title: AB11339

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 9 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
human sample collection: skin samples were obtained through punch biopsy (4 mm), 10 cm distal to the elbow and placed in saline containing tubes on ice and then transferred to cold FACS buffer (EDTA pH8.0 2mM, BSA 0.5% in PBS). Whole blood samples were collected at the time of skin biopsy, were placed in EDTA-containing tubes (Beckton Dickenson) on ice and diluted 1:1 with ice cold FACS buffer. Skin and blood samples immediately transported to the lab.
Skin cell suspension and blood mononuclear cells were stained with the following antibodies: CD45 (PerCp/Cyanine, 3040285.5, Biolegend), CD90 (PE 328144, Biolegend), LGR5 (PE, 373803, Biolegend), CD55 (FITC, 311306, Biolegend). All FACS antibodies were used with a 1:100 dilution. Samples were filtered through a 40μm strainer before commencing sorting. Single cell sorting was performed using FACSAria Fusion cell sorter (BD Biosciences, San Jose, CA). After doublets exclusion, isolated live cells were single-cell sorted into 384-well cell capture plates containing 2μL of lysis solution and barcoded poly(T) reverse-transcription (RT) primers for single-cell RNA-seq. Four empty wells were kept in each 384-well plate as a no-cell control for data analysis. Immediately after sorting, each plate was spun down to ensure cell immersion into the lysis solution, snap frozen on dry ice, and stored at –80°C until processed. Cells were analyzed using BD FACSDiva software (BD Bioscience) and FlowJo software (FlowJo, LLC).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

value: Skin


title: AB11336

status: Public on Apr 04 2022

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: Forearm skin

treatment_protocol:
treatment protocol (1): To generate gentle and efficient single-cell suspensions from human skin tissue, we used Miltenyi human whole skin dissociation kit (catalog num. 130-101-540), which combines mechanical dissociation with enzymatic degradation of the extracellular adhesion proteins. In short, first we cut the skin biopsy into small pieces (< 1mm) and transferred them into gentleMACS C Tube containing 435µL of Buffer and 65 µL of enzyme mix. Next, samples were incubated in a water bath at 37 °C for 1h. After incubation we diluted the samples by adding 0.5 mL of cold cell culture medium, tightly closed C Tube and attached it upside down onto the sleeve of the gentleMACS dissociator, and run the gentleMACS Program h_skin_01. After a short centrifugation step to collect the sample material at the tube bottom, we applied the cell suspension to a 70 µm pre-separation filter, placed on a 15 mL tube, and washed with ice cold FACS buffer. Then, we centrifuged the cell suspension at 300×g for 10 minutes at 4°C and aspirated the supernatant completely. Finally, after red blood cell lysis (Sigma) for 5min at 4°C, centrifugation at 300×g for 10 minutes at 4°C, and washing, we resuspended the cells for FACS staining and sorting.
treatment protocol (2): Blood mononuclear cell separation was performed by density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with blood cells. Centrifugation (460g, 25min) was performed at 10°C, and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After red blood cell lysis (Sigma) for 5 minutes at 4°C, centrifugation at 300×g for 10 minutes at 4°C, and washing, we resuspended the cells for FACS staining and sorting.

tag: tissue

tag: selection marker

tag: patient id


title: E87_Aggrewell

city: Bergen

first: Helge

last: Ræder

address: Dept of Pediatrics, Haukeland University Hospital

department: Department of Clinical Science

country: Norway

institute: University if Bergen

description:
Sample 14
Raw_Counts_All_Samples.csv

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq2 software (Illumina inc.).
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 21.0.4 was used to demultiplex the raw sequencing reads according to the sample indices.
The reads were then mapped to the Human genome GRCh38 and annotated using the ENSEMBL GRCh38 v. 98 gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: hiPSC-derived beta like cells at Stage7

growth_protocol: The directed differentiation of hiPSCs to β-like cells was performed as previously described (7, 8). To reduce variability between different differentiations we performed the original differentiation in parallel in the same multiwell-plate for all conditions with the same batch of differentiation cocktail. At the end of Stage 5, 5.0 million cells were embedded in alginate beads, as previously described (13), 2.4 million cells were used to form cell aggregates (11) and approximately 5 million were kept in adherent culture. The beads, aggregates and planar cultures were differentiated until ST7 as previously described (7, 14).

extract_protocol:
RNA from cell clusters were isolated using  Qiagen RNeasy kit. RNA from alginate capsules were snap freeze in the kit lysis buffer, without de-algination, RNA were then isolated by following the recommended process.
The library preparation was done using the QIAseq UPX 3’ Transcriptome Kit (QIAGEN). A total of 10 ng (sample 1-7), 2.5 ng (sample 8-14) purified RNA was converted into cDNA NGS libraries. During reverse transcription, each sample was tagged with a unique ID, and each RNA molecule was tagged with a unique molecular index (UMI). The samples were then pooled into one tube for downstream processing. Quality control of the library preparation was performed using capillary electrophoresis (Agilent DNA 7500 Chip) and the libraries were quantified using qPCR.

treatment_protocol: Different cell lins were differentiated in Aggrewell plates (3D), encapsulated in Alginate, or in 2D conditation respectively.

tag: condition

tag: iPSc cell line

tag: genotype


title: AB11337


title: AB11335


title: FAH5F

city: Aarhus N

first: Paul

middle: Vinu

last: Salachan

state: Aarhus

address: Brendstrupgårdsvej 21A

country: Denmark

institute: Aarhus University

description: sampled at high temperature point after 12 fluctuation cycles during adult stage

data_processing:
The raw reads were checked for quality using FastQC (Andrews, 2010) and trimmed using trimmomatic based on a minimum length of 80 bp. Alignment of the trimmed reads was done using HISAT2 with default settings (Kim et al., 2015). StringTie (Pertea et al., 2015) was used to assemble the transcripts based on Drosophila melanogaster reference genome. All the transcripts were further merged using StringTie merge. The StringTie was run again with the B option on the merged transcripts to produce Ballgown input table files.
hisat2 -p 19 --dta -t -q -x
stringtie align_1/${sample}.bam -o align_1/${sample}.gtf -p 19 -G drosGTF/Dros_mel.BDGP6.92.chr.gtf
stringtie --merge -p 19 -o align_1/stringtie_merged.gtf -G drosGTF/Dros_mel.BDGP6.92.chr.gtf align_1/mergelist.txt
stringtie -e -B align_1/${sample}.bam -o align_1/ballgown/${sample}/${sample}.gtf -p 19 -G align_1/stringtie_merged.gtf
Genome_build: BDGP6
Supplementary_files_format_and_content: .csv file containing count data for all samples, generated using a python script provided by the developers of StringTie

organism: Drosophila melanogaster

source_name: Whole organism

growth_protocol: Experimental animals were kept in vials with 7ml standard Drosophila food medium. Adult flies were tipped to fresh food containing vials every second day

extract_protocol:
Extrraction and Library construction performed by Novogene using standard protocols.
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Experimental animals subjected to constant temperature at 19 degree centigrade or a fluctuating temperature with a mean of 19 and an amplitude of plus or minus 8 degree centigrade. The treatment was continued for 7 days during larval development and for 13 days during adult stage, during which animals were taken for RNA sequencing at different timepoints

tag: treatment

value: fluctuating

tag: Sex

value: female

tag: timepoint

tag: lifestage

value: adult


title: E75_Aggrewell

description:
Sample 13
Raw_Counts_All_Samples.csv


title: Control_RNAseq C2

city: xian

first: Miaomiao

last: Jin

address: yangling

country: China

institute: northwest A&F university

data_processing:
TopHat (version 2.0.12) was used to map the paired-end clean reads to the reference goat genome and to build the index of the reference genome with Bowtie (Version 2.2.3)
Cufflinks (version 2.1.1) was used to assemble the mapped reads from TopHat2 (version 2.0.12)
Cuffdiff was used to calculate FPKM of the lncRNAs and coding genes in all libraries
Assembly: ASM170441v1
Supplementary files format and content: gtf were generated by cufflinks. FPKM were caculated by cuffdiff.

organism: Capra hircus

source_name: Ear marginal tissue

extract_protocol:
Total RNA was isolated from in vitro fertilization (IVF) goat embryos at the two-cell and eight-cell stages and somatic cell nuclear transfer(SCNT) 8-cell embyos. We used the Qubit® RNA Assay Kit and Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) to detect RNA concentration. RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was employed for RNA integrity evaluation, and SMART-SeqTM v4 UltraTM Low RNA Kit for Sequencing (Clontech) was used to obtain the amplified cDNA in accordance with the manufacturer’s instructions.
The Covaris system sheared the cDNA samples prior to library preparation. Moreover, sequencing libraries (IVF-2c  IVF-8c and SCNT-8c) were generated using NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, USA) in accordance with the manufacturer’s instructions, and index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was conducted on a cBot Closter Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) in accordance with the manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina HiseqTM 2500 platform, and 125-bp paired-end reads were generated.

value: Ear marginal tissue

tag: cell type

value: GFFs cells

value: Control

value: transfected with pcDNA3.1 using Lipofectamine 3000


title: D13_Aggrewell

description:
Sample 11
Raw_Counts_All_Samples.csv


title: AB11421


title: AB11334


title: Control_RNAseq C1


title: FAH3F

description: sampled at high temperature point after 6 fluctuation cycles during adult stage


title: SCNT_8c_RNAseq

source_name: early embryo

value: early embryo

value: embryo

value: somatic cell nuclear transfer

value: somatic cell nuclear transfer 8-cell embyos


title: Over3720_RNAseq Over37202

value: Overexpress

value: transfected with pcDNA3.1(+)-lncRNA3720 using Lipofectamine 3000


title: IVF_8c_RNAseq

value: in vitro fertilization

value: in vitro fertilization 8-cell embyos


title: D94_Aggrewell

description:
Sample 12
Raw_Counts_All_Samples.csv


title: FAH2F


title: FAH4F


title: 6F_Aggrewell

description:
Sample 10
Raw_Counts_All_Samples.csv


title: AB10170

source_name: Peripheral blood

value: Blood


title: 6D_Alg

description:
Sample 17
Alg_Expression_raw_counts.csv

value: Alginate Group


title: FAH3M

value: fluctuating

value: male


title: 6D_Aggrewell

description:
Sample 9
Raw_Counts_All_Samples.csv


title: FAH2M

value: adult


title: AB10168

value: Skin


title: AB10169


title: IVF_2c_RNAseq

value: in vitro fertilization 2-cell embyos


title: CLL4

description: sampled at low temperature point after 6 fluctuation cycles during larval stage

value: control

value: unknown

value: larvae


title: E87_2D

description:
Sample 7
Raw_Counts_All_Samples.csv


title: AB10167

source_name: Lung

value: Lung


title: 6A_Aggrewell

description:
Sample 8
Raw_Counts_All_Samples.csv


title: AB10166


title: CLL3


title: CLL2


title: D13_2D

description:
Sample 4
Raw_Counts_All_Samples.csv


title: FAH1M


title: AB10165


title: FAH1F

value: female


title: AB10163


title: AB10164


title: CLH4

description: sampled at high temperature point after 6 fluctuation cycles during larval stage


title: 6F_2D

description:
Sample 3
Raw_Counts_All_Samples.csv


title: CLL1


title: CLH3


title: E75_2D

description:
Sample 6
Raw_Counts_All_Samples.csv


title: 6D_2D

description:
Sample 2
Raw_Counts_All_Samples.csv


title: AB10162


title: D94_2D

description:
Sample 5
Raw_Counts_All_Samples.csv


title: CLH1


title: 6A_2D

description:
Sample 1
Raw_Counts_All_Samples.csv


title: CLH2


title: AB10161


title: PDX366 ISL2 KO Rep2

city: Chicago

first: Meric

last: Kinali

address: Robert Lurie Biomedical research Building 303 E Superior St

department: Ob/gyn

country: USA

institute: Northwestern University

data_processing:
RNA-Seq data werealigned to the human reference genome (hg19) using HISAT23(v. 2.1.0)with the default paired-end mode settings.
The resulting sam files were sorted by the read name and converted to bam file using samtools 4(v. 1.9) sortcommand.Then the bam files were sorted by mapping position and indexed using corresponding samtools commands.
RNA-Seq data were quantified against gencode (v27lift37) annotation using Stringtie 5(v. 1.3.4d)withthe default settings
Genome_build: hg19
Supplementary_files_format_and_content: GTF files

source_name: PDX-derived cell line

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen #74104) by following manufacturer's instructions. mRNA was isolated by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs # 7490S).
RNA-Seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs # E7420S) by following the manufacturer's instructions.

value: Pancreas


title: CAL8F

description: sampled at low temperature point after 12 fluctuation cycles during adult stage


title: AB10157


title: TAC KO biological rep 2

type: RNA

city: Albany

first: Ben

last: Boivin

state: NY

address: 257 Fuller road

institute: SUNY Polytechnic Institute

description: Heart ventricles

hyb_protocol: Samples were hybridized by Genome Quebec using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes  Hybridize 16 hours at 48° at 60rpm

scan_protocol: Hybridized target cRNA was stained with streptavidin phycoerythrin and arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488 nm

data_processing: Differential analysis was performed using LIMMA, a linear model fit to each gene separately. Normalized expression values were reported, together with expression values centered in reference to a specific control group. A heatmap was generated where Euclidean distance was used for hierarchical clustering of miRNA hits.

label: biotin

organism: Mus musculus

source_name: Heart KO TAC 4w

label_protocol: Samples were processed by Genome Quebec using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA 4.0 according to the manufacturer's instructions

growth_protocol: hearts harvested from 8w mice

extract_protocol: Hearts were harvested and ventricles were rapidly removed, snap-frozen in liquid N2, and stored at -80 C. Ventricles were pulverized under liquid N2 and total RNA was extracted using Trizol

treatment_protocol: 4w transaortic constriction to induce cardiac hypertrophy

tag: age

value: 8 weeks

value: Heart

value: PTP1B cKO


title: PDX366 Parental Rep2


title: AB10160


title: CAL8M


title: TAC KO biological rep 3

description: Heart ventricles


title: AB10159


title: PDX366 ISL2 KO Rep1


title: CAL7F


title: AB10158


title: mPanc96 ISL2 KO Rep2

source_name: PDAC cell line


title: TAC WT biological rep 1

description: Heart ventricles

source_name: Heart WT TAC 4w

value: wild-type


title: TAC WT biological rep 3

description: Heart ventricles


title: TAC WT biological rep 2

description: Heart ventricles


title: TAC KO biological rep 1

description: Heart ventricles


title: Sham KO biological rep 1

description: Heart ventricles

source_name: Heart KO Sham 4w


title: Sham KO biological rep 3

description: Heart ventricles


title: AB10155


title: CAL7M


title: m2_relapse_tumor1

city: Stanford

first: Michael

middle: F.

last: Clarke

state: CA

address: 265 Campus Dr

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

data_processing:
we used the public server at usegalaxy.org to analyze the data
sequence quality control was done multiple times using FASTQC  and MultiQC
Trim Galore! to trim the reads, HISAT2 to map reads to the mm10 reference genome, featureCounts to count the aligned reads, limma-voom to filter out lowly expressed genes and provides information on differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts and and differentially expression in genes between primary and relapse tumors

source_name: mouse mammary tumor, relapse tumor

growth_protocol: All mice used for this study were maintained at the Stanford Animal Facility in accordance with the guidelines of the animal care use committee.

extract_protocol:
Tumor cells were sorted using FACS directly into RNAprotect. RNA was extracted using the RNeasy micro kit (catalog #74004, Qiagen), according to manufacturer’s instructions.
At least 300 ng RNA was shared for input. Library preparation, sequencing, and initial quality control was performed by Novogene (Beijing, China). Briefly, mRNA was enriched using oligo(dT) beads followed by library generation using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB), according to manufacturer’s instructions. To allow for sequencing different samples at the same time, adaptor sequences were added to each library.
RNA sequencing; NEBNext® UltraTM RNA Library Prep Kit for Illumina®

treatment_protocol: Mice bearing tumors were euthanized and tumors were resected. Fluorescent status tumor was confirmed under the microscope. Small chunks were saved in 4% PFA exchanged for 70% EtOH the next day for immunohistochemistry. Remainder of the tumor was was mechanically dissociated and digested in DMEM/F12 (catalog #12634028, Gibco) with collagenase and hyaluronidase (catalog #07912, STEMCELL Technologies Inc.) and DNAse I (Catalog #LS002139, Worthington) for 2.5 hr with gentle pipetting every 30 min. The remainder of the protocol has previously been described (Prater 2013 Methods Mol Biol) with minor revisions. In short, after lysing red blood cells for 5 min in ACK (catalog #BW10548E Lonza), tumor cells were treated for 5 min with pre-warmed 0.25% Trypsin-EDTA (catalog #25-510, GenClone), followed by pre-warmed dispase (catalog #07913, STEMCELL Technologies Inc.) mixed with DNAse I (catalog #LS002139, Worthington) for 2 min. Next, cells were filtered through a 40 μm mesh, washed and resuspended in HBSS (catalog #21022CV, Corning) + 2% FBS (catalog #FB-01, Omega Scientific) + PSA (catalog #15240112, Gibco).

tag: strain

value: mammary tumor

value: Krt14-Cre mT/mG Trp53f/f MMTV-rtTA TetO-KrasG12D


title: Sham WT biological rep 3

description: Heart ventricles

source_name: Heart WT Sham 4w


title: Sham KO biological rep 2

description: Heart ventricles


title: PDX366 Parental Rep1


title: AB10156


title: mPanc96 ISL2 KO Rep1


title: m2_primary_tumor2

source_name: mouse mammary tumor, primary tumor


title: m2_primary_tumor1


title: CAL6F


title: CAL6M


title: AB10154


title: AB10153

value: Blood


title: Sham WT biological rep 2

description: Heart ventricles


title: m2_relapse_tumor2


title: Sham WT biological rep 1

description: Heart ventricles


title: AB10152


title: CAL5F


title: CAL5M

value: male


title: mPanc96 WT Rep1


title: mPanc96 WT Rep2


title: m1_relapse_tumor1


title: m1_relapse_tumor2


title: CAL4M

description: sampled at low temperature point after 6 fluctuation cycles during adult stage

value: adult


title: m1_primary_tumor2


title: AB10149


title: CAL4F


title: AB10151


title: m1_primary_tumor1


title: AB10150


title: AB10148


title: AB10147


title: CAL2M


title: CAL3M


title: CAL2F


title: AB10145

value: Skin


title: AB10146


title: CAL3F


title: CAL1F


title: JR20878

city: Houston

first: Swarnima

last: Singh

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Library strategy: TCR-seq
scRNA-seq reads were mapped to the mouse genome(mm10) and transcripts were quantified using CellRanger V3.0.2 using default parameters.
scTCR-seq(VDJ) reads were mapped and alligned to the GRCm38 v2.2.0 vdj genome assembly available from 10X Genomics using CellRanger V3.0.2
Genome_build: mm10 for scRNA-seq and GRCm38 for scTCR-seq
Supplementary_files_format_and_content: For scRNA-seq, the sparse matrix of the filtered feature-barcode output from “cellranger count” run in Market Exchange Format (MEX) were compressed into a zipped tarball (tar.gz). Specifically, it contains three files: feature names, barcode sequences, and matrix of three columns with the first two column corresponding to the index of feature and barcode while the third column being the gene expression value. For scTCR-seq, high-level and detailed annotations of each contig output from “cellranger vdj” in comma-separated values (CSV) format for all of the samples were combined

source_name: Mammary Tumors

extract_protocol: Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell, 96 rxns PN-1000071 for scTCR-seq and Chromium Single Cell 5’ Library & Gel Bead Kit, 16 rxns PN-1000006 for scRNA-seq

treatment_protocol: 3 week treatment course with cyclophosphamide and pexidartinib

tag: library type

value: VDJ

value: Balb/c

value: Mammary tumor

value: CD45+ Immune Cells

tag: treatment status

value: Treated


title: JR20879


title: 16802


title: 17742


title: AB10143


title: AB10144


title: JR20877

data_processing:
scRNA-seq reads were mapped to the mouse genome(mm10) and transcripts were quantified using CellRanger V3.0.2 using default parameters.
scTCR-seq(VDJ) reads were mapped and alligned to the GRCm38 v2.2.0 vdj genome assembly available from 10X Genomics using CellRanger V3.0.2
Genome_build: mm10 for scRNA-seq and GRCm38 for scTCR-seq
Supplementary_files_format_and_content: For scRNA-seq, the sparse matrix of the filtered feature-barcode output from “cellranger count” run in Market Exchange Format (MEX) were compressed into a zipped tarball (tar.gz). Specifically, it contains three files: feature names, barcode sequences, and matrix of three columns with the first two column corresponding to the index of feature and barcode while the third column being the gene expression value. For scTCR-seq, high-level and detailed annotations of each contig output from “cellranger vdj” in comma-separated values (CSV) format for all of the samples were combined

value: GEX


title: CAH8M

value: control


title: CAH8F

value: female


title: AB10142


title: CAH7M


title: JR20876


title: metastasis, sample 7

type: genomic

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Data from a metastasis of the left adrenal gland

hyb_protocol: DNA samples were hybridized to Agilent Human Genome CGH microarray 180K (Agilent Technologies, Santa Clara, CA, USA). Oligonucleotide array-CGH was performed using the standard version of the manufacturer’s instructions. Microarrays were scanned using the Agilent scanner G2565BA. Images were extracted using Agilent Feature Extraction software. Data were normalized using the printtiploess function implemented in the snapCGH package.

scan_protocol: Chromosomal imbalances of each sample were detected using the DNAcopy function implemented in snapCGH. To allow the direct comparison of all samples, the resulting chromosomal areas were combined to define the smallest non-overlapping chromosomal (SNOC) regions of deletions or amplifications. The SNOC regions were refined by eliminating those associated with less than five probes. In addition, if two contiguous probes belonging to the same SNOC region were separated by more than one million nucleotides the region was fragmented. Finally, gain and/or loss of those resulting chromosomal regions were further estimated for each sample by calculating the median of the normalized log2-ratios of their related probes.

data_processing: In order to classify samples based on both array-CGH and transcriptomic data, we used the multiple factor analysis (MFA) function implemented in the FactoMineR package (6). This method is an extension of the Principal Component Analysis (PCA) and allows studying tables in which individuals (samples) are described by several groups of (quantitative and/or qualitative) variables; i.e. SNOC regions for array-CGH data and gene expression for transcriptomic data.

molecule: genomic DNA

source_name: metastasis, left adrenal gland

label_protocol: standard Agilent prototocol

extract_protocol: Total RNA was extracted from biological samples using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions with a maximum of 30 mg frozen tissue.

treatment_protocol: no treatment

tag: type

value: tumor tissue

tag: organ

value: adrenal gland

source_name: human DNA

value: normal tissue


title: metastasis, sample 6

description: Data from a metastasis of the right adrenal gland

source_name: metastasis, right adrenal gland


title: 17746_HKCJVDMXX

tag: tissue


title: metastasis, sample 5


title: metastasis, sample 9


title: AB10141

source_name: Forearm skin

tag: selection marker


title: AB10140

tag: patient id


title: 17746_HFLJYDRXX


title: metastasis, sample 8


title: metastasis, sample 4


title: CAH6M

source_name: Whole organism


title: AB10139


title: CAH7F


title: metastasis, sample 3


title: CAH6F


title: 16805

value: Untreated


title: metastasis, sample 2

description: Data from tumor thrombus of the vena cava

source_name: tumor thrombus

value: thrombus


title: AB10138


title: primary tumor, sample 3

description: Data from primary tumor of a clear cell renal cell carcinoma

source_name: primary tumor, right kidney

value: kidney


title: primary tumor, sample 5


title: metastasis, sample 1


title: primary tumor, sample 4


title: primary tumor, sample 2


title: Intravascular fraction of spleen ILCs [SIVP1]

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina BCL to FASTQ file converter (bcl2fastq) v2.20.0.422
Cellranger Pipeline 3.0.1
Assembly: GRCh38
Supplementary files format and content: 10X Genomics .h5 file (contains valid cell barcodes, features, and reads)

source_name: Spleen ILCs from MISTRG humanized mice

growth_protocol: Spleen cells were isolated from two months old MISTRG mice that were irradiated and transplanted with human CD34+ HSPCs from umbilical cord blood. To obtain sufficient cells, spleen cells were pooled from ten MISTRG mice, engrafted with three pooled batches of human CD34+ cells to reduce the impact of HSPC donor variability.

extract_protocol:
Further processing of sorted ILCs (GEM generation, barcoding, cleanup, cDNA amplification) were done using reagents and protocol from 10x Genomics Chromium Single Cell 3' Reagent kit v2
Library construction was done using protocol and reagents from 10x Genomics Chromium Single Cell 3' Reagent kit v2

treatment_protocol: HSPC-engrafted MISTRG mice were injected intravenously (IV) with 2 μg of phycoerythrin (PE)-conjugated anti human CD45 antibody (clone HI30) 5 minutes before spleen harvest without any prior perfusion. Spleens were mechanically dissociated with a syringe plunger before passing through a 70 µm filter to obtain a single cell suspension before cell sorting. Human ILCs were then purified as live CD45+CD127+CD94-CD3-TCRab-Lin-CD34- lymphocytes and divided into intravascular (IV-CD45-PE+) and extravascular (IV-CD45-PE-) ILCs. Lineage (Lin) markers included CD11c, CD14, CD19, CD123, FceRI.

tag: cell population

value: Live human CD45+CD127+CD94-CD3-TCRab-Lin-CD34- IV-CD45-PE+ lymphocytes

tag: host strain

value: MISTRG mice


title: CAH5M

value: male

value: adult


title: Gao2

value: Balb/c


title: Tissue (extravascular) fraction of spleen ILCs [SIVN1]

value: Live human CD45+CD127+CD94-CD3-TCRab-Lin-CD34- IV-CD45-PE- lymphocytes


title: CAH4M


title: primary tumor, sample 1


title: AB10137

source_name: Lung

value: Lung


title: AB10136

value: Skin


title: 16800

value: GEX

value: Mammary tumor

value: CD45+ Immune Cells


title: CAH4F

value: control

value: female


title: CAH3M


title: BNI-FNS-51

city: beijing

first: zhao

last: fu

address: No. 6 Tiantan Xili Dongcheng District

institute: Beijing Neurosurgical Institute

data_processing:
Illumina Casava1.7 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 Million of library size (FPKM) were calculated using a protocol. 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.
hg38
Genome_build: tab-delimited text files include FPKM values for each Sample .
Supplementary_files_format_and_content: Matrix table with raw gene abundance measurements (FPKM) for every gene and every sample

source_name: cell line

extract_protocol:
Primary  tumour and PDX tumour  flash frozen on dry ice, and RNA was harvested using Trizol reagent. VAHTS Stranded mRNA-seq Library Prep Kit for Illumina®(Cat#NR602-02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue/cell type

value: cell

tag: germline mutation

value: NF2 LOH


title: BNI-VS-52


title: BNI-VS-50


title: CAH5F

tag: treatment

tag: Sex


title: Gao1

value: Untreated


title: PDX-NF2-FNS-05

source_name: PDX

value: xenografts


title: AB10133


title: AB10134


title: AB10135

source_name: Peripheral blood

value: Blood


title: PDX-NF2-VS-04


title: AB10131


title: AB10132


title: CAH2M

tag: timepoint

tag: lifestage


title: PDX-NF2-VS-02


title: CAH2F


title: AB10130


title: NF2-FNS-05

source_name: primary NF2-associated schwannoma

value: tumor tissue


title: CAH1M

value: male


title: AB10129


title: NF2-VS-04


title: CAH1F

value: adult


title: NF2-VS-02


title: CAH3F


title: AB10128


title: Hkh-2_2

status: Public on Apr 03 2022

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

country: United Kingdom

institute: The Francis Crick Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were processed using RMA implemented in the affy bioconductor package

source_name: HCT116 isogenic cell line KRASwt (homologous recombination)

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 1% L-glutamine

extract_protocol: RNeasy Kit

treatment_protocol: Cells were treated with 25 ng/ml docycycline or vehicle control for 3 days or 6 days

tag: cell line


title: Hkh-2_1

value: HCT116 isogenic cell line KRASwt (homologous recombination)


title: Hke3_3


title: HCT116_1

source_name: parental HCT116 KRASG13D

value: parental HCT116 KRASG13D


title: HCT116_sh-KRAS_1e+5_veh_d6_2

source_name: sh-KRAS-inducible HCT116, 6-day vehicle

value: sh-KRAS-inducible HCT116


title: HCT116_sh-KRAS_1e+5_dox_d6_1

source_name: sh-KRAS-inducible HCT116, 6-day doxycycline


title: HCT116_3


title: HCT116_sh-KRAS_1e+5_veh_d6_3


title: Hke3_1


title: Hke3_2


title: HCT116_sh-KRAS_1e+5_dox_d6_3


title: HCT116_2


title: HCT116_sh-KRAS_1e+5_veh_d6_1


title: Hkh-2_3


title: HCT116_sh-KRAS_5e+5_veh_d3_2

source_name: sh-KRAS-inducible HCT116, 3-day vehicle


title: HCT116_sh-KRAS_5e+5_veh_d3_1


title: HCT116_ctl_5e+5_veh_d3_2

source_name: HCT116, 3-day culture


title: HCT116_ctl_5e+5_dox_d3_2

source_name: HCT116, 3-day doxycyline


title: HCT116_sh-KRAS_5e+5_veh_d3_3


title: HCT116_sh-KRAS_5e+5_dox_d3_1

source_name: sh-KRAS-inducible HCT116, 3-day doxycycline


title: HCT116_ctl_5e+5_veh_d3_3


title: HCT116_sh-KRAS_1e+5_dox_d6_2


title: HCT116_sh-KRAS_5e+5_dox_d3_3


title: HCT116_sh-KRAS_5e+5_dox_d3_2


title: HCT116_ctl_5e+5_veh_d3_1


title: HCT116_ctl_5e+5_dox_d3_3


title: HCA-7 cells, Pcad sgRNA3, rep3

city: Cleveland

first: Pranab

last: Mukherjee

state: OH

address: 9500 Euclid Avenue

department: Infection and Immunity

institute: Cleveland Clinic

data_processing:
Paired-ended reads were checked for quality with FastQC (v0.11.3) [ref: http://www.bioinformatics.babraham.ac.uk/projects]
Reads were aligned using Rsubread::Subread
Gene counts were determined by the number of uniquely aligned, unambiguous reads (Subread: featureCounts, v1.5.2) and annotated by alignment to the human genome (GRCh38.p10 using Gencode Release 27 annotations).
Raw counts were loaded into R (v3.6.2 and 4.1.2, R Core Team 2021), and Counts were filtered to exclude transcripts that were expressed at low levels (counts per million reads mapped [CPM] < 1)
Differential expression (DE) analysis was conducted using R packages edgeR and Limma, subsequent analyses were performed using standard R packages (tidyverse, dunn.test, EnhancedVolcano, clusterProfiler)
Assembly: GRCh38.p10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human colonic epithelial cells

growth_protocol: All cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), HEPES, non-essential amino acids, and penicillin-streptomycin antibiotic, at 37 degree, 5% CO2 incubator.

extract_protocol:
RNA was isolated using the Qiagen Mini RNeasy Kit
RNA-SEQ libraries were generated using Illumina TruSEQ kits following the manufacturer’s protocol

treatment_protocol: Stable P-cadherin-depleted IEC cells were generated by transduction with P-cadherin sgRNAs containing lentiviruses and subsequent puromycin selection (5 μg/ml) for 7 days. Likewise, control IEC were generated by transduction with control sgRNA containing lentivirus and puromycin selection.

value: Pcad sgRNA3

tag: genotype

value: P-cadherin knockdown

value: colon

tag: cell type

value: Primary human intestinal epithelial cells


title: HCA-7 cells, Pcad sgRNA1, rep4

value: Pcad sgRNA1


title: HCA-7 cells, Pcad sgRNA3, rep4


title: HCT116_ctl_5e+5_dox_d3_1


title: VCaP siAR plus siOPRK1 replicate4

city: Kyoto

first: Yuki

last: Makino

address: 54 Shogoinkawahara-cho, Sakyo-ku

department: Urology

country: Japan

institute: Kyoto University Graduate School of Medicine

description:
Biological replicate 4 of 4. VCaP treated with siAR plus OPRK1 (combo-siRNA).
VCaP-raw.data.xlsx

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing:
Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array.
Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

source_name: prostate cancer cells

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

growth_protocol: VCaP was cultured in DMEM, supplemented with 10% fetal bovine serum (FBS), 12.5 mM HEPES, penicillin and streptomycin at 37°C in humidified air containing 5% CO2. AIVCaP was established from the parental VCaP cultured in phenol-red-free DMEM medium with 8% CSFBS plus 2% FBS.

extract_protocol: Total RNA was extracted using an RNeasy Mini kit (QIAGEN, Hilden, Germany). RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: For in vitro siRNA silencing, the cells were transfected with specific siRNA oligos using Lipofectamine RNAiMAX (Thermo Fisher Scientific K.K., Tokyo, Japan) according to the manufacturer’s instruction.

value: VCaP (CRL-2876)

value: prostate cancer cells

value: siAR plus siOPRK1


title: VCaP siAR plus siOPRK1 replicate3

description:
Biological replicate 3 of 4. VCaP treated with siAR plus OPRK1 (combo-siRNA).
VCaP-raw.data.xlsx


title: HCA-7 cells, Pcad sgRNA1, rep3


title: HCA-7 cells, Pcad sgRNA1, rep1


title: HCA-7 cells, control,, rep3

value: control


title: HCA-7 cells, Pcad sgRNA1, rep2


title: VCaP siAR alone replicate4

description:
Biological replicate 4 of 4. VCaP treated with siAR alone (single siRNA).
VCaP-raw.data.xlsx

value: siAR alone


title: VCaP siAR plus siOPRK1 replicate1

description:
Biological replicate 1 of 4. VCaP treated with siAR plus OPRK1 (combo-siRNA).
VCaP-raw.data.xlsx


title: VCaP siAR plus siOPRK1 replicate2

description:
Biological replicate 2 of 4. VCaP treated with siAR plus OPRK1 (combo-siRNA).
VCaP-raw.data.xlsx


title: VCaP siAR alone replicate3

description:
Biological replicate 3 of 4. VCaP treated with siAR alone (single siRNA).
VCaP-raw.data.xlsx


title: AIVCaP siAR plus siOPRK1 replicate1

description: Biological replicate 1 of 4. AIVCaP treated with siAR plus OPRK1 (combo-siRNA).

growth_protocol: AIVCaP was established from the parental VCaP cultured in phenol-red-free DMEM medium with 8% CSFBS plus 2% FBS.

value: AIVCaP (androgen-independent subline of VCaP (CRL-2876))


title: AIVCaP siAR plus siOPRK1 replicate4

description: Biological replicate 4 of 4. AIVCaP treated with siAR plus OPRK1 (combo-siRNA).


title: AIVCaP siAR plus siOPRK1 replicate3

description: Biological replicate 3 of 4. AIVCaP treated with siAR plus OPRK1 (combo-siRNA).


title: VCaP siAR alone replicate1

description:
Biological replicate 1 of 4. VCaP treated with siAR alone (single siRNA).
VCaP-raw.data.xlsx


title: AIVCaP siAR plus siOPRK1 replicate2

description: Biological replicate 2 of 4. AIVCaP treated with siAR plus OPRK1 (combo-siRNA).


title: AIVCaP siAR alone replicate3

description: Biological replicate 3 of 4. AIVCaP treated with siAR alone (single siRNA).


title: HCA-7 cells, control,, rep2


title: HCA-7 cells, control,, rep1


title: HCA-7 cells, Pcad sgRNA3, rep2


title: HCA-7 cells, Pcad sgRNA3, rep1


title: AIVCaP siAR alone replicate1

description: Biological replicate 1 of 4. AIVCaP treated with siAR alone (single siRNA).


title: AIVCaP siAR alone replicate4

description: Biological replicate 4 of 4. AIVCaP treated with siAR alone (single siRNA).


title: AIVCaP siAR alone replicate2

description: Biological replicate 2 of 4. AIVCaP treated with siAR alone (single siRNA).


title: HCA-7 cells, control,, rep4


title: VCaP siAR alone replicate2

description:
Biological replicate 2 of 4. VCaP treated with siAR alone (single siRNA).
VCaP-raw.data.xlsx


title: donor_22549_MSA

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

data_processing:
Reads alignment: STAR
Gene level summarization: featureCounts
Normalization: DESeq2
Assembly: GRCh37
Supplementary files format and content: *txt, raw counts by gene and sample

source_name: post-mortem cerebellum (white matter: oligodendrocytes)

extract_protocol:
Oligodendrocytes were stained by using a modified H&E staining protocol adapted from Ordway et al. [49]. A total of 300 oligodendrocytes per sample were captured using Arcturus CapSure Macro LCM Caps (Applied Biosystems) with the following settings: UV speed at 676 um/s and UV current at 2%. RNA was extracted immediately after cell capture using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
Library preparation was carried out using  the SMARTer® Stranded Total RNA-Seq Kit - Pico Input (Clontech/Takara) was used, including the integrated removal of rRNAs

value: Female

tag: age at death

tag: post mortem interval (hours)

tag: diagnosis

value: MSA-P

tag: source

value: New South Wales Brain Tissue Resource Center, Sydney, Australia


title: donor_22699_MSA

value: Male

value: MSA-C


title: donor_22514_MSA


title: donor_SU548_control


title: donor_03.63_control

value: Brain and Body Donor Program, Sun City, Arizona


title: donor_98.34_control


title: donor_12.18_MSA

value: MSA


title: donor_22494_MSA


title: donor_99.02_control


title: donor_04.56_MSA


title: donor_06.21_control


title: donor_SU720_control


title: donor_P82_10_CTRL

data_processing:
Read alignment: STAR
Gene level summarization: featureCounts
Normalization: DESeq2
Assembly: GRCh37
Supplementary files format and content: *txt, raw counts by gene and sample

source_name: post-mortem cerebellum (white matter)

extract_protocol:
Total DNAse-treated RNA was extracted in TRI Reagent (Zymo, #R2050) from ~ 5 mg of tissue using Rino Tubes (Next Advance , #13503) with one 0.1 mL scoop of Stainless Steel Beads 0.9 – 2.0 mm blend RNase Free (Next Advance, #SSB14B), Bullet Blender Gold (Next Advance, model BB24-AU), and Zymo Direct-zol-96 RNA (#R2054) utilizing the kit’s DNase I digestion step. Extracted RNA was then assayed on an Agilent TapeStation 4200 and Agilent RNA ScreenTape (#5067-5576). The mean RNA integrity number equivalent (RINe) and concentration for MSA cases were 3.42 and 77.6ng/μl, and Control cases were 3.59 and 64.76 ng/μl, respectively
Following TempO-Seq Assay User Guide (version 2.0), 1μl of the extracted RNA from each of the 96 samples processes separately into the TempO-Seq Human Whole Transcriptome Assay (BioSypder, index set C, #200615).  This assay is based on a proprietary 3’ mRNA capture protocol, using probes for protein-coding mRNA. Thus, extracted RNA was not rRNA depleted or poly(A)-selected.  A total of sixteen cycles of PCR, on a QuantStudio 6 Flex Instrument (ThermoFisher), were used to amplify the 96 ligated samples. The 96 samples were pooled into one library and then purified using NucleoSpin Gel and PCR clean-up kit (Macherey-Nagel, #740609). The final library was sequenced according to the TempO-Seq Assay User Guide (version 2.0, 50 bp read1 x 9 bp index1 x 9 bp index2) on the NextSeq 500/550 High Output v2 kit (Illumina, 75 cycles, #FC-404-2005) on a NextSeq 500 (Illumina), at a final concentration of 1.6 pM with 2% PhiX. For sequencing, the BioSpyder TempO-Seq Custom Index 1 Sequencing Primer was used at 0.3 μM final concentration diluted in HT1 buffer (illumina, see nextseq-custom-primers-guide-15057456-01). Final library concentration was determined via the mean of three replicates using the Qubit dsDNA BR Assay (invitrogen, #Q32853) on a Qubit 2 Fluorometer (Invitrogen).

tag: clinical diagnosis

value: HC

tag: neuropathological diagnosis

value: Queen Square Brain Bank for Neurological Disorders (London, UK)


title: donor_P75_10_CTRL


title: donor_P8_12_MSA


title: donor_P76_6_CTRL


title: donor_P91_10_MSA


title: donor_P75_8_CTRL


title: donor_P79_9_MSA


title: donor_P90_10_MSA


title: donor_P75_4_MSA


title: donor_P78_6_CTRL


title: donor_P87_8_MSA


title: donor_P73_6_CTRL


title: donor_P74_7_MSA


title: donor_P74_8_MSA


title: donor_P72_7_CTRL


title: donor_P72_11_MSA


title: donor_P70_6_MSA


title: donor_P66_12_MSA


title: donor_P66_10_CTRL


title: donor_P64_3_CTRL


title: donor_P59_10_MSA


title: donor_P64_10_MSA


title: donor_P61_9_CTRL


title: donor_P51_5_MSA


title: donor_P64_11_CTRL


title: donor_P67_10_CTRL


title: donor_P57_7_MSA


title: donor_P51_8_CTRL


title: donor_P5_13_CTRL


title: donor_P50_6_CTRL


title: donor_P66_11_CTRL


title: donor_P48_10_MSA


title: donor_P44_4_MSA


title: donor_P53_3_MSA


title: donor_P43_13_CTRL


title: donor_P55_11_MSA


title: donor_P69_8_MSA


title: donor_P45_12_MSA


title: donor_P47_11_CTRL


title: donor_P45_4_CTRL


title: donor_P48_6_CTRL


title: donor_P50_12_MSA


title: donor_P43_12_MSA


title: donor_P58_10_CTRL


title: donor_P58_7_MSA


title: donor_P48_7_CTRL


title: donor_P43_9_MSA


title: donor_P41_9_CTRL


title: donor_P39_8_MSA


title: CAL1M

description: sampled at low temperature point after 6 fluctuation cycles during adult stage

source_name: Whole organism

value: male

value: adult


title: donor_P31_11_CTRL


title: donor_P40_12_MSA


title: donor_P31_4_MSA


title: donor_P29_12_CTRL


title: donor_P34_5_CTRL


title: donor_P32_9_CTRL


title: donor_P36_14_CTRL


title: donor_P42_12_MSA


title: donor_P28_9_MSA


title: donor_P34_2_MSA


title: donor_P16_7_CTRL


title: donor_P19_3_MSA


title: donor_P18_3_CTRL


title: donor_P38_2_MSA


title: donor_P22_6_MSA


title: donor_P14_12_MSA


title: donor_P22_13_CTRL


title: donor_P26_5_MSA


title: donor_P39_5_MSA


title: donor_P13_11_MSA


title: donor_P38_8_MSA


title: donor_P11_17_CTRL


title: donor_P24_8_MSA


title: donor_P25_9_MSA


title: donor_P05_11_MSA


title: donor_P19_5_MSA


title: donor_P05_9_MSA


title: donor_P11_6_MSA


title: donor_P05_5_CTRL


title: donor_P03_8_MSA


title: donor_P04_5_CTRL


title: donor_P01_11_CTRL


title: donor_C9_99_CTRL


title: Donor_78_IL15_CCR5+_cells

city: St. Louis

first: Yuhao

last: Li

state: MO

address: 425 S. Euclid Ave, BJCIH 7403

department: Department of Medicine

institute: Washington University School of Medicine

data_processing: Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a (Dobin et al., 2013). Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5 (Liao et al., 2014). Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2 (Wang et al., 2012). Counts were first filtered by removing genes where greater than half of the samples had Counts per million (cpm) values less than 1 using python version 3.8.5.

source_name: CD4+ T cells

growth_protocol: CD4+ T cells were purified from the buffy coat of uninfected donors by Ficoll gradient separation followed by negative selection with MojoSort™ Human CD4 T Cell Isolation Kit (Biolegend) or EasySep™ Human CD4+ T Cell Isolation Kit (Stem Cell Technology).  Purified CD4+ T cells (106 cells/mL) were cultured in RPMI 1640 medium supplemented with 10% FCS, penicillin (100 unit/mL) and streptomycin (100 µg/mL).

extract_protocol:
CCR5+ and CCR5- CD4+ T cells were sorted, and total RNA was extracted using Direct-zol RNA kit (Zymo Research). The cDNA library was prepared using strand-specific RNA-sequencing protocols. Samples were prepared according to library kit manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate activated cells, CD4+ T cells were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies at 1μg/mL (BioLegend) for 3 days in the presence of 20 ng/mL IL-2. Stimulated CD4+ T cells were cultured with 20 ng/mL IL-7 or IL-15. Fresh medium was provided every 3 days to keep the cell densities at 1-2*106 cells/mL.  Activated blood CD4+ T cells were cultured with the presence of IL-15 for 6 days.

tag: donor


title: donor_C8_98_CTRL


title: 8-EtOH-Male

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Partek Flow
Sequence reads were trimmed to remove adaptor sequence/low-quality sequence using Partek Flow (CutAdapt)
Trimmed sequence reads were mapped to miRbase22 mature sequences from RGSC5.0/rn5 using PartekFlow
Raw read counts quantified using PartekFlow
Assembly: RGSC5/0/rn5
Supplementary files format and content: tab-delimited text files include raw read values for each sample

organism: Rattus norvegicus

source_name: brain (right hippocampus)

growth_protocol: Male rats raised in normal environment in accredited housing facility on alternating light/dark cycle.

extract_protocol:
Right hippocampus was dissected from each animal following euthanasia.
RNA was harvested using Trizol plus RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Small RNA protocol, following manufacturer's protocols.

treatment_protocol: Adult male Sprague Dawley rats (n=8 per group, N= 16) were injected with ethanol (4 g/kg) in early adulthood (P70-80) and euthanized 3 hr later.

tag: tissue

value: brain (right hippocampus)

tag: strain

value: Sprague Dawley

tag: time

value: 3 hours post injection

value: EtOH


title: 3-EtOH-Male

tag: treatment


title: 9-Veh-Male

tag: Sex

value: Veh


title: 4-EtOH-Male


title: 24-EtOH-Male


title: 23-EtOH-Male


title: Donor_78_IL15_CCR5-_cells


title: donor_C18_93_CTRL


title: donor_P02_7_MSA


title: Male KO mouse liver 1

city: Miyazaki

first: Koichi

last: Yano

state: Miyazaki

address: 5200 Kihara, Kiyotake

department: Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine

institute: University of Miyazaki

hyb_protocol: Fifteen micrograms of fragmented cRNA from each sample was hybridized to a pre-equilibrated Clariom S mouse microarray chip, which was then washed and stained.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, USA)

data_processing:
Normalization and expression value calculations were performed using Genespring. (Agilent Technologies, Santa Clara, CA, USA). Fold change 1.5 or more related to cell cycle was considered.
Summarization Algorithm: ExonSSTRMAWithoutStabilization

source_name: Male KO mouse liver

label_protocol: Amplification and biotin labeling of fragmented cDNA was performed using the biotin labeling system (WT PLUS Reagent Kit, Thermo Fisher Scientific, Rockford, IL, USA) in duplicate.

extract_protocol: Total RNA was prepared using Trizol (Invitrogen, Carlsbad, CA, USA).

tag: strain background

tag: age

value: 8 weeks

value: liver


title: Donor_77_IL15_CCR5+_cells


title: 20-Veh-Male


title: 16-EtOH-Male


title: Male KO mouse liver 3


title: Male KO mouse liver 2


title: 7-EtOH-Male


title: Donor_77_IL15_CCR5-_cells


title: Male WT mouse liver 3

source_name: Male WT mouse liver

value: WT


title: donor_C3_0_CTRL


title: donor_C1_99_CTRL

value: Female


title: Male WT mouse liver 1


title: 15-EtOH-Male

value: Male


title: 19-Veh-Male


title: Tumor tissue of case 21 [34Ca]

city: Zhengzhou

first: Haiyang

last: Du

state: Henan

address: 156 Jinshui East Road, Zhengzhou, Henan, China

institute: Henan University of Chinese Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tumor tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA was purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany) after passing the quality control. Sample RNA was amplified and labeled using the Low Input Quick Amp LabelingKit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US) and standard procedures for the amplification of mRNA in total RNA. The labeled RNA was purified using the RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

value: Tumor tissue


title: donor_C06_0_CTRL


title: donor_C04_99_CTRL


title: donor_C08_99_CTRL


title: donor_C04_97_CTRL


title: 10-Veh-Male


title: donor_C04_0_CTRL


title: donor_C07_0_CTRL


title: donor_C02_99_CTRL


title: Roots 8mM nitrate at 720 ppm of CO2 replicate 3

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina).
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The reads were assembled using Trinity 2.11.0 (Haas et al., 2013, Nature Protocols 8:1494-512). Contigs lower than 400 pb were eliminated, for the rest of contigs the redundancy was reduced using CD-HIT-EST software (Fu et al., 2012, Bioinformatics 28: 3150-3152).
The final transcriptome was used as the reference for the read mapping that was performed with Bwa-mem2 (Vasimuddin et al., 2019, IPDPS). The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
Assembly: Assembled reference transcriptome
Supplementary files format and content: raw_counts.txt: Tab-delimited text file includes raw counts for each sample. The column id is the sequence identifier.
Supplementary files format and content: Pinaster_CO2_final_a.fasta: Fasta file includes the assembled reference transcriptome.

organism: Pinus pinaster

source_name: Roots

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a luminal intensity of 100 μmol m−2 s−1, a constant temperature of 25 °C and watered twice a week with distilled water.

extract_protocol:
Total root RNA from maritime pine seedlings was isolated following the protocol described by Liao et al. (2004, Preparative Biochemistry & Biotechnology 34: 209-214) and modified by Canales et al. (2012, Frontiers in Plant Science 3: 100). The RNA concentration and purity were determined via spectrophotometry on a Nanodrop ND-1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. RNA quality was also determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK).
RNA sequencing was conducted by aScidea Computational Biology Solutions S.L. sequencing company (Barcelona, Spain). Only RNA samples with a RIN > 7 in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) were used for library preparation. RNA libraries for sequencing were prepared starting with 1 µg of total RNA and using TruSeq RNA kits (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Clustering was performed on a cBot cluster generation system using an Illumina NovaSeq paired-end read cluster generation kit according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). The samples were sequenced on an Illumina NovaSeq 6000 as paired-end reads of 150 bp length.

treatment_protocol: One-month-old maritime pine seedlings were used for this experiment. Pine seedlings were randomly subdivided into three different groups, relocated into forestall seedbeds and irrigated with 80 mL of a solution that contains macro- and micronutrients without any nitrogen source (1.16 mM KCl; 0.63 mM KH2PO4; 0.35 mM MgSO4·7H2O; 0.17 mM CaCl2·H2O; 80 μM EDTA-FeSO4; 25.9 μM H3BO3; 10.2 μM MnCl2·4H2O; 1.3 μM ZnSO4·7H2O; 0.7 μM CuSO4·5H2O; 0.1 μM Na2MoO4·2H2O). After three days of acclimation, the control group was irrigated with 80 mL of water, the second group was supplied with 80 mL of 0.1 mM NH4Cl and the third group was supplied with 80 mL of 3 mM NH4Cl. Root samples were collected before the irrigation and at two different time points after the treatments (2 and 24 hours) and immediately frozen in liquid nitrogen. Ten seedlings were collected and pooled per each sample. This experiment was carried out three independent times.

tag: provenance

value: Segura-Alcaraz

tag: developmental stage

value: 2-month-old seedling

value: Roots

tag: treatment 1

value: Nitrate 8mM

tag: treatment 2

value: CO2 720 ppm

tag: biological replicate


title: Tumor tissue of case 20 [33Ca]


title: CybbKO RPM F4/80low 3

city: St Louis

first: Mary

middle: C

last: Dinauer

state: Missouri

address: 660 South Euclid Ave

department: Pathology & Immunology

institute: Washington University In St Louis

description: No treatment

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies). The extracted signal was  quantile-normalizated using Partek.

source_name: Mouse resident peritoneal macrophage (B220-CD115+ F4/80low MHCIIhigh)

label_protocol: RNA samples were amplified using SIGMA WTA2 RNA amplification system. Amplified cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul). The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes. Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol. cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf

extract_protocol: Qiagen RNAeasy micro plus

tag: genotype

value: CGD

value: Peritoneal lavage

tag: gender


title: CybbKO RPM F4/80low 2

description: No treatment


title: Roots 8mM nitrate at 720 ppm of CO2 replicate 2


title: Tumor tissue of case 12 [17Ca]


title: Tumor tissue of case 9 [12Ca]


title: Tumor tissue of case 17 [25Ca]


title: Roots 8mM nitrate at 720 ppm of CO2 replicate 1


title: CybbKO RPM F4/80high 1

description: No treatment

source_name: Mouse resident peritoneal macrophage (B220-CD115+ F4/80high MHCII-)


title: CybbKO RPM F4/80low 1

description: No treatment


title: Tumor tissue of case 10 [13Ca]


title: WRPM F4/80low 3

description: No treatment


title: Tumor tissue of case 15 [23Ca]


title: CybbKO RPM F4/80high 3

description: No treatment


title: Tumor tissue of case 18 [26Ca]


title: Tumor tissue of case 14 [21Ca]


title: Tumor tissue of case 13 [19Ca]


title: WRPM F4/80low 2

description: No treatment


title: CybbKO RPM F4/80high 2

description: No treatment


title: Tumor tissue of case 19 [28Ca]


title: Tumor tissue of case 16 [24Ca]


title: Tumor tissue of case 11 [16Ca]


title: Male WT mouse liver 2


title: Tumor tissue of case 8 [11Ca]


title: Tumor tissue of case 6 [9Ca]


title: Tumor tissue of case 7 [10Ca]


title: WRPM F4/80low 1

description: No treatment


title: Tumor tissue of case 4 [6Ca]


title: Tumor tissue of case 5 [8Ca]


title: Roots 8mM nitrate at 400 ppm of CO2 replicate 2

value: CO2 400 ppm


title: Roots 8mM nitrate at 400 ppm of CO2 replicate 3


title: Replicate B (sample 10) for d28 KO2 hESC-derived neuronal culture RNA replicates [G95_S10_B_KO2]

city: Cincinnati

first: Bruce

middle: J

last: Aronow

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Four independent culture replicates of immature d7 and mature d28 iN cells were lysed and RNA was extracted using the RNeasy kit (Qiagen). RNA-seq libraries were generated from total RNA using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).
Paired-end sequencing (2 x 150 base-pair reads) was performed using the Illumina Next-seq 500 platform (UMass Amherst Genomics Core).
For d7 samples, raw sequencing reads were processed using in-house RNA-Seq data processing software Dolphin at University of Massachusetts Medical School. Paired reads Fastq files generated from the NextSeq 500 was imported in the Dolphin analysis suite. The FastQ files were subjected to quality check using FastQC. The high quality read pairs first were filtered out using ribosomal RNAs with bowtie2. STAR (2.6.0c) alignment tool was used to align the reads to the reference transcriptome. RSEM (v1.2.28) was used to quantify the expression levels of genes. The reference transcriptome refSeq annotation, UCSC hg19 refGene was used.
For d28 samples, we first built a human + mouse reference (Homo_sapiens GRCh38 v96 and Mus_musculus GRCm38 v96) with a concatenated human-mouse index using the index command in Kallisto (v 0.46.0). d28 RNA-sequencing reads from Fastq files were pseudo-aligned to the concatenated reference genome using the Kallisto quant command and transcripts were assigned to proper species reference. For each Kallisto-processed human-mouse sample, expression matrices of raw count values and TPM (transcript per million) were constructed for human-specific transcripts.
Assembly: We built a human + mouse reference (Homo_sapiens GRCh38 v96 and Mus_musculus GRCm38 v96) with a concatenated human-mouse index using the index command in Kallisto (v 0.46.0).
Supplementary files format and content: d28 RNA-sequencing reads from Fastq files were pseudo-aligned to the concatenated reference genome using the Kallisto quant command and transcripts were assigned to proper species reference. For each Kallisto-processed human-mouse sample, expression matrices of raw count values and TPM (transcript per million) were constructed for human-specific transcripts.

source_name: Human cortical excitatory neurons

growth_protocol: Human induced cortical excitatory neurons were cultured as previously described using forced expression of Ngn2 transcription factor (Zhang et al., 2013, Neuron). All samples were induced into neurons using this method. Day 7 neurons were cultured without mouse glia and Day 28 neurons were cultured with mouse glia from Day 3 of the induction protocol.

extract_protocol:
Rneasy kit (Qiagen) was used to isolate total RNA from all samples. Dnase treatment step was added to remove genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CRISPR/Cas9 mediated gene editing generated two independent cell lines from H1 hESC WT. They were named CASK KO#1 and CASK KO#2. From these cell lines, neuronal induction was performed and samples were collected.

tag: cell type

value: hESC-derived neurons cultured with mouse glia

value: H1 hESC background CASK KO#2


title: Replicate D (sample 12) for d28 KO2 hESC-derived neuronal culture RNA replicates [G95_S12_D_KO2]


title: WRPM F4/80high 3

description: No treatment


title: Replicate C (sample 11) for d28 KO2 hESC-derived neuronal culture RNA replicates [G95_S11_C_KO2]


title: Roots 8mM ammonium at 720 ppm of CO2 replicate 2

value: Ammonium 8 mM


title: Roots 8mM nitrate at 400 ppm of CO2 replicate 1


title: Replicate A (sample 9) for d28 KO2 hESC-derived neuronal culture RNA replicates [G95_S9_A_KO2]


title: Roots 8mM ammonium at 400 ppm of CO2 replicate 3


title: Tumor tissue of case 3 [5Ca]


title: Replicate C (sample 7) for d28 KO1 hESC-derived neuronal culture RNA replicates [G95_S7_C_KO1]

value: H1 hESC background CASK KO#1


title: Roots 8mM ammonium at 720 ppm of CO2 replicate 3


title: Tumor tissue of case 1 [2Ca]


title: Roots 8mM ammonium at 400 ppm of CO2 replicate 1


title: WRPM F4/80high 2

description: No treatment

value: 12 wks


title: Tumor tissue of case 2 [4Ca]


title: WRPM F4/80high 1

description: No treatment

value: WT


title: Roots 8mM ammonium at 720 ppm of CO2 replicate 1


title: Roots 8mM ammonium at 400 ppm of CO2 replicate 2


title: Replicate D (sample 8) for d28 KO1 hESC-derived neuronal culture RNA replicates [G95_S8_D_KO1]


title: Normal tissue of case 19 [28normal]

source_name: Normal tissue

value: Normal tissue


title: Replicate B (sample 6) for d28 KO1 hESC-derived neuronal culture RNA replicates [G95_S6_B_KO1]


title: Normal tissue of case 14 [21normal]


title: Normal tissue of case 17 [25normal]


title: Normal tissue of case 21 [34normal]


title: Normal tissue of case 13 [19normal]


title: Normal tissue of case 16 [24normal]


title: Normal tissue of case 10 [13normal]


title: Stem 8mM nitrate at 720 ppm of CO2 replicate 3

source_name: Stem

value: Stem


title: Normal tissue of case 8 [11normal]


title: Normal tissue of case 18 [26normal]


title: Replicate A (sample 5) for d28 KO1 hESC-derived neuronal culture RNA replicates [G95_S5_A_KO1]


title: Normal tissue of case 12 [17normal]


title: Replicate D (sample 4) for d28 WT hESC-derived neuronal culture RNA replicates [G95_S4_D_WT]

value: H1 hESC background WT


title: Normal tissue of case 7 [10normal]


title: Stem 8mM nitrate at 720 ppm of CO2 replicate 2

value: Segura-Alcaraz


title: Normal tissue of case 6 [9normal]


title: Normal tissue of case 9 [12normal]


title: Stem 8mM nitrate at 720 ppm of CO2 replicate 1

value: 2-month-old seedling


title: Normal tissue of case 15 [23normal]


title: Replicate C (sample 3) for d28 WT hESC-derived neuronal culture RNA replicates [G95_S3_C_WT]


title: Replicate B (sample 2) for d28 WT hESC-derived neuronal culture RNA replicates [G95_S2_B_WT]


title: Stem 8mM nitrate at 400 ppm of CO2 replicate 2


title: Replicate A (sample 1) for d28 WT hESC-derived neuronal culture RNA replicates [G95_S1_A_WT]


title: LEN mutant 3 dpa heart

city: Madison

first: Kwangdeok

last: Shin

state: WI

address: 4451 WISCONSIN INSTITUTE FOR MEDICAL RESEARCH II

institute: University of Wisconsin - Madison

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 using HISAT2
featurecount was used to get count of each gene
Assembly: GRCz11
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: amputated heart

extract_protocol:
Hearts were homogenized immediately after dissection and RNA was extracted using Trizol reagent. .
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ekkwill

value: LEN[delta]/[delta]

value: 3 days post-amputation


title: Stem 8mM nitrate at 400 ppm of CO2 replicate 3

value: Nitrate 8mM


title: Wild type 3 dpa heart

value: LEN+/+


title: Normal tissue of case 4 [6normal]


title: Normal tissue of case 11 [16normal]


title: LEN mutant uninjured heart

source_name: uninjured heart

value: uninjured


title: Stem 8mM ammonium at 720 ppm of CO2 replicate 3

value: CO2 720 ppm


title: Replicate C (sample 11) for d7 KO2 hESC-derived neuronal culture RNA replicates [G29_S11_C_KO2]

value: hESC-derived neurons

value: H1 hESC background CASK KO#2


title: Replicate D (sample 12) for d7 KO2 hESC-derived neuronal culture RNA replicates [G29_S12_D_KO2]


title: Wild type uninjured heart


title: Normal tissue of case 5 [8normal]


title: Replicate B (sample 10) for d7 KO2 hESC-derived neuronal culture RNA replicates [G29_S10_B_KO2]


title: Stem 8mM ammonium at 720 ppm of CO2 replicate 2

value: Ammonium 8 mM


title: Normal tissue of case 20 [33normal]


title: Knockout Ipsilateral [3592 IL KO]

city: Pittsburgh

first: Md Nabiul

last: Hasan

state: PA

address: 3501 Fifth Avenue

department: Neurology

institute: University of Pittsburgh

description: 3592 IL KO

data_processing:
Partek Flow 8.0 platform was used for data analysis
RNA-Seq reads, obtained in FASTQ format, were subjected to sequence quality checks using QA/QC tool of Partek Flow. The reads were mapped against the mouse reference genome mm10 using STAR aligner
Reads were quantified using "Quantify to annotation model (Partek E/M)" tool with the default settings
Differentially expressed genes (DEGs) were identified by comparing gene reads between Ko-IL vs Ctrl-IL and KO-CL vs Ctrl-CL mice derived CD11b+ cells. DEGs were analyzed using Partek GSA algorithm by applying multiple statistical models to each individual gene in order to account for each gene’s varying response to different experimental factors, and differing data distributions.  Genes with adjusted p-value ≤ 0.05 and Log2 fold change ≥ 1.2 or ≤ -1.2 were considered as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with differentially expressed genes (DEGs) for each comparision
Supplementary files format and content: Raw counts

source_name: CD11b+ cells isolated from TBI hemisphere

extract_protocol:
Single cell suspension of microglia/myeloid cells from the ipsilateral and contralateral hemispheres from wild-type and Nhe1-KO brains after 3-days of traumatic brain injury were prepared using Neural Tissue Dissociation Kit (Miltenyi Biotec, Germany) following manufacturers protocol. CD11b+ microglia/myeloid cells were sorted by MACS. Total RNA was extracted using Direct-zol RNA MicroPrep kit (Zymo Research).
Library was prepared using Smart Seq v4 library preparation kit according to manufacturers instructions

value: Brain tissue

value: 8-12 weeks old

value: Tamoxifen


title: w1l

description:
WT 12 wks CD11blow
Naive
WT_12W_CD11blow AM

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount.
Sailfish was used to produce isoform estimated counts.
Assembly: Mus musculus Ensemble R76
Supplementary files format and content: Tab-delimited text files include read count values for each Sample

source_name: BAL AM (CD45+ Ly6G-SIglecF + CD11c+)

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

value: Pooled BAL cells

tag: group

value: CD45+ Ly6G-SIglecF + CD11c+ CD11blow


title: w2l


title: Normal tissue of case 2 [4normal]

value: Normal tissue


title: Stem 8mM ammonium at 720 ppm of CO2 replicate 1

value: Segura-Alcaraz

value: 2-month-old seedling

value: Stem


title: Normal tissue of case 3 [5normal]


title: Knockout contralateral  [3592 CL KO]

description: 3592 CL KO

source_name: CD11b+ cells isolated from non lesion hemisphere


title: Stem 8mM nitrate at 400 ppm of CO2 replicate 1

value: CO2 400 ppm


title: HCT116 ShSrx cells 1

city: Lexington

first: Qiou

last: Wei

state: KY

address: 324 HSRB, 1095 VA Drive

institute: University of Kentucky College of Medicine

description: total RNA extracted using Qiagen kit

hyb_protocol: standard

scan_protocol: Affymetrix chip standard

data_processing: TAC or Partek Flow recommended

source_name: HCT116 cells

label_protocol: Superscript III indirect cDNA labelling system (invitrogen)

growth_protocol: normal cell culture medium and conditions.

extract_protocol: Qiagen RNA mini kit

treatment_protocol: none.

tag: srx depetion

value: cancer cells ShSrx

tag: assays

value: DNA microarry


title: HCT116 ShSrx cells 3

description: total RNA extracted using Qiagen kit


title: HCT116 control ShNT cells 2

description: total RNA extracted using Qiagen kit

value: cancer cells control


title: HCT116 ShSrx cells 2

description: total RNA extracted using Qiagen kit


title: Normal tissue of case 1 [2normal]

tag: tissue


title: HCT116 control ShNT cells 1

description: total RNA extracted using Qiagen kit


title: Replicate D (sample 8) for d7 KO1 hESC-derived neuronal culture RNA replicates [G29_S8_D_KO1]

value: H1 hESC background CASK KO#1


title: Replicate A (sample 9) for d7 KO2 hESC-derived neuronal culture RNA replicates [G29_S9_A_KO2]

value: hESC-derived neurons


title: HCT116 control ShNT cells 3

description: total RNA extracted using Qiagen kit


title: Stem 8mM ammonium at 400 ppm of CO2 replicate 3


title: Stem 8mM ammonium at 400 ppm of CO2 replicate 1


title: Stem 8mM ammonium at 400 ppm of CO2 replicate 2


title: Needles 8mM nitrate at 720 ppm of CO2 replicate 3

source_name: Needles

value: Needles

value: Nitrate 8mM

value: CO2 720 ppm


title: Knockout Ipsilateral [791 IL KO]

description: 791 IL KO

tag: strain

value: Brain tissue

value: 8-12 weeks old


title: c1l

description:
CGD 12wks CD11blow
Naive
CGD_12W_CD11blow AM

value: CGD/CYBB KO (C57BL/6)

value: Pooled BAL cells


title: c2l

value: CD45+ Ly6G-SIglecF + CD11c+ CD11blow


title: w3l


title: Knockout contralateral  [791 CL KO]

description: 791 CL KO

tag: treatment

value: Tamoxifen


title: Needles 8mM nitrate at 720 ppm of CO2 replicate 2

value: Segura-Alcaraz

value: 2-month-old seedling


title: Replicate C (sample 7) for d7 KO1 hESC-derived neuronal culture RNA replicates [G29_S7_C_KO1]


title: Needles 8mM nitrate at 720 ppm of CO2 replicate 1


title: c2h

description:
CGD 12wks CD11bhigh
Naive
CGD_12W_CD11bhigh AM

value: CD45+ Ly6G-SIglecF + CD11c+ CD11bhigh


title: Replicate C (sample 3) for d7 WT hESC-derived neuronal culture RNA replicates [G29_S3_C_WT]

value: H1 hESC background WT


title: c1h


title: Wildtype Ipsilateral [3551 IL WT]

description: 3551 IL WT


title: Replicate D (sample 4) for d7 WT hESC-derived neuronal culture RNA replicates [G29_S4_D_WT]


title: Replicate A (sample 5) for d7 KO1 hESC-derived neuronal culture RNA replicates [G29_S5_A_KO1]


title: Knockout Ipsilateral [784 IL KO]

description: 784 IL KO


title: Replicate B (sample 6) for d7 KO1 hESC-derived neuronal culture RNA replicates [G29_S6_B_KO1]


title: Knockout contralateral  [788 CL KO]

description: 788 CL KO


title: wy3l

description:
WT 4wks CD11blow
Naive
WT_4W_CD11blow AM


title: Wildtype contralateral  [3551 CL WT]

description: 3551 CL WT


title: c3h


title: Needles 8mM nitrate at 400 ppm of CO2 replicate 2

value: CO2 400 ppm


title: Replicate B (sample 2) for d7 WT hESC-derived neuronal culture RNA replicates [G29_S2_B_WT]


title: c3l


title: Wildtype Ipsilateral [3546 IL WT]

description: 3546 IL WT


title: Wildtype contralateral  [3546 CL WT]

description: 3546 CL WT


title: Wildtype Ipsilateral [3545 IL WT]

description: 3545 IL WT


title: Needles 8mM nitrate at 400 ppm of CO2 replicate 1


title: Needles 8mM ammonium at 720 ppm of CO2 replicate 3

value: Ammonium 8 mM


title: Needles 8mM nitrate at 400 ppm of CO2 replicate 3


title: Needles 8mM ammonium at 720 ppm of CO2 replicate 2


title: wy2l


title: cy1l

description:
CGD 4wks CD11blow
Naive
CGD_4W_CD11blow AM


title: HB79N

city: Sao Paulo

first: Ana

middle: Cristina

last: Victorino Krepischi

address: Rua do Matao 277

department: Genética e Biologia Evolutiva

country: Brazil

institute: Universidade de São Paulo

data_processing:
FASTQ files aligned against the ribosomal reference sequence using BWA version 0.7.17-r1188.
Non-ribossome-aligned reads alignment against the reference sequence of the human genome GRCh37 / hg19 using STAR version 2.6.1a_08-27.
Normalization using FPKM metrics with a Python 3 developed script.
Assembly: GRCh37 / hg19
Supplementary files format and content: Table with raw gene counts for every gene and every sample

source_name: Control sample

extract_protocol:
Fourteen fresh-frozen primary HBLs and five control liver samples (non-tumoral matched liver tissues) were surgically obtained from patients enrolled in Brazilian cancer institutions. Total RNA samples were isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol. Microfluidics-based electrophoresis (Bioanalyzer, Agilent Technologies, USA) was performed to verify the RNA quality.
The total RNA extracted from the samples was used to build cDNA libraries using the TruSeq®Stranded Total RNA LT- kit (with Ribo-Zero TM Gold) (Illumina, USA).

tag: tissue type

value: Liver tissue


title: Replicate A (sample 1) for d7 WT hESC-derived neuronal culture RNA replicates [G29_S1_A_WT]

value: hESC-derived neurons


title: Needles 8mM ammonium at 720 ppm of CO2 replicate 1

value: Needles


title: Wildtype Ipsilateral [3541 IL WT]

description: 3541 IL WT


title: HB15N


title: Wildtype contralateral  [3541 CL WT]

description: 3541 CL WT


title: wy1l


title: cy3l

description:
CGD 4wks CD11blow
Naive
CGD_4W_ CD11blow AM


title: HB17N


title: cy2l


title: HB48N


title: Needles 8mM ammonium at 400 ppm of CO2 replicate 2


title: Needles 8mM ammonium at 400 ppm of CO2 replicate 3


title: P

description:
CGD_CD11bhigh_12wk
CGD_hi_12wk.narrowPeak.gz
CGD_hi_12wk.fc.signal.bigwig

library_source: genomic

data_processing:
Sequencing reads were demultiplexed and aligned to human genome (mm10) by bowtie2 (versoin 2.2.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab ATAC-seq and DNase-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines, version 0.33)
Assembly: hg19
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase followed by

treatment_protocol: Cells were sorted into RPMI1640 + 20% heat-inactivated FBS.

value: Mouse Alveolar macrophage (CD45+ Ly6G-SIglecF+ CD11c+)

value: 12 wks


title: HB79T

source_name: Tumor sample

value: Tumor


title: HB30N


title: HB48T


title: Wildtype contralateral  [3545 CL WT]

description: 3545 CL WT

value: Brain tissue

value: 8-12 weeks old


title: Male.SNI3.mPFC

city: Guang Zhou

first: dai

middle: wei

last: ping

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road

institute: Sun Yat-sen University

data_processing:
Raw data of fastq format was processed by Trimmomatic(v.0.36) to aquire the clean reads.
Clean reads were mapping to NCBI Rfam databases, to remove the rRNA sequences by Bowtie2 (v2.33)
Reference genome of Mus musculus and gene model annotation files were downloaded from genome website directly. Theremaining mRNA sequences were mapped to reference genome by Hisat2 (2.1.0)
HTSeq-count(v.0.9.1) was used to obtain the read count and function information of each gene. And in order to compare the gene expression among samples, RPKM of each gene was caculated.
Differentially expressed genes of  samples based different treatment were performed using the edgeR (v3.34.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample ...

source_name: Brain

extract_protocol:
The mPFC and ACC were dissected out with a 15G puncher and snap-frozen on dry ice. Total RNA was isolated using RNAeasy Micro Kit following the manufacturer’s protocol (Qiagen, Hilden, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: medial prefrontal cortex

value: 3 month old

value: Spared nerve injury

value: male


title: Male.SNI3.ACC

value: anterior cingulate cortex


title: Needles 8mM ammonium at 400 ppm of CO2 replicate 1

value: Segura-Alcaraz

value: 2-month-old seedling


title: HB46T


title: 20065FL-02-02-12

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

data_processing:
trimming/raw data cleaning - flexbar and data quality check - fastqc
additional adaptors removal - NGmerge
bwa - alignment
atacseq filtration for aligned reads/marking duplicates - samtools, samjdk, picard, own scripts
peak calling with background tissues - genrich
annotation and resutls data manipulation - R (own scripts)
Assembly: Sscrofa11.1
Supplementary files format and content: compressed gzip file containing raw peaks

organism: Sus scrofa

source_name: liver

growth_protocol: All pigs were female and they were maintained at Pig Test Station under the same feeding and housing conditions and were slaughtered when they reached 100±2 kg.

extract_protocol:
Up to twenty minutes letter, liver tissue was sampled  in media tissue-specific for liver tissue (William’s E medium with 1x hepatocyte plating/thawing medium A; Thermofisher). Then samples were transported in +4C to the laboratory. Then they were centrifuged and undergone 10-minutes digestion in 37°C using 1xAcutase (Stempro). After that, they will be filtered by using a 70um cell strainer (Sigma), washed with 10% FCS DMEM/F12 (Gibco) and then slowly frozen in cryotubes with cryoprotectant Cryostor 10 (Stemcell) and Mr Frosty™ Freezing Container to the temperature -80°C.
ATAC libraries were prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme) according to attached protocol.

tag: breed

value: Zlotnicka White

tag: day

tag: Sex

value: female

value: liver

tag: shear force

value: low fat content_600

tag: replicant


title: 20065FL-02-02-14


title: Male.SNI1.mPFC

tag: age


title: HB42T


title: N

description:
CGD_CD11blow_4wk
CGD_lo_4wk.narrowPeak.gz
CGD_lo_4wk.fc.signal.bigwig

source_name: CGD CD11blow_4wk

value: CGD/CYBB KO (C57BL/6)


title: O

description:
CGD_CD11blow_12wk
CGD_lo_12wk.narrowPeak.gz
CGD_lo_12wk.fc.signal.bigwig

value: Mouse Alveolar macrophage (CD45+ Ly6G-SIglecF+ CD11c+)


title: 20065FL-02-02-11

value: high fat content_600


title: 20065FL-02-02-13


title: Male.SNI1.ACC


title: HB40T

value: Tumor


title: HB47T


title: 20065FL-02-02-09


title: I

description:
WT_CD11blow_4wk
WT_lo_4wk.narrowPeak.gz
WT_lo_4wk.fc.signal.bigwig


title: Male.SNI2.ACC


title: M


title: Male.Sham3.ACC

value: Sham


title: Male.Sham2.mPFC


title: J


title: HB41T


title: Male.Sham3.mPFC


title: 20065FL-02-02-10


title: K


title: Male.SNI2.mPFC


title: 20065FL-02-02-07


title: F

value: 12 wks


title: HB35T


title: Male.Sham2.ACC


title: HB39T


title: Male.Sham1.ACC


title: 20065FL-02-02-04


title: Female.SNI3.mPFC

value: medial prefrontal cortex


title: H


title: HB30T


title: 20065FL-02-02-08


title: G


title: Female.SNI3.ACC

value: 3 month old


title: 20065FL-02-02-02


title: 20065FL-02-02-01


title: B

description:
WT_CD11blow_12wk
WT_lo_12wk.narrowPeak.gz
WT_lo_12wk.fc.signal.bigwig


title: TC28a2 HYPERTROPHY3

city: Seoul

first: Dong Suk

last: Yoon

address: Yonsei-ro 50-1

department: Orthopaedic Surery

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Illumina bcl2fastq v2.20.0.422 software was used for basecalling.
Sequenced reads were trimmed for adoptor sequence using cutadapt v1.18.
mapped to rn5 whole genome using TopHat v2.0.13 and calculate abundance using cuffdiff v2.2.1.
Assembly: rn5
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: Normal chondrocyte cell line TC28a2

growth_protocol: Basically, TC28a2 cells were cultured in DMEM-HG containing 10% fetal bovine serum (FBS; Gibco, Grand Island NY, USA) and 1% antibiotic–antimycotic solution (Invitrogen) at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using Trizol reagent following the protocols provided by the manufacturer.
RNA libraries were prepared for sequencing according to TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E using TruSeq Stranded Total RNA LT Sample Prep Kit (Gold). The reagent was NovaSeq 6000 S4 Reagent Kit. Sequencing protocol was NovaSeq 6000 System User Guide Document # 1000000019358 v02

treatment_protocol: TC28a2 cells were cultured in DMEM-HG supplemented with 1% FBS, 1% insulin Transferrin Selunium-A (ITS, Invitrogen), 100 ng/ml BMP-2 (R&D Systems Inc.), 10 ng/ml GDF-5 (PeproTech, Rosemont, IL, USA), 1 μM 3,3,5-Triiodo-L-thyronine (T3) (Sigma-Aldrich), 50 μg/ml L (+)-Ascorbic acid (Sigma-Aldrich), 10 nM dexamethasone (Sigma-Aldrich), 10 mM β-glycerophosphate (Sigma-Aldrich) and 1% antibiotic–antimycotic solution. The hypertrophic medium was replaced every 2 days for 5 days.

tag: cell line

value: Normal chondrocytes

value: Costal cartilage

value: Hypertrophic medium


title: 20065FL-02-01-14

value: low fat content_200


title: HB38T


title: Male.Sham1.mPFC

value: male


title: E

tag: genotype


title: Day 6_Il13-3

city: Boston

first: Yae-Huei

last: Liou

state: MA

address: 665 Huntington Ave.

department: MET

institute: Harvard School of Public health

description:
Lee_processed-2
47-WT_B6_Day_6_IL13_Pre_S31

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.10 )
Quality control for individual samples (CLC Genomics Workbench v.10 )
Mapping against the reference genome (CLC Genomics Workbench v.10 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.10)
Normalisation by scaling 10.000.000 reads per sample per transcript (TPM),
Genome_build: Genome_build: mouse mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM, Total counts, TPM, and CPM values for each Sample

source_name: imortalized mouse preadipocyte

growth_protocol: Sample are day 0 or day 6 differentiated preadipocyte.

extract_protocol:
RNA was harvest by spin column.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. 2 ug total RNA was used as input.

treatment_protocol: with or without Il13 pre-treatment for 16hr

value: wild type

tag: agent

tag: time point

value: Day 6


title: Day 6_Il13-4

description:
Lee_processed-2
48-WT_B6_Day_6_IL13_Pre_S32


title: 20065FL-02-02-06

value: Zlotnicka White

value: female

value: liver


title: HB31T


title: 20065FL-02-01-13


title: Female.SNI1.ACC

value: anterior cingulate cortex

value: Spared nerve injury

tag: gender


title: TC28a2 HYPERTROPHY2

tag: cell type


title: Day 6_Il13-1

description:
Lee_processed-2
45-WT_B6_Day_6_IL13_Pre_S29


title: HB15T

value: Tumor


title: HB28T


title: C

value: Mouse Alveolar macrophage (CD45+ Ly6G-SIglecF+ CD11c+)


title: 20065FL-02-01-12


title: Female.SNI2.ACC


title: 20065FL-02-02-05

value: high fat content_600


title: TC28a2 HYPERTROPHY1


title: D

value: 12 wks

value: CGD/CYBB KO (C57BL/6)


title: Female.SNI2.mPFC

value: medial prefrontal cortex

value: 3 month old


title: TC28a2 CTRL2

value: Normal chondrocytes

value: Costal cartilage

value: Growth medium


title: Female.SNI1.mPFC


title: 20065FL-02-01-11

value: high fat content_200


title: Day 6_Il13-2

description:
Lee_processed-2
46-WT_B6_Day_6_IL13_Pre_S30

value: wild type

value: Day 6


title: 20065FL-02-02-03

value: Zlotnicka White

value: female

value: low fat content_600


title: A


title: Day 6-4

description:
Lee_processed-2
44-WT_B6_Day_6_S28


title: Female.Sham3.mPFC

value: Sham


title: Female.Sham3.ACC

value: anterior cingulate cortex


title: TC28a2 CTRL1


title: Female.Sham2.mPFC


title: 20065FL-02-01-10

value: liver

value: low fat content_200


title: Day 6-3

description:
Lee_processed-2
43-WT_B6_Day_6_S27


title: 20065FL-02-01-09


title: Female.Sham2.ACC


title: Day 6-1

description:
Lee_processed-2
41-WT_B6_Day_6_S25


title: HAEC_after_24h_2

city: Changchun

first: luya

last: pu

address: No. 126 Xinmin St, Changchun, Jilin

institute: Jilin University

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform, and 150-bp paired-end reads were generated. Approximately 98.19 M raw reads for each sample were generated. Raw data (raw reads) in fastq format were first processed using Trimmomatic software. In this step, clean data (clean reads) were obtained by removing reads containing adapter and ploy-N or low-quality reads from raw data.
Approximately 13.47 M clean reads for each sample were retained for subsequent analyses. Sequencing reads were mapped to the human genome (GRCh38) using HISAT2. For mRNAs, the FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained using HTSeq-Count. For lncRNAs, the transcriptome from each dataset was assembled independently using the Cufflinks 2.0 program. All transcriptomes were pooled and merged to generate a final transcriptome using Cuffmerge.
RNA expression profile data were analyzed with the DESeq2 package of R. By setting the | log2FoldChange | ≥ 1 and P value ≤ 0.05 as criteria, DE lncRNAs and DE mRNAs were screened for subsequent analysis.
Assembly: hg18
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human aortic endothelial cells

extract_protocol:
Total RNA of the three groups of HAECs was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, Cat. No. RS-122-2301) according to the manufacturer’s instructions. RNA (1 μg) from each sample was used for library construction. First, ribosomal RNA (rRNA) was removed using Ribo-Zero Gold rRNA Removal Kit (Illumina), and RNA was fragmented using a fragment reagent. Subsequently, sequencing libraries were constructed using rRNA-depleted RNA. Finally, products were puriﬁed (Agencourt AMPure XP, BECKMAN COULTER), and library quality was assessed using the Agilent Bioanalyzer 2100 system.

value: Human aortic-derived endothelial cells

value: 24h recovery after Lss treatment


title: Day 0_Il13-4

description:
Lee_processed-1
24-WT_B6_Day_0_IL13_Pre_S16

value: Day 0


title: 20065FL-02-01-08


title: HAEC_after_24h_1


title: 20065FL-02-01-07


title: Female.Sham1.ACC

value: 3 month old


title: HAEC_12dy_12h_3

value: Treated with Lss of 12 dyn/cm2 for 12h


title: Female.Sham1.mPFC

value: medial prefrontal cortex


title: Day 0_Il13-3

description:
Lee_processed-1
23-WT_B6_Day_0_IL13_Pre_S15


title: HAEC_12dy_12h_1


title: Day 0_Il13-1

description:
Lee_processed-1
21-WT_B6_Day_0_IL13_Pre_S13


title: HAEC_12dy_12h_2


title: 20065FL-02-01-04


title: Day 0_Il13-2

description:
Lee_processed-1
22-WT_B6_Day_0_IL13_Pre_S14


title: 20065FL-02-01-05