title: biol rep 1, S.aureus+ S. anginosus + tonsillar cells , test, 3h

description: BR1.reads aligned against S. aureus from bacterial mix with host at 3h


title: swi6-delta set1-delta _9me2_IP_rep2_endogenous

status: Public on Sep 26 2023

type: SRA

city: Waltham

first: Melissa

last: Seman

address: 415 South St

country: USA

institute: Brandeis University

library_source: genomic

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA, and normalized using bamCompare with subtraction of input and RPKM
Supplementary files format and content: bigwig files from bamCompare

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: YEA, grown to log phase at 32C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIP-seq libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. 1 ng of DNA was used as starting material.

tag: genotype

value: swi6-delta set1-delta

tag: chip antibody

tag: treatment

value: IP

tag: cell type

value: fission yeast


title: biol rep 2, S.aureus+ S. anginosus + tonsillar cells , test, 3h

city: Tromsø

first: Anne

middle: Merethe

last: Hanssen

address: Hansine Hansens veg 18

department: Medical Biology

country: Norway

institute: University of Tromsø

description: BR2.reads aligned against S. aureus from bacterial mix with host at 3h

library_source: transcriptomic

data_processing:
RNA seq reads were generated from 12  samples in two runs of RNA-seq. The overall pipeline for RNA-seq data analysis included generating FASTQ-format files containing reads sequenced from an NGS platform, quality control and trimming, aligning reads to an annotated reference genome, and quantifying expression of genes.
Each library produced between 45 – 184 million reads, were pre-processed for quality check using FASTQC/0.11.9-Java-11. Filtering (removable of adaptor dimer reads) and trimming (removable of low-quality bases) was performed by Trimmomatic/0.39-Java-11. Then, only those sequences with a quality score Q > equal to 20 and a minimum of 55 nucleotide sequence lengths were retained in the dataset.
The final quality check was performed in the trimmed file. S. aureus TR145 strain was used as a reference genome for the mapping performed by Bowtie2/2.4.4-GCC-10.3.0. For all the samples, percentage of mapping efficacy was retrieved from Bowtie2 and sorted by Samtools/1.14-GCC-11.2.0.
Further, the gene count matrix for gene expression analysis was identified using the featureCounts program implemented in the SourceForge Subread package.
Differentially expressed genes analysis of the test group and the control group (each group has three biological replicates per conditions) was analyzed using the DESeq R package (1.38.0).
DEGs were calculated under log2|FoldChnage|(log2|FC|) > 2 and a false discovery rate (FDR) adjusted p (padj) < 0.05.
Supplementary files format and content: raw RNA seq reads generated after RNA sequencing for each Samples (total 12)
Supplementary files format and content: tab-delimited text files include count matrix complied after feature count tool for each Sample

molecule: total RNA

organism: Staphylococcus aureus

source_name: HTEpiC- Human tonsils epithelial cells

growth_protocol: The bacterial strains grown to log phase OD600nm =0.8 -1.2 were diluted to OD600nm = 0.36 – 0.42 (corresponding to 0.6 - 1.2 x 108 CFU/ml) and seeded into wells with host cells at a Multiplicity of Infection (MOI) of 5.

extract_protocol:
After 1 and 3h post-infection, the media was aspirated, and the host cells were washed twice with fresh media to remove unbound bacteria. The host cells were then trypsinized and lysed with Triton-X. The released bacterial mix was then collected from three technical replicates and pooled together for RNA extraction. Plate enumeration, adhesion assay and cytotoxicity assay were also performed.
Total RNA extracted from three replicates of S. aureus cocultured with S. anginosus in the absence/presence of host cells collected at time points of 1 h and 3 h were processed for RNA-seq library preparation. The samples were sequenced on an Illumina 550 platform, with dual indexes, and paired-end mode. The final sequencing concentration was 1.8 pM.
Prior to RNA libraries for RNA-seq, depletion of bacterial rRNA was performed with the RiboCop rRNA depletion kit for Gram-Positive Bacteria (G+), according to the manufacturer’s protocol. In total 12 samples were processed for libraries construction using Lexogen’s CORALLTM Total RNA-Seq Kit with RiboCop following the manufacturer's protocols.

tag: cell line

value: HTEpiC- Human tonsils epithelial cells

value: primary epithelial cell line

tag: time

value: bacterial mix with Host

tag: group


title: swi6-delta mst2-delta _9me2_IP_rep2_endogenous

value: swi6-delta mst2-delta


title: swi6-delta mst2-delta set1-delta _9me2_IP_rep2_endogenous

value: swi6-delta mst2-delta set1-delta


title: biol rep 1, S. aureus + S. anginosus, control, 3h

description: BR1.reads aligned against S. aureus from bacterial mix without host at 3h

value: bacterial mix without Host


title: Starch_D2

city: Campinas

first: Joaquim

last: Martins Junior

state: SP

address: Rua Giuseppe Maximo Scolfaro 10000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Paired-end reads (2x100pb) were filtered by quality and presence of adaptors using Trimmomatic v0.38 and rRNA reads were filtered using SortmeRNA v. 2.0.
QC reads were mapped into the Xanthomonas citri pv. citri str. 306 genome using Bowtie2 algorithm.
Differential gene expression analysis was based on counting data and performed using the Bioconductor DESeq2 package using the R platform, by paired comparison against the control (Glucose) condition.
Transcripts showing differential expression (log2-fold change ≥1 and ≤-1) relative to the control condition (Glucose) were determined by applying p-ajusted ≤ 0.05 as the threshold.
Genome_build: Xanthomonas
Assembly: European Nucleotide Archive ASM716v1
Assembly: genome-build-accession GCA_000007165.1
Supplementary files format and content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix tab-delimited file include TPM values for each Sample
Supplementary files format and content: Matrix tab-delimited file include DESeq2 results

organism: Xanthomonas citri pv. citri

source_name: Bacterial culture

growth_protocol: Strains and plasmids used in this study are listed in Supplementary Table 5.  E. coli cells were cultured in Lysogeny broth (LB) medium or LB agar plates at 37℃. X. citri 306 strains were cultured in LBON medium (1% m/v bacto peptone and 0.5% m/v yeast extract) and on LBON agar plates at 28℃. When required, media were supplemented with antibiotics: ampicillin (100 µg/ml) or kanamycin (50 µg/ml).

extract_protocol:
Total RNA samples were extracted from 15 mL X. citri 306 cultures grew at mid-exponential phase (as described above) using the TRIzol/chloroform protocol (41). Genomic DNA was removed by treatment with DnaseI (Invitrogen™) and then then the samples were treated with RNaseOUT (Invitrogen™), followed by purification with the Rneasy Mini Kit (Qiagen), according to the manufacturer’s recommendations. The absorbance analyzes were performed in a NanoDrop spectrophotometer (Thermo Scientific) and the integrity of the samples evaluated in the Agilent 2100 Bioanalyzer (Agilent Technologies). Prior to the tests, the samples were quantified on a Qubit® 2.0 Fluorometer using the RNA BR assay kit (Life Technologies).
For cDNA library preparation, only RNA samples free of genomic DNA contamination and with values of RIN (RNA Integrity Number) greater than 7 were used. Then, 2-2.5 µg of RNA was used for depletion of rRNA using the Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria – Epicenter Biotechnologies). The preparation of the cDNA libraries was performed using the TruSeq Stranded mRNA kit (Illumina Inc.) according to the manufacturer’s protocol. Samples quality was accessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and libraries were quantified via qPCR using the KAPA Library Quantification Kit (Illumina)

treatment_protocol: For growth curve analysis, X. citri 306 strain was cultured in LBON medium (1% m/v bacto peptone and 0.5% m/v yeast extract) containing 100 µg. mL−1 ampicillin at 30 °C and 200 rpm until mid-exponential phase. Then, the cultures were centrifuged for 5 minutes at 6000 g and the harvested cells were washed once with the modified minimal medium XVM2 (40) (XVM2m, without sucrose and fructose) supplemented with glucose, cellobiose or starch (5 mg. mL-1), and transferred to a 20 mL culture medium for an initial OD600 nm = 0.01. Growth analyses were performed at 30 °C and 200 rpm, being monitored through OD600 nm readings at times 0h, 8h, 14h, 20h, 26h, 32h, 36h, 44h and 52h in triplicate (Supplementary Figure 1).

tag: strain

tag: carbon source

value: Starch

tag: biological replicate


title: biol rep 1, S.aureus+ S. anginosus + tonsillar cells , test, 1h

description: BR1.reads aligned against S. aureus from bacterial mix with host at 1h


title: WT_9me2_IP_rep2_endogenous

value: WT


title: swi6-delta mst2-delta set1-delta _9me2_input_rep1_endogenous

value: input


title: Starch_B1


title: swi6-delta mst2-delta _9me2_input_rep1_endogenous


title: swi6-delta _9me2_input_rep1_endogenous


title: swi6-delta set1-delta _9me2_input_rep1_endogenous


title: Starch_A2


title: WT_9me2rep1_9me3_rep2_input_endogenous


title: Starch_C1


title: swi6-delta _9me2_IP_rep2_endogenous


title: Cellobiose_D2

value: Cellobiose


title: LB_ON_A1


title: swi6-delta mst2-delta set1-delta _9me2_IP_rep1_endogenous


title: Cellobiose_C2


title: WT_9me2_IP_rep1_endogenous


title: LB_ON_D1


title: biol rep 1, S. aureus + S. anginosus, control, 1h

description: BR1.reads aligned against S. aureus from bacterial mix without host at 1h


title: LB_ON_C1


title: swi6-delta mst2-delta _9me2_IP_rep1_endogenous


title: swi6-delta _9me2_IP_rep1_endogenous


title: clr4-delta _9me3_input_rep2_ectopic


title: LB_ON_B1


title: Cellobiose_A1


title: mst2-delta set1-delta _9me3_input_rep2_ectopic

value: mst2-delta set1-delta


title: swi6-delta set1-delta _9me2_IP_rep1_endogenous


title: Cellobiose_B1


title: swi6-delta mst2-delta set1-delta _9me3_input_rep2_ectopic


title: WT_9me3_input_rep2_ectopic


title: swi6-delta _9me3_input_rep2_ectopic


title: swi6-delta mst2-delta _9me3_input_rep2_ectopic


title: swi6-delta set1-delta _9me3_input_rep2_ectopic


title: NAF normal 4

city: Houston

first: Minsun

last: Jeon

address: 2121 W Holcombe Blvd

institute: Texas A&M Institute of Biosciences & Technology

library_source: other

data_processing:
cfDNA sequenced reads were aligned to the Human Reference Genome Build GRCh38 (hg38) via bwa-meth (version 0.2.2). MethylDackel (version 0.5.2) was used to extract methylation levels from each sample.
Assembly: hg38
Supplementary files format and content: bedgraph (contains methylation levels for each sample)

molecule: other

organism: Homo sapiens

source_name: Nipple aspirate fluid

extract_protocol:
cfDNA was isolated from NAF using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s protocol.
WGBS libraries were generated using Pico Methyl-Seq Library Kit (Zymo Research).
Whole-genome bisulfite sequencing (WGBS)

tag: tissue

value: Nipple aspirate fluid

tag: disease state

value: Healthy


title: NAF cancer 1

value: Breast Cancer


title: K18-hACE2 mice, 35, COVID-19 48 hours post infection

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

library_source: transcriptomic single cell

data_processing:
The demultiplexing , barcode processing , gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/6.1)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Lung

extract_protocol: Lungs were isolated and minced with forceps and scissors. They were further enzymatically digested with 2 mg/mL collagenase (Sigma) and 80 U/mL DNase I (Sigma) in 2 mL serum-free medium for 60 min at 37°C. Digested tissues were passed through a sterile 70 mm filter (Fisher Scientific) and 40 mm filter (Miltenyi Biotec) to generate a single cell suspension. After washing, cell suspensions were incubated with 2 ml of ACK Lysing Buffer (Cat #A1049201, Gibco) for 2 min and washed twice. 1x106 cells per condition were collected as whole lung single cell population. Cell numbers and viability were validated by Countess II (Thermo Fisher) prior to preparation of single cell RNAseq library.

value: Lung

value: Female

tag: infection

value: 48 hours post infection


title: NAF normal 3


title: NAF cancer 3


title: K18-hACE2 mice, 32, COVID-19 48 hours post infection


title: NAF normal 1


title: K18-hACE2 mice, COVID-19 day 4 post infection [re-analysis]

description:
10x-Genomics
re-analysis of GSM5352467

value: 4 days post infection


title: clr4-delta _9me3_IP_rep2_ectopic

value: IP

value: fission yeast


title: swi6-delta mst2-delta _9me3_IP_rep2_ectopic

value: swi6-delta mst2-delta


title: NAF cancer 2


title: NAF normal 2


title: Tula8_Day7

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

description:
Tula8.Day7_S57_L002
MM_252_raw_gene_count.txt

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina TruSeq adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.36.0 and glmmSeq v0.2.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated via PAXgene Blood miRNA Kits, per product instruction, with automated processing through QIAcube instrumentation.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: All samples were collected into PAXgene Blood RNA tubes (Qiagen) and stored per product recommendation the same day of collection.

value: Whole blood

value: Day 7

value: Tulathromycin

tag: sequencing lane

tag: individual id


title: Tula8_Day56

description:
Tula8.Day56_S60_L002
MM_252_raw_gene_count.txt

value: Day 56


title: swi6-delta _9me3_IP_rep2_ectopic


title: WT_9me3_IP_rep2_ectopic

value: WT


title: Tula8_Day21

description:
Tula8.Day21_S59_L002
MM_252_raw_gene_count.txt

value: Day 21


title: mst2-delta set1-delta _9me3_IP_rep2_ectopic

value: mst2-delta set1-delta


title: Tula8_Day3

description:
Tula8.Day3_S56_L002
MM_252_raw_gene_count.txt

value: Day 3


title: Tula8_Day14

description:
Tula8.Day14_S58_L002
MM_252_raw_gene_count.txt

value: Day 14


title: Tula8_Day0

description:
Tula8.Day0_S55_L002
MM_252_raw_gene_count.txt

value: Day 0


title: mst2-delta set1-delta _9me3_input_rep1_ectopic

value: input


title: swi6-delta mst2-delta set1-delta _9me3_input_rep1_ectopic

value: swi6-delta mst2-delta set1-delta


title: swi6-delta mst2-delta set1-delta _9me3_IP_rep2_ectopic


title: Tula7_Day7

description:
Tula7.Day7_S51_L002
MM_252_raw_gene_count.txt


title: Tula7_Day56

description:
Tula7.Day56_S54_L002
MM_252_raw_gene_count.txt


title: swi6-delta set1-delta _9me3_IP_rep2_ectopic

value: swi6-delta set1-delta


title: swi6-delta set1-delta _9me3_input_rep1_ectopic


title: swi6-delta mst2-delta _9me3_input_rep1_ectopic


title: Tula7_Day3

description:
Tula7.Day3_S50_L002
MM_252_raw_gene_count.txt


title: Tula7_Day14

description:
Tula7.Day14_S52_L002
MM_252_raw_gene_count.txt


title: Tula7_Day21

description:
Tula7.Day21_S53_L002
MM_252_raw_gene_count.txt


title: swi6-delta _9me3_input_rep1_ectopic


title: Tula6_Day7

description:
Tula6.Day7_S45_L002
MM_252_raw_gene_count.txt


title: Tula6_Day56

description:
Tula6.Day56_S48_L002
MM_252_raw_gene_count.txt


title: Tula7_Day0

description:
Tula7.Day0_S49_L002
MM_252_raw_gene_count.txt


title: WT_9me3_input_rep1_ectopic


title: swi6-delta set1-delta _9me3_IP_rep1_ectopic


title: mst2-delta set1-delta _9me3_IP_rep1_ectopic


title: swi6-delta mst2-delta set1-delta _9me3_IP_rep1_ectopic


title: Tula6_Day14

description:
Tula6.Day14_S46_L002
MM_252_raw_gene_count.txt


title: clr4-delta _9me2_input_rep2_ectopic


title: swi6-delta mst2-delta _9me3_IP_rep1_ectopic


title: clr4-delta _9me3_input_rep1_ectopic


title: Tula6_Day3

description:
Tula6.Day3_S44_L002
MM_252_raw_gene_count.txt


title: swi6-delta _9me3_IP_rep1_ectopic


title: WT_9me3_IP_rep1_ectopic


title: Tula5_Day7

description:
Tula5.Day7_S39_L002
MM_252_raw_gene_count.txt


title: Tula6_Day21

description:
Tula6.Day21_S47_L002
MM_252_raw_gene_count.txt


title: swi6-delta mst2-delta set1-delta _9me2_input_rep2_ectopic


title: Tula5_Day56

description:
Tula5.Day56_S42_L002
MM_252_raw_gene_count.txt


title: mst2-delta set1-delta _9me2_input_rep2_ectopic


title: Tula5_Day3

description:
Tula5.Day3_S38_L002
MM_252_raw_gene_count.txt


title: swi6-delta mst2-delta _9me2_input_rep2_ectopic


title: Tula5_Day21

description:
Tula5.Day21_S41_L002
MM_252_raw_gene_count.txt


title: swi6-delta set1-delta _9me2_input_rep2_ectopic


title: Tula5_Day14

description:
Tula5.Day14_S40_L002
MM_252_raw_gene_count.txt


title: swi6-delta _9me2_input_rep2_ectopic


title: Tula4_Day3

description:
Tula4.Day3_S32_L002
MM_252_raw_gene_count.txt


title: clr4-delta _9me3_IP_rep1_ectopic


title: Tula4_Day56

description:
Tula4.Day56_S36_L002
MM_252_raw_gene_count.txt


title: clr4-delta _9me2_IP_rep2_ectopic


title: Tula4_Day21

description:
Tula4.Day21_S35_L002
MM_252_raw_gene_count.txt


title: Tula4_Day7

description:
Tula4.Day7_S33_L002
MM_252_raw_gene_count.txt


title: WT_9me2_input_rep2_ectopic


title: swi6-delta set1-delta _9me2_IP_rep2_ectopic


title: Tula6_Day0

description:
Tula6.Day0_S43_L002
MM_252_raw_gene_count.txt


title: swi6-delta _9me2_IP_rep2_ectopic


title: Tula4_Day14

description:
Tula4.Day14_S34_L002
MM_252_raw_gene_count.txt


title: swi6-delta mst2-delta _9me2_IP_rep2_ectopic


title: Tula3_Day56

description:
Tula3.Day56_S30_L002
MM_252_raw_gene_count.txt


title: WT_9me2_IP_rep2_ectopic


title: clr4-delta _9me2_input_rep1_ectopic


title: Tula3_Day7

description:
Tula3.Day7_S27_L002
MM_252_raw_gene_count.txt


title: Tula4_Day0

description:
Tula4.Day0_S31_L002
MM_252_raw_gene_count.txt


title: Tula5_Day0

description:
Tula5.Day0_S37_L002
MM_252_raw_gene_count.txt


title: Tula3_Day21

description:
Tula3.Day21_S29_L002
MM_252_raw_gene_count.txt


title: swi6-delta mst2-delta set1-delta _9me2_input_rep1_ectopic


title: swi6-delta set1-delta _9me2_input_rep1_ectopic


title: swi6-delta mst2-delta set1-delta _9me2_IP_rep2_ectopic


title: mst2-delta set1-delta _9me2_input_rep1_ectopic


title: Tild8_Day7

description:
Tild8.Day7_S3_L003
MM_252_raw_gene_count.txt

value: Tildipirosin


title: Tula3_Day0

description:
Tula3.Day0_S25_L002
MM_252_raw_gene_count.txt


title: swi6-delta _9me2_input_rep1_ectopic


title: mst2-delta set1-delta _9me2_IP_rep2_ectopic

value: IP


title: swi6-delta mst2-delta _9me2_input_rep1_ectopic

value: fission yeast


title: WT_9me2_input_rep1_ectopic


title: mst2-delta set1-delta _9me2_IP_rep1_ectopic


title: Tild8_Day56

description:
Tild8.Day56_S6_L003
MM_252_raw_gene_count.txt


title: Tild8_Day3

description:
Tild8.Day3_S2_L003
MM_252_raw_gene_count.txt


title: Tild8_Day21

description:
Tild8.Day21_S5_L003
MM_252_raw_gene_count.txt


title: swi6-delta mst2-delta set1-delta _9me2_IP_rep1_ectopic


title: Tild8_Day0

description:
Tild8.Day0_S1_L003
MM_252_raw_gene_count.txt


title: Tild8_Day14

description:
Tild8.Day14_S4_L003
MM_252_raw_gene_count.txt


title: Tula3_Day3

description:
Tula3.Day3_S26_L002
MM_252_raw_gene_count.txt


title: swi6-delta set1-delta _9me2_IP_rep1_ectopic


title: Tild7_Day7

description:
Tild7.Day7_S81_L002
MM_252_raw_gene_count.txt


title: Tula3_Day14

description:
Tula3.Day14_S28_L002
MM_252_raw_gene_count.txt


title: swi6-delta _9me2_IP_rep1_ectopic


title: Tild7_Day56

description:
Tild7.Day56_S84_L002
MM_252_raw_gene_count.txt


title: swi6-delta mst2-delta _9me2_IP_rep1_ectopic

value: swi6-delta mst2-delta


title: Tild7_Day21

description:
Tild7.Day21_S83_L002
MM_252_raw_gene_count.txt

value: Whole blood


title: Tild7_Day3

description:
Tild7.Day3_S80_L002
MM_252_raw_gene_count.txt


title: WT_9me2_IP_rep1_ectopic


title: Tild5_Day7

description:
Tild5.Day7_S75_L002
MM_252_raw_gene_count.txt

value: Day 7


title: Tild7_Day0

description:
Tild7.Day0_S79_L002
MM_252_raw_gene_count.txt


title: Tild5_Day56

description:
Tild5.Day56_S78_L002
MM_252_raw_gene_count.txt


title: Tild7_Day14

description:
Tild7.Day14_S82_L002
MM_252_raw_gene_count.txt


title: Tild5_Day3

description:
Tild5.Day3_S74_L002
MM_252_raw_gene_count.txt


title: Tild3_Day3

description:
Tild3.Day3_S68_L002
MM_252_raw_gene_count.txt


title: Tild5_Day21

description:
Tild5.Day21_S77_L002
MM_252_raw_gene_count.txt


title: Tild5_Day14

description:
Tild5.Day14_S76_L002
MM_252_raw_gene_count.txt


title: Tild5_Day0

description:
Tild5.Day0_S73_L002
MM_252_raw_gene_count.txt


title: clr4-delta _9me2_IP_rep1_ectopic


title: Tild3_Day56

description:
Tild3.Day56_S72_L002
MM_252_raw_gene_count.txt


title: Tild2_Day7

description:
Tild2.Day7_S63_L002
MM_252_raw_gene_count.txt


title: Tild3_Day7

description:
Tild3.Day7_S69_L002
MM_252_raw_gene_count.txt


title: Tild3_Day14

description:
Tild3.Day14_S70_L002
MM_252_raw_gene_count.txt


title: Tild3_Day0

description:
Tild3.Day0_S67_L002
MM_252_raw_gene_count.txt


title: Tild2_Day3

description:
Tild2.Day3_S62_L002
MM_252_raw_gene_count.txt


title: Tild3_Day21

description:
Tild3.Day21_S71_L002
MM_252_raw_gene_count.txt


title: Tild2_Day56

description:
Tild2.Day56_S66_L002
MM_252_raw_gene_count.txt


title: Tild2_Day21

description:
Tild2.Day21_S65_L002
MM_252_raw_gene_count.txt


title: Tild2_Day14

description:
Tild2.Day14_S64_L002
MM_252_raw_gene_count.txt


title: Tild10_Day56

description:
Tild10.Day56_S12_L003
MM_252_raw_gene_count.txt


title: Tild10_Day3

description:
Tild10.Day3_S8_L003
MM_252_raw_gene_count.txt


title: Tild10_Day14

description:
Tild10.Day14_S10_L003
MM_252_raw_gene_count.txt


title: Tild2_Day0

description:
Tild2.Day0_S61_L002
MM_252_raw_gene_count.txt


title: Tild10_Day21

description:
Tild10.Day21_S11_L003
MM_252_raw_gene_count.txt


title: Tild10_Day7

description:
Tild10.Day7_S9_L003
MM_252_raw_gene_count.txt


title: Oxyt9_Day7

description:
Oxyt9.Day7_S81_L003
MM_252_raw_gene_count.txt

value: Oxytetracycline


title: Oxyt9_Day56

description:
Oxyt9.Day56_S84_L003
MM_252_raw_gene_count.txt

value: Day 56


title: Tild10_Day0

description:
Tild10.Day0_S7_L003
MM_252_raw_gene_count.txt


title: Oxyt9_Day21

description:
Oxyt9.Day21_S83_L003
MM_252_raw_gene_count.txt


title: Oxyt9_Day14

description:
Oxyt9.Day14_S82_L003
MM_252_raw_gene_count.txt


title: Canine Atopic Drematitis Patient 1 after therapy 7

type: RNA

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

hyb_protocol: according to the Agilent's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: whole blood form atopic dog 7 after immunotherapy

label_protocol: according to the Agilent's protocol

growth_protocol: not applicable

extract_protocol: Total RNA extracted using Rneasy Protect Animal Blood Kit following manufacturer's instructions (Qiagen, USA)

treatment_protocol: Blood collection into Rneasy Protect Animal Blood Tubes  (Qiagen, USA).

tag: sampling method

value: venous whole blood collected into Rneasy Protect Animal Blood Tubes (Qiagen, USA)

tag: health condition

value: Canine Atopic Drematitis dog 7  after 6 months immunotherapy

source_name: common reference sample compsed of total RNAs isolated from whole blood from 13 healthy dogs


title: Canine Atopic Drematitis Patient 1 after therapy 6

source_name: whole blood form atopic dog 6 after immunotherapy

value: Canine Atopic Drematitis dog 6  after 6 months immunotherapy


title: Canine Atopic Drematitis Patient 1 after therapy 5

source_name: whole blood form atopic dog 5 after immunotherapy

value: Canine Atopic Drematitis dog 5  after 6 months immunotherapy


title: Oxyt9_Day0

description:
Oxyt9.Day0_S79_L003
MM_252_raw_gene_count.txt


title: Canine Atopic Drematitis Patient 1 after therapy 3

source_name: whole blood form atopic dog 3 after immunotherapy

value: Canine Atopic Drematitis dog 3  after 6 months immunotherapy


title: Canine Atopic Drematitis Patient 4

source_name: whole blood form atopic dog 4

value: Canine Atopic Drematitis dog 4


title: Canine Atopic Drematitis Patient 7

source_name: whole blood form atopic dog 7

value: Canine Atopic Drematitis dog 7


title: Canine Atopic Drematitis Patient 6

source_name: whole blood form atopic dog 6

value: Canine Atopic Drematitis dog 6


title: Canine Atopic Drematitis Patient 1 after therapy 2

source_name: whole blood form atopic dog 2 after immunotherapy

value: Canine Atopic Drematitis dog 2  after 6 months immunotherapy


title: Canine Atopic Drematitis Patient 1 after therapy 4

source_name: whole blood form atopic dog 4 after immunotherapy

value: Canine Atopic Drematitis dog 4  after 6 months immunotherapy


title: Oxyt6_Day7

description:
Oxyt6.Day7_S75_L003
MM_252_raw_gene_count.txt


title: Canine Atopic Drematitis Patient 1 after therapy 1

source_name: whole blood form atopic dog 1 after immunotherapy

value: Canine Atopic Drematitis dog 1  after 6 months immunotherapy


title: Canine Atopic Drematitis Patient 5

source_name: whole blood form atopic dog 5

value: Canine Atopic Drematitis dog 5


title: Canine Atopic Drematitis Patient 1

source_name: whole blood form atopic dog 1

value: Canine Atopic Drematitis dog 1


title: Canine Atopic Drematitis Patient 3

source_name: whole blood form atopic dog 3

value: Canine Atopic Drematitis dog 3


title: Healthy Dog Patient Control 7

source_name: whole blood from healthy dog

value: healthy dog


title: Healthy Dog Patient Control 6


title: Oxyt6_Day3

description:
Oxyt6.Day3_S74_L003
MM_252_raw_gene_count.txt

value: Whole blood

value: Day 3

value: Oxytetracycline


title: Oxyt9_Day3

description:
Oxyt9.Day3_S80_L003
MM_252_raw_gene_count.txt


title: Oxyt6_Day21

description:
Oxyt6.Day21_S77_L003
MM_252_raw_gene_count.txt

value: Day 21


title: Oxyt6_Day56

description:
Oxyt6.Day56_S78_L003
MM_252_raw_gene_count.txt

value: Day 56


title: Oxyt6_Day0

description:
Oxyt6.Day0_S73_L003
MM_252_raw_gene_count.txt

value: Day 0


title: Oxyt6_Day14

description:
Oxyt6.Day14_S76_L003
MM_252_raw_gene_count.txt

value: Day 14


title: Canine Atopic Drematitis Patient 2

source_name: whole blood form atopic dog 2

value: venous whole blood collected into Rneasy Protect Animal Blood Tubes (Qiagen, USA)

value: Canine Atopic Drematitis dog 2


title: Oxyt5_Day7

description:
Oxyt5.Day7_S69_L003
MM_252_raw_gene_count.txt

source_name: Whole blood

value: Day 7


title: Z1_1-209_mut_OE_3

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
Raw sequence reads from RNA-seq experiments quality checked using FastQC
Reads were then trimmed for adaptors and filtered using Trim Galore
Trimmed reads were mapped to Hg38, using HISAT2 in paired-end mode.
Reads were converted to bigwig (bw) files using bamCoverage
Assembly: hg38
Supplementary files format and content: Stranded bigwig (bw) files, either individual replicates or average bw tracks

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto cells were cultured in DMEM medium (+Glutamax) supplemented with 10% FBS and Pen-Strep

extract_protocol:
Total RNA was extracted using Trizol (Ambion) and Dnase treated using TURBO Dnase
Ribodepletion and strand specific libraries were prepared by BGI Tech Solutions

value: HeLa Kyoto

tag: genotype

value: + DOX


title: Oxyt5_Day56

description:
Oxyt5.Day56_S72_L003
MM_252_raw_gene_count.txt


title: Healthy Dog Patient Control 8

source_name: common reference sample compsed of total RNAs isolated from whole blood from 13 healthy dogs


title: Z1_1-209_mut_OE_1


title: Z1_1-209_mut_OE_2


title: Oxyt5_Day3

description:
Oxyt5.Day3_S68_L003
MM_252_raw_gene_count.txt


title: Z1_1-209_WT_OE_3


title: Oxyt5_Day21

description:
Oxyt5.Day21_S71_L003
MM_252_raw_gene_count.txt


title: Oxyt5_Day14

description:
Oxyt5.Day14_S70_L003
MM_252_raw_gene_count.txt


title: Z1_1-209_WT_OE_2


title: Z1_1-209_WT_OE_1


title: Healthy Dog Patient Control 2


title: Oxyt5_Day0

description:
Oxyt5.Day0_S67_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day7

description:
Oxyt4.Day7_S63_L003
MM_252_raw_gene_count.txt


title: siZFC3H1+Z1_FL(mut)_2

tag: sirna treatment


title: Oxyt4_Day56

description:
Oxyt4.Day56_S66_L003
MM_252_raw_gene_count.txt

tag: treatment


title: siZFC3H1+Z1_FL(mut)_1


title: siZFC3H1+Z1_FL(WT)_2


title: Healthy Dog Patient Control 5


title: Healthy Dog Patient Control 3


title: siZFC3H1+Z1_FL(WT)_3


title: Oxyt4_Day21

description:
Oxyt4.Day21_S65_L003
MM_252_raw_gene_count.txt


title: Healthy Dog Patient Control 1


title: Healthy Dog Patient Control 4


title: Oxyt4_Day14

description:
Oxyt4.Day14_S64_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day7

description:
Oxyt2.Day7_S57_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day56

description:
Oxyt2.Day56_S60_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day0

description:
Oxyt4.Day0_S61_L003
MM_252_raw_gene_count.txt


title: siZFC3H1_3

value: - DOX


title: siZFC3H1_2


title: siZFC3H1+Z1_FL(WT)_1


title: Oxyt2_Day3

description:
Oxyt2.Day3_S56_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day21

description:
Oxyt2.Day21_S59_L003
MM_252_raw_gene_count.txt


title: DU145_RANKL50_solo_2

city: Chuo-ku

first: Jun

last: Nakayama

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center

data_processing:
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Assembly: hg19

source_name: Human prostate cancer cell lines

growth_protocol: Human prostate cancer cell lines were either mono-cultured or co-cultured with MG63 by NICO-1 (Ginreilab) in αMEM (gibco) with 10% FBS (gibco) and 1% antibiotic–antimycotic solution (AA,gibco) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
cDNA libraries for RNA sequencing were established from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for selecting poly-A mRNA followed by strand-specific library preparation using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech). The resulting double-stranded library fragments were further processed into single-stranded circular DNA (sscDNA), which is the final form of MGI library. The sscDNA libraries were quantified by Qubit ssDNA Assay Kit and used for generating DNA nanoballs (DNBs) by rolling circle replication reaction. DNBs were then loaded into a flow cell for sequencing on DNBSEQ-G400 platform (MGI tech), according to the manufacturer’s instructions.

value: Human prostate cancer cell line

tag: cell type

value: Osteolytic prostate cancer

tag: cell lines

tag: culture condition

value: mono-culture

tag: with rankl

value: Yes

tag: co-culture with osteoblasts or osteoclasts


title: DU145_RANKL50_solo_1


title: siZFC3H1+Z1_FL(mut)_3

tag: cell line


title: Oxyt2_Day14

description:
Oxyt2.Day14_S58_L003
MM_252_raw_gene_count.txt

value: Whole blood

tag: time


title: Oxyt4_Day3

description:
Oxyt4.Day3_S62_L003
MM_252_raw_gene_count.txt

tag: tissue

value: Day 3


title: Oxyt2_Day0

description:
Oxyt2.Day0_S55_L003
MM_252_raw_gene_count.txt

value: Oxytetracycline


title: DU145_RANKL50_RAW_1

value: co-culture

value: Osteoclasts(RAW246.7 cells)


title: DU145_RANKL50_RAW_2


title: DU145_MG63_2

value: No

value: Osteoblasts(MG63 cells)


title: Oxyt1_Day7

description:
Oxyt1.Day7_S51_L003
MM_252_raw_gene_count.txt


title: Oxyt1_Day3

description:
Oxyt1.Day3_S50_L003
MM_252_raw_gene_count.txt


title: Oxyt1_Day56

description:
Oxyt1.Day56_S54_L003
MM_252_raw_gene_count.txt

value: Day 56


title: Oxyt1_Day21

description:
Oxyt1.Day21_S53_L003
MM_252_raw_gene_count.txt

value: Day 21


title: C4-2B_RANKL50_solo_2

value: Osteoblastic prostate cancer


title: C4-2B_RANKL50_RAW_2


title: C4-2B_RANKL50_solo_1


title: C4-2B_RANKL50_RAW_1


title: Oxyt1_Day0

description:
Oxyt1.Day0_S49_L003
MM_252_raw_gene_count.txt

value: Day 0


title: NC7_Day7

description:
NC7.Day7_S15_L001
MM_252_raw_gene_count.txt

value: Day 7

value: Negative Control


title: Oxyt1_Day14

description:
Oxyt1.Day14_S52_L003
MM_252_raw_gene_count.txt

value: Day 14


title: siZFC3H1_1

value: HeLa Kyoto

value: - DOX


title: C4-2B_MG63_2

value: Human prostate cancer cell line


title: NC7_Day56

description:
NC7.Day56_S18_L001
MM_252_raw_gene_count.txt

value: Whole blood


title: C4-2B_MG63_1


title: NC5_Day56

description:
NC5.Day56_S12_L001
MM_252_raw_gene_count.txt


title: NC7_Day21

description:
NC7.Day21_S17_L001
MM_252_raw_gene_count.txt


title: NC5_Day7

description:
NC5.Day7_S9_L001
MM_252_raw_gene_count.txt


title: C4-2_MG63_2


title: C4-2_RANKL50_solo_1

value: mono-culture

value: Yes


title: NC7_Day0

description:
NC7.Day0_S13_L001
MM_252_raw_gene_count.txt


title: 22Rv1_RANKL50_solo_1

value: Osteolytic prostate cancer


title: C4-2_RANKL50_solo_2


title: C4-2_RANKL50_RAW_1

value: co-culture

value: Osteoclasts(RAW246.7 cells)


title: DU145_MG63_1

value: No

value: Osteoblasts(MG63 cells)


title: C4-2_MG63_1


title: NC5_Day21

description:
NC5.Day21_S11_L001
MM_252_raw_gene_count.txt

value: Day 21


title: 22Rv1_RANKL50_RAW_2


title: NC5_Day0

description:
NC5.Day0_S7_L001
MM_252_raw_gene_count.txt


title: 22Rv1_RANKL50_RAW_1


title: NC5_Day3

description:
NC5.Day3_S8_L001
MM_252_raw_gene_count.txt

value: Day 3


title: NC15_Day7

description:
NC15.Day7_S33_L001
MM_252_raw_gene_count.txt


title: NC5_Day14

description:
NC5.Day14_S10_L001
MM_252_raw_gene_count.txt


title: 22Rv1_MG63_2


title: 22Rv1_MG63_1


title: NC15_Day3

description:
NC15.Day3_S32_L001
MM_252_raw_gene_count.txt


title: NC15_Day56

description:
NC15.Day56_S36_L001
MM_252_raw_gene_count.txt

value: Day 56


title: DU145_3


title: NC7_Day3

description:
NC7.Day3_S14_L001
MM_252_raw_gene_count.txt


title: NC15_Day21

description:
NC15.Day21_S35_L001
MM_252_raw_gene_count.txt


title: DU145_2


title: NC7_Day14

description:
NC7.Day14_S16_L001
MM_252_raw_gene_count.txt


title: C4-2_RANKL50_RAW_2

value: Osteoblastic prostate cancer


title: 22Rv1_RANKL50_solo_2


title: DU145_1


title: NC13_Day56

description:
NC13.Day56_S30_L001
MM_252_raw_gene_count.txt

value: Negative Control


title: NC13_Day7

description:
NC13.Day7_S27_L001
MM_252_raw_gene_count.txt

value: Day 7


title: NC15_Day0

description:
NC15.Day0_S31_L001
MM_252_raw_gene_count.txt

value: Day 0


title: NC13_Day3

description:
NC13.Day3_S26_L001
MM_252_raw_gene_count.txt


title: C4-2_3


title: C4-2B_1


title: C4-2B_2


title: NC13_Day14

description:
NC13.Day14_S28_L001
MM_252_raw_gene_count.txt

value: Day 14


title: C4-2_2

value: Human prostate cancer cell line


title: NC13_Day21

description:
NC13.Day21_S29_L001
MM_252_raw_gene_count.txt

value: Whole blood


title: C4-2B_3

value: mono-culture


title: 22Rv1_2


title: NC13_Day0

description:
NC13.Day0_S25_L001
MM_252_raw_gene_count.txt


title: C4-2_1


title: 22Rv1_1


title: 22Rv1_3


title: NC12_Day3

description:
NC12.Day3_S20_L001
MM_252_raw_gene_count.txt


title: NC12_Day56

description:
NC12.Day56_S24_L001
MM_252_raw_gene_count.txt


title: NC12_Day14

description:
NC12.Day14_S22_L001
MM_252_raw_gene_count.txt


title: NC12_Day21

description:
NC12.Day21_S23_L001
MM_252_raw_gene_count.txt


title: NC12_Day0

description:
NC12.Day0_S19_L001
MM_252_raw_gene_count.txt


title: NC1_Day7

description:
NC1.Day7_S3_L001
MM_252_raw_gene_count.txt


title: NC15_Day14

description:
NC15.Day14_S34_L001
MM_252_raw_gene_count.txt


title: NC1_Day3

description:
NC1.Day3_S2_L001
MM_252_raw_gene_count.txt


title: leaf,R-loop,Cold_2

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

country: China

institute: Nanjing Agricultural University

description: DRIP-seq

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

growth_protocol: Seeds of Nipponbare (Oryzasativa 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

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


title: leaf,R-loop,CK_3

description: DRIP-seq

value: grow in the normal conditions


title: leaf,R-loop,Cold_3

description: DRIP-seq


title: leaf,R-loop,CK_2

description: DRIP-seq


title: leaf,R-loop,Cold_1

description: DRIP-seq


title: NC1_Day21

description:
NC1.Day21_S5_L001
MM_252_raw_gene_count.txt


title: NC12_Day7

description:
NC12.Day7_S21_L001
MM_252_raw_gene_count.txt


title: Cold-RH

data_processing:
DRIP-seq
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

source_name: leaf,RH,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.

tag: antibody

value: Rnase H

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


title: Cold-DRIP_rep2

source_name: leaf,R-loop,Cold


title: Cold-DRIP_rep1


title: leaf,R-loop,CK_1

description: DRIP-seq


title: Cold_rep2

source_name: leaf,RNA-seq,Cold


title: CK-DRIP_rep1

source_name: leaf,R-loop,CK


title: CK-DRIP_rep2


title: Flor8_Day3

description:
Flor8.Day3_S14_L002
MM_252_raw_gene_count.txt

value: Florfenicol


title: Flor8_Day56

description:
Flor8.Day56_S18_L002
MM_252_raw_gene_count.txt


title: Flor8_Day7

description:
Flor8.Day7_S15_L002
MM_252_raw_gene_count.txt


title: Flor8_Day21

description:
Flor8.Day21_S17_L002
MM_252_raw_gene_count.txt

value: Day 21


title: Flor8_Day14

description:
Flor8.Day14_S16_L002
MM_252_raw_gene_count.txt


title: Cold_rep1


title: lowP_12SIII-2

city: Thuwal

first: Jian You

last: Wang

state: Not Specified

address: 4700 King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900, Kingdom of Saudi Arabia

country: Saudi Arabia

institute: KAUST

description:
gene_fpkm
lowP_12SIIIvslowP_WT_deg

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly (ensemblplants_oryza_sativa_japonica_group_irgsp_1_0_gca_001433935_1). Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Differential gene expression was examined using DESeq2
Assembly: ensemblplants_oryza_sativa_japonica_group_irgsp_1_0_gca_001433935_1
Supplementary files format and content: FPKM, DESeq2 output

organism: Oryza sativa

source_name: 3-week-old root tissues

extract_protocol:
Total rice root RNA was extracted with TRIzol (Invitrogen, https://www.thermofisher.com/de/de/home.htmL) using a Direct-zol RNA Miniprep Plus Kit following the manufacturer’s instructions (ZYMO RESEARCH; USA).
The cDNA libraries were constructed following standard protocols

value: 3-week-old root tissues

tag: cultivar

value: cv. Nipponbare

value: Low Pi


title: CK_rep2

source_name: leaf,RNA-seq,CK


title: NC1_Day56

description:
NC1.Day56_S6_L001
MM_252_raw_gene_count.txt

value: Day 56

value: Negative Control

tag: sequencing lane


title: Flor7_Day7

description:
Flor7.Day7_S9_L002
MM_252_raw_gene_count.txt

value: Day 7

tag: individual id


title: NC1_Day14

description:
NC1.Day14_S4_L001
MM_252_raw_gene_count.txt

value: Day 14


title: lowP_12SIII-1

description:
gene_fpkm
lowP_12SIIIvslowP_WT_deg


title: lowP_WT-3

description:
gene_fpkm
lowP_12SIIIvslowP_WT_deg

value: WT


title: lowP_WT-2

description:
gene_fpkm
lowP_12SIIIvslowP_WT_deg


title: Flor7_Day3

description:
Flor7.Day3_S8_L002
MM_252_raw_gene_count.txt

value: Whole blood

value: Day 3


title: Flor7_Day0

description:
Flor7.Day0_S7_L002
MM_252_raw_gene_count.txt

value: Day 0


title: Wt_Dead

city: Boston

middle: Ryan

last: Sullivan

state: Massachusetts

address: 140 The Fenway

department: Pharmaceutical Sciences

institute: Northeastern University

data_processing:
Unknown, performed by Novogene
Assembly: hg18
Supplementary files format and content: raw gene counts of all samples in excel format, along with basic gene information

source_name: Blood

growth_protocol: NK cells were culted with 500 IU/ml IL2 in NK MACS media for several days prior to experiment

extract_protocol:
RNA was extracted and prepared using QIAGEN Rneasy kit
Novogene ultra-low input

treatment_protocol: CAR NK were transfected with lentiviral infection. Lentivirus was produced by co-transfecting HEK293 cells with transfer plasmid pHIV-CD19-CAR-GFP plasmid, packaging plasmid pCMV-Δ8.9, envelope pCMV-BaEV and pAdvantage (Promega) using the TransIT-LT1 transfection reagent (Mirus Bio). Culture supernatants were harvested at 24h and 36h.

value: Blood

value: Primary cells

value: Cancer and immune cells


title: lowP_WT-1

description:
gene_fpkm
lowP_12SIIIvslowP_WT_deg


title: CK_rep1

value: leaf

value: grow in the normal conditions


title: Flor6_Day7

description:
Flor6.Day7_S3_L002
MM_252_raw_gene_count.txt

value: Florfenicol


title: Flor7_Day56

description:
Flor7.Day56_S12_L002
MM_252_raw_gene_count.txt


title: NC1_Day0

description:
NC1.Day0_S1_L001
MM_252_raw_gene_count.txt


title: lowP_12SIII-3

description:
gene_fpkm
lowP_12SIIIvslowP_WT_deg

value: 3-week-old root tissues


title: Flor6_Day56

description:
Flor6.Day56_S6_L002
MM_252_raw_gene_count.txt


title: Flor7_Day14

description:
Flor7.Day14_S10_L002
MM_252_raw_gene_count.txt


title: CAR_NoK_2


title: Flor7_Day21

description:
Flor7.Day21_S11_L002
MM_252_raw_gene_count.txt

value: Day 21


title: +P_12SIII-2

description:
gene_fpkm
Pi_12SIIIvsPi_WT_deg

value: cv. Nipponbare

value: +Pi


title: CAR_K_2


title: Flor8_Day0

description:
Flor8.Day0_S13_L002
MM_252_raw_gene_count.txt


title: Flor6_Day3

description:
Flor6.Day3_S2_L002
MM_252_raw_gene_count.txt


title: Flor6_Day0

description:
Flor6.Day0_S1_L002
MM_252_raw_gene_count.txt


title: HDAC8_SKMEL28-3

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

description:
raw-counts.txt
EV_SKMEL28.vs.HDAC8_SKMEL28.fc.txt

data_processing:
Short reads were trimmed with trimmomatic and mapped to the human transcriptome using the STAR aligner.
Gene expression was quantified with RSEM and differential expression analysis was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab delimited file of pseudo-counts for each gene in each sample
Supplementary files format and content: Tab delimited file of fold change and P-value for the contrast between the two experimental conditions

growth_protocol: 1 million HDAC8 and EV expresing melanoma cells were harvested from melanoma cells grown to 70% confluence in 175 cm2 flasks.

extract_protocol:
RNA was harvested using Aurum total RNA kit (BioRad). 500 ng of total RNA was used for the construction of sequencing libraries.
rRNAs first were removed by Illumina Ribo-Zero Plus rRNA depletion Kit f(Part# 20040526, Illumina) following the manufacturer’s protocol, then the depleted RNA were used for library construction with NEBNext®Ultra™II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog # E7760L).

value: melanoma

value: plasmid expressing HDAC8 added

value: forced HDAC8 expression

tag: biorep


title: Flor6_Day21

description:
Flor6.Day21_S5_L002
MM_252_raw_gene_count.txt


title: Flor4_Day7

description:
Flor4.Day7_S81_L001
MM_252_raw_gene_count.txt

value: Day 7


title: +P_12SIII-1

description:
gene_fpkm
Pi_12SIIIvsPi_WT_deg


title: Wt_Live


title: HDAC8_SKMEL28-2


title: Flor4_Day3

description:
Flor4.Day3_S80_L001
MM_252_raw_gene_count.txt

value: Whole blood


title: Flor4_Day56

description:
Flor4.Day56_S84_L001
MM_252_raw_gene_count.txt

value: Day 56


title: +P_12SIII-3

description:
gene_fpkm
Pi_12SIIIvsPi_WT_deg


title: Flor4_Day21

description:
Flor4.Day21_S83_L001
MM_252_raw_gene_count.txt


title: +P_WT-3

description:
gene_fpkm
Pi_12SIIIvsPi_WT_deg

value: WT


title: HDAC8_SKMEL28-1


title: Flor6_Day14

description:
Flor6.Day14_S4_L002
MM_252_raw_gene_count.txt

value: Day 14


title: +P_WT-2

description:
gene_fpkm
Pi_12SIIIvsPi_WT_deg


title: Flor4_Day0

description:
Flor4.Day0_S79_L001
MM_252_raw_gene_count.txt

value: Day 0


title: EV_SKMEL28-3

value: EV plasmid added

value: control


title: Flor3_Day7

description:
Flor3.Day7_S75_L001
MM_252_raw_gene_count.txt


title: Flor3_Day56

description:
Flor3.Day56_S78_L001
MM_252_raw_gene_count.txt


title: Flor3_Day3

description:
Flor3.Day3_S74_L001
MM_252_raw_gene_count.txt

value: Day 3


title: EV_SKMEL28-1


title: +P_WT-1

description:
gene_fpkm
Pi_12SIIIvsPi_WT_deg


title: EV_SKMEL28-2


title: Flor3_Day0

description:
Flor3.Day0_S73_L001
MM_252_raw_gene_count.txt

value: Florfenicol


title: Flor3_Day21

description:
Flor3.Day21_S77_L001
MM_252_raw_gene_count.txt


title: Flor3_Day14

description:
Flor3.Day14_S76_L001
MM_252_raw_gene_count.txt


title: Flor10_Day56

description:
Flor10.Day56_S24_L002
MM_252_raw_gene_count.txt


title: nCT, ST medium, 72h, flow, rep2

city: Kyoto

first: ASAKO

last: INOHAYA

address: Shogoin, Sakyoku

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

data_processing:
Adapter sequences and low-quality reads were trimmed from the raw sequencing reads using Trim_Galore (RRID: SCR_011847)
The resulting reads were aligned to the human reference genome (GRCh38) using STAR and guided by gene models from the Ensembl v98 release
Reads mapped to ribosomal RNA were removed using SAMtools IntersectBed
The number of reads mapped to exons was calculated using featureCounts
Assembly: GRCh38
Supplementary files format and content: command separated files containing expected read counts

source_name: 409B2 iPSC

growth_protocol: nCTs were cultured in A83-01, CHIR99021, and EGF(ACE) medium or ST medium for 48 or 72 hours under static condition or 10 dyn/cm2 shear stress.

extract_protocol:
Total RNA was extracted using the Rneasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol
RNA libraries were prepared  for sequencing using standard Illumina protocols

treatment_protocol: nCT was incubated in ACE medium (NDiff227, 1 mM A83-01, 2 mM CHIR99021, and 50 ng/ml recombinant human EGF on iMatrix silk).  The nCTs were treated with ST medium (NDiff 227, 4% KnockOut Serum Replacement , 2 µM forskolin ) to induce ST differentiation

value: 409B2 iPSC

value: naive human pluripotent stem cell-derived cytotrophoblast stem cell

tag: tratment(medium)

value: ST medium

tag: treatment(flow

value: _shear_stress):flow 72h


title: Flor10_Day3

description:
Flor10.Day3_S20_L002
MM_252_raw_gene_count.txt


title: nCT, ST medium, 72h, flow, rep3


title: Flor4_Day14

description:
Flor4.Day14_S82_L001
MM_252_raw_gene_count.txt


title: nCT, ST medium, 72h, flow, rep1


title: nCT, ST medium, 72h, static, rep3

value: _shear_stress):static 72h


title: Flor10_Day0

description:
Flor10.Day0_S19_L002
MM_252_raw_gene_count.txt


title: Flor10_Day21

description:
Flor10.Day21_S23_L002
MM_252_raw_gene_count.txt

value: Day 21


title: Enro9_Day7

description:
Enro9.Day7_S63_L001
MM_252_raw_gene_count.txt

value: Enrofloxacin


title: Flor10_Day14

description:
Flor10.Day14_S22_L002
MM_252_raw_gene_count.txt


title: Enro9_Day56

description:
Enro9.Day56_S66_L001
MM_252_raw_gene_count.txt


title: nCT, ST medium, 72h, static, rep2


title: Enro9_Day3

description:
Enro9.Day3_S62_L001
MM_252_raw_gene_count.txt


title: Enro9_Day21

description:
Enro9.Day21_S65_L001
MM_252_raw_gene_count.txt


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

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

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.

organism: Drosophila subobscura

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

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: Dsuz.ovary.2 small-RNA-Seq

organism: Drosophila suzukii


title: Enro9_Day14

description:
Enro9.Day14_S64_L001
MM_252_raw_gene_count.txt

value: Whole blood

tag: treatment


title: Enro8_Day7

description:
Enro8.Day7_S57_L001
MM_252_raw_gene_count.txt

value: Day 7


title: nCT, ST medium, 48h, flow, rep3

tag: cell type

value: _shear_stress):flow 48h


title: Flor10_Day7

description:
Flor10.Day7_S21_L002
MM_252_raw_gene_count.txt


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


title: Enro9_Day0

description:
Enro9.Day0_S61_L001
MM_252_raw_gene_count.txt


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

organism: Drosophila biarmipes


title: Enro8_Day3

description:
Enro8.Day3_S56_L001
MM_252_raw_gene_count.txt


title: Enro8_Day56

description:
Enro8.Day56_S60_L001
MM_252_raw_gene_count.txt

value: Day 56


title: Enro8_Day21

description:
Enro8.Day21_S59_L001
MM_252_raw_gene_count.txt


title: nCT, ST medium, 48h, flow, rep1


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


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

value: somatic follicle cells


title: Enro8_Day14

description:
Enro8.Day14_S58_L001
MM_252_raw_gene_count.txt

value: Day 14


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

organism: Drosophila azteca


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


title: nCT, ST medium, 48h, static, rep3

value: _shear_stress):static 48h


title: nCT, ST medium, 72h, static, rep1


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


title: Enro6_Day3

description:
Enro6.Day3_S50_L001
MM_252_raw_gene_count.txt

value: Day 3


title: Enro6_Day7

description:
Enro6.Day7_S51_L001
MM_252_raw_gene_count.txt


title: Enro8_Day0

description:
Enro8.Day0_S55_L001
MM_252_raw_gene_count.txt

value: Day 0


title: Enro6_Day21

description:
Enro6.Day21_S53_L001
MM_252_raw_gene_count.txt


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


title: nCT, ST medium, 48h, static, rep2

value: 409B2 iPSC


title: nCT, ST medium, 48h, static, rep1

value: naive human pluripotent stem cell-derived cytotrophoblast stem cell


title: Enro6_Day0

description:
Enro6.Day0_S49_L001
MM_252_raw_gene_count.txt


title: Enro5_Day7

description:
Enro5.Day7_S45_L001
MM_252_raw_gene_count.txt


title: Enro6_Day14

description:
Enro6.Day14_S52_L001
MM_252_raw_gene_count.txt


title: nCT, ST medium, 48h, flow, rep2

value: ST medium


title: MYC/SMARCA4_tumor_2

type: genomic

city: Hamburg

first: Ulrich

last: Schüller

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulfite conversion was performed with the EZ DNA Methylation kit (Zymo Research, CA, USA) before amplification, fragmentation, and hybridization to the Illumina Infinium Mouse Methylation BeadChip using standard Illumina protocol

scan_protocol: Illumina iScan microarray scanner

data_processing:
SeSAMe
Normalized beta values generated with openSesame (491 orthologous sites used for clustering) is provided in the Matrix_processed.txt.

label: cy3, cy5

source_name: tumor, fresh frozen biopsy

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from frozen tissue (n=2) was isolated using the NucleoSpin Tissue kit (Macherey-Nagel, Düren, DE), whereas DNA isolation from FFPE tissue (n=1) was performed using the Maxwell RSC DNA FFPE kit (Promega Corporation, WI, USA).

tag: host/recipient strain

value: brain

tag: age (days)

tag: tissue type

value: tumor, fresh frozen biopsy


title: nCT, ACE medium, 72h, static, rep3

tag: cell line

value: ACE medium

value: _shear_stress):static 72h


title: T9

city: Yangling

first: shenye

last: qu

address: LiTai road Yangling, shaanxi

institute: Northwest A&F university

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of parasite was sequenced run with Illumina 4000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating 4 billon paired-end reads of bp length
Prior to assembly, the low quality reads were removed. After that, a total of 80 G bp of cleaned ,paired-end reads were produced.
The mapped reads of each sample were assembled using StringTie. All transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
we aligned reads  to the UCSC (http://genome.ucsc.edu/) I. multifiliis reference genome using HISAT package,
Assembly: GCA_000220395.1/ v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Ichthyophthirius multifiliis

source_name: G5 strain

growth_protocol: All parasites naturally infected goldfish at favorable condition (22-23℃, freshwater)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeqsample preparation kit (Illumina, San Diego, USA),

treatment_protocol:
The parasites on fish skin were treated with magnolol at various concentrations (1.5 mg/L for 0.5 h and 1 h)
The parasites on fish skin were treated with magnolol at various concentrations (3.5 mg/L for 1 h)

value: G5 strain

value: parasite

tag: genotype

value: WT

value: drug treatment (3.5 mg/L magnolol)

tag: time


title: T8


title: MYC/SMARCA4_tumor_1

tag: tissue


title: Enro5_Day56

description:
Enro5.Day56_S48_L001
MM_252_raw_gene_count.txt

value: Whole blood

value: Day 56

value: Enrofloxacin


title: Enro6_Day56

description:
Enro6.Day56_S54_L001
MM_252_raw_gene_count.txt


title: MYC/SMARCA4_tumor_3

source_name: tumor, FFPE punch

value: tumor, FFPE punch


title: nCT, ACE medium, 72h, static, rep2


title: Enro5_Day3

description:
Enro5.Day3_S44_L001
MM_252_raw_gene_count.txt

value: Day 3


title: T7


title: Enro5_Day21

description:
Enro5.Day21_S47_L001
MM_252_raw_gene_count.txt

value: Day 21


title: Enro5_Day14

description:
Enro5.Day14_S46_L001
MM_252_raw_gene_count.txt

value: Day 14


title: T5

value: drug treatment (1.5 mg/L magnolol)


title: T6


title: Enro2_Day7

description:
Enro2.Day7_S39_L001
MM_252_raw_gene_count.txt

value: Day 7


title: Enro5_Day0

description:
Enro5.Day0_S43_L001
MM_252_raw_gene_count.txt

value: Day 0


title: WM164HDAC8-3

description: HDAC8 expression vector

data_processing:
Short reads were trimmed with trimmomatic and mapped to the human transcriptome using the STAR aligner.
Gene expression was quantified with RSEM and differential expression analysis was performed with DESeq2.
Supplementary files format and content: tab delimited file of pseudo-counts for each gene in each condition
Supplementary files format and content: Excel file of fold change and P-value for all differentially expressed genes in each contrast

source_name: melanoma cell line

extract_protocol:
RNA was harvested using Aurum total RNA kit (BioRad). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina RNA-Seq library Prep following manufacturer's protocols.

value: melanoma cell line

value: melanoma

value: HDAC8 expression vector


title: T4

value: G5 strain


title: Enro2_Day56

description:
Enro2.Day56_S42_L001
MM_252_raw_gene_count.txt

source_name: Whole blood


title: Enro2_Day14

description:
Enro2.Day14_S40_L001
MM_252_raw_gene_count.txt


title: Enro2_Day3

description:
Enro2.Day3_S38_L001
MM_252_raw_gene_count.txt


title: WM164HDAC8-2

description: HDAC8 expression vector


title: Enro10_Day7

description:
Enro10.Day7_S69_L001
MM_252_raw_gene_count.txt


title: T3

value: parasite


title: T2

value: WT


title: Enro2_Day0

description:
Enro2.Day0_S37_L001
MM_252_raw_gene_count.txt


title: Enro2_Day21

description:
Enro2.Day21_S41_L001
MM_252_raw_gene_count.txt


title: nCT, ACE medium, 72h, static, rep1

value: 409B2 iPSC

value: naive human pluripotent stem cell-derived cytotrophoblast stem cell

value: ACE medium

value: _shear_stress):static 72h


title: Enro10_Day3

description:
Enro10.Day3_S68_L001
MM_252_raw_gene_count.txt

value: Whole blood

value: Enrofloxacin


title: Enro10_Day21

description:
Enro10.Day21_S71_L001
MM_252_raw_gene_count.txt

value: Day 21


title: Enro10_Day56

description:
Enro10.Day56_S72_L001
MM_252_raw_gene_count.txt

value: Day 56


title: C5


title: Enro10_Day14

description:
Enro10.Day14_S70_L001
MM_252_raw_gene_count.txt

value: Day 14


title: U056_GEX

city: Durham

first: Joseph

middle: Ruixin

last: Chen

state: North Carolina

address: R323  Pegram 1340 Campus Drive

department: National Institute of Aging

institute: National Institute of Health

data_processing:
Sequences mapped to reference genome and single cell transcriptomes via Cellranger
Cells filtered and clustered via Seurat
Supplementary files format and content: Seurat Object containing meta data tied to donor and stimulation status

source_name: Peripheral Blood

growth_protocol: Stimulated with LLL antigen

extract_protocol:
Sorted for  LLL antigen binding
10x Genomics

value: Peripheral Blood

value: CD8+ T cells


title: WM164-2

description: empty expression vector

value: melanoma cell line

value: empty expression vector


title: T1

value: drug treatment (1.5 mg/L magnolol)


title: WM164-3

description: empty expression vector

value: melanoma


title: Enro10_Day0

description:
Enro10.Day0_S67_L001
MM_252_raw_gene_count.txt

value: Day 0


title: WM164-1

description: empty expression vector


title: C4

value: G5 strain

value: parasite

value: WT


title: Ceft8_Day56

description:
Ceft8.Day56_S42_L003
MM_252_raw_gene_count.txt

value: Ceftiofur


title: C3


title: WM164HDAC8-1

description: HDAC8 expression vector

value: HDAC8 expression vector


title: human_blastocyst_B4_8

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: blastocyst

tag: batch

value: fair


title: Ceft8_Day3

description:
Ceft8.Day3_S38_L003
MM_252_raw_gene_count.txt

value: Whole blood

value: Day 3

tag: sequencing lane


title: human_blastocyst_B4_7


title: C2


title: Ceft8_Day21

description:
Ceft8.Day21_S41_L003
MM_252_raw_gene_count.txt

value: Day 21

tag: individual id


title: Ceft8_Day0

description:
Ceft8.Day0_S37_L003
MM_252_raw_gene_count.txt


title: Ceft8_Day14

description:
Ceft8.Day14_S40_L003
MM_252_raw_gene_count.txt

value: Day 14


title: C1


title: Ceft6_Day56

description:
Ceft6.Day56_S36_L003
MM_252_raw_gene_count.txt

value: Day 56


title: Ceft6_Day7

description:
Ceft6.Day7_S33_L003
MM_252_raw_gene_count.txt

value: Day 7


title: Ceft8_Day7

description:
Ceft8.Day7_S39_L003
MM_252_raw_gene_count.txt


title: human_blastocyst_B4_5

value: good


title: Ceft6_Day3

description:
Ceft6.Day3_S32_L003
MM_252_raw_gene_count.txt


title: Ceft6_Day14

description:
Ceft6.Day14_S34_L003
MM_252_raw_gene_count.txt


title: human_blastocyst_B4_4

value: high


title: human_blastocyst_B4_6


title: Ceft5_Day7

description:
Ceft5.Day7_S27_L003
MM_252_raw_gene_count.txt


title: Ceft6_Day21

description:
Ceft6.Day21_S35_L003
MM_252_raw_gene_count.txt


title: SGK1/3 DKO + DMXAA (rerun) [dKO_D_V_Re]

city: Chapel Hill

first: Johnny

middle: Victor

last: Castillo Cabrera

state: NC

address: 450 West Drive

institute: University of North Carolina

description:
dKO_D_V_Re
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

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

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.

value: macrophage

value: SGK1/SGK3 double KO

value: DMXAA 10μg/mL 2 hours


title: SGK1/3 DKO + DMXAA (rerun) [dKO_D_W_Re]

description:
dKO_D_W_Re
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_blastocyst_B4_3


title: SGK1 KO + DMXAA (rerun) [S1_D_S_Re]

description:
S1_D_S_Re
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: SGK1 KO


title: Ceft5_Day56

description:
Ceft5.Day56_S30_L003
MM_252_raw_gene_count.txt

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina TruSeq adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.36.0 and glmmSeq v0.2.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample


title: human_blastocyst_B4_2


title: Ceft5_Day3

description:
Ceft5.Day3_S26_L003
MM_252_raw_gene_count.txt


title: Ceft5_Day21

description:
Ceft5.Day21_S29_L003
MM_252_raw_gene_count.txt


title: human_blastocyst_B4_1


title: Ceft5_Day14

description:
Ceft5.Day14_S28_L003
MM_252_raw_gene_count.txt


title: Ceft5_Day0

description:
Ceft5.Day0_S25_L003
MM_252_raw_gene_count.txt

value: Day 0


title: SGK1 KO no treatment [S1_F]

description:
S1_F
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: no treatment


title: human_blastocyst_B3_3


title: Ceft6_Day0

description:
Ceft6.Day0_S31_L003
MM_252_raw_gene_count.txt

value: Ceftiofur


title: SGK1 KO + DMXAA [S1_D_R]

description:
S1_D_R
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_blastocyst_B3_4

value: blastocyst


title: Ceft4_Day7

description:
Ceft4.Day7_S21_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day21

description:
Ceft4.Day21_S23_L003
MM_252_raw_gene_count.txt


title: SGK1 KO no treatment [S1_E]

description:
S1_E
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: Ceft4_Day3

description:
Ceft4.Day3_S20_L003
MM_252_raw_gene_count.txt


title: SGK1 KO + DMXAA [S1_D_Q]

description:
S1_D_Q
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: Ceft3_Day7

description:
Ceft3.Day7_S15_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day0

description:
Ceft4.Day0_S19_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day56

description:
Ceft4.Day56_S24_L003
MM_252_raw_gene_count.txt


title: SGK1 KO + DMXAA [S1_D_P]

description:
S1_D_P
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_blastocyst_B3_1

value: fair


title: human_blastocyst_B3_2


title: Ceft3_Day56

description:
Ceft3.Day56_S18_L003
MM_252_raw_gene_count.txt

value: Whole blood


title: WT no treatment (rerun) [EV_D_J_Re]

description:
EV_D_J_Re
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: WT (empty vector sgRNA)


title: Ceft4_Day14

description:
Ceft4.Day14_S22_L003
MM_252_raw_gene_count.txt


title: Ceft3_Day3

description:
Ceft3.Day3_S14_L003
MM_252_raw_gene_count.txt

value: Day 3


title: SGK1 KO + DMXAA [S1_D_O]

description:
S1_D_O
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: Ceft3_Day21

description:
Ceft3.Day21_S17_L003
MM_252_raw_gene_count.txt

value: Day 21


title: human_morula_B3_4

value: morula

value: bad


title: Ceft3_Day14

description:
Ceft3.Day14_S16_L003
MM_252_raw_gene_count.txt

value: Day 14


title: SGK1 KO no treatment [S1_D]

description:
S1_D
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: Ceft3_Day0

description:
Ceft3.Day0_S13_L003
MM_252_raw_gene_count.txt


title: human_morula_B3_3


title: Ceft10_Day7

description:
Ceft10.Day7_S45_L003
MM_252_raw_gene_count.txt

value: Day 7


title: human_morula_B3_2


title: human_8C_B4_6

value: high


title: WT + DMXAA [EV_D_M]

description:
EV_D_M
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: macrophage


title: WT + DMXAA [EV_D_N]

description:
EV_D_N
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: DMXAA 10μg/mL 2 hours


title: WT + DMXAA [EV_D_L]

description:
EV_D_L
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_blastocyst_B2_1


title: Ceft10_Day14

description:
Ceft10.Day14_S46_L003
MM_252_raw_gene_count.txt


title: WT no treatment [EV_C]

description:
EV_C
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_8C_B4_3


title: WT + DMXAA [EV_D_K]

description:
EV_D_K
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: Ceft10_Day0

description:
Ceft10.Day0_S43_L003
MM_252_raw_gene_count.txt


title: Ceft10_Day3

description:
Ceft10.Day3_S44_L003
MM_252_raw_gene_count.txt


title: Ceft10_Day21

description:
Ceft10.Day21_S47_L003
MM_252_raw_gene_count.txt


title: human_8C_B4_4


title: WT no treatment [EV_B]

description:
EV_B
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: ATAC_dmel_ovary_rep2

description: 6 ovaries

data_processing:
genome build/assembly: dm6
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 melanogaster

source_name: ovary

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

value: wild type

tag: Sex

value: female


title: human_8C_B4_5


title: ATAC_dmel_ovary_rep1

description: 6 ovaries


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


title: Dmel.ovary_FC.3 small-RNA-Seq

value: somatic follicle cells


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


title: human_8C_B4_2


title: WT no treatment [EV_A]

description:
EV_A
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: no treatment


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


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


title: Ceft10_Day56

description:
Ceft10.Day56_S48_L003
MM_252_raw_gene_count.txt

extract_protocol:
Total RNA was isolated via PAXgene Blood miRNA Kits, per product instruction, with automated processing through QIAcube instrumentation.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols.

value: Day 56

value: Ceftiofur


title: human_8C_B4_1


title: SGK1/3 dKO no treamtent [dKO_I]

description:
dKO_I
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: SGK1/SGK3 double KO


title: THC-COOH 2

city: Rehovot

first: Ofer

last: Gover

address: Hertzel 229

department: Biochemistry and Nutrition

country: Israel

institute: Hebrew University Jerusalem

data_processing:
fastq files were generated by the usage bcl2fastq-v2.20.0.422 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the Rattus norvegicus genome build Rnor_6.0 using STAR (2.7.3a)
Deduplication (UMI is in read 2) was carried out by flagging all reads that were mapped to the same gene and had the same UMI (read 2 has the UMI)
Reads were counted using Ensembl annotations, build 104 (1000 bases of the 3’ UTR), using HTSeq-Counts (version 0.11.2), and corrected for UMI saturation
Normalization and differential expression analysis were performed using DESeq2 (1.26.0)
Assembly: Rnor_6.0
Supplementary files format and content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary files format and content: Excel file includes the normalized counts (DESeq Normalization)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Enteric glial cell lines

growth_protocol: Enteric glial cell lines (EGC/PK060399egfr) were purchased from the American type culture collection (ATCC). Cells were thawed and grown in 75 mm2 flasks to 70% confluence in DMEM medium containing 10% (Sigma Aldrich, USA) fetal bovine serum (FBS) (Biological industries), 0.5% penicillin-streptomycin (Biological industries), at 37°C under 5% CO2. Cells were trypsinized (using 0.25%) (Invitrogen, Carlsbad CA, USA) and transferred every 2-3 days.

extract_protocol:
RNA was extracted using TRI reagent (Sigma GmBH, Mannheim, Germany) in combination with PureLink column-based kit (Thermo Fisher, Waltham USA). RNA was quantified using Nanodrop 2000 (Thermo Fisher, Waltham, USA) and RNA integrity was confermed using Tapestation. 10ng was used for library creation for MarsSeq sequening.
A bulk adaptation of the MARS-Seq protocol (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019)
Briefly, 30 ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter, Indianapolis, IN), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR. Libraries were quantified by Qubit and TapeStation.

treatment_protocol: Cells were incubeted for 1h without treatment, with 0.1hg/mL pure THC, 10nM pure THC-COOH, 10ug/L Sparstolonin B (Ssnb) (positive control). After 1h 1ug/mL LPS (E. coli 0111:B4) was added for 24h. After 24h media was removed and RNA was extracted using MN NucleoSpin RNA Kit.

value: Enteric glial cell lines

value: 1h 10nM THC-COOH then 24h LPS


title: Dmel.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: RiboZero


title: human_8C_B3_9

value: good


title: THC-COOH 1


title: human_8C_B3_8

value: bad


title: SGK1/3 dKO no treamtent [dKO_H]

description:
dKO_H
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: SGK1/3 dKO no treamtent [dKO_G]

description:
dKO_G
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: Dmel.ovary.3


title: THC 2

value: 1h 0.1ug/mL THC then 24h LPS


title: Dmel.ovary.2


title: human_8C_B3_7

value: fair


title: human_8C_B3_6


title: THC 1


title: SGK1/3 dKO + DMXAA [dKO_D_T]

description:
dKO_D_T
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: macrophage


title: human_8C_B3_5


title: SGK1/3 dKO + DMXAA [dKO_D_X]

description:
dKO_D_X
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: DMXAA 10μg/mL 2 hours


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

value: ovary


title: EGC untreated 2


title: Dmel.ovary.1


title: LPS 2

value: 1ug/ml LPS 24h


title: Splenic B-cells, ODN plus IM156_2

city: Seoul

first: Lucy Eunju

last: Lee

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Division of Rheumatology, Department of Internal Medicine

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk (> average Q20)
Trimmed sequence reads were mapped to GRCm38/mm10 using Bowtie2 and Bedtools
Read count extraction and normalization were performed using EdgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Splenic B-cells

growth_protocol: An ODN-injected mouse model was established on the basis of a previous report (Krogmann AO, Lusebrink E, Steinmetz M, et al. Proinflammatory stimulation of toll-like receptor 9 with high dose CpG ODN 1826 impairs endothelial regeneration and promotes atherosclerosis in mice. PLoS One. 2016;11:e0146326). All mice were maintained under specific pathogen-free conditions at a controlled temperature (23 ± 3°C) and relative humidity (40–60%).

extract_protocol:
Total RNA was isolated from splenic B cells using TRIzol reagent (Invitrogen), and samples of 3 μg of total RNA were prepared from each condition with three experimental replicates.
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Seven-week-old B6 mice (C57BL/6; Orient Bio) were injected i.p. with 50 μg ofODN(class B CpG-ODN 1826; Bioneer) on days 1 and 3. Mice in the IM156 treatment group were given an i.p. injection of IM156 (ImmunoMet Therapeutics) (30 mg/kg) on days 0 and 2.
On day 4, the mice were euthanized, and spleens were collected for further analysis.

tag: strain

value: Splenic B-cells

value: WT

value: CpG-ODN 1826 (50 mcg) plus IM156 (30 mg/kg), i.p. injected

value: ODN on day 1 and 3, IM156 on day 0 and 2


title: Splenic B-cells, ODN plus IM156_3


title: Splenic B-cells, ODN plus IM156_1


title: EGC untreated 1


title: Splenic B-cells, IM156_3

value: IM156 (30 mg/kg), i.p. injected

value: on day 0 and 2


title: SGK3 KO + DMXAA [S3_D_4]

description:
S3_D_4
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: SGK3 KO


title: LPS 1

value: Enteric glial cell lines


title: SGK3 KO + DMXAA [S3_D_5]

description:
S3_D_5
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_8C_B3_2

value: high


title: SGK3 KO + DMXAA [S3_D_3]

description:
S3_D_3
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: SGK1/3 dKO + DMXAA [dKO_D_U]

description:
dKO_D_U
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: SGK1/SGK3 double KO


title: human_8C_B2_1


title: Splenic B-cells, IM156_2


title: Splenic B-cells, IM156_1


title: SGK3 KO + DMXAA [S3_D_1]

description:
S3_D_1
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_4C_B4_5


title: Splenic B-cells, ODN_3

value: class B CpG-ODN 1826 (50 mcg), i.p. injected

value: on day 1 and 3


title: Splenic B-cells, ODN_2


title: SGK3 KO no treatment [S3_3]

description:
S3_3
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: no treatment


title: human_4C_B4_3


title: P8 CAR+ D8 - mRNA

city: Sydney

first: Fabio

last: Luciani

address: High St. Kensington

country: Australia

institute: UNSW

description: poly A RNA

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

source_name: CAR T

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

value: CAR T

tag: library type

value: mRNA


title: P8 CAR- D21 - ADT

description: Antibody-derived oligonucleotide (ADT)

molecule: protein

source_name: PBMC

value: PBMC

value: ADT


title: Splenic B-cells, ODN_1

value: Splenic B-cells

tag: treatment


title: human_4C_B4_2


title: P8 CAR- D8 - ADT

description: Antibody-derived oligonucleotide (ADT)

tag: cell type


title: P8 CAR- D21 - mRNA

description: poly A RNA


title: SGK3 KO no treatment [S3_2]

description:
S3_2
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: macrophage


title: human_4C_B4_1


title: Splenic B-cells, Control_3

value: WT

value: seven week-old mice


title: P8 CAR- Preinfusion - ADT

description: Antibody-derived oligonucleotide (ADT)

value: Preinfusion


title: WT + DMXAA [EV_D_5]

description:
EV_D_5
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: WT (empty vector sgRNA)

value: DMXAA 10μg/mL 2 hours


title: P8 CAR+ D8 - ADT

description: Antibody-derived oligonucleotide (ADT)


title: P8 CAR- Preinfusion - mRNA

description: poly A RNA


title: Splenic B-cells, Control_2


title: SGK3 KO + DMXAA [S3_D_2]

description:
S3_D_2
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: SGK3 KO


title: Splenic B-cells, Control_1


title: WT + DMXAA [EV_D_4]

description:
EV_D_4
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: WT + DMXAA [EV_D_3]

description:
EV_D_3
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: P7 CAR+ D24 - ADT

description: Antibody-derived oligonucleotide (ADT)


title: P8 CAR- D8 - mRNA

description: poly A RNA


title: human_4C_B4_4

value: high


title: human_4C_B3_7


title: human_4C_B3_8


title: SGK3 KO no treatment [S3_1]

description:
S3_1
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_4C_B3_6

value: fair


title: WT + DMXAA [EV_D_1]

description:
EV_D_1
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: WT + DMXAA [EV_D_2]

description:
EV_D_2
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_4C_B3_5


title: P7 CAR+ D24 - mRNA

description: poly A RNA


title: P7 CAR- D24 - mRNA

description: poly A RNA


title: WT no treatment [EV_3]

description:
EV_3
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: NIH, 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

source_name: NIH 3T5

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: NIH 3T3

value: fibroblast

tag: chip antibody

tag: drug-treatment

value: DMSO

value: non-heat shock


title: NIH, HS, DMSO, Pol2S5P, rep2

source_name: NIH 3T3

value: heat shock


title: NIH, NHS, CCG203971, Pol2S5P, rep2

source_name: NIH 3T4


title: human_4C_B3_4


title: P7 CAR- Preinfusion - ADT

description: Antibody-derived oligonucleotide (ADT)

value: PBMC


title: NIH, HS, CCG203971, Pol2S5P, rep2


title: WT no treatment [EV_2]

description:
EV_2
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: no treatment


title: human_4C_B3_9


title: human_8C_B3_4

value: good


title: NIH, NHS, DMSO, Pol2S5P, rep1


title: P7 CAR- Preinfusion - mRNA

description: poly A RNA

value: mRNA


title: WT + Sanofi-14h + DMXAA [EV_14h_5]

description:
EV_14h_5
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: macrophage

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


title: P2 CAR+ D24 - ADT

description: Antibody-derived oligonucleotide (ADT)

value: CAR T

value: ADT


title: P7 CAR- D24 - ADT

description: Antibody-derived oligonucleotide (ADT)


title: human_4C_B3_2


title: WT + Sanofi-14h + DMXAA [EV_14h_4]

description:
EV_14h_4
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: WT (empty vector sgRNA)


title: NIH, NHS, CCG203971, Pol2S5P, rep1


title: NIH, NHS, DMSO, MAL, rep1

value: MAL


title: human_4C_B2_2

value: high


title: human_4C_B3_1


title: NIH, HS, DMSO, MAL, rep1


title: human_4C_B2_1


title: P2 CAR+ Product - ADT

description: Antibody-derived oligonucleotide (ADT)

value: Product


title: WT + Sanofi-14h + DMXAA [EV_14h_3]

description:
EV_14h_3
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: NIH, HS, DMSO, Pol2S5P, rep1

value: NIH 3T3


title: P2 CAR+ D24 - mRNA

description: poly A RNA


title: WT + Sanofi-14h + DMXAA [EV_14h_1]

description:
EV_14h_1
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt


title: human_2C_B4_7


title: P2 CAR+ Product - mRNA

description: poly A RNA


title: NIH, HS, CCG203971, Pol2S5P, rep1

value: fibroblast


title: human_2C_B4_6


title: human_4C_B3_3

value: fair


title: P2 CAR- D31 - mRNA

description: poly A RNA


title: SGK1/3 dKO + DMXAA [dKO_5]

description:
dKO_5
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: SGK1/SGK3 double KO

value: DMXAA 10μg/mL 2 hours


title: Validation_SHH_MB_3

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, tumor

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

value: FFPE, tumor

tag: age (days)


title: human_2C_B4_5


title: P2 CAR- D24 - ADT

description: Antibody-derived oligonucleotide (ADT)

value: PBMC


title: Validation_SHH_MB_2


title: human_2C_B4_4


title: P2 CAR- D24 - mRNA

description: poly A RNA


title: SGK1/3 dKO + DMXAA [dKO_4]

description:
dKO_4
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

tag: cell line


title: Validation_SHH_MB_1

tag: genotype


title: Control_Cerebellum_3

source_name: FFPE, cerebellum

value: FFPE, cerebellum

value: injection of 0.4 mg tamoxifen on postnatal day 3


title: SGK1/3 dKO + DMXAA [dKO_3]

description:
dKO_3
grcm39gcM27_geneCount.txt
grcm39gcM27_gene_tpm.txt

value: macrophage