title: Control 60 vs. heat 60

city: Seoul

first: Hye Yun

last: Moon

state: Seoul

address: , 221 Heukseok-dong, Dongjak-gu

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

description:
dye-swapping, total genes spotted twice on glass surface.
Control 60 (P. angusta DL1 strain, cultivated for 60min after exponential growth) vs. heat 60 (P. angusta DL1 strain, cultivated for 60min with 55 degree temperature after exponential growth)

hyb_protocol: The resultant cDNAs were purified, incubated at 80°C for 10 min and at 50°C for 20 min, and then applied to the prehybridized slide. The array was incubated in a dark humidified chamber at 43 to 53°C for 6 to 12 h.

scan_protocol: Hybridized slides were scanned with a ScanArray 5000 scanner (Packard, Billerica, CA) using the appropriate photomultiplier tube value to obtain the highest signal intensity without saturation. Using GenePix Pro 4.0 software (Axon, Foster City, CA), the spot intensity was quantified for each channel and transferred to Microsoft Excel spreadsheets.

data_processing: All arrays were analyzed by using Quintet, an R-based unified cDNA microarray data analysis system with GUI. The clustering of genes with the similar expression patterns across the time points was carried out by using the K-Means clustering program.

organism: Ogataea angusta

label_protocol: Target cDNAs were labeled with a 3DNA Submicro EX expression array detection kit (Genisphere, Hatfield, PA) as previously described. Briefly, a mixture of total RNA (50 μg) and oligo(dT) tagged with either Cy3- or Cy5-specific 3DNA capture sequence was heated at 80°C for 10 min and quickly chilled on ice for 2 to 3 min. A 5x reverse transcriptase buffer containing 0.1 mM dithiothreitol, deoxynucleoside triphosphate mixture, RNase inhibitor, and 200 U of reverse transcriptase (Invitrogen, Carlsbad, CA) was added to the mixture and incubated at 42°C for 2 h.

extract_protocol: Total RNA was isolated by hot phenol method and further purified with RNeasy mini purification kits (QIAGEN, Valencia, CA). The quality and amount of total RNA were checked by electrophoresis on 1.2% formaldehyde agarose gels and by UV/Vis spectrophotometry (serial no. 2598; NanoDrop Technology, Wilmington, DE).

treatment_protocol: DL1 were cultivated in YPD medium to exponential phase. And then the cells were exposured in 55 degree temperature and incubated for each time 15, 30, 60 min.

tag: strain

value: Control

tag: time

value: 60 min

value: Heat


title: KW939_CD4_C1

status: Public on Jul 31 2022

type: SRA

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

description: single cell

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM with default parameters. Reads aligning to features were counted from the alignment bam files with the htseq-count script from HTSeq(17) with parameters: -r pos -m union -s no. Counts were aggregated accross the 2 lanes for each cell to give the raw counts matrix
Genome_build: hg38
Supplementary_files_format_and_content: Counts matrix with raw feature counts for each cell

molecule: total RNA

organism: Homo sapiens

source_name: single cell

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation and frozen in FCS containing 10% DMSO and stored at –80°C for later use. T cells were sorted on the FACS Aria fusion (BD, USA) using CD3-PERCPCy5.5 (Biolegend, clone HIT3A), CD4-APC/Cy7 (BD Biosciences, clone RPA-T4), and CD8-Viogreen (Miltneyi Biotec, clone BW135/80). CD56-FITC (Biolegend, clone 5.1H11) was used to gate out NK cells and propidium iodide to exclude dead cells (Miltenyi Biotec).
Single cells were sorted into a 96 well plate directly into 3ul of lysis buffer. Library preparation and sequencing was performed by Oxford Genomics Centre (Oxford University, United Kingdom)
Paired end single cell sequencing using Smartseq2

treatment_protocol: Single cell RNA sequencing was performed in 3 patients on T cells isolated from 30–50 ml peripheral blood collected at two weeks after transplantation

tag: cell type

value: CD4 T


title: KW939_CD8_C1

description: single cell

value: CD8 T


title: D2 female water biol rep 6

city: Baltimore

first: Mahashweta

last: Basu

state: MD

address: 670 W. Baltimore Street

country: USA

institute: Institute for Genome Sciences

data_processing:
Samples were sequenced on an Illumina HiSeq 4000 with a 75 bp paired-end read.
An average of 64–100 million reads were obtained for each sample.
Reads were aligned to the mouse genome (Mus_musculus.GRCm38) using TopHat (version 2.0.8; maximum number of mismatches = 2; segment length = 30; maximum multi-hits per read = 25; maximum intron length = 50,000).
The number of reads that aligned to the predicted coding regions was determined using HTSeq.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Raw counts file (without normalization)
Supplementary files format and content: File is in text format with first column as gene ensemble IDs and second its counts.

organism: Mus musculus

source_name: nucleus accumbens

extract_protocol:
RNA was extracted with a DNase step (Qiagen) using the RNeasy mini kit (Qiagen #74104) by adding lysis buffer supplemented with beta mercaptoethanol.
Libraries were prepared from10ng of RNA using the Smart-Seq v4 kit (Takara).

treatment_protocol: Polyribosomes were immunoprecipitated from NAc of D1-Cre-RiboTag and A2A-Cre-RiboTag mice. four 14-gauge NAc tissue punches per mouse (4 mice pooled/sample) were collected on Day 10 of fentanyl abstinence. Tissue punches were homogenized by douncing in 1 mL homogenization buffer, and the supernatant was incubated with 5 µl anti-HA antibody (Covance #MMS-101 R) at 4ºC overnight with constant rotation. Samples were then incubated with 400 uL of protein G magnetic beads (Life Technologies #100.09D) overnight at 4ºC with constant rotation. Beads were washed in a magnetic rack with high-salt buffer.

tag: tissue

value: nucleus accumbens

tag: Sex

value: female

value: Drd2 neurons

tag: genotype

value: A2ACre x Rpl22HA

tag: treatment

value: water abstinence


title: D2 female water biol rep 4


title: D2 female water biol rep 5


title: D2 female water biol rep 3


title: Testis_ind5

city: NOUZILLY

first: Sophie

last: Fouchécourt

state: FRANCE

address: Centre Val de Loire

country: France

institute: INRA

data_processing:
control quality with FastQC software
alignment with STAR software (version 2.604a) on annotated exons
counting with featureCounts software (version 1.6.3)
differentially expressed gene analysis using SARTools-DESeq2 R package (Varet et al, 2016, PloS one, 11(6):e0157022)
Genome_build: Genome Reference Consortium Chicken Build 6a/GCA 00002315.5 (https://www.ncbi.nlm.nih.gov/genome/111?genome_assembly_id=451987)
Supplementary_files_format_and_content: featureCounts matrix table

organism: Gallus gallus

source_name: individual 5_Testis

extract_protocol:
Total RNA was isolated from frozen tissues using Macherey-Nagel Nucleo-Spin® RNA kit according to the manufacturer’s instructions and  mRNA were selected using poly-T beads
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA sample prep kit
RNA-seq experiments (paired-end read length of 2x150 pb) have been performed on an Illumina NovaSeq 6000 with the Illumina NovaSeq 6000 sequencing kits

tag: breed

value: Leghorn

tag: individual id

value: individual 5

tag: age

value: male

value: Testis


title: Lung_ind5

source_name: individual 5_Lung

value: Lung


title: KW939_CD8_B1

description: single cell


title: KW939_CD4_B1

description: single cell


title: D2 female water biol rep 1


title: D2 female fentanyl biol rep 5

value: fentanyl abstinence


title: Muscle_ind5

source_name: individual 5_Muscle

value: Muscle


title: D2 female fentanyl biol rep 4


title: D2 female fentanyl biol rep 3


title: KW939_CD8_A1

description: single cell


title: D2 female fentanyl biol rep 2


title: KW939_CD4_A1

description: single cell


title: Control 15 vs. heat 15

type: RNA

description:
dye-swapping, total genes spotted twice on glass surface.
Control 15 (P. angusta DL1 strain, cultivated for 15min after exponential growth) vs. heat 15 (P. angusta DL1 strain, cultivated for 15min with 55 degree temperature after exponential growth)

value: Control

value: 15 min


title: KW939_CD8_H12

description: single cell


title: D2 female fentanyl biol rep 1


title: D2 male water biol rep 6


title: Control 30 vs. heat 30

description:
dye-swapping, total genes spotted twice on glass surface.
Control 30 (P. angusta DL1 strain, cultivated for 30min after exponential growth) vs. heat 30 (P. angusta DL1 strain, cultivated for 30min with 55 degree temperature after exponential growth)

value: 30 min

value: Heat


title: D2 female water biol rep 2


title: D2 male water biol rep 5


title: Kidney_ind5

source_name: individual 5_Kidney

value: Kidney


title: D2 female fentanyl biol rep 6

value: nucleus accumbens


title: Intestine_ind5

source_name: individual 5_Intestine

value: Intestine


title: P1_SClysatecontrol_F12

description: single cell

value: single cell lysate from non-control wells


title: D2 male water biol rep 2

value: Drd2 neurons

value: A2ACre x Rpl22HA


title: D2 male water biol rep 3

value: water abstinence


title: Brain_ind5

source_name: individual 5_Brain

value: Leghorn

value: individual 5

value: Brain


title: Heart_ind5

source_name: individual 5_Heart

value: male

value: Heart


title: KW939_CD8_F12

description: single cell

value: CD8 T


title: KW939_CD8_G12

description: single cell


title: Testis_ind4

source_name: individual 4_Testis

value: individual 4

value: Testis


title: Liver_ind5

source_name: individual 5_Liver

value: Liver


title: D2 male fentanyl biol rep 6

value: fentanyl abstinence


title: KW939_CD8_E12

description: single cell


title: D2 male fentanyl biol rep 2


title: HD1_CD8_100_D12

description: single cell


title: D2 male fentanyl biol rep 4


title: D2 male fentanyl biol rep 3


title: D2 male fentanyl biol rep 1


title: D2 male fentanyl biol rep 5


title: D1 female water biol rep 6

value: female

value: Drd1 neurons

value: Drd1Cre x Rpl22HA


title: Lung_ind4

source_name: individual 4_Lung

value: Lung


title: D1 female water biol rep 5

value: nucleus accumbens


title: Muscle_ind4

source_name: individual 4_Muscle

value: Muscle


title: Liver_ind4

source_name: individual 4_Liver


title: D1 female water biol rep 4

value: water abstinence


title: D1 female water biol rep 3


title: D2 male water biol rep 1

value: Drd2 neurons

value: A2ACre x Rpl22HA


title: KW939_CD8_100_C12

description: single cell


title: D2 male water biol rep 4


title: KW939_CD4_100_C12

description: single cell

value: CD4 T


title: KW939_CD8_B12

description: single cell


title: Intestine_ind4

source_name: individual 4_Intestine

value: Leghorn

value: male

value: Intestine


title: Kidney_ind4

source_name: individual 4_Kidney

value: individual 4

value: Kidney


title: D1 female fentanyl biol rep 6


title: D1 female water biol rep 2


title: D1 female fentanyl biol rep 4


title: Brain_ind4

source_name: individual 4_Brain

value: Brain


title: D1 female water biol rep 1


title: D1 female fentanyl biol rep 5

value: fentanyl abstinence


title: D1 female fentanyl biol rep 3

value: female


title: KW939_CD4_B12

description: single cell

source_name: single cell


title: D1 female fentanyl biol rep 1

source_name: nucleus accumbens

value: Drd1 neurons


title: D1 female fentanyl biol rep 2

value: Drd1Cre x Rpl22HA


title: KW939_CD8_A12

description: single cell

value: CD8 T


title: HD1_CD4_100_D12

description: single cell


title: Testis_ind3

source_name: individual 3_Testis

value: individual 3

value: Testis


title: D1 male water biol rep 4

value: nucleus accumbens

value: water abstinence


title: Heart_ind4

source_name: individual 4_Heart

value: Heart


title: KW939_CD4_A12

description: single cell

value: CD4 T


title: D1 male water biol rep 3


title: Muscle_ind3

source_name: individual 3_Muscle

value: Leghorn

value: Muscle


title: D1 male water biol rep 6

value: male


title: KW939_CD4_F11

description: single cell


title: D1 male water biol rep 5


title: D1 male fentanyl biol rep 4


title: Lung_ind3

source_name: individual 3_Lung

value: Lung


title: KW939_CD4_G11

description: single cell


title: KW939_CD4_E11

description: single cell


title: KW939_CD4_H11

description: single cell


title: UREΔ/+;Tet2-/-_oxBS8

city: Bronx

first: Britta

last: Will

state: NY

address: 1300 Morris Park Avenue, Chanin Bldg., Rm. #401

department: Cell Biology

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
library strategy: OxBS-seq (Oxidative bisulfite sequencing)
adapters were trimmed from fastq files using trim_galore 0.4.0 with default parameters
reads were aligned to the PhiX RTA genome using bowtie2 with parameters: -N 1   Mapped reads were filtered away.
bisulfite mapping was performed with Bismark version 0.14.5 using default parameters.
Duplicate reads were marked with picard-tools 1.92.
number of methylated reads were counted  at each loci with mpileup2methylation.py
Genome_build: mm10
Supplementary_files_format_and_content: The output files are in bedGraph-like format with columns:  Chromosome, Position of C (0-based), Position of C +1, Percentage reads methylated, Count methylated reads, Total read count, Strand

molecule: genomic DNA

extract_protocol:
Total bone marrow cells were isolated from the femurs, tibiae, pelvic bones and spines of mice and were treated with 1x ACK lysing buffer pH 7.4 to lyse the red blood cells. cKit+ Lymph- Ery- cells were  FACS-purified and gDNA was extracted using the Puregene Cell and Tissue kit (Qiagen)
oxBS-seq library construction was performed using the Ovation Ultralow Methyl-Seq with TrueMethyl oxBS kit and the M01320 v10 manual (Nugen/Tecan)

value: bone marrow

value: cKit+ Lymph- Ery- HSPC

tag: disease state

value: AML

tag: ure

value: HET

value: KO


title: Heart_ind3

source_name: individual 3_Heart


title: D1 male fentanyl biol rep 3

value: Drd1 neurons

value: Drd1Cre x Rpl22HA

value: fentanyl abstinence


title: D1 male water biol rep 1


title: Kidney_ind3

source_name: individual 3_Kidney

value: individual 3

value: Kidney


title: KW939_CD4_D11

description: single cell


title: D1 male fentanyl biol rep 6

value: nucleus accumbens


title: D1 male fentanyl biol rep 2


title: KW939_CD8_D11

description: single cell

value: CD8 T


title: D1 male fentanyl biol rep 1


title: URE+/+;Tet2-/-_oxBS4

value: Normal

value: WT


title: Liver_ind3

source_name: individual 3_Liver

value: Leghorn

value: Liver


title: URE+/+;Tet2+/-_oxBS3


title: D1 male fentanyl biol rep 5

value: male


title: P2_SClysatecontrol_F11

description: single cell

value: single cell lysate from non-control wells


title: D1 male water biol rep 2

value: water abstinence


title: UREΔ/+;Tet2+/+_oxBS2

value: bone marrow

value: cKit+ Lymph- Ery- HSPC


title: Brain_ind3

source_name: individual 3_Brain

value: Brain


title: Testis_ind2

value: Testis


title: URE+/+;Tet2+/+_oxBS1


title: UREΔ/+;Tet2-/-_BS8

data_processing:
adapters were trimmed from fastq files using trim_galore 0.4.0 with default parameters
reads were aligned to the PhiX RTA genome using bowtie2 with parameters: -N 1   Mapped reads were filtered away.
bisulfite mapping was performed with Bismark version 0.14.5 using default parameters.
Duplicate reads were marked with picard-tools 1.92.
number of methylated reads were counted  at each loci with mpileup2methylation.py
Genome_build: mm10
Supplementary_files_format_and_content: The output files are in bedGraph-like format with columns:  Chromosome, Position of C (0-based), Position of C +1, Percentage reads methylated, Count methylated reads, Total read count, Strand

value: AML

value: HET

value: KO


title: Muscle_ind2

source_name: individual 2_Muscle

value: individual 2

value: Muscle


title: UREΔ/+;Tet2+/-_BS6


title: KW939_CD4_B11

description: single cell

value: CD4 T


title: Kidney_ind2

value: individual 3

value: Kidney


title: UREΔ/+;Tet2+/-_oxBS6


title: KW939_CD8_C11

description: single cell

value: CD8 T


title: UREΔ/+;Tet2+/-_oxBS5


title: UREΔ/+;Tet2+/-_BS5


title: Intestine_ind3

source_name: individual 3_Intestine

value: Leghorn

value: Intestine


title: UREΔ/+;Tet2+/+_BS2

value: Normal

value: WT


title: KW939_CD4_A11

description: single cell


title: Lung_ind2

source_name: individual 2_Lung

value: male

value: Lung


title: UREΔ/+;Tet2-/-_oxBS7

value: bone marrow

value: cKit+ Lymph- Ery- HSPC


title: UREΔ/+;Tet2-/-_BS7

value: AML


title: KW939_CD8_B11

description: single cell


title: Liver_ind2

source_name: individual 2_Liver

value: Liver


title: URE+/+;Tet2+/+_BS1


title: KW939_CD4_C11

description: single cell


title: FCH7HF7CCX2_L7_CHKPE85219100041 URE  /+;Tet2-/-

data_processing:
Reads were pre-processed with bbduk.sh from the BBTools suite (adapter removal and quality trimming), aligned to GRCm38 with bowtie2 (v. 2.4.1) with the parameters --no-mixed --no-discordant --very-sensitive -k 10 -X 2000, and duplicates were removed with samblaster (v.0.1.26). Mitochondrial reads were removed with sambamba (v0.7.1), and the remaining reads sorted by name using sambamba, then filtered to keep uniquely aligned read pairs using samtools (1.10.2) with the parameters -F 0x900 -f 0x0002.
Peaks were called using Genrich (v.0.6), excluding the blacklisted regions from ENCODE mm10 (https://www.encodeproject.org/files/ENCFF547MET/). Individual peaks were called in the leukemic and non-leukemic samples and the union of the peaks from both groups was used as potential peaks to perform differential testing within the csaw framework (peaks called by local enrichment), as previously described (Reske et al., 2020).
Alternatively, csaw from Bioconductor 3.11 was used to identify significant enrichment in cis-regulatory elements from the Integrative and Discriminative Epigenome Annotation System (IDEAS) database from the Validated Systematic IntegratiON (VISION) project (Xiang et al., 2020). In that case, peaks were normalized using csaw loess-normalization at FDR < 0.001.
Genome_build: GRCm38
Supplementary_files_format_and_content: matrix; logFC column represents the score column and logCPM represents the signalValue column.

source_name: Bone marrow

extract_protocol:
Total bone marrow cells were isolated from the femurs, tibiae, pelvic bones and spines of mice and were treated with 1x ACK lysing buffer pH 7.4 to lyse the red blood cells. cKit+ Lymph- Ery- cells were  FACS-purified and gDNA was extracted using the Puregene Cell and Tissue kit (Qiagen)
ATACseq library construction was performed as previously described (Corces et al 2017)

value: HET

value: KO


title: URE+/+;Tet2+/-_BS3


title: FCH7HF7CCX2_L6_CHKPE85219100040 URE  /+;Tet2-/-


title: Heart_ind2

source_name: individual 2_Heart

value: individual 2

value: Heart


title: KW939_CD4_H10

description: single cell

value: CD4 T


title: KW939_CD8_A11

description: single cell


title: KW939_CD4_G10

description: single cell


title: URE+/+;Tet2-/-_BS4


title: Intestine_ind2

source_name: individual 2_Intestine


title: Brain_ind2

source_name: individual 2_Brain

value: Brain


title: FCH7HF7CCX2_L6_CHKPE85219100038 URE  /+;Tet2+/-


title: Kidney_ind1

source_name: individual 1_Kidney

value: individual 1

value: Kidney


title: FCH7HF7CCX2_L7_CHKPE85219100039 URE  /+;Tet2+/-


title: KW939_CD8_H10

description: single cell

source_name: single cell

value: CD8 T


title: KW939_CD8_G10

description: single cell


title: FCH7HF7CCX2_L8_CHKPE85219100037 URE+/+;Tet2-/-

value: Normal


title: Lung_ind1

source_name: individual 1_Lung

value: Leghorn


title: Muscle_ind1

source_name: individual 1_Muscle

value: male

value: Muscle


title: Testis_ind1

source_name: individual 2_Testis

value: Testis


title: FCH7HF7CCX2_L8_CHKPE85219100036 URE+/+;Tet2+/-

value: cKit+ Lymph- Ery- HSPC

value: WT


title: KW939_CD8_F10

description: single cell


title: FCH7HF7CCX2_L7_CHKPE85219100035 URE  /+;Tet2+/+


title: KW939_CD4_E10

description: single cell


title: KW939_CD4_F10

description: single cell


title: FCH7HF7CCX2_L6_CHKPE85219100034 URE+/+;Tet2+/+


title: Liver_ind1

source_name: individual 1_Liver

value: Liver


title: Intestine_ind1

source_name: individual 1_Intestine

value: Intestine


title: KW939_CD8_E10

description: single cell


title: D56_R2_PE

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

institute: CNRS

description:
Biological Replica 2 for rpsAΔ56, sequenced Pair End.
Deseq2_Transcriptomics_WT-rpsAdel56.xlsx

data_processing:
Basecalling pipeline for NextSeq 500 system by Vertis, Germany.
Adapter sequences and poor quality reads removed with Trimmomatic.
Reads alignment on E. coli MG1655 genome (NC_000913.3) using BOWTIE2 (very sensitive end-to-end protocol with maximum 2 mismatches allowed).
Reads per feature counted with HTseq. The protocol chosen is interception non-empty.
Differential analysis with DEseq2.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Deseq2_Transcriptomics_WT-rpsAdel56.xlsx: Table obtained by DEseq2 reporting the Fold Changes, p-values and p-adj-values.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: D56 E. coli bacterial cells

growth_protocol: The bacteria were grown in LB at 37°C under constant agitation until DO600 = 0.4.

extract_protocol:
RNAs were extracted according to the FastRNA Pro protocol (Qbiogene).
The rRNA-depleted RNA samples (RiboZero) were fragmented with ultrasound (4 pulses of 30 sec at 4°C) followed by a treatment with antarctic phosphatase and re-phosphorylated with polynucleotide kinase (PNK). Afterwards oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). The cDNAs have a size range of 200-500 bp. The cDNA pool was either paired-end sequenced using 2x75 bp read length (Replica R2 samples) or single-end sequenced using 50 bp read length on an Illumina NextSeq 500 system.
Adapter ligation on fragmented RNA samples.


title: KW939_CD8_D10

description: single cell


title: Heart_ind1

source_name: individual 1_Heart


title: D56_R1_SE

description:
Biological Replica 1 for rpsAΔ56, sequenced Single End.
Deseq2_Transcriptomics_WT-rpsAdel56.xlsx


title: WT_R2_PE

description:
Biological Replica 2 for WT, sequenced Pair End.
Deseq2_Transcriptomics_WT-rpsAdel56.xlsx

source_name: WT E. coli bacterial cells


title: Brain_ind1

source_name: individual 1_Brain


title: WT_R1_SE

description:
Biological Replica 1 for WT, sequenced Single End.
Deseq2_Transcriptomics_WT-rpsAdel56.xlsx


title: KW939_CD8_C10

description: single cell


title: KW939_CD4_C10

description: single cell


title: KW939_CD4_D10

description: single cell


title: HU086-HU089-K562-WT-IAA-EdU

city: Beijing

first: Zhengrong

last: Zhangding

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description: for identification of early replication regions

data_processing:
Library strategy: Nail-seq
The "RepFind" pipeline was applied as described in  Liu et al., 2021.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage

source_name: cultured cell

growth_protocol: The authenticated K562 cells (3111C0001CCC000039, National Infrastructure of Cell line resource, China) were cultured in the RPMI1640 with 15% FBS as described.

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation of BrdU (by antibody on Protein G beads) and then EdU (by streptavidin beads).
After on-beads ligation, purified DNA was tagged with Illumina sequencing primers and sequenced on Hi-seq, 2×150 bp.
Nail-seq (Liu et al., 2021)

treatment_protocol:
cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 3h, labelled by EdU and then BrdU, each for 15 min and purified EdU-enriched DNA
EdU-and-BrdU labeling, G1-arrested WT or RAD21-depleted cells were released into fresh medium for 3 or 4 hours, respectively.Then, cells were labeled by 20 uM EdU for 15 min, washed with pre-warmed fresh medium, and then incubated with 50 uM BrdU for 15 min. Of note, Dox and IAA persisted in the medium during release and labeling with nucleoside analogs. After that, cells were thoroughly washed by ice-cold PBS and subjected to FACS purification of RAD21-depletion cells.

tag: cell line

tag: clone

tag: label

value: EdU


title: High OD= 1.0 rep2

city: Braunschweig

first: Yi-Hui

last: Lai

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Raw reads were saved in FASTQ format. Quality control   and adapter clipping were done using fastq-mcf tool of ea-utils
Sequenced reads were then mapped to  whole genome  of E. coli strain BW25113 (genebank: CP009273.1)using Rockhopper
The raw counts of reads were normalized diﬀerential expression analysis were performed with the R   package-limma (version 3.42.2)
Genome_build: E. coli BW25113
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Escherichia coli

source_name: Escherichia coli BW25113

growth_protocol: Overnight cultures were grown in iron-limited MHB medium at 37 °C.

extract_protocol:
RNA was extracted by applying the RNAeasy Mini Kit (Qiagen cat. 74104) and followed by the DNase   treatment (Qiagen cat. 79254). Total RNA quality and integrity were assessed using the 5200   Fragment Analyzer System (Agilent Technologies). By applying NEBNext® Ultra™ II   Directional RNA Library Prep Kit (New England BioLabs), total RNA library was generated from   1 mg total RNA after rRNA depletion through Ribo-off rRNA Depletion Kit (Bacteria) (Vazyme   BioTech Co.Ltd.).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bacterial pellets were treated with LP-600 at the concentration of 0.0625, 128 µg/ml or DMSO as vehicle control and were harvested at OD 600= 0.5 or 1.0.

value: High-dose

tag: time-point


title: High OD= 1.0 rep3


title: HU086-HU089-K562-Rad21-mAC-4-IAA-EdU

treatment_protocol:
cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 4h, labelled by EdU and then BrdU, each for 15 min and sorted for mClover-negative cells,  purified genomic DNA and enriched EdU-labelled DNA
EdU-and-BrdU labeling, G1-arrested WT or RAD21-depleted cells were released into fresh medium for 3 or 4 hours, respectively.Then, cells were labeled by 20 uM EdU for 15 min, washed with pre-warmed fresh medium, and then incubated with 50 uM BrdU for 15 min. Of note, Dox and IAA persisted in the medium during release and labeling with nucleoside analogs. After that, cells were thoroughly washed by ice-cold PBS and subjected to FACS purification of RAD21-depletion cells.

value: RAD21-mAID-mClover (RAD21-depleted)


title: Low OD= 1.0 rep3

value: Low-dose


title: HU086-HU089-K562-WT-IAA-BrdU

treatment_protocol:
cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 3h, labelled by EdU and then BrdU, each for 15 min and purified BrdU-enriched DNA
EdU-and-BrdU labeling, G1-arrested WT or RAD21-depleted cells were released into fresh medium for 3 or 4 hours, respectively.Then, cells were labeled by 20 uM EdU for 15 min, washed with pre-warmed fresh medium, and then incubated with 50 uM BrdU for 15 min. Of note, Dox and IAA persisted in the medium during release and labeling with nucleoside analogs. After that, cells were thoroughly washed by ice-cold PBS and subjected to FACS purification of RAD21-depletion cells.

value: BrdU


title: KW939_CD8_B10

description: single cell


title: High OD= 1.0 rep1


title: HU086-HU089-K562-Rad21-mAC-4-IAA-BrdU

treatment_protocol:
cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 4h, labelled by EdU and then BrdU, each for 15 min and sorted for mClover-negative cells,  purified genomic DNA and enriched BrdU-labelled DNA
EdU-and-BrdU labeling, G1-arrested WT or RAD21-depleted cells were released into fresh medium for 3 or 4 hours, respectively.Then, cells were labeled by 20 uM EdU for 15 min, washed with pre-warmed fresh medium, and then incubated with 50 uM BrdU for 15 min. Of note, Dox and IAA persisted in the medium during release and labeling with nucleoside analogs. After that, cells were thoroughly washed by ice-cold PBS and subjected to FACS purification of RAD21-depletion cells.


title: HU086-HU089-K562-Rad21-mAC-1-IAA-EdU


title: KW939_CD4_B10

description: single cell

value: CD4 T


title: EdUHU-K562-WT+IAA-RPKM-rmblacklist-1k.bw

data_processing:
The "RepFind" pipeline was applied as described in  Liu et al., 2021.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation of EdU.
After on-beads ligation, purified DNA was tagged with Illumina sequencing primers and sequenced on Hi-seq, 2×150 bp.
Nail-seq (Liu et al., 2021)

treatment_protocol:
cells were treat with CDK4/6 inhibitor for 42h, at 24h and 6h prior to release, dox and IAA were added respectively, cells were released into EdU/HU/DOX/IAA for 24h, and mClover negative cells were sorted for NAIL-seq libraries
cells were treat with CDK4/6 inhibitor for 42h, at 24h and 6h prior to release, dox and IAA were added respectively, cells were released into EdU/HU/DOX/IAA for 24h, and mClover negative cells were sorted for NAIL-seq libraries


title: HU086-HU089-K562-Rad21-mAC-1-IAA-BrdU


title: Low OD= 1.0 rep2


title: Low OD= 1.0 rep1


title: KW939_CD8_A10

description: single cell


title: HU090_B24_K562_RAD21-mAC_4_IAA_G1_antiMCM5_ChIP-input

description: Comparing the disribution of chromatin-bound MCM5 after RAD21 depletion.

data_processing:
Trimmed the adapter sequences in the reads using cutadapt
Aligned reads to the human genome(assembly hg19) using BWA-MEM
The bigwig files were generated using bamCoverage with RPKM normalization
Signals were normalized to fold change defined by the ratio of ChIP-ed signals over input signals by bigwigCompare
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing signal of MCM ChIP-seq and fold-change of ChIP-ed sample to input.

extract_protocol:
Collected cells were fixed by 1% formaldehyde (Sigma, F1635, fresh-made) for 10 min at 25oC and quenched by 125 mM glycine (VWR-amerasco 0167) for 5 min. Thoroughly washed by PBS, cells were lysed on ice for 15 min with ice-cold NP40 lysis buffer (10 mM Tris-HCl, pH 7.5; 150 mM NaCl; 0.05% NP40) supplied with protease inhibitors (PIs) (Bimake, B14012). The nuclei fraction was isolated, washed by PBS/1 mM EDTA, and then lysed with glycerol buffer (20 mM Tris-HCl, pH 8.0; 75 mM NaCl; 0.5 mM EDTA; 0.85 mM DTT; 50% glycerol) and nuclei lysis buffer (10 mM HEPES, pH 7.6; 1 mM DTT; 7.5 mM MgCl2; 0.2 mM EDTA; 0.3 M NaCl; 1 M urea; 1% NP40). The chromatin was pelleted by centrifuge, washed twice by PBS/1 mM EDTA, and eventually suspended in sonication buffer (20 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM EDTA; 0.1% SDS; 1% Triton X-100; 4 mM CaCl2) with PIs. Chromatin fractions were then treated with 50 U MNase (NEB, M2047S) for 10-12 min at 37oC, and the digestion was quenched by adding 5 mM EGTA and 5 mM EDTA. After that, pre-digested chromatin was sonicated by a Biorupter (Energy: High; On: 30 s; Off: 60 s; 15 cycles; 4oC). 30 mL of soluble chromatin fraction was kept as input and the rest was subjected to ChIP analysis.
For ChIP-seq, an antibody against  MCM5 (1:50; Abcam, ab75975) was incubated with the soluble chromatin fraction for 2 hours at 4oC. 40 mL protein G dynabeads (Invitrogen, 10003D) were then added overnight. Next, beads were sequentially washed by high-salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.0) for twice, LiCl buffer (0.25 M LiCl; 1% NP-40; 10 mM Tris-HCl; pH 8.0, 1 mM EDTA) for once, and TE buffer for three times. Chromatin bound on beads was eluted twice with elution buffer (20 mM Tris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) at 65 oC, each for 15 min. Eluate fraction was treated with RNase A (Thermo Fisher, EN0531), Proteinase K (Invitrogen, 25530015), and de-crosslinked at 65 oC overnight. Purified DNA was end-repaired, tailed with poly-dC, tagged with biotin, captured by Streptavidin C1 beads (Invitrogen, 65002), and ligated with an adapter. The beads-bound DNA was thoroughly washed, tagged with Illumina sequences, and sequenced with Hi-seq (2×150 bp).

treatment_protocol:
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.

tag: antibody

value: none (input)


title: Gene expression in MM.1S cells cultured with HA under shear stress

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

country: Japan

institute: Jichi Medical University

hyb_protocol: Labeled cRNAs were hybridized with SurePrint G3 Human Gene Expression 8x60K version 3.0 Microarray (Agilent-072363) in Agilent In Situ Hybridization buffer Kit Plus enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Arrays were scanned on an Agilent G2505C scanner. Images were quantified using the Agilent Feature Extraction Software (version 12.0.3.1).

data_processing: Agilent Feature Extraction Software (version 12.0.3.1) was used for background subtraction and LOWESS normalization.

source_name: MM.1S cells

label_protocol: RNA samples (50 ng) were primed with T7 primer at 65°C for 10 min and reversed transcribed at 40°C for 2 h in the presence of AffinityScript, followed by T7 transcription in the presence of Cy3- or Cy5-CTP at 40°C for 2 h.

growth_protocol: We cultured KMS12 and MM.1S cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted after 24 hours using Trizol according to manufacturer's instructions.

treatment_protocol: KMS12 and MM.1S cells were cultured with the conditioned medium from bone marrow stromal cells under shear stress or without shear force for 24 hours.

tag: condition

value: Cultured under shear stress

value: 24 hours in culture


title: Gene expression in KMS12 cells cultured with HA without shear stress

source_name: KMS12 cells

value: Cultured without shear stress

tag: time


title: Gene expression in MM.1S cells cultured with HA without shear stress


title: HCT116 transfected siKRT80_1

city: Kagoshima city

first: Ryutaro

last: Yasudome

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Digestive Surgery, Breast and Thyroid Surgery

institute: Kagoshima University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2600D Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 12.1.1.1

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1 (Agilent)

source_name: HCT116 transfected siKRT80_1

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: HCT116 transfected siKRT80_1


title: Gene expression in KMS12 cells cultured with HA under shear stress


title: EdUHU-K562-CTCF-mAC-5C9-RPKM-rmblacklist-1k.bedgraph

description: cells were treat with CDK4/6 inhibitor for 42h, at 24h and 6h prior to release, dox and IAA were added respectively, cells were released into EdU/HU/DOX/IAA for 24h, and mClover negative cells were sorted for NAIL-seq libraries

value: CTCF-mAID-mClover


title: Control OD= 1.0 rep3

tag: strain

value: Control


title: HU090_B23_K562_RAD21-mAC_1_IAA_G1_antiMCM5_ChIP-input


title: KW939_CD4_A10

description: single cell

tag: cell type


title: HU090_B22_K562_WT_IAA_G1_antiMCM5_ChIP-input

treatment_protocol:
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were collected and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.


title: HCT116


title: pooled liver_WT mice_HFD

city: Ann Arbor

first: Sujuan

last: Wang

state: MI

address: 2800 Plymouth Road

department: Molecular & Integrative Physiology

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse Gene 2.1 ST, and were washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460).

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.4.0

label: Biotin

source_name: pooled mice liver, WT mice after 12 weeks HFD

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: All mice are housed on a 12 hours:12 hours light/dark cycle at 25℃ with free access to water and regular chow (26.8% kcal from protein, 16.6% kcal from fat, and 56.4% kcal from starch).

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and chloroform.

treatment_protocol: At the age of 2 months, WT and E4bp4-LKO male mice were fed high-fat diet for 12 weeks.

tag: gender

value: male

tag: tissue

value: liver


title: HCT116 transfected siKRT80_2

source_name: HCT116 transfected siKRT80_2

tag: treatment

value: HCT116 transfected siKRT80_2


title: pooled liver_E4bp4-LKO mice_HFD

source_name: pooled mice liver, E4bp4-LKO mice after 12 weeks HFD

tag: genotype


title: HU090_B21_K562_RAD21-mAC_4_IAA_G1_antiMCM5_ChIP

treatment_protocol:
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover-negative cells were sorted and then subjected to ChIP-seq procedure with MCM5 antibody(Abcam, ab75975).
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.

value: MCM5 antibody(Abcam, ab75975)


title: KW939_CD4_H9

description: single cell

source_name: single cell


title: HU090_B20_K562_RAD21-mAC_1_IAA_G1_antiMCM5_ChIP


title: HU088-K562-WT-IAA-repeat2-24h-EdU-S4, rep2

description: Depicting replication timing in K562 WT cells.

data_processing:
Library strategy: NAIL-seq
Following NAIL-seq "RepFind" pipeline as described in Liu et al., 2021
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, bedgraph (S50 curve of WT replicates 1 and 2) files

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation EdU (by streptavidin beads).
Following NAIL-seq protocol as described in Liu et al., 2021

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S4 fraction with Hoechest

value: WT

tag: fraction


title: HU090_B19_K562_WT_IAA_G1_antiMCM5_ChIP

treatment_protocol:
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were collected and then subjected to ChIP-seq procedure with MCM5 antibody(Abcam, ab75975).
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.


title: Control OD= 1.0 rep2


title: HU088-K562-WT-IAA-repeat2-24h-EdU-S3, rep2

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S3 fraction with Hoechest


title: Control OD= 1.0 rep1


title: KW939_CD4_G9

description: single cell

treatment_protocol: Single cell RNA sequencing was performed in 3 patients on T cells isolated from 30–50 ml peripheral blood collected at two weeks after transplantation


title: HU088-K562-WT-IAA-repeat2-24h-EdU-S1, rep2

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S1 fraction with Hoechest


title: High OD= 0.5 rep3

value: High-dose


title: HU088-K562-WT-IAA-repeat2-24h-EdU-S2, rep2

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S2 fraction with Hoechest


title: KW939_CD8_G9

description: single cell

value: CD8 T


title: HU088-K562-WT-IAA-repeat2-24h-EdU-G2, rep2

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the G2 fraction with Hoechest


title: High OD= 0.5 rep2

treatment_protocol: Bacterial pellets were treated with LP-600 at the concentration of 0.0625, 128 µg/ml or DMSO as vehicle control and were harvested at OD 600= 0.5 or 1.0.


title: KW939_CD4_F9

description: single cell


title: HU088-K562-WT-IAA-repeat2-24h-EdU-G1, rep2

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the G1 fraction with Hoechest


title: HU088-K562-WT-IAA-repeat1-24h-EdU-S4, rep1


title: High OD= 0.5 rep1


title: KW939_CD8_F9

description: single cell


title: HU088-K562-WT-IAA-repeat1-24h-EdU-S1, rep1


title: HU088-K562-WT-IAA-repeat1-24h-EdU-G1, rep1


title: HU088-K562-WT-IAA-repeat1-24h-EdU-S3, rep1


title: Low OD= 0.5 rep2

value: Low-dose


title: Low OD= 0.5 rep3


title: HU088-K562-WT-IAA-repeat1-24h-EdU-G2, rep1


title: HU088-K562-WT-IAA-repeat1-24h-EdU-S2, rep1


title: KW939_CD8_E9

description: single cell


title: KW939_CD8_H9

description: single cell


title: KW939_CD4_D9

description: single cell


title: KW939_CD8_D9

description: single cell


title: HU085_B22_PRO_seq_K562_RAD21_mAC_4_IAA_G1

description: Comparing the expression difference of WT and RAD21-depleted cells

data_processing:
Library strategy: PRO-seq
The adapter sequences on R1 and R2 were trimmed using cutadapt.
Reads were aligned to a combined genome (assembly hg19 combined with dm6) using bowtie.
Duplicates or reads with multiple alignments, and reads in the blacklist regions were removed.
Reads uniquely aligned to hg19 were normalized by the spike-in reads with a normalization factor measured by 1000000 / (the number of reads aligned to the dm6 genome).
Genome_build: combined genome (assembly hg19 combined with dm6)
Supplementary_files_format_and_content: bigwig files containing transcription signal.

extract_protocol:
Cell nuclears were isolated and subjected to nuclear run-on for PRO-seq libraries as described in Mahat et al., 2016.
Following PRO-seq description in Mahat et al., 2016.

treatment_protocol:
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to nuclear run-on following the PRO-seq procedure.
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to nuclear run-on following the PRO-seq procedure.

value: RAD21-mAID-mClover (RAD21-depleted)

value: nascent RNA


title: HU085_B21_PRO_seq_K562_RAD21_mAC_1_IAA_G1


title: Low OD= 0.5 rep1


title: HU085_B18_PRO_seq_K562_WT_IAA_replicate2_G1

treatment_protocol:
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were collected and then subjected to nuclear run-on following the PRO-seq procedure.
Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to nuclear run-on following the PRO-seq procedure.


title: Control OD= 0.5 rep3


title: HU085_B17_PRO_seq_K562_WT_IAA_replicate1_G1


title: Control OD= 0.5 rep2


title: HU088_K562_WT_IAA_repeat2_c_MYC

data_processing:
Library strategy: PEM-seq
Followed the PEM-Q pipeline described in Liu et al., 2021
Genome_build: hg19
Supplementary_files_format_and_content: tab file (The .tab file is a new result file that have been stated in Liu et al., 2021 with PEM-Q pipeline. Briefly, it is a new version of file that contains the translocation information identified by PEM-seq, including the position and sequence of prey. In addition, it also contains the insertion and deletion information induced by Cas9 cutting.)

extract_protocol: Followed the PEM-seq protocol that described in Yin et al., 2019.

treatment_protocol:
The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) cells.
The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: KW939_CD8_C9

description: single cell

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM with default parameters. Reads aligning to features were counted from the alignment bam files with the htseq-count script from HTSeq(17) with parameters: -r pos -m union -s no. Counts were aggregated accross the 2 lanes for each cell to give the raw counts matrix
Genome_build: hg38
Supplementary_files_format_and_content: Counts matrix with raw feature counts for each cell


title: HU088_K562_WT_IAA_repeat1_c_MYC


title: HU088_K562_WT_IAA_repeat3_TP53


title: Control OD= 0.5 rep1


title: KW939_CD4_E9

description: single cell

value: CD4 T


title: KW939_CD4_C9

description: single cell


title: HU088_K562_WT_IAA_repeat2_TP53


title: KW939_CD8_B9

description: single cell


title: HU088_K562_WT_IAA_repeat1_TP53


title: HU088_K562_WT_IAA_repeat3_c_MYC


title: HU088_K562_RAD21_mAC_4_IAA_repeat3_c_MYC

treatment_protocol:
The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.
The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: HU088_K562_RAD21_mAC_4_IAA_repeat2_c_MYC


title: HU088_K562_RAD21_mAC_4_IAA_repeat3_TP53


title: HU088_K562_RAD21_mAC_4_IAA_repeat1_c_MYC


title: HU088_K562_RAD21_mAC_4_IAA_repeat2_TP53


title: KW939_CD4_B9

description: single cell


title: KW939_CD8_A9

description: single cell


title: KW939_CD4_A9

description: single cell


title: KW939_CD4_H8

description: single cell


title: HU088_K562_RAD21_mAC_4_IAA_repeat1_TP53


title: HU088_K562_RAD21_mAC_1_IAA_repeat2_c_MYC


title: Spleen ILC1, control, rep3

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality check, removal of poor quality reads, and adaptor trimming of RNA sequencing reads were performed using fastp (v0.23.0).
Read data was aligned to the mouse genome (mm10) with Hisat2 (version 2.1.0)
The aligned reads were used for the transcript quantification by using featureCounts from the subread package (version 1.6.5)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen ILC1s

extract_protocol:
200 ILC1s [CD3(-)NK1.1(+)NKp46(+)CD49a(+)CD49b(lo)IL-7R(+)] and NK cells [CD3(-)NK1.1(+)NKp46(+)CD49a(-)CD49b(+)] were sorted from the liver and the spleen by BD FACSAria 3, and cells were lysed by Buffer RLT (QIAGEN). Then total RNA was harvested using Agencourt AMPure XP (Beckman Coulter) size selection beads. Takara SMART-seq HT kit (Takara Bio) was used with all extracted RNA for cDNA synthesis. Takara SMART-seq Library Prep kit (Takara Bio) was used with 1 ng of cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Takara HT Plus kit protocols

tag: age

value: Spleen


title: Spleen ILC1, RARα403, rep3

value: Ncr1-Cre; Rosa26-RARalpha403


title: vehicle_4hour_rep3

city: Toronto

first: Denise

middle: D

last: Belsham

state: ON

address: 1 Kings College Circle MSB3346

department: Physiology

country: Canada

institute: University of Toronto

hyb_protocol: Samples were quantified to assess total RNA quantity and purity and sent to The Princess Margaret Genomics Centre, Toronto, ON, Canada for hybridization, purification, immobilization and image counting according to standard procedures.

scan_protocol: standard nanostring protocol

data_processing:
Data were processed, normalized and analyzed using nSolver Analysis Software v1.0 (NanoString), by the University Health Network Microarray Centre, Toronto, ON, Canada
To calculate the normalization factor code counts were normalized to positive controls via the geometric mean method.  Then the top 100 genes and geometric mean method were used to determine the Codeset normalization factor, and  perfom final normalization of the data.

label_protocol: standard nanostring protocol

growth_protocol: The cell line was grown in high glucose 5.5 mM glucose DMEM containing 5% Fetal Bovine Serum and 1% Pencillin-Streptomycin

extract_protocol: Total RNA containing miRNAs were extracted using the mirVana miRNA isolation kit from Thermofisher Scientific (Waltham, MA, USA) Catalog Number: AM1560

treatment_protocol: mHypoE-46 cells were treated with either vehicle (PBS) or 100 nM of Insulin and harvested at both 4 hours and 24 hours afterwards to compare before and after the development of insuiln resistance in this model as described in the paper PMID:19887566

tag: Sex

value: embryonic hypothalmic neuronal cell line

tag: genotype/variation

value: expressing Neuropeptide Y/Agouti-related Peptide

value: vehicle (Phosphate Buffered Saline, PBS)

tag: time point

value: 4 hours post treatment


title: vehicle_24hour_rep3

value: male

tag: cell line

value: 24 hours post treatment


title: HU088_K562_RAD21_mAC_1_IAA_repeat3_TP53

tag: clone


title: KW939_CD8_H8

description: single cell

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation and frozen in FCS containing 10% DMSO and stored at –80°C for later use. T cells were sorted on the FACS Aria fusion (BD, USA) using CD3-PERCPCy5.5 (Biolegend, clone HIT3A), CD4-APC/Cy7 (BD Biosciences, clone RPA-T4), and CD8-Viogreen (Miltneyi Biotec, clone BW135/80). CD56-FITC (Biolegend, clone 5.1H11) was used to gate out NK cells and propidium iodide to exclude dead cells (Miltenyi Biotec).
Single cells were sorted into a 96 well plate directly into 3ul of lysis buffer. Library preparation and sequencing was performed by Oxford Genomics Centre (Oxford University, United Kingdom)
Paired end single cell sequencing using Smartseq2


title: Spleen ILC1, control, rep2


title: KW939_CD4_G8

description: single cell


title: H358-CDDP-n2

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

description: replicate 2

data_processing:
Raw reads were were aligned on the human reference genome (hg19) using STAR (version 2.5.3a) (Dobin et all, 2013).
A coverage track was generated using bamCoverage (Ramírez et al., 2016) for each alignement files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: polyA RNA

source_name: Non-small cell lung cancer cell line

growth_protocol: Cells were cultured in RPMI-1640-Glutamax medium (GibcoBRL, Life Technologies, Cergy Pontoise, France), supplemented with 10% (v/v) heat-inactivated fetal calf serum (GibcoBRL), in 5% CO2 at 37°C.

extract_protocol:
RNA from whole cells was extracted with TRIzol Reagent (ThermoFischer Scientific) according to the manufacturer’s instructions, and 1 µl of GlycoBlue (ThermoFisher Scientific) was added for RNA precipitation. RNA was treated with TURBO DNase I (ThermoFisher Scientific) and quantified using a Nanodrop 2000 spectrophotometer (ThermoFischer Scientific). For sequencing, RNA samples were analyzed using an RNA 2100 Bioanalyzer (Agilent).
Total RNA was subjected to DNAse I treatment. 500 ng of good quality RNA (RIN > 9) were used for Illumina compatible library preparation using the TruSeq Stranded total RNA protocol allowing to take into account strand information. A first step of ribosomal RNA depletion was performed using the RiboZero Gold kit (Illumina). After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. Libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche). Sequencing was carried out on the NovaSeq 6000 instrument from Illumina based on a 2*100 cycle mode (paired-end reads, 100 bases) using a S1 flow cell in order to obtain around 100 million clusters (200 million raw paired-end reads) per sample.

treatment_protocol: Treatment with cisplatin (Selleckchem, Euromedex, Souffelweyersheim, France) was done at 100 µM for 24 hours. Treatment with vehicle (DMSO) was done in parallel.

value: Cisplatin

tag: extract

value: Total cells


title: KW939_CD8_G8

description: single cell


title: Liver NK, control, rep3

source_name: Liver NK cells

value: Liver

value: NK cells


title: H358-CDDP-n1

description: replicate 1


title: insulin_4hour_rep3

value: 100 nM of Insulin


title: H358-DMSO-n1

description: replicate 1

value: Vehicle (DMSO)


title: H358-DMSO-n2

description: replicate 2


title: HU088_K562_RAD21_mAC_1_IAA_repeat3_c_MYC

value: RAD21-mAID-mClover (RAD21-depleted)


title: Liver NK, RARα403, rep3


title: KW939_CD4_F8

description: single cell


title: KW939_CD8_F8

description: single cell

value: CD8 T


title: SK-BR-3 lapatinib resistance cell

first: Daeun

last: Jeong

address: Daehak-ro 101

department: Cancer research institute

institute: Seoul National University

description: Biological replicate 1 of 1. SK-BR-3 LR cells, untreated, harvested after several passages.

data_processing:
Mapped the readers to the reference genome using the HISAT2 (v2.0.5) program considering the splice, and then creaste the alinged reads, proceeded with transcript assembly through String Tie (v1.3.3b) program using the information of reference based on aligned reads.
Take raw signal (FPKM) +1 to facilitate logarithm, and convert this value to log2 based transformation. After logarithm, it influences bilogical meaning in the comparison between samples. To reduce possible systematic bias, use quantile normalization, a sample-to-sample normalization method to correct the data (using the 'preprocessCore' R library)
Calculate the amount of expression obtained by transcript quantification of each sample as a normalization value considering transcript length and depth of coverage. The expression profile was extracted by performing within normalization with Fragment Per Kilobase of transcript per Million mapped reads (FPKM)
Genome_build: hg18
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

growth_protocol: SK-BR-3 parental cells and LR cells were grown for passages 4. RPMI with 10% fetal bovine serum and 10 μg/mlgentamicin at 37℃ in a 5% CO2/95% air humidified atmosphere.

extract_protocol:
Randomly fragmented the purified RNA for sequencing with a short read and reverse-transcribed the cleaved RNA fragment into cDNA. 6 µg of total RNA were primed with 2 µl of DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of RTase (Invitrogen), and dNTP.
Attached different adapters to both ends of the prepared cDNA fragment and ligated them. cDNA fragments were amplified with PCR. Seuencing service was provided by Macrogen Inc. Hybrid service was also provided by Macrogen.

treatment_protocol: Nothing was treated.

value: female

value: SK-BR-3 lapatinib resistance cell


title: HU088_K562_RAD21_mAC_1_IAA_repeat1_c_MYC


title: SK-BR-3 parental cell

description: Biological replicate 1 of 1. Control SK-BR-3 parental cells, untreated, harvested after several passages.

value: Control SK-BR-3 parental cell


title: Liver NK, RARα403, rep2

value: Ncr1-Cre; Rosa26-RARalpha403


title: KW939_CD4_E8

description: single cell

value: CD4 T


title: HU088_K562_RAD21_mAC_1_IAA_repeat2_TP53


title: Spleen ILC1, RARα403, rep2

value: Spleen


title: KW939_CD8_E8

description: single cell


title: HU088_K562_RAD21_mAC_1_IAA_repeat1_TP53


title: Liver ILC1, control, rep3

source_name: Liver ILC1s


title: Liver ILC1, RARα403, rep3


title: Sample_25_abdomen_RECURRENT1

city: Los Angeles

first: Michelle

last: Jones

state: CA

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description:
matrix column name
Sample_25_Recurrent

data_processing:
WGBS reads were aligned to the human reference genome (build GRCh38) using BISCUIT. Duplicate reads were marked using Picard Tools
Methylation rates were called using BISCUIT. CpGs with fewer than 5 reads of coverage were excluded from further analysis. Adapter sequences were trimmed using TrimGalore, using default parameters for Illumina sequencing platforms
Quality control was performed using PicardTools as well as MultiQC. Bisulfite non-conversion was checked using the Biscuit QC module in MultiQC
Assembly: hg38
Supplementary files format and content: Text file matrix containing methylation beta values for all CpGs with coverage >= 5 after masking for partially methylated domains as described in paper methods.
Supplementary files format and content: Text file matrix containing methylation beta values for all CpGs with coverage >= 5 WITHOUT masking for partially methylated domains as described in paper methods

source_name: ovarian cancer tumors

extract_protocol:
Fresh frozen tumors were embedded in optimal cutting temperature compound, bisected and mounted and two slides were made for hematoxylin and eosin (H&E) staining. Each punch was divided into three pieces, two of which were used for genomic DNA (gDNA) extraction using the Machery-Nagel Nucleospin DNA Kit
Libraries were constructed using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, MI), and amplified using no more than 6 cycles of PCR. Libraries were sequenced to at least 30x coverage

value: ovarian cancer tumors

tag: tumor source_tissue

value: abdomen

tag: tumor type_(primary,_recurrence)

tag: brca genotype

value: BRCA non-carrier


title: Sample_15_omentum_RECURRENT1

description:
matrix column name
Sample_15_Recurrent

value: omentum


title: Sample_22_lymph nodes_RECURRENT1

description:
matrix column name
Sample_22_Recurrent

value: lymph nodes


title: Sample_21_gallbladder_RECURRENT2

description:
matrix column name
Sample_21_Recurrent

value: gallbladder


title: Sample_25_right ovary_PRIMARY

description:
matrix column name
Sample_25_Primary

value: right ovary

value: PRIMARY


title: Sample_15_left ovary_PRIMARY

description:
matrix column name
Sample_15_Primary

value: left ovary


title: KW939_CD8_D8

description: single cell


title: Sample_21_left ovary_PRIMARY

description:
matrix column name
Sample_21_Primary


title: Liver NK, control, rep2

tag: strain

value: Liver

value: NK cells


title: KW939_CD4_D8

description: single cell

tag: cell type


title: Sample_17_brain_RECURRENT1

description:
matrix column name
Sample_17_Recurrent

value: brain


title: Sample_28_lymph nodes_RECURRENT1

description:
matrix column name
Sample_28_Recurrent


title: Sample_12_pelvic_lymph_node_RECURRENT2

description:
matrix column name
Sample_12_Recurrent

value: pelvic lymph node


title: Sample_22_left ovary_PRIMARY

description:
matrix column name
Sample_22_Primary


title: KW939_CD8_C8

description: single cell

value: CD8 T


title: Spleen ILC1, RARα403, rep1

value: Ncr1-Cre; Rosa26-RARalpha403


title: Liver ILC1, RARα403, rep2


title: Liver ILC1, control, rep2


title: KW939_CD8_B8

description: single cell


title: KW939_CD4_C8

description: single cell

value: CD4 T


title: Sample_28_left ovary_PRIMARY

description:
matrix column name
Sample_28_Primary


title: Sample_12_left ovary_PRIMARY

description:
matrix column name
Sample_12_Primary


title: Sample_20_lymph nodes_RECURRENT2

description:
matrix column name
Sample_20_Recurrent


title: Sample_17_omentum_PRIMARY

description:
matrix column name
Sample_17_Primary


title: Liver NK, control, rep1


title: Liver NK, RARα403, rep1


title: Sample_18_spleen_RECURRENT1

description:
matrix column name
Sample_18_Recurrent

value: spleen


title: Liver ILC1, RARα403, rep1


title: Sample_20_ovary_PRIMARY

description:
matrix column name
Sample_20_Primary

value: ovarian cancer tumors

value: ovary


title: KW939_CD4_A8

description: single cell


title: KW939_CD4_B8

description: single cell


title: Sample_16_bowel_RECURRENT1

description:
matrix column name
Sample_16_Recurrent

value: bowel

value: BRCA non-carrier


title: Sample_13_spleen_RECURRENT2

description:
matrix column name
Sample_13_Recurrent


title: Sample_27_right adnexa_PRIMARY

description:
matrix column name
Sample_27_Primary

value: right adnexa


title: Liver ILC1, control, rep1


title: KW939_CD4_H7

description: single cell


title: Spleen ILC1, control, rep1

value: Spleen


title: SG G1ILC, rep2

source_name: Salivary gland group 1 ILCs

extract_protocol:
2,000 IL-7R(-) ILC1s [CD3(-)NK1.1(+)NKp46(+)CD49a(+)CD49b(lo)IL-7R(-)], IL-7R(+) ILC1s [CD3(-)NK1.1(+)NKp46(+)CD49a(+)CD49b(lo)IL-7R(+)], bone marrow immature ILC1s [CD3(-)NK1.1(+)NKp46(+)CD49a(+)CD49b(lo)], bone marrow and liver NK cells [CD3(-)NK1.1(+)NKp46(+)CD49a(-)CD49b(+)], fetal liver group 1 ILCs [CD3(-)NK1.1(+)NKp46(+)CD49a(int)CD49b(int)], small intestinal lamina propria ILC1s [CD3(-)NK1.1(+)NKp46(+)CD27(+)IL-7R(+)], and salivary gland group 1 ILCs [CD3(-)NK1.1(+)NKp46(+)CD49a(+)CD49b(+)] were sorted by BD FACSAria 3, and cells were lysed by Buffer RLT (QIAGEN). Then total RNA was harvested using Agencourt AMPure XP (Beckman Coulter) size selection beads. Takara SMART-seq HT kit (Takara Bio) was used with all extracted RNA for cDNA synthesis. Takara SMART-seq Library Prep kit (Takara Bio) was used with 1 ng of cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Takara HT Plus kit protocols

value: Salivary glands

value: group 1 ILCs

value: wild type


title: Sample_13_left ovary_PRIMARY

description:
matrix column name
Sample_13_Primary

value: left ovary

value: PRIMARY


title: Sample_23_lymph nodes_RECURRENT2

description:
matrix column name
Sample_23_Recurrent

value: lymph nodes


title: SG G1ILC, rep1


title: Sample_16_right adnexa_PRIMARY

description:
matrix column name
Sample_16_Primary


title: Sample_24_colon_RECURRENT2

description:
matrix column name
Sample_24_Recurrent

value: colon


title: Sample_23_omentum_PRIMARY

description:
matrix column name
Sample_23_Primary

value: omentum


title: Sample_27_lymph nodes_RECURRENT1

description:
matrix column name
Sample_27_Recurrent


title: Sample_14_rectum_RECURRENT3

description:
matrix column name
Sample_14_Recurrent

value: rectum


title: KW939_CD8_G7

description: single cell

value: CD8 T


title: Sample_26_vagina_RECURRENT1

description:
matrix column name
Sample_26_Recurrent

value: vagina


title: LV NK, rep2

source_name: Adult liver NK cells

value: Liver

value: NK cells


title: Sample_14_right ovary_PRIMARY

description:
matrix column name
Sample_14_Primary

value: ovarian cancer tumors

value: right ovary


title: KW939_CD4_F7

description: single cell

value: CD4 T


title: KW939_CD8_A8

description: single cell


title: Sample_5_pelvis_RECURRENT3

description:
matrix column name
Sample_5a_Recurrent

value: pelvis

value: BRCA1:L598X (1912T>A) and BRCA2:8765delAG


title: KW939_CD8_F7

description: single cell


title: Sample_6_right inguinal lymph node_RECURRENT1

description:
matrix column name
Sample_6_Recurrent

value: right inguinal lymph node


title: Sample_24_right ovary_PRIMARY

description:
matrix column name
Sample_24_Primary

value: BRCA non-carrier


title: LPL ILC1, rep3

source_name: Small intestinal lamina propria ILC1s

value: Small intestinal lamina propria

value: wild type


title: KW939_CD8_H7

description: single cell


title: Sample_18_right ovary_PRIMARY

description:
matrix column name
Sample_18_Primary

value: PRIMARY


title: KW939_CD4_E7

description: single cell


title: KW939_CD8_E7

description: single cell


title: Sample_26_right ovary_PRIMARY

description:
matrix column name
Sample_26_Primary


title: LPL ILC1, rep1


title: LV NK, rep1


title: Sample_9_omentum_PRIMARY

description:
matrix column name
Sample_9_Primary


title: LPL ILC1, rep2


title: Sample_2_left ovary_PRIMARY

description:
matrix column name
Sample_2_Primary

value: left ovary

value: BRCA2:exon 11 6174delT


title: Sample_5_left ovary_PRIMARY

description:
matrix column name
Sample_5_Primary


title: KW939_CD4_G7

description: single cell


title: Sample_8_omentum_RECURRENT1

description:
matrix column name
Sample_8_Recurrent

value: omentum


title: Sample_6_pelvic lymph nodes_PRIMARY

description:
matrix column name
Sample_6_Primary

value: pelvic lymph nodes


title: Sample_4_spleen_RECURRENT1

description:
matrix column name
Sample_4_Recurrent

value: spleen


title: Sample_5_pelvis_RECURRENT1

description:
matrix column name
Sample_5_Recurrent


title: KW939_CD8_D7

description: single cell

value: CD8 T


title: Sample_10_pelvis_RECURRENT2

description:
matrix column name
Sample_10a_Recurrent


title: LPL ILC1, rep4


title: Sample_8_right ovary_PRIMARY

description:
matrix column name
Sample_8_Primary


title: Sample_3_diaphragm_RECURRENT3

description:
matrix column name
Sample_3a_Recurrent

value: diaphragm


title: Sample_3_pelvis_RECURRENT2

description:
matrix column name
Sample_3_Recurrent

value: ovarian cancer tumors


title: BM NK, rep3

source_name: Bone marrow NK cells

value: Bone marrow

value: NK cells


title: KW939_CD8_C7

description: single cell


title: Sample_6_left inguinal lymph node_RECURRENT1

description:
matrix column name
Sample_6a_Recurrent

value: left inguinal lymph node


title: KW939_CD8_A7

description: single cell


title: KW939_CD4_D7

description: single cell

value: CD4 T


title: BM NK, rep1


title: Sample_3_left ovary_PRIMARY

description:
matrix column name
Sample_3a_Primary


title: KW939_CD4_C7

description: single cell


title: Sample_4_right ovary_PRIMARY

description:
matrix column name
Sample_4_Primary

value: right ovary


title: FL G1ILC, rep1

source_name: Fetal liver group 1 ILCs

value: Fetal liver

value: group 1 ILCs


title: Sample_10_omentum_PRIMARY

description:
matrix column name
Sample_10_Primary


title: FL G1ILC, rep2

value: wild type


title: FL G1ILC, rep3


title: Sample_10_left side wall_RECURRENT1

description:
matrix column name
Sample_10_Recurrent

value: left side wall


title: Sample_3_right ovary_PRIMARY

description:
matrix column name
Sample_3_Primary

value: PRIMARY


title: KW939_CD4_B7

description: single cell


title: BM iILC1, rep2

source_name: Bone marrow immature ILC1s

value: immature ILC1s


title: Sample_1_right ovary_PRIMARY

description:
matrix column name
Sample_1a_Primary


title: Sample_1_omentum_PRIMARY

description:
matrix column name
Sample_1_Primary

value: omentum


title: FL G1ILC, rep4


title: BM NK, rep2


title: BM iILC1, rep1


title: KW939_CD8_H6

description: single cell


title: KW939_CD8_B7

description: single cell


title: Sample_11_diaphragm_PRIMARY

description:
matrix column name
Sample_11_Primary


title: 7R(+)ILC1, rep2

source_name: Adult liver IL-7R(+) ILC1s

value: Liver

value: IL-7R(+) ILC1s


title: KW939_CD4_H6

description: single cell


title: Sample_1_colon_RECURRENT2

description:
matrix column name
Sample_1a_Recurrent

value: colon


title: BM iILC1, rep3


title: Sample_19_diaphragm_RECURRENT1

description:
matrix column name
Sample_19_Recurrent

value: diaphragm

value: BRCA non-carrier


title: Sample_19_left ovary_PRIMARY

description:
matrix column name
Sample_19_Primary

value: ovarian cancer tumors

value: left ovary


title: Sample_1_rectum_RECURRENT1

description:
matrix column name
Sample_1_Recurrent

value: rectum


title: KW939_CD4_A7

description: single cell

value: CD4 T


title: RA FLS Myr2

city: Guangzhou

first: Yu

last: Kuang

state: Guangdong

address: 58 Zhongshan 2nd Road, Yuexiu District

department: Rheumatology and Immunology

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: rheumatoid fibroblast-like synoviocytes

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: treated with Myr for 24 hours


title: 7R(+)ILC1, rep1

value: wild type


title: Sample_11_abdominal wall_RECURRENT1

description:
matrix column name
Sample_11_Recurrent

value: abdominal wall


title: KW939_CD4_F6

description: single cell


title: KW939_CD8_G6

description: single cell

value: CD8 T


title: KW939_CD4_G6

description: single cell


title: Sample_9_spleen_RECURRENT3

description:
matrix column name
Sample_9_Recurrent

value: spleen


title: Sample_7_small intestine_RECURRENT2

description:
matrix column name
Sample_7_Recurrent

value: small intestine


title: 7R(+)ILC1, rep3

value: Liver


title: KW939_CD8_F6

description: single cell


title: 7R(-)ILC1, rep4

source_name: Adult liver IL-7R(-) ILC1s

value: IL-7R(-) ILC1s


title: Sample_7_left adenexa_PRIMARY

description:
matrix column name
Sample_7_Primary

value: left adenexa

value: PRIMARY


title: RA FLS Myr3


title: RA FLS Myr1


title: RA FLS DMSO3

value: untreated


title: RA FLS DMSO1


title: 7R(-)ILC1, rep3


title: KW939_CD4_E6

description: single cell


title: RA FLS DMSO2


title: KW939_CD8_E6

description: single cell


title: 7R(-)ILC1, rep2


title: 7R(-)ILC1, rep1


title: Cold_polysomal_Col0_20d_R1

city: Stillwater

first: Ramanjulu

last: Sunkar

state: OK

address: 359 Noble Research Center

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

data_processing:
Alignment was done to Col-0 reference genome/annotation file TAIR10 obtained from ensembl using STAR aligner with the following parameters :  STAR --runThreadN 10 --readFilesIn -outSAMattributes All --outSAMtype BAM SortedByCoordinate. All non-unique reads were discarded from downstream analysis.
Raw reads were counted for transcripts IDs annotated by ensembl using htseq package and parameters : htseq-count -f bam -s reverse -q -i gene_id -r pos
Mapped read coverage was split into + and minus strand fractions and macs2 callpeak was then used to call m6A peaks on each strand, respectively, using parameters --nomodel --extsize 50 genome size was set to ½ the transcriptome using -g 32542107 and with an pvalue cutoff of < 0.05. m6A peaks are provided in bedgraph format in supplementary excel file.
Genome_build: TAIR10
Supplementary_files_format_and_content: m6A peaks are presented in a narrowPeak format , raw read count files are presented as txt files.

organism: Arabidopsis thaliana

source_name: 20d seedling

growth_protocol: 20 day old Arabidopsis Seedlings were grown in 1/2 MS agar plates under 12hr dark/12 hr light condition at 22C

extract_protocol:
Following control or treatment, seedlings were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Trizol according to manufacturers instructions.
The total RNA from each sample was quantified using a NanoDrop ND-1000 instrument. The mRNAs were isolated from the total RNA samples and chemically fragmented to around 100-nt sizes. MeRIP was performed to enrich m6A methylated mRNA fragments with anti-N6-methyadenosine (m6A) antibody. The RNA-seq libraries for both the m6A immunoprecipitated RNAs and the input RNAs were prepared with a KAPA Stranded mRNA-seq Kit.
The barcoded libraries were denatured to single-stranded DNAs, captured on Illumina flow cells, amplified in situ as sequencing clusters, and sequenced for 150 cycles on Illumina HiSeq 4000 system per the manufacturer,s instructions.

treatment_protocol: Seedlings were subjected to either 4C for 24 hrs or untreated as Control.

value: whole 20d old seedling

value: 24 hr cold treated at 4C

tag: ecotype


title: Control_polysomal_Col0_20d_R1

tag: tissue


title: KW939_CD8_D6

first: Paul

last: Moss

address: Vincent Drive

institute: University of Birmingham

description: single cell


title: Control_polysomal_Col0_20d_R2

tag: treatment


title: Cold_polysomal_Col0_20d_R2


title: Control_mRNAseq_Col0_20d_R3


title: KW939_CD8_C6

description: single cell


title: P6_blank_H7

description: single cell

organism: blank sample

value: blank


title: Control_mRNAseq_Col0_20d_R2


title: P5_blank_H8

description: single cell


title: KW939_CD4_C6

description: single cell

value: CD4 T


title: KW939_CD8_B6

description: single cell


title: 24hr-KO-5pGEX

city: Daejeon

first: Jiung

address: 291, Daehak-ro, Yuseong-gu

institute: KAIST

data_processing:
Cell Ranger (10X Genomics) was used for align reads, generate gene-cell matrices and perform clustering and gene expression analysis
Samples were aligned using the mouse genome 10-3.0.0 (Mm10, 10X genomics)
Genome_build: Mm10
Supplementary_files_format_and_content: Feature, barcode, matrix

source_name: CD4+cells in spleen

growth_protocol: Ift20 f/f or Ift20 f/f CD4 cre mice were housed in specific pathogen free (SPF) facility or KAIST, Korea.

extract_protocol:
Naive CD4 T  cells or activated CD4 T cells were collected and washed with cold wash buffer, composed of DPBS, with 1% bovine calf serum and 1% penicillin-streptomycin, and stained for 30 min on ice with antibodies. Cells were stained with anti-mouse CD4-FITC, CD3-PE and 7-AAD. 7-AAD-negative, CD3-positive and CD4-positive live immune cells were sorted with FACS Aria.
library were constructed with Chromium Next GEM Single Cell 5p RNA library v1.1 (10x genomics) following manufacturer's instruction.

treatment_protocol: CD4+ T cells for T cell activation were extracted from spleens of Ift20f/f or Ift20f/f CD4cre mice. Following single cell isolation, the MagnisortTM Mouse CD4 naïve T cell Enrichment Kit (Invitrogen) was used to obtain purified naïve T cells. Naïve CD4 + T cells were activated with 1-μg/mL anti-CD3 (Invitrogen) and 1-μg/mL anti-CD28 antibodies (BioLegend) for 24 hours.

value: Spleen

value: anti-CD3 (1μg/mL) + anti-CD28  (1μg/mL) for 24hours

tag: genotype

value: Ift20 f/f CD4 cre

value: 7AAD-CD3+CD4+ cell


title: 24hr-WT-5pGEX

value: Ift20 f/f


title: 0hr-WT-5pGEX

value: DPBS


title: Papain-KO

source_name: Immune cells in lung

growth_protocol: Ift20 f/f or Ift20 f/f CD4 cre mice were housed in specific pathogen free (SPF) facility of KAIST, Korea.

extract_protocol:
Single cells were collected from mouse lung tissues and washed with cold wash buffer, composed of DPBS, with 1% bovine calf serum and 1% penicillin-streptomycin, and stained for 30 min on ice with antibodies. Cells were stained with anti-mouse CD45.2-PE and 7-AAD. 7-AAD-negative and CD45.2-positive live immune cells were sorted with FACS Aria.
library were constructed with Chromium Single Cell 3p RNA library v3 (10x genomics) following manufacturer's instruction.

treatment_protocol: Ift20 f/f or Ift20 f/f CD4 cre mice were administered 25-μg of papain intranasally for three consecutive days to sensitize them to the allergen. On day 14 after first administration of papain, mice were challenged with the same concentration of papain administered via intranasal injection. Immune cells were harvested from lung tissue on day 15.

value: Lung

value: Papain

value: CD45.2+ immune cell


title: P5_blank_G8

city: Birmingham

description: single cell

source_name: single cell


title: P3_blank_H10

description: single cell


title: KW939_CD4_D6

description: single cell


title: KW939_CD8_A6

description: single cell

value: CD8 T


title: Cold_mRNAseq_Col0_20d_R3


title: DPBS-KO


title: Papain-WT


title: Cold_mRNAseq_Col0_20d_R1


title: P3_blank_G10

description: single cell


title: Cold_mRNAseq_Col0_20d_R2


title: KW939_CD4_A6

description: single cell


title: P4_blank_H9

description: single cell


title: Control_mRNAseq_Col0_20d_R1


title: DPBS-WT


title: P6_blank_G7

description: single cell


title: TBEV_negative_for_NudC_CapClip_rep3

city: Copenhagen N

first: Jeppe

last: Vinther

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

description:
CapZyme-seq protocol
FeatureCount_TBEV_NudC_CapClip_output.txt

data_processing:
Library strategy: CapZyme-seq
Illumina bcl2fastq was used to create fastq files
Sequenced reads were trimmed for adaptor sequence (cutadapt -a AGATCGGAAGAGCACACGTCT -q 20 -m 15) and mapped to RNA sequences (viral RNA, rRNA, snoRNA, tRNA and mRNA (TPM>2) using  (bowtie2 --norc --very-sensitive)
Counts for the 5' end of different RNA were obtained using the featureCounts function from the Subread package using a SAF file specifing the first 100 nts of each RNA.
Example code for the processing of the sequencing data is available at https://github.com/jeppevinther/CapZyme
Supplementary files format and content: Tab-delimited text files include FeatureCounts output, raw counts
Supplementary files format and content: Matrix table with raw 5'  counts for every RNA (first 100nt) and every sample in experiment

organism:
Homo sapiens
Tick-borne encephalitis virus

source_name: Human SH-SY5Y cell line

extract_protocol:
RNA extraction was performed by Trizol treatment followed on-column DNase I digestion and RNA purification using RNA Clean & Concentrator kit-5
RNA was enzymatically treated with de-capping enzymes that specifically convert different 5’ cap structures to 5’ monophosphates. 5’-phosphate dependent adapter ligation was performed followed by reverse transcription. Libraries were generated using PCR with custom Illumina compatible primers.

value: Human SH-SY5Y cell line

tag: enzymatic treatment

value: negative

tag: virus

value: Tick-borne encephalitis virus

tag: molecule subtype

value: TEX treated total RNA


title: Control_MeRIP_Col0_20d_R3

value: whole 20d old seedling

value: untreated

tag: antibody

value: m6A IP


title: P4_blank_G9

description: single cell

value: blank


title: insulin_24hour_rep3

tag: Sex

value: male

value: embryonic hypothalmic neuronal cell line

tag: genotype/variation

value: expressing Neuropeptide Y/Agouti-related Peptide

value: 100 nM of Insulin

tag: time point

value: 24 hours post treatment


title: Control_MeRIP_Col0_20d_R1


title: Control_MeRIP_Col0_20d_R2


title: P1_blank_G12

description: single cell


title: TBEV_NudC_rep3

value: NudC


title: P2_blank_G11

description: single cell


title: P1_blank_H12

description: single cell


title: KW939_CD4_B6

description: single cell

value: CD4 T


title: TBEV_CapClip_rep3

value: CapClip


title: Cold_MeRIP_Col0_20d_R2

value: 24 hr cold treated at 4C


title: TBEV_negative_for_NudC_CapClip_rep2

value: Human SH-SY5Y cell line


title: vehicle_4hour_rep2

tag: cell line

value: vehicle (Phosphate Buffered Saline, PBS)

value: 4 hours post treatment


title: TBEV_NudC_rep2

value: Tick-borne encephalitis virus

value: TEX treated total RNA


title: insulin_4hour_rep2


title: Cold_MeRIP_Col0_20d_R3

value: whole 20d old seedling


title: TBEV_CapClip_rep2


title: Cold_MeRIP_Col0_20d_R1

value: m6A IP


title: P2_blank_H11

description: single cell

value: blank


title: vehicle_24hour_rep2

value: male


title: vehicle_4hour_rep1

value: embryonic hypothalmic neuronal cell line


title: insulin_24hour_rep2

value: expressing Neuropeptide Y/Agouti-related Peptide


title: TBEV_negative_for_NudC_CapClip_rep1

value: negative


title: CHKV_AtNUDX23_rep2

description:
CapZyme-seq protocol
FeatureCount_CHIKV_output.txt

organism:
Homo sapiens
Chikungunya virus

source_name: Human TIG3 cell line

value: Human TIG3 cell line

value: Chikungunya virus

value: Total RNA


title: CHKV_Rpp_rep2

value: Rpp


title: CHKV_neg_rep2


title: TBEV_CapClip_rep1

value: CapClip


title: G3 Roots

city: Toledo

first: Carolina

last: Escobar

address: Avenida Carlos III, s/n

country: Spain

institute: University of Castilla-La Mancha

description: Treatment (infected roots)

data_processing:
MethylC-seq data was processed using the pipeline available at https://github.com/seb-mueller/snakemake-bisulfite (commit f12bb6) in GitHub.
The pipeline performed quality control using FastQC (version 0.11.8). Raw reads were trimmed for adapters, quality-trimmed and filtered using Trim Galore (version 0.5.0).
A combined genome was constructed by concatenation the genomes (in fasta format) of A. thaliana (TAIR10, including the chloroplast and mitochondrial genome), M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017) and Lambda phage into a single fasta format reference. Reads were then mapped to the constructed reference with Bismark (version 0.20.0; Krueger and Andrews, 2011), using the following parameters: L,0,-0.4.
The SAM alignment generated by Bismark were further processed into BAM format and subsequently imported for further processing into the R package methylKit version 0.99.2 (Akalin et al., 2012).
To identify differential methylated regions (DMRs), we  defined various regions in form of adjacent non-overlapping window of 200 base pairs (referred to as bins), which were posteriorly checked for overlapping different genomic regions, including genes, promoters and transposable elements as specified in Araport11 (06/2016; Cheng et al., 2017). Promoters were considered as 1000 base pairs (bp) upstream until 200 bp downstream of the transcription start site.
For each region, the containing methylated and unmethylated cytosines were counted (separately for each library, each region and each context [CHH, CHG, CG]) and tested for differential methylation using a logistic regression approach using the “MN” over-dispersion correction as implemented in MethylKit. DMRs are then defined if the difference of methylation proportion between the gall samples and the controls was higher than 15% and a FDR (q-value) of less than 0.05 and covered by at least two biological replicates of the treatment or control.
Genome_build: A. thaliana (TAIR10) and M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017)
Supplementary_files_format_and_content: File with DMRs (in different DNA methylation contexts); .csv

source_name: Roots

growth_protocol: Arabidopsis thaliana plants were were grown in controlled environment chambers under 16 h/8 h of light/dark at 23ºC

extract_protocol:
Galls and control roots were collected at 3 days post infection and frozen on liquid nitrogen. Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657)
The libraries were prepared using the NEXTflex Bisulfite-Seq Library Prep Kit (BiooScientific), following the manufacturer's instructions. The fragment size distribution of the libraries were checked in the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit. The libraries were then sequenced in one lane of an Illumina HiSeq 4000 PE100 platform. Two of the libraries (RC2 and RC3) were sequenced in an Illumina® HiSeq X PE150 (San Diego, California, USA). Both steps were performed by the company AllGenetics & Biology SL.

treatment_protocol: Arabidopsis plants were inoculated at 5 days post germination at the root tip with approximately 20 freshly-hatched Meloidogyne J2 each plant. The inoculated and non-inoculated plants were then kept in the dark for 2 days. During the first 48 hours, the infections and control roots growth were accessed. After 2 days, the plates containing both inoculated and non-inoculated plants were maintained in the light, covered by a gauze. For more details concerning this protocol please see Olmo et al. (2017; doi: 10.1007/978-1-4939-6831-2_5).

tag: developmental stage

value: Aprox. 9-days-old plants (3 days post infection)

tag: agent

value: Infected with Meloidogyne javanica


title: RC1 Roots

description: Control (non-infected roots)

value: Non-infected


title: CHKV_neg_rep1


title: vehicle_24hour_rep1

value: vehicle (Phosphate Buffered Saline, PBS)

value: 24 hours post treatment


title: TBEV_negative_rep3

description:
CapZyme-seq protocol
FeatureCount_TBEV_output.txt

value: Human SH-SY5Y cell line

value: Tick-borne encephalitis virus

value: TEX treated total RNA


title: CHKV_AtNUDX23_rep1


title: insulin_4hour_rep1

value: male

value: 100 nM of Insulin

value: 4 hours post treatment


title: TBEV_NudC_rep1

value: NudC


title: EdUHU-K562-Rad21-mAID-1-RPKM-rmblacklist-1k

data_processing:
Library strategy: NAIL-seq
R1 and R2 reads were stitched using PEAR
The stitched reads were aligned to the human genome (assembly hg19) by BWA-MEM (-k 20)
PCR duplicates were distinguished by random molecular barcodes (RMBs) and only one was kept.
Reads with mapping quality (MAPQ) ≥ 30 were kept for further analysis.
We used samtools to convert .sam files into .bam files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage

source_name: cultured cell

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation of EdU.
After on-beads ligation, purified DNA was tagged with Illumina sequencing primers and sequenced on Hi-seq, 2×150 bp.

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into EdU/HU/DOX/IAA for 24h, and mClover negative cells were sorted

tag: clone

value: RAD21-mAID-mClover (RAD21-depleted)


title: TBEV_negative_rep2

value: negative


title: G1 Roots

description: Treatment (infected roots)


title: CHKV_Rpp_rep1

value: Human TIG3 cell line

value: Chikungunya virus

value: Total RNA


title: TBEV_AtNUDX23_rep3


title: 12.HE-1We-m1-S12-all-R1-001

city: Nouzilly

first: joelle

last: dupont

address: Centre Val de Loire

institute: INRA

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.4.6 and bcl2fastq 2.15.0
Adapter sequences were trimmed with Cutadapt-1.3, only reads longer than 10 bp were kept for analysis
Sequences were aligned to the cow genome (bosTau8.fa) with TopHat2 using default parameters
Mapped reads were assigned to features with htseq-count (intersection-nonempty mode)
Differential expression analysis was performed with DESeq2,
Genome_build: bosTau8.fa
Supplementary_files_format_and_content: tabulated .txt file containing DESeq2 results

organism: Bos taurus

source_name: HE dairy cows one week after calving (animals were fed with HE since one month before calving)

extract_protocol:
Total RNA from the fat tissue of three cows per group was extracted using a RNeasy Midi kit (Qiagen®, Courtaboeuf, France) and purified using a DNAfree kit (Invitrogen by Life Technologies), according to the manufacturer’s recommendations.
Directional RNA-Seq libraries were constructed using the TruSeq Stranded Total RNA library prep kit (Illumina), following the manufacturer’s instructions, using 750 ng of total RNA.

tag: breed

value: Prim Holstein

tag: cow status

value: primiparous

tag: diet

value: HE (high energy diet) since one month before calving

value: one week after calving

value: subcutaneous adipose tissue


title: 13.HE-16We-m2-S13-all-R1-001

source_name: HE dairy cows 16 weeks after calving (animals were fed with HE since one month before calving)

value: 16 weeks after calving

tag: tissue


title: 11.HE-1We-m1-S11-all-R1-001


title: TBEV_Rpp_rep3

tag: cell type

value: Human SH-SY5Y cell line

value: Rpp

value: Tick-borne encephalitis virus


title: insulin_24hour_rep1

value: male

value: embryonic hypothalmic neuronal cell line

value: expressing Neuropeptide Y/Agouti-related Peptide

tag: treatment

value: 100 nM of Insulin

value: 24 hours post treatment


title: 15.HE-16We-m2-S15-all-R1-001


title: TBEV_Rpp_rep1

tag: enzymatic treatment

value: TEX treated total RNA


title: G2 Roots

description: Treatment (infected roots)

tag: ecotype

value: Aprox. 9-days-old plants (3 days post infection)

value: Infected with Meloidogyne javanica


title: 14.HE-16We-m2-S14-all-R1-001

value: Prim Holstein


title: TBEV_Rpp_rep2

tag: virus

tag: molecule subtype


title: 9.LE-16We-m1-S9-all-R1-001

source_name: LE dairy cows 16 weeks after calving (animals were fed with LE since one month before calving)

value: primiparous

value: LE (low energy diet) since one month before calving


title: 10.HE-1We-m1-S10-all-R1-001

value: HE (high energy diet) since one month before calving

value: one week after calving


title: 6.LE-1We-m2-S6-all-R1-001

source_name: LE dairy cows one week after calving (animals were fed with LE since one month before calving)

value: subcutaneous adipose tissue


title: TBEV_AtNUDX23_rep2

value: Human SH-SY5Y cell line


title: EdUHU-K562-Rad21-mAID-4-RPKM-rmblacklist-1k

first: Zhengrong

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

tag: genotype

value: RAD21-mAID-mClover (RAD21-depleted)


title: Instructed ESC- ATAC_rep1

city: Bethsda

first: Vittorio

last: Sartorelli

address: 50 South Dr.

department: NIAMS

institute: NIH

description: bulk ATAC-seq

data_processing:
ChIP-seq reads were mapped to the mm10 genome assembly using Bowtie version 1.1.1,allowing two mismatches, after adapter sequences were removed using trimgalore version0.6.6.
RNA-seq reads were mapped to the mm10 genome assembly using TopHat version 2.1.1 with the default configurations after adapter sequences were removed using trimgalore version 0.6.6.
peaks were called using MACS 1.4.2 (Zhang et al., 2008)  with the following setting: a p value (1.0E-05).
Gene expression values (RPKM: Reads Per Kilobase exon per Million mapped reads) were calculated using Partek Genomics Suite 7.18.
scRNA-seq reads were processed with CellRanger ver. 3.1.0  and bcl2fastq/2.20.0 to generate fastq files with default parameters.
scATAC-seq reads were processed with Cellranger-atac ver. 1.1.0  and bcl2fastq/2.20.0 to generate fastq files with default parameters.
omics reads were processed with cellranger-arc/2.0.0 and bcl2fastq/2.20.0 to generate fastq files with default parameters.
For clustering, filtering, variable gene selection, dimensionality reduction of scRNA(single cell RNA) are performed using the Seurat ver.4.1.0 (Butler et al., 2018).
For clustering, filtering, variable gene selection, dimensionality reduction of scATAC(single cell ATAC) are performed using the Signac ver.1.5.0 (Stuart et al., 2019).
The pseudotemporal Analyses of scRNA(single cell RNA) was performed using Monocle v.3.0.0, Slingshot(ver 2.2.0) (Street et al., 2018)  and tradeSeq(ver 1.8.0) (Van den Berge et al., 2020).
Hi-C  reads were mapped to the mm10 genome assembly using BWA (Li and Durbin, 2010),filtering reads that aligned to more than two places in the genome and low mapping quality score (MAPQ <30).
Hi-C downstream analysis was performed with HOMER (Heinz et al., 2010)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include barcodes,gene names, and UMI counts  for each Sample.

source_name: Instructed ESC

growth_protocol: ESCs were plated on 0.1% gelatin and cultured in DMEM supplemented with 15% FBS, 1% penicillin-streptomycin,2 mM L-glutamine, 0.1 mM non-essential amino acids, 0.1% β-mercaptoethanol, 1,500 U/ml LIF and 2i inhibitors. Somites were dissected from embryoes, sorted and processed for RNAseq and ATACseq assays.

extract_protocol:
RNA was extracted using Trizol. For ChIP cells were  lysed in RIPA buffer as described in Mousavi et al., 2012. ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013)
For RNA-seq, poly (A)+ mRNA libraries were generated  using NEBNext Ultra II RNA library preparation kit for Illumina (NEB #E7490). Single-cell RNA-seq libraries were prepared using a Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (P/N 1000121, 10x Genomics) and scATAC seq performed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x genomics, 1000175). Single Cell Multiome ATAC+ Gene Expression (10x Genomics kit, CG000338). Hi-C experiments were performed using the Arima-HiC kit (A510008GFP)
Bulk RNAseq, Bulk ATAC seq, ChIPseq, scRNA, scATAC, snRNA and scATAC from the same cell (multiomeic) and HiC

treatment_protocol: ESCs differentiation was induced as described inChalet al., 2015. ESC were plated on gelatin-coated plates in serum-free N2B27 medium and BMP4 10ng/ml for 2 days. cells were shifted to MEM, 1%FBS, 14% KSR,10ng/ml Rspo3, 0.5% DMSO and 0.1 μM LDN19318 for 4 days. Subsequently, medium was changed to DMEM, 1%FBS, 14% KSR,  10 ng/ml Rspo3, 10 ng/ml HGF,2 ng/ml IGF-1,20 ng/ml FGF-2  and 0.1 μM LDN193189 for additional 2 days..

tag: sample type

value: Differentiated ESC


title: 8.LE-16We-m1-S8-all-R1-001

tag: time point

value: 16 weeks after calving


title: TBEV_negative_rep1

value: negative

value: Tick-borne encephalitis virus


title: 7.LE-16We-m1-S7-all-R1-001


title: Instructed ESC- ATAC_rep2

description: bulk ATAC-seq


title: TBEV_AtNUDX23_rep1


title: 4.LE-1We-m2-S4-all-R1-001


title: 5.LE-1We-m2-S5-all-R1-001


title: Mouse Embryonic Fibroblasts, replicate 3

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Samples were analyzed using UTAP software (Kohen et al. 2019). Reads were trimmed using CutAdapt (Martin 2011) (parameters: -a ADAPTER1 -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic - alignSoftClipAtReferenceEnds No).
Sample counting was done using STAR, quantifying mm10 RefSeq annotated genes. Further analysis was done for genes having a minimum of five reads in at least one sample. Normalization of the counts and differential expression analysis was performed using DESeq2 (Love et al. 2014) with the parameters betaPrior = true, cooksCutoff = false, and independentFiltering = false.
Assembly: mm10

source_name: MEF

growth_protocol: Cell were cultured on MEFs in humdified 5%Co2 , 21% O2 incubator

extract_protocol:
RNeasy mini RNA kit
Bulk MARS-seq
3 primed library

treatment_protocol: Doxycycline treatment for different time points decribed in each sample. Some samples were treated with LPA as indicated.

tag: cell line

value: ICR


title: Extra-embryonic Endoderm Stem Cells, replicate 1

source_name: Extra-embryonic Endoderm Stem Cells (XEN)


title: Naïve ESC- ATAC_rep1

description: bulk ATAC-seq

source_name: Naïve ESC

value: ESC-Naive


title: 2-1Mo-m1-S2-all-R1-001

source_name: dairy cows one month before calving before diet experiment


title: Mouse Embryonic Fibroblasts, replicate 2


title: Naïve ESC- ATAC _rep2

description: bulk ATAC-seq


title: Extra-embryonic Endoderm Stem Cells, replicate 3


title: Mouse Embryonic Fibroblasts, replicate 1