNA_CBMS1_scRR3_WholeS_027


title: iPSC-derived pericytes 3

description: Library name: iPE_3


title: N_D0_3

city: Beijing

first: Shaojun

last: Liang

address: 18 Shuangqing Road

institute: Chinese academy of sciences

data_processing:
Sequencing was performed with an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Reads were filtered and mapped to the reference genome sequence with Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: The fragments per kilobase of exon per million fragments mapped (FPKM) method was used to calculated gene expression

source_name: liver

extract_protocol:
The samples for RNA-seq were collected in TriZol. 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following

value: liver

value: the mixture  of LX2, iPSC_N-derived EC and iPSC-derived HE

value: hepatic stellate cells, endothelial cels and hepatic endoderm

value: wt


title: N_D0_2


title: DNA_RPE1_scRR3_MidS_Lot2_013


title: N_D0_1


title: DNA_RPE1_scRR3_MidS_Lot2_012


title: RNA_CBMS1_scRR3_WholeS_019

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: mm10
Supplementary files format and content: txt, bedGraph

value: embryonic stem cell


title: iPSC-derived pericytes 1

description: Library name: iPE_1


title: RNA_CBMS1_scRR3_WholeS_026


title: RNA_CBMS1_scRR3_WholeS_016


title: iPSC-derived endothelial cells 5

description: Library name: iEC_5

source_name: iPSC-derived endothelial cells

value: iPSC-derived endothelial cells


title: AC19_D0_3

value: the mixture  of LX2, iPSC_AC19-derived EC and iPSC-derived HE


title: iPSC-derived pericytes 2

description: Library name: iPE_2


title: DNA_RPE1_scRR3_MidS_Lot2_011


title: RNA_CBMS1_scRR3_WholeS_013


title: AC19_D0_2


title: iPSC-derived endothelial cells 4

description: Library name: iEC_4


title: DNA_RPE1_scRR3_MidS_Lot1_009


title: RNA_CBMS1_scRR1_WholeS_128


title: iPSC-derived endothelial cells 3

description: Library name: iEC_3


title: DNA_RPE1_scRR3_MidS_Lot1_007


title: AC19_D0_1


title: RNA_CBMS1_scRR1_WholeS_127


title: RNA_CBMS1_scRR1_WholeS_125


title: iPSC-derived endothelial cells 2

description: Library name: iEC_2


title: iPSC-derived endothelial cells 1

description: Library name: iEC_1


title: DNA_RPE1_scRR3_MidS_Lot1_003


title: PHH_3

value: PHH

value: hepatocyte


title: PHH_1


title: DNA_RPE1_scRR3_MidS_Lot1_006


title: HEp2, 1.5hpi, rep1

city: Ithaca

first: Joel

last: Baines

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: Library name: HEp2_1

data_processing:
Adapter trimming, genome alignment and conversion to strand-specific BigWigs using pipeline available here: https://github.com/Danko-Lab/proseq2.0
Assembly: Hg38 human genome build,  HSV-1 F in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: Library size and HSV-1 genome copy normalized HSV-1 aligned strand-specific bigwig files
Library strategy: PRO-Seq

molecule: nuclear RNA

organism:
Homo sapiens
Human alphaherpesvirus 1

growth_protocol: HEp-2 cells were maintained in DMEM supplemented with 10% NBS and pen/strep

extract_protocol:
Nuclei were extracted and nuclear run-on with biotinylated nucleotides performed as described in: Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086 and Journal of virology 92.8 (2018): doi:10.1128/JVI.02184-17
Constructed as detailed in Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol: Cells were infected with HSV-1 at anMOI of 5 and infection allowed to proceed for 1.5hpi . Time 0 indicates time after 1h viral adsorption at 4°C. Performed in duplicate

value: lung epithelial carcinoma cells

tag: virus infection

value: HSV-1 F

tag: hours post-infection


title: DNA_RPE1_scRR3_MidS_Lot2_014


title: RNA_CBMS1_scRR1_WholeS_123


title: RNA_CBMS1_scRR1_WholeS_126


title: BRACO-19, 1.5hpi, rep3

description: Library name: BRACO19_3

treatment_protocol: Cells were infected with HSV-1 at anMOI of 5 and infection allowed to proceed for 1.5hpi in the presence of 25µM BRACO-19 or DMSO. Time 0 indicates time after 1h viral adsorption at 4°C. Performed in triplicate.

value: BRACO-19 (25µM)


title: RNA_CBMS1_scRR1_WholeS_124


title: DNA_RPE1_scRR1_MidS_008


title: HEp2, 1.5hpi, rep2

description: Library name: HEp2_2


title: PHH_2


title: DNA_RPE1_scRR3_MidS_Lot1_019


title: DNA_RPE1_scRR3_MidS_Lot1_013


title: RNA_CBMS1_scRR1_WholeS_120


title: RNA_CBMS1_scRR1_WholeS_121


title: DNA_RPE1_scRR1_MidS_007


title: N_MPTA_3

value: the mixture  of LX2, iPSC_N-derived EC and iPSC-derived HLC

value: hepatic stellate cells, endothelial cels and hepatocyte like cells

value: 60 ng / mL microplastics and 100 nM TBBPA


title: N_TBBPA_3

value: 100 nM TBBPA


title: RNA_CBMS1_scRR1_WholeS_119


title: DNA_RPE1_scRR1_MidS_005


title: RNA_CBMS1_scRR3_WholeS_012


title: DMSO, 1.5hpi, rep2

description: Library name: DMSO_2

value: DMSO


title: DNA_RPE1_scRR1_MidS_004


title: RNA_CBMS1_scRR1_WholeS_118


title: N_MPTA_1

value: liver


title: N_TBBPA_2


title: DMSO, 1.5hpi, rep1

description: Library name: DMSO_1


title: N_MP_3

value: 60 ng / mL microplastics


title: DNA_RPE1_scRR1_MidS_016


title: BRACO-19, 1.5hpi, rep2

description: Library name: BRACO19_2


title: RNA_CBMS1_scRR1_WholeS_115


title: ATRX KD, 1.5hpi, rep3

description: Library name: ATRX_KD_3

data_processing:
Adapter trimming, genome alignment and conversion to strand-specific BigWigs using pipeline available here: https://github.com/Danko-Lab/proseq2.0
Assembly: Hg38 human genome build, , HSV-1 F in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: Library size and HSV-1 genome copy normalized HSV-1 aligned strand-specific bigwig files
Library strategy: PRO-Seq

treatment_protocol: Cells were reverse transfected with 50nM ATRX siRNA or Neg non-targeting control. After 48h cells were infected with HSV-1 at anMOI of 5 and infection allowed to proceed for 1.5hpi. Time 0 indicates time after 1h viral adsorption at 4°C. Performed in triplicate.

value: 50nM Neg ATRX siRNA


title: DNA_RPE1_scRR1_MidS_003


title: N_TBBPA_1

value: wt


title: N_MP_1


title: RNA_CBMS1_scRR1_WholeS_116

value: embryonic stem cell


title: DNA_RPE1_scRR1_MidS_015


title: BRACO-19, 1.5hpi, rep1

description: Library name: BRACO19_1


title: ATRX KD, 1.5hpi, rep2

description: Library name: ATRX_KD_2


title: DNA_RPE1_scRR1_MidS_006


title: RNA_CBMS1_scRR1_WholeS_113


title: DMSO, 1.5hpi, rep3

description: Library name: DMSO_3


title: N_MPTA_2


title: DNA_RPE1_scRR1_MidS_013


title: Neg ctrl KD, 1.5hpi, rep3

description: Library name: Neg_ctrl_KD_3

value: 50nM Neg ctrl siRNA


title: RNA_CBMS1_scRR1_WholeS_111


title: Neg ctrl KD, 1.5hpi, rep2

description: Library name: Neg_ctrl_KD_2


title: RNA_CBMS1_scRR3_WholeS_011


title: N_MP_2


title: N_ctrl_1


title: RNA_CBMS1_scRR1_WholeS_110


title: Neg ctrl KD, 1.5hpi, rep1

description: Library name: Neg_ctrl_KD_1


title: AC19_MPTA_3

value: the mixture  of LX2, iPSC_AC19-derived EC and iPSC-derived HLC


title: RNA_CBMS1_scRR1_WholeS_109


title: AC19_MPTA_2


title: RNA_RPE1_scRR3_G0_003

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: hg38
Supplementary files format and content: txt


title: AC19_MPTA_1


title: RNA_CBMS1_scRR1_WholeS_108


title: DNA_RPE1_scRR1_MidS_010


title: N_ctrl_3


title: 1.5hpi, ATRX, rep2

description: Library name: ATRX_2

data_processing:
QC and alignment: https://github.com/Baines-Lab/Public/blob/main/ATRX_ChIP_Seq/QC_align.sh
RPGC normalization to generate bigwig files using deepTools bamCoverage
Peaks called using MACS3: (https://github.com/Baines-Lab/Public/blob/main/ATRX_ChIP_Seq/MACS3.sh)
Assembly: Hg38 human genome build,  HSV-1 F in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: RPGC normalized bigwig files for hg38 reads
Supplementary files format and content: RPGC normalized bigwig files for HSV reads

extract_protocol:
Cells werecrosslinked with 2mM ethylene glycol-bis(succinimidylsuccinate) (EGS)for 45 min at room temperature, followed by a 1% formaldehyde fixation for 8 min. After quenching and lysis, chromatin was sonicated using a Bioruptor Plus (Diagenode) (45 cycles of 30s on/30s off, 4C)
NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645S, NEB), without size selection

treatment_protocol: 10^8 Cells were infected with HSV-1 at anMOI of 5 and infection allowed to proceed for 1.5hpi. Time 0 indicates time after 1h viral adsorption at 4°C. Performed in triplicate.

value: ATRX (Abcam, #ab97508)


title: RNA_CBMS1_scRR1_WholeS_104


title: DNA_RPE1_scRR1_MidS_014


title: ATRX KD, 1.5hpi, rep1

description: Library name: ATRX_KD_1


title: RNA_RPE1_scRR3_G0_015


title: DNA_RPE1_scRR1_MidS_011


title: 1.5hpi, ATRX, rep3

description: Library name: ATRX_3


title: AC19_ctrl_3


title: 1.5hpi, IgG, rep3

description: Library name: IgG_3

value: IgG (Abcam, #ab171870)


title: N_ctrl_2


title: 1.5hpi, ATRX, rep1

description: Library name: ATRX_1

value: lung epithelial carcinoma cells


title: RNA_CBMS1_scRR1_WholeS_103


title: RNA_RPE1_scRR3_MidS_Lot2_009


title: DNA_RPE1_scRR1_MidS_012


title: AC19_ctrl_2


title: AC19_ctrl_1


title: RNA_CBMS1_scRR1_WholeS_101


title: RNA_CBMS1_scRR1_WholeS_102


title: 1.5hpi, IgG, rep2

description: Library name: IgG_2

value: HSV-1 F


title: RNA_RPE1_scRR3_MidS_Lot2_008


title: 1.5hpi, IgG, rep1

description: Library name: IgG_1


title: RNA_RPE1_scRR3_MidS_Lot2_007


title: 1.5hpi, input, rep3

description: Library name: Input_3


title: RNA_RPE1_scRR3_MidS_Lot2_016


title: RNA_CBMS1_scRR3_WholeS_005


title: 1.5hpi, input, rep2

description: Library name: Input_2


title: RNA_CBMS1_scRR3_WholeS_007


title: WT_10uM_iCB_rep2

city: Valencia

first: Pedro

middle: L.

last: Rodriguez

state: Valencia

address: C/ Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

description: Library name: N11_iCB

data_processing:
After quality analysis with FastQC and read cleaning and adaptor trimming with cutadapt, clean reads were mapped to reference genome of Solanum lycopersicum SL4.0 using STAR. Read counts table produced by STAR was used to perform the differential expression analysis with DESeq2.
Assembly: SL4.0  (https://solgenomics.net/ftp/tomato_genome/assembly/build_4.00/)
Supplementary files format and content: tab-delimited text fille includes raw counts for each sample

organism: Solanum lycopersicum

source_name: whole seedlings

growth_protocol: Solanum lycopersicum seedlings (3 d.a.g.) were transferred from plates to flashes with liquid media during 8 days

extract_protocol:
RNA was harvested using E.Z.N.A.® Plant RNA Kit (Omega Biotek).
The library was constructed using the DNBSEQ Eukaryotic Strand-specific mRNA library kit (BGI Genomics, Shenzhen, China)

treatment_protocol: the medium was refreshed, and it was supplemented with 0.1% DMSO (mock) or 10 μM ABA or 20 μM iSB09 or 10 µM iCB. Samples were collected after 3 hours of incubation

value: whole seedlings

value: WT

value: 10µM iCB


title: WT_10uM_iCB_rep3

description: Library name: N12_ICB


title: WT_10uM_iCB_rep1

description: Library name: N10_iCB


title: RNA_RPE1_scRR3_MidS_Lot2_015


title: 14 dpi sample 2

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
The data were analyzed by following the description of CTK pipeline (https://doi.org/10.1093/bioinformatics/btw653)
3' adapter were trimmed by cutadapt (v1.18) by two steps to remove the adapters (NNNNNNNNAGATCGGAAGAGCGTCGTG, NNNNNNNNAGATCGGAAGAGCGTCGTGT, AGATCGGAAGAGCGTCGTG, and AGATCGGAAGAGCGTCGTGT) with parameters(--times 1 -e 0.1 -O 1 --quality-cutoff 5 -m 20)
The trimmed reads were mapped to danRer10 by STAR (2.7.4a)
Reads were counted after PCR duplicates were collapsed.
Assembly: danRer10
Supplementary files format and content: csv file with reads count for given exons

organism: Danio rerio

source_name: zebrafish hearts

extract_protocol: Van Nostrand, Eric L., et al. "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)."Nature methods13.6 (2016): 508-514.

value: zebrafish hearts

tag: group

value: 14 days post injury

tag: fraction

value: IP

value: Z-CAT transgenic fish

value: Tamoxifen treatment


title: RNA_CBMS1_scRR3_WholeS_004

extract_protocol:
Single cells were collected into 0.2 ml PCR tubes by cell sorter or manually picked and lysed in RamDA-seq lysis buffer (TOYOBO, #RMD-101) containing 2 mg/ml Dynabeads™ MyOne™ Carboxylic Acid (Invitrogen, #65011). Genomic DNA was trapped on the beads, while RNA was released into the lysis buffer. The isolated DNA on magnetic beads was subjected to whole-genome amplification (WGA) and Next-Generation Sequencing (NGS) library preparation, as described in scRepli-seq (Takahashi et al., Nat Genet 2019). The DNA-seq (scRepli-seq) data was used to assess genome-wide DNA copy numbers, karyotype G1-phase cells, and analyze the replication state of S-phase cells. In parallel, the RNA isolated in the supernatant was subjected to scRamDA-seq (Hayashi et al., Nat Commun 2018) using the GenNext®RamDA-seq™ Single Cell Kit (TOYOBO, #RMD-101) according to the manufacturer’s instructions with modifications.
Sample and library preparation for scRR-seq-DNA (scRepli-seq): Genomic DNA was subjected to WGA with a SeqPlex kit (Sigma, SEQXE) in a 30-µl reaction volume, per the manufacturer’s instructions. Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads (1.7× reaction volume), and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The gDNA was then purified with Agencourt AMPure XP SPRI beads (2.0× reaction volume) and eluted in 20 µl of 1/10× Elution Buffer (Qiagen). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu). We could easily distinguish single cells from zero or two cells by quantification of DNA with MultiNA, which provided reassurance that the gDNA was indeed derived from single cells. Then NGS libraries were constructed using the NGS LTP Library Preparation Kit (KAPA, KK8232) with a SeqCap adapter kit A/B (Roche, 07141530001/07141548001) or NEXTflex DNA barcode (Bio Scientific, NOVA), or the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England BioLabs , #E7645) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, Set 2) (New England BioLabs , #E7600S, #E7780S ) or NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, Set 2, Set 3, Set 4) (New England BioLabs , #E7355L, E7500L, E7710L, E7730L). Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).  Library preparation for scRR-seq-RNA scRamDA-seq NGS libraries were generated by using the Nextera® XT Library Prep Kit 24 Samples (illumina, #15032350, #15032352) with Nextera® XT Index Kit v2 Set A 96 indexes-samples (Illumina, #15052163) according to the manufacturer’s instructions with modifications. Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).


title: RNA_RPE1_scRR3_MidS_Lot2_014


title: 14 dpi sample 1


title: 1.5hpi, input, rep1

description: Library name: Input_1


title: RNA_RPE1_scRR3_MidS_Lot2_013


title: RNA_CBMS1_scRR3_WholeS_001


title: 14 days post injury (dpi) prior to pulldown

value: input


title: RNA_RPE1_scRR3_MidS_Lot2_012


title: CTRL04_ChorioamnioticMembranes

city: Seattle

first: Kristina

last: Adams Waldorf

state: Washington

address: 750 Republican Street, E Building, Room E360

department: OBGYN

institute: University of Washington

description: Library name: Z12353_MemInoc

data_processing:
Initial processing and fastq generation was done using cellranger v7.2
Generation of count matricies was done using cellranger v7.2
Aggregation of count matricies was done using cellranger v7.2
Assembly: Mmul_10
Supplementary files format and content: h5 format aggregate filtered count matrix

organism: Macaca nemestrina

source_name: MemInoc

extract_protocol:
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)

value: MemInoc


title: DNA_8CEmbryo2_Cell8_025

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: mm10
Supplementary files format and content: txt
Library strategy: scRepli-seq

source_name: 8-cell embryo

value: 8-cell embryo


title: CTRL04_ChorionicVillous

description: Library name: Z12353_CV

source_name: CV

value: CV


title: DNA_8CEmbryo2_Cell7_024


title: Uninjured sample 2

value: Uninjured


title: Uninjured sample 1


title: RNA_RPE1_scRR3_MidS_Lot2_011


title: CTRL03_Decidua

description: Library name: M10190_Decidua

source_name: Decidua

value: Decidua


title: Uninjured prior to pulldown


title: RNA_RPE1_scRR3_MidS_Lot1_007


title: DNA_8CEmbryo2_Cell5_022


title: RNA_CBMS1_scRR3_WholeS_002

value: embryonic stem cell


title: CTRL03_ChorionicVillous

description: Library name: M10190_CV


title: DNA_8CEmbryo1_Cell7_021


title: DNA_8CEmbryo2_Cell6_023


title: RNA_RPE1_scRR3_MidS_Lot1_006


title: CTRL04_Decidua

description: Library name: Z12353_Decidua


title: CTRL03_ChorioamnioticMembranes

description: Library name: M10190_MemInoc


title: CTRL02_ChorioamnioticMembranes

description: Library name: A10007_MemInoc


title: RNA_RPE1_scRR3_MidS_Lot1_019


title: RNA_RPE1_scRR3_MidS_Lot1_003


title: DNA_8CEmbryo2_Cell3_017


title: CTRL02_ChorionicVillous

description: Library name: A10007_CV


title: DNA_8CEmbryo2_Cell2_016


title: C.pCMV6.TGF

city: Fukuoka

first: Sae

last: Oka

address: 3-1-1 Maidashi Higashi-ku

institute: Kyushu University

description: Library name: Sample8

data_processing:
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Quality of total RNAs were assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0. After poly (A) + RNA enrichment by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), double-stranded cDNA libraries (RNA-seq libraries) were prepared using QIAseq UPX 3' Transcriptome Kit (QIAGEN, 333088) and MGIEasy Universal Library Conversion Kit (App-A) (MGI, 1000004155) according to the manufacturer’s instruction. RNA-seq libraries were sequenced using paired end reads (150nt of read1 and read2) on a DNBSEQ-G400RS instrument (MGI Tech). Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.6.7), Trimmomatic (version 0.39), and cutadapt (version 3.7) software. Trimmed reads were then mapped to Rattus norvegicus mRatBN7.2 using STAR (version 2.7.10a). Reads on annotated genes were counted using featureCounts (version 2.0.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcripts. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0). The list of differentially expressed genes detected by DESeq2 (basemean > 5 and fold-change < 0.25, or basemean > 5 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include CPM (FPKM, peak) values for each sample.
Supplementary files format and content: gene-CPM_name.txt

organism: Rattus norvegicus

source_name: the cervical loop of rat mandibular incisors

extract_protocol:
Total RNA was extracted using the RNeasy® Mini Kit (Qiagen, 74904).
RNA quality was assessed using a NanoDrop One spectrophotometer Thermo Fisher Scientific, Waltham, MS, USA), and only samples with an RNA Integrity Number of 9.0 or higher were used for further analysis. Libraries were prepared using the QIAseq UPX 3' Transcriptome Kit (Qiagen, Venlo, Netherlands, 333088) and the MGIEasy Universal Library Conversion Kit (App-A) (MGI, Shenzhen, China, 1000004155). Paired-end sequencing (150 bp) was performed on the DNBSEQ-G400 platform (MGI, Shenzhen, China). The quality of raw sequencing reads was evaluated using FastQC, and adapters and low-quality reads were removed using Trim Galore!, Trimmomatic, and Cutadapt. Clean reads were mapped to the Rat (Rattus norvegicus) genome assembly mRatBN7.2 using the STAR aligner, and gene-level read counts were obtained using featureCounts. Differential gene expression analysis was conducted using the DESeq2 package (version 1.20.0). Genes with a false discovery rate (FDR) < 0.05 were considered statistically significant.

value: a dental epithelial cell line

value: Control


title: C.pCMV6.ODAM.TGF

description: Library name: Sample7

value: the cervical loop of rat mandibular incisors


title: C.pCMV6.ODAM.N

description: Library name: Sample6


title: RNA_RPE1_scRR3_MidS_Lot1_009


title: A.pCMV6.TGF

description: Library name: Sample4

value: AmeloD-overexpressing


title: RNA_RPE1_scRR3_MidS_Lot1_013


title: CTRL08_Decidua

description: Library name: Z15198_Decidua


title: RNA_RPE1_scRR1_MidS_008


title: DNA_8CEmbryo2_Cell1_015


title: CTRL02_Decidua

description: Library name: A10007_Decidua


title: DNA_8CEmbryo1_Cell4_014


title: RNA_RPE1_scRR1_MidS_006


title: A.pCMV6.ODAM.TGF

description: Library name: Sample3


title: DNA_8CEmbryo1_Cell6_020


title: RNA_RPE1_scRR1_MidS_007


title: DNA_8CEmbryo1_Cell3_013


title: A.pCMV6.ODAM.N

description: Library name: Sample2


title: CTRL08_ChorionicVillous

description: Library name: Z15198_CV


title: RNA_RPE1_scRR1_MidS_005


title: DNA_8CEmbryo1_Cell2_012


title: CTRL07_Decidua

description: Library name: Z15060_Decidua


title: A.pCMV6.N

description: Library name: Sample1


title: C.pCMV6.N

description: Library name: Sample5


title: CTRL07_ChorioamnioticMembranes

description: Library name: Z15060_MemInoc


title: RNA_RPE1_scRR1_MidS_004


title: DNA_8CEmbryo1_Cell1_011


title: Intestinal Organoid Differentiated from IPS2

city: Kansas City

first: Tamara

last: Potapova

state: Missouri

institute: Stowers Institute for Medical Research

description: Library name: Minigut_iPS-2

data_processing:
Alignment to chm13 (v2.0) using the bisulfite sequencing aligner Bismark (v0.24.0) with the local parameter set (--local).
Alignments were deduplicated and extracted into bed coverage format to give a C and T count at each reference position. Complementary CpGs on the two strands were merged into a single site. Positions were later filtered by requiring coverage of 5 or more reads.
To assess rDNA alone, reads were aligned to the reference sequence KY962518.1 instead of chm13. The bismark local alignment option was used but reads were not deduplicated. This is due to the high copy number of the rDNA gene which creates many real duplicate alignments that are useful for methylation quantificaiton. Methylation extraction was performed to give bed coverage files with CpGs merged from both strands. Positions were filtered by requiring coverage of 10 or more reads.
Assembly: chm13 v2.0
Supplementary files format and content: Bed coverage files for whole genome and KY962518.1 alignments
Supplementary files format and content: The columns are unlabelled but have the format of: chromosome, start position, end position, methylation percentage, count methylated, count unmethylated.
Library strategy: EM-seq

source_name: hydatidiform mole

extract_protocol:
Genomic DNA was isolated using QIAamp DNA Micro Kit (Qiagen).
For HG002 LCLs, iPSc and organoids, methyl-seq Next Generation Sequencing libraries were generated from 100ng of DNA, and the library construction was performed according to the manufacturer’s directions for the NEBNext Enzymatic Methyl-seq kit (New England Biolabs, #E7120L) with 5 cycles of library PCR amplification. Equal molar libraries were pooled, quantified, and sequenced on the AVITI (Element Biosciences) on a 2x150bp Cloudbreak Freestyle High Output flow cell (Cat. No. 860-00013), using AVITI OS 3.2.0 with the following read length: 8 bp Index1, 8 bp Index2, 151 bp Read1, and 151 bp Read2. Following sequencing, Bases2Fastq was run to demultiplex reads for all libraries and generate FASTQ files.

value: hydatidiform mole

value: extraembryonic tissues

value: genomic DNA

value: paired-end


title: CTRL07_ChorionicVillous

description: Library name: Z15060_CV


title: Intestinal Organoid Differentiated from IPS1

description: Library name: Minigut_iPS-1


title: RNA_8CEmbryo2_Cell7_024

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: mm10
Supplementary files format and content: txt


title: RNA_8CEmbryo2_Cell8_025


title: CTRL01_Decidua

description: Library name: Z15006_Decidua


title: RNA_RPE1_scRR1_MidS_003


title: CTRL08_ChorioamnioticMembranes

description: Library name: Z15198_MemInoc


title: CTRL01_ChorioamnioticMembranes

description: Library name: Z15006_MemInoc


title: RNA_RPE1_scRR1_MidS_015


title: Cerebral Organoid Differentiated from IPS2

description: Library name: Minibrain_iPS-2


title: Cerebral Organoid Differentiated from IPS1

description: Library name: Minibrain_iPS-1


title: RNA_8CEmbryo2_Cell6_023


title: RNA_RPE1_scRR1_MidS_016


title: CTRL01_ChorionicVillous

description: Library name: Z15006_CV


title: RNA_8CEmbryo2_Cell5_022


title: HG002 IPS1 Sendai Virus

description: Library name: GM27730_iPS-2


title: RNA_RPE1_scRR1_MidS_014


title: RNA_8CEmbryo1_Cell7_021


title: CTRL06_ChorionicVillous

description: Library name: R06147a_CV


title: HG002 IPS1 Episomal delivery

description: Library name: GM26105_iPS-1


title: RNA_RPE1_scRR1_MidS_013


title: RNA_8CEmbryo1_Cell6_020


title: HG002 LCL

description: Library name: GM24385_LCL


title: RNA_RPE1_scRR1_MidS_012


title: CTRL10_Decidua

description: Library name: R10195_decidua


title: RNA_8CEmbryo2_Cell3_017


title: CTRL10_ChorioamnioticMembranes

description: Library name: R10195_meminoc


title: RNA_RPE1_scRR1_MidS_010


title: Liver_WT_10mMMtz_3

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

institute: Shiv Nadar Institution of Eminence

description:
Library name: Mtz10_3
Mtz10_3

data_processing:
Reads were mapped to GRCz11 using HiSat2. Gene Counts were extracted using FeatureCounts.
Assembly: GRCz11
Supplementary files format and content: Counts in tab-separated format

molecule: polyA RNA

source_name: Liver

growth_protocol: Wild-type zebrafish larvae raised under standard conditions

extract_protocol:
Microdisected livers were lysed and RNA purified using Promega ReliaPrep™ RNA Miniprep Systems for Tissues
Performed by Novogene using poly A enrichment

treatment_protocol: Animals treated with Vehicle, 1 mM Metronidazole, 10 mM Metronidazole for 24 hours

value: Liver

value: Wild-type

value: 10 mM Metronidazole

tag: replicate

value: Replicate 3


title: RNA_RPE1_scRR1_MidS_011

city: Tsu-shi

first: Rawin

last: Poonperm

institute: Mie University


title: CTRL10_ChorionicVillous

description: Library name: R10195_CV


title: Liver_WT_10mMMtz_2

description:
Library name: Mtz10_2
Mtz10_2

value: Replicate 2


title: RNA_8CEmbryo2_Cell2_016

value: 8-cell embryo


title: CTRL05_ChorioamnioticMembranes

description: Library name: L10152_meminoc

value: MemInoc


title: RNA_RPE1_scRamDA_G0_001


title: RNA_8CEmbryo1_Cell4_014


title: Liver_WT_10mMMtz_1

description:
Library name: Mtz10_1
Mtz10_1

value: Replicate 1


title: Liver_WT_1mMMtz_3

description:
Library name: Mtz1_3
Mtz1_3

value: 1 mM Metronidazole


title: Liver_WT_1mMMtz_2

description:
Library name: Mtz1_2
Mtz1_2


title: RNA_8CEmbryo2_Cell1_015


title: RNA_RPE1_scRamDA_G0_002


title: Liver_WT_1mMMtz_1

description:
Library name: Mtz1_1
Mtz1_1


title: RNA_RPE1_scRamDA_MidS_009


title: CTRL05_ChrorionicVillous

description: Library name: L10152_CV

value: CV


title: RNA_RPE1_scRamDA_MidS_008


title: RNA_8CEmbryo1_Cell3_013


title: RNA_8CEmbryo1_Cell2_012


title: CTRL09_Decidua

description: Library name: J08186_decidua

value: Decidua


title: CTRL09_ChorioamnioticMembranes

description: Library name: J08186_meminoc


title: RNA_RPE1_scRamDA_MidS_007


title: CTRL09_ChorionicVillous

description: Library name: J08186_CV


title: RNA_8CEmbryo1_Cell1_011


title: Liver_WT_Control_3

description:
Library name: Vehicle_3
WT_3

value: Vehicle


title: Liver_WT_Control_2

description:
Library name: Vehicle_2
WT_2


title: RNA_RPE1_scRamDA_MidS_006


title: Chicken fibroblast DF1 cells, Non-targeting control RfxCas13d crRNA, biological replicate 3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

description: Library name: rfx_nt_grna_rep3

data_processing:
Skewer 0.2.2 (Jiang et al., 2014) was used to trim poor quality bases from the 3' end of reads, with a phred threshold of 20. Kallisto v0.48.0 (Bray et al., 2016) was then used to map reads to the chicken transcriptome (Ensembl v113).
Transcript read counts were then imported into R v4.4.2 and aggregated to gene level. Differential expression was conducted with DESeq2 v1.44.0 (Love et al., 2014) after removing genes with low counts (defined as <10 counts per sample on average across all samples in the comparison).
Assembly: Gallus_gallus.bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Gene count matrix in TSV format

organism: Gallus gallus

source_name: Cultured fibroblast

growth_protocol: The chicken fibroblast DF1 cells (American Type Culture Collection number: CRL–12203) were maintained in Dulbecco’s Modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FCS), 2mM L-glutamine, 10mM Hepes, 1.5% (w/v) sodium bicarbonate, 100 U/mL penicillin, and 100µg/mL of streptomycin. Cells were incubated at 37⁰C in 5% CO2.

extract_protocol:
Twenty-four hours post-transfection, RNA was extracted and purified from DF1 cells using RNeasy Plus Mini Kit (Qiagen) and the integrity of the RNA was measured using a 2100 Bioanalyser (Agilent).
The RNA was sent to the Australian Genome Research Facility, Melbourne, Australia (AGRF) for RNA sequencing with n=3 samples per group. Poly-A enrichment was carried out to eliminate ribosomal RNA.

treatment_protocol: To generate stable RfxCas13d and HfCas13d expressing cell lines, DF1 cells were seeded at a density of 1 × 106 cells/well in a 6-well plate 24 h prior to transfection. Cells were co-transfected with 2 µg of appropriate  Tol2-RfxCas13d or HfCas13d and 2 µg pTrans, complexed with 10 μL Lipofectamine 2000 (L2000) (Catalogue No. 11668019, Thermo Fisher Scientific, Waltham, MA, USA). To select for stable Cas13d expressing cells, transfected cells were maintained in media containing 1 μg/mL of puromycin (Catalogue No. A1113803, Thermo Fisher, Massachusetts, USA) for at least 14 days. DF1-Cas13d or DF1-HfCas13d cells were seeded at a density of 2 × 105 cells/well in a 24-well plate. Subsequently, 24 hours post seeding, cells were transfected in triplicates with 500 ng of crDsRed#2, or crNS, 100 ng of pCMV-DsRed and 100 ng pCAG-GFP.

value: Cultured fibroblast

value: RfxCas13d non targeting crRNA control


title: 50uMFOH_Biorep2

description:
Library name: Sample 27
Experiment 3

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3)
Read mapping was performed with STAR (v2.7.10) for experiment 1 and Kalisto for experiments 2 and 3.
Feature quantification was performed using RSEM (v1.3.3) for experiment 1 and Kallisto for experiments 2 and 3.
Read counts loaded into R and were normalized using edgeR’s (v1.14.5) Trimmed Mean of M values (TMM) algorithm.
Experiment 1: Subsequent values were then converted to counts per million (cpm). Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups. The file “AllQuantified Genes.tsv” contains the results of the qlfTest for all genes in addition to the normalized counts per million. Experiment 2/3: Differential expression was performed using DEseq2 against groups.
Assembly: ASM18296v3
Supplementary files format and content: Tab-separated values file contains raw counts for each sample
Supplementary files format and content: Tab-separated values file contains the results of the qlfTest for all genes in addition to the normalized counts per million

source_name: SC5314 derived

value: SC5314 derived

value: 50 µM E,E-farnesol added a time 0


title: 50uMFOH_Biorep4

description:
Library name: Sample 29
Experiment 3


title: Liver_WT_Control_1

description:
Library name: Vehicle_1
WT_1


title: Chicken fibroblast DF1 cells, DsRed targeting RfxCas13d crRNA, biological replicate 3

description: Library name: rfx_dsred_grna_rep3

value: RfxCas13d DsRed targeting crRNA


title: ileum, Diet containing 21 % crude protein diet, rep4

city: Chuzhou

first: xiaorong

last: he

address: No. 9 Donghua Road, Fengyang County

institute: Anhui Science and Technology University

description: Library name: MG3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: anser_cygnoides_domesticus/NCBI/GooseV1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Anser cygnoides

source_name: ileum

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: ileum

value: Diet containing 21 % crude protein diet


title: ileum, Diet containing 21 % crude protein diet, rep5

description: Library name: MG4


title: 50uMFOH_Biorep3

description:
Library name: Sample 28
Experiment 3

extract_protocol:
Total RNA was extracted using the hot-phenol method  and further cleaned up using the RNeasy mini kit (Qiagen). RNA quality was assessed by gel, spectrophotometric analysis (Spectramax Plus 384, Molecular Devices), and bioanalyzer analysis (Agilent). RNA samples sent for sequencing had a RIN > 8 and absorbance 260/280 of >2.0. RNA was quantified for sequencing by Quibit (Thermofischer Scientific). Samples were treated with DNase (RNAse free); Invitrogen.
Illumina’s Stranded mRNA prep with 10bp IDT for Illumina indices


title: RNA_RPE1_scRamDA_MidS_004

address: 1577 Kurimamachiya


title: ileum, Diet containing 21 % crude protein diet, rep1

description: Library name: MG1


title: Chicken fibroblast DF1 cells, Non-targeting control RfxCas13d crRNA, biological replicate 2

description: Library name: rfx_nt_grna_rep2


title: CTRL05_Decidua

description: Library name: L10152_decidua


title: RNA_RPE1_scRamDA_MidS_016


title: RNA_RPE1_scRamDA_MidS_002


title: RNA_RPE1_scRamDA_MidS_005


title: Chicken fibroblast DF1 cells, Non-targeting control RfxCas13d crRNA, biological replicate 1

description: Library name: rfx_nt_grna_rep1


title: ileum, Diet containing 21 % crude protein diet, rep3

description: Library name: MG2


title: RNA_RPE1_scRamDA_MidS_015


title: ileum, Basal diet containing 18 % crude protein diet, rep7

description: Library name: CG4


title: Chicken fibroblast DF1 cells, Non-targeting control HfCas13d crRNA, biological replicate 3

description: Library name: hf_nt_grna_rep3

value: HfCas13d non targeting crRNA control


title: Chicken fibroblast DF1 cells, DsRed targeting RfxCas13d crRNA, biological replicate 2

description: Library name: rfx_dsred_grna_rep2


title: pTDH3-CWH8_Biorep4

description:
Library name: Sample 25
Experiment 3


title: ileum, Basal diet containing 18 % crude protein diet, rep6

description: Library name: CG3


title: RNA_RPE1_scRamDA_MidS_013


title: Chicken fibroblast DF1 cells, Non-targeting control HfCas13d crRNA, biological replicate 2

description: Library name: hf_nt_grna_rep2


title: pTDH3-CWH8_Biorep3

description:
Library name: Sample 24
Experiment 3


title: pTDH3-CWH8_Biorep2

description:
Library name: Sample 23
Experiment 3


title: ileum, Basal diet containing 18 % crude protein diet, rep3

description: Library name: CG1


title: RNA_RPE1_scRamDA_MidS_012


title: Chicken fibroblast DF1 cells, DsRed targeting RfxCas13d crRNA, biological replicate 1

description: Library name: rfx_dsred_grna_rep1


title: 50uMFOH_Biorep1

description:
Library name: Sample 26
Experiment 3


title: ileum, Diet containing 21 % crude protein diet + 0.3 % lactulose, rep6

description: Library name: LS4


title: Chicken fibroblast DF1 cells, DsRed targeting HfCas13d crRNA, biological replicate 3

description: Library name: hf_dsred_grna_rep3

value: HfCas13d DsRed targeting crRNA


title: Chicken fibroblast DF1 cells, Non-targeting control HfCas13d crRNA, biological replicate 1

description: Library name: hf_nt_grna_rep1


title: RNA_RPE1_scRamDA_MidS_011


title: RNA_RPE1_scRamDA_MidS_010


title: RNA_RPE1_scRamDA_MidS_014


title: MAY1375_BioRep_2-3

description:
Library name: Sample 20
Experiment 3

value: WT


title: pTDH3-CWH8_Biorep1

description:
Library name: Sample 22
Experiment 3


title: Chicken fibroblast DF1 cells, DsRed targeting HfCas13d crRNA, biological replicate 1

description: Library name: hf_dsred_grna_rep1


title: ileum, Basal diet containing 18 % crude protein diet, rep4

description: Library name: CG2


title: ileum, Diet containing 21 % crude protein diet + 0.3 % lactulose, rep2

description: Library name: LS1


title: ileum, Diet containing 21 % crude protein diet + 0.3 % lactulose, rep5

description: Library name: LS3


title: MAY1375_BioRep_2-4

description:
Library name: Sample 21
Experiment 3


title: RNA_RPE1_scRamDA_MidS_001


title: Chicken fibroblast DF1 cells, DsRed targeting HfCas13d crRNA, biological replicate 2

description: Library name: hf_dsred_grna_rep2


title: MAY1375_BioRep_2-2

description:
Library name: Sample 19
Experiment 3


title: PRO-seq, THP1, OTS 4 hours, release with AZ5576 10 min

status: Public on Aug 25 2025

first: Jennifer

middle: Rose

last: Devlin

state: Victoria

address: Peter MacCallum Cancer Centre, 300 Grattan Street

department: The Sir Peter MacCallum Department of Oncology at Peter MacCallum Cancer Centre

institute: University of Melbourne

description: Library name: THP1-OTS-AZ

data_processing:
Adaptor sequences were removed using CutAdapt (v.1.9) and trimmed reads were aligned to the human hg19 genome or the combined hg19/dm6 genome using hisat2 (v.2.1.0) or bowtie2 (v.2.3.4.1)
Bam files were generared using samtools (v.1.9) and bigWig files were generated using Deeptools (v.3.0.0) bamCompare (normaliseUsing CPM or RPKM, smoothLength 150 or 30, extend 200, binSize 50 or 10). For TT-seq bigWig files were generated using scaleFactor based on D.melanogaster S2 spike-in.
Average profiles and metagene occupancy heatmaps were generated using Deeptools computeMatrix scale-regions and reference-point, and plotHeatmap functions
Assembly: hg19, dm6
Supplementary files format and content: bigWig
Library strategy: PRO-seq

source_name: Blood

growth_protocol: THP1 cells were maintained in RPMI-16410 supplemented with 10% FBS, 2mM GlutaMax, 100U/mL penicillin and 100ug/mL streptomycin at 37C and 5% CO2

extract_protocol:
For PRO-seq nuclei were isolated and subjected to in vitro transcription reaction (37C, 3min) with 0.05mM biotin-11-CTP. Nuclear RNA was isolated by phenol-chloroform extraction and ethanol precipitation. Nuclear RNA was hydrolysed using 1M NaOH and buffer exchange was performed using BioRad Micro Bio-Spin P30 columns. Biotin-11-CTP labelled RNA was enriched using Streptavidin-linked dynabeads and enriched RNA was isolated by phenol-chloroform extraction and ethanol precipitation.
Libraries were generated using the NEBNext Ultra II Directional RNA Library prep kit and NEBNext rRNA Depletion kit as per manufacturer's instructions

treatment_protocol: For PRO-seq exponentially growing cells were treated with DRB (100uM) for 4 hours and OTS964 (156nM), or with OTS964 (156nM) for 4 hours prior to washout and treatment with DMSO, OTS964 (156nM) or AZ5576 (170nM) for 10 minutes.

value: Blood

value: Acute myeloid leukemia


title: PRO-seq, THP1, OTS 4 hours, release with DMSO 10 min

description: Library name: THP1-OTS-DMSO


title: PRO-seq, THP1, OTS 4 hours, release with OTS964 10 min

description: Library name: THP1-OTS-OTS


title: PRO-seq, THP1, DRB 4 hours and OTS 1 hour, release with DMSO 10 min

description: Library name: THP1-DRB-OTS-DMSO


title: PRO-seq, THP1, DRB 4 hours and OTS 1 hour, release with OTS964 10 min

description: Library name: THP1-DRB-OTS-OTS


title: PRO-seq, THP1, DRB 4 hours and OTS 1 hour, release with AZ5576 10 min

description: Library name: THP1-DRB-OTS-AZ


title: PRO-seq, THP1, DRB 4 hours, release with AZ5576 170nM 10 min, exp2

extract_protocol:
For PRO-seq nuclei were isolated and subjected to in vitro transcription reaction (37C, 3min) with 0.05mM biotin-11-CTP. Nuclear RNA was isolated by phenol-chloroform extraction and ethanol precipitation. Nuclear RNA was hydrolysed using 1M NaOH and buffer exchange was performed using BioRad Micro Bio-Spin P30 columns. Biotin-11-CTP labelled RNA was enriched using Streptavidin-linked dynabeads and enriched RNA was isolated by phenol-chloroform extraction and ethanol precipitation.
For TT-seq total RNA was isolated by phenol-chloroform extraction and isopropanoal precipiation. Isolated human RNA was combined with a D.melanogaster S2 4SU-labelled RNA spike-in (5%) and the RNA mixture was fragmented by sonication using the Covaris S220 and AFA Fiber tubes at maximum power for 15 seconds. Fragmented 4sU-labelled RNA was biotinylated using EZ-link HPDP-Biotin and enriched using Miltenyi uMACS streptavidin beads and columns. Enriched RNA was purified using the Qiagen RNeasy MinElute kit as per manufacturer's instructions.
Libraries were generated using the NEBNext Ultra II Directional RNA Library prep kit and NEBNext rRNA Depletion kit as per manufacturer's instructions

treatment_protocol:
For PRO-seq exponentially growing cells were treated with DMSO, OTS964 (156nM) or AZ'5576 (170nM) for 2 hours; cells were treated with DRB (100uM) for 4 hours prior to washout and treatment with DMSO, OTS964 (156nM) or AZ5576 (170nM) for 10 minutes.
For TT-seq exponentially growing cells were treated with DMSO or OTS964 (156nM) for 30 minutes and pulse labelled with 1mM 4sU for the final 5 minutes.

value: Acute myeloid leukeamia


title: PRO-seq, THP1, DRB 4 hours, release with OTS964 156nM 10 min, exp2


title: PRO-seq, THP1, DRB 4 hours, release with AZ5576 170nM 10 min, exp1


title: PRO-seq, THP1, DRB 4 hours, release with DMSO 10 min, exp2


title: ileum, Diet containing 21 % crude protein diet + 0.3 % lactulose, rep3

description: Library name: LS2


title: PRO-seq, THP1, DRB 4 hours, release with DMSO 10 min, exp1


title: PRO-seq, THP1, DRB 4 hours, release with OTS964 156nM 10 min, exp1


title: PRO-seq, THP1, DRB 4 hours, no release, exp1


title: PRO-seq, THP1, DRB 4 hours, no release, exp2