title: SM3-07-KANG-3

city: Hangzhou

first: yuanlin

last: qi

address: No. 666, Wusu Street, Lin'an District

department: Donghu Campus

institute: Zhejiang A&F University

description:
Library name: SM3-07-KANG-3
The resistant group was treated with Streptomyces sclerogranulatus

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NAM 5.0  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NAM 5.0
Supplementary files format and content: tab-delimited text files include gene count for each Sample

organism: Zea mays

source_name: whole body

extract_protocol:
RNA was extracted from plant whole body using TRIzol reagent. Briefly, plant whole body samples were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: whole body


title: 4X-H2Av-NC14-1

status: Public on Jul 14 2026

type: SRA

city: Denton

first: Fanju

last: Meng

state: TX

address: 1155 Union Circle #305220

department: Biological Sciences

country: USA

institute: University of North Texas

description: Library name: 4X-H2Av-NC14-1

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed for adaptors using TrimGalore (version 0.6.10), and then mapped to the D. melanogaster reference genome (dm6) or zebrafish genome (GRCz11) using STAR (version 2.7.11b)
The transcript-level abundance was quantified with Salmon and then aggregated using tximport to obtain gene-level quantification.
Subsequent differential expression analysis was done using DESeq2
Statistical tests and plots for data visualization were generated in R and GraphPad
Assembly: dm6 and GRCz11
Supplementary files format and content: txt files with TPM count table and DEseq2 results

molecule: total RNA

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol: Drosophila embryos of roughly the correct stage were observed by confocal imaging until they reached the desired timepoint and then flash frozen.

extract_protocol:
Embryos were then macerated in TRIzol with a needle to extract RNA and purified using Direct-Zol™ RNA MiniPrep Kit (Zymo Research) according to manufacturer’s protocol.
RNA libraries for batch 1, 2 and 5 were prepared with Illumina total RNA with rRNA depletion, and RNA libraries for batch 3 and 4 were prepared with SMART-Seq Total RNA Pico Input with UMIs according to user manual.

tag: tissue

value: whole embryo

tag: developmental stage

tag: genotype

tag: batch


title: SM3-07-KANG-2

country: China

description:
Library name: SM3-07-KANG-2
The resistant group was treated with Streptomyces sclerogranulatus

tag: treatment


title: 1X_NC13_3

description: Library name: 1X_NC13_3


title: 4X-H2Av-NC13-2

description: Library name: 4X-H2Av-NC13-2


title: CD8_plus_Tcells_E2ko_3

city: Würzburg

first: Stefan

last: Klein-Hessling

address: Josef-Schneider-Str. 2

department: Institute of Pathology

country: Germany

institute: University of Würzburg

data_processing:
Base calling with Illumina NextSeq RTA v3.9.25
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to mouse genome (GRCm39) using STAR (Dobin et al., 2013) v2.7.2b with default parameters based on RefSeq annotation version 109
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 109 for GRCm39) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
Assembly: GRCm39
Supplementary files format and content: Character (TAB) separated value file containing raw mRNA abundance measurements

organism: Mus musculus

source_name: CD8+ T cells

growth_protocol: Purified splenic CD8+T cells from 8-16 weeks old mice were activated for 2 d on antiCD3 (3µg/ml) antibody coated plastic dishes in the presence of antiCD28 (1µg/ml) and hIL-2 (50U/ml). Afterwards the cells were persistently stimulated by plate bound aCD3 (3µg/ml) Abs in medium containing IL-7 (50ng/ml) and IL-15 (15ng/ml) for additional 4 days.

extract_protocol:
RNA preparation was carried out using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was > 8.3. cDNA libraries were prepared from total RNA with TruSeq mRNA Stranded Library Prep Kit from Illumina according to manufacturer’s instructions (1/2 volume). Libraries were quantified by QubitTM Flex Fluorometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with DNA 1000 Kit (Agilent). The average size of the pool were approximately 300 bp. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at 25 million reads/sample in single-end mode with 100 nt read length on the NextSeq 2000 platform (Illumina).

tag: cell type

value: CD8+ T cells

tag: Sex

value: male


title: CD8_plus_Tcells_E2ko_2


title: SM3-07-KANG-1

description:
Library name: SM3-07-KANG-1
The resistant group was treated with Streptomyces sclerogranulatus


title: H-4,20 months

city: Beijing

first: di

last: deng

address: No. 11, Beisanhuan East Road, Chaoyang District, Beijing

institute: Beijing University of Chinese Medicine

description:
Library name: Sample12
R-NH-15

data_processing:
Raw reads of fastq format were firstly processed using fastpi and the low quality reads were removed to obtain the clean reads.
Assembly: mm39
Supplementary files format and content: FPKMi of each gene was calculated and the read counts of each gene were obtained

source_name: hippocampus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

value: hippocampus

value: WT

value: H


title: 1X_NC11_combine

description: Library name: 1X_NC11_combine


title: CD8_plus_Tcells_E2ko_1


title: SM3-07-GAN-3

description:
Library name: SM3-07-GAN-3
The susceptible group was treated with Streptomyces sclerogranulatus


title: CD8_plus_Tcells_WT_5

value: wildtype


title: 2X-H2Av-NC14-3

description: Library name: 2X-H2Av-NC14-3


title: 1X_NC11_3

description: Library name: 1X_NC11_3


title: 2X-H2Av-NC14-2

description: Library name: 2X-H2Av-NC14-2


title: SM3-07-GAN-2

description:
Library name: SM3-07-GAN-2
The susceptible group was treated with Streptomyces sclerogranulatus


title: CD8_plus_Tcells_WT_4


title: 1X_Egg_combine

description: Library name: 1X_Egg_combine

value: Egg


title: 1X_NC13_combine

description: Library name: 1X_NC13_combine


title: 1X_Egg_2_121024

description: Library name: 1X_Egg_2_121024


title: SM3-07-GAN-1

description:
Library name: SM3-07-GAN-1
The susceptible group was treated with Streptomyces sclerogranulatus


title: CD8_plus_Tcells_WT_3


title: FJSM-07-KANG-3

description: Library name: FJSM-07-KANG-3

value: The resistant group was treated with Streptomyces murinus.


title: 2X-H2Av-NC13-3

description: Library name: 2X-H2Av-NC13-3


title: 1XDL_NC14_combine

description: Library name: 1XDL_NC14_combine

value: Jabba heterozygous mutant


title: CD8_plus_Tcells_WT_2


title: 2X-H2Av-NC13-2

description: Library name: 2X-H2Av-NC13-2


title: FJSM-07-KANG-2

description: Library name: FJSM-07-KANG-2


title: CD8_plus_Tcells_WT_1


title: Egg_4X_3

description: Library name: Egg_4X_3


title: FJSM-07-GAN-3

description: Library name: FJSM-07-GAN-3

value: The susceptible group was treated with Streptomyces murinus


title: 4C Klf14 distal CB-KO/KO MAT

city: Vancouver

first: Louis

last: Lefebvre

state: BC

address: 5.503-2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
4C-seq library construction and mapping were generated using c4ctus (https://github.com/NoordermeerLab/c4ctus)
4C-seq scores from the distal viewpoint were generated using a running mean over 21 restriction fragments.
Assembly: mm39
Supplementary files format and content: 4C-seq scores were converted to bigWig format using bedtools (Quinlan et al., 2010) and bedGraphToBigWig (UCSC).

molecule: genomic DNA

source_name: ESC

growth_protocol: Hybrid ESC lines BC (C57BL/6J x CAST) and CB (CAST x C57BL/6J) were derived from blastocysts in M2 media, and cultured in serum-free 2i conditions as described (Hayashi & Saitou 2013; Ying et al. 2008). ESCs were transitioned and maintained in serum+LIF conditions.

extract_protocol:
Allele-specific in-nucleus 4C-seq was performed as in (Llères et al. 2019) and described in detail in (Miranda et al, 2022; in press).
Libraries were constructed as described (Miranda et al, 2022; in press) containing Illumina Truseq adapter sequences, and sequenced on a single-end Illumina Nextseq2000 100 cycles P2 run.
4C-seq

tag: strain

value: CAST x C57BL/6

value: ESC

value: Mest gDMR pKO

tag: viewpoint

value: Klf14 distal


title: 4C Klf14 distal CB-mKO MAT

value: Mest gDMR mKO


title: 1XDL_NC11_combine

description: Library name: 1XDL_NC11_combine


title: 4C Klf14 distal CB-WT MAT

value: Mest gDMR WT


title: FJSM-07-GAN-1

description: Library name: FJSM-07-GAN-1

value: whole body


title: Egg_4X_1

description: Library name: Egg_4X_1

value: whole embryo


title: 4C Klf14 distal BC-KO/KO PAT

value: C57BL/6 x CAST

value: Mest gDMR KO/KO


title: Nphp3mut1/mut2 mouse 3

city: Brussels

first: Patrick

last: Jacquemin

address: 75, Avenue Hippocrate bte B1.75.03

country: Belgium

institute: de Duve Institute SSS/DDUV

description: Library name: S562

data_processing:
fastq files were processed using Trimmomatic (v0.38) to remove low quality reads, HISAT2 (v2.2.1)  to align reads to the mouse genome (GRCm38), and featureCounts from Subread (v2.0.0)  to obtain gene counts.
Assembly: GRCm38
Supplementary files format and content: Tab-delimated text file including raw counts for each sample

source_name: adipocytes

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, AM1912) according to the manufacturer’s instructions.
Sequencing libraries were prepared from rRNA-depleted RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: adipocytes


title: Egg_2X_3

description: Library name: Egg_2X_3


title: 1XDL_Egg_combine

description: Library name: 1XDL_Egg_combine


title: Egg_2X_2

description: Library name: Egg_2X_2


title: 4C Klf14 distal BC-WT PAT


title: 1XDL_Egg_3

description: Library name: 1XDL_Egg_3


title: HDCA3

status: Public on Jul 13 2026

city: Chiba

first: Eunyoung

last: Lee

address: 1-8-1 Inohana, Chuo-ku

department: Department of Medical Physiology

country: Japan

institute: Chiba University, Graduate School of Medicine

description: Library name: sample9

data_processing:
Sequencing was performed on the Illumina HiSeq 1500 platform using the TruSeq Rapid SBS Kit (Illumina, FC-402-4002) in the 50-base single-end mode.
The TopHat program (version 1.3.2 with default parameters) was used to align reads to a mouse reference genome (mm10).
Then, gene expression values were calculated as reads per kilobase of exon unit per million mapped reads using the Cufflinks program (version 2.0.2).
Assembly: mm10
Supplementary files format and content: Plain text file includes raw counts for each sample.
Supplementary files format and content: Plain text file includes FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from the liver using RNeasy lipid Kit (Qiagen).
Libraries were prepared using a TruSeq RNA Sample Prep Kit (Illumina, 20020594)

treatment_protocol: Mice were treated with different diets (ND, 60% HFD, or 60% HFD+0.25% HDCA) for 12 weeks from 8 weeks. Liver was dissected under fed condition.

value: Liver

value: WT

value: 60% high fat det plus 0.25% HDCA


title: HDCA2

description: Library name: sample8


title: HDCA1

description: Library name: sample7


title: HFD3

description: Library name: sample6

value: 60% high fat diet


title: HFD1

description: Library name: sample4


title: ND3

description: Library name: sample3

value: normal diet


title: ND1

description: Library name: sample1


title: ND2

description: Library name: sample2


title: CBMS1 mESC, BrdU-IP-seq, aphidicolin G2M, rep2

city: Kobe

first: Jothivanan

last: Elumalai

state: Hyogo

address: 2-2-3, Minatojima Minamimachi, Chuo-ku

department: Biosystems Dynamics Research (BDR)

institute: RIKEN

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For BrdU-IP Repli-seq: After removing duplicate reads and filtering blacklist regions, we counted the reads and calculated reads per million for each 100-kb non-overlapping window in early- and late-S fractions. Then, RT is determined by calculating log2(early/late) for each 100-kb window. All the BrdU-IP RT profiles were quantile normalized before downstream analysis.
For BrdU-IP G2M-seq: After removing duplicate reads and filtering blacklist regions, we counted the reads and calculated reads per million for each 100-kb non-overlapping window in untreated and aphidicolin-treated conditions. Then, aphidicolin-induced G2/M replication is determined by calculating log2(aphidicolin/untreated) for each 100-kb window.
Assembly: hg19, mm9
Supplementary files format and content: log2(early/late) RT (.bedGraph)
Supplementary files format and content: log2(aphidicolin/untreated) G2M replication (.bedGraph)
Library strategy: BrdU-IP-seq

source_name: Embryo

growth_protocol: Human osteosarcoma cells (U2OS) were cultured in DMEM (Nacalai, 08459-64) supplemented with 10% FBS (Sigma, 172012) and maintained at 37°C with 5% CO2. CBMS1 mouse embryonic stem cells (mESCs) have been described (Murakami et al, Development, 2011) and grown in 2i/LIF medium as described (Hayashi et al, Nat. Protoc. 2013).

extract_protocol:
75% ethanol fixed cells were stained with Propidium iodide (Nacalai tesque, 29037), then early- and late-S phase cell population (at least 10,000 cells/fraction) were sorted by a Sony SH800 or MA900 cell sorter. Extracted DNA was sonicated by a Bioruptor UCD-250 (Sonic Bio). BrdU-incorporated DNA was immunoprecipitated using anti-BrdU antibody (BD Biosciences Pharmingen, #555627).
BrdU-immunoprecipitated DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed from early- and late-replicating DNA after WGA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

treatment_protocol: Cells were subjected to treatment with or without 0.4 μM aphidicolin for 24 hours and labelled with 50 μM BrdU for 30 minutes before harvesting.

value: Embryo

tag: cell line

value: CBMS1 mESC

value: Embryonic Stem Cells

value: Aphidicolin


title: CBMS1 mESC, BrdU-IP-seq, untreated G2M, rep2

value: Untreated


title: CBMS1 mESC, BrdU-IP-seq, aphidicolin G2M, rep1


title: CBMS1 mESC, BrdU-IP-seq, untreated G2M, rep1


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 045

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For single-G1 karyotype analysis: After marking the duplicate reads, copy number analysis was conducted using the AneuFinder package v1.22.0 within R v4.1.3. Initially, duplicate reads, blacklist regions (available at https://github.com/Boyle-Lab/Blacklist) and reads with a mapping quality (MAPQ) below 10 were filtered out. Uniquely mapped reads were counted within each 500-Kb genomic window, adjusted for GC content (GC.BSgenome=BSgenome.Hsapiens.UCSC.hg19 for humans and BSgenome.Mmusculus.UCSC.mm9 for mouse, method="loess"), and copy number segmentation was executed using the "findCNVs" function (method='edivisive', R=50) of the AneuFinder package. For quality control (QC), multivariate clustering was applied, and clusters with a spikiness value exceeding 1 were eliminated.
For Log2percentile RT: We followed our established procedure to generate binarized replication timing (RT) profiles for each of the 14 fractions of S-phase or single-cells under analysis, along with their respective percentage replication scores (Miura et al, Nat. Protoc. 2020). The percentage replication score of each S-phase fraction or single-cells was utilized to compute their raw, non-binarized replication timing profile, termed as "log2repliscore RT".
Assembly: hg19, mm9
Supplementary files format and content: CNV states (.txt)
Supplementary files format and content: log2percentile RT (.txt)
Library strategy: scRepli-seq

extract_protocol:
Single cells were sorted with a Sony SH800 or MA900 cell sorter. Sample preparations were performed as described (Miura et al, Nat. Protoc. 2020). DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE).
NGS libraries were constructed for amplied DNA using an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions.

treatment_protocol: Cells were subjected to treatment with or without 0.4 μM aphidicolin for 24 hours and labelled with 10 μM EdU for 60 and 15 minutes before harvesting, respectively.


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 044


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 041


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 040


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 039


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 038


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 035


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 036


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 032


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 033


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 030


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 029


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 028


title: 2X-H2Av-NC14-1

description: Library name: 2X-H2Av-NC14-1


title: 1XDL_NC14_3

description: Library name: 1XDL_NC14_3

value: Jabba heterozygous mutant


title: 2X-H2Av-NC13-1

description: Library name: 2X-H2Av-NC13-1


title: FJSM-07-GAN-2

description: Library name: FJSM-07-GAN-2

value: The susceptible group was treated with Streptomyces murinus


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 026


title: 1XDL_NC11_1

description: Library name: 1XDL_NC11_1


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 025


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 027


title: 4C Klf14 distal BC-pKO PAT

value: ESC

value: Mest gDMR pKO

value: Klf14 distal


title: Nphp3mut1/mut2 mouse 2

description: Library name: S561


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 023


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 022


title: Nphp3mut1/mut2 mouse 1

description: Library name: S560


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 021


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 020


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 031


title: HFD2

description: Library name: sample5


title: 1XDL_NC13_combine

description: Library name: 1XDL_NC13_combine

value: whole embryo


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 016


title: Egg_4X_2

description: Library name: Egg_4X_2

value: Egg


title: 1XDL_NC13_3

description: Library name: 1XDL_NC13_3


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 018


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 015


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 014


title: FJSM-07-KANG-1

description: Library name: FJSM-07-KANG-1

value: whole body

value: The resistant group was treated with Streptomyces murinus.


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 019


title: Egg_2X_1

description: Library name: Egg_2X_1


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 024


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 012


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 013


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 011


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 010


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 008


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 009


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 006


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 004


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 007


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 017


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 005


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 003


title: CBMS1 mESC, scRepli-seq, untreated singleS 046


title: CBMS1 mESC, scRepli-seq, untreated singleS 047


title: CBMS1 mESC, scRepli-seq, untreated singleS 044


title: CBMS1 mESC, scRepli-seq, untreated singleS 040


title: CBMS1 mESC, scRepli-seq, untreated singleS 041


title: CBMS1 mESC, scRepli-seq, untreated singleS 037


title: CBMS1 mESC, scRepli-seq, untreated singleS 042


title: CBMS1 mESC, scRepli-seq, untreated singleS 038


title: CBMS1 mESC, scRepli-seq, untreated singleS 034


title: CBMS1 mESC, scRepli-seq, untreated singleS 036


title: CBMS1 mESC, scRepli-seq, untreated singleS 035


title: CBMS1 mESC, scRepli-seq, untreated singleS 032


title: CBMS1 mESC, scRepli-seq, untreated singleS 031


title: CBMS1 mESC, scRepli-seq, untreated singleS 030


title: CBMS1 mESC, scRepli-seq, untreated singleS 028


title: CBMS1 mESC, scRepli-seq, untreated singleS 029


title: CBMS1 mESC, scRepli-seq, untreated singleS 027


title: CBMS1 mESC, scRepli-seq, untreated singleS 026


title: CBMS1 mESC, scRepli-seq, untreated singleS 025


title: CBMS1 mESC, scRepli-seq, untreated singleS 021


title: CBMS1 mESC, scRepli-seq, untreated singleS 019


title: CBMS1 mESC, scRepli-seq, untreated singleS 018


title: CBMS1 mESC, scRepli-seq, untreated singleS 017


title: CBMS1 mESC, scRepli-seq, untreated singleS 016


title: CBMS1 mESC, scRepli-seq, untreated singleS 015


title: CBMS1 mESC, scRepli-seq, untreated singleS 023


title: CBMS1 mESC, scRepli-seq, untreated singleS 014


title: CBMS1 mESC, scRepli-seq, untreated singleS 013


title: CBMS1 mESC, scRepli-seq, untreated singleS 011


title: CBMS1 mESC, scRepli-seq, untreated singleS 009


title: CBMS1 mESC, scRepli-seq, untreated singleS 010


title: CBMS1 mESC, scRepli-seq, untreated singleS 008


title: CBMS1 mESC, scRepli-seq, untreated singleS 007


title: CBMS1 mESC, scRepli-seq, untreated singleS 006


title: CBMS1 mESC, scRepli-seq, untreated singleS 005


title: CBMS1 mESC, scRepli-seq, untreated singleS 003


title: CBMS1 mESC, scRepli-seq, untreated singleS 033


title: CBMS1 mESC, scRepli-seq, untreated singleS 002


title: CBMS1 mESC, scRepli-seq, untreated singleS 001


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 048


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 046


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 042


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 041


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 040


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 039


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 038


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 036


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 047


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 035


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 045


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 044


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 043


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 034


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 033


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 032


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 031


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 030


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 029


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 028


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 027


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 026


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 025


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 024


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 037


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 023


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 022


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 021


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 020


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 019


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 001


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 018


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 017


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 002


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 016


title: CBMS1 mESC, scRepli-seq, untreated singleS 045


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 015


title: CBMS1 mESC, scRepli-seq, untreated singleS 043


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 014


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 013


title: CBMS1 mESC, scRepli-seq, untreated singleS 039


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 012


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 010


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 011


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 009


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 008


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 007


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 006


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 005


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 004


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 002


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 003


title: CBMS1 mESC, scRepli-seq, aphidicolin singleG1 001


title: CBMS1 mESC, scRepli-seq, untreated singleG1 047


title: CBMS1 mESC, scRepli-seq, untreated singleG1 048


title: CBMS1 mESC, scRepli-seq, untreated singleS 022


title: CBMS1 mESC, scRepli-seq, untreated singleS 024


title: CBMS1 mESC, scRepli-seq, untreated singleG1 045


title: CBMS1 mESC, scRepli-seq, untreated singleG1 046


title: CBMS1 mESC, scRepli-seq, untreated singleG1 044


title: CBMS1 mESC, scRepli-seq, untreated singleG1 043


title: CBMS1 mESC, scRepli-seq, untreated singleS 020


title: CBMS1 mESC, scRepli-seq, untreated singleG1 042


title: CBMS1 mESC, scRepli-seq, untreated singleG1 041


title: CBMS1 mESC, scRepli-seq, untreated singleG1 040


title: CBMS1 mESC, scRepli-seq, untreated singleG1 039


title: CBMS1 mESC, scRepli-seq, untreated singleG1 037


title: CBMS1 mESC, scRepli-seq, untreated singleG1 036


title: CBMS1 mESC, scRepli-seq, untreated singleG1 035


title: CBMS1 mESC, scRepli-seq, untreated singleG1 038


title: CBMS1 mESC, scRepli-seq, untreated singleG1 034


title: CBMS1 mESC, scRepli-seq, untreated singleG1 032


title: CBMS1 mESC, scRepli-seq, untreated singleG1 031


title: CBMS1 mESC, scRepli-seq, untreated singleG1 029


title: CBMS1 mESC, scRepli-seq, untreated singleG1 028


title: CBMS1 mESC, scRepli-seq, untreated singleG1 027


title: CBMS1 mESC, scRepli-seq, untreated singleG1 026


title: CBMS1 mESC, scRepli-seq, untreated singleG1 025


title: CBMS1 mESC, scRepli-seq, untreated singleG1 023


title: CBMS1 mESC, scRepli-seq, untreated singleG1 020


title: CBMS1 mESC, scRepli-seq, untreated singleG1 019


title: CBMS1 mESC, scRepli-seq, untreated singleG1 018


title: CBMS1 mESC, scRepli-seq, untreated singleG1 017


title: CBMS1 mESC, scRepli-seq, untreated singleG1 016


title: CBMS1 mESC, scRepli-seq, untreated singleG1 015


title: CBMS1 mESC, scRepli-seq, untreated singleG1 014


title: CBMS1 mESC, scRepli-seq, untreated singleG1 013


title: CBMS1 mESC, scRepli-seq, untreated singleG1 012


title: CBMS1 mESC, scRepli-seq, untreated singleG1 009


title: CBMS1 mESC, scRepli-seq, untreated singleG1 011


title: CBMS1 mESC, scRepli-seq, untreated singleG1 008


title: CBMS1 mESC, scRepli-seq, untreated singleG1 007


title: CBMS1 mESC, scRepli-seq, untreated singleG1 006


title: CBMS1 mESC, scRepli-seq, untreated singleG1 005


title: CBMS1 mESC, scRepli-seq, untreated singleG1 004


title: CBMS1 mESC, scRepli-seq, untreated singleG1 003


title: CBMS1 mESC, scRepli-seq, untreated singleG1 002


title: CBMS1 mESC, scRepli-seq, untreated singleG1 001


title: [RNA-Seq] EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (3)

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-ku

institute: Kumamoto University

data_processing:
We conducted deep sequencing using NovaSeq X Plus (Illumina Inc., San Diego, CA). Trimming, alignment (to mouse genome mm10), and Read counts were performed by Trimmomatic, Hisat2, and featureCounts, respectively. Moreover, TPM was cultulate from the data of read number by R-base.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TPM, RPKM, and Read number for each Sample.

source_name: bone marrow

extract_protocol:
HSCs were directly sorted into lysis buffer for the library construction
After 100 cells were sorted, first strand cDNA were synthesized followed by generating 2nd strand by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) . Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .

value: bone marrow

value: Hemtopoietic stem cells


title: [RNA-Seq] EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (1)


title: [RNA-Seq] EPCRHigh HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (3)


title: [RNA-Seq] EPCRHigh HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (4)


title: [RNA-Seq] EPCRHigh HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (2)


title: [RNA-Seq] EPCRHigh HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (1)


title: [RNA-Seq] EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (4)


title: CBMS1 mESC, scRepli-seq, untreated singleG1 033


title: [RNA-Seq] EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (1)


title: [RNA-Seq] EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (2)


title: [RNA-Seq] EPCRHigh HSCs cultured under control conditions for 1 day (4)


title: [RNA-Seq] EPCRHigh HSCs cultured under control conditions for 1 day (3)


title: [RNA-Seq] EPCRHigh HSCs cultured under control conditions for 1 day (1)


title: EHEC hnrS triple deletion pZE12::hnrS replicate 3

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: Library name: EHEC_comp_3

data_processing:
FASTQ files were processed with READemption v2.0.4 (Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma, Bioinformatics, Volume 30, Issue 23, December 2014, Pages 3421–3423, https://doi.org/10.1093/bioinformatics/btu533)
Assembly: NC_002695.2
Supplementary files format and content: Output tables from READemption displaying log2FC for genoem features and FDR. Three files have been provided pairwise contrasts between WT, ∆hnrS, and ∆hnrS pZE12::hnrS

organism: Escherichia coli O157:H7 str. Sakai

source_name: whole cells

growth_protocol: E. coli str. Sakai and isogenic strains grown in MEM-HEPES (Sigma M7278) supplemented with 0.1% glucose and 250 nM Fe(NO3)3 at 37°C with shaking until OD600 0.8

extract_protocol:
Total RNA was extracted from E. coli O157:H7 str. Sakai using a guanidinium thiocyanate–phenol method (Tollervey D, Mattaj IW. 1987. Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U-snRNPs. Embo j 6:469-76.)
Total RNA-seq library contruction was performed at Novogene (Singapore). From the supplier: "ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification."

treatment_protocol: No treatment

value: whole cells

value: hnrS1-2 pZE12::hnrS

value: mid-exponential phase (OD0.8) in supplemented MEM-HEPES media


title: EHEC hnrS triple deletion pZE12::hnrS replicate 2

description: Library name: EHEC_comp_2


title: [RNA-Seq] EPCRLow HSCs cultured under control conditions for 1 day (4)


title: EHEC hnrS triple deletion pZE12::hnrS replicate 1

description: Library name: EHEC_comp_1


title: CBMS1 mESC, scRepli-seq, untreated singleG1 022

value: Embryo

value: CBMS1 mESC

value: Embryonic Stem Cells


title: [RNA-Seq] EPCRLow HSCs cultured under control conditions for 1 day (1)


title: EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (4)

data_processing:
After deep sequencing using Hi-seq 2000 system (Illumina Inc.) with 150 bps paired-end reads, trimming, alignment (to mouse genome mm10), peak calling, and quantification were performed using Trimmomatic, Bowtie2, MACS2, and HOMER, respectively.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
HSCs were directly sorted into lysis buffer for the library construction
Omni-ATAC-seq was performed as previously described with minor modifications (Corces et al., 2017; Umemoto et al., 2022).


title: EHEC wild type replicate 3

description: Library name: EHEC_WT_3

value: WT


title: EHEC hnrS triple deletion replicate 3

description: Library name: EHEC_hnrS_3


title: EHEC hnrS triple deletion replicate 1

description: Library name: EHEC_hnrS_1


title: EHEC hnrS triple deletion replicate 2

description: Library name: EHEC_hnrS_2


title: [RNA-Seq] EPCRLow HSCs cultured under control conditions for 1 day (2)


title: [RNA-Seq] EPCRLow HSCs cultured under control conditions for 1 day (3)


title: EHEC wild type replicate 1

description: Library name: EHEC_WT_1


title: EHEC wild type replicate 2

description: Library name: EHEC_WT_2


title: EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (2)


title: EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (1)


title: EPCRHigh HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (3)


title: EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (4)


title: EPCRHigh HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (1)


title: EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (3)


title: EPCRHigh HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (2)


title: EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (2)


title: EPCRHigh HSCs cultured under control conditions for 1 day (3)


title: EPCRHigh HSCs cultured under control conditions for 1 day (2)


title: EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (1)


title: EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (3)


title: EPCRLow HSCs cultured under control conditions for 1 day (3)


title: CBMS1 mESC, scRepli-seq, untreated singleG1 030

value: Untreated


title: EPCRHigh HSCs cultured under control conditions for 1 day (1)


title: CBMS1 mESC, scRepli-seq, untreated singleG1 024


title: EPCRLow HSCs cultured under control conditions for 1 day (1)


title: EPCRLow HSCs cultured under control conditions for 1 day (2)


title: CBMS1 mESC, scRepli-seq, untreated singleG1 021


title: M07e_KO_Replicate_3

city: Little Rock

first: Samrat

last: Roy Choudhury

state: AR

address: 13 Children's Way, Arkansas Children's Research Institute

institute: University of Arkansas for Medical Sciences

description: Library name: Sample_6

data_processing:
Quality control (QC) of raw sequencing data from the Illumina HiSeq platform was performed using FastQC. Low-quality reads were filtered with Trimmomatic, removing adapters, reads with >5% ambiguous bases (N), and >50% low-quality bases (Q < 20). Clean reads were re-evaluated using FastQC before alignment to the hg38 reference genome using Bismark and HISAT2. Bisulfite sequencing data were processed with C-to-T conversions to account for methylation states, retaining the best strand alignment. MspI digestion efficiency was assessed to ensure RRBS enrichment of CpG-rich regions. Methylation site detection was performed with Bismark, calculating methylation levels as ML = mC / (mC + umC), where mC represents methylated cytosines. A whole-genome methylation map was generated, and average methylation levels were computed for CG contexts. Sample comparisons included Pearson correlation analysis (20 Kb/bin), UPGMA-based hierarchical clustering, and Principal Component Analysis (PCA) to assess methylation profile similarities. Differentially Methylated Regions (DMRs) were identified using methylKit with a 500 bp sliding window and a 10% methylation difference cutoff (q-value < 0.01). DMRs were annotated using gene transcripts and CpG island data to map associated genomic regions (e.g., promoters, exons, introns).
Assembly: hg38
Supplementary files format and content: Raw methylation count in tab tab delimited format

organism: Homo sapiens

growth_protocol: M07e cells were grown in RPMI-1640, supplemented with 20% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin and 10 ng/mL GM-CSF.

extract_protocol:
Genomic DNA was extracted from AML cell lines and primary cells using the AllPrep DNA/RNA Kits, Qiagen, following the manufacturer’s instructions. DNA purity and concentration were assessed using a Qubit fluorometer. The integrity of the extracted DNA was evaluated using a bioanalyzer.
Genomic DNA (500 ng) was digested using the MspI restriction enzyme, which targets CpG-rich regions. The fragmented DNA was then end-repaired, A-tailed, and ligated to methylated adapters using the Zymo-Seq RRBS Library Kit. Bisulfite conversion was performed using the Zymo EZ DNA Methylation Kit according to the manufacturer’s protocol. Converted DNA was PCR-amplified, size-selected, and purified before sequencing.

value: Acute Megakaryoblastic Leukemia Cells

value: DNMT3B knockout


title: M07e_KO_Replicate_2

description: Library name: Sample_5


title: M07e_KO_Replicate_1

description: Library name: Sample_4


title: M07e_C_Replicate_3

description: Library name: Sample_3


title: M07e_C_Replicate_2

description: Library name: Sample_2


title: M07e_C_Replicate_1

description: Library name: Sample_1


title: LPS day 9; Fabp5 KO mouse

city: Denver

first: Fabienne

middle: Sabrina

last: Gally

state: Colorado

address: 1400 Jackson Street, K827

institute: National Jewish Health

description: Library name: LPS_day9_KO

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files compressed with gzip
Supplementary files format and content: Integrated Seurat object

molecule: polyA RNA

source_name: Lung

extract_protocol:
Lung cells were digested using Liberase TM (0.25 mg/ml) and Dnase (125 ug/ml). CD45+ cells were enriched using magnetic beads per manufacturer’s instructions (StemCell Technologies).
Libraries were performed according to manufacturer's instructions (single cell 3' protocol, 10X genomics)

value: Lung

value: Fabp5 KO

value: LPS


title: Parse WT kit 5 samples

city: Cleveland

first: Tyler

middle: J

last: Alban

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description:
Library name: All_samples
Parse Biosciences

data_processing:
ParseBio WT v2  was utilized along the alignment via Split-Pipe Pipeline v1.0.3p using mm10 genome.
After QC Seurat was used with Harmony to batch correct data for unsupervised clustering
Assembly: mm10
Supplementary files format and content: Parse splitpipe outputs: all_genes.csv, cell_metadata.csv, count_matrix.mtx used to created count matrix

source_name: NPC

extract_protocol:
Parse Biosciences single cell RNAseq capture kit
To induce differentiation, NPC cells were plated on dishes coated with 10 μg/ ml laminin (Sigma-Aldrich) and cultured in NeuroCult Basal Medium containing NeuroCult Differentiation Supplement (Stemcell Technologies). After 21 days of induction at 5% CO2 and 37 °C, cells were harvested and performed the single cell RNASeq experiments.

value: NPC

value: pooled samples (Wildtype  and Parkin KO)


title: DDC mouse liver replicate 3

city: Harbin

first: Wenjing

last: Sun

address: Baojian road

institute: Harbin Medical University

description:
Library name: DDC3
Liver tissue from a C57BL/6J mouse fed a 1% DDC diet, biological replicate 3

data_processing:
Raw reads were filtered using Cutadapt to remove adapter sequences, poly(A)/poly(G) reads, reads containing more than 5% unknown nucleotides, and low-quality reads with more than 20% bases having a Q score ≤ 20. Clean read quality was assessed using FastQC.
clean reads were aligned to the mouse reference genome using HISAT2.
Transcript assembly and gene expression quantification were performed using StringTie. Gene expression abundance was calculated as FPKM values.
Differentially expressed genes between groups were identified using DESeq2 based on raw count data. Genes with an adjusted P value < 0.05 and the predefined fold-change threshold were considered differentially expressed.
Functional enrichment analysis of differentially expressed genes was performed using Gene Ontology and KEGG pathway analysis. Gene set enrichment analysis was performed using GSEA software and MSigDB gene sets.
Assembly: Mus musculus reference genome [GRCm38/mm10 ]
Supplementary files format and content: Tab-delimited text file containing raw gene counts for all samples.
Supplementary files format and content: Tab-delimited text file containing normalized gene expression values, reported as FPKM, for all samples.

growth_protocol: C57BL/6J mice were maintained under specific pathogen-free conditions with free access to food and water under a 12-h light/dark cycle.

extract_protocol:
Total RNA was extracted from mouse liver tissues using TRIzol reagent according to the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent Bioanalyzer 2100 system with the RNA 6000 Nano LabChip Kit. RNA samples with an RNA integrity number greater than 7.0 were used for library construction.
Polyadenylated mRNA was purified from total RNA using Dynabeads Oligo(dT) beads and fragmented under elevated temperature. The fragmented RNA was reverse-transcribed into cDNA, followed by second-strand cDNA synthesis using dUTP. After end repair, A-tailing, adapter ligation, size selection and UDG treatment, the libraries were amplified by PCR. The final cDNA libraries had an average insert size of approximately 300 ± 50 bp and were sequenced on an Illumina NovaSeq 6000 platform using a 150-bp paired-end strategy.

treatment_protocol: Mice in the DDC group were fed a diet containing 1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine for 4 weeks to induce cholestatic liver injury and biliary fibrosis. Control mice were fed a standard diet for the same duration.

value: Liver

value: wild type

value: 1% DDC diet

value: batch 1


title: LPS day 9; WT mouse

description: Library name: LPS_day9_WT


title: CBMS1 mESC, scRepli-seq, untreated singleG1 010


title: DDC mouse liver replicate 4

description:
Library name: DDC4
Liver tissue from a C57BL/6J mouse fed a 1% DDC diet, biological replicate 4


title: DDC mouse liver replicate 2

description:
Library name: DDC2
Liver tissue from a C57BL/6J mouse fed a 1% DDC diet, biological replicate 2


title: DDC mouse liver replicate 1

description:
Library name: DDC1
Liver tissue from a C57BL/6J mouse fed a 1% DDC diet, biological replicate 1


title: Control mouse liver replicate 4

description:
Library name: Control4
Liver tissue from a control C57BL/6J mouse, biological replicate 4

value: standard diet


title: Control mouse liver replicate 3

description:
Library name: Control3
Liver tissue from a control C57BL/6J mouse, biological replicate 3


title: Control mouse liver replicate 2

description:
Library name: Control2
Liver tissue from a control C57BL/6J mouse, biological replicate 2


title: Control mouse liver replicate 1

description:
Library name: Control1
Liver tissue from a control C57BL/6J mouse, biological replicate 1


title: Syn D14 liver EC

city: Columbus

first: Katherine

middle: E

last: Miller

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
Library name: Syn_D14_liver_EC
10x Genomics Flex fixed scRNAseq, singleplex, BC001

data_processing:
Raw BCL files were converted to FASTQ format using Cell Ranger v8.0.0 mkfastq, and alignment to the mm10 Flex probe set was performed using Cell Ranger v8.0.0 multi with default settings, including filtering, barcode counting, and UMI quantification. Downstream analysis was conducted in R v4.3.3 using Seurat v5 [PMCID: PMC10928517].
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
Endothelial cells were collected 4 days or 14 days after transplant and isolated from the liver via flow staining and sorting for Cd45- Cd11b+ Cd31+.
Up to 10,000 cells per condition were targeted for scRNA-seq via the 10x Genomics Flex singleplex kit (BC001) following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq6000.

treatment_protocol: Female mice received either a syngeneic or allogeneic hematopoietic stem cell transplant.

value: Female

value: cKit selected

value: CD45.2 B6D2F1/J (F1 hybrid cross B6xDBA2)


title: Syn D4 liver EC

description:
Library name: Syn_D4_liver_EC
10x Genomics Flex fixed scRNAseq, singleplex, BC001


title: Allo D4 liver EC

description:
Library name: Allo_D4_liver_EC
10x Genomics Flex fixed scRNAseq, singleplex, BC001

value: Flow sorted endothelial cells (Cd45-Cd11b-Cd31+)


title: Allo D14 liver EC

description:
Library name: Allo_D14_liver_EC
10x Genomics Flex fixed scRNAseq, singleplex, BC001


title: Sternum bone marrow cells

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

description:
Library name: sternum
Live CD45+B220-CD11b-Thy1.2+CD4+CD8+ cells from sternum bone marrow were sorted with FACS Aria II

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 9.0.1. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
See methods for more details
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices, matrices with gene symbols, and barcodes for each sample

source_name: Sternum bone marrow cells

extract_protocol:
10X Genomics Chromium Single Cell preparation
NGS Illumina NextSeq

value: Sternum bone marrow cells


title: Skull bone marrow cells

description:
Library name: skull
Live CD45+B220-CD11b-Thy1.2+CD4+CD8+ cells from skull bone marrow were sorted with FACS Aria II.

source_name: Skull bone marrow cells

value: Skull bone marrow cells


title: M07e_Replicate-2

description: Library name: Sample_4

data_processing:
Paired-end libraries were sequenced on an Illumina NovaSeq platform, generating 150–200 million read pairs per replicate. Data processing followed the Dovetail® Target Enrichment Workflow (https://dovetail-capture.readthedocs.io/en/latest/). Reads were aligned using BWA-MEM (v0.7.17-r1198-dirty) with the -5SP parameters, deduplicated, and formatted as pairs using Pairtools (v1.0.1). Promoter-based chromatin loop interactions were identified at 5 kb resolution by pooling deduplicated alignments from replicates and analyzing with CHiCAGO (v1.26.0). Differential loops were detected using ChicDiff (v0.6), with results output in BEDPE format.
Assembly: hg38
Supplementary files format and content: .hic files for each sample
Supplementary files format and content: contact matrix for each sample

growth_protocol: CD34+ hematopoietic stem cells (HSCs) were expanded in StemSpan SFEM II media supplemented with 1% L-glutamine, 1% penicillin-streptomycin, and growth factors: TPO (50 ng/µL), EPO (5 ng/µL), SCF (100 ng/µL), IL-3 (10 ng/µL), IL-6 (10 ng/µL), and FLT-3L (10 ng/µL). Megakaryocyte (MK) progenitors were derived by treating CD34+ HSCs with StemSpan™ Megakaryocyte Expansion Supplement (100X) following the manufacturer’s instructions. Flow cytometry confirmed the purity of HSCs (CD34+) and MK progenitors (CD41+). M07e cells were grown in RPMI-1640, supplemented with 20% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin and 10 ng/mL GM-CSF. K-562 cells were were grown in RPMI-1640, supplemented with 20% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells are crosslinked with formaldehyde to preserve chromatin interactions, followed by chromatin digestion using a restriction enzyme.  DNA purity and concentration were assessed using a Qubit fluorometer. The integrity of the extracted DNA was evaluated using an Agilent Tapestation.
For Promoter capture Hi-C (PCHi-C) libraries were prepared using the Dovetail® Pan Promoter™ Assay (Catalog #35013E, Cantata Bio), following the manufacturer’s protocol.

value: Acute Megakaryoblastic Leukemia Cells

value: WT


title: [RNA-Seq] EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (4)

value: bone marrow

value: Hemtopoietic stem cells


title: dura cells

description:
Library name: dura
Live CD45+B220-CD11b-Thy1.2+CD4+CD8+ cells from the dura were sorted with FACS Aria II.

source_name: dura cells

value: dura cells


title: [RNA-Seq] EPCRHigh HSCs expanded after 4-daya culture of EPCRHigh HSCs in the presence of R162 (2)


title: M07e_Replicate-1

description: Library name: Sample_3


title: Sternum cells. BCR

description:
Library name: Sternum cells. BCR
Live CD45+CD3e-CD138-CD19+ B cells and CD45+IgD-CD3e-CD138+TACI+ antibody-secreting cells (ASCs) were sorted with FACS Aria II.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 9.0.1. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
See methods for more details
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices, matrices with gene symbols, and barcodes for each sample, as well as vdj filtered contig outputs

source_name: Sternum bone marrow

value: Sternum bone marrow


title: CD34_HSC_Replicate_2

description: Library name: Sample_2

source_name: CD34+ Hematopoietic Stem Cells

value: CD34+ Hematopoietic Stem Cells

value: Hematopoietic Stem Cells


title: Skull cells, BCR

description:
Library name: Skull cells, BCR
Live CD45+CD3e-CD138-CD19+ B cells and CD45+IgD-CD3e-CD138+TACI+ antibody-secreting cells (ASCs) were sorted with FACS Aria II.

source_name: Skull bone marrow

value: Skull bone marrow


title: CD34_HSC_Replicate_1

description: Library name: Sample_1


title: Sternum cells. GEX

description:
Library name: Sternum cells. GEX
Live CD45+CD3e-CD138-CD19+ B cells and CD45+IgD-CD3e-CD138+TACI+ antibody-secreting cells (ASCs) were sorted with FACS Aria II.


title: MVV, Naked target DNA (fragmented by sonication), rep3

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Library name: MVV_Naked_biol_rep3
MVV intasome integration into naked sonicated yeast DNA

data_processing:
Nanopore reads containing the vDNA end (5'-CCATGACA, 5'-CTCTAGCA, or 5'-ATCTCGCA for PFV, HIV-1, and MVV, respectively; only precise match was considered) and the linker (5'-TAAGGGACT; allowing one mismatch) sequence tags in converging orientations, with at least 15 bp of intervening sequence, were cropped and brought into sense orientation with respect to integrated viral DNA end.
Cropped reads were aligned to the yeast SacSer3 assembly using BLAT version 3.5 96 with the following options: stepSize 5, repMatch 2253, minScore 20, minIdentity 0. Only matches that started immediately at the vDNA and linker junctions with overall less than 12% mismatches, (Q gap bases + T gap bases + mismatch)/match < 0.12, and were used for further analysis. Mathched with non-unique combinations of genomic positions of integration (T start) and linker ligation sites (T end) were considered PCR duplicates and counted only once. To avoid reads originating from linker ligation to ends of yeast genomic DNA fragments, all matches within 10 bp of a XbaI or NheI site were removed. Processed PSL files represent Blat alignment files pruned of duplicates and reads originated from linker ligations to XbaI or NheI genomic DNA ends. The merged processed files contain only matches with the distance between the integration site and the linked target DNA fragementation site is less than 150 bp (this distance is found in column 11 of each PSL file for each mapped integration site). The data from the merged and filtered psl files were used to construct the histograms shown in the publication.
Assembly: SacCer3
Supplementary files format and content: BLAT alignment psl files

organism: Saccharomyces cerevisiae

extract_protocol:
organic extraction
Chromatinized or naked yeast DNA was incubated with purified retroviral intasomes. Chromatinized reaction products were fragmented using Fenton reaction in the presence of copper (II) cloride, mercaptopropionic acid, and hydrogen peroxide. DNA was then deproteinized,  repaired with phi29 DNA polymerase and processed for dA tailing. End-prepped DNA was ligated to a linker (obtained by annealing 5'-phosphorylated and 3'-blocked 5'-GTCCCTT AAGCGGAG with 5'- GTAATAC GACTCAC TATAGGGCC TCCGCTT AAGGGACT). The products,  PCR amplified using primers specific to the linker and viral DNA ends, were sequenced using Nanopore technology.

treatment_protocol: Genomic DNA extracted from BY4741 cells was sheared by digestion with NheI and XbaI prior to chromatinization with human histones, including H4(S47C)-phenanthroline conjugate with or without Lys36Me3 modification on histone H3. For naked target DNA control condition, the DNA was additionally sheared by sonication.

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: MVV, Naked target DNA (fragmented by sonication), rep2

description:
Library name: MVV_Naked_biol_rep2
MVV intasome integration into naked sonicated yeast DNA


title: Skull cells, GEX

description:
Library name: Skull cells, GEX
Live CD45+CD3e-CD138-CD19+ B cells and CD45+IgD-CD3e-CD138+TACI+ antibody-secreting cells (ASCs) were sorted with FACS Aria II.


title: Brain tumor tissues, BCR

description:
Library name: Brain tumor tissues, BCR
8-wks-old mice were intracranially injected with 1x10^5 cells of CT2A. After 14 days of injection, tissues were harvested and PNA+ cells were magnetically sorted from tissues. After that, DAPI-negative live cells were sorted with FACS Aria III

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 9.0.1. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
See methods for more details
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices, matrices with gene symbols, and barcodes for each sample, as well as vdj filtered contig outputs.

source_name: Brain tumor

value: Brain tumor


title: MVV, Naked target DNA (fragmented by sonication), rep1

description:
Library name: MVV_Naked_biol_rep1
MVV intasome integration into naked sonicated yeast DNA


title: [RNA-Seq] EPCRLow HSCs generated after 4-daya culture of EPCRHigh HSCs under control conditions for 1 day (3)


title: Skull bone marrow cells, BCR

description:
Library name: Skull bone marrow cells, BCR
8-wks-old mice were intracranially injected with 1x10^5 cells of CT2A. After 14 days of injection, tissues were harvested and PNA+ cells were magnetically sorted from tissues. After that, DAPI-negative live cells were sorted with FACS Aria III

source_name: Skull

value: Skull


title: MVV, Me3, LEDGF, rep2

description:
Library name: MVV_Me3_LEDGF_biol_rep2
MVV intasome integration into H3K36Me3 chromatinized yeast DNA supplemented with 8nM LEDGF


title: Brain tumor tissues, GEX

description:
Library name: Brain tumor tissues, GEX
8-wks-old mice were intracranially injected with 1x10^5 cells of CT2A. After 14 days of injection, tissues were harvested and PNA+ cells were magnetically sorted from tissues. After that, DAPI-negative live cells were sorted with FACS Aria III


title: MVV, Me3, LEDGF, rep1

description:
Library name: MVV_Me3_LEDGF_biol_rep1
MVV intasome integration into H3K36Me3 chromatinized yeast DNA supplemented with 8nM LEDGF


title: Skull bone marrow cells, GEX

description:
Library name: Skull bone marrow cells, GEX
8-wks-old mice were intracranially injected with 1x10^5 cells of CT2A. After 14 days of injection, tissues were harvested and PNA+ cells were magnetically sorted from tissues. After that, DAPI-negative live cells were sorted with FACS Aria III


title: MVV, Me3, rep2

description:
Library name: MVV_Me3_biol_rep2
MVV intasome integration into H3K36Me3 chromatinized yeast DNA


title: TA_Young_2

city: Rome

first: Andrea

last: Bracaglia

address: Via Antonio Scarpa 16

country: Italy

institute: University of Rome La Sapienza

description:
Library name: 144173_ID3405_4-D_Young_rep2
Fresh-frozen tibialis anterior muscle derived from two different 5 months-old C57BL/6 mice

data_processing:
Raw sequencing data and .json file obtained with Loupe Browser were processed with 10x Genomics spaceranger pipeline
The reads wre aligned to 10mm mouse genome with spaceranger default parameters to generate h5 matrix
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 h5 matrix with barcodes and gene expression count
Supplementary files format and content: V13Y08-028.json json file with spatial coordinates
Supplementary files format and content: lam.tif image in tif format of laminin immunofluorescence staining
Supplementary files format and content: col.tif image in tif format of collagen immunofluorescence staining
Supplementary files format and content: dapi.tif image in tif format of dapi staining
Library strategy: Spatial Transcriptomics

source_name: Tibialis anterior muscle

growth_protocol: C57BL/6 mice were mainated in a pathogen-free animal facility under standard 12h light/12h dark cycle at 21°C with access to red house and to standard chow and water ad libitum

extract_protocol:
Fresh-fozen muscles were embebbed in OCT and 10 μm sections were cut at the cryostat
Spatial transcriptomics sequencing libraries were prepared with 10X Genomics Visium spatial gene expression slides and reagent kit according to manufacturer's instructions

value: Tibialis anterior muscle


title: MVV, Me3, rep1

description:
Library name: MVV_Me3_biol_rep1
MVV intasome integration into H3K36Me3 chromatinized yeast DNA


title: [RNA-Seq] EPCRHigh HSCs cultured under control conditions for 1 day (2)


title: MVV, Me0, rep3

description:
Library name: MVV_Me0_biol_rep3
MVV intasome integration into H3K36Me0 chromatinized yeast DNA


title: TA_Young_1

description:
Library name: 144172_ID3405_3-C_Young_rep1
Fresh-frozen tibialis anterior muscle derived from 5 months-old C57BL/6 mice


title: TA_Old_2

description:
Library name: 144171_ID3405_2-B_Old_rep_2
Fresh-frozen tibialis anterior muscle derived from two different 24 months-old C57BL/6 mice


title: MVV, Me0, rep2

description:
Library name: MVV_Me0_biol_rep2
MVV intasome integration into H3K36Me0 chromatinized yeast DNA


title: TA_Old_1

description:
Library name: 144170_ID3405_1-A_Old_rep_1
Fresh-frozen tibialis anterior muscle derived from two different 24 months-old C57BL/6 mice


title: Resistant,Panicle,normal night temperature,inoculated B.glumae,rep 1

status: Public on Jul 15 2026

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Library name: R_NT_P1

data_processing:
RNA-Seq reads were first trimmed with Trim Galore version 0.6.4 (Krueger, 2019; Martin, 2011) which includes filtering reads shorter than 30 bp and low-quality ends from reads (Phred score: <20) and the option of removing reads with Ns. The quality of reads before and after trimming was confirmed using FastQC version 0.12.1 (Andrews, 2019)
The filtered reads were then aligned to the Oryza sativa Japonica genome (EnsemblPlants IRGSP-1.0; GCA_001433935.1) using STAR version 2.7.10b (Dobin et al., 2013) with default parameters and --sjdbOverhang of 149. The alignment files generated by STAR were then used to generate gene counts using Subread version 2.0.0 (featureCounts), with default parameters (Liao et al., 2014). A data matrix of gene counts for all samples was created using a custom Python script, which was used for further differential gene expression analysis
Differential gene expression analysis was performed separately for the resistant and susceptible accessions using DESeq2 version 1.38.3 (Love et al., 2014). A Wald test was employed to calculate p-values, and genes with a Benjamini-Hochberg adjusted p-value less than 0.05 and a log2 fold change greater than 1 were considered differentially expressed
Assembly: EnsemblPlants IRGSP-1.0; GCA_001433935.1
Supplementary files format and content: A tab-delimited data matrix of raw feature counts with features (genes) in rows and sample names in columns.

organism: Oryza sativa

source_name: panicle

growth_protocol: The selected accessions were grown until heading stage in the greenhouse.

extract_protocol:
Panicles were ground using 1600 MiniG® automated tissue homogenizer (Spex Sample Prep, Metuchen NJ), and total RNA was extracted using Trizol reagent (Life Technologies, Carlsbad, CA). RNA was precipitated with 5M Potassium Acetate pH 5.2, and 100% ice-cold ethanol and air-dried. RNA pellets were resuspended in 20 µl of RNAse-free water
RNA purity and integrity was evaluated using the ExperionTM Automated Electrophoresis system (BioRad, Hercules, CA).  RNA sequencing was performed by Novogene (Davis, CA) for 150 bp paired-end read sequencing on the Illumina PE250 platform

treatment_protocol: Emerging panicles were inoculated with B. glumae (Pathogen, P) or treated with water (Mock, M) and maintained at normal night temperature (22C) and high night temperature (28C) conditions for 3 days.

value: panicle

value: B.glumae inoculation


title: MVV, Me0, rep1

description:
Library name: MVV_Me0_biol_rep1
MVV intasome integration into H3K36Me0 chromatinized yeast DNA


title: TAMs from Late stage tumor (15day) replicate 3

first: Huan

last: Wang

address: 38 Life Science Park Road

institute: National Center for Protein Sciences, Beijing

description: Library name: Late-3

data_processing:
All samples passed quality control based on the results of FastQC.
Reads were aligned to the mouse genome assembly mm10.GRCm38 using HISAT2.
The aligned reads were counted using FeatureCounts.
Differentially expressed genes were determined with DESeq2 program
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor

extract_protocol:
Total RNA was isolated with RNeasy plus Mini Kit (Qiagen) according the manufacturer's protocol.
Library preparation was performed with Hieff NGS™ Ultima Dual-mode RNA Library Prep Kit according the manufacturer's protocol.

value: Tumor

value: TAM

value: Non


title: HIV-1, Naked target DNA (fragmented by sonication), rep6

description:
Library name: HIV1_Naked_biol_rep6
HIV-1 intasome integration into naked sonicated yeast DNA


title: TAMs from Late stage tumor (15day) replicate 2

description: Library name: Late-2

value: WT


title: HIV-1, Naked target DNA (fragmented by sonication), rep5

description:
Library name: HIV1_Naked_biol_rep5
HIV-1 intasome integration into naked sonicated yeast DNA


title: TAMs from Late stage tumor (15day) replicate 1

description: Library name: Late-1


title: TAMs from early stage tumor (8day) replicate 3

description: Library name: Early-3


title: HIV-1, Naked target DNA (fragmented by sonication), rep4

description:
Library name: HIV1_Naked_biol_rep4
HIV-1 intasome integration into naked sonicated yeast DNA


title: HIV-1, Naked target DNA (fragmented by sonication), rep3

description:
Library name: HIV1_Naked_biol_rep3
HIV-1 intasome integration into naked sonicated yeast DNA


title: TAMs from early stage tumor (8day) replicate 2

description: Library name: Early-2


title: HIV-1, Naked target DNA (fragmented by sonication), rep2

description:
Library name: HIV1_Naked_biol_rep2
HIV-1 intasome integration into naked sonicated yeast DNA


title: TAMs from early stage tumor (8day) replicate 1

description: Library name: Early-1


title: HIV-1, Naked target DNA (fragmented by sonication), rep1

description:
Library name: HIV1_Naked_biol_rep1
HIV-1 intasome integration into naked sonicated yeast DNA


title: Brequiner treated wounded skin tissue 3 (day 9)

city: Maebashi

first: Akihiko

last: Uchiyama

state: Gunma

department: Dermatology

institute: Gunma University

description: Library name: B4_2_S23genesresults

data_processing:
Reads were aligned to the mm10 assembly of the mouse genome (NCBI Build 38, obtained from the UCSC Genome Browser website) using STAR aligner. Gene-level raw count data were used for downstream analyses. RNA-seq data were analyzed using the iDEP Genomics Suite (https://bioinformatics.sdstate.edu/idep/). Relative log expression (RLE) plots were used to assess data normalization and quality.
Differential gene expression analysis was performed using the Wald test for pairwise comparisons. For human samples, publicly available RNA-seq datasets comparing PG lesional skin and normal skin were analyzed. In mouse samples, brequinar-treated skin was compared with vehicle-treated skin and with unwounded skin. Gene Ontology (GO) terms (p < 0.01, fold change > 4 for human and p < 0.05, fold change > 1.5 for mouse) were obtained using ToppGene (https://toppgene.cchmc.org/).
Assembly: mm 10
Supplementary files format and content: csv file including normalized count value for all samples

source_name: Skin

extract_protocol:
Total RNA from skin tissue and cells were isolated using a RNeasy Mini Kit (Qiagen, Valencia, California). Total 100 ng
Library preparation was carried out using the KAPA mRNA HyperPrep kit (KAPA BIOSYSTEMS, KK8580) according to the manufacturer’s protocols. Library quality was assessed using an Agilent 4200 TapeStation (Agilent, CA, US). Paired-end sequencing was performed on a NextSeq 2000 platform (Illumina).

value: Skin

value: Brequiner and wound


title: HIV-1, Me3, LEDGF, rep3

description:
Library name: HIV1_Me3_LEDGF_biol_repl3
HIV-1 intasome integration into H3K36Me3 chromatinized yeast DNA supplemented with 8nM LEDGF


title: DO_3_2

city: Schlieren

first: Ataman

last: Sendoel

address: Wagistrasse 12

department: Institute of Regenerative Medicine

country: Switzerland

institute: University of Zurich

description:
Library name: DO_3_2
dial-out nested PCR for sgRNA amplification for 120h gastruloids, Replicate 2

library_source: other

data_processing:
Bioinformatic analysis of single-cell sequencing data: Raw sequencing data in the form of BCL files, were demultiplexed using Illumina bcl2fastq v2.20 with default settings. Up to one mismatch in the sample barcode sequences was allowed. Resulting fastq files were processed using the BD Rhapsody Pipeline (version 1.9.1) hosted at the Seven Bridges’ cloud platform (https://www.sevenbridges.com/). A custom mouse reference genome, based on Gencode vM25 (GRCm38.p6), was generated and combined with the 669 sgRNAs sequences. Based on STAR aligner, a custom STAR reference genome was created and the Refined Putative Cell Calling option was disabled during the pipeline execution. For downstream analysis, unique molecular identifier (UMI) count data was corrected by BD Genomics Recursive Substitution Error Correction (RSEC).  Bioinformatic analysis of dial-out data: PCR dial-out data was processed using an in-house custom Python script as previously described. Three 9-nucleotide cell barcodes were extracted from the 97 possible barcodes from Read 1. Up to one mismatch was allowed for each barcode (Hamming distance of 1). The script retrieved the 8-nucleotide UMI sequences from Read 1 as per the BD manual. For valid barcodes, sgRNAs were identified in Read 2 by performing an exact match search for the 20-nucleotide sgRNA sequence. Following UMI deduplication sgRNA UMI counts per cell were computed. In case of multiple sgRNAs detected for an individual cell, specific sgRNA assignment was only performed if the cells UMI count exceeded the 99th percentile.  Processing of single-cell RNA sequencing data: The Scrublet Python package was used for duplet detection and removal on each individual sample. Expected doublet rates were adjusted based on estimates by the BD Rhapsody scanner. Genes expressed at least 5 cells were retained. Following filtering, 4 datasets from 2 different screen replicates were combined in Seurat using the Harmony package. Data from Cnot8 KO, Cnot7 KO and Control organoids comes from a single cartridge/whole transcriptome assembly, with no need for integration. Only cells containing detected sgRNAs and classified as singlets were selected for further analysis. Cells were filtered based on the following criteria: UMI counts > 500, UMI counts lower than the 0.99 quantile (to remove outliers) and mitochondrial gene content < 20%. Filtered datasets were then processed using Seurat’s standard pipeline.
Bulk RNA sequencing data analysis: Paired-end RNA-seq data was processed using the Nextflow RNA-seq pipeline (https://github.com/nf-core/rnaseq) version 3.14.0 as previously described. In short, the FastQC program was used for quality control, followed by quality and adapter trimming using TrimGalore. Read alignment was performed to the Gencode vM25 (GRCm38.p6) reference by STAR. Reads were quantified using Salmon. Quality control of analysis pipelines was done by MultiQC.    Ribosome profiling data analysis: UMI- tools in combination with a custom “regular expression pattern” were used to extract ribosome footprints from fastq files. Footprints above minimal length cutoff of 20 nt were extracted, along with sample barcode 5 nt in length. For further processing adapter sequences (AGATCGGAAG) were moved to the 7 nt UMI sequence of the fastq header. Removal of reads aligning to rRNAs and tRNAs was performed using bowtie2 v2.2.5. All remaining reads were aligned to the Gencode vM25 (GRCm38.p6) reference genome by STAR v2.7.11a allowing up to one mismatch (--outFilterMismatchNmax 1) and a maximum of 20 multimappers (--outFilterMultimapNmax 20). UMI deduplication of the aligned bam files was performed using the UMI-tools dedup command. Reads mapping to the CDS regions of the genome in forward strand were counted by featureCounts program.
Nanopore data bioinformatic analysis and poly(A) length estimation: Raw nanopore reads in .pod5 format were basecalled and mapped to the reference mouse genome GRCm38 (primary assembly, obtained from the GENCODE website) using the Dorado software [https://github.com/nanoporetech/dorado] version 0.8.3 with the model rna004_130bps_sup@v5.1.0. Dorado is the software package developed and supported by Oxford Nanopore Technologies for the processing of raw nanopore data obtained on their platform. Dorado uses a deep learning-based algorithm for basecalling (transforming nanopore current data to nucleotide sequence), minimap2 aligner [PMID: 29750242] for read alignment to the genome, and a separate heuristic algorithm for estimating poly(A) tail length in each read. Importantly, successfully estimated tail lengths are stored as the “pt:i” tags in the output .bam files, while the basecalled sequences of reads contain only short fragments of poly(A) tails which are not informative for actual length of the poly(A) tails. Identification of the poly(A) tails in the reads was configured to tolerate non-adenine gaps up to 3 nt in length: tail_interrupt_length = 3. We further retained only uniquely mapped reads with mapping quality above or equal to one (in minimap2 output, quality=0 indicates that a read is a multimapper that aligns equally well to more than one genomic loci) and present “pt:i” tag. In total, ~8.1 mln reads were retrieved from four samples (two bioreplicates for each of the two conditions: Cnot8 KO and Control), with ~1.7 to ~2.5 mln reads per sample. Read counting was performed by featureCounts.
For a subset of analyses, the WTA reads were aligned and quantified with STARsolo (STAR v2.7.11b) against the Gencode vM25 (GRCm38.p6) genome, using the BD Rhapsody bead cell-barcode and UMI configuration (CB_UMI_Complex mode with single-mismatch whitelist matching).
Assembly: Gencode Mouse vM25 (GRCm38.p6)
Supplementary files format and content: Comma-separated value files and matrix files with count numbers, *_counts.csv.gz files contain Cell Barcode, Gene Symbol and RSEC adjusted counts.
Supplementary files format and content: Some single-cell WTA gene-expression matrices are provided in the standard STARsolo output format - three files per sample: *_matrix.mtx.gz (genes x cells, integer UMI counts) with *_barcodes.tsv.gz (composite cell barcodes) and _features.tsv.gz (Ensembl gene ID, gene symbol, feature type). Dial-out sgRNA files (_DO.csv.gz) give the per-cell sgRNA assignment with columns: cell_barcode, cell_index, sgRNA, umi_count, sgrna_detected.

molecule: other

source_name: Gastruloids

growth_protocol: Mouse embryonic stem cell culture: The dual T/Brachyury-mCherry, SOX1-GFP reporter (SBR) mouse ES cell line was cultured in in tissue culture treated 6 well plates (Thermo Scientific, 140675), in DMEM with Glutamax (Gibco, 7001569) supplemented with 10% FCS (XXX), Penicillin-Streptomycin (100U/ml, 100µg/ml respectively), non-essential amino acids (0.1 mM, Gibco, 11140050), sodium pyruvate (1mM, Thermo Scientific, 11360070), , beta-mercaptoethanol (0.11 mM, Gibco, 21985023) , 3 µM CHIR99021 (SML1046), 1 µM PD0325901 (S1036), 100u/mL LIF (produced in house). Cells were split every 48-72h, by accutase treatment followed by centrifugation at 200 g, 4min and seeding between 75 000 and 150 000 cells per well.

extract_protocol:
Gastruloids were generated as described previously. In short, murine embryonic stem cells (mESCs) are washed twice with PBS, followed by a detachment using Accutase (AT-104) for 4 min at 37C, 5% CO2. Cells were collected in 4.5 ml of embryonic stem cell medium with 10% fetal calf serum. Cells were centrifuged 200xg, 4min, 4°C and then resuspended in 10 ml PBS, followed by a second spin and PBS wash. Finally, cells were resuspended in 1 ml of N2B27 and counted using a hemocytometer. 40 µl of N2B27 with 300 cells per well were seeded in low adhesion 96 well plates (CLS7007-24EA) and incubated for 48h at 37C, 5% CO2. After 48 hours gastruloids were pulsed with 150uL of N2B27 supplemented with 3uM CHIR99021 (SML1046-5MG). Medium was refreshed using N2B27 every 24 hours for the extend of culture (between 120-144h). 120h gastruloids were harvested using P1000 cut-tips and subjected to single cell sequencing. In short gastruloids were collected in 15 ml tubes, washed once with PBS and incubated with accutase for 15 mins at 37C. Cell suspensions were resuspended using low adhesion tips and centrifuged 200xg, 4min, 4C. For sorting, cells were resuspended in FACS buffer (2% FCS and 0.5 ng/ul DAPI in PBS), passed through a 35 µm filter cap into 5 ml FACS tubes and sorted for GFP+ populations using a BD FACSAria III cell sorter using a 70 µM nozzel. Sorted cells were then spun down 15 min at 400xg, 4°C and then resuspended in BD sample buffer. Unsorted gastruloids were harvested and processed the same way, resuspended in sample buffer and then passed through 35 µm cell filters 3 times. Single cell suspensions were prepared for sequencing using the BD Rhapsody Single-Cell Analysis System with the BD Rhapsody Cartridge Kit (633733). Bead based reverse transcription, amplification and sequencing library production was performed following manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 2.0).                                                                   Samples for Nanopore direct RNA-seq: Samples for Nanopore direct RNA-sequencing were harvested at 72 h of gastruloid development. Gastruloids were harvested using cut P1000 tips, collected in 15 ml tubes and washed 2 times in PBS+CHX. Supernatant was removed, and organoids were flash frozen in liquid nitrogen. Frozen organoids were then resuspended in ribosome lysis buffer (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase, 100µg/mL CHX), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and flash frozen in liquid nitrogen, before being stored at -80 °C before downstream processing.                    Samples for ribosome profiling: Ribosome profiling experiments were performed as previously described, with minor modifications for gastruloids. In short, gastruloids were harvested at indicated time points using cut P1000 tips and collected into 15 ml tubes. Gastruloids were washed 2 times in PBS+CHX, supernatant was removed, and organoids were flash frozen in liquid nitrogen. Frozen organoids were then resuspended in ribosome lysis buffer (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase, 100µg/mL CHX), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and flash frozen in liquid nitrogen, before being stored at -80 °C before downstream processing. Samples for RNA degradation: Gastruloids at 96 h of development were treated with 10 µM Actinomycin D (ThermoScientific, 11805017) in N2B27 and gastruloids were harvested after 0, 2 and 4 h of treatment. Gastruloids were harvested at indicated time points using cut P1000 tips and flash frozen. Frozen organoids were then resuspended in ribosome lysis buffer without cyclohexamide (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and RNA was purified using the DirectZol RNA kit. Purified RNA was submitted for library preparation and sequencing to Novogene.
Reverse transcription from beads and sequencing library production was carried out according to the manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 1.0). Library construction protocol for RNA-seq: RNA was isolated from lysates gastruloids at indicated time points as described in the Ribosome profiling section using TRIzol®  LS Reagent (Invitrogen, 10296028) and column purified with a Direct-zol RNA MiniPrep kit (Zymo Research, R2052). Libraries were prepared and sequenced at Novogene. Library construction protocol for Other:  As previously described, the sgRNA-containing region was amplified from the BD Rhapsody beads using a nested KAPA Polymerase reaction. In the first polymerase reaction (PCR1), the Rhapsody beads from each separate cartridges were resuspended and distributed into 4 separate 50 µL reactions  (100 µl KAPA HiFi HotStart ReadyMix (Roche 07958935001), 6 µl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 6 µl reverse primer (5′-TCTTGTGGAAAGGACGA-3′, 10 μM), 12 μl Bead RT/PCR Enhancer reagent from BD Biosciences and 72 μl nuclease-free water for a total volume of 200 μl). PCR1 conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 25 cycles of denaturation 95 °C for 30 s, annealing 53 °C for 30 s, extension 72 °C for 20 s and a final extension of 10 min at 72 °C. The 4 x 50 µl PCR1 product was pooled, and beads were removed using a magnet. Amplicons were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, A63881) following manufacturer’s instructions. 3 μl of cleaned up PCR1 was used as template for PCR 2 (25 µL KAPA HiFi HotStart Ready Mix, 2 μl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 2 μl reverse primer (CAGACGTGTGCTCTTCCGATCTCTTGTGGAAAGGACGAAACA*C*C*G-3′, 10 μM), 18 μl nuclease-free water) for a total volume of 50 μl. PCR2 conditions were as follows: initial denaturation at 95 °C for 3 min, followed by 10 cycles of denaturation 95 °C for 30 s, annealing 60 °C for 3 min, extension 72 °C for 60 s, and a final extension of 5 min at 72 °C. Agencourt AMPure XP beads were used to clean up PCR2 product according to the manufacturer’s instructions  before the indexing PCR. Indexing PCR was performed according to BD Biosciences ‘mRNA Targeted Library Preparation’ protocol (doc ID: 210968 rev. 3.0). Library construction protocol for Ribo-seq: Ribosome profiling was conducted with some adjustments of the original method (64, 65). For RNA digestion, cell lysates were incubated with 1 U/µg of RNase 1 (Epicentre/Lucigen, 10U/µL) for 45 minutes at room temperature. Reaction was stopped by adding 4 µL of SUPERase Inhibitor (20 U/µL, SUPERase-InTM RNase Inhibitor Thermo Scientific AM2694). To eliminate free nucleotides and isolate ribosome-protected fragments, the RNase I-treated samples were processed using Amersham MicroSpin S-400 HR columns (Cytiva, 27514001). RNA extraction was performed utilizing TRIzol® LS Reagent (Invitrogen 10296028) in combination with the Direct-zolTM RNA MiniPrep kit (Zymo Research, R2052). Total RNA concentration was measured using QubitTM RNA broad range kit (Invitrogen, Q10210). Ribosome footprints were excised and extracted from a 15% TBE-UREA gel (Invitrogen, EC68852BOX) using the 20nt, 22nt, 27nt, 30nt and 60nt oligonucleotides mix as markers (1 µL of 10 µM dilution in 19µL RNase-free H2O). Extraction was performed overnight with RNA extraction buffer (300mM NaOAc pH=5.5, 1mM EDTA, 0.25% v/v SDS). T4 PNK (NEB, M0201S) end-healing reaction was performed on the ribosome footprints for 1 hour at 37˚C. Linker ligation reaction followed using T4 RnI truncated K227Q (NEB, M0351L) in combination with 20 µM of preadenylated linker for 3 hours at 22˚C (50% w/v PEG-8000, 10X T4 RNA ligase, preadenylated linker, T4 RnI truncated K227Q). Ribosomal RNA was depleted using biotinylated rRNA depletion oligos (2 µM) by mixing 10 µL of sample with 10 µL of oligo mix and incubated for 2 minutes at 80˚C, followed by a gradual decrease in temperature to 25˚C. MyOne Streptavidin dynabeads (Life Technologies, 65001) were used to recover the samples. Reverse transcription was performed on the Ribosomal RNA-free samples using SuperScriptTM IV Reverse Transcriptase (Invitrogen, 18090050). Footprints were excised and extracted from a 15% TBE-UREA gel. Extraction was performed overnight with DNA extraction buffer (10mM Tris-HCl pH=8, 300mM NaCl, 1mM EDTA). cDNA was circularized using CircLigase II (100 U/µL, Biosearch, CL4115K) for 1 hour at 60˚C. cDNA was amplified using Phusion High-Fidelity DNA polymerase (Thermo Scientific, F530S) using an individual index per sample. 6-12 cycle amplicons were visualized using an 8% TBE non-denaturing polyacrylamide gel to determine optimal cycle number. PCR was carried out with 7-9 cycles and analyzed on an 8% TBE non-denaturing polyacrylamide gel (Invitrogen, EC61252BOX). DNA was excised from gel and extracted using DNA extraction buffer by incubating overnight with gentle shaking. DNA was recovered and precipitated in 10 mM Tris-HCl pH=8. DNA was quantified using Qubit TM 1X dsDNA High Sensitivity Assay (Invitrogen, Q33230) and quality was verified using the Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626). Samples were pooled and prepared for sequencing.               Nanopore direct RNA-seq: RNA was isolated from ribosome profiling lysate buffer lysates using Direct-zol RNA Kit, according to manufacturer’s instruction. Nanopore direct RNA-sequencing library preparation was performed using the Direct RNA Sequencing Kit (SQK-RNA004) according to manufacturer’s instructions. Samples were loaded onto MinION flow cells (FLO-MIN114).

value: Gastruloids

value: SBR

value: mESCs/gastruloid cells


title: DO_3_1

description:
Library name: DO_3_1
dial-out nested PCR for sgRNA amplification for 120h gastruloids, Replicate 2


title: DO_2_2

description:
Library name: DO_2_2
dial-out nested PCR for sgRNA amplification for 120h gastruloids, Replicate 1


title: HIV-1, Me3, LEDGF, rep2

description:
Library name: HIV1_Me3_LEDGF_biol_repl2
HIV-1 intasome integration into H3K36Me3 chromatinized yeast DNA supplemented with 8nM LEDGF


title: HIV-1, Me3, LEDGF, rep1

description:
Library name: HIV1_Me3_LEDGF_biol_repl1
HIV-1 intasome integration into H3K36Me3 chromatinized yeast DNA supplemented with 8nM LEDGF


title: DO_2_1

description:
Library name: DO_2_1
dial-out nested PCR for sgRNA amplification for 120h gastruloids, Replicate 1


title: HIV-1, Me3, rep2

description:
Library name: HIV1_Me3_biol_repl2
HIV-1 intasome integration into H3K36Me3 chromatinized yeast DNA


title: HIV-1, Me3, rep1

description:
Library name: HIV1_Me3_biol_repl1
HIV-1 intasome integration into H3K36Me3 chromatinized yeast DNA


title: WTA_3_2

description:
Library name: WTA_3_2
scRNA-seq WTA of 120h gastruloids, CROP-seq-GFP , Replicate 2


title: HIV-1, Me0, rep3

description:
Library name: HIV1_Me0_biol_rep3
HIV-1 intasome integration into H3K36Me0 chromatinized yeast DNA


title: WTA_3_1

description:
Library name: WTA_3_1
scRNA-seq WTA of 120h gastruloids, CROP-seq-GFP , Replicate 2


title: WTA_2_2

description:
Library name: WTA_2_2
scRNA-seq WTA of 120h gastruloids, CROP-seq-GFP, Replicate 1


title: HIV-1, Me0, rep2

description:
Library name: HIV1_Me0_biol_rep2
HIV-1 intasome integration into H3K36Me0 chromatinized yeast DNA


title: HIV-1, Me0, rep1

description:
Library name: HIV1_Me0_biol_rep1
HIV-1 intasome integration into H3K36Me0 chromatinized yeast DNA


title: WTA_2_1

description:
Library name: WTA_2_1
scRNA-seq WTA of 120h gastruloids, CROP-seq-GFP, Replicate 1


title: PFV, Naked target DNA (fragmented by sonication), rep3

description:
Library name: PFV_Naked_rep3
PFV intasome integration into naked sonicated yeast DNA


title: Gast_38_120h_RNA

description:
Library name: Gast_38_4_RNA
RNA sequencing from 120h gastruloids, Replicate 3


title: Gast_38_96h_RNA

description:
Library name: Gast_38_3_RNA
RNA sequencing from 96h gastruloids, Replicate 3


title: PFV, Naked target DNA (fragmented by sonication), rep2

description:
Library name: PFV_Naked_rep2
PFV intasome integration into naked sonicated yeast DNA


title: PFV, Naked target DNA (fragmented by sonication), rep1

description:
Library name: PFV_Naked_rep1
PFV intasome integration into naked sonicated yeast DNA


title: Gast_38_72h_RNA

description:
Library name: Gast_38_2_RNA
RNA sequencing from 72h gastruloids, Replicate 3


title: Gast_38_48h_RNA

description:
Library name: Gast_38_1_RNA
RNA sequencing from 48h gastruloids, Replicate 3


title: PFV, Me3, rep2

description:
Library name: PFV_Me3_biol_rep2
PFV intasome integration into H3K36Me3 chromatinized yeast DNA


title: PFV, Me3, rep1

description:
Library name: PFV_Me3_biol_rep1
PFV intasome integration into H3K36Me3 chromatinized yeast DNA


title: Gast_37_120h_RNA

description:
Library name: Gast_37_4_RNA
RNA sequencing from 120h gastruloids, Replicate 2


title: PFV, Me0, rep1

description:
Library name: PFV_Me0_biol_rep1
PFV intasome integration into H3K36Me0 chromatinized yeast DNA


title: Gast_37_96h_RNA

description:
Library name: Gast_37_3_RNA
RNA sequencing from 96h gastruloids, Replicate 2


title: Gast_37_72h_RNA

description:
Library name: Gast_37_2_RNA
RNA sequencing from 72h gastruloids, Replicate 2


title: Pseudomonas syringae pv. phaseolicola Cunea #6_18, infected with phage pphageB21; control

city: Heverlee

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 20

department: Biosystems

institute: KU Leuven

description: Library name: Sample 6

data_processing:
Real time basecalling and demultiplexing by the Guppy software (v3.2.10) in high accuracy mode.
read processing, mapping and identification of the viral transcription start sites (TSS) and termination sites (TTS) was performed according to the ONT-cappable-seq2 automated data-analysis workflow (https://github.com/LoGT-KULeuven/ONT-cappable-seq2)
Assembly: KIL3b (KU130131), KIL5 (KU130130), pphageB21 (MZ868714.1), f2 (NC_013638), KNP (NC_047827)
Supplementary files format and content: .txt files contain information on the location and efficiency of transcription start and termination sites of the phages

organism:
Pseudomonas savastanoi pv. phaseolicola
Pseudomonas phage pphageB21

source_name: bacterial cells infected with phage

growth_protocol: An overnight culture of the bacterial host was diluted in 30 ml of fresh culture medium and grown to an OD600 of 0.3. At this point phages were added  and samples were taken throughout the entire infection cycle of the phage

extract_protocol:
All samples were pooled together and homogenized. The resulting sample was subjected to hot phenol treatment and ethanol precipitation to extract and purify the RNA
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCB109)

treatment_protocol: Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.

value: bacterial cell

value: no enrichment

tag: infection stage

value: infected with phage pphageB21


title: Gast_37_48h_RNA

description:
Library name: Gast_37_1_RNA
RNA sequencing from 48h gastruloids, Replicate 2


title: Pseudomonas syringae pv. phaseolicola Cunea #6_18, infected with phage pphageB21; enriched

description: Library name: Sample 5

value: enriched for primary transcripts


title: Pseudomonas syringae pv. porri CFBP 1770, infected with phage KIL3b; control

description: Library name: Sample 2

organism:
Pseudomonas coronafaciens pv. porri
Pseudomonas phage vB_PsyM_KIL3b

value: infected with phage KIL3b


title: Gast_36_120h_RNA

description:
Library name: Gast_36_4_RNA
RNA sequencing from 120h gastruloids, Replicate 1


title: Gast_36_96h_RNA

description:
Library name: Gast_36_3_RNA
RNA sequencing from 96h gastruloids, Replicate 1


title: Pseudomonas syringae pv. porri CFBP 1770, infected with phage KIL3b; enriched

description: Library name: Sample 1


title: D2

city: Zhanjiang City

first: Xiao

state: Guangdong Province

address: No. 57 South Renmin Avenue

institute: Affiliated Hospital of Guangdong Medical University

description: Library name: D2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count and FPKM value for each Sample

source_name: early spontaneous abortion following IVF/ICSI-ET as the disease group

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: Endometrial Villi


title: D3

description: Library name: D3

value: early spontaneous abortion following IVF/ICSI-ET as the disease group


title: Resistant,Panicle,high night temperature,inoculated B.glumae,rep 1

description: Library name: R_HT_P1

value: panicle

value: B.glumae inoculation


title: Gast_36_48h_RNA

description:
Library name: Gast_36_1_RNA
RNA sequencing from 48h gastruloids, Replicate 1


title: Gast_36_72h_RNA

description:
Library name: Gast_36_2_RNA
RNA sequencing from 72h gastruloids, Replicate 1


title: D1

description: Library name: D1