title: POS parental rep 3

city: Raleigh

first: Hiroyuki

last: Mochizuki

state: NC

address: 1060 William Moore Dr

institute: North Carolina State University

description: POS parental cell line

data_processing:
standard RNA data processing used
The software package Real Time Analysis (RTA), was used to generate raw bcl, or base call files, which were then de-multiplexed by sample into fastq files.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.38 with parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50.
The trimmed sequence reads were mapped to CanFam3.1 using TopHat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks and compared using cuffdiff.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: CSV files of comparison of differences in FPKM between samples.

organism: Canis lupus familiaris

source_name: Osteosarcoma

extract_protocol:
Total RNA was extracted from tissue samples using an RNeasy mini kit (Qiagen, USA) and assessed for RNA sample integrity using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies, USA).
Purification of messenger RNA (mRNA) was performed using oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA). Complementary DNA (cDNA) libraries for Illumina sequencing were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Mulitplex Oligos for Illumina (NEB) using the manufacturer-specified protocol. Briefly, the mRNA was chemically fragmented and primed with random oligos for first strand cDNA synthesis. Second strand cDNA synthesis was then carried out with dUTPs to preserve strand orientation information. The double-stranded cDNA was then purified, end repaired and “a-tailed” for adaptor ligation. Following ligation, the samples were selected a final library size (adapters included) of 400-550 bp using sequential AMPure XP bead isolation (Beckman Coulter, USA). Library enrichment was performed and specific indexes for each sample were added during the protocol-specified PCR amplification. The amplified library fragments were purified and checked for quality and final concentration using an Agilent 2200 Tapestation (D1000 chip, Agilent Technologies, USA) combined with a Qubit fluorometer (ThermoFisher, USA).

tag: tissue

value: Osteosarcoma cell line

tag: phenotype

value: parental cell line


title: Pat 04_IPNB - premalignant

status: Public on Jan 05 2021

type: genomic

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

description: Infinium MethylationEPIC

hyb_protocol: supplier protocol (Illumina)

scan_protocol: supplier protocol (Illumina)

data_processing: supplier software (GenomeStudio)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Pat 04

label_protocol: supplier protocol (Illumina)

extract_protocol: AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) as recommended by the manufacturer with following modifications: After addition of xylene, samples were incubated at 56°C for 2 min followed by two ethanol washes. The first proteinase K digestion was done with 20 µl at 56°C for 30 min. The DNA was eluted twice with 30 µl H2O.

tag: disease state

value: IPNB - premalignant


title: opc12-72_pooled_male_2

type: SRA

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

country: USA

institute: University of Virginia

description:
opc12-72
rsem_opc.csv

library_source: transcriptomic

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the mouse (GRCm38.82) transcriptome using RSEM. Reference ERCC sequences were also provided for the alignment.
RSEM options for pool-and-split controls and 10-cell samples: --bowtie2 --single-cell-prior --paired-end (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts, paired end reads)
RSEM options for bulk samples: --bowtie2 (Bowtie2 transcriptome aligner)
Comma-separated values (CSV) file includes read counts from RSEM
Genome_build: GRCm38.82
Supplementary_files_format_and_content: 2020_03_20_opc_allcompiled.csv (read counts)

molecule: polyA RNA

organism: Mus musculus

source_name: Brain oligodendrocyte precursor cells

extract_protocol:
PCR amplification
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads
All samples were cryoembedded and sectioned onto glass slides. Cell samples were isolated via laser capture microdissection prior to RNA extraction, reverse transcription, and RNA amplification

tag: genotype

tag: time

value: 12 dpi (days following tamoxifen treatment start)

tag: sample type

value: pool-and-split control

tag: Sex

value: male

tag: section thickness (µm)


title: POS parental rep 2

description: POS parental cell line

molecule: total RNA


title: memory.CD8.TCR+media.4h 3

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.2.1
Aligned reads are converted to BAM files using samtools. BAM files are subsequently converted to BED files using bedtools. Unpublished python scripts were used to calculate raw reads and RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes among different conditions.
Genome_build: mm10

source_name: sleen

growth_protocol: Naïve WT and Tslpr-/- P14 T cells were isolated for use in vitro and in vivo from the spleens of naïve WT and Tslpr-/- P14 mice and purified using a negative selection CD8+ T cell kit (Stem Cell Technologies). To generate memory CD8+ T cells for use in vivo or in vitro, 5 x 104 (influenza infections) or 105 (LCMV infections) WT or Tslpr-/- naïve P14 cells were injected i.v. into naïve C57BL/6 mice, and the following day the mice were infected with either 103 EID50 of PR8-33 i.n. or 2 x 106 pfu LCMV Armstrong i.p. At >30 days p.i. the spleens were harvested and memory WT and Tslpr-/- P14 cells purified using a negative selection CD8+ T cell kit (Stem Cell Technologies). A sample of the cells were stained with Thy1.1, Thy1.2, CD8, CD44, Va2 and Live/Dead stain to determine the number of P14 T cells. Equal numbers of naïve or memory WT and Tslpr-/- P14 were combined; verification that equal numbers of WT and Tslpr-/- were added was determined by flow cytometry using the same antibodies listed above, and 2.5 x 104 (influenza) or 103 (LCMV) naive P14 T cells or 104 (influenza) or 103 (LMCV) memory P14 T cells of each population (WT and Tslpr-/-) were co-transferred i.v. into naive C57BL/6 mice. On the day following cell transfer, the mice were infected with either 103 EID50 of PR8-33 i.n. or 2 x 106 pfu LCMV Armstrong i.p.  For the assessment of the homeostasis of naïve and memory P14 cells in vivo, equal numbers of naïve or memory WT and Tslpr-/- P14 T cells (~1-2 x 106 total cells) were co-transferred into naïve C57BL/6 mice.

extract_protocol:
For RNA-seq, RNA was isolated from sorted P14 T cells at the indicated time points using the Zymo RNA miniprep kit (Zymo Research), and 500 ng RNA was used for RNA-Seq library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were excised and purified with Zymoclean Gel DNA Recovery Kit (Zymo Research).
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq3000 system.

treatment_protocol: 1 x 106 CD8+ T cells were plated in 0.75 ml/well in 48 well plates or 2 x 106 CD8+ T cells were plated in 1.5 ml/well total volume in 24 well plates with either medium or 100 ng/ml TLSP (R&D systems) with or without stimulation. For in vitro stimulation of naïve cells, the plates were pre-coated with 2 mg/ml anti-CD3e (BioXcell) and 1 mg/ml of soluble anti-CD28 was added. For in vitro stimulation of memory cells, 1 mg/ml of soluble anti-CD3 was added.

tag: strain

tag: cell type

value: CD8+ T cells

tag: sorted cell

value: memory

tag: treatment

value: TCR+media 4h


title: memory.CD8.media.24h 3

value: media 24h


title: 8.Late.Epi

city: OSLO

first: Agate

last: Noer

address: Kirkeveien 166

department: Ophthalmology

country: Norway

institute: Oslo University Hospital, Ullevaal

description: Genomic DNA from formalin-fixed paraffin-embedded uveal melanoma sections

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan system

data_processing: Illumina’s GenomeStudio V2011.1 Methylation Module V1.9

source_name: Uveal melanoma

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extraction was carried out using the QIAamp DNA FFPE Tissue Kit (Qiagen, Venlo, NL) according to the manufacturers’ recommendations. DNA was purified using the Zymo PCR inhibitor removal kit (Zymo, Irvine, CA, US). DNA concentration was determined using Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, US). Quality control of DNA samples was performed using the Infinium HD FFPE QC Assay (Illumina, San Diego, CA, US) protocol according to Illumina’s recommendations. Samples were kept at -20 C˚ until bisulphite conversion using Zymo EZ DNA Methylation kit (Zymo). 500 ng of genomic DNA from each sample was converted. Samples underwent restoration using the Illumina Infinium HD Restore protocol (Illumina), and 4 μl of bisulphite-converted restored DNA was used for hybridization on the Infinium Human Methylation 450 BeadChip (Illumina), following the Illumina Infinium HD Methylation protocol (Illumina).

tag: gender

value: F

tag: histology

value: Epi

tag: relapse

value: Late


title: opc12-73_pooled_female_1

description:
opc12-73
rsem_opc.csv

value: female


title: Pat 02_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 02


title: opc12-75_pooled_female_1

description:
opc12-75
rsem_opc.csv


title: POS parental rep 1

description: POS parental cell line


title: PBMCs from Healthy 2

city: Bangkok

first: Natthaya

last: Chuaypen

address: 1873 Rama 4 road, Pathumwan

country: Thailand

institute: Chulalongkorn University

description:
Control
Controls_vs_Treatments HepG2.txt,Controls_vs_Treatments Huh7.txt
RCM5

data_processing:
The quality of the raw sequencing reads were assessed with the FastQC v.0.11.2 software. The raw sequencing reads were subjected to trimming process with Trimmomatic v.0.32 software. The surviving paired-end reads were aligned to the Homo sapiens reference genome (Ensembl GRCh38 genome) with HISAT2 v.2.1.0 software. The alignment files were analyzed individually with the StringTie version 1.3.3b software to detect and quantify previously known transcripts. Invidual annotation files generated from transcript assembly process were merged together parsimoniously using StringTie version 1.3.3b. With the merged annotation file.
The expression unit calculated is FPKM, Fragments Per Kilobase Million. Besides, differential expression (DE) analysis was performed according to the given comparison groups . The expression fold change between each comparison group were calculated and log-transformed. Multiple output files were generated by DESeq2 version 1.16.1 and the detail files information are described in the table of result files below. Significant DE genes or transcripts (q-value < 0.05) were extracted for each comparison groups and cancer type.
Genome_build: HG19
Supplementary_files_format_and_content: text files were generated using DESeq2 version 1.16.1 and represented FPKM for each sample , fold change and p-value compared between Control and Treatment groups

source_name: PBMCs

growth_protocol: The liver cancer cells were obtained from Nation Institutes of Biomedical Innovation, Health and Nutrition JCRB Cell Bank (Osaka, Japan) including HepG2 (JCRB1054) and Huh7 (JCRB0403). The Cells were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37 ºc 5 % CO2 in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

extract_protocol:
PBMCs were collected from Transwell culture six well plates and RNA was harvested using Trizol reagent.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified (by AxyPrep Mag PCR Clean-up (Axygen)) double-stranded cDNA was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer ( Agilent Technologies, Palo Alto, CA, USA ) , and quantified by Qubit 2.0 Fluorometer ( Invitrogen, Carlsbad, CA, USA ).

treatment_protocol: Indirect or co-culture liver cancer cells with PBMCs from healthy were performed in Transwell culture six well plates (Costar, France). The liver cancer cells were seeded into plate (106 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37 ºc 5 % CO2. The PBMCs from healthy were plated on permanent membrane culture of Transwell (2 × 106 cells) and incubated for 4 hours at 37 ºc 5 % CO2.

tag: cell line

tag: blood

value: PBMCs


title: BL03-D-4 in YPM

city: Guangzhou

first: Li

middle: Bu

last: Su

address: No. 100, Xianlie Middle Road, Guangzhou, 510070, PR China

country: China

institute: Guangdong Institute of Microbiology

description: different expression gene.xls

data_processing:
SeqPrep  (https://github.com/jstjohn/SeqPrep)  used for basecalling
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads  ere separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
To identify DEGs (differential expression genes) between two different samples, the expression  level of each transcript was calculated according to the transcripts per million reads (TPM)  method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) [3] was used to quantify gene abundances
Supplementary_files_format_and_content: Xls file was genarated according to the transcripts per million reads (TPM)  method to identify DEGs (differential expression genes) between two different samples

organism: Saccharomyces cerevisiae

growth_protocol: For cultivation, a single colony was picked up from a freshly YPD plate and trans-ferred to 5 mL of YPD medium. After cultured at 200 rpm and 30°C, 1 mL seed culture was inoculated into a 250 mL shake-ﬂask with 50 mL YPD medium, modified YPD me-dia (YPM) or YPD media supplemented with different chemicals to an optical density (OD600) of 0.05 and then allowed to incubate at 30 °C for 24 h.

extract_protocol:
Total RNA of different yeast cells was isolated after about 24 h cultivation using the HiPure Yeast RNA Kit (Magen, Guangzhou, China) according to the manufactur-er’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain type


title: BL03-D-4 in YPD

description: different expression gene.xls


title: memory.CD8.media.4h 3

value: media 4h


title: opc12-70_pooled_female_2

description:
opc12-70
rsem_opc.csv


title: memory.CD8.media.0h 2

value: media 0h


title: Pat 14_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 14


title: opc12-69_ten-cell_female_2

description:
opc12-69
rsem_opc.csv

value: 10-cell sample


title: P.for #12, Ovary

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

data_processing:
Genome mapping: TopHat2
Expression profiling: FeatureCounts
Genome_build: P. formosa genome (GCF_000485575.1)
Supplementary_files_format_and_content: csv; gene expression counts

organism: Poecilia formosa

source_name: Ovary

growth_protocol: We used one clone of P. formosa as well as F1 interspecies hybrids produced by mating a female P. mexicana and a male P. latipinna for our study. Founder fish for clonal fish of the laboratory strain of P. formosa were collected from the Canal Principal E at Ciudad Mante, Tamaulipas, Mexico, where P. mexicana is the sperm-donor host species. A clonal lineage of this P. formosa collection was maintained in the aquarium for over about 70 generations before dissections of organs for transcriptome profiling was performed. Founder fish of the P. mexicana and P. latipinna originated from Laguna Champaxan at Altamira, Tamaulipas, Mexico. F1 interspecies hybrids were produced by mating a single virgin female P. mexicana and a male P. latipinna under regular aquarium breeding conditions.    P. formosa clone and F1 interspecies hybrids were from a single female and the same brood. They were raised under identical conditions in the fish room of the Biocenter of the University of Würzburg, and were size and age (3 months) matched.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Thermo Fisher Scientific, Waltham, USA) according to the supplier’s recommendation. All samples were treated with DNase. Total RNA concentration was determined using a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY, USA). RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) to confirm that RIN scores were above 8.0 prior to sequencing.
Library construction follows Illumina TruSeq mRNA sequencing library preparation protocol

treatment_protocol: no treatment

tag: age

value: 3 month old

tag: tissue

value: Ovary


title: memory.CD8.TCR+TSLP.24h 2

value: TCR+TSLP 24h


title: Pat 03_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 03

tag: disease state

value: IPNB - premalignant


title: opc12-68_ten-cell_female_2

description:
opc12-68
rsem_opc.csv

tag: genotype

tag: time

value: 12 dpi (days following tamoxifen treatment start)


title: HMPOS extravasation-positive rep 3

description: HMPOS extravasation-positive subline

value: Osteosarcoma cell line

tag: phenotype

value: exravasion-positive subline


title: Pat 02_bile duct control - normal

description: Infinium MethylationEPIC

value: bile duct control - normal


title: memory.CD8.TCR+media.24h 2

value: CD8+ T cells

value: memory

value: TCR+media 24h


title: P.for #12, Brain

source_name: Brain

tag: Sex

value: Brain


title: memory.CD8.media+TSLP.24h 2

tag: strain

value: media+TSLP 24h


title: 6.No.Epi

value: F

value: Epi

value: No


title: 5.Late.Mix

value: Mix

value: Late


title: memory.CD8.media+TSLP.4h 3

tag: cell type

value: media+TSLP 4h


title: PBMCs from Healthy 1

description:
Control
Controls_vs_Treatments HepG2.txt,Controls_vs_Treatments Huh7.txt
RCM4

value: PBMCs


title: 9.Late.Spi

value: Spi


title: 2.Early.Spi

value: M

value: Early


title: P.for #11, Ovary

value: 3 month old

value: female

value: Ovary


title: opc12-71_pooled_female_2

description:
opc12-71
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

tag: sample type

value: pool-and-split control

tag: section thickness (µm)


title: 3.Early.Epi

tag: gender


title: opc12-65_pooled_male_1

description:
opc12-65
rsem_opc.csv

value: male


title: 7.No.Spi

tag: histology


title: Pat 01_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 01

value: IPNB - premalignant


title: memory.CD8.media.24h 2

value: CD8+ T cells

tag: sorted cell

value: memory

tag: treatment

value: media 24h


title: HMPOS extravasation-positive rep 2

description: HMPOS extravasation-positive subline

value: Osteosarcoma cell line

value: exravasion-positive subline


title: opc12-67_pooled_male_1

description:
opc12-67
rsem_opc.csv


title: P.for #11,   Liver

source_name: Liver

value: Liver


title: HMPOS extravasation-positive rep 1

description: HMPOS extravasation-positive subline


title: memory.CD8.TCR+TSLP.4h 2

value: TCR+TSLP 4h


title: opc12-64_ten-cell_male_1

description:
opc12-64
rsem_opc.csv

value: 10-cell sample


title: P.for #11, Brain

value: Brain


title: memory.CD8.TCR+media.4h 2

value: TCR+media 4h


title: opc12-63_ten-cell_male_2

description:
opc12-63
rsem_opc.csv


title: P.for #4, Ovary

value: 3 month old


title: 11.No.Spi

value: F

value: Spi

tag: relapse

value: No


title: 4.Late.Spi

value: M

value: Late


title: opc12-62_ten-cell_male_2

description:
opc12-62
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

value: male


title: D17 extravasation-positive rep 3

description: D17 extravasation-positive subline


title: memory.CD8.media+TSLP.4h 2

value: CD8+ T cells

value: memory

value: media+TSLP 4h


title: opc12-61_pooled_male_2

description:
opc12-61
rsem_opc.csv

value: pool-and-split control


title: P.for #4, Brain

value: female


title: P.for #4,  Liver

value: Liver


title: memory.CD8.media.4h 2

value: media 4h


title: memory.CD8.media.0h 1

value: media 0h


title: Pat 06_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 06

value: bile duct control - normal


title: D17 extravasation-positive rep 2

description: D17 extravasation-positive subline

value: Osteosarcoma cell line

value: exravasion-positive subline


title: P.for #3, Ovary

value: 3 month old

value: Ovary


title: Pat 01_bile duct control - normal

description: Infinium MethylationEPIC


title: opc12-59_pooled_male_1

description:
opc12-59
rsem_opc.csv


title: memory.CD8.TCR+TSLP.24h 1

value: TCR+TSLP 24h


title: D17 extravasation-positive rep 1

description: D17 extravasation-positive subline


title: P.for #3,  Liver


title: memory.CD8.TCR+media.24h 1

value: TCR+media 24h


title: 1.Early.Spi

value: M

value: Spi

value: Early


title: P.for #3, Brain

value: Brain


title: opc12-60_ten-cell_male_2

description:
opc12-60
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

value: 10-cell sample

value: male


title: memory.CD8.TSLP.24h 1

value: CD8+ T cells

value: memory

value: TSLP 24h


title: Pat 09_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 09

value: bile duct control - normal


title: HLT8

city: Galway

first: Oliver

last: Carroll

address: Newcastle Rd

country: Ireland

institute: National University of Galway, Ireland

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the human reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. All statistical analysis was performed using R free software. With the package DESeq2, a comparison of gene expression between the groups of samples was performed.
The Wald test was used to generate p-values and Log2 fold changes.
Genome_build: The reads were then mapped to the Ovis aries reference genome available on NCBI using the STAR aligner
Supplementary_files_format_and_content: read counts

organism: Ovis aries

source_name: healthy, animal 4

extract_protocol:
Each sample, weighing approximately 50 mg, was finely minced and extracted in TRIzol (Thermo Fisher Scientific) by beads grinding using a TissueLyser LT (Qiagen) set at 50 oscillations per min (Qiagen). Two cycles of 10 min each were performed at 4°C and samples were visually inspected to ensure a complete homogenisation. RNA extraction was then carried out by chloroform precipitation and purified using RNeasy Mini Spin Columns (Qiagen).
RNA sequencing library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina followed by manufacturer's instructions (New England Biolabs). Briefly, mRNA was first enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 ¡C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (Invitrogen) as well as by quantitative PCR (KAPA Biosystems).
The sequencing libraries were clustered on one lane of a patterned flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 or equivalent instrument in High Output Mode according to manufacturer's instructions. The samples were sequenced using a 2x150 paired end configuration. Image analysis and base calling were conducted by the HiSeq Control Software.

treatment_protocol: Samples from healthy and infarcted (ischemic core, border and remote regions) hearts were harvested immediately after explantation, as described above, and stored in RNAlater (Thermo Fisher Scientific).

value: heart

tag: heart region

value: left ventricle

tag: specific zone

value: healthy


title: opc12-57_ten-cell_female_1

description:
opc12-57
rsem_opc.csv

value: female


title: HLT6

source_name: healthy, animal 3

tag: tissue


title: P.for #12,   Liver

tag: age

value: 3 month old

value: Liver


title: OE5-MG rep3

city: Wuhan

first: Zheng-Wei

last: Fu

state: Hubei

address: Bayi road

department: College of Life Sciences

institute: Wuhan University

data_processing:
RNA-seq: SOAPnuke v1.5.2 software used for basecalling with parameters -l 15 -q 0.5 -n 0.1.
RNA-seq: HISAT2 v2.0.4 software used for alignment with parameters -p 8 -phred64 -sensitive -I 1 -X 10000.
RNA-seq: Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using HTSeq-count.
ChIP-seq: SOAPnuke v1.5.2 software used for basecalling with parametersr -l 10 -q 0.4 -n 0.1 -Q 2 -c 25 -5 1.
ChIP-seq: SOAPaligner v2.21t software used for alignment with parameters soap_mm_gz -p 4 -v 2 -s 35.
ChIP-seq: Tag-enriched regions were identified by SICER (Zang, C. et al., 2009 Bioinformatics) with a window size of 200 bp and gap size of 600 bp.
ChIP-seq: Peak annotation was performed using the R package ChIPseeker (Yu, G. et al., 2015 Bioinformatics).
Genome_build: Tair10 (http://www.arabidopsis.org/)
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include RPKM values; ChIP-seq: wig files were generated using SICER with a window size of 200 bp and gap size of 600 bp.

organism: Arabidopsis thaliana

growth_protocol: Five-day-old seedlings grown on medium containing 1/2 strength MS solid medium.

extract_protocol:
RNA was extracted using TRIzol reagent and mRNA was enriched with magnetic beads with Oligo (dT); Genomic DNA for ChIP-seq analysis  were digested by micrococcal nuclease.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols; ChIP genomic DNA libraries were prepared for sequencing using Illumina Paired-End DNA Sample Prep kit.

tag: genotype/variation

value: seedlings

value: 200 μM MG for 12h


title: opc12-56_ten-cell_male_2

description:
opc12-56
rsem_opc.csv

tag: genotype

tag: time


title: OE5-MG rep2


title: memory.CD8.media.24h 1

value: media 24h


title: HLT5

source_name: healthy, animal 2


title: HLT1

source_name: healthy, animal 1


title: opc12-54_ten-cell_female_2

description:
opc12-54
rsem_opc.csv

source_name: Brain oligodendrocyte precursor cells

tag: Sex


title: memory.CD8.media+TSLP.4h 1

source_name: sleen

tag: strain

value: media+TSLP 4h


title: memory.CD8.TCR+media.4h 1

tag: cell type

value: TCR+media 4h


title: OE5-MG rep1


title: OE5-NaCl rep3

value: 100 mM NaCl for 12h


title: HYD4-F

source_name: 21 days post-hydrogel animal 4

value: remote

value: 21 days post-hydrogel


title: HYD3-F

source_name: 21 days post-hydrogel animal 3


title: OE5-NaCl rep2


title: opc12-58_ten-cell_male_1

description:
opc12-58
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

tag: sample type

value: 10-cell sample

value: male


title: memory.CD8.media.4h 1

value: CD8+ T cells

value: memory

value: media 4h


title: opc12-52_ten-cell_male_1

description:
opc12-52
rsem_opc.csv

tag: section thickness (µm)


title: opc12-53_ten-cell_male_1

description:
opc12-53
rsem_opc.csv


title: HYD2-F

source_name: 21 days post-hydrogel animal 2

value: heart

value: left ventricle


title: OE5-NaCl rep1


title: HYD1-F

source_name: 21 days post-hydrogel animal 1


title: naive.CD8.media.24h 3

value: naive


title: opc12-50_ten-cell_female_1

description:
opc12-50
rsem_opc.csv

value: female


title: naive.CD8.TSLP.24h 3

value: TSLP 24h


title: HYD4-BZ

value: border


title: OE5-mock rep2

value: seedlings


title: opc12-55_ten-cell_male_2

description:
opc12-55
rsem_opc.csv


title: naive.CD8.TSLP.24h 2


title: OE5-mock rep1


title: opc12-48_ten-cell_female_1

description:
opc12-48
rsem_opc.csv


title: naive.CD8.media.24h 2

value: media 24h


title: HYD3-BZ


title: OE1-MG rep3

value: 200 μM MG for 12h


title: HYD2-BZ


title: naive.CD8.TSLP.24h 1


title: opc12-49_ten-cell_female_1

description:
opc12-49
rsem_opc.csv


title: opc12-47_ten-cell_female_2

description:
opc12-47
rsem_opc.csv


title: HYD1-BZ


title: naive.CD8.TCR+media.4h 3

value: TCR+media 4h


title: OE1-MG rep2


title: naive.CD8.media.4h 3


title: opc12-45_pooled_female_2

description:
opc12-45
rsem_opc.csv

value: pool-and-split control


title: OE1-MG rep1


title: opc12-51_ten-cell_female_1

description:
opc12-51
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)


title: HYD3-IS

value: ischemic

value: 21 days post-hydrogel


title: opc12-46_ten-cell_female_1

description:
opc12-46
rsem_opc.csv

value: 10-cell sample


title: naive.CD8.TCR+TSLP.24h 3

value: CD8+ T cells

value: TCR+TSLP 24h


title: OE1-NaCl rep3

value: 100 mM NaCl for 12h


title: OE5-mock rep3


title: opc12-44_pooled_female_2

description:
opc12-44
rsem_opc.csv


title: HYD2-IS

value: heart

value: left ventricle


title: memory.CD8.TCR+TSLP.4h 1

value: memory

value: TCR+TSLP 4h


title: naive.CD8.TCR+media.24h 3

value: naive

value: TCR+media 24h


title: OE1-NaCl rep2

value: seedlings


title: HYD1-IS


title: OE1-NaCl rep1


title: opc12-43_pooled_female_1

description:
opc12-43
rsem_opc.csv

value: female


title: naive.CD8.TCR+TSLP.24h 2


title: opc12-42_pooled_female_1

description:
opc12-42
rsem_opc.csv


title: 28D4-F

source_name: 28 days post-infarct, animal 4

value: remote

value: 28 days post-infarct


title: OE1-mock rep3


title: naive.CD8.TCR+media.24h 2


title: HYD4-IS


title: opc12-41_pooled_male_2

description:
opc12-41
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

value: pool-and-split control

value: male


title: 28D3-F

source_name: 28 days post-infarct, animal 3


title: opc12-40_ten-cell_male_2

description:
opc12-40
rsem_opc.csv

value: 10-cell sample


title: naive.CD8.TCR+TSLP.24h 1

value: CD8+ T cells


title: naive.CD8.TCR+media.24h 1


title: opc12-66_pooled_male_1

description:
opc12-66
rsem_opc.csv


title: naive.CD8.media.4h 2

value: media 4h


title: 28D2-F

source_name: 28 days post-infarct, animal 2


title: 28D1-F

source_name: 28 days post-infarct, animal 1


title: naive.CD8.media.4h 1


title: opc12-38_pooled_female_2

description:
opc12-38
rsem_opc.csv


title: glyI2-MG rep2

value: 200 μM MG for 12h


title: 28D4-BZ

value: heart

value: border


title: glyI2-MG rep3


title: opc12-37_ten-cell_female_2

description:
opc12-37
rsem_opc.csv


title: naive.CD8.media.24h 1

value: media 24h


title: opc12-36_pooled_female_2

description:
opc12-36
rsem_opc.csv


title: glyI2-NaCl rep3

value: 100 mM NaCl for 12h


title: 28D2-BZ

value: left ventricle


title: opc12-35_pooled_female_2

description:
opc12-35
rsem_opc.csv


title: OE1-mock rep2


title: 28D1-BZ


title: naive.CD8.TCR+TSLP.4h 3

value: naive

value: TCR+TSLP 4h


title: opc12-34_ten-cell_male_1

description:
opc12-34
rsem_opc.csv


title: OE1-mock rep1

value: seedlings


title: opc12-39_ten-cell_male_2

description:
opc12-39
rsem_opc.csv


title: naive.CD8.TCR+media.4h 2

value: TCR+media 4h


title: naive.CD8.TSLP.4h 3

value: TSLP 4h


title: glyI2-NaCl rep2


title: opc12-33_ten-cell_male_1

description:
opc12-33
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)


title: glyI2-NaCl rep1


title: 28D3-IS

value: ischemic

value: 28 days post-infarct


title: glyI2-mock rep3


title: glyI2-MG rep1


title: opc12-32_ten-cell_female_1

description:
opc12-32
rsem_opc.csv

value: 10-cell sample

value: female


title: 28D3-BZ


title: naive.CD8.TCR+media.4h 1

value: CD8+ T cells


title: glyI2-mock rep2


title: 28D2-IS


title: glyI2-mock rep1


title: opc12-31_ten-cell_female_1

description:
opc12-31
rsem_opc.csv


title: naive.CD8.TCR+TSLP.4h 2


title: 28D1-IS


title: naive.CD8.TSLP.4h 2


title: opc12-29_pooled_male_2

description:
opc12-29
rsem_opc.csv

value: pool-and-split control

value: male


title: 28D4-IS

value: heart


title: 7D4-F

source_name: 7 days post-infarct, animal 4

value: remote

value: 7 days post-infarct


title: 7D3-F

source_name: 7 days post-infarct, animal 3

value: left ventricle


title: naive.CD8.TCR+TSLP.4h 1

value: naive


title: WT-MG rep2

value: wild type

value: 200 μM MG for 12h


title: opc12-28_ten-cell_female_2

description:
opc12-28
rsem_opc.csv


title: 7D2-F

source_name: 7 days post-infarct, animal 2


title: naive.CD8.media.0h 3

value: media 0h


title: WT-MG rep1

value: seedlings


title: opc12-26_pooled_male_1

description:
opc12-26
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)


title: WT-NaCl rep3

value: 100 mM NaCl for 12h


title: WT-NaCl rep2


title: 7D4-BZ

value: border


title: 7D1-F

source_name: 7 days post-infarct, animal 1


title: 7D2-BZ


title: opc12-30_pooled_female_1

description:
opc12-30
rsem_opc.csv


title: P.mex/lat #14_Brain

organism: Poecilia mexicana x Poecilia latipinna

source_name: Brain

value: 3 month old

value: Brain


title: WT-NaCl rep1


title: WT-mock rep3


title: opc12-24_pooled_female_1

description:
opc12-24
rsem_opc.csv

value: female


title: naive.CD8.media.0h 1

value: CD8+ T cells


title: P.mex/lat #14_Liver

source_name: Liver

value: Liver


title: opc12-23_ten-cell_male_2

description:
opc12-23
rsem_opc.csv

value: 10-cell sample

value: male


title: 7D1-BZ

value: heart

value: 7 days post-infarct


title: P.mex/lat #13_Ovary

source_name: Ovary

value: Ovary


title: opc12-22_pooled_male_2

description:
opc12-22
rsem_opc.csv

source_name: Brain oligodendrocyte precursor cells

value: pool-and-split control


title: P.mex/lat #13_Liver


title: 7D3-IS

value: left ventricle

value: ischemic


title: opc12-27_pooled_male_1

description:
opc12-27
rsem_opc.csv


title: WT-mock rep2

value: wild type

value: seedlings


title: WT-mock rep1


title: 7D4-IS


title: opc12-21_pooled_male_2

description:
opc12-21
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)


title: naive.CD8.media.0h 2

source_name: sleen

value: naive

value: media 0h


title: 7D3-BZ

value: border


title: P.mex/lat #13_Brain

value: 3 month old

value: female

value: Brain


title: WT-MG rep3

value: 200 μM MG for 12h


title: beta'greAB-_RNET-seq_rep2

city: Tianjin

first: Zhe

last: Sun

address: 32 West 7th Ave

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
nascent RNA
betaprime_greAB-_RNET-seq_rep1_5prime_R1_positive_strand.wig.gz
betaprime_greAB-_RNET-seq_rep1_5prime_R1_negative_strand.wig.gz

data_processing:
Library strategy: RNET-seq
Basecalling was performed by RTA 1.18.
Adaptor and barcode were removed by cutadapt 1.18.
For RNET-seq, duplicates were removed by bbmap 38.22.
RNET-seq reads were aligned to E. coli MG1655 genome NC_000913.2 using bowtie 1.2.2 with parameters -q -p 10 -v 1 -m 1 --best --strata. RNA-seq reads were mapped to the genome by STAR 2.6.1.
For RNET-seq, the counts of all uniquely aligned reads whose the 5’ ends mapped were recorded and counted in each coordinate by bedtools 2.27.1. For RNA-seq, the raw counts of aligned reads in each gene were calculated by HTseq 0.11.2.
Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.2
Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped.
Supplementary_files_format_and_content: hRpoD_and_hRpoDgreAB-_TPM.csv: Comma-separated text file includes the TMP values for each sample.

organism: Escherichia coli str. K-12 substr. W3110

growth_protocol: The overnight cell cultures were diluted in 100 ml LB medium (OD600 = 0.02) and incubated at 37 ºC to mid-log phase (OD600 = 0.5).

extract_protocol:
The cells collected were resuspended and lysed by 120 kU Ready-Lyse lysozyme (Lucigen), 400 U RNase I (Invitrogen) and 40 U alkaline phosphatase (NEB) at room temperature for 10 min. The chromosomal DNA with RNAP binding was pelleted and treated with 300 U RNase I, 6 U Turbo DNase (Invitrogen) and 100 U DNase I (Roche) by vortexing at room temperature for 10 min. After centrifugation, the supernatant containing ECs was transferred to mix with Ni-NTA beads for 1 hour at 4 ºC with continuous shaking (1000 rpm). The beads were washed and ternary complexes immobilized on the beads were further digested by 100 U RNase I, 2 U Turbo DNase and 40 U DNase I for 30 min at room temperature. The beads were washed and loaded onto 0.5 ml Ultrafree-MC centrifugal filters (Millipore). The immobilized ECs were eluted with wash buffer containing 0.3 M imidazole. The nucleic acids in the eluates were extracted once with phenol:chloroform:isoamylalcohol (PCI; 25:24:1) and once with chloroform. The top water phase was collected and the nucleic acids were precipitated by isopropanol at -80 ºC for 30 min. After centrifugation, the nucleic acids pellet was washed by 80% ethanol and air dried. The resultant pellet was dissolved in nuclease-free water. The DNA was removed by 2 U Turbo DNase and 10 U DNase I at 37 ºC for 15 min. The residual RNA was extracted by PCI and precipitated by isopropanol.
Libraries were constructed based on the modified protocol of NET-seq (Mayer, A. and Churchman, L. S. Nat Protoc. 2016). Briefly, a barcode DNA linker was ligated to 3' end of nascent RNA. The resulting RNA-DNA chimera was reverse transcribed by using PrimeScript Reverse Transcriptase and a 5' phosphorylated reverse transcription primer. The cDNA between 75-100 nt were excised after running 10% Urea-TBE gel, extracted and precipitated by isopropanol. The purified cDNA was circularized by ssDNA ligase (Takara) and applied to PCR the sequencing library using Illumina index primers and PrimeSTAR Max DNA polymerase (Takara). The DNA product excised from gel was extracted and purified for Illumina sequencing.

value: beta' greAB-

value: W3110 6xHis-rpoC greA::tet greB::amp

tag: growth


title: opc12-20_ten-cell_male_2

description:
opc12-20
rsem_opc.csv

value: 10-cell sample

value: male


title: P.mex/lat #12_Ovary

value: Ovary


title: beta'greAB-_RNET-seq_rep1


title: 7D2-IS

value: heart

value: left ventricle

value: 7 days post-infarct


title: opc12-19_pooled_female_2

description:
opc12-19
rsem_opc.csv

value: pool-and-split control


title: 7D1-IS

value: ischemic


title: P.mex/lat #12_Liver

value: Liver


title: Sham-50mg-12

city: Kunming

first: Hong-Yi

last: Zheng

state: Yunnan

address: No. 32 jiaochang East Road, Wuhua District

institute: Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean data were obtained from raw data by removing adapter sequences and trimming reads with poly-N and low quality reads (the percentage of low quality bases is over 50% in a read).
The subsequent workflows of alignment, assembly and mapping for these RNA-seq data were all completed in https://usegalaxy.org.
Clean reads from all libraries were aligned to Ensembl (http://asia.ensembl.org/) Mus musculus reference genome (Mus_musculus. GRCm38.p6) using HISAT2 v 2.2.1
The mapped reads of each library were assembled using StringTie v2.1.3.Gtf files generated by Stringtie were converted to gene count matrix by Ballgown v2.22.
Genome_build: Mus_musculus. GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using the RNeasy Plus Mini Kit (Qiagen, Germany). Illumina TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
All libraries were constructed and sequenced with PE 250 using the Illumina Novaseq6000 platform according to standard procedures.

value: Heart

value: post natal day 45

value: wild type

value: Sham-operation group treated with 50mg/kg/d gastrodin


title: beta'WT_RNET-seq_rep2

description:
nascent RNA
betaprime_WT_RNET-seq_rep1_5prime_R1_positive_strand.wig.gz
betaprime_WT_RNET-seq_rep1_5prime_R1_negative_strand.wig.gz

value: beta' WT

value: W3110 rpoC-6xHis::kan


title: beta'WT_RNET-seq_rep1


title: P.mex/lat #12_Brain

value: 3 month old

value: female

value: Brain


title: opc12-18_ten-cell_male_1

description:
opc12-18
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

value: 10-cell sample

value: male


title: opc12-17_ten-cell_male_1

description:
opc12-17
rsem_opc.csv


title: opc12-16_ten-cell_female_1

description:
opc12-16
rsem_opc.csv


title: P.mex/lat #11_Liver


title: Sham-5mg-10

value: Sham-operation group treated with 5mg/kg/d gastrodin


title: P.mex/lat #11_Brain


title: sigma70greAB-_RNET-seq_rep1

description:
nascent RNA
sigma70greAB-_RNET-seq_rep1_5prime_R1_positive_strand.wig.gz
sigma70greAB-_RNET-seq_rep1_5prime_R1_negative_strand.wig.gz

value: sigma70 greAB-

value: W3110 6xHis-rpoD greA::tet greB::amp


title: opc12-15_ten-cell_female_1

description:
opc12-15
rsem_opc.csv


title: sigma70WT_RNET-seq_rep2

description:
nascent RNA
sigma70WT_RNET-seq_rep1_5prime_R1_positive_strand.wig.gz
sigma70WT_RNET-seq_rep1_5prime_R1_negative_strand.wig.gz

value: sigma70 WT

value: W3110 6xHis-rpoD


title: opc12-14_ten-cell_male_2

description:
opc12-14
rsem_opc.csv


title: Sham-5mg-9

value: Heart


title: Sham-0mg-8

value: post natal day 45

value: Sham-operation group treated with menstruum


title: P.mex/lat #10, Ovary

value: Ovary


title: opc12-13_pooled_male_2

description:
opc12-13
rsem_opc.csv

value: pool-and-split control


title: P.mex/lat #10, Liver

value: Liver


title: sigma70WT_RNET-seq_rep1


title: Sham-0mg-7

value: wild type


title: opc12-12_ten-cell_female_2

description:
opc12-12
rsem_opc.csv

value: female


title: AngII-50mg-6

value: AngII modeling group treated with 50mg/kg/d gastrodin


title: sigma70greAB-_RNET-seq_rep2


title: P.mex/lat #10, Brain

value: 3 month old

value: Brain


title: Sham-50mg-11

value: Sham-operation group treated with 50mg/kg/d gastrodin


title: WT-2

city: Zhejiang Province

first: kang

last: ren

address: Yuhangtang Road No.388

institute: Zhejiang University

data_processing:
Data filtering steps. Prior to assembly, the low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed. software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT, version 2.0, parameters -l fr-first strand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts. software StringTie,version 1.3.0, parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Beauveria bassiana

source_name: Beauveria bassiana

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ARSEF 2860

value: hyphal

tag: characteristics

value: genotype:wild type


title: opc12-11_ten-cell_female_2

description:
opc12-11
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

value: 10-cell sample


title: WT-1


title: AngII-50mg-5

value: Heart


title: opc12-10_pooled_male_1

description:
opc12-10
rsem_opc.csv

value: male


title: AngII-5mg-4

value: post natal day 45

value: AngII modeling group treated with 5mg/kg/d gastrodin


title: dim5_3

value: genotype:dim5 mutant


title: P.mex/lat #4, Brain


title: dim5_2


title: opc12-08_ten-cell_male_1

description:
opc12-08
rsem_opc.csv


title: opc12-09_ten-cell_male_1

description:
opc12-09
rsem_opc.csv


title: AngII-5mg-3


title: dim5_1


title: dme_seedling_rep3

city: Seoul

first: Yeonhee

last: Choi

state: Gwanak-gu

address: 1 Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
Fragments with low quality reads or reads with adaptors were filtered using Trimmomatic (v.0.36)
We mapped filtered reads onto reference genome using HISAT2 (v2.1.0) identifying a total of 24,739 genes
Reads were assembled into transcripts using StringTie (v2.1.3)
Annotation was conducted using the TAIR10 FASTA sequence and the TAIR10 genome GTF annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: whole seedlings

growth_protocol: seedlings were grown in MS plastes

extract_protocol:
RNA was harvested using Qiagen RNeasy Plant Mini Kit(Cat. No. 74904)
Libraries were generated from BGI(the Beijing Genomics Institute)

value: dme/-

value: whole seedlings


title: dme_seedling_rep2


title: WT-3


title: naive.CD8.TSLP.4h 1

value: CD8+ T cells

tag: sorted cell

value: naive

value: TSLP 4h


title: P.mex/lat #4, Liver

value: 3 month old

value: female

value: Liver


title: P.mex/lat #4, Ovary

value: Ovary


title: sigma70greAB-_RNA-seq_rep3

data_processing:
Basecalling was performed by RTA 1.18.
Adaptor and barcode were removed by cutadapt 1.18.
For RNET-seq, duplicates were removed by bbmap 38.22.
RNET-seq reads were aligned to E. coli MG1655 genome NC_000913.2 using bowtie 1.2.2 with parameters -q -p 10 -v 1 -m 1 --best --strata. RNA-seq reads were mapped to the genome by STAR 2.6.1.
For RNET-seq, the counts of all uniquely aligned reads whose the 5’ ends mapped were recorded and counted in each coordinate by bedtools 2.27.1. For RNA-seq, the raw counts of aligned reads in each gene were calculated by HTseq 0.11.2.
Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.2
Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped.
Supplementary_files_format_and_content: hRpoD_and_hRpoDgreAB-_TPM.csv: Comma-separated text file includes the TMP values for each sample.

extract_protocol:
Cells were resuspended in TRIzol (Invitrogen) and incubated for 4 min at 95 ºC to disrupt the cells. The total RNA was purified by PCI extraction and chloroform extraction. After centrifugation, equal volume of isopropanol was added to the top water phase to precipitate the total RNA. The genomic DNA was digested by 50 U DNase I for 30 min at room temperature. The RNA was then purified by RNeasy Mini Kit (Qiagen).
Libraries were generated using TruSeq Standard Total RNA Library Prep Kit (Illumina).

value: sigma70 greAB-

value: W3110 6xHis-rpoD greA::tet greB::amp


title: opc12-06_pooled_male_1

description:
opc12-06
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

value: pool-and-split control


title: AngII-0mg-1

value: Heart

value: wild type

tag: treatment

value: AngII modeling group treated with menstruum


title: WT_seedling_rep3


title: sigma70greAB-_RNA-seq_rep1


title: opc12-05_ten-cell_female_1

description:
opc12-05
rsem_opc.csv

value: 10-cell sample


title: opc12-25_ten-cell_female_1

description:
opc12-25
rsem_opc.csv


title: HFD - Experiment 3

city: Odense M

first: Susanne

last: Mandrup

state: Fyn

address: Campusvej 55

department: Department of Biochemistry and Molecular Biologi

country: Denmark

institute: University of Southern Denmark

data_processing:
Fastq files were generated from raw sequencing data using Cellranger mkfastq.
Count matrices were generated from fastq files using zUMIs.
Genome_build: mm10
Supplementary_files_format_and_content: *.mtx: MatrixMarket files containing a sparse matrix of raw gene counts for all barcodes (with more than 0 counts) and genes
Supplementary_files_format_and_content: *.barcodes: tab-seperated text files containing the names of all barcodes (column names for the MatrixMarket files)
Supplementary_files_format_and_content: *.genes: tab-seperated text files containing the names of all genes (row names for the MatrixMarket files)
Supplementary_files_format_and_content: *.qc: tab-seperated text files containing the names of barcodes that passed quality-filtering

molecule: nuclear RNA

source_name: epididymal white adipose tissue

extract_protocol:
10x Genomics Chromium 3' v3 Single Cell Gene Expression Kit
Mice were euthanized by CO2 treatment and subsequently, subjected to cardiac perfusion using 1x PBS. eWAT was surgically removed and minced in nuclei preparation buffer (NPB) [10 mM HEPES, 1.5 mM MgCl2, 10mM KCl, 250 mM sucrose, 0.001% IGEPAL CA-630, 0.2 mM DTT, 1U/µL RNase inhibitor] on ice. The samples were further homogenized in 1.5 ml NPB using a 7 mL dounce tissue grinder, applying 10 strokes with the loose pestle and 10 strokes with the tight pestle. The homogenate was filtered through a 70 µm cell strainer and centrifuged to obtain nuclei at 1000 g for 10 min at 4 °C. The nuclear pellet was resuspended in 2 mL NPB and centrifuged at 1000 g for 10 min at 4 °C. The pellet was resuspended in nuclei resuspension buffer [20 mM Tris, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.001% IGEPAL CA-630, 0.2 mM DTT, 1U/µL RNase inhibitor]. The nuclei were counted using Bürker pattern counting chamber and 10,000-12,000 nuclei were submitted for snRNA-seq using the 10x Genomics system.

treatment_protocol: Wild-type mice were fed a low-fat or high-fat diet for 18 or 22 weeks.

tag: diet

value: HFD

tag: week


title: sigma70greAB-_RNA-seq_rep2


title: WT_seedling_rep2

value: whole seedlings


title: sigma70WT_RNA-seq_rep3

value: sigma70 WT

value: W3110 6xHis-rpoD


title: WT_seedling_rep1


title: opc12-03_pooled_male_1

description:
opc12-03
rsem_opc.csv

value: male


title: AngII-0mg-2

value: post natal day 45


title: sigma70WT_RNA-seq_rep2


title: LFD - Experiment 3

value: LFD


title: LFD - Experiment 2

extract_protocol:
10x Genomics Chromium 3' v2 Single Cell Gene Expression Kit
Mice were euthanized by CO2 treatment and subsequently, subjected to cardiac perfusion using 1x PBS. eWAT was surgically removed and minced in nuclei preparation buffer (NPB) [10 mM HEPES, 1.5 mM MgCl2, 10mM KCl, 250 mM sucrose, 0.001% IGEPAL CA-630, 0.2 mM DTT, 1U/µL RNase inhibitor] on ice. The samples were further homogenized in 1.5 ml NPB using a 7 mL dounce tissue grinder, applying 10 strokes with the loose pestle and 10 strokes with the tight pestle. The homogenate was filtered through a 70 µm cell strainer and centrifuged to obtain nuclei at 1000 g for 10 min at 4 °C. The nuclear pellet was resuspended in 2 mL NPB and centrifuged at 1000 g for 10 min at 4 °C. The pellet was resuspended in nuclei resuspension buffer [20 mM Tris, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.001% IGEPAL CA-630, 0.2 mM DTT, 1U/µL RNase inhibitor]. The nuclei were counted using Bürker pattern counting chamber and 10,000-12,000 nuclei were submitted for snRNA-seq using the 10x Genomics system.


title: opc12-02_ten-cell_male_2

description:
opc12-02
rsem_opc.csv


title: T47D_ZNF528-AS1 OE

city: Jinan

first: Qifeng

last: Yang

state: Shandong

address: Wenhua West Road No.44

department: Department of Breast Surgery

institute: Qilu Hospital

data_processing:
Illumina software used for basecalling.
HISAT2 was used for alignment, mapping reads to the genome
StringTie was used for String Assembly
HTSeq was used for estimating gene expression level
DESeq for 2 groups of biological replicates, while DEGseq for 2 individual samples
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw and normalized gene counts for every gene and every sample

source_name: breast cancer cells

growth_protocol: RPMI-1640 supplemented with 10% FBS, supplemented with penicillin and streptomycin, and 0.25ug/ml puromycin

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: stable transfection of pCDH and pCDH-ZNF528-AS1 vectors

value: ER+ breast cancer cells

value: transfection with pCDH-ZNF528-AS1 vectors

tag: cell line


title: T47D_pCDH

value: transfection with pCDH vectors


title: dme_seedling_rep1

value: dme/-

tag: tissue


title: opc12-07_ten-cell_male_1

description:
opc12-07
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)


title: LFD - Experiment 1


title: opc12-01_ten-cell_female_2

description:
opc12-01
rsem_opc.csv

value: female


title: HFD - Experiment 2


title: opc12-04_ten-cell_male_2

description:
opc12-04
rsem_opc.csv


title: Sample 35_RNASeq_FFiTreg-MLN

status: Public on Jan 04 2021

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description:
Gene Expression
C*.mLN_iTreg_85FF_m2

data_processing:
The raw bulk ATAC-Seq files were processed using the ENCODE-DCC pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) automated through Cromwell (https://github.com/broadinstitute/cromwell). Shortly, adapter sequences were trimmed (Cutadapt) prior to genome map with Bowtie2. Subsequently, mapped reads were filtered with Samtools. Next, sequencing enriched regions, associated to chromatin accessible peaks were called with MACS2 and filtered by running IDR, Irreproducible Discovery Rate, algorithm with a 10% threshold. Later, filtered peak regions were annotated by using HOMER software tools.
The raw bulk ChIP-Seq files were processed using the ENCODE-DCC pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) automated through Cromwell (https://github.com/broadinstitute/cromwell). Shortly, adapter sequences were trimmed by Cutadapt prior to the genome mapping with BWA and filtered subsequently using Samtools. Next, sequencing enriched regions associated to the transcription factor binding sites were called with SPP and filtered by running IDR, Irreproducible Discovery Rate, algorithm with a 5% threshold. Later, filtered peak regions were annotated by the HOMER software suite of tools. Comprehensive motif screening was performed with MEME-ChIP by using promoter originated, length-normalized reads to a 500 kb.
The raw fastq sequencing files were processed together with the gencode mouse annotation database (v. M21), by running kallisto (v. 0.46.0) to calculate the transcript abundances. Next, the abundance files were submitted to the sleuth (v. 0.30.0) pipeline based on R, for transcript abundance normalization, gene expression analysis and statistics. The quantified transcripts were combined into genes for the downstream analysis. Batch effects were evaluated through principal component analysis and removed with Limma. To capture significantly expressed genes we performed a likelihood ratio test between a null model and our experimental design using an adjusted p-value of 0.05 as threshold. The selected features were clustered using k-means and represented as a heatmap to define group gene signatures. Pairwise comparisons between groups were performed using the Wald-test and significant genes were considered for downstream analysis by having an adjusted p-value smaller than 0.05 and a log2 foldchange of 1.
The single cell RNA-Seq fastq files originated from the Chromium 10x libraries were processed with Cell Ranger (v. 3.0.2) for cell barcode aggregation, genome alignment, and UMI transcript quantification. The matrix of gene counts was analyzed with the Seurat (v. 3.1.2) package for the R environment. For downstream analysis, the top 3000 genes containing the highest standardized variance and expression were pre-selected. The detected cell clusters were visualized by performing Uniform Manifold Approximation and Projection (UMAP) algorithm. Cluster signatures were determined by the Wilcoxon Rank Sum test and genes containing adjusted p-values smaller than 0.01 were considered significant. For pseudotime trajectory analysis, the Seurat dataset was converted into a ‘SingleCellExperiment’ object and used within Slingshot and Monocle.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: kallisto abundances
Supplementary_files_format_and_content: h5: kallisto abundances and bootstrap estimates for sleuth
Supplementary_files_format_and_content: 10x mtx: UMI counts
Supplementary_files_format_and_content: 10x features.tsv: feature names
Supplementary_files_format_and_content: 10x barcodes.tsv: single cell barcodes
Supplementary_files_format_and_content: bb:  Indexed binary files containing annotated peaks
Supplementary_files_format_and_content: narrowpeak: text (BED6+4) files containing annotated peaks
Supplementary_files_format_and_content: bed: interval file containing annotated chip peaks
Supplementary_files_format_and_content: bigwig: Indexed binary files containing dense continuous data of read mapping

extract_protocol:
Atac-Seq: ATAC-Seq was performed on 5,000-40,000 FACS-purified cells from 2-9 mice. In brief, cells were lysed in lysis buffer for 1 minute and transposed with Tagment DNA Enzyme 1 (Illumina) for 30 minutes. DNA was cleaned up using a MinElute DNA purification Kit (Qiagen), followed by barcoding and library preparation by the Nextera DNA Library preparation kit (Illumina) according to manufacturer’s guidelines and sequenced on an Illumina Illumina NextSeq 500.
ChIP-Seq: Cells were fixed in 1% formaldehyde for 20min, quenched with 0.15M glycine and washed in PBS. 2x106 were then sorted and lysed for 30min at 4ºC. Cells were then sonicated for 22 minutes at 30 seconds on/off using the Bioruptor sonicator (Diagenode) and spun down. 10% was frozen for input, the remaining 90% was incubated with anti-ThPOK antibody bound to goat anti-rabbit M280 magnetic beads (Invitrogen) overnight at 4ºC prior to washing with RIPA buffer and overnight decrosslinking at 65ºC. DNA was then eluted off beads into TE buffer and, along with input, purified using the Zymogen DNA clean & concentrator kit. DNA was sequenced using NextSeq2500. To obtain Tregs, Foxp3RFP reporter mice were injected with IL-2/aIL-2 complex as previously described for 3 consecutive days for Treg expansion. CD4+ T cells were isolated from the spleen and mLNs and sorted as Thy1+TCRb+CD4+CD8a–RFP+.
RNA-Seq: Sorted cells (300-800) were lysed in TCL buffer (Qiagen, 1031576) supplemented with 1% βmercaptoethanol. RNA was isolated using RNAClean XP beads (Agentcourt, A63987), reversibly transcribed, and amplified. Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 550.
Single Cell Sequencing: Lymphocytes were sorted, counted for viability and immediately subjected to library preparation. The scRNA-Seq library was prepared using the 10x Single Cell Chromium system, according to the manufacturer’s instructions at the Genomics core of Rockefeller University and was sequenced on an Illumina NextSeq 550 to a minimum sequencing depth of 50,000 reads per cell using read lengths of 26 bp read 1, 8 bp i7 index, 98 bp read 2.

tag: strain background

tag: mouse id

value: Female

value: iTreg-MLN


title: HeartPos2_ATACSeq

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ATACSeq reads were aligned to the mm10 genomes using Bowtie2 (v 2.3.5.1) maximum insert size  set to 2000 (-X 2000)
Resulting SAM file from Bowtie2 were filtered for quality and converted to BAM using samtools v1.19 (samtools view -h -F 4 -q 10 -bS). Duplicate reads were removed using picard tools (https://broadinstitute.github.io/picard/)
NarrowPeak file were generated using Genrich peak caller (https://github.com/jsh58/Genrich), excluding chrM and chrY for peak identification (genrich -j -v -y  -r  -e chrM, chrY -E $BLACKLIST). BLACKLIST regions file for mm10 was downloaded from https://github.com/Boyle-Lab/Blacklist/tree/master/lists
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated from bedGraph files generated by generich.

extract_protocol:
NuTRAP/Cdh5-Cre (NuTRAP from Roh, 2017, Cell Reports) animals were generated to GFP tag endothelial cell nuclei. Total nuclei were isolated from whole hearts of 8-12week old male animals. Endothelial cell nuclei (GFP+) were isolated by flow cytometry in addition to non-endothelial nuclei (GFP-).
100-50,000 purified  GFP+ ("Pos") and GFP- ("Neg") nuclei were processed for ATACSeq, using the protocol outlined in Buenrostro, et al 2013, using 2.5uL of Tn5 per 50,000 nuclei.

tag: genotype/variation

tag: age

value: 8-12 weeks

value: heart

value: endothelial cell (GFP+) nuclei

value: 2.5uL per 50,000 nuclei


title: Sample 32_RNASeq_FFiTreg-IEL

description:
Gene Expression
C*.IEL_iTreg_67FF_m2

tag: Sex

tag: genotype

value: iTreg-iEL


title: HeartNeg2_ATACSeq

tag: cell type

value: non-endothelial cell (GFP-) nuclei


title: Sample 34_RNASeq_FFiTreg-MLN

description:
Gene Expression
C*.mLN_iTreg_81FF_m1

value: Male


title: HFD - Experiment 1

value: HFD


title: Sample 30_RNASeq_FFiTreg-IEL

description:
Gene Expression
C*.IEL_iTreg_10FF_m6


title: Sample 31_RNASeq_FFiTreg-IEL

description:
Gene Expression
C*.IEL_iTreg_59FF_m1


title: Differentiated_RNA-seq [SLX-12349.D706_D508]

city: London

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

data_processing:
Reads were mapped to the human reference (hg19). ChIP-seq and ATAC-seq samples were mapped using BWA (version 0.7.12) and RNA-seq samples using STAR aligner (version 2.6.0c).
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0).
H3K27AC, H3K27me3 and ATAC-seq samples: Average fragment size was determined using the ChIPQC Bioconductor package, and peak calling was performed with MACS2 (version 2.1.0), using fragment size as an extension size (--extsize parameter).
H3K9me3 samples: Enriched domains were called with EDD
ChIP-seq and ATAC-seq normalised coverage files (.bw) were generated using THOR.
RNA-seq counts were calculated using Rsubread.
Genome_build: hg19
Supplementary_files_format_and_content: .bw = coverage files
Supplementary_files_format_and_content: .narrowPeak/.bed = peak files
Supplementary_files_format_and_content: .txt = counts

growth_protocol: Keratinocytes were cultured in Epilife (Gibco) suppremented with human keratinocyte growth supprement (HKGS, Gibco).

extract_protocol:
For ChIP-seq, lysates were cralified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-seq, RNA was purified from using the Qiagen RNeasy plus kit according to the manufacturer's instructions.
For ChIP-seq, libraries were prepared using the NEB-Next Ultra II DNA Library Prep Kit (E7645, New England Biolabs) according to the manufacturer's instructions. For RNA-seq, libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: To induce differentiation in culture, keratinocytes were treated with 500 nM of phorbol 12-myristate 13-acetate (PMA, Sigma, P8139) for 48 h after become confluent.

value: Skin-derived primary keratinocyte

tag: passage

tag: condition

value: Differentiated


title: Differentiated_RNA-seq [SLX-12349.D707_D507]


title: Differentiated_RNA-seq [SLX-12349.D707_D506]


title: Sample 28_RNASeq_FFiexTreg-IEL

description:
Gene Expression
C*.exTregIEL_66FF_m2

value: exTreg-IEL


title: Differentiated_RNA-seq [SLX-12349.D707_D503]


title: Growing_RNA-seq [SLX-12349.D708_D501]

value: Growing


title: Differentiated_RNA-seq [SLX-12349.D708_D505]


title: Growing_RNA-seq [SLX-12349.D706_D507]


title: Growing_RNA-seq [SLX-12349.D706_D504]


title: Growing_RNA-seq [SLX-12349.D706_D506]


title: Growing_RNA-seq [SLX-12349.D707_D505]


title: sigma70WT_RNA-seq_rep1

tag: strain

value: sigma70 WT

value: W3110 6xHis-rpoD

tag: growth


title: Growing_RNA-seq [SLX-12349.D706_D501]


title: Growing_RNA-seq [SLX-12349.D707_D501]


title: Differentiated_RNA-seq [SLX-12349.D706_D502]


title: Differentiated_RNA-seq [SLX-12349.D707_D508]


title: Differentiated_RNA-seq [SLX-12349.D706_D503]


title: Sample 33_RNASeq_FFiTreg-MLN

description:
Gene Expression
C*.mLN_iTreg_45FF_m6


title: Rtel1f/f Ad-GFP MOCK Input biological replicate 1

first: Simon

middle: J

last: Boulton

address: 1 Midland Rd

institute: The Francis Crick Institute

description: DRIP-seq

data_processing:
Library strategy: DRIP-seq
The nf-core/chipseq pipeline (version 1.2.1; Ewels et al., 2020; https://doi.org/10.5281/zenodo.3966161) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was " nextflow run nf-core/chipseq --input design.csv --genome mm10 --gtf refseq_genes.gtf --single_end -profile crick -r 1.2.1".
All data was processed relative to the mouse UCSC mm10 genome (Karolchik et al., 2004). Gene annotation files in GTF format were originally downloaded from UCSC on February 19th 2016.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Genome_build: mm10
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/chipseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 broadPeak files generated using from the nf-core/chipseq pipeline command defined above.

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Rtel1F/F;WT RNH1-GFP MEFs were grown in DMEM supplemented with 10% FBS.

extract_protocol:
5x106 cells were collected, washed in PBS and resuspended in 1.6 ml of TRIS-EDTA buffer pH8.0. Cells were lysed by addition 50 μl SDS 20% and 5 μl ProteinaseK 20 mg/ml (Roche), mix gently and incubated overnight at 37°C. DNA was extracted with phenol/chloroform in phase lock tubes, precipitated with EtOH/sodium acetate, washed three times with 70% EtOH, and resuspended in TE. DNA was digested with EcoRI, HindIII, BsrGI, SspI and XbaI (NEB) restriction enzymes overnight at 37°C and DNA was isolated as described above and 4.4 μg of digested DNA was diluted in 500 μl TE buffer pH8.0 aliquots. For DRIP-seq, three IPs with the S9.6 antibody per condition were performed in parallel to obtain enough material for library construction. For each aliquot of digested DNA, 50 μl was kept as input and 50 μl of 10x binding buffer (100 mM NPO4 pH7.0, 1.4 M NaCl, 0.5% Triton X-100) and 10 μl of S9.6 antibody was added to the rest and incubated overnight at 37°C. Protein A Dynabeads (Roche 10002D) were added for 2 h. Bound beads were washed 3 times in binding buffer 1x and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, Proteinase K) for 45 min at 55°C. DNA was purified as described and resuspended in 20 μl 10 mM TrisHCl, pH 8.0. Three IPs per condition were pooled and 5 μl was withdrawed and efficiency of IP was assessed by QPCR. Once quality of S9.6 IP was verified, pooled IPs were treated with RNaseA for 1 h at 37°C and sonicated using a Covaris sonicator (11 cycles of 15 sec ON / 90 sec OFF)
Libraries were constructed using the NEB NEBNext® Ultra™ II DNA Library Prep Kit following the manufacturer’s instructions

treatment_protocol: Rtel1F/F;WT RNH1-GFP MEFs were infected with GFP or Cre-GFP adenovirus, after 48 h doxycycline (2 μg/ml) was added and cells were collected after 48 h

value: Mouse Embryonic Fibroblasts

value: Rtel1F/F;WT RNH1-GFP MEFs

value: Ad-GFP infected;mock treated


title: Sample 27_RNASeq_FFiexTreg-IEL

description:
Gene Expression
C*.exTregIEL_58FF_m1


title: Rtel1f/f Ad-GFP +DOX Input biological replicate 1

description: DRIP-seq

value: Ad-GFP infected; doxycycline treated


title: Rtel1f/f Ad-Cre +DOX Input biological replicate 1

description: DRIP-seq

value: Ad-Cre infected; doxycycline treated


title: Rtel1f/f Ad-Cre MOCK Input biological replicate 1

description: DRIP-seq

value: Ad-Cre infected; mock treated


title: Differentiated_RNA-seq [SLX-12349.D708_D504]


title: Rtel1f/f Ad-Cre MOCK DRIP biological replicate 1

description: DRIP-seq


title: Rtel1f/f Ad-GFP +DOX DRIP biological replicate 1

description: DRIP-seq


title: Rtel1f/f Ad-Cre +DOX DRIP biological replicate 1

description: DRIP-seq


title: Tlr7ko-5

city: Iowa City

first: Scott

middle: Matthew

last: Lieberman

state: IA

address: 500 Newton Road, 2191A ML

institute: University of Iowa

data_processing:
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project (https://github.com/chapmanb/bcbio-nextgen; version 1.0.8)
Reads were aligned to mm10 (genome FASTA and annotations derived from ftp://ftp.ensembl.org/pub/release-97/fasta/mus_musculus/) reference genomes using the ultra-rapid ‘hisat2’ aligner (ver 2.1.0)
Concurrently, reads were also quantified against the transcriptome using the ‘salmon’ aligner (ver 0.9.1), yielding estimated counts and values in length-normalized TPM (transcripts per million).
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package from Bioconductor
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with the counts that have been adjusted for library size factors and gene lengths
Supplementary_files_format_and_content: Matrix table with the raw counts

source_name: lacrimal gland

extract_protocol:
Qiagen Rneasy Plus Mini kit
RNA was prepared for sequencing using Illumina HiSeq 4000

value: NOD

value: Tlr7 knockout

value: male

value: lacrimal gland


title: Tlr7ko-4


title: Tlr7ko-3


title: 1_MC_sorted

type: RNA

city: Freiburg

first: Anne

last: Loesslein

address: Breisacherstr. 115

department: CCI

institute: Universität Freiburg

description: mouse bone marrow, monocytes

hyb_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix  GeneChip WT Pico Reagent Kit User Guide (Affymetrix, Inc., Santa Clara, CA, USA).

scan_protocol: For scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

label: biotin

source_name: mouse bone marrow, monocytes

label_protocol: Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin.

growth_protocol: animal facilities of the University of Freiburg under  specific pathogen-free conditions

extract_protocol: Bones were flushed with full medium. Cells were extracted from bone marrow by magnetic cell separation and fluorescence-activated cell sorting. Total RNA was extracted from sorted cells with the Rneasy Micro Kit (Qiagen) as per manufacturer's instructions.


title: 2_MC_MCSF_48h

description: monocytes cultured in M-CSF 48hours

source_name: monocytes cultured in M-CSF 48hours


title: 2_cMoP_MCSF_48h

description: cMoP cultured in M-CSF 48hours

source_name: cMoP cultured in M-CSF 48hours


title: 1_MC_MCSF_plusLMMS_48h

description: monocytes cultured in M-CSF and Lipomannan from M. smegmatis 48hours


title: 1_MC_MCSF_48h

description: monocytes cultured in M-CSF 48hours


title: 1_cMoP_MCSF_plusLMMS_48h

description: cMoP cultured in M-CSF and Lipomannan from M. smegmatis 48hours


title: 2_MC_MCSF_plusLMMS_48h

source_name: monocytes cultured in M-CSF and Lipomannan from M. smegmatis 48hours


title: Tlr7ko-1


title: Tlr7ko-2


title: Sample 29_RNASeq_FFiexTreg-IEL

description:
Gene Expression
C*.exTregIEL_9FF_m6

value: Female


title: Ifnar1ko-3

value: Ifnar1 knockout


title: 2_cMoP_MCSF_plusLMMS_48h

source_name: cMoP cultured in M-CSF and Lipomannan from M. smegmatis 48hours


title: Ifnar1ko-2


title: 2_MC_sorted

description: mouse bone marrow, monocytes


title: 1_cMoP_sorted

description: mouse bone marrow, cMoP

source_name: mouse bone marrow, cMoP


title: Def6 KO cOB Og0 rep2

city: NEW YORK

first: Kazuki

last: Inoue

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

data_processing:
fastp(https://github.com/OpenGene/fastp) was used to evaluate quality of sequenced reads and trim contaminated adaptor portions of sequenced reads.
RNA-seq reads were aligned to the mouse genome (mm10) using HISAT2. HTseq was subsequently used to count reads in features and then edgeR was used to estimate the transcript abundances as CPM (counts per million) values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: Calvaial bone

growth_protocol: osteoblastic cells were isolated from the calvarial bone of newborn (0-3d) mice by enzymatic digestion in α-MEM with 0.1% collagenase and 0.2% dispase and were cultured in α-MEM medium (ascorbic acid free, Invitrogen)  with 10% FBS (Invitrogen).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) was used to purify poly-A+ transcripts and generate libraries with multiplexed barcode adaptors following the manufacturer’s instructions.

treatment_protocol: Calvarial cells were cultured in osteogenic medium containing α-MEM with 10% FBS supplemented with 100 μg/mL ascorbic acid and 10 mM β-glycerophosphate to induce osteoblast differentiation. The osteogenic media were exchanged every two days.


title: 1_cMoP_MCSF_48h

description: cMoP cultured in M-CSF 48hours


title: Rtel1f/f Ad-GFP MOCK DRIP biological replicate 1

description: DRIP-seq


title: Def6 KO cOB Og12 rep2


title: Def6 WT cOB Og12 rep2

value: WT


title: WT-3

value: wild-type


title: WT-1


title: WT-2


title: Growing_RNA-seq [SLX-12349.D708_D503]

value: Skin-derived primary keratinocyte

value: Growing


title: Def6 KO cOB Og12 rep1


title: Def6 KO cOB Og0 rep1


title: 2_cMoP_sorted

description: mouse bone marrow, cMoP


title: Def6 WT cOB Og12 rep1


title: Def6 WT cOB Og0 rep1


title: AR14_H3K27me3

city: Chicago

first: Alexander

last: Ruthenburg

state: Illinois

address: 920 E 58th St

department: Molecular Genetics and Cell Biology

institute: The University of Chicago

data_processing:
Reference genome was modified to contain sequences of semi-synthetic nucleosome barcodes.
(AR13 only) NEXTflex qRNA-Seq Kit v2 Molecular barcodes were decoded and unique reads were selected using softwere for deconvolution provided by Bioo Scientific. Molecular barcodes were trimmed by removing 12bp from 5' end.
Reads were mapped to GRCm38/mm10+barcodes reference genome, using Bowtie2 (Langmead et al., 2009), end-to-end, sensitive preset.
SAM files were filtered to reject unmapped and unpaired reads, as well as fragments with length > 200bp and Phred quality score < 20.
Paired reads were merged into single interval of the fragment.
BEDTools genomecov(Quinlan and Hall, 2010) waw used to calculate bedgraphs of the genome coverage. BEDTools unionbedg was used to merge IP and input bedgraphs of genome coverage into multiple entry interval file of genome coverage.
Number of DNA fragments coming from semi-synthetic nucleosome standards were counted for each barcode and IP efficiency was calculated for each histone mark.
IP efficiency correction has been applied to calculate HMD as in (Grzybowski et al., 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig (Score). Score: HMD - histone modification density; genome_coverage - sequencing depth; transHMD - HMD of transbivalent nucleosomes; HMD_H3K9me3_correction - HMD after correcting for H3K9me3 off-specificity

source_name: Embryonic stem cells

growth_protocol: Mouse Embryonic Stem Cells (mESC) E14 cell line (129/Ola background) (Hooper et al., 1987) were grown at 37°C, 5% CO2, 95% humidity in ES media high glucose DMEM (Invitrogen) supplemented with 15% (v/v) FBS (Gibco), 2mM L-glutamine (Gibco), 1% (v/v) non-essential amino acids (Gibco), 1X Penicillin/Streptomycin (Gibco), 0.1 mM  2-mercaptoethanol (Gibco), 1000U/mL LIF (ESG1107, Millipore), 3 µM CHIR99021 (04-0004, Stemgent), 1 µM PD0325901 (04-0006, Stemgent), sterile filtered 0.1 µm membrane, stored in 4°C for up to 1 week. E14 cells were cultured on dishes coated with 0.1% gelatin (Sigma) without feeder cells, and passaged daily in 1:3 ratio (media was changed 3 hours prior passage). Cells were harvested at 80-90% confluence, with media changed at least 3 hours prior.

extract_protocol: ICeChIP has been done as previously described (Brand et al., 2008; Grzybowski et al., 2015). Briefly, ~100M plate adherent cells were released using Accutase (Millipore), quenched with complete medium and collected (500rcf, 5 min., 4°C). Subsequent steps have been done on ice, cells after each wash were collected by centrifugation (500rcf, 5 min., 4°C). Cells were washed twice with 10mL PBS, twice with 5mL of buffer N (15 mM Tris pH 7.5, 15 mM NaCl, 60 mM KCl, 8.5% (w/v) Sucrose, 5 mM MgCl2, 1 mM CaCl2 1 mM DTT, 1x RL Protease Inhibitor Cocktail). Cell’s membrane was lysed by adding 1volume of the 2x Lysis Buffer (Buffer N supplemented with 0.6% NP-40 substitute (Sigma)) to the single cell suspension in 2 PCVs (packed cell volumes) of Buffer N. After 10 minute incubation on ice, nuclei were collected by centrifugation and resuspended in at least 6 PNV (packed nuclei volumes) of buffer N. Subsequently nuclei were layered over 7.5 mL Sucrose Cushion N (15 mM Tris pH 7.5, 15 mM NaCl, 60 mM KCl, 30% (w/v) Sucrose, 5 mM MgCl2, 1 mM CaCl2 1 mM DTT, 1x RL Protease Inhibitor Cocktail, 50 µg/mL BSA(NEB)) in a 50 ml centrifuge tube. Nuclei were spun through the sucrose cushion in swinging bucket rotor at 500g for 12 min., 4°C. Nuclei were resuspended in 2 PNVs of buffer N, total nuclei acid content was measured spectroscopically at 260nm by Nanodrop (Thermo Scientific) (1A260 = 50 ng/µl), prior to measurement, DNA was stripped from chromatin by adding 18ul – 98 ul of 2M NaCl and DNA was fragmented by vortexing and water bath sonication. The amount and quality of nuclei was measured using a hemocytometer. The apparent concentration of chromatin was adjusted to 1ug/ul with Buffer N. The following semi synthetic standards were then spiked in: Symmetrical H3K4me3, H3K9me3, H3K27me3, H3K36me3, H3K79me2, H3K4me3/H3K27me3 cis bivalent, asymmetrical H3K4me3 , H3K4me3/H3K27me3 trans-bivalent. To fragment the DNA, we aliquoted 100 µg of chromatin and added 1Worthington unit of Micrococcal nuclease(Worthington) per 4.785µg of chromatin (measured at 260nm, 1A260 = 50 ng/µl), incubated at 37C for 12 minutes. Digestion was stopped by adding 1/10 volume of 11x MNase stop buffer (110mM EGTA, 110mMEDTA pH 8.0). Nuclei were lysed by slowly adding 5 M NaCl while mixing on a vortex (lowest setting) to the final concentration of 600 mM NaCl. Insoluble material has been spun down at 18000rcf, 1min. 4°C.   Hydroxyapatite (HAP) chromatography has been done as described in (Brand et al., 2008). Briefly, 66mg of hydroxyapatite (HAP) resin (Bio-Rad Macro-Prep® Ceramic Hydroxyapatite Type I 20 μm) was rehydrated with 200 μL of HAP buffer 1 (3.42 mM Na2HPO4 and 1.58 mM NaH2PO4 final pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 μM PMSF). Subsequently, 100 µg of digested soluble chromatin was added to the rehydrated resin and incubated for 10 minutes at 4C on a rotator. Afterwards, resin slurry was transferred to the centrifugal filter unit (Millipore Ultrafree MC–HV Centrifugal Filter 0.45 μm). Resin was washed 4 times with 200 μl of HAP buffer 1, 4 times with 200 μl of HAP buffer 2 (3.42 mM Na2HPO4 and 1.58 mM NaH2PO4 final pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 μM PMSF), and eluted 3 times with 50 µl HAP elution buffer (342 mM Na2HPO4 and 158 mM NaH2PO4 final pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 μM PMSF), each wash/elution step was accompanied by centrifugation step (600rcf, 30s, 4°C). Concentration of the chromatin was evaluated spectroscopically by Nanodrop (Thermo Scientific) (1A260 = 50 ng/µl). Apparent concentration of the chromatin was adjusted to 20 ng/µl with ChIP buffer 1 with BSA (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% (v/v) glycerol, 0.1% (v/v) NP-40 substitute, 100µg/ml BSA(NEB)).  ICeChIP was performed as previously described (Grzybowski et al., 2015) with following modifications: αH3K4me3 ChIP- 5µg chromatin, 2µg 304M3B-1xHRV3C(Hattori et al., 2016), 40µl Streptavidin M-280 Dynabeads (Invitrogen). αH3K9me3 ChIP- 3µg chromatin, 0.5µg 309M3B(Hattori et al., 2016), 10µl Streptavidin M-280 Dynabeads (Invitrogen). αH3K27me3 ChIP - 0.8µg chromatin, 0.6µg CST C36B11 lot 8, 5µl Protein G Dynabeads (Invitrogen).  Aforementioned volumes of magnetic beads were washed twice with 200µl ChIP buffer 1 with BSA. Antibodies were resuspended in 100 µl of ChIP buffer 1 with BSA; subsequently, magnetic beads were collected using magnetic rack, supernatant was removed, and magnetic beads were resuspended with the antibody solution and incubated for at least 1hr at 4°C on a rotator. Afterwards unbound antibody was washed away with two 200µl washes of ChIP buffer 1 with BSA. Streptavidin beads were additionally washed twice with 200µl of ChIP buffer 1 with BSA supplemented with 5µM biotin for 10 min at °4C on a rotator for each wash, followed by wash with 200µl ChIP buffer 1 with BSA. Supernatant was removed on a magnetic rack and specific amount of chromatin, mentioned at the beginning of this chapter, was used to resuspend the magnetic beads. Chromatin was incubated with antibody-beads conjugates for 10-15 minutes at 4°C on a rotator.    Subsequently, magnetic beads were washed two times with 200µl ChIP buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% (v/v) glycerol, 0.1% (v/v) NP-40 substitute, 100 µg/ml BSA(NEB)), and one time with 200µl ChIP buffer 3(10 mM Tris pH 7.5, 250 mM LiCl, 1mM EDTA, 0.5% Na•Deoxycholate, 0.5%(v/v) NP 40 substitute, 100 µg/ml BSA(NEB)), 10 minute, at 4°C, on a rotator with tube change after each wash. These washes were followed by quick 200µl ChIP buffer 1 (without BSA) wash and 200µl TE wash (10mM Tris-HCl pH 8.0, 1mM EDTA). Chromatin was released from the resin using 50µl ChIP elution buffer(50 mM Tris pH 7.5, 1 mM EDTA, 1% w/v SDS) at 55°C for 5 minutes. Elution was supplemented with 200mM NaCl, 10mM EDTA, 10µg of Proteinase K (Roche) and incubated at 55°C for 2 hours. DNA was isolated using 3 volumes of Serapure HD (1mg/ml of 1µm, hydrophobic, carboxylated, Sera-Mag SpeedBeads (GE 65152105050250), 20% PEG-8000, 2.5 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.05% Tween-20, filter sterilized prior to addition of  magnetic beads), incubated for 5 minutes at room temperature, collected with magnetic rack and washed twice with +200µl of 75% ethanol, on a magnetic rack without disturbing the magnetic beads. Subsequently, ethanol was carefully removed, and DNA was eluted by resuspending beads in 50µl of TE buffer, magnetic beads were collected using magnetic rack and supernatant was moved to a new tube. In order to limit DNA loss, all operations have been performed using 250µl siliconized tubes.   Sequential ICeChIP was performed in the same manner as described above with following changes. For the primary IP we have used 5µg of HAP purified chromatin, 2µg 304M3B-1xHRV3C – HRV3C cleavable, biotinylated, αH3K4me3 Fab (Hattori et al., 2016), immobilized on 40µl Streptavidin M-280 Dynabeads (Invitrogen). After 10 minutes incubation of chromatin with Fab-resin conjugate, resin was washed three times with 200µl ChIP buffer 1 with 100µg/ml BSA, each wash consisted of 10 minutes incubation at 4°C on a rotator, followed by tube change. Subsequently, resin was briefly washed with 200ul ChIP buffer 1 with 100µg/ml BSA, and chromatin was released from the resin with 20µl of ChIP buffer 1 supplemented with 100µg/ml BSA and 4µg HRV3C incubated on ice for 60 minutes, elution step was repeated one more time and both elutions were combined. Primary elution was added to 0.6µg CST C36B11, αH3K27me3 mAb, immobilized on 5µl of Protein G Dynabeads(Invitrogen) for 10 minutes, at 4°C, on a rotator. Subsequently, magnetic beads were washed two times with 200µl ChIP buffer 2, and one time with 200µl ChIP buffer 3, 10 minute, at 4°C, on a rotator with tube change after each wash. These washes were followed by quick wash with 200µl ChIP buffer 1 (without BSA). Chromatin was released from the resin using 50µ

tag: chip antibody

tag: amplification cycles

tag: map quality cut-off

tag: mononucleosome cut-off

tag: reference genome

value: mm10 (GRCm38)


title: AR14_H3K4me3


title: AR14_Bivalent


title: AR14_Input


title: AR14_H3K9me3


title: AR13_H3K4me3


title: AR13_H3K4me3-to-H3K27me3


title: AR13_Input


title: A14-LENA-MNP technical replicate 3

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: MNP, LENA, Animal A14, technical replicate 3

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for demultiplexing.
tab-delimited text files include gene counting for each sample
Genome_build: ss102 (Ensembl 91)
Supplementary_files_format_and_content: reads counts

organism: Sus scrofa

source_name: MNP

extract_protocol:
Total RNA from sorted cells was extracted using the Arcturus PicoPure RNA Isolation kit (ThermoFisher Scientiﬁc, St Aubin, France) according to the manufacturer’s instructions. The RNase-Free DNase Set (Qiagen, France) was used to remove contaminating DNA. RNA integrity was assessed using an RNA 6000 Pico kit on a Bioanalyzer 2100 (Agilent Technologies).
1 to 3 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina).

value: Large White

value: MNP

tag: infected

value: yes

tag: virus

value: LENA

tag: original name (to remove)

tag: animal id


title: A14-FL-MNP technical replicate 4

description: MNP, FL, Animal A14, technical replicate 4

value: FL


title: A14-LENA-MNP technical replicate 1

description: MNP, LENA, Animal A14, technical replicate 1


title: A14-LENA-MNP technical replicate 2

description: MNP, LENA, Animal A14, technical replicate 2


title: A14-LENA-MNP technical replicate 4

description: MNP, LENA, Animal A14, technical replicate 4


title: A14-FL-MNP technical replicate 3

description: MNP, FL, Animal A14, technical replicate 3


title: A14-CTRL-MNP technical replicate 2

description: MNP, CTRL, Animal A14, technical replicate 2

value: no


title: A14-CTRL-MNP technical replicate 3

description: MNP, CTRL, Animal A14, technical replicate 3


title: A14-CTRL-MNP technical replicate 1

description: MNP, CTRL, Animal A14, technical replicate 1


title: A13-LENA-MNP technical replicate 4

description: MNP, LENA, Animal A13, technical replicate 4


title: A13-LENA-MNP technical replicate 2

description: MNP, LENA, Animal A13, technical replicate 2


title: A13-LENA-MNP technical replicate 3

description: MNP, LENA, Animal A13, technical replicate 3


title: A14-CTRL-MNP technical replicate 4

description: MNP, CTRL, Animal A14, technical replicate 4


title: A14-FL-MNP technical replicate 2

description: MNP, FL, Animal A14, technical replicate 2


title: A13-FL-MNP technical replicate 3

description: MNP, FL, Animal A13, technical replicate 3


title: A14-FL-MNP technical replicate 1

description: MNP, FL, Animal A14, technical replicate 1


title: A13-FL-MNP technical replicate 2

description: MNP, FL, Animal A13, technical replicate 2


title: A13-LENA-MNP technical replicate 1

description: MNP, LENA, Animal A13, technical replicate 1


title: A13-FL-MNP technical replicate 1

description: MNP, FL, Animal A13, technical replicate 1


title: A12-LENA-MNP technical replicate 4

description: MNP, LENA, Animal A12, technical replicate 4


title: A13-FL-MNP technical replicate 4

description: MNP, FL, Animal A13, technical replicate 4


title: A13-CTRL-MNP technical replicate 1

description: MNP, CTRL, Animal A13, technical replicate 1


title: A13-CTRL-MNP technical replicate 2

description: MNP, CTRL, Animal A13, technical replicate 2


title: Humanized_HuR_KD4

city: Bethesda

first: Haiming

last: Cao

address: 9000 Rockville Pike

institute: NIH

data_processing:
Sequenced reads were trimmed using trimgalore
For wild type mice liver,trimmed reads were aligned tomouse (mm10) genome using HISAT2 align with parameters --no-mixed --no-discordant.  For humanized mice livers, trimmed reads were aligned to a combined human (b38) and mouse (mm10) genome using HISAT2 align with parameters --no-mixed --no-discordant
Aligned reads were transformed into .bam files and sorted by coordinate using sambamba view and sambamba sort.
Read counts were generated using the featureCounts program from the subread package with parameters -p -P and were normalized as TPM (Transcripts Per Million).
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

source_name: liver

growth_protocol: Male C57BL/6 mice from the Jackson Laboratory were used for all experiments. Groups of co-housed mice were randomly assigned to experimental groups with age and weight matched between groups.TK-NOG mice, in which a herpes simplex virus type 1 thymidine kinase (TK) transgene under a mouse albumin promoter is expressed within the liver of highly immune-deficient NOG mice, were obtained from Taconic Biosciences. The TK converts an antiviral medication ganciclovir (GCV) into a toxic product that allows selective elimination of TK positive cells in vivo. The cryopreserved primary human hepatocytes were obtained from Thermo Fisher Scientific. The humanized TK-NOG mice were prepared as previously described (Hasegawa, M. et al.). Briefly, The TK-NOG mice at 8-9 weeks old received an i.p. injection of GCV at a dose of 25 mg/kg. One week later, 50ul volume of 1  106 human primary hepatocytes suspended in HBSS solution were transplanted via intra-splenic injection. 8-12 weeks after transplantation, the serum human albumin in the mice were measured as an index of the extent of human hepatocytes replacement. Humanized TK-NOG mice with serum human albumin levels above 0.5 mg/ml were used for experiments, in which human hepatic genes could be reliably detected by q-PCR. Reference paper PMID: 21238430.

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

treatment_protocol: HuR shRNA adenoviruses were delivered into WT or humanized mice intravenously at 2 × 109 pfu/mouse for both control virus and HuR shRNA virus . After seven days, liver tissue samples were harvested after a four hours fasting and stored immediately in liquid nitrogen till further analysis.

value: TKNOG

tag: host organism

value: TKNOG Mus musculus

tag: xenograft organism

value: Homo sapiens


title: A12-LENA-MNP technical replicate 2

description: MNP, LENA, Animal A12, technical replicate 2


title: Humanized_HuR_KD3


title: Humanized_Lacz4


title: A13-CTRL-MNP technical replicate 3

description: MNP, CTRL, Animal A13, technical replicate 3


title: Humanized_Lacz3


title: Humanized_HuR_KD2


title: A13-CTRL-MNP technical replicate 4

description: MNP, CTRL, Animal A13, technical replicate 4


title: WT_Lacz6


title: Humanized_HuR_KD1


title: Humanized_Lacz1


title: Humanized_Lacz2


title: A12-LENA-MNP technical replicate 3

description: MNP, LENA, Animal A12, technical replicate 3


title: A12-LENA-MNP technical replicate 1

description: MNP, LENA, Animal A12, technical replicate 1


title: WT_Lacz4


title: A12-FL-MNP technical replicate 1

description: MNP, FL, Animal A12, technical replicate 1


title: WT_Lacz5


title: A12-FL-MNP technical replicate 3

description: MNP, FL, Animal A12, technical replicate 3


title: A12-FL-MNP technical replicate 4

description: MNP, FL, Animal A12, technical replicate 4


title: A12-FL-MNP technical replicate 2

description: MNP, FL, Animal A12, technical replicate 2


title: WT_Lacz3


title: A12-CTRL-MNP technical replicate 4

description: MNP, CTRL, Animal A12, technical replicate 4


title: WT HuR KD6


title: WT_Lacz2


title: WT HuR KD4


title: WT HuR KD5


title: A11-LENA-MNP technical replicate 3

description: MNP, LENA, Animal A11, technical replicate 3


title: WT HuR KD3


title: A12-CTRL-MNP technical replicate 2

description: MNP, CTRL, Animal A12, technical replicate 2


title: WT HuR KD2


title: WT_Lacz1


title: WT HuR KD1


title: A12-CTRL-MNP technical replicate 1

description: MNP, CTRL, Animal A12, technical replicate 1


title: A12-CTRL-MNP technical replicate 3

description: MNP, CTRL, Animal A12, technical replicate 3


title: A11-FL-MNP technical replicate 3

description: MNP, FL, Animal A11, technical replicate 3


title: A11-LENA-MNP technical replicate 4

description: MNP, LENA, Animal A11, technical replicate 4


title: A11-LENA-MNP technical replicate 1

description: MNP, LENA, Animal A11, technical replicate 1


title: A11-FL-MNP technical replicate 4

description: MNP, FL, Animal A11, technical replicate 4