title: THP-1 HA LPS 4

status: Public on Nov 30 2022

type: SRA

city: Frankfurt

first: Dmitry

last: Namgaladze

address: Theodor Stern Kai 7

country: Germany

institute: Goethe University Frankfurt

description: Normalized counts HA_LPS

library_source: transcriptomic

data_processing:
Demultiplexed FASTQ ﬁles were generated with bcl2fastq2 software (Illumina).
Processed reads were subsequently mapped to the human genome (GRCh38) using Bluebee online platform (Lexogen).
Differential expression was evaluated using DESeq2 Pipeline (Bluebee)
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: Tab-delimited text files contain the normalized read counts for each condition

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA of non-treated and LPS-treated THP-1 cells was isolated using RNeasy Mini Kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI 12nt set B1 (Lexogen)

tag: cell line

tag: cell type

value: Myeloid leukemia

tag: genotype

value: ACLY H760A

tag: treatment

value: LPS 100 ng/ml 3h


title: THP-1 KO LPS 4

description: Normalized counts KO_LPS

value: ACLY knockout


title: THP-1 WT LPS 4

description: Normalized counts WT_LPS

value: wild type


title: THP-1 SA 4

description: Normalized counts SA

value: ACLY S455A

value: untreated


title: THP-1 SA LPS 3

description: Normalized counts SA_LPS


title: THP-1 HA 4

description: Normalized counts HA


title: THP-1 KO 4

description: Normalized counts KO


title: THP-1 WT 4

description: Normalized counts WT


title: THP-1 SA LPS 4

description: Normalized counts SA_LPS


title: THP-1 HA LPS 3

description: Normalized counts HA_LPS


title: THP-1 HA 3

description: Normalized counts HA


title: THP-1 KO LPS 3

description: Normalized counts KO_LPS


title: THP-1 KO 3

description: Normalized counts KO


title: THP-1 WT LPS 3

description: Normalized counts WT_LPS


title: THP-1 WT 3

description: Normalized counts WT


title: THP-1 SA LPS 2

description: Normalized counts SA_LPS


title: THP-1 SA 2

description: Normalized counts SA


title: THP-1 HA 2

description: Normalized counts HA


title: THP-1 KO LPS 2

description: Normalized counts KO_LPS


title: THP-1 HA LPS 2

description: Normalized counts HA_LPS


title: THP-1 WT 2

description: Normalized counts WT


title: THP-1 SA LPS 1

description: Normalized counts SA_LPS


title: THP-1 WT LPS 2

description: Normalized counts WT_LPS


title: THP-1 KO 2

description: Normalized counts KO


title: THP-1 SA 1

description: Normalized counts SA


title: THP-1 HA LPS 1

description: Normalized counts HA_LPS


title: THP-1 SA 3

description: Normalized counts SA


title: THP-1 WT LPS 1

description: Normalized counts WT_LPS


title: THP-1 HA 1

description: Normalized counts HA


title: THP-1 WT 1

description: Normalized counts WT


title: FA_2

city: Uppsala

first: Ankita

last: Pal

address: Husargatan 3

department: Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

data_processing:
Illumina HiSeq 4000 used for sequencing
CUTADAPT used for removing adapter sequence and low-quality reads (q >= 20)
BWA used for reads mapping and alignment to reference genome (GenBank accession no. NC_000913.3)
Samtools used for compressing alignment files and sorting
FeatureCounts used for assigning counts at gene level
EdgeR used for differential gene expression analysis
Genome_build: Reference genome used: E.coli K12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: tab delimited .txt file containing raw reads count (Raw_counts_msi.txt)

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

source_name: Bacteria grown in M9 + glucose  under anaerobic fermentative conditions

growth_protocol: Escherichia coli cells grown in a bioreactor under anaerobic fermentation conditions with M9 + glucose at 37 degree Celcius and 150 rpm till exponential phase

extract_protocol:
Total RNA extraction was done using the TRIzol-chloroform method. DNase treatment was done to remove any DNA contamination. Dnase treated RNA was treated with MEGAclear to remove small-RNA and produce high-quality RNA after which enrichment for mRNA was done using the MicrobExpress Kit.
Paired-end, strand specific libraries for RNA sequencing were prepared using NEBNext Ultra Directional RNA library kit.The sequencing was carried out on HiSeq 4000  using 2x150 bp paired-end reads.

treatment_protocol: Escherichia coli cells grown in a bioreactor under anaerobic conditions with M9+glucose at 37 degree Celcius and 150 rpm and total RNA extracted at exponential phase

tag: sample group

value: ΔfnrΔarcA (FA)

tag: growth phase

value: exponential phase of growth

tag: molecule subtype

value: Ribo-depleted mRNA


title: FI_1

value: ΔfnrΔihf (FI)


title: THP-1 KO 1

description: Normalized counts KO


title: FI_2


title: WT 2


title: WT 1


title: AI_1

value: ΔarcAΔihf (AI)


title: AI_2


title: Patient11372

city: Ann Arbor

first: Matthias

last: Kretzler

state: MI

address: 1150 W. Medical Center Dr.

department: Internal Medicine

country: USA

institute: University of Michigan

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 or above (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
SoupX and DoubletFinder were employed as noted per sample in the supplemental materials for this manuscript. DoubletFinder was run on all default settings for all samples. SoupX was run on default for most of the samples, but a few samples had excess ambient RNA that required specific consideration, as outlined in the supplemental.
To replicate the SoupX findings with the materials here, the raw files need to be placed into a folder called "raw_feature_bc_matrix", while the processed files need to be placed into a folder called "filtered_feature_bc_matrix". These two folders then need to be placed into a separate folder, which is referred to in calling load10X for SoupX.
Seurat 4.1.1 was run on all samples. All nuclei were subset to include nuclei that had an nFeature count between 500 and 5000 and had less than 10% mitochondrial gene presence in the overall sample.
Data were normalized using the log-normalization method, variable features were found using the vst method. RPCA-based integration was then conducted on all samples and integrated using the "IntegrateData" function with dimensions set to 1:30. Data were then scaled, subjected to a PCA, neighbors were calculated with dimensions at 1:30. Clusters were found at a resolution of 0.6 and projected onto a UMAP. Cell clusters were identified in an unbiased approach using KPMP and PREMIERE cell type markers.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney cortex

extract_protocol:
Cortical human kidney biopsies that had been preserved in RNALater underwent microdissection to remove glomeruli. These biopsied materials were then subjected to a nuclear extraction protocol from the Kidney Precision Medicine Project.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics)

value: Kidney and immune cells

tag: tissue

value: Kidney cortex

tag: disease state

value: nephrotic syndrome


title: Patient11442

description: 10x Genomics


title: Patient11344

description: 10x Genomics


title: Patient11382

description: 10x Genomics


title: Patient11343

description: 10x Genomics


title: Patient11443

description: 10x Genomics


title: Patient11381

description: 10x Genomics


title: E1 mutant strain

city: Talca

first: Angela

last: Contreras

state: Talca

address: Av San Miguel 3605

country: Chile

institute: Universidad Católica del Maule

data_processing:
Raw reads were normalized through RPKM (reads per kilo base per million reads) method using the Qseq program (Conesa et al., 2016). Publicly available transcriptome data sets were downloaded from the NCBI’s database and they were mapped using the QSeq program of DNASTAR.
Assembly: Oenococcus oeni PSU-1 NCBI ID: 203123
Supplementary files format and content: En este analisis se compararon dos cepas de Oenococcus oeni (PSU1 y E1) con una cepa de referencia. Para la comparación se utilizaron datos  RPKM 2 para evaluar la señal de RNAseq para cada muestra y cada gen. Se uso la prueba t de Student con corrección de error de Benjamini Hochberg. La comparación de expresiones diferenciales se realizó entre: 1) Tratamiento 1 (PSU-1) vs control; 2) Tratamiento 2 (E1) vs control y 3) Tratamiento 2 frente a tratamiento 1.

organism: Oenococcus oeni

source_name: strain

extract_protocol:
Bacterial RNA was extracted using kit E.Z.N.A™ (Omega Biotek, USA) and treated with DNAsa I (Omega Biotek, USA), following the manufacturer’s instructions. All the samples were suspended on DEPC water and dried using RNAstable® tubes (Biomatrica, USA).The concentration of total RNA was determined  using the Qubit® RNA Assay Kit (Life Technologies). In order to evaluate the quality of the total RNA, RNA integrity value (RIN) was determined using the Agilent RNA 6000 Nano Reagents and RNA Nano Chips in Agilent 2100 Bioanalyzer (Agilent Technologies). 0.5-1.5 ug of total RNA was used to remove the DNA contamination using Baseline-ZERO™ DNase (Epicentre) following the manufacturer's instructions followed by purification using the RNA Clean & Concentrator-5 columns (Zymo Research). DNA free RNA samples were used for rRNA removal by using Ribo-Zero™ Magnetic Gold Kit (Epidemiology; Illumina) and final purification was performed using the RNA Clean & Concentrator-5 columns (Zymo Research). rRNA depleted samples were used for library preparation using the TruSeq™ RNA LT Sample Preparation Kit (Illumina) according to the manufacturer’s instructions.
The final concentration of all the libraries were measured using the Qubit® dsDNA HS Assay Kit (Life Technologies), and the average library size was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies). The libraries were then pooled in equimolar ratios of 2nM, and 8pM of the library pool was clustered using the cBot (Illumina) and sequenced paired end for 300 cycles using the HiSeq 2500 system (Illumina).

value: strain

value: strain is a complete cell

value: bacterium

value: mutant strain

value: mutagenized strain using random mutagenesis with EMS


title: Patient11371

description: 10x Genomics


title: PSU1 parental strain

value: WT

value: untreated strain


title: Patient11341

description: 10x Genomics


title: Vs1 (RNA-seq)

city: Zhengzhou

first: Gao-Pu

last: Zhu

state: Henan

address: No. 3, Weiwu Road

department: Non-timber Forest Research and Development Center

country: China

institute: Chinese Academy of Forestry

data_processing:
A cDNA library constructed by technology from the pooled RNA from all samples of grape was sequenced run with Illumina 4000 sequence platform.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) Vitis vinifera reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.
HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie.
Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
The miRNA-seq raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs.
The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
To predict the genes targeted by most aboundant miRNAs, computational target prediction algorithms (TargetFinder) were used to identify miRNA binding sites. The GO terms and KEGG Pathway of most aboundant miRNA targets were also annotated
Raw sequencing reads were obtained using Illumina's software to remove adaptors and low quality reads. The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline .
The degradome reads were mapped to the mRNA downloaded from www （ JGI , NCBI or other databases,or mapped to the species transcripts from transcriptome  sequencing） . Only the perfect matching alignment(s) for the given read would be kept for degradation analysis .
The degradation group sequence can match different numbers of reads on different sites on the same mRNA, and the predicted sequences at these sites may haven't corresponding miRNAs. The degradation group sequence can match different numbers of reads on different sites on the same mRNA, and the predicted sequences at these sites may haven't corresponding miRNAs. Detailed results with specific alignment information form a long_outfile file with AlignmentScore (Targetfinder penalty), AlignmentRange (pairing site), CleaveageSite (cutting site), Category (segmentation),P-value (P value), Raw_reads, Rep_Norm_reads (matches that match multiple sites for site normalization). Without alignment information, only AlignmentScore (Targetfinder score), AlignmentRange (pairing site), CleaveageSite (cutting site), Category (type), P-value (P value), Raw_reads, Rep_Norm_reads are listed. The (multi-site normalized reads) information is a simple list of miRNA and target gene relationships for the "Degradome_result.xlsx" file.
All resulting reads (t-signature) were reverse-complemented and aligned to the miRNA identified in our study.
All the identified targets were subjected to BlastX analysis to search for similarity, and then to GO analysis to uncover the miRNA-gene regulatory network on the basis of biological process ,cellular component and molecular function .
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-37/plants/gtf/vitis_vinifera v37
Supplementary_files_format_and_content: mRNA include FPKM values for each Sample ;miRNA expression use the norm values for each Sample.

organism:
Vitis vinifera
Schisandra chinensis

source_name: Vitis vinifera

growth_protocol: Both grafted types of plants had grown in the same area for 25 years

extract_protocol:
In harvest season, the samples were selected that quick-frozen in liquid nitrogen, and stored at below 80°C until use. Total RNA and small RNA were extracted using Polysaccharide Polyphenol Plant MicroRNA Extraction Kit (LabHelper, Beijing, China) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no special treatment

tag: type

value: graft hybrids of Schisandra chinensis + Vitis vinifera

tag: time

value: 25 years

value: LEAF, PHLOEM, BERRY


title: THP-1 KO LPS 1

description: Normalized counts KO_LPS

value: Myeloid leukemia

value: ACLY knockout

value: LPS 100 ng/ml 3h


title: Vs3 (RNA-seq)


title: Patient11342

description: 10x Genomics


title: Vs2 (RNA-seq)


title: Induced 1

city: Philadelphia

first: Renato

middle: V.

last: Iozzo

state: PA

address: 1020 Locust Street

institute: Thomas Jefferson University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: triple-negative malignant mouse breast cancer cell line

value: Tie2CreER;ERKi C57BL/6J mice

value: Tamoxifen

value: Day 22


title: Induced 2


title: Induced 4


title: Induced 5


title: Induced 6


title: ARVF_SW033291_rep4

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Medicine

institute: University of Colorado Anschutz Medical Campus

data_processing:
No data correction was applied to the samples, and reads obtained were equally distributed across samples.
Reads were processed with Trim Galore! (v.0.6.4_dev, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to verify quality and trim adapters and low-quality ends.
Trimmed reads were aligned with STAR (v.2.7.5c) to the rat genome (Rnor_6.0) with Ensembl (v.101, https://ensembl.org) annotations in a single pass using default settings for gene counting (--quantMode GeneCounts).
Reads were loaded into R (v.3.3.3) for processing [R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/]).
Transcripts with < 1 read per million mapped in all samples (61%) were removed before differential expression (DE) analysis with DESeq2 (v.1.14).
Genes were considered differentially expressed with adjusted p-value < 0.05 and fold change > 1.5.
Assembly: Rnor_6.0
Supplementary files format and content: Excel workbook; raw counts

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Heart

growth_protocol: Adult rat ventricular fibroblasts were cultured in DMEM/F-12 containing 20% fetal bovine serum

extract_protocol:
Total RNA was collected from ARVFs from 4 biological replicates using the Direct-zol RNA Miniprep Kit (Zymo Research R2051) according to the manufacturer’s instructions.
Following mRNA selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490S), cDNA libraries were prepared from 1 µg of mRNA using a single NEBNext Ultra Directional Library Preparation Kit for Illumina® (New England Biolabs E7420S) according the manufacturer’s protocol.

treatment_protocol: In DMEM/F-12 containing 0.1% fetal bovine serum, ARVFs were treated with DMSO, TGFβ, SW033291, or TGFβ+SW033291 for 48 hours

value: Heart

value: Fibroblast

value: Wild-type


title: ARVF_TGFβ_SW033291_rep2


title: ARVF_TGFβ_SW033291_rep4


title: ARVF_TGFβ_SW033291_rep1


title: Induced 7


title: ARVF_TGFβ_SW033291_rep3


title: Control 1

value: Control


title: Control 2


title: ARVF_TGFβ_rep4

value: TGF[beta]


title: Control 3


title: Control 4


title: ARVF_SW033291_rep3


title: Control 5


title: ARVF_SW033291_rep2


title: ARVF_SW033291_rep1


title: ARVF_TGFβ_rep3


title: ARVF_TGFβ_rep2


title: Induced 3


title: ARVF_DMSO_rep4

value: DMSO


title: ARVF_TGFβ_rep1


title: ARVF_DMSO_rep3


title: ARVF_DMSO_rep1


title: ARVF_DMSO_rep2


title: Subject-NN023, Biopsy-6wks Post-2nd-Exposure

city: Chicago

first: Kurt

middle: Q

last: Lu

state: IL

address: 303 E Chicago Ave

department: Dermatology

institute: Northwestern University

data_processing:
The quality of reads, in FASTQ format, was evaluated using FastQC. Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt.
Trimmed reads were aligned to the Human genome (hg38) using STAR.
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg38 obtained from Ensembl.
Assembly: hg38
Supplementary files format and content: tab deliminted text file contains raw counts for all samples

source_name: Skin

extract_protocol:
Snap-frozen biopsies were immersed in Trizol and extracted according to manufacturer's protocol
Tru-seq Stranded Total RNA was used for library prep

tag: individual

value: Skin

tag: Sex

value: Male

tag: age

tag: condition

value: 6wks Post-2nd-Exposure Mild

value: Placebo


title: Subject-MN021, Biopsy-6wks Post-2nd-Exposure

value: Female


title: Subject-MN004, Biopsy-6wks Post-2nd-Exposure

value: VitaminD


title: Subject-RN034, Biopsy-6wks Post-2nd-Exposure


title: Subject-KN022, Biopsy-6wks Post-2nd-Exposure

value: 6wks Post-2nd-Exposure Severe


title: Subject-SN026, Biopsy-6wks Post-2nd-Exposure


title: Subject-TN027, Biopsy-6wks Post-2nd-Exposure


title: Subject-KN025, Biopsy-6wks Post-2nd-Exposure


title: Subject-SN019, Biopsy-6wks Post-2nd-Exposure


title: Subject-KN013, Biopsy-6wks Post-2nd-Exposure


title: Subject-SN009, Biopsy-6wks Post-2nd-Exposure


title: KO_0h

city: Jinan

first: Lifen

last: Gao

address: 44 Wenhua Xi Road, Jinan, Shandong, 250012 P. R. China

institute: Shandong University

data_processing:
RNA-seq was performed using BGISEQ-500 platform.
Sequence reads were filtered by SOAPnuke software. Reads containing adaptor, with unknown base N content greater than 10% A and low quality (we defined the ratio of bases with quality value below 15 to the total number of bases of the reads as more than 50% reads are low-quality reads) were removed
Clean reads were mapped to mm10 using  HISAT software (Total Mapping Ratio: 96.49%)
RSEM software was then used to calculate the expression level of genes and transcripts
Assembly: mm10
Supplementary files format and content: xls files include log2Fold Change(KO_0h/WT_0h)

source_name: peritoneal cavity

extract_protocol:
Cells were then cultured with DMEM supplemented with 10% FBS and 1% PS.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: peritoneal cavity

value: peritoneal macrophages

value: Tim-4 KO


title: AB1_ChIP-seq

city: Vienna

first: Rohit

middle: Anil

last: Dnyansagar

address: Althanstrasse 14 (UZA1) A-1090 Wien

department: Department of Molecular Evolution and Development

country: Austria

institute: University of Vienna

library_source: genomic

data_processing:
For RNA-seq reads were trimmed of adapter sequences ATTACTCGTATAGCCT, TCCGGAGAATAGAGGC, CGCTCATTCCTATCCT, GAGATTCCGGCTCTGA, ATTCAGAAAGGCGAAG, CTGAAGCTCAGGACGT, TAATGCGCGTACTGAC, CGGCTATGTATAGCCT,TCCGCGAAATAGAGGC, TCTCGCGCCCTATCCT, AGCGATAGGGCTCTGA, TCCGGAGATAATCTTA, CGCTCATTCAGGACGT, GAATTCGTATAGAGGC using cutadapt v1.8.1
Trimmed reads were aligned to N. vectensis genome (v1) using STAR aligner (v2.5.3a)
unaligned reads were then filtered
Transcripts per million (TPM) per transcript was calculated from reads that didn't align to RepBase were quasi-aligned to GENCODE v19 protein coding and lincRNA transcripts using Sailfish v0.6.3
Reads aligned to genomic features were counted with featureCounts (Subread v1.6.2)
The counts files generated were used as input to DESeq2 (v1.6.0)
Genes with Log2fold change of 1 and FDR corrected p-value (q-value) of 0.05 are considered as differentially expressed.
For ChIP-seq Trimmed reads were aligned to N.vectensis genome (v1) using BWA aligner using the BWA-MEM algorithm
ChIP-seq peaks were called using Peakzilla
Genome_build: https://mycocosm.jgi.doe.gov/Nemve1/Nemve1.home.html
Supplementary_files_format_and_content: tab separated values

molecule: genomic DNA

organism: Nematostella vectensis

source_name: whole embryo

growth_protocol: Nematostella polyps were kept at 18°C and largely in the dark. Spawning was induced by a combination of light and elevated temperature. Embryos were raised at 21°C

extract_protocol:
embryos at gastrula stage were fixed with 2% formaldehyde for 12 min. Nuclei were collected by Dounce homogenizing the embryos. Chromatin was fragmented to an average size of 100-200bp using a Covaris S1 ultrasonicator
library preparation according to Illumina ChIP-seq DNA Sample Prep Kit instructions (Catalog number IP-102-1001). The quantity and quality (size distribution) of the libraries was confirmed using an Agilent Bioanalyzer.

treatment_protocol: Custom-made antibodies: A 6xHis-tagged full-length clone of Nematostella Brachyury was expressed in E. coli strain BL21. After transformation, bacteria were grown overnight in LB supermedium + Ampicillin. Then, 10 ml LB medium /Ampicillin were inoculated with 500   ul of overnight culture, grown for 3 h (O.D. 600 = 0,5-0,6), IPTG was added to a final concentration of 1 mM, and bacteria culture was incubated for 21 h at 4  C. Brachyury protein was purified using Ni-NTA agarose (Qiagen), followed by polyacrylamide gel electrophoresis. The Brachyury band at ~50 kDa was excised and used to inject two rabbits (PRIMM Biotech).

value: Embryo cells

tag: developmental stage

value: gastrula

tag: sample type

value: Bulk ChIP-seq


title: Subject-EN016, Biopsy-6wks Post-2nd-Exposure


title: FA_1

value: ΔfnrΔarcA (FA)

value: exponential phase of growth

value: Ribo-depleted mRNA


title: Subject-EN005, Biopsy-6wks Post-2nd-Exposure


title: Subject-JN033, Biopsy-6wks Post-2nd-Exposure


title: Input_ChIP-seq


title: Subject-JN032, Biopsy-6wks Post-2nd-Exposure


title: AB2_ChIP-seq


title: Subject-JN015, Biopsy-6wks Post-2nd-Exposure


title: WT_0h

value: wild type


title: Subject-EN012, Biopsy-6wks Post-2nd-Exposure

value: Skin


title: Subject-AN020, Biopsy-6wks Post-2nd-Exposure


title: Subject-HN031, Biopsy-6wks Post-2nd-Exposure

value: Male


title: Subject-EN030, Biopsy-6wks Post-2nd-Exposure


title: Subject-AN017, Biopsy-6wks Post-2nd-Exposure

value: 6wks Post-2nd-Exposure Mild


title: Subject-AN011, Biopsy-6wks Post-2nd-Exposure


title: Subject-TN027, Biopsy-72hrs Post-2nd-Exposure

value: 72hrs Post-2nd-Exposure Mild

value: Placebo


title: HL60_NTX301, day2, rep3

type: genomic

city: Daejeon

first: Byungho

last: Lim

address: 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea

country: South Korea

institute: KRICT

description: DNA methylation data from drug treated AML cells

hyb_protocol: A pair of bead-bound probes is used to detect the presence of T or C by hybridization.

scan_protocol: Standard Illumina procedures using Illumina iScan scanner.

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: biotin

source_name: NTX-301 treatment

label_protocol: Hybridization by a pair of bead-bound probes is followed by single-base extension with a labeled nucleotide.

growth_protocol: Leukimia cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) in a CO2 incubator.

extract_protocol: Genomic DNA was extracted by using DNA Mini kit (Qiagen).

treatment_protocol: During 48h, DMSO, NTX-301 (60nM), and DAC (60nM) were treated to 1x106 MV4-11 and HL-60 cells plated on 10cm dishes in triplicates.

tag: disease

value: AML

tag: time point


title: CAPN3-point-mutation , no muscle injury 2

city: Shanghai

first: Jiajun

last: Qiu

address: West BeiJing Road

institute: Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequenced fragments are randomly interrupted by mRNA, and in order to determine which genes these segments are transcribed from, the quality controlled clean reads need to be compared to the reference genome. HISAT2 software was used to quickly and accurately compare Clean Reads with the reference genome to obtain the positioning information of Reads on the reference genome.
After the quantification of gene expression is completed, it is necessary to statistically analyze the expression data and screen for genes with significantly different expression levels in different states. Variance analysis is mainly divided into three steps.    First, normalization of the original readcount, mainly to correct the depth of sequencing.  The statistical model then calculates the probability of hypothesis testing (pvalue).  Finally, multiple hypothesis test corrections were performed to obtain the FDR value (false discovery rate, PADJ is its common form).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count matrix of each gene

source_name: muscle cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
NEB ordinary library: using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system, and then the RNA strand was degraded with RNaseH, and the second cDNA strand was synthesized under the DNA polymerase I system using dNTPs as raw materials. The purified double-stranded cDNA was repaired at the end, A-tailed and ligated to the sequencing linker, and about 250-300 bp of cDNA was screened with AMPure XP beads, PCR amplification was performed, and the PCR products were purified again using AMPure XP beads, and finally the library was obtained. The kit for library construction is NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

tag: cell type

value: muscle cell

value: CAPN3-point-mutation , no muscle injury


title: Subject-AN029, Biopsy-6wks Post-2nd-Exposure

value: Female

value: 6wks Post-2nd-Exposure Severe

tag: treatment

value: VitaminD


title: CAPN3-point-mutation , muscle injury 1

value: CAPN3-point-mutation , muscle injury


title: CAPN3-point-mutation , muscle injury 2


title: Subject-AN028, Biopsy-6wks Post-2nd-Exposure


title: CAPN3-point-mutation , no muscle injury 3


title: Normal control, no muscle injury 1

value: no muscle injury


title: Subject-SN009, Biopsy-72hrs Post-2nd-Exposure


title: MV411_DAC, day2, rep2

source_name: DAC treatment


title: HL60_DAC, day2, rep1


title: Normal control, muscle injury 3

value: muscle injury


title: Subject-AN014, Biopsy-6wks Post-2nd-Exposure


title: CAPN3-point-mutation , no muscle injury 1


title: MV411_DMSO, day2, rep2

source_name: DMSO treatment


title: HL60_DAC, day2, rep2


title: MV411_DAC, day2, rep1


title: HL60_NTX301, day2, rep2


title: CAPN3-point-mutation , muscle injury 3


title: MV411_NTX301, day2, rep1


title: HL60_DMSO, day2, rep3


title: Subject-MN021, Biopsy-72hrs Post-2nd-Exposure


title: Subject-AN007, Biopsy-6wks Post-2nd-Exposure


title: Normal control, muscle injury 2


title: MV411_NTX301, day2, rep3


title: HL60_NTX301, day2, rep1


title: Initial segment of the murine epididymis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Reads were aligned against the mouse genome (mm10) and counted by StarSolo.
Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 49 cells in total that did not express at least 300 genes or had an mitochondrial content greater than 10%. Further, we filtered genes if they were detected in less than 30 cells (<0.2%).
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: mm10
Supplementary files format and content: starsolo output matrix

source_name: extravasular CD45+

growth_protocol: Mice were maintained under SPF conditions for 10 weeks prior organ collection (to obtain adult epididymis).

extract_protocol:
Organ were collected and single cell suspension was prepared by mechanical separation (chopping), followed by enzymatic digestion (1.5 mg/ml collagenase D, 60 U/ ml Dnase I, 60 U/ml hyaluronidase type I-S in DMEM, 45 minutes at 37°C) and aspiration through 20G needle. Subsequently, red blood lysis was performed for 3 minutes using RBS lysis buffer (Qiagen). Cells were staining with PerCP-Cyanine 5.5-conjugated CD45.1 antibody (BioLegend, RRID: AB_893346). Single live CD45.1+CD45.2- immune cells (extravasular CD45+ cells) were sorted using an BD Aria Fusion flow cytometer.
Single cell suspensions were prepared using the 10x Genomics Single Cell 3' v2 Reagent Kit user guide. Approporiate volume for droplet generationas assessed by Tryptan Blue staining and hemacytometer. Reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo FIsher). cDNA was recovered using 10x-associated Recovery Agent followed by amplification and purification using SPRIselect beads (Beckman) following manufacturer´s recommendation. Samples were diluted in a 4:1 ratio with elution buffer (Qiagen) prior to determining cDNA concentration using a Bioanalyzer (Agilent Technologies). Sequencing libraries were prepared using 10x Chromium and processed as recommended by the methods provided from 10x Genomics. Raw vase call files obtained from HiSeq2500 sequencer were demultiplexed into FastQ files.

treatment_protocol: Mice were intravenously injected with an APC/Cyanine 7-conjugated anti-mouse CD45.2 antibody (Clone 104, BioLegend, RRID:AB_830789) five minutes prior to euthanasia allowing a discrimination of intra- and extravasular CD45+ cells during FACS.

tag: strain

value: C57BL/6J, WT, 10 weeks old

tag: Stage

value: adult

value: extravasular CD45+


title: HL60_DMSO, day2, rep1


title: Subject-SN026, Biopsy-72hrs Post-2nd-Exposure

value: Skin

value: 72hrs Post-2nd-Exposure Severe


title: Normal control, no muscle injury 3


title: MV411_DMSO, day2, rep1


title: MV411_NTX301, day2, rep2


title: Subject-JN033, Biopsy-72hrs Post-2nd-Exposure

value: Male


title: Normal control, muscle injury 1


title: HL60_DMSO, day2, rep2


title: Subject-SN019, Biopsy-72hrs Post-2nd-Exposure


title: MV411_DAC, day2, rep3


title: Caput epididymidis


title: Normal control, no muscle injury 2


title: MV411_DMSO, day2, rep3


title: Vv_DGD (degradome)

organism: Vitis vinifera

source_name: Vitis vinifera (All samples mixed)

value: Self-root Vitis vinifera

value: 25 years

value: LEAF, PHLOEM, BERRY


title: HL60_DAC, day2, rep3

value: AML


title: Subject-RN034, Biopsy-72hrs Post-2nd-Exposure

value: 72hrs Post-2nd-Exposure Mild

value: Placebo


title: Subject-NN023, Biopsy-72hrs Post-2nd-Exposure


title: Subject-KN022, Biopsy-72hrs Post-2nd-Exposure

value: Female


title: Subject-MN004, Biopsy-72hrs Post-2nd-Exposure

value: VitaminD


title: Corpus epididymidis


title: Subject-KN025, Biopsy-72hrs Post-2nd-Exposure


title: Cauda epididymidis


title: Subject-EN012, Biopsy-72hrs Post-2nd-Exposure


title: Subject-JN015, Biopsy-72hrs Post-2nd-Exposure


title: Subject-HN031, Biopsy-72hrs Post-2nd-Exposure


title: Subject-GN003, Biopsy-72hrs Post-2nd-Exposure


title: Subject-KN013, Biopsy-72hrs Post-2nd-Exposure


title: Subject-JN032, Biopsy-72hrs Post-2nd-Exposure


title: Subject-AN028, Biopsy-72hrs Post-2nd-Exposure


title: Vv3 (miRNA-seq)


title: Subject-EN030, Biopsy-72hrs Post-2nd-Exposure


title: Vv2 (miRNA-seq)


title: Subject-EN016, Biopsy-72hrs Post-2nd-Exposure


title: Subject-EN005, Biopsy-72hrs Post-2nd-Exposure


title: IT2P1

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the rat (Rnor_6.0) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: Rnor_6.0
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd: Sprague Dawley SD (Harlan) were fed ad lib using a standard rat diet and ad lib tap water. The F0 generation consisted of three male controls and five ifosfamide treated males. The F1 generation consisted of: ifosfamide females n=24, control females n=34, ifosfamide males n=18, and control males n=25. The F2 generation consisted of: ifosfamide females n=51, control females n=47, ifosfamide males n=43, and control males n=51. F1 and F2 generation control and ifosfamide lineages were housed in the same room and racks with lighting, food and water. Non-littermate females and males aged 80-90 days from the F1 generation of ifosfamide or control lineages were bred to other unrelated F1 generation individuals within their lineage group to obtain F2 generation offspring. Efforts were made to cull litters to 10 rats per litter, however in the F1 generation controls there were two litters of 12 rats and one litter of 15 rats.

extract_protocol:
The epididymis was dissected free of fat and connective tissues, then, after cutting open the cauda, placed into 6 mL of phosphate buffer saline (PBS) for 20 min at room temperature. Further incubation at 4 ºC will immobilize the sperm. The tissue was then minced, the released sperm was pelleted at 4 ºC 3000 x g for 10 min, then resuspended in NIM buffer and stored at -80 ºC for further processing. An appropriate amount of rat sperm suspension was used for DNA extraction. Somatic cells and debris were removed by brief sonication (Fisher Sonic Dismembrator, model 300, power 25), then centrifugation and washing 1–2 times in 1X PBS. The resulting pellet was resuspended in 820 μL DNA extraction buffer and 80 μL 0.1 M DTT added, then incubated at 65 °C for 15 min. Eighty μL proteinase K (20 mg/mL) was added and the sample was incubated at 55 °C for 2−3 h under constant rotation. Protein was removed by addition of protein precipitation solution (300 μL, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500 x g for 30 min at 4 °C. One ml of the supernatant was precipitated with 2 μL of GlycoBlue (Invitrogen, AM9516) and 1 mL of cold 100 % isopropanol. After incubation, the sample was spun at 13,500 x g for 30 min at 4 °C, then washed with 70 % cold ethanol. The pellet was air-dried for about 5 min then resuspended in 100 μL of nuclease free water. For the MeDIP procedure, F1 generation samples were pooled, with three to four samples per pool and six pools each for both the ifosfamide and control lineage. F2 generation samples were pooled as well, with seven samples per pool for the control lineage, and eight or nine samples per poor for the ifosfamide lineage. Genomic DNA was sonicated and run on 1.5 % agarose gel for fragment size verification. The sonicated DNA was then diluted with 1X TE buffer to 400 μl, then heat-denatured for 10 min at 95 °C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight on a rotator at 4 °C. The following day magnetic beads (Dynabeads M280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and 50 μl of beads were added to the 500 μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 h on a rotator at 4 °C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250 μl digestion buffer (5 mM Tris PH 8, 10.mM EDTA, 0.5 % SDS) with 3.5 μl Proteinase K (20 mg/mL), and incubated for 2−3 h on a rotator at 55 °C. DNA clean-up was performed using a Phenol-Chloroform-Isoamyl-Alcohol extraction, and the supernatant precipitated with 2 μl of GlycoBlue (20 mg/mL), 20 μl of 5 M NaCl and 500 μl ethanol in -20 °C freezer for one to several hours. The DNA precipitate was pelleted, washed with 70 % ethanol, then dried and resuspended in 20 μl H2O or 1X TE. DNA concentration was measured in Qubit (Life Technologies) with the ssDNA kit (Molecular Probes Q10212).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Male rats were treated with 8.5 mg/kg of the chemotherapeutic agent ifosfamide (intraperitoneally), once every three days for three treatments, starting when they were 26 days old (days 26, 29, and 32) of rat pubertal development. Ifosfamide injection solution was 7.65 mg/mL ifosfamide in 1x PBS (phosphate buffered saline), filter sterilized. Control rats were treated with 1.1 mL/kg 1X PBS. Only F0 generation individuals received ifosfamide treatments and they exhibited no gross pathology upon dissection. All experimental protocols for procedures using the rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252). All methods were performed in accordance with the relevant guidelines and regulations.

value: Sprague Dawley SD (Harlan)

value: Sperm

tag: generation

tag: treatment lineage

value: ifosfamide


title: IT2P3


title: IT2P4


title: IT2P5


title: Subject-CN024, Biopsy-72hrs Post-2nd-Exposure

tag: tissue


title: Vv1 (miRNA-seq)

tag: type


title: Subject-AN029, Biopsy-72hrs Post-2nd-Exposure


title: IT1P6


title: IT2P6


title: Subject-AN017, Biopsy-72hrs Post-2nd-Exposure


title: IT2P2


title: 5818_hippo_SYP_PSD95_double_negative_3

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Combined_5818h_sorted_NC_transcript_counts_rRNA_MT_filtered.tsv

data_processing:
Base-calling was performed with the standard Illumina NextSeq500 procedure.
The 3’ polyA tail of cDNA on Read 1 was trimmed with cutadapt v3.1, the Read 2 covering cell barcode sequences was assigned to a pre-defined barcode list.
Reads with successfully assigned cell barcodes were extracted with umi_tools extract (v1.0.1). Extracted Read 1 was mapped to the hg19 genome (or a combined genome of hg19 and mm10) with STAR v2.5.3a, and the uniquely mapped reads with mapping q score no smaller than 250 was used for downstream analysis.
The filtered reads were assigned to genes by featureCounts  v2.0.1 with appropriate Gencode annotation gtf files. (stradness parameter: -s 2)
For the reads with unambiguously assigned gene features, umi_tools “count” command was used to generate the transcript-based or exon-based digital gene expression matrix (parameter: --per-gene --gene-tag=XT --per-cell –method=directional).
Nuclei with mitochondrial UMI fraction higher than 5% were removed. Synapses with mitochondrial UMI fraction smaller than 5% were removed. Next, genes on chrMT and rRNA genes (based on Ensembl annotation) were removed from downstream analysis.
Assembly: hg19 and mm10
Supplementary files format and content: tab-delimited files include the transcript-based, intron-based, and exon-based UMI count matrix for each sample.

source_name: Hoechst-negative subneuronal compartments from frozen postmortem human prefrontal cortical tissues

extract_protocol:
The frozen brain tissues were homogenized by Dounce Homogenizer, and the homogenate was fixed by incubating with 3% PFA at room temperature for 10 min. Hoechst-postive single nuclei and Hoechst-negative single synapses were sorted out by FANS.
Total-RNA based transcriptome library was generated with MATQ-Drop chemistry.

value: prefrontal cortical tissues


title: 5818_hippo_SYP_PSD95_double_negative_4


title: Subject-AN014, Biopsy-72hrs Post-2nd-Exposure


title: IT1P4


title: Subject-AN007, Biopsy-72hrs Post-2nd-Exposure


title: IT1P5


title: 5818_hippo_SYP_PSD95_double_negative_2


title: Subject-AN020, Biopsy-72hrs Post-2nd-Exposure


title: IT1P3


title: Subject-TN027, Biopsy-72hrs Post-1st-Exposure

value: 72hrs Post-1st-Exposure Mild

value: Untreated


title: 5818_hippo_SYP_PSD95_double_negative_1


title: IT1P2


title: 5818_hippo_SYP_PSD95_double-positive_4

description: Combined_5818h_sorted_PP_transcript_counts_rRNA_MT_filtered.tsv


title: Rapa treated p53

first: Christian

last: Sell

state: Pennsylvania

address: 245 N 15th St, Room

department: Biochemistry

institute: Drexel University

description: Note: This sample was not used in the analysis and no processed data are provided

data_processing:
Fasq files were transferred to Basepair bioinformatic platform and analyzed using the Cut and Tag pipeline developed by Basepair
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&TAG

source_name: HCF

growth_protocol: MEM, 10% fetal bovine serum, 2mM glutamine, no antibiotics. Cells were cultured at 37C at 5% CO2, 5% O2.

extract_protocol:
Wjole cells were utilized according to the Active Motif Cut and Tag protocol.
libraries were prepared using Illumina i5 and i7 primers. Quality control was perfomed using bioanalyzer chips performed by GeneWiz, sequencing was performed by GeneWiz

treatment_protocol: Cells were used at early passage (20-30population doublings), late passage (>50 population doublings), or late passage cultured in the continous presence of 1nM rapamycin

tag: cell line

value: HCF

value: Human cardiac fibroblast

tag: cut and_tag_antibody


title: Subject-SN026, Biopsy-72hrs Post-1st-Exposure

tag: individual

value: Skin

tag: Sex

value: 72hrs Post-1st-Exposure Severe


title: IT1P1


title: IT0P5


title: Subject-AN011, Biopsy-72hrs Post-2nd-Exposure

tag: age

tag: condition

value: 72hrs Post-2nd-Exposure Severe


title: 5818_hippo_SYP_PSD95_double-positive_3


title: Subject-RN034, Biopsy-72hrs Post-1st-Exposure


title: 5818_hippo_SYP_PSD95_double-positive_2


title: Subject-SN019, Biopsy-72hrs Post-1st-Exposure


title: Subject-SN009, Biopsy-72hrs Post-1st-Exposure


title: IT0P4


title: Subject-NN023, Biopsy-72hrs Post-1st-Exposure

value: Male


title: IT0P3


title: 5818_hippo_SYP_PSD95_double-positive_1


title: IT0P2


title: 5844_PFC_synapse_6


title: IT0P1


title: 5844_PFC_synapse_5


title: Subject-MN004, Biopsy-72hrs Post-1st-Exposure


title: Subject-KN025, Biopsy-72hrs Post-1st-Exposure


title: IC2P5

value: PBS


title: 5844_PFC_synapse_4


title: IC2P6


title: Subject-KN022, Biopsy-72hrs Post-1st-Exposure


title: 5844_PFC_synapse_3


title: Subject-KN013, Biopsy-72hrs Post-1st-Exposure


title: IC2P4


title: 5844_PFC_synapse_2


title: Subject-JN033, Biopsy-72hrs Post-1st-Exposure


title: 5844_PFC_synapse_7


title: Subject-MN021, Biopsy-72hrs Post-1st-Exposure


title: 5844_Hippo_synapse_7


title: IC1P6

description:
f1.results.csv.gz
f1cvsf2t.results.csv.gz


title: Subject-HN031, Biopsy-72hrs Post-1st-Exposure


title: 5844_Hippo_synapse_5


title: Subject-JN032, Biopsy-72hrs Post-1st-Exposure


title: Subject-GN003, Biopsy-72hrs Post-1st-Exposure


title: IC2P1


title: IC1P4


title: IC2P2


title: 5844_Hippo_synapse_6


title: 5844_Hippo_synapse_4


title: Subject-EN030, Biopsy-72hrs Post-1st-Exposure


title: 5844_Hippo_synapse_3


title: Subject-EN016, Biopsy-72hrs Post-1st-Exposure


title: IC1P3


title: IC1P1


title: 5844_Hippo_synapse_2


title: Subject-EN012, Biopsy-72hrs Post-1st-Exposure


title: Subject-EN005, Biopsy-72hrs Post-1st-Exposure


title: IC1P2


title: 5844_Hippo_synapse_1


title: IC2P3


title: Subject-JN015, Biopsy-72hrs Post-1st-Exposure


title: 5844_Hippo_nucleus_4

source_name: Nuclei from frozen postmortem human prefrontal cortical tissues


title: IC0P5


title: 5844_Hippo_nucleus_3

source_name: Nuclei from frozen postmortem human hippocampal tissues

value: hippocampal tissues


title: 5844_PFC_synapse_1


title: IC0P4


title: IC1P5


title: Subject-AN029, Biopsy-72hrs Post-1st-Exposure


title: Subject-AN028, Biopsy-72hrs Post-1st-Exposure


title: 5818_PFC_synapse_8


title: Subject-AN020, Biopsy-72hrs Post-1st-Exposure


title: 5844_Hippo_nucleus_2


title: Subject-AN017, Biopsy-72hrs Post-1st-Exposure


title: IC0P2


title: 48h_Purm_DMSO_N2 [4535_Z]

city: Dortmund

first: Jana

last: Flegel

state: NRW

address: Otto-Hahn-Straße 11

department: Chemical Biology

institute: Max Planck Institute of Molecular Physiology

data_processing:
Analysis was done at Max Planck Genome center in Cologne using the CLC Workbench (Version 12.0 & CLC Genomics Server Version 11.0) using the following steps:
’Trim Reads’
'RNA-Seq Analysis‘
Strand specific = Reverse‘
‘Differential Expression for RNA-Seq’
Genome_build: GRCm38
Supplementary_files_format_and_content: .txt files contain raw counts

growth_protocol: 120 000 C3H10T1/2 cells per well were seeded in a volume of 3 mL DMEM containing 1 mM sodium pyrovate and 10 % heat inactivated FCS into 6-well plates and incubated for 48 h at 37°C and 5 % CO2 to 80 % confluence.

extract_protocol:
For collection of the samples, the medium was aspirated from the wells and cells were washed once with 1 mL PBS. Afterwards 600 µL of RLT buffer (from RNeasy Plus Mini kit, #74134) was added to each well and the cells were collected in RNase free 1.5 mL tubes (supplemented with the RNeasy Plus Mini kit, #74134). For complete lysis, the cells were snap frozen once in liquid nitrogen and thawed on ice. The total RNA was extracted using the RNeasy plus mini kit (including the optional on column DNase I digest) according to the manufacturer’s instructions. RNA concentrations and qualities were accessed with the Qubit 4.0 fluorometer, using the QubitTM RNA BR assay kit and the QubitTM RNA IQ assay kit, according to the instructions of the manufacturer. Until further usage, the isolated RNA was snap frozen and stored at -80°C.  RNeasy plus mini kit (Qiagen, #74134)  DNase MAX kit (Qiagen, #15200)
RNA quality and quantity was assessed by Agilent Bioanalyser Nanochip. Next, Poly-A RNA was enriched from 500 ng total RNA by the "®Poly(A) mRNA Magnetic Isolation Module" (New England Biolabs) and directional RNA-seq libraries were prepared as described in "Ultra™ II Directional RNA Library Prep Kit for Illumina" (New England Biolabs). Library concentration was enriched by PCR with dual barcoded primers. Concentration of the libraries were determined by Qubit HS kit (Thermo) and the fragment size and quality of libraries screened by Agilent TapeStation.
Libraries were then diluted and pooled on a liquid handling station (Biomek i7, Beckman Coulter). Sequencing-by-synthesis was done on an Illumina HiSeq 3000 device at the Max Planck Genome center Cologne in paired-end read mode 2 x 150 bp with a HiSeq 3000 PE Cluster Kit and a HiSeq 3000 SBS Kit (300 cycle). Finally, data was trimmed to 1 x 150 bp.

treatment_protocol: Cells were treated either with 1.5 µM purmorphamine + DMSO, only DMSO, with 1.5 µM purmorphamine and 1 nM Picoberin, or 1.5 µM purmorphamine and 100 nM Picoberin, or DMSO and 100 nM Picoberin for 24h, 48h, 96h or 7 days. In all conditions, the final DMSO concentration was 0.25 %.

tag: developmental stage

value: embryo

tag: clone

value: Clone 8


title: IC0P1


title: 5818_PFC_synapse_7


title: 5818_PFC_synapse_6


title: Subject-AN011, Biopsy-72hrs Post-1st-Exposure

value: Female


title: Subject-AN014, Biopsy-72hrs Post-1st-Exposure


title: 5818_PFC_synapse_5


title: 24h_DMSO_DMSO_N2 [4535_X]


title: 24h_Purm_1nM_N2 [4535_W]


title: Subject-AN007, Biopsy-72hrs Post-1st-Exposure


title: Subject-CN024, Biopsy-72hrs Post-1st-Exposure


title: Subject-TN027, Biopsy-Baseline

value: Unexposed


title: 5818_PFC_synapse_3


title: 24h_Purm_100nM_N2 [4535_V]


title: Subject-SN026, Biopsy-Baseline


title: 24h_Purm_DMSO_N2 [4535_U]


title: 5818_PFC_synapse_2


title: IC0P3

value: Sprague Dawley SD (Harlan)

value: Sperm


title: Subject-SN019, Biopsy-Baseline


title: 7d_DMSO_100nM_N1 [4535_T]


title: 5844_Hippo_nucleus_1


title: 5818_Hippo_synapse_7

source_name: Hoechst-negative subneuronal compartments from frozen postmortem human hippocampal tissues


title: 24h_DMSO_100nM_N2 [4535_Y]


title: 7d_Purm_1nM_N1 [4535_R]


title: 5818_Hippo_synapse_6


title: Subject-NN023, Biopsy-Baseline


title: Subject-SN009, Biopsy-Baseline


title: 7d_Purm_100nM_N1 [4535_Q]


title: 5818_Hippo_synapse_5


title: 5818_PFC_synapse_4

value: prefrontal cortical tissues


title: 5818_Hippo_synapse_4


title: 7d_Purm_DMSO_N1 [4535_P]


title: Subject-MN004, Biopsy-Baseline


title: 96h_DMSO_100nM_N1 [4535_O]


title: 5818_Hippo_synapse_3


title: 5818_Hippo_synapse_2


title: Subject-MN021, Biopsy-Baseline


title: 96h_DMSO_DMSO_N1 [4535_N]


title: Subject-KN025, Biopsy-Baseline


title: Subject-KN013, Biopsy-Baseline


title: 96h_Purm_1nM_N1 [4535_M]


title: Subject-KN022, Biopsy-Baseline


title: 5818_PFC_nucleus_2


title: 5818_Hippo_synapse_1


title: 5818_PFC_synapse_1


title: Subject-JN033, Biopsy-Baseline


title: 96h_Purm_100nM_N1 [4535_L]


title: 5818_PFC_nucleus_1


title: 96h_Purm_DMSO_N1 [4535_K]


title: Subject-RN034, Biopsy-Baseline


title: 7d_DMSO_DMSO_N1 [4535_S]


title: 48h_DMSO_100nM_N1 [4535_J]


title: 5818_Hippo_nucleus_3


title: 5818_Hippo_nucleus_2


title: Subject-JN015, Biopsy-Baseline


title: Subject-HN031, Biopsy-Baseline


title: 5818_Hippo_nucleus_1


title: Subject-GN003, Biopsy-Baseline


title: Subject-EN030, Biopsy-Baseline


title: 48h_Purm_100nM_N1 [4535_G]


title: 48h_Purm_DMSO_N1 [4535_F]


title: Old amino acid suplementation_TIG-1_rep4

city: Ibaraki

first: Tomonori

last: Kimura

state: Osaka

address: 7-6-8 Saito-Asagi

department: Center for Rare Disease Research

country: Japan

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

data_processing:
The sequenced read was mapped to the human tRNA sequences using Blast version 2.2.26, and was aligned to the 25 nucleotides of 3' end of tRNA sequences without any mismatches.
The aligned read with 3'-end CCA was regarded to be derived from charged tRNA, whereas the read ended with 3'-end CC was from uncharged tRNA. Charging ratios were determined as 3'-end CCA–aligned reads over the sum of 3'-end CCA– and CC–aligned reads. Abundancy ratio of tRNA isodecoder was calculated based on the sum of 3'-end CCA– and CC–aligned reads of each isodecoder.
Genome_build: hg19
Supplementary_files_format_and_content: Individual alignment files mapping tRNA to isodecoder with read counts

source_name: old TIG-1 cells

growth_protocol: TIG-1 20 (JCRB0501) cells from JCRB were grown in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was extracted once the cells reached 70-90% confluency. Small RNA was isolated using Isogen2. After ethanol precipitation, periodate oxidation of small RNA was carried out in 100 mM NaOAc/HOAc, pH 5.2, freshly prepared 50 mM NaIO4 at 27°C for 30 minutes. The reaction was quenched with 100 mM glucose for 5 minutes at 27°C. tRNA was then purified by denaturing 15% PAGE(5M Urea, 1× TBE), and eluted from the gel overnight in TE.   For β-elimination and deacylation, tRNA was treated in 150 mM Tris-HCl, pH 9.0, at 37 °C for 30 min. tRNA was demethylated as previously described (Zheng 2015).
RNA libraries were prepared for sequencing using TGIRT.
tRNA-Seq

treatment_protocol: All replicates were incubated with amino acid free medium for 15h and two of them were suplemented with amino acids.

tag: tissue for primary cancer

value: Lung

tag: genetics

value: fetal lung

value: treated with amino acids for 1h

value: TIG-1 cells


title: Subject-EN012, Biopsy-Baseline

value: Skin

tag: treatment

value: Untreated


title: 24h_Purm_1nM_N1 [4535_C]

tag: cell type

tag: strain


title: Subject-EN005, Biopsy-Baseline


title: 24h_DMSO_DMSO_N1 [4535_D]


title: Subject-JN032, Biopsy-Baseline


title: 24h_DMSO_100nM_N1 [4535_E]


title: Old amino acid suplementation_TIG-1_rep3


title: Old amino acid suplementation_TIG-1_rep1


title: Subject-CN024, Biopsy-Baseline


title: Subject-AN029, Biopsy-Baseline


title: 48h_DMSO_DMSO_N1 [4535_I]


title: 7d_DMSO_100nM_N3 [4535_BH]


title: 7d_DMSO_DMSO_N3 [4535_BG]


title: Old_amino acid starvation_TIG-1_rep5

value: untreated


title: Subject-AN028, Biopsy-Baseline

value: Male


title: Old_amino acid starvation_TIG-1_rep3


title: 48h_Purm_1nM_N1 [4535_H]


title: Old_amino acid starvation_TIG-1_rep4


title: Subject-AN020, Biopsy-Baseline


title: Old amino acid suplementation_TIG-1_rep5


title: 7d_Purm_DMSO_N3 [4535_BD]


title: Old_amino acid starvation_TIG-1_rep2


title: Subject-EN016, Biopsy-Baseline


title: Old_amino acid starvation_TIG-1_rep1


title: Subject-AN014, Biopsy-Baseline


title: Old amino acid suplementation_TIG-1_rep2


title: Subject-AN011, Biopsy-Baseline


title: Young amino acid suplementation_TIG-1_rep5

source_name: young TIG-1 cells


title: Young amino acid suplementation_TIG-1_rep4


title: CUT&RUN Control - Input DNA

city: Baltimore

first: Yi

address: 511 WBSB, 725 N. Wolfe St.

department: Biological Chemistry

institute: Johns Hopkins University, School of Medicine

data_processing:
Library strategy: CUT&RUN-Seq
Analysis of the sequencing data followed the protocol of (Zheng et al., 2020). Sequencing adaptors were trimmed from the raw reads using Trim Galore. Trimmed reads were mapped to the human reference genome (GRCh38.p13) using Bowtie2. For spike-in calibration, the trimmed reads were additionally mapped to the E.coli reference genome (ASM584v2). Mapped BAM files were filtered by samtools view and converted to BED format using bedtools bamtobed. The BED files were spike-in calibrated and converted to genomic coverage bedgraph files using the bedtools genomecov function. Peak calling was performed with SEACR under the stringent mode, using the bedgraph file of IgG as control. Differential binding analysis was performed using Diffbind, using the mapped BAM reads (to human and E.coli reference genomes) from Bowtie2 and the called peaks from SEACR as input. The differential binding sites were annotated with ChIPSeeker.
Genome_build: GRCh38.p13
Genome_build: ASM584v2 (for spike-in calibration)
Supplementary_files_format_and_content: bigwig files were generated using the mapped BAM reads.
Supplementary_files_format_and_content: A tabular file generated by Diffbind that contains the differential binding sites of EZH2, comparing expression of Dual-specificity Aptamer vs. Individual Aptamers in Wnt - samples
Supplementary_files_format_and_content: A tabular file generated by Diffbind that contains the differential binding sites of EZH2, comparing expression of Dual-specificity Aptamer vs. Individual Aptamers in Wnt + samples

source_name: Cultured Cells

growth_protocol: Cells were cultured in DMEM with 1 g/L glucose, pyruvate and GlutaMAX (Gibco), supplemented with 10% heat-inactivated Fetal bovine serum, 200 U/mL penicillin and 200 µg/mL streptomycin.

extract_protocol:
At 24 hr post-transfection, cells were monodispersed by scrapping and pipetting. Nuclei from 5E5 cells were isolated for each reaction. CUT&RUN was performed using the CUTANA CUT&RUN kit (EpiCypher 14-1048), following the kit manual. 500 ng of EZH2 antibody (CST 5246) or Rabbit IgG (EpiCypher 13-0042k) was used in each 50 μL of binding reaction. After chromatin digestion, 0.5 ng of E.coli genomic DNA (kit included) was spiked-in to each reaction with the Stop Buffer. After chromatin release, DNA fragments were purified by Phenol:Chloroform extraction and isopropanol precipitation. Concentrations of DNA were measured using the Qubit 1X dsDNA HS Assay Kit (Invitrogen Q33230).
Preparation of Sequencing Library was performed using the NEBNext Ultra II DNA Library Prep Kit (NEB E7103L), and NEBNext Multiplex Oligos for Illumina (NEB E6440S). 6 ng DNA from each CUT&RUN reaction was used as the starting material. A negative control (Input) with 6 ng of sonication-sheard genomic DNA from HEK293T cells was included. Prepared DNA library was dissolved in nuclease-free water, and submitted to GENEWIZ (South Plainfield, NJ, USA) for sequencing. Sequencing was performed on an Illumina HiSeq 4000 sequencer in 2x150 bp mode.

treatment_protocol: 2E6 HEK293T cells were seeded per 10cm dish and transfection was performed after 24 hr (at 40% - 60% confluency). 1.5 μg of plasmids encoding Individual or Dual-speficity aptamers were dissolved in 100 μL Opti-MEM medium. 6 μg of TransIT-X2 Transfection Reagent (Mirus Bio) was added to the mixture, incubated at room temperature for 20 min and distributed evenly into the cell culture. Media were changed to fresh DMEM at 6 hr post-transfection. At 20 hr post-transfection, culture media were changed to fresh DMEM (Wnt-) or 50% (v/v) Wnt3A-conditioned DMEM (Wnt+).

tag: cut&run antibody


title: Subject-AN007, Biopsy-Baseline

source_name: Skin


title: 7d_Purm_1nM_N3 [4535_BF]


title: Young amino acid suplementation_TIG-1_rep1


title: 96h_Purm_100nM_N3 [4535_AZ]


title: 96h_Purm_1nM_N3 [4535_BA]


title: CUT&RUN Control - IgG

value: Normal Rabbit IgG (EpiCypher 13-0042k)


title: 7d_Purm_100nM_N3 [4535_BE]


title: Young amino acid suplementation_TIG-1_rep2


title: CUT&RUN Dual-specificity Aptamer_Wnt+_Rep1

value: EZH2 (Cell Signaling, 5246S)


title: 24h_Purm_100nM_N1 [4535_B]

value: embryo


title: 96h_DMSO_DMSO_N3 [4535_BB]

value: Clone 8


title: Young_amino acid starvation_TIG-1_rep4


title: 96h_DMSO_100nM_N3 [4535_BC]


title: 48h_DMSO_100nM_N3 [4535_AX]


title: Subject-AN017, Biopsy-Baseline

value: Female


title: 96h_Purm_DMSO_N3 [4535_AY]


title: Young_amino acid starvation_TIG-1_rep3


title: Young_amino acid starvation_TIG-1_rep5


title: CUT&RUN Dual-specificity Aptamer_Wnt+_Rep2


title: CUT&RUN Dual-specificity Aptamer_Wnt+_Rep3


title: 48h_DMSO_DMSO_N3 [4535_AW]


title: 48h_Purm_1nM_N3 [4535_AV]


title: CUT&RUN Individual Aptamers_Wnt+_Rep3


title: CUT&RUN Individual Aptamers_Wnt+_Rep2


title: Young amino acid suplementation_TIG-1_rep3


title: CUT&RUN Individual Aptamers_Wnt+_Rep1


title: 48h_Purm_100nM_N3 [4535_AU]


title: Young_amino acid starvation_TIG-1_rep1


title: 48h_Purm_DMSO_N3 [4535_AT]


title: ISRIB treated_rep5

data_processing:
The sequenced read was mapped to the human genome sequences using Blast version 2.2.26.
Genome_build: hg19
Supplementary_files_format_and_content: Individual alignment files mapping mRNA with read counts

source_name: TIG-1 cells

extract_protocol:
RNA was extracted once the cells reached 70-90% confluency. Cells were lysed in the presence of lysis buffer (20 mM Tris (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1%Triton X-100, 100 μg/mL CHX). For ribosome-protected mRNA fragment library preparation, the RNA amount was measured by Qubit and 10 μg of total RNA was digested with RNase I (Promega) at 20U for 45 min at 25°C. Ribosomes are pelleted from the digested lysate by ultracentrifugation through a sucrose cushion, and then RNA is extracted from the pellet. 25–34 nt fragments were size-selected after electrophoresis through a 15% TBE-Urea gel.
Library was prepared by using NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs). Sequencing was performed on an Illumina Nextseq 500 platform in a 75-base single-end mode (illumina).

treatment_protocol: All replicates were incubated with amino acid free medium for 15h and one of them were suplemented with ISRIB.

value: treated with ISRIB


title: CUT&RUN Dual-specificity Aptamer_Wnt-_Rep3


title: 24h_DMSO_DMSO_N3 [4535_AR]


title: 24h_DMSO_100nM_N3 [4535_AS]


title: ISRIB treated_rep3


title: CUT&RUN Dual-specificity Aptamer_Wnt-_Rep1


title: ISRIB treated_rep4


title: CUT&RUN Dual-specificity Aptamer_Wnt-_Rep2


title: Young_amino acid starvation_TIG-1_rep2


title: 24h_Purm_1nM_N3 [4535_AQ]


title: 24h_Purm_100nM_N3 [4535_AP]


title: DMSO_rep5

value: vehicle


title: 24h_Purm_DMSO_N3 [4535_AO]


title: ISRIB treated_rep1


title: CUT&RUN Individual Aptamers_Wnt-_Rep3


title: CUT&RUN Individual Aptamers_Wnt-_Rep2


title: 7d_DMSO_DMSO_N2 [4535_AM]


title: ISRIB treated_rep2


title: CUT&RUN Individual Aptamers_Wnt-_Rep1


title: 7d_Purm_1nM_N2 [4535_AL]


title: DMSO_rep4


title: 18mo mouse bulk retina, IOP, day2, polyA RNA-Seq, replicate 2

city: Irvine

first: Dorota

last: Skowronska-Krawczyk

state: California

address: 837 Health Sciences Rd, Gillespie Neuroscience Research Facility, Room#2226, Bench#8

department: Physiology & Biophysics

institute: UC Irvine

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_19/

data_processing:
All clean-reads were mapped to Mus musculus reference genome mm10 by STAR v2.7.8a. Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification. The uniquely mapped tags in exons on minus strand (one isoform per locus) were quantified by analyzeRepeats.pl. Raw reads count was normalized to experiment totals and performed differential expression by DESeq v1.24.0 program.
For mRNA quantification, mm10 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
Differentially regulated RNA expression features were found via the homer tool - getDiffExpression.pl with the differential Expression Calculation program DESeq2. The significance cutoffs were log2fold>1, FDR<0.05 for up-regulated genes and log2fold<-1, FDR<0.05 for down-regulated genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bulk retina

extract_protocol:
Fresh bulk mouse retina tissue were collected and homogenized thoroughly in TRIzol Reagent (15596026, Invitrogen) followed by RNA isolation. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The poly-adenylated (poly-A) transcripts from the isolated total RNA sample were enriched and performed strand specific mRNA-Seq TruSeq libraries preparation for sequencing using standard Illumina protocols

treatment_protocol: Each mouse underwent unilateral hydrostatic pressure-induced IOP elevation to 30 mmHg, with the contralateral eye left as an untreated control. To ensure a sterile environment, compounds were prepared under the tissue culture hood using sterile PBS. The final solution was filtered through a 0.22-μm PES membrane just before injection. Tips, tubes, and syringes were sterile.

value: bulk retina

tag: genotype

value: WT

value: unilateral IOP (constant 30mmHg IOP for 1 hour)

tag: date of tissue collection after treatment

value: day 2 from IOP


title: DMSO_rep2

value: Lung

value: fetal lung


title: 18mo mouse bulk retina, IOP, day2, polyA RNA-Seq, replicate 1

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_17/

tag: tissue


title: 18mo mouse bulk retina, contralateral control, day2, polyA RNA-Seq, replicate 2

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_15/

value: unilateral untreated control


title: 7d_Purm_100nM_N2 [4535_AK]


title: DMSO_rep1

tag: cell line

value: TIG-1 cells


title: 7d_Purm_DMSO_N2 [4535_AJ]


title: 18mo mouse bulk retina, contralateral control, day2, polyA RNA-Seq, replicate 1

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_13/


title: GCN2KD_rep4

extract_protocol:
RNA was extracted once the cells reached 70-90% confluency. Cells were lysed in the presence of lysis buffer (20 mM Tris (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1%Triton X-100, 100 μg/mL CHX). For ribosome-protected mRNA fragment library preparation, the RNA amount was measured by Qubit and 10 μg of total RNA was digested with RNase I (Promega) at 20U for 45 min at 25°C. Ribosomes are pelleted from the digested lysate by ultracentrifugation through a sucrose cushion, and then RNA is extracted from the pellet. 25–34 nt fragments were size-selected after electrophoresis through a 15% TBE-Urea gel.
Library was prepared by using NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs). Sequencing was performed on an Illumina Nextseq 500 platform in a 75-base single-end mode (illumina).
Ribo-seq

treatment_protocol: Cells were allowed to reach 50–70% confluency prior to transfection, and then were transfected with 50 nM siGenome siGCN2 (#M-005314-02-0005, Dharmacon, Waltham, MA). As a control siGENOME Non-Targeting siRNA Pool #1 (Dharmacon) was used. Transfections were performed using Lipofectamine RNAiMAX (Invitrogen) following the manufacturer’s procedure. Thereafter, cells were incubated for 48 hours at 37 °C in a humidified chamber supplemented with 5% CO2.

value: GCN2 siRNA treated


title: GCN2KD_rep3


title: 3mo mouse bulk retina, IOP, day2, polyA RNA-Seq, replicate 2

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_4/


title: 96h_DMSO_100nM_N2 [4535_AI]


title: 3mo mouse bulk retina, IOP, day2, polyA RNA-Seq, replicate 1

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_2/


title: 96h_DMSO_DMSO_N2 [4535_AH]


title: 96h_Purm_1nM_N2 [4535_AG]


title: 3mo mouse bulk retina, contralateral control, day2, polyA RNA-Seq, replicate 1

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_1/


title: 96h_Purm_DMSO_N2 [4535_AE]


title: DMSO_rep3


title: Control_rep3

value: Non-targetting siRNA treated


title: GCN2KD_rep1


title: Control_rep4


title: GCN2KD_rep2


title: 7d_DMSO_100nM_N2 [4535_AN]


title: 96h_Purm_100nM_N2 [4535_AF]


title: 48h_DMSO_DMSO_N2 [4535_AC]


title: 48h_Purm_1nM_N2 [4535_AB]


title: Control_rep1


title: Veh.3_S60

city: Indianapolis

first: Reuben

last: Kapur

state: IN

address: 1044 W Walnut St

institute: Indiana University

data_processing:
Data is mapping to genome UCSC mm10 using STAR software
counts data are extract using featureCounts
Assembly: UCSC mm10
Supplementary files format and content: Gene counts in txt file

source_name: WBM Dnmt3aKO Transplant

growth_protocol: Whole bonemarrow cells of Dnmt3a knockout mice were transplanted into irradiated C57/BL6 recipietns and terated with vheicle or PI3Kalpha/beta inhibitor (75mg/kg) for 21 days.

extract_protocol:
Total RNA was extrated and purified with Quiagen Rneasy Plus Micro Kit Cat # 74034
Clontech SMART-Seqv4 Ultra Low Input RNA Kit (Cat#634889), 24rxns; Illumina Nextera XT DNA Lib Kit. Dual Index

treatment_protocol: Mice bearing Leukemic Dnmt3a null BM cells were treated with vheicle or PI3Kalpha/beta inhibitor (75mg/kg) for 21 days, later BM cells harvested

value: WBM Dnmt3aKO Transplant

value: Primary Mouse BM cells

value: vehicle group

value: vehicle-Dnmt3aKO TRPs


title: Bay.5_S63

value: PI3K inhibitor group

value: PI3Ki-Dnmt3aKO TRPs

value: PI3Kalpha/beta inhibitor treated


title: Bay.3_S62


title: Bay.1_S61


title: Amino acid suplementation_rep4

treatment_protocol: All replicates were incubated with amino acid free medium for 15h and one of them were suplemented with amino acids.

value: treated with amino acids for 1h


title: 48h_DMSO_100nM_N2 [4535_AD]

value: embryo

value: Clone 8


title: Control_rep2


title: 3mo mouse bulk retina, contralateral control, day2, polyA RNA-Seq, replicate 2

description:
FPKM_CTRLvsIOP_3movs18mo.txt
Column name in processed data: QX_3/

value: bulk retina

value: WT

value: day 2 from IOP


title: Veh.2_S59

value: vehicle


title: 48h_Purm_100nM_N2 [4535_AA]


title: Amino acid suplementation_rep3

value: Lung

value: fetal lung

value: TIG-1 cells


title: Veh.1_S58

value: WBM Dnmt3aKO Transplant


title: 24h_Purm_DMSO_N1 [4535_A]


title: Amino acid suplementation_rep2


title: Amino acid suplementation_rep1


title: Vs3 (miRNA-seq)

first: Gao-Pu

institute: Chinese Academy of Forestry

data_processing:
A cDNA library constructed by technology from the pooled RNA from all samples of grape was sequenced run with Illumina 4000 sequence platform.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) Vitis vinifera reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.
HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie.
Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
The miRNA-seq raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs.
The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
To predict the genes targeted by most aboundant miRNAs, computational target prediction algorithms (TargetFinder) were used to identify miRNA binding sites. The GO terms and KEGG Pathway of most aboundant miRNA targets were also annotated
Raw sequencing reads were obtained using Illumina's software to remove adaptors and low quality reads. The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline .
The degradome reads were mapped to the mRNA downloaded from www （ JGI , NCBI or other databases,or mapped to the species transcripts from transcriptome  sequencing） . Only the perfect matching alignment(s) for the given read would be kept for degradation analysis .
The degradation group sequence can match different numbers of reads on different sites on the same mRNA, and the predicted sequences at these sites may haven't corresponding miRNAs. The degradation group sequence can match different numbers of reads on different sites on the same mRNA, and the predicted sequences at these sites may haven't corresponding miRNAs. Detailed results with specific alignment information form a long_outfile file with AlignmentScore (Targetfinder penalty), AlignmentRange (pairing site), CleaveageSite (cutting site), Category (segmentation),P-value (P value), Raw_reads, Rep_Norm_reads (matches that match multiple sites for site normalization). Without alignment information, only AlignmentScore (Targetfinder score), AlignmentRange (pairing site), CleaveageSite (cutting site), Category (type), P-value (P value), Raw_reads, Rep_Norm_reads are listed. The (multi-site normalized reads) information is a simple list of miRNA and target gene relationships for the "Degradome_result.xlsx" file.
All resulting reads (t-signature) were reverse-complemented and aligned to the miRNA identified in our study.
All the identified targets were subjected to BlastX analysis to search for similarity, and then to GO analysis to uncover the miRNA-gene regulatory network on the basis of biological process ,cellular component and molecular function .
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-37/plants/gtf/vitis_vinifera v37
Supplementary_files_format_and_content: mRNA include FPKM values for each Sample ;miRNA expression use the norm values for each Sample.

source_name: Vitis vinifera

extract_protocol:
In harvest season, the samples were selected that quick-frozen in liquid nitrogen, and stored at below 80°C until use. Total RNA and small RNA were extracted using Polysaccharide Polyphenol Plant MicroRNA Extraction Kit (LabHelper, Beijing, China) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: type

value: graft hybrids of Schisandra chinensis + Vitis vinifera

tag: time

value: 25 years

value: LEAF, PHLOEM, BERRY


title: DNMT3a_KO_2_1

data_processing:
Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) was set at default and used for aligning the quality filtered RNA sequence reads, against the whole mouse reference genome mm10.
StringTie (Version 1.2.1) was used with default parameters to quantitate the transcripts
R (EdgeR) package was used for differential gene expression analysis of RNA-Seq expression profiles.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MxCre+v: Dnmt3a-/- BM cells

growth_protocol: BM cells harvested from Wildtype and Dnmt3a knockout  mice were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). total RNA was used for the construction of sequencing libraries.After extract total RNA and treated with DNase I, Oligo(dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA are fragmented.Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.Illumina Hiseq platform was used for sequencing.

treatment_protocol: BM cells cultured in RPMI supplemented with IL3 (10ng/ml), SCF (50ng/ml) in RPMI, and week1 culture cells were utilized for RNAsequencing..

value: MxCre+v:Dnmt3a-/- BM cells

value: Primary Mouse BM cells

value: Dnmt3a knockdown

value: IL3,SCF supplemented culture

value: week 1


title: Amino acid starvation_rep4

value: untreated


title: DNMT3a_KO_3_1


title: DNMT3a_KO_1_1


title: Vs2 (miRNA-seq)

treatment_protocol: no special treatment


title: Amino acid starvation_rep3


title: Amino acid starvation_rep2


title: Vs1 (miRNA-seq)


title: WT2_1

source_name: MxCre+v: Dnmt3a+/+ BM cells

value: MxCre+v:Dnmt3a+/+ BM cells


title: Amino acid starvation_rep1


title: WT3_1

value: WT


title: Dermal_suplimentation_rep3

source_name: primary dermal fibroblast

growth_protocol: Cells from ATCC were cultured in the recommended media.

extract_protocol:
RNA was extracted once the cells reached 70-90% confluency. Small RNA was isolated using Isogen2. After ethanol precipitation, periodate oxidation of small RNA was carried out in 100 mM NaOAc/HOAc, pH 5.2, freshly prepared 50 mM NaIO4 at 27°C for 30 minutes. The reaction was quenched with 100 mM glucose for 5 minutes at 27°C. tRNA was then purified by denaturing 15% PAGE(5M Urea, 1× TBE), and eluted from the gel overnight in TE.   For β-elimination and deacylation, tRNA was treated in 150 mM Tris-HCl, pH 9.0, at 37 °C for 30 min. tRNA was demethylated as previously described (Zheng 2015).
RNA libraries were prepared for sequencing using TGIRT.

tag: tissues

value: Dermal

value: treated with amino acids for 1h

tag: atcc number


title: WT1_1


title: Dermal_suplimentation_rep1


title: T cells mRNA

city: Marseille

first: Rudy

last: AUSSEL

address: Parc Scientifique et Technologique de Luminy

country: France

institute: CIML

description: 53448 T cells were isolated from 44 spleen from 44 C57BL/6Rj mice and processed using the Chromium Single Cell 3’ kit from 10X genomics (California, USA) for the library preparation and the Illumina HiSeq4000 . FASTQ raw files were processed using Cell Ranger software (v2.1.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.

data_processing:
FASTQ raw files were processed using Cell Ranger software (v2.1.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads   were aligned to the mouse mm10 genome.
Quality control (QC) was performed to remove poor quality cells thanks to in-house developed R scripts using Seurat v3 R package.
Expression data were normalized using the Seurat R package NormalizeData function (using logNormalize method and scale factor of 10000).
Expression data were centered and regressed from the number of UMI factor using the Seurat R package ScaleData function (centering true and scaling false).
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files containing cell barcodes, features and count matrix for mRNA, HTO and ADT libraries, csv files containing expression matrix.

source_name: Spleen

extract_protocol:
Cells were extracted from pooled spleens isolated from seven 2-week-old- and two 5-week-old-WT mice, nine 1-week-old-, eleven 1.5-week-old-, six 2-week-old-, five 2.5-week-old-, three 3-week-old-, and one 5-week-old-LatY136F mice, and T cells were enriched using the EasySep Mouse T Cells Isolation Kit (Stemcell). Each purified T cell sample was then labeled with a specific Hashtag (TotalSeq™ anti-mouse Hashtag antibody #A0301-A0308, Biolegend), a mix of 6 calibrated TotalSeq™-A anti-mouse specific antibodies (CD27, CD25, CD39, TCRb, PD-1, CD103), and a cocktail of 6 fluorescently-labeled anti-mouse antibodies plus a viability dye. Cells were then sorted as live singlets, CD11b– IA/IE–CD90.2+ CD6+ expressing either CD4+ or CD8+. After sorting, cells were washed in PBS - 0.04% BSA as recommended by the 10xGenomics sample preparation protocol and kept on ice until counting was performed.
2 to 3 samples were mixed at a concentration of 1200 cells /µl and loaded in 2 to 3 lanes at a maximum concentration of 12,000 cells per lane and run on a Chromium-controller (10X Genomics, Pleasanton). Single-cell RNA-Seq libraries, HTO libraries and ADT libraries were generated using the Chromium Single Cell 3′ V3 kit (10X Genomics) according to the manufacturer’s instructions.

tag: mouse strain

value: Spleen (n=44)

tag: mouse age

value: WT mice:2 week (n= 7); 5 weeks (n=2).  mutant mice :1 week (n= 9); 1,5 weeks (n=11); 2 weeks (n=6); 2,5 weeks (n= 5); 3 weeks (n=3); 5 weeks (n=1)


title: NC--replicate 1

city: Nanjing

first: Ruyi

last: Fan

state: Jinngsu

address: 1 Shanghai Road

department: Department of Periodontics

institute: Nanjing Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes readcount values for each Sample

source_name: human Periodontal Ligament

growth_protocol: hPDLCs were cultured by α‐MEM with 10% FBS

extract_protocol:
hPDLCs were washed with 1 X PBS for 3 times, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hPDLCs were treated with  LPS,  P. gingivalis 33277 OMVs,  P. gingivalis W83 OMVs

value: human Periodontal Ligament

value: hPDLCs

value: fibroblast


title: LPS-replicate 2

value: LPS


title: NC--replicate 3


title: LPS-replicate 3


title: NC--replicate 2


title: T cells HTO


title: T cells ADT


title: Progeria‐GM08398‐P13‐R1

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: Tennessee

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github https://github.com/dekkerlab/cMapping
Iterative correction was performed using method described by Imakaev et al.
Assembly: hg19
Supplementary files format and content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 40 kb, 100 kb, 250 kb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 2.5 Mb bin size

source_name: Skin fibroblast (Coriell: https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM08398&Product=CC)

growth_protocol: Fibroblast lines were grown to confluency prior to crosslinking.

extract_protocol:
Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing. Samples were then digested overnight with HindIII or DpnII (as indicated per sample). Ends were filled in with biotin and ligated. Then, crosslinking was reversed.
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

value: skin fibroblast

tag: passage

value: Passage 13


title: Dermal_starvation_rep3


title: SNI-5d-rep-3

city: Los Angeles

first: Yuyan

last: Cheng

state: CA

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

institute: UCLA

data_processing:
For RNA-seq, raw sequenced reads were mapped to the reference genome Mus musculus (mm10) refSeq (refFlat) using STAR with default parameter.
Data quality was assessed on base-quality calls, nucleotide composition of sequences, insert sizes, per cent of uniquely aligned reads and transcript coverage using custom scripts and Picard Tools.
Total counts of read fragments aligned to candidate gene regions were derived using the Salmon program with mouse mm10 refSeq (refFlat table) as a reference.
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene counts in tsv format

source_name: Dorsal Root Ganglion Neurons

extract_protocol:
Samples were dissociated in papain, followed by FACS sorting. For RNA-seq, RNA from 5,000 – 10,000 FACS-sorted DRG neurons were isolated with RNeasy Micro Kit (Qiagen), and RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), following manufacturers’ protocols.
The cDNA was fragmented to 300 base pairs (bp) using the Covaris M220 (Covaris), and then the manufacturer’s instructions were followed for end repair, adaptor ligation, and library amplification. The libraries were quantified by the Qubit dsDNA HS Assay Kit (Molecular Probes); Library size distribution and molar concentration of cDNA molecules in each library were determined by the Agilent High Sensitivity DNA Assay on an Agilent 2200 TapeStation system.

value: Sciatic Nerve Injury

tag: time post crush


title: OMV2--replicate 2

value: P. gingivalis W83 OMVs


title: SNI-5d-rep-1


title: OMV2--replicate 3


title: SNI-1d-rep-3


title: LPS-replicate 1


title: Dermal_starvation_rep2


title: Lung_suplimentation_rep3

source_name: primary lung fibroblast

value: Lung


title: SNI-5d-rep-2


title: Dermal_starvation_rep1


title: OMV2--replicate 1


title: Lung_suplimentation_rep2


title: Dermal_suplimentation_rep2


title: Lung_suplimentation_rep1


title: OMV1 -replicate 3

value: P. gingivalis 33277 OMVs


title: SNI-1d-rep-1


title: OMV1 -replicate 2


title: Lung_starvation_rep3

value: untreated


title: SNI-0d-rep-1

value: Naïve


title: OMV1 -replicate 1

value: WT


title: SNI-0d-rep-3


title: Lung_starvation_rep2


title: SNI-0d-rep-2


title: Lung_starvation_rep1


title: MDA-F471 CSCs replicate 2

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Sequenced raw reads were first subjected to quality control (QC) using FastQC.
Trimmomatic was used to remove adapter sequences, low quality bases as well as reads with lengths shorter than 36 base pairs.
Reads were then mapped to the reference mouse genome (UCSC mm 10) using the fast splice-aware aligner HISAT2.
Transcripts were assembled using StringTie and normalization was carried out using DESEQ2 considering both transcript length and depth of coverage after which read conts were computed for each transcript/gene.
Assembly: mm10
Supplementary files format and content: Read counts for all samples in one tab-delimited txt file

source_name: MDA-F471 cells

growth_protocol: MDA-F471 cells were maintained in a humidified incubator at 37 degrees Celcius with 5 CO2 and in DMEM F-12 medium (Sigma-Aldrich) supplemented with 10% feta bovine serum (FBS), 1% penicillin-streptomycin antibiotics (Lonza), and plasmocin prophylactic (Invivogen). Derivation of CSCs as 3D spheres was performed using sphere formation assays as described previously. Three biological replicates of MDA-F471 cell suspensions were embedded in growth actor-reduced Matrigel (from Corning) in a 1:1 ration with medium.

extract_protocol:
Total RNA was purified from MDA-F471 cells and the spheres (6 samples) using the RNeasy Plus Kit (Qiagen) according to the manufacturer's protocol
The Ribo-zero RNA removal kit was used to remove ribosomal RNAs from total RNA samples. Paired-end libraries (101 bp reads) were prepared from 500 ng total RNA using the TruSeq stranded total RNA LT sample kit (Illumina) according to the manufacturer's instructions.

value: MDA-F471 cells

value: Mouse lung adenocarcinoma cells

value: CSCs/spheres


title: MDA-F471 CSCs replicate 1


title: MDA-F471 CSCs replicate 3


title: MDA-F471 cells replicate 3

value: Parental


title: MDA-F471 cells replicate 2


title: SNI-1d-rep-2


title: MDA-F471 cells replicate 1


title: Amino acid suplementation_rep3

description: small RNA

extract_protocol:
RNA was extracted once the cells reached 70-90% confluency. Small RNA was isolated using Isogen2. After ethanol precipitation, periodate oxidation of small RNA was carried out in 100 mM NaOAc/HOAc, pH 5.2, freshly prepared 50 mM NaIO4 at 27°C for 30 minutes. The reaction was quenched with 100 mM glucose for 5 minutes at 27°C. tRNA was then purified by denaturing 15% PAGE(5M Urea, 1× TBE), and eluted from the gel overnight in TE.   For β-elimination and deacylation, tRNA was treated in 150 mM Tris-HCl, pH 9.0, at 37 °C for 30 min. tRNA was demethylated as previously described (Zheng 2015).
RNA libraries were prepared for sequencing using NEBNext Small RNA Library Prep Set for Illumina.

treatment_protocol: Both replicates were incubated with amino acid free medium for 15h and one replicate was suplemented with amino acids.

tag: tissue for primary cancer

value: fetal lung

value: treated with amino acids for 1h


title: Amino acid suplementation_rep2

description: small RNA

tag: treatment


title: GFP_Naive-rep-5

data_processing:
For RNA-seq, raw sequenced reads were mapped to the reference genome Mus musculus (mm10) refSeq (refFlat) using STAR with default parameter.
Data quality was assessed on base-quality calls, nucleotide composition of sequences, insert sizes, per cent of uniquely aligned reads and transcript coverage using custom scripts and Picard Tools.
Total counts of read fragments aligned to candidate gene regions were derived using the Salmon program with mouse mm10 refSeq (refFlat table) as a reference.
Differential expression analysis was conducted with limma-voom.
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene counts in tsv format

value: Naive

value: wild-type


title: GFP_Naive-rep-4


title: Amino acid suplementation_rep1

description: small RNA

tag: cell type


title: Pneumonia2

first: Dianyin

last: Yang

address: 150, Jimo Road, Pudong District

institute: Shanghai East hospital

data_processing:
After sequencing on Illumina Novaseq 6000 sequencer, double-end reads were harvested. q30 was used for quality control, and cutadapt software (v1.9.3) was used to de-join and remove low quality reads to obtain high quality reads. circRNA, LncRNA and mRNA were analyzed separately using different methods.
circRNA: High quality reads were compared to the reference genome/transcriptome using STAR software (v2.5.1b), and circular RNA detection and identification were performed using DCC software (v0.4.4)
The identified circular RNAs were also annotated using the circBase database and Circ2Traits. Data normalization and differentially expressed circRNA screening were then performed using edgeR software (v3.16.5). GO and KEGG analysis of the genes from which the differential circRNAs originated was also performed.
LncRNA & mRNA: using hisat2 software (v2.1), high quality reads were aligned to the human reference genome (UCSC HG19).Then, FPKM of transcript-level LncRNA and gene-level mRNA were obtained using cuffdiff software (part of the cufflinks software suite) guided by gtf gene annotation files.
(Fragments per kilobase of exon per million fragments mapped) values as expression profiles of LncRNA and mRNA, and ploidy changes and p-values between two/groups of samples were calculated to screen for differentially expressed LncRNA and mRNA.
Based on the proximity relationship, the target genes of LncRNAs were predicted, and GO and KEGG pathway analysis of target genes were performed. GO and KEGG pathway analysis of differential mRNAs were also performed.
Assembly: HG19
Supplementary files format and content: excel format

source_name: plasma

extract_protocol:
RNA was extracted using trizol reagent
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA)

value: plasma

tag: disease state

value: pneumonia patients without sepsis


title: Sepsis2

value: pneumonia-induced sepsis


title: Sepsis3


title: Pneumonia3


title: Sepsis1


title: GFP_Naive-rep-2

tag: strain


title: Amino acid starvation_rep3

description: small RNA


title: Pneumonia1