title: WT + Sanofi-14h + DMXAA [EV_14h_2]

description:
EV_14h_2
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: Pretreat Sanofi-14h (SGKi) 500nM for 2hr prior to DMXAA 10μg.mL for 2 hours)


title: P2 CAR- Preinfusion - ADT

status: Public on Sep 26 2023

type: SRA

city: Sydney

first: Fabio

last: Luciani

address: High St. Kensington

country: Australia

institute: UNSW

description: Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT counts) was performed using the 10x genomics Cell Ranger pipeline aligning to the GRCh38 genome builds. A custom protocol was used to add AbSeq to the count matrix
Further processing was done with Seurat v3.0.0 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Single PBMC and CAR T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the 10x protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols
Single cell AbSEQ libraries were prepared for sequencing using standard Illumina protocols

tag: patient

tag: cell type

value: PBMC

tag: library type

value: ADT

tag: time

value: Preinfusion


title: SGK1/3 dKO + DMXAA [dKO_2]

city: Chapel Hill

first: Johnny

middle: Victor

last: Castillo Cabrera

state: NC

address: 450 West Drive

country: USA

institute: University of North Carolina

description:
dKO_2
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

library_source: transcriptomic

data_processing:
STAR v2.7.9a
Paired-end reads were mapped to mouse reference genome GRCm39 and Gencode vM27 annotation
StringTie v2.2.0
Gene expression were estimated based on Gencode vM27 gene annotation as TPM, gene count (prepDE.py3 script)
Assembly: GRCm39
Supplementary files format and content: tab-delimited gene counts x sample matrix with gene information
Supplementary files format and content: tab-delimited gene TPM x sample matrix with gene information

molecule: total RNA

organism: Mus musculus

growth_protocol: RAW264.7 cells of the indicated genotypes were grown in DMEM supplemented with 10% FCS and pen/strep.

extract_protocol:
Total RNA was extracted using Quick-RNA miniprep kit (Zymo Research). Greater than 1 microgram of RNA was sent for RNA sequencing.
Libraries were constructed at Novogene. polyA-tailed mRNA was enriched with olig(dT) beads. mRNA was randomly fragmented with fragmentation buffer and cDNA was synthesized with random hexamer primers prior to second strand synthesis (Illumina). Terminal repair, A ligation, and sequencing adaptor ligation were performed prior to size selection and PCR enrichment.

treatment_protocol: Cells were stimulated with 10μg/mL DMXAA for 2 hours or left untreated. A portion of cells were pretreated for 2 hours prior to stimulation with either vehicle (DMSO) or 500nM Sanofi-14h.

tag: cell line

value: macrophage

tag: genotype

value: SGK1/SGK3 double KO

tag: treatment

value: DMXAA 10μg/mL 2 hours

tag: batch


title: P2 CAR- D31 - ADT

description: Antibody-derived oligonucleotide (ADT)


title: Control_Cerebellum_2

city: Hamburg

first: Ulrich

last: Schüller

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
usegalaxy.eu and Rstudio
Low quality reads were detected using FastQC (Galaxy Version 0.73+galaxy0), and reads with average quality <20 were trimmed with Trimmomatic (Galaxy Version 0.38.1)
Reads were aligned to the GRCm39 (mm39) mouse reference genome using STAR aligner (Galaxy Version 2.7.8a+galaxy1; length of genome sequence around annotated junction = 100, using basic 2 pass-mapping,excluding alignements with indels or soft clippings, MAPQ value for unique mapper filter = 60, number of genome bins for coordinate-sorting = 50 and maximum number of loci anchor allowed to map to = 50)
Gene expression was quantified with featureCounts (Galaxy Version 2.0.1+galaxy2)
VST-normalized files were generated by DEseq2 (Galaxy Version 2.11.40.7+galaxy2)
Assembly: mm39
Supplementary files format and content: tab-delimited text files include featureCounts for each sample
Supplementary files format and content: comma separated values file includes normalized data for all samples

source_name: FFPE, cerebellum

extract_protocol:
RNA was harvested from FFPE tissue using the Maxwell RSC RNA FFPE kit (Promega Corporation, WI, USA) following manufacturer's protocol
Ribosomal RNA was depleted with the RiboCop Human/Mouse/Rat V2 kit before library preparation with the CORALL Total RNA-seq V2 kit (both Lexogen GmbH, Vienna, AT) following manufacturer's protocol

tag: tissue

value: FFPE, cerebellum

tag: age (days)

value: injection of 0.4 mg tamoxifen on postnatal day 3


title: human_2C_B4_1

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Short-read RNA-Seq raw reads underwent adapter trimming and quality control using Trim Galore (v0.6.6) with default parameters. Filtered reads were aligned to the GRCh38 reference genome together with the Ensembl v102 gene annotation reference database with STAR (v2.7.5b) using the two-pass mapping approach with default parameters. Finally, RSEM (v1.3.3) was used to calculate gene and isoform-level expression using the following parameters: rsem-calculate-expression –alignments --strandedness none --paired-end --estimate-rspd.
Genome_build: hg38
Supplementary_files_format_and_content: TSV file containing gene counts

source_name: embryo

extract_protocol:
Donated embryos were thawed using the Quinn's Advantage Thaw Kit (SAGE) following the manufacturer’s instructions. Single embryos were lysed to release mRNA, which was primed using a modified oligo-dT primer and reverse-transcribed using template switching technology to generate full-length cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech, Takara; Cat# 634897), following the manufacturer’s instructions. The first-strand cDNA templates were then amplified using 14-16 cycles of LD-PCR and then purified using AMPure XP beads (Beckman Coulter).
Illumina sequencing libraries were prepared by following the Nextera XT DNA Library Preparation Kit (Illumina, # FC-131-1024) workflow, as recommended by the manufacturer. Briefly, 0.7 – 1 ng of amplified full-length cDNA from each sample was ultrasonically sheared using a Covaris AFA system, while also simultaneously ligated with adapters by tagmentation. Individual indices were then ligated onto the tagmented cDNA templates via PCR. The libraries were sequenced on an S1 200 flowcell on the NovaSeq platform as 100 nt or 125 nt paired-end reads at a depth of 50 million reads per sample.

value: high


title: Control_Cerebellum_1


title: P2 CAR- Preinfusion - mRNA

description: poly A RNA

library_source: transcriptomic single cell

molecule: polyA RNA

value: mRNA


title: P1 CAR+ D13 - ADT

description: Antibody-derived oligonucleotide (ADT)

source_name: CAR T

value: CAR T


title: human_2C_B3_6

value: good


title: P1 CAR+ D13 - mRNA

description: poly A RNA


title: WT no treatment [EV_1]

description:
EV_1
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: WT (empty vector sgRNA)

value: no treatment


title: human_2C_B3_5

value: fair


title: human_2C_B4_3


title: P1 CAR- D13 - ADT

description: Antibody-derived oligonucleotide (ADT)


title: MYC_SMARCA4_tumor_2

source_name: FFPE, tumor

value: FFPE, tumor

value: transplanted with MYC overexpressing SMARCA4-deficient granule cell precursors


title: ko-si-crypt-2

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

country: China

institute: Tsinghua University

data_processing:
RNA of these cells was extracted by RNeasy mini kit (74,104, Qiagen) as manuals.
cDNA libraries were conducted with the Ovation RNA-Seq System V2 kit and subjected to high_x0002_throughput sequencing on an Illumina Novaseq 6000 PE150
Sequencing reads were aligned to mouse genome reference (mm10) using STAR (Spliced Tran_x0002_scripts Alignment to a Reference)
Differential expression analysis was performed using the R package DESeq2 based on gene counts
Assembly: mm10
Supplementary files format and content: tab-delated text file of deseq2 results and normalized counts for each samples of crypt
Supplementary files format and content: tab-delated text file of deseq2 results and normalized counts for each samples of villus

source_name: crypt tissue

extract_protocol:
freshly collected epithelial cells from Gli1-CreERT2; Rosa26-tdTomato mice and Gli1-PtgscKO mice. RNA was purified using the RNeasy Kit 9 (mf167-01; Mei5 Biotech).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Small intestine

value: crypt tissue

tag: strain background


title: ko-si-villus-1

source_name: villus tissue

value: villus tissue


title: ko-si-villus-2


title: human_2C_B3_4


title: P1 CAR- D13 - mRNA

description: poly A RNA

value: PBMC


title: MYC_SMARCA4_tumor_1


title: ko-si-crypt-1


title: human_2C_B3_2


title: wt-si-villus-2

value: WT


title: SGK1/3 dKO + DMXAA [dKO_1]

description:
dKO_1
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: macrophage

value: SGK1/SGK3 double KO

value: DMXAA 10μg/mL 2 hours


title: human_2C_B4_2

value: high


title: wt-si-villus-1


title: MYC_SMARCA4_tumor_4


title: P1 CAR- D7 - ADT

description: Antibody-derived oligonucleotide (ADT)

value: ADT


title: human_2C_B3_1


title: KO input

city: Tsukuba

first: Tsukasa

last: Nabekura

state: Ibaraki

address: 1-1-1 Tennodai

department: Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance

country: Japan

institute: University of Tsukuba

library_source: genomic

data_processing:
CLC Genomics Workbench
Sequencing read FASTQ files were imported to CLC Genomics Workbench as paired-end reads.
Assembly: mm10
Supplementary files format and content: bedgraph

molecule: genomic DNA

source_name: Spleen

extract_protocol:
NK cells were purified and ixed with 1% formaldehyde, washed with TBSE buffer, and resuspended in 1% SDS lysis buffer. Cells were sonicated and immunoprecipitation was performed with anti-H3K4me3 polyclonal Ab and anti-H3K27ac polyclonal Ab, and bound to Dynabeads Protein A. Beads were reverse-crosslinked and DNA was recovered.
ChIP DNA was processed into DNA sequencing library using NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: Spleen

value: Natural killer cells

tag: cell subset

value: Naïve

value: Themis2 KO NK-CreERT2

tag: ly49h status

tag: infection

value: Day 0

tag: chip antibody


title: human_2C_B2_1


title: P1 CAR- Preinfusion - ADT

description: Antibody-derived oligonucleotide (ADT)

value: Preinfusion


title: MYC_SMARCA4_tumor_3

value: FFPE, tumor

value: transplanted with MYC overexpressing SMARCA4-deficient granule cell precursors


title: P1 CAR- D7 - mRNA

description: poly A RNA

value: mRNA


title: Memory_KO_H3K4me3_003

value: Memory

value: Day 28 post-MCMV infection

value: H3K4me3 (Abcam, ab8580)


title: wt-si-crypt-2

value: Small intestine

value: crypt tissue

value: WT


title: human_1C_B4_3

value: high


title: P1 CAR- Preinfusion - mRNA

description: poly A RNA

value: PBMC


title: human_1C_B4_2


title: Memory_KO_H3K4me3_002

value: Spleen


title: human_1C_B4_1


title: Memory_KO_H3K4me3_001

value: Natural killer cells


title: BHFS4 [RNA]

city: Nanning

first: Lingjie

last: Deng

address: a. Department of Prenatal Diagnosis and Genetic Diseases, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, Guangxi, China

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.8.4)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: GRCh37
Supplementary_files_format_and_content: The xlsx format file contains the FPKM value of gene in every sample

source_name: placenta

extract_protocol:
Placental tissues were collected immediately after abortion, stored in RNAlater solution at 4 °C for 12–16 h and then stored at -80 °C. RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: placenta

tag: classification

value: BHFS

value: --SEA/--SEA


title: BHFS5 [RNA]

institute: The First Affiliated Hospital of Guangxi Medical University


title: Memory_WT_H3K4me3_003

value: WT NK-CreERT2


title: human_1C_B3_7


title: Veh_M1

city: Nanjing

first: Yuanqing

last: Gao

state: CHINA

address: nanjing medical university, jiangning, nanjing, china

institute: Nanjing Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: Genome_build: mm10
Supplementary files format and content: 4_genes_fpkm_expression.txt includes FPKM value for each sample

source_name: brain

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: The neonates were gavaged with either vehicle or PLX3397 from P9 to P15

value: brain

value: Vehicle


title: human_1C_B3_5


title: Memory_WT_H3K4me3_001


title: BHFS2 [RNA]


title: Veh_F1


title: WT input

value: Naïve

value: Day 0


title: Naïve_KO_H3Kme3_003

value: Themis2 KO NK-CreERT2


title: Veh_M2


title: Veh_F2


title: NF5 [RNA]

value: normal fetus

value: [alpha][alpha]/[alpha][alpha]


title: PLX_M1


title: Naïve_KO_H3Kme3_002

value: H3K4me3 (Abcam, ab8580)


title: Memory_WT_H3K4me3_002

value: Memory

value: Day 28 post-MCMV infection


title: wt-si-crypt-1

value: Small intestine

value: crypt tissue

value: WT


title: human_1C_B3_3

value: high


title: BHFS1 [RNA]

value: placenta

value: BHFS


title: human_8C_B3_3


title: human_1C_B3_4


title: NF4 [RNA]


title: human_1C_B3_8


title: BHFS3 [RNA]

value: --SEA/--SEA


title: Naïve_KO_H3Kme3_001

value: Spleen

value: Natural killer cells


title: human_1C_B3_2


title: NF3 [RNA]


title: PLX_F2

value: brain


title: Naïve_WT_H3K4me3_003

value: Naïve

value: WT NK-CreERT2

value: Day 0


title: PLX_F1


title: NF2 [RNA]

value: normal fetus

value: [alpha][alpha]/[alpha][alpha]


title: human_1C_B3_1


title: Naïve_WT_H3K4me3_002

value: H3K4me3 (Abcam, ab8580)


title: PLX_M2


title: Naïve_WT_H3K4me3_001


title: human_1C_B2_1


title: human_1C_B1_2


title: Primary hepatocytes-S100a16-KD3

first: Wen-Song

last: Zhang

state: Jiangsu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Primary hepatocytes

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Primary hepatocytes

value: S100A16 knockdown

value: alcohol-feeding


title: Primary hepatocytes-S100a16-KD2


title: human_1C_B1_1


title: Memory_KO_H3K27ac_003

value: Memory

value: Themis2 KO NK-CreERT2

value: Day 28 post-MCMV infection

value: H3K27ac (Abcam, ab4729)


title: Memory_KO_H3K27ac_002


title: S24_60mM.KNO3_2.5nM.isoxaben_shift_rep3

city: Madison

first: Sarah

middle: J

last: Whitcomb

state: WI

address: 502 Walnut St

department: Cereal Crops Research Unit

institute: USDA-ARS

description:
24-60mMisx-shift
S24
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt

data_processing:
data filtering (removing adapter sequence, contamination, and low-quality reads) with SOAPnuke (BGI); filter parameters："-n 0.03 -l 20 -q 0.4 -A 0.28"; delete the entire read if more than 28% match the adapter sequence; delete the entire read if there are more than 40% bases having a quality value lower than 20; delete the entire read if there are more than 3% N in the read
read alignment with STAR v2.7.9a
counts per gene normalized by median of ratios method with DESeq2 v1.32.0
Assembly: TAIR10 release 51
Supplementary files format and content: cts_str2_STARout_allsamples.txt : tab-delimited text file, STAR read counts per gene in each sample
Supplementary files format and content: nCts_DESeq2_allsamples.txt : tab-delimited text file, DESeq2 normalized  read counts per gene in each sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Seedlings grown vertically on 1x MS media with 0.8% agar, modified to contain either 6 mM or 60 mM KNO3. Three days stratification, then moved to growth cabinet set to 21C/19C 16h/8h light/dark, under LED lighting at 100 uE.

extract_protocol:
Frozen roots added to 2 mL tube with 5 mm zirconia ball. Frozen tissue ground with Retsch Mill. Qiagen Rneasy Plant Mini Kit used to extract RNA.
Libraries prepared using polyA enrichment by BGI (Hong-Kong) for DNBSEQ platform.

treatment_protocol: Long term treatment: seedlings grown on KNO3-adjusted media containing 2.5 nM isoxaben or mock - roots harvested 6 days after stratification. Shift/short-term experiment: seedlings grown on polyester mesh on KNO3-adjusted media, then on day 5 shifted to media containing the same concentration of KNO3 with 2.5 nM isoxaben or mock - roots harvested at 6 days after stratification.

value: root


title: Primary hepatocytes-S100a16-KD1


title: Primary hepatocytes-WT3

value: WT


title: Primary hepatocytes-WT2


title: Memory_KO_H3K27ac_001

value: Spleen

value: Natural killer cells


title: KO T cells, G4 (G) treatment, R2

city: WuHan

first: TeDing

last: Chang

state: HuBei

address: No.1095, Jiefang Avenue, Qiaokou

institute: HuaZhong University of science and technology

data_processing:
Quality control: Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp (v0.21.0) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis .
Reads mapping  The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.1.0.
Assembly: mm10
Supplementary files format and content: tab10-delimited .txt file includes raw counts for each Sample
Supplementary files format and content: tab10-delimited .xlsx file includes TPM counts for each Sample

growth_protocol: Splenocytes were maintained in RPMI with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃. Treatment protocol:

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit fluorescence or microplate analyzer was used for quality control and quantification of the products.

treatment_protocol: Splenocytes were separated from Lrrc8af/f and Lrrc8af/f Cd4-Cre;OT-I mice. The splenocytes were stimulated with indicated peptides (unstime/ SIINFEKL-10pM(NL)/ SIINFEKL-1000pM(NH)/ SIIGFEKL-1000nM(G4)) for 6 hours. The OT-I CD8+ T cells were labeled with Va2-PE/CD8-A700 and sorted for the sequencing.

value: T cell

value: Lrrc8a knockout

value: G4 treatment


title: KO T cells, G4 (G) treatment, R3


title: WT T cells, G4 (G) treatment, R3

value: wild type


title: S23_60mM.KNO3_2.5nM.isoxaben_shift_rep2

description:
23-60mMisx-shift
S23
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: WT T cells, G4 (G) treatment, R2


title: KO T cells, G4 (G) treatment, R1


title: Memory_WT_H3K27ac_003

value: WT NK-CreERT2


title: Primary hepatocytes-WT1


title: Memory_WT_H3K27ac_002


title: NF1 [RNA]

value: placenta

value: normal fetus

value: [alpha][alpha]/[alpha][alpha]


title: S21_60mM.KNO3_shift_rep3

description:
21-60mM-shift
S21
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: Control / 9527-AN-0002

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

description: Control / 9527-AN-0002

data_processing:
Paired-end RNA sequencing reads were trimmed and filtered for quality using Trimgalore v0.6.7 (Krueger et al., 2023). Trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) (Dobin et al., 2013) v2.7.9a with the –quantMode GeneCounts parameter against the mm10 mouse genome and GENCODE comprehensive gene annotations (Release M23). On average 178 million uniquely mapped reads were acquired per sample. DESeq2 package v1.34.0 (Love et al. 2014) was used to perform normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: Pancreas

growth_protocol: Following isolation, islets were treated with 200μl of chilled 1-Thioglycerol/Homogenization Solution (Promega #AS1280), vortexed briefly, and stored at -80°C until RNA isolation the following day

extract_protocol:
RNA was isolated from islets from ~15-week-old male mice (WT and Kcnk16 L114P (L/P)) using Maxwell® 16 LEV simplyRNA Purification Kits (Catalog no. AS1280, Promega, USA)
RNA-seq libraries for RNA-seq was prepared using NEBNext Ultra II Directional RNA Library Prep Kit and protocol (P/N: E7760L) per manufacturer recommendations.

value: Pancreas

value: pancreatic islets

value: Control


title: Talk-1_L114P / 9527-AN-0001

description: Talk-1_L114P / 9527-AN-0001


title: WT T cells, G4 (G) treatment, R1


title: Naïve_KO_H3K27ac_003

value: Naïve

value: Themis2 KO NK-CreERT2

value: Day 0


title: S20_60mM.KNO3_shift_rep2

description:
20-60mM-shift
S20
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt

value: root


title: KO T cells, N4 Low (NL) dose treatment, R3

value: Spleen

value: NL dose treatment


title: S19_60mM.KNO3_shift_rep1

description:
19-60mM-shift
S19
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: Memory_WT_H3K27ac_001

value: Natural killer cells

value: Memory

value: Day 28 post-MCMV infection

value: H3K27ac (Abcam, ab4729)


title: Talk-1_L114P / 9454-AN-0007

description: Talk-1_L114P / 9454-AN-0007


title: Control / 9454-AN-0008

description: Control / 9454-AN-0008


title: WT T cells, N4 Low (NL) dose treatment, R3

value: T cell

value: wild type


title: Talk-1_L114P / 9454-AN-0006

description: Talk-1_L114P / 9454-AN-0006


title: KO T cells, N4 Low (NL) dose treatment, R2

value: Lrrc8a knockout


title: Naïve_KO_H3K27ac_001


title: Naïve_KO_H3K27ac_002


title: S18_6mM.KNO3_2.5nM.isoxaben_shift_rep3

description:
18-6mMisx-shift
S18
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: S17_6mM.KNO3_2.5nM.isoxaben_shift_rep2

description:
17-6mMisx-shift
S17
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: WT T cells, N4 Low (NL) dose treatment, R2


title: Naïve_WT_H3K27ac_003

value: WT NK-CreERT2


title: S22_60mM.KNO3_2.5nM.isoxaben_shift_rep1

description:
22-60mMisx-shift
S22
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: Talk-1_L114P / 9454-AN-0004

description: Talk-1_L114P / 9454-AN-0004

value: Pancreas


title: KO T cells, N4 Low (NL) dose treatment, R1


title: Control / 9454-AN-0002

description: Control / 9454-AN-0002

value: pancreatic islets


title: Naïve_WT_H3K27ac_002


title: Control / 9454-AN-0001

description: Control / 9454-AN-0001

value: Control


title: WT T cells, N4 Low (NL) dose treatment, R1


title: S15_6mM.KNO3_shift_rep3

description:
15-6mM-shift
S15
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: Naïve_WT_H3K27ac_001

value: Naïve


title: KO T cells, N4 High (NH) dose treatment, R3

value: NH dose treatment


title: TNFR2KO-2

city: Ottawa

first: Seung-Hwan

last: Lee

state: Ontario

address: 451 Smyth Road

department: Biochemistry, Immunology and Microbiology

country: Canada

institute: University of Ottawa

description: WT_2 and TNFR2KO_2 samples were isolated from the same pooled spleen sample generated from 3 treated NSG mice.

data_processing:
Trimmed first 15bp to remove low quality base calls using Trimmomatic (Version 1.4).
Alignment to mouse genome (mm10) assembly Kallisto (Version 0.46.1).
Gene level quanitification using Tximport (Version 1.26.1)
Assembly: mm10
Supplementary files format and content: csv file including raw counts for each sample

extract_protocol:
Spleens were harvested, and a single-cell suspension was generated following red blood cell lysis and filtration through a 70-uM filter. NK cells were enriched from the spleen by negative selection using the Mojosort Mouse NK cell isolation kit. Ly49H+ (CD45.1 or CD45.2) cells were sorted with the Sony SH800. RNA was extracted using the purelink RNA mini kit (Thermofisher).
Poly-A enriched (stranded) library. Performed by Genome Quebec in Montreal, Quebec, Canada.
RNA-Seq perfomed using 100bp paired-end sequencing by Novaseq 6000. Performed by Genome Quebec.

treatment_protocol: Ly49H+ natural killer (NK) cells from CD45.1-WT and CD45.2-TNFR2 knockout (KO) mice were co-transferred into NSG mice. The mice were then infected with murine cytomegalovirus (MCMV). On day 3.5 post-infection, Ly49H+ cells (CD45.1 or CD45.2) were isolated using flow sorting and analyzed using bulk RNA-seq.

value: CD45.2 Ly49H+ NK

value: TNFR2 Knockout

value: Adoptive Transfer and MCMV Infection


title: Memory KO_002

data_processing:
CLC Genomics Workbench
Sequencing read FASTQ files were imported to CLC Genomics Workbench as paired-end reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized expression values

extract_protocol:
Total RNA in sorted NK cell subsets was isolated using a TRIzol reagent and the yield was monitored using an Agilent Bioanalyzer RNA 6000 Pico Kit.
RNA libraries for RNA-seq were prepared by using a SMART-seq Stranded Kit.

value: Spleen

value: Themis2 KO NK-CreERT2


title: Memory KO_003

value: Natural killer cells

value: Memory


title: WT T cells, N4 High (NH) dose treatment, R3


title: S13_6mM.KNO3_shift_rep1

description:
13-6mM-shift
S13
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt

value: root


title: KO T cells, N4 High (NH) dose treatment, R2

value: T cell


title: Memory KO_001

value: Day 28 post-MCMV infection


title: Memory WT_003


title: WT-1

description: WT_1 and TNFR2KO_1 samples were isolated from the same pooled spleen sample generated from 3 treated NSG mice.

value: CD45.1 Ly49H+ NK

value: Wild Type


title: TNFR2KO-1


title: S10_60mM.KNO3_2.5nM.isoxaben_rep1

description:
10-60mMisx
S10
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: WT-2


title: WT T cells, N4 High (NH) dose treatment, R2

value: wild type


title: S11_60mM.KNO3_2.5nM.isoxaben_rep2

description:
11-60mMisx
S11
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: oocyte, KO, MII stage2

city: Hangzhou

first: Long

last: Bai

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: oocyte

growth_protocol: GV stage oocytes were cultured in M16 medium in humidified atmosphere with 5% CO2 at 37C

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

value: oocyte

value: KO

value: MII stage


title: Memory WT_002

value: WT NK-CreERT2


title: S09_60mM.KNO3_rep3

description:
09-60mM
S09
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: KO T cells,N4 High (NH) dose treatment, R1

value: Lrrc8a knockout

value: NH dose treatment


title: oocyte, KO, MII stage1


title: WT T cells, N4 High (NH) dose treatment, R1


title: Memory WT_001


title: S08_60mM.KNO3_rep2

description:
08-60mM
S08
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: KO T cells, Control, R3

value: Control


title: S14_6mM.KNO3_shift_rep2

description:
14-6mM-shift
S14
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: oocyte, KO, GVBD stage2

value: GVBD stage


title: Naïve KO_003

value: Spleen

value: Naive

value: Themis2 KO NK-CreERT2

value: Day 0


title: S07_60mM.KNO3_rep1

description:
07-60mM
S07
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt

value: root


title: S12_60mM.KNO3_2.5nM.isoxaben_rep3

description:
12-60mMisx
S12
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: WT T cells, Control, R3

value: T cell


title: oocyte, KO, GVBD stage1


title: Naïve KO_002

value: Natural killer cells


title: S06_6mM.KNO3_2.5nM.isoxaben_rep3

description:
06-6mMisx
S06
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: Naïve KO_001


title: KO T cells, Control, R2


title: oocyte, KO, GV stage2

value: GV stage


title: S05_6mM.KNO3_2.5nM.isoxaben_rep2

description:
05-6mMisx
S05
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: oocyte, KO, GV stage1


title: WT T cells, Control, R2

value: wild type


title: Naïve WT_003


title: S04_6mM.KNO3_2.5nM.isoxaben_rep1

description:
04-6mMisx
S04
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: S16_6mM.KNO3_2.5nM.isoxaben_shift_rep1

description:
16-6mMisx-shift
S16
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: Naïve WT_002


title: oocyte, WT, MII stage1

value: oocyte

value: WT


title: KO T cells, Control, R1


title: Long-lived Ly49H- NK_003

value: Long-lived

value: Day 28 post-MCMV infection


title: S03_6mM.KNO3_rep3

description:
03-6mM
S03
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: oocyte, WT, GVBD stage2


title: oocyte, WT, MII stage2

value: MII stage


title: S01_6mM.KNO3_rep1

description:
01-6mM
S01
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: GFP-2 RNA-seq

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

data_processing:
zebracall software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using hisat2
Mapped reads were ennotated by Stingtie with gencode.vM22.annotation.gtf
Read counts were generated by featurecounts
FPKM were calculated followed the standard formula "count/((transcript length in kb)*(total count/1000000)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each Sample ...

source_name: Muscle Stem Cells

extract_protocol:
Muscle Stem Cell isolation followed the  Nature protocol paper ''Isolation of Skeletal Muscle Stem Cells by Fluorescence-Activated Cell Sorting''
RNA libraries were prepared for sequencing using SMART-seq2 method

tag: strain

value: Muscle Stem Cells

tag: age

value: 33 months

value: GFP virus infection


title: Naïve WT_001

value: Spleen

tag: cell type

value: WT NK-CreERT2


title: S02_6mM.KNO3_rep2

description:
02-6mM
S02
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt


title: CPEB4-2 RNA-seq

value: CPEB4 virus infection


title: Long-lived Ly49H- NK_002


title: oocyte, WT, GVBD stage1

value: GVBD stage


title: ATAC_dpse_ovary_rep2

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: 10-12 ovaries

data_processing:
genome build/assembly: GCF_009870125
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

organism: Drosophila pseudoobscura

source_name: ovary

growth_protocol: All Drosophila species were maintained at room temperature on species-specific food.

extract_protocol:
The freshly dissected instact ovaries were directly lysed in ATAC-Resuspension Buffer (RSB, 10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2 in nuclease free water) containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and washed out with cold ATAC-RSB containing 0.1% Tween-20.
The transposition reaction was performed with 25 μl 2x TD buffer from and 2.5 μl transposase (100nM final) from Illumina Tagment DNA Enzyme and Buffer Small Kit (Illumina 20034197), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O at 37°C for 30 minutes in a thermomixer with 1000 RPM mixing. Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) was used for a clean-up. The transposed fragments were amplified for 5 cycles [72 °C for 5 min, 98 °C for 30 s (98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min) × 5] using NEBNext 2x MasterMix and primer pairs of the universal primer Ad1 and the index primers Ad2. This was followed by qPCR amplification to determine additional cycle number. Amplified DNA was purified using Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and eluted in 20 μl H2O. AMPure XP beads (Beckman Coulter) were used for double-sided bead purification. 100-600 bp fragments were selected using Blue Pippin (Sage Science).

value: ovary

tag: Sex

value: female


title: oocyte, WT, GV stage2


title: Long-lived Ly49H- NK_001

value: Natural killer cells


title: CPEB4-1 RNA-seq


title: GFP-1 RNA-seq


title: oocyte, WT, GV stage1

value: GV stage


title: ATAC_dpse_ovary_rep1

description: 10-12 ovaries

value: wild type


title: IgG RIP-seq rep2

description: Immunoprecipitated RNA

data_processing:
Library strategy: RIP-seq
zebracall software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using hisat2
Mapped reads were ennotated by Stingtie with gencode.vM22.annotation.gtf
Read counts were generated by featurecounts
FPKM were calculated followed the standard formula "count/((transcript length in kb)*(total count/1000000)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each Sample ...

value: 3 months


title: ATAC_dyak_ovary_rep3

description: 12 ovaries

data_processing:
genome build/assembly: droYak2
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

organism: Drosophila yakuba


title: Effector Ly49H- NK_002

value: Effector

value: Day 10 post-MCMV infection


title: Effector Ly49H- NK_003


title: ATAC_dyak_ovary_rep2

description: 10 ovaries


title: oocyte, KO, GV stage, input

data_processing:
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/).
Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeMus musculus(Version: v101).
Peak calling and diff peak analysis were performed by R package exomePeak2 (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: mm10

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs withE. coliDNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: oocyte

value: KO


title: IgG RIP-seq rep1

description: Immunoprecipitated RNA

value: Muscle Stem Cells


title: WT T cells, Control, R1

value: T cell

value: Control


title: Effector Ly49H- NK_001

value: Spleen


title: ATAC_dyak_ovary_rep1

description: 6 ovaries


title: oocyte, KO, GV stage, m6A peaks


title: Input RNA-seq rep2

description: Total RNA


title: Naïve Ly49H- NK_003

value: Naive

value: Day 0


title: Input RNA-seq rep1

description: Total RNA


title: oocyte, WT, GV stage, input

value: WT


title: Dyak.ovary.2 small-RNA-Seq

data_processing:
Trim Galore! (v0.6.4, --stringency 30 -e 0.1 -a TGCTTGGACTACATATGGTTGAGGGTTGTA --length 18 -q 0) was first run to remove an abundant rRNA sequence, followed by a second run (--stringency 5 -e 0.1 --length 18 --max_length 35 -q 0) to remove adapter sequences (specified using ‘-a’), and any flanking random nucleotides (‘--clip_R1’ and/or ‘--three_prime_clip_R1’ with appropriate arguments).
The processed reads were mapped to a miRNA hairpin database (miRBase release 22.1) using bowtie (v1.2.3, -S -n 2 -M 1 -p 20 --best --strata --nomaqround --chunkmbs 1024) with ‘--un’ and ‘--max’ to extract unmapped reads.
Reads not mapping to miRNAs were aligned to the respective reference genomes using bowtie (-S -n 2 -M 1 -p 20 --best --strata --nomaqround --chunkmbs 1024).
Multi-mapping reads were extracted into a separate BAM file using awk (MQ<10).
The BAM files were converted to bigWig using bamCoverage from deepTools (Ramírez et al., 2016) (v3.3.2, --binSize 1 --ignoreForNormalization chrM  --normalizeUsing CPM --exactScaling --skipNonCoveredRegions --minFragmentLength 23 --maxFragmentLength 30) and additionally ‘--filterRNAstrand’ to separate the two strands, ‘---scaleFactor’ to scale counts per million to reflect all mapped reads, and optionally ‘--minMappingQuality 50’ when extracting uniquely mapped reads.
Supplementary files format and content: bigWig showing read coverage per position. File name indicate species, genome assembly, strand, and sample.

extract_protocol:
Small RNAs were isolated using the TraPR Small RNA Isolation Kit (Lexogen) following the manufacturer's instructions. The soma-enrichment sRNA-seq libraries were generated for 13 species (2 replicates each) similar to published protocols (Akkouche et al., 2013; Chirn et al., 2015), with modifications.  In brief, 75-100 ovary pairs were dissected in ice-cold PBS.  Ovaries were dissociated for 18 minutes in 0.25% Trypsin (Sigma-Aldrich) at 25˚C, shaking at 800 rpm.  Dissociated tissue was pushed through a 40 µm nylon mesh (Greiner Bio-one) washed with equal volume Schneider 2 medium (Thermo Fisher Scientific) and then pelleted.  Cell count was quantified using the Luna-FL (Logos Biosystems).  Cells were pelleted and directly used as input for sRNA isolation using the TraPR Small RNA Isolation Kit (Lexogen).
sRNA libraries were generated using the Small RNA-Seq Library Prep Kit (Lexogen) with minor modifications.  Both primers A3 and A5 as well as the primer RTP were used at 0.5x.

value: ovary

tag: enrichment

tag: assembly


title: Dyak.ovary.3 small-RNA-Seq


title: t539, LSN

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
To be updated.
Assembly: mm10
Supplementary files format and content: readcount.txt

source_name: Lung tumor

growth_protocol: SCLC tumors were harvested at necropsy and were flash-frozen

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen #74106) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed
The libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit.  Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell. Sequencing reads were mapped to the mm10 genome by STAR. Statistics for differentially expressed genes were calculated by DESeq2.

tag: disease state

value: SCLC

value: Lung tumor

value: tumor cell

tag: genotype

value: RPP

value: LSN


title: CPEB4 RIP-seq rep2

description: Immunoprecipitated RNA

value: 3 months


title: Naïve Ly49H- NK_001

value: Natural killer cells


title: Long-lived Ly49H+ NK_003

value: Long-lived

value: Day 28 post-MCMV infection


title: Dyak.ovary.1 small-RNA-Seq


title: CPEB4 RIP-seq rep1

description: Immunoprecipitated RNA

value: Muscle Stem Cells


title: t536, LSN

tag: treatment


title: Dyak.ovary_FC.1 small-RNA-Seq

tag: tissue

value: somatic follicle cells


title: Long-lived Ly49H+ NK_002


title: pZE-FliX_3

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
fastq records trimming (cutadapt 3.7)
short reads mapping (rilseq 0.74)
wiggle file generation (deeptools 3.5.1)
Supplementary files format and content: wiggle file

organism: Escherichia coli K-12

source_name: MG1655(crl-) + pZE-FliX

growth_protocol: Bacterial strains were grown at 37˚C , shaking at 250 rpm, in LB rich medium and samples were collected at OD~0.2.

extract_protocol:
Standard TRIzol protocol was used for total RNA extraction.
Library construction was carried out based on the RNAtag-Seq methodology (Shishkin et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018)

treatment_protocol: Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen by liquid nitrogen.

value: Escherichia coli K-12

tag: genotype/variation

value: Constitutive overexpression of FliX

tag: growth


title: Long-lived Ly49H+ NK_001

value: Spleen

tag: cell subset


title: t757, Vehicle

value: Vehicle


title: pZE-FliX_2


title: Dyak.ovary_FC.2 small-RNA-Seq


title: t533, Vehicle


title: Dyak.ovary.4

data_processing:
Removal of adators using Trim Galore! (v0.6.4, --stringency 6 -e 0.1).
Alignment to the reference genome using HiSeq2 (v2.2.0, -max-seeds 100 -q -k 1).
Converting to bigWig and scaling to cpm using bamCoverage from deeptools (v3.3.2, --binSize 1 --ignoreForNormalization chrM  --normalizeUsing CPM --exactScaling --skipNonCoveredRegions, and additionally --filterRNAstrand and --scaleFactor).
Supplementary files format and content: bigWig showing read coverage per position. File name indicate species, genome assembly, strand, and sample.

extract_protocol:
Ovaries from 10-20 flies were dissected in ice-cold PBS and total RNA was extracted using TRIzol.  Briefly, ovaries were lysed in TRIzol (Thermo Fisher Scientific), and RNA was phase separated using chloroform (Sigma-Aldrich).   Total RNA in the aqueous fraction was precipitated using 100% isopropanol, washed with 70% ethanol, and dissolved in nuclease free water (Invitrogen).  Ribosomal RNA was depleted using RiboPOOL (siTOOLs, Biotech) following the manufacturer's protocol. The indicated RiboZero libraries were prepared as previously described (Kneuss et al., 2019, PMID: 31416967).
RNA-seq libraries were produced using NEBNext Ultra Directional Library Prep Kit for Illumina, following the manufacturer’s instructions for rRNA depleted RNA.

tag: rrna depletion

value: RiboPOOL


title: pZE_3_control for pZE-FliX

source_name: MG1655(crl-) + pZE

value: Control library of pZE-FliX


title: pZE-FliX_1


title: Dyak.ovary.3

value: ovary


title: LSN+PD-L1-27

description: 10x Genomics

data_processing:
Cell ranger version 6.0.2 pipeline (10× Genomics) was used to align sequencing data to the custom mouse reference genome and generate the gene-level counts matrix.
Assembly: Custom reference genome was established by adding EGFP and Cas9 sequence to the mouse genome (mm10-2020-A).
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mice were euthanized and lung tumors dissected and finely minced mechanically using a razor blade and then enzymatically digested with Mouse Tumor Dissociation Kit (Miltenyi Biotec, #130-096-730) following the manufacturer’s instruction.
For each sample, about 16,000 cells were loaded onto a 10× Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium Next GEM Single Cell 5' Kit v2 kit (10× Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq were normalized to 4 nM concentration and pooled. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform.

value: Lung tumor


title: Naïve Ly49H- NK_002

value: Naive

tag: ly49h status

tag: infection

value: Day 0


title: Effector Ly49H+ NK_003

value: Effector

value: Day 10 post-MCMV infection


title: oocyte, WT, GV stage, m6A peaks

value: oocyte

value: WT

value: GV stage


title: pZE_2_control for pZE-FliX


title: LSN+PD-L1-18

description: 10x Genomics

value: tumor cell

value: RPP


title: Dyak.ovary.2


title: Effector Ly49H+ NK_001

value: Natural killer cells


title: Effector Ly49H+ NK_002


title: Dyak.ovary.1


title: pZE_1_control for pZE-FliX

value: Escherichia coli K-12


title: Naïve Ly49H+ NK_003

value: Spleen


title: t534, LSN

value: SCLC

value: LSN


title: LSN+PD-L1-12

description: 10x Genomics


title: pZE-3

data_processing:
fastq records trimming (cutadapt 2.3)
short reads mapping and wiggle file generation (rilseq 0.60)
Genome_build: ecoli-k12-MG1655-NC_000913-3
Supplementary_files_format_and_content: wiggle file

growth_protocol: Bacterial strains were grown at 37˚C, shaking at 250 rpm, in LB rich medium and samples were collected at OD~0.2.

value: Control library of pZE-MotR*


title: LSN-26

description: 10x Genomics


title: Dpse.ovary.2 small-RNA-Seq

value: ovary


title: Dpse.ovary.1 small-RNA-Seq


title: LSN-13

description: 10x Genomics

value: Lung tumor


title: Naïve Ly49H+ NK_001

value: Naive


title: Dpse.ovary_FC.2 small-RNA-Seq

value: somatic follicle cells


title: PD-L1-25

description: 10x Genomics


title: PD-L1-09

description: 10x Genomics


title: pZE-MotR*-3

source_name: MG1655(crl-) + pZE-MotR*

value: Constitutive overexpression of MotR*


title: S3-CTRL_HRO_3

city: Leipzig

first: Sebastian

last: Canzler

address: Permoserstraße 15

department: Deparment Computational Biology

institute: Helmholtz-Centre for Environmental Research - UFZ

data_processing:
To build the reference for Cell Ranger, human genome (hg38) as well as gene annotation (Ensembl 87) were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger (options: ‘-‑attribute=gene_biotype:protein_coding -‑attribute=gene_biotype:lincRNA -‑attribute=gene_biotype:antisense’).
Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference.
The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software (v2.1.0) provided by 10X Genomics with the option ‘--expect-cells’ set to 5000. All other options were used as per default.
All other options were used as per default.
Assembly: human genome  hg38 (Ensembl V87)
Supplementary files format and content: Tab-delimited text files incude cell-barcode names as well as gene names corresponding to the count data in matrix.mtx. The h5ad-file includes the processed count data after the scanpy workflow descripted in the puplication.

source_name: Human retinal organoid cells

growth_protocol: Human retinal organoids (HROs) were differentiated from an established hiPSC line (5A line from Lojewski et al.) and using a protocol modified from previous works (Lowe et al., Zhu et al.).

extract_protocol:
21.8 µl of the cells suspension (an estimated number of 9,000-11,000 cells) were carefully mixed with reverse transcription reaction mix using the Chromium Single Cell 3’ Library & Gel beads chemistry v2 and loaded into a Chromium Single Cell A Chip (10X Genomics, Pleasanton, CA). During the encapsulation process in the 10X Genomics Chromium system (Zheng et al., 2017), the cells lysed within the droplet and released polyadenylated RNA bound to the barcoded bead that was captured with the cell.
Following the guidelines of the 10X Genomics user manual, the droplets were directly subjected to reverse transcription, the emulsion was broken and cDNA was purified using Dynabeads MyOne Silane (ThermoFisher Scientific). After the amplification of cDNA with 10 cycles, it underwent purification and a quality control check on the Fragment Analyzer. The cDNA was fragmented for five minutes and dA-tailed, followed by an adapter ligation step and an indexing PCR of 10 cycles in order to generate libraries.
After quantification, the libraries were sequenced on an Illumina NextSeq 500 machine using a high-output flowcell in PE mode (R1: 26 cycles; I1: 8 cycles; R2: 57 cycles), thus generating 220 mio. fragments at minimum per sample.

treatment_protocol: One individual whole HRO (N=1 experiment) at day 200 of differentiation was dissociated using the Papain Dissociation System (Worthington Industries). Dissociated cells were resuspended in PBS with 0,04% BSA, passed through a 50m filter (CellTrics, Sysmex) to remove cell clumps and processed for sequencing immediately. Cells were counted in a Neubauer chamber.

value: Human retinal organoid cells

value: untreated


title: Dpse.ovary_FC.1 small-RNA-Seq


title: BHFS5 [miRNA]

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Genome_build: GRCh38
Supplementary_files_format_and_content: The xlsx format file contains the counts of miRNAs in every sample

extract_protocol:
Placental tissues were collected immediately after abortion, stored in RNAlater solution at 4 °C for 12–16 h and then stored at -80 °C. RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta

tag: classification

value: BHFS

value: --SEA/--SEA


title: pZE-MotR*-2


title: BHFS4 [miRNA]


title: Dpse.ovary.2

value: RiboPOOL


title: Vehicle-24

description: 10x Genomics

value: tumor cell

value: RPP

value: Vehicle


title: Dpse.ovary.1


title: Vehicle-14

description: 10x Genomics


title: BHFS3 [miRNA]


title: Naïve Ly49H+ NK_002

value: Spleen

value: Natural killer cells

value: Day 0


title: pZE

value: Control library of pZE-FliX-S


title: pZE-FliX-S

source_name: MG1655(crl-) + pZE-FliX-S

value: Constitutive overexpression of FliX-S


title: BHFS1 [miRNA]


title: CflarLKO-CDE 28 days#3

city: Miyama, Funabashi-shi

first: Yuichi

last: Tsuchiya

state: Chiba

department: Pharmaceutical Sciences

institute: Toho University

data_processing:
Sequences were mapped to mouse reference genome GRCm39 using Bowtie2 software.
TCC-GUI was used to normalize sequence count data and conduct differential gene-expression analysis.
Genome_build: GRCm39 (mm39)
Supplementary_files_format_and_content: "Fgf18Tg-normal vs NonTg-normal.xlsx" file compares the gene expressions of the livers from Fgf18Tg mice and NonTg mice (N=3 each).
Supplementary_files_format_and_content: "CflarLKO-normal vs CflarLKO-CDE 2 days.xlsx" file compares the gene expressions of the livers of CflarLKO mice fed either normal diet or CDE diet for 2 days (N=3 each).
Supplementary_files_format_and_content: "CflarFF-CDE 28 days vs CflarLKO-CDE 28 days.xlsx" file compares the gene expressions of the livers of CflarFF and CflarLKO mice fed CDE diet for 28 days (N=3 each).

source_name: CflarLKO mouse fed CDE diet for 28 days

growth_protocol: Mice were housed in a controlled environment with a 12:12-h light-dark cycle.

extract_protocol:
Total RNAs were purified from mouse liver using Sepasol-RNA I SuperG (09379-55, Nacalai Tesque).
PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711). To perform reverse transcription and template-switching, beads were then suspended in 10 μL of RT mix [1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2, 1 U/μL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/μL Superscript II (Thermo Fisher Scientific), and 1uM of trP1-TSO], and incubated for 60 min at 42ºC and immediately cooled on ice. Beads were washed once with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with 10mM Tris-HCl (pH 8.0).   To amplify the total cDNA, beads containing cDNA was resuspended with 25 uL of first PCR mix [0.4 μM of primers (Illumina-i7- [BC]-trP1, NH2-3' WTA), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems)], and the thermal cycling was performed as the following condition: for 3 min at 95°C, 12 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The first PCR products were purified by an Agencort AM Pure XP kit (Beckman-Coulter) at a 0.6:1 ratio of reagents to sample and eluted with 25 μL of nuclease-free water. 6.3uL of purified first PCR product was mixed with the 8.7 µl of second PCR mix [0.4 μM of primers (Illumina-i7, NH2-3' WTA), and 1x KAPA Hifi Hotstart ReadyMix and the thermal cycling was performed as the following condition: for 3 min at 95°C, 5 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The second PCR products were purified by an Agencort AM Pure XP kit at a 0.6:1 ratio of reagent to sample and eluted with 15 μL of 10 mM Tris-HCl (pH 8.0). 100 ng of the whole-transcriptome library was subjected to fragmentation/ end-repair/polyA-tailing/ligation using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) and 1.875 pmol of illumine adapter-bulk according to manufacturer instructions. Reaction products were purified using a double-size selection of Agencort AM Pure XP kit (reagent: sample ratio = 0.4:1 → 0.7:1) and then eluted with 10 μL of nuclease-free water. Barcoding mix [12.5 μL; 2× NEBNext Ultra II Q5 (New England Biolabs), 1 µM ILMN-[UDI]-i5 primer, and 1 µM ILMN-[UDI]-i7 primer] was added into 7.5 μL of eluate, and PCR was performed using the following program: for 30 sec at 98ºC, 9 cycles of 10 sec at 98ºC and 75 sec at 65ºC, followed by 5 min at 65ºC and hold at 4ºC. Reaction products were purified twice using a double-size selection of Agencort AM Pure XP kit (0.5:1 → 0.8:1) and eluted with 12 μL of nuclease-free water.

treatment_protocol: For the CDE diet, eight-week-old female mice were housed individually and fed the choline-deficient diet (02960034, MP Biomedicals) and drinking water containing 0.15% DL-ethionine (E5139, Sigma) for 2 or 28 days.

tag: strain

value: liver

value: CflarLKO


title: BHFS2 [miRNA]


title: Dmoj.ovary.3 small-RNA-Seq

organism: Drosophila mojavensis

value: ovary


title: CflarLKO-CDE 28 days#2


title: pZE-1

value: Control library of pZE-MotR*


title: pZE-2


title: CflarLKO-CDE 28 days#1


title: pBR-lacI-FliX-S_1

source_name: MG1655(crl-) + pBR-lacI-FliX-S

value: pBR-lacI-FliX-S_1, FliX-S is overexpressed with 1 mM IPTG

value: 1 Mm IPTG, OD ~ 0.2


title: CflarFF-CDE 28 days#3

source_name: CflarFF mouse fed CDE diet for 28 days

value: CflarFF


title: NF5 [miRNA]

source_name: placenta

value: placenta

value: normal fetus

value: [alpha][alpha]/[alpha][alpha]


title: pBR-lacI-FliX-S_0

value: Control library of pBR-lacI-FliX-S_1, 0 mM IPTG

value: 0 Mm IPTG, OD ~ 0.2


title: ATAC_dsim_ovary_rep1

description: 6 ovaries

data_processing:
genome build/assembly: droSim1
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

organism: Drosophila simulans

value: wild type

value: female


title: Dmoj.ovary_FC.2 small-RNA-Seq

value: somatic follicle cells


title: NF3 [miRNA]


title: Dmoj.ovary_FC.1 small-RNA-Seq


title: pZE-MotR*-1

value: Constitutive overexpression of MotR*


title: CflarFF-CDE 28 days#2


title: NF4 [miRNA]


title: Dmoj.ovary.2

value: RiboPOOL


title: Dsim.ovary.3 small-RNA-Seq


title: Dmoj.ovary.4 small-RNA-Seq


title: CflarFF-CDE 28 days#1

value: liver


title: NonTg-normal#3

source_name: NonTg mouse fed normal diet

value: NonTg


title: NF1 [miRNA]


title: Dsim.ovary.2 small-RNA-Seq

value: ovary


title: Dvir.ovary.3 small-RNA-Seq

organism: Drosophila virilis


title: Dmoj.ovary.1


title: Cold-DNase-seq

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

data_processing:
For RNA-seq analyses, the quality of raw reads was assessed using FastQC (Kroll et al. 2014). Raw reads were cleaned after removal of adapters and poor-quality bases using Trimmomatic (version 0.39) (Bolger et al. 2014). Clean reads were aligned to the rice reference genome using Hisat2 (version 2.1.0) (Kim et al. 2015). The number of reads mapped to each gene was counted using FeatureCounts (version 1.6.4) (Liao et al. 2014). FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values were calculated to represent the gene expression levels.
For DRIP-seq data analyses, the raw data were processed for removal of adapter and low-quality bases using TrimGalore (version0.4.3,Babraham Bioinformatics). Clean reads were aligned to the rice reference genome (MSU version7.0) using Bowtie (Langmead et al. 2009) with the following parameters‐‐best‐‐strata -m 1 - x 800. Additional duplicate reads were removed by using the SAMtools rmdup,version1.4 (Li et al. 2009). The strand-specific reads were separated using flags of SAM files. The direction of R-loops was determined according to the direction of the R2 reads (R1 for the paired-end reads) aligned to the genome.
Assembly: MSU v7.0

organism: Oryza sativa Japonica Group

source_name: leaf,DH,Cold

growth_protocol: Seeds of Nipponbare (Oryza sativa ssp. japonica) were pre-germinated at room temperature under dark conditions for 3 days. Uniformly germinated seeds were individually put into 96-well PCR plates with bottom cut. Each plate with germinated seeds were put into the liquid culture medium for continuing to grow under a mean temperature as 28/22°C and 12 h/12 h for a light-dark cycle in the greenhouse.

extract_protocol:
Uniformly germinated seeds were individually put into 96-well PCR plates with bottom cut. Each plate with germinated seeds were put into the liquid culture medium for continuing to grow under a mean temperature as 28/22°C and 12 h/12 h for a light-dark cycle in the greenhouse.
Total RNA was extracted from CK and COLD seedlings, respectively, using the RNeasy plant Mini kit (Qiagen, 74904). After removal of genomic DNA contamination using DNase I treatment, approximately 30 µg total RNA was used for mRNA enrichment using oligo (dT) conjugated magnetic beads.The DNA-RNA hybrid immunoprecipitation (DRIP) experiment and DRIP-seq libraries were conducted as described before

treatment_protocol: At the 13th day, a half of PCR plates with seedlings were continued to grow in the normal conditions (CK) and another half were grown at 4℃ for cold treatment. After a 24 h cold treatment (COLD), two biological replicates of CK and cold treated (COLD) seedlings were collected and stored at −80°C for later use.

value: leaf

tag: antibody

value: DNase 1

value: After a 24 h  grown at 4℃ for cold treatment(cold)


title: NonTg-normal#2


title: NonTg-normal#1


title: Dsim.ovary.1 small-RNA-Seq


title: CK-DNase-seq

source_name: leaf,DH,CK

value: grow in the normal conditions


title: Dvir.ovary.2 small-RNA-Seq


title: Dmoj.ovary.1 small-RNA-Seq


title: Dsim.ovary_FC.1 small-RNA-Seq


title: Dsim.ovary_FC.2 small-RNA-Seq


title: Dvir.ovary_FC.2 small-RNA-Seq


title: Fgf18Tg-normal#3

source_name: Fgf18Tg mouse fed normal diet


title: CK_input

source_name: leaf,input,CK

value: ChIP,input


title: Dsim.ovary.4


title: NF2 [miRNA]

value: placenta

value: normal fetus


title: Dvir.ovary_FC.1 small-RNA-Seq


title: Dvir.ovary.1 small-RNA-Seq


title: Dsim.ovary.3


title: Dsim.ovary.2


title: Cold-H3K36me3


title: S2, NHS, DMSO, Pol2S5P, rep2

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
ChIP-Seq data sets were aligned using Bowtie2
Assembly: dm6 (BDGP6.87), mm10 (GRCm38)
Supplementary files format and content: bigwig files were generated using DeepTools with RPKM normalization method

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Mammalian cell line NIH 3T3 was cultured in DMEM supplemented with 10 % Fetal Bovine Serum (FBS) and maintained in humidified 95% air by 5% CO2 incubator at + 37°C. Schneider cell line (S2R+) cultured in Schneider’s Drosophila Medium (Thermo Fisher Scientific) supplemented with 10% heat inactivated fetal bovine serum (Thermo Fisher Scientific) and 1 x antibiotic-antimycotic solution (penicillin, streptomycin, Amphotericin B; Thermo Fisher Scientific) at +25°C incubator.

extract_protocol:
samples were were fixed in 1% PFA for 10 min at RT, homogenized using a pestle in 300 ml of RIPA buffer, and sonicated with Bioruptor (Diagenode). Immunoprecipitations were carried out with 5 µg antibody overnight at 4°C in a rotating wheel.
ChIP libraries were prepared for Illumina NextSeq 500 using NEBNext ChIP-Seq DNA Sample Prep Master Mix Set for Illumina (NEB E6240) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB E7335) according to the manufacturer’s protocols.

treatment_protocol: Drug treatment was done for allocated timepoints (10 mins with the inhibitors at NH condition) followed by heat shock for 20 mins either in 37°C waterbath (S2R+ cells) or 42°C waterbath (NIH 3T3 cells).

value: embryo

tag: cell line

tag: chip antibody

tag: drug-treatment

value: DMSO

value: non-heat shock


title: Dvir.ovary.4

source_name: ovary

tag: assembly


title: CK-H3K36me3


title: Dsim.ovary.1


title: Dvir.ovary.3


title: S2, NHS, CCG1423, Pol2S5P, rep2


title: CK-H3K27me3


title: S2, NHS, DMSO, IgG, rep2

value: IgG


title: Dvir.ovary.2


title: S2, NHS, CCG1423, IgG, rep2


title: Dper.ovary.1 small-RNA-Seq

organism: Drosophila persimilis

tag: enrichment


title: Dvir.ovary.1


title: Fgf18Tg-normal#2

tag: genotype


title: Fgf18Tg-normal#1


title: Cold-H3K4me3

tag: treatment


title: Dtak.ovary.2 small-RNA-Seq

organism: Drosophila takahashii

tag: tissue


title: Cold-H3K27ac


title: S2, HS, DMSO, IgG, rep2

value: heat shock


title: Dtak.ovary.1 small-RNA-Seq


title: Dper.ovary.2


title: Dper.ovary_FC.1 small-RNA-Seq

value: somatic follicle cells


title: Dtak.ovary_FC.2 small-RNA-Seq


title: Dtak.ovary_FC.1 small-RNA-Seq


title: S2, HS, CCG1423, Pol2S5P, rep2


title: Cold-H3K27me3


title: Dper.ovary.2 small-RNA-Seq


title: CK-H3K27ac


title: S2, HS, CCG1423, IgG, rep2


title: Dper.ovary.1

value: RiboPOOL


title: ATAC_dper_ovary_rep2

description: 10-12 ovaries

data_processing:
genome build/assembly: GCF_003286085
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

value: wild type

tag: Sex

value: female


title: Cold-H4K12ac


title: S2, NHS, DMSO, Pol2S5P, rep1


title: ATAC_dsuz_ovary_rep2

description: 10-12 ovaries

data_processing:
genome build/assembly: GCF_013340165
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

organism: Drosophila suzukii

value: ovary


title: ATAC_dper_ovary_rep1

description: 10-12 ovaries


title: S2, HS, DMSO, Pol2S5P, rep2


title: CK-H3K4me3

value: leaf


title: Cold-H3K9ac


title: ATAC_dfic_ovary_rep2

description: 10-12 ovaries

data_processing:
genome build/assembly: GCF_018152265
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

organism: Drosophila ficusphila


title: S2, NHS, CCG1423, Pol2S5P, rep1


title: S2, HS, DMSO, Pol2S5P, rep1


title: Dper.ovary_FC.2 small-RNA-Seq


title: CK-H3K9ac


title: ATAC_dbia_ovary_rep1

description: 10-12 ovaries

data_processing:
genome build/assembly: GCF_018148935
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

organism: Drosophila biarmipes


title: ATAC_dbia_ovary_rep2

description: 10-12 ovaries


title: Mouse HGG-MYCN_7

status: Public on Sep 25 2023

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

data_processing:
All samples were demultiplexed and then processed with the 10x Genomics CellRanger v6.0.2 pipeline.
For all samples, the raw 10X scRNA-seq data was converted to fastq format with CellRanger's mkfastq function.
CellRanger's count algorithm was then used to align the data against the murine reference transcriptome mm10, version 2020-A.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tumor

extract_protocol:
Tumors of four hGFAP-cre::TP53Fl/Fl::lsl-MYCNFl/wt mice were isolated and minced. To prepare single-cell suspensions, samples were digested with papain and DNAse, and passed through a 40 µm cell strainer. Red blood cells were depleted using red-blood-cell  lysis buffer and non-vital cells were removed using 7-Aminoactinomycin D staining. 10,000 vital cells were used as input for scRNA-seq.
Dual-index libraries were generated with Chromium Single Cell 3’ v3.1 technology (10x Genomics) and sequenced using a NextSeq 2000 sequencing instrument (high-throughput kit, 100 cycles).

value: brain tumor

tag: age

value: 70 days


title: Mouse HGG-MYCN_4

value: 43 days


title: S2, HS, CCG1423, Pol2S5P, rep1


title: Mouse HGG-MYCN_5

value: male


title: Mouse HGG-MYCN_2

extract_protocol:
Tumors of three hGFAP-cre::TP53Fl/Fl::lsl-MYCNFl/wt mice were isolated and minced. To prepare single-cell suspensions, samples were digested with papain and DNAse, and passed through a 40 µm cell strainer. Red blood cells were depleted using red-blood-cell  lysis buffer and non-vital cells were removed using 7-Aminoactinomycin D staining. 10,000 vital cells were used as input for scRNA-seq.
Single-index libraries were generated with Chromium Single Cell 3’ v3.1 technology (10x Genomics) and sequenced using a NextSeq 2000 sequencing instrument (high-throughput kit, 100 cycles).

value: 77 days


title: ATAC_dsuz_ovary_rep1

description: 10-12 ovaries


title: Mouse HGG-MYCN_1


title: CK-H4K12ac

value: grow in the normal conditions


title: WT, Input, Rep A

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: Wild Type

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to HG38 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using masc2 (v 2.0.10.20131216) with the "broad-peak" settings (enrichment relative to input samples)
Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for input samples)

growth_protocol: Human SH-SY5Y neuroblastoma cells (94030304, Sigma-Aldrich) were cultured in complete Dulbecco’s Modified Eagle Medium (61965–059, Gibco) supplemented with 1% non-essential amino acids (11140035, Gibco), 1% penicillin-streptomycin (15140122, Gibco) and 10% fetal bovine serum (FBS; 10270106, Gibco). Cells were grown at 37°C with saturated humidity and 5% CO2

extract_protocol:
Cells were washed twice with cold PBS and lysed (Buffer B; PN 520237, Covaris). Nuclei were washed (Buffer C; PN 520237, Covaris) and resuspend in sonication buffer (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% N-lauroylsarcosine sodium salt and fresh 0.1% Na-deoxycholate and proteinase inhibitors). Chromatin was fragmented by sonication with a Bioruptor to an average size of 100-400 bp and brought to 1% TritonX-100. A 50 μL aliquot was saved as input, whereas 500 μL each was incubated with 5 μg antibody, overnight at 4°C. Protein A magnetic beads (16-661, Merk Millipore) were washed three times with 0.5% BSA in PBS and added for 5 h at 4°C. DNA-protein complex was recovered, washed and eluted overnight at 65°C (GeneJET PCR purification; K0701, Thermo Fisher Scientific).
Library preparation from 5 ng purified chromatin was performed using NebNext Ultra II DNA Library Prep with magnetic purification beads (E7103S, NewEngland Biolabs) and multiplex oligonucleotides (Dual Index Primers; E7600S, NewEngland Biolabs), followed by adaptor ligation according to the manufacturer’s protocol. Quality controls of amplified chromatin fragments were performed on Bioanalyzer 2100 (Agilent Technologies) and Qubit V4 (Thermo Fisher Scientific). Next-generation sequencing was performed on NextSeq2000 (Illumina) with the P2 reagents kit V3 (100 cycles; Illumina)

value: Wild Type


title: WT, H3K27me3, ChIP, Rep B

description: Wild Type

value: H3K27me3 antibody (C36B11, Cell Signalling)


title: 232P, INPUT, Rep A

description: Input for 232P knock out Rep 1

value: 232P knock out


title: 232P, INPUT, Rep B

description: Input for 232P knock out Rep 2


title: 232P, H3K27me3, ChIP, Rep B

description: 232P knock out Rep 2


title: NHBE IAV-WT scRNAseq

city: Seattle

first: Daniel

last: Blanco-Melo

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

data_processing:
Initial read filtering, read counting and cell filtering were processed using PIPseeker v2.1 with custom genome containing both human and IAV/PR8/34 references.
Filtered count matrix was first processed through SoupX software to infer ambient contamination of viral RNAs (Young and Behjati, 2020). The SoupX-corrected count matrix was further filtered for low and high UMI counts and percentage of mitochondria reads.
The filtered matrix was processed using Seurat v4.9 following the standard analysis pipeline to normalize read counts and generate UMAP layout (Hao et al., 2021).
hg38, AF389122.1, AF389121.1, AF389120.1, AF389119.1, AF389118.1, AF389117.1, AF389116.1, AF389115.1
Tab delimited value files and matrix files

molecule: other

source_name: Normal Human Bronchial Epithelial Cells

extract_protocol:
NHBE cells were infected with IAV-WT at MOI of 3 for 12 hours. At 12 hpi, dead cells were washed off the plate, and the live cells were trypsinized and washed in PBS and centrifuged at 300xg for 5 minutes. The cells were counted to ensure >90% viability and concentrated to 2.12x10E6 cells per mL.
A total of 10 μL of cells were hence loaded into PIPseq T20 3’ Single Cell RNA kit v4.0 (Fluent BioSciences, (Clark et al., 2023) reaction tube to be processed, intended to capture 10,000 cells. Following the manufacturer’s protocol, the transcripts from cells were barcoded, and processed for Illumina sequencing on NextSeq2000 platform using P3-100 cycle kit. A total of 267 million reads were assigned to the sample.
Fluent BioSciences PIPseq 3' single cell RNA-seq

value: Normal Human Bronchial Epithelial Cells

tag: cell type

value: Primary Lung Cells

value: WT

value: Influenza A Virus WT


title: WT, INPUT, Rep B

description: Wild Type


title: 232P, H3K27me3, ChIP, Rep A

description: 232P knock out Rep 1


title: ATAC_dfic_ovary_rep1

description: 10-12 ovaries

value: wild type


title: 231K, INPUT, Rep A

description: Input for 231K knock out Rep 1

value: 231K knock out


title: Mouse HGG-MYCN_3

value: 92 days


title: 231K, H3K27me, ChIP, Rep B

description: 231K knock out Rep 2


title: KRASG12D, Trametinib Sample 3

city: Dallas

first: Michael

last: Dellinger

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Centre

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
Tram_3_S14

data_processing:
Gene expression analyses were performed using Partek Flow software
Single-end reads were aligned to the human reference genome (hg38) using STAR
gene expression was quantified using RefSeq annotations
Expression counts were normalized using Counts Per Million (CPM). Genes with low expression in all samples were excluded.
Assembly: hg38
Supplementary files format and content: KRAS_GFP_CPM_Compiled.xlsx, xlsx File format,CPM Values,Gene ID,Gene name,P-value, FDR,Log2 Ratios, Fold Change etc.
Supplementary files format and content: Tram_vs_DMSO_CPM_Compiled.xlsx, xlsx File format,CPM Values,Gene ID,Gene name,P-value, FDR,Log2 Ratios, Fold Change etc.

source_name: dermis of juvenile foreskin

growth_protocol: Primary Human Dermal Lymphatic Endothelial Cells (HDLEC) (C-12216) were maintained in EGM-2MV media (LONZA CC-3125).

extract_protocol:
RNA was then isolated with a Qiagen RNeasy Plus Mini Kit (Qiagen, #74314).
Samples were submitted to the Next Generation Sequencing Core for library preparation with the TruSeq RNA library prep kit

treatment_protocol: Primary human LECs were infected with lentivirus particles. Twenty-four hours later, the media was replaced with standard growth media. To assess the impact of trametinib on KRASG12D-LECs, primary human LECs were infected with lentivirus particles, and the media was replaced with normal growth media 24 hours later. Forty-eight hours after infecting cells, they were treated with DMSO or trametinib (10 nM) for approximately 16 hours.

value: dermis of juvenile foreskin

value: HDLEC

value: Trametinib


title: 231K, H3K27me, ChIP, Rep A

description: 231K knock out Rep 1


title: KRASG12D, DMSO Sample 2

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
DMSO_2_S10

value: Primary Human Dermal Lymphatic Endothelial Cells

value: DMSO


title: 231K, INPUT, Rep B

description: Input for 231K knock out Rep 2


title: KRASG12D, DMSO Sample 1

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
DMSO_1_S9


title: KRASG12D Sample 3

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
KRAS3_S13


title: KRASG12D Sample 1

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
KRAS1_S11


title: GFP Sample 3

description:
Cells were transfected GFP-expressing  lentivirus particles  to express GFP
GFP3_S1

value: GFP


title: STEM-PD #3 at thaw

type: genomic

city: Lund

first: Malin

last: Parmar

department: Department of Experimental Medical Science, Lund University

country: Sweden

institute: Wallenberg Neuroscience Center, MultiPark and Lund Stem Cell Centre

description: Genomic DNA extracted from human ventral midbrain dopaminergic precursors was genotyped using Human CytoSNP-12 v2.1 BeadChip (Illumina).

hyb_protocol: As per standard Illumina protocol

scan_protocol: The BeadChip array was scanned with the iScan (Illumina)

data_processing:
The scanned data files were processed by GenomeStudio GT module (Illumina). BluFuse Multi (Illumina) was used to call genotype and calculate LogR ratio and B allele frequency using a manifest file (HumanCytoSNP-12v2-1_L1.bpm) and a cluster file (HumanCytoSNP-12v2-1_L (1).egt) supplied by Illumina.
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

label_protocol: C-Bio and A-DPN

growth_protocol: Cell lines were grown according to standard culturing conditions, and as described in the relative manuscript

extract_protocol: Genomic DNA was extracted using QIAGEN Dneasy mini kit according to manufacturer's instruction.

tag: gender

value: Female


title: KRASG12D Sample 2

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
KRAS2_S12


title: WT, H3K27me3, ChIP, Rep A

description: Wild Type

value: Wild Type


title: KRASG12D, DMSO Sample 3

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
DMSO_3_S11


title: GFP Sample 2

description:
Cells were transfected GFP-expressing  lentivirus particles  to express GFP
GFP2_BC6H_S14


title: GFP Sample 1

description:
Cells were transfected GFP-expressing  lentivirus particles  to express GFP
GFP1_S7


title: STEM-PD #1 fourteen passages after thawing

source_name: ventral midbrain dopaminergic precursors


title: RC17 master cell bank four passages after thawing

description: Genomic DNA extracted from human human embryonic stem cells was genotyped using Human CytoSNP-12 v2.1 BeadChip (Illumina).

source_name: embryonic stem cells


title: RC17 master cell bank two passages after thawing


title: STEM-PD #1 at thaw


title: RC17 master cell bank at thaw


title: KRASG12D, Trametinib Sample 1

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
Tram_1_S12


title: KMS12BM.BATF2.isotype2

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

data_processing:
FASTQ files were quality trimmed with TrimGalore! (v0.6.4) and CutAdapt (v2.5)
Quality and adapter trimmed FASTQ files were mapped to the GRCh38 reference genome using bowtie2 (v2.3.5.1)
Putative PCR duplicate reads were marked in BAM files using Samtools (v1.10)
Factor-bound (‘peaks’) regions were determined using MACS2 (v2.1.1.20160309)
The union of all accessible regions was determined and reads mapping to these regions for each sample was assessed using the ‘summarizeOverlaps’ function of the GenomicAlignments package (v1.30.0) in R (v4.1.2)
Regions that overlapped ENCODE blacklisted regions were removed.
Assembly: GRCh38 reference genome (GRCh38.d1.vd1.fa)

source_name: multiple myeloma

growth_protocol: RPMI 1640 supplemented with 5% FBS and 1X glutamineGlutaMAX (Gibco), without antibiotics

extract_protocol:
Chromatin from approximately 2 × 10e7 cells were used for each ChIP-Seq reaction
ChIPed DNA fragments were blunt-ended, ligated to adaptors.

treatment_protocol: Cells were transduced with empty vector (EV) or BATF2 expression constructs

value: multiple myeloma

value: Rabbit IgG (R&D, AB-105-C, ER11)

value: BATF2 vector


title: KMS12BM.BATF2.IRF4

value: IRF4 (Santa Cruz, sc-6059, k1209)


title: KMS12BM.EV.IRF4

value: empty vector


title: KMS12BM.EV.isotype