title: E24_rep3: nsPEF, 24 h, TM3, replicate 3

source_name: nsPEF, 24 h, TM3, replicate 3

value: nanosecond pulsed electric field (nsPEF)-exposed


title: 20070005a_202817030109_R07C01

status: Public on Oct 20 2021

type: genomic

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

country: USA

institute: University of Michigan

hyb_protocol: Bisulfite conversion was performed using 350 ng input FFPE DNA with the Zymo EZ DNA Methylation Kit following manufacturer recommendations

scan_protocol: BeadChips were scanned and image data recorded by an iScan Reader with Methylation NXT settings

data_processing:
Methylation Profiles were generated using the GenomeStudio (v2011.1) Analysis Software with the Methylation Module and MethylationEPIC_v-1-0_B4 Manifest (Illumina). Raw data were pre-processed with R packages minfi and ChAMP.
the 'processed_beta_values_all.txt' contains average Beta

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: oral cavity_regimen 1_Baseline

label_protocol: Standard Illumina protocol

extract_protocol: The corresponding areas on unstained slides were microdissected for DNA isolation using the QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany). All DNA samples were treated with RNAse using the QIAquick Nucleotide Removal Kit (Qiagen, Hilden, Germany). DNA quantity was assessed using the Qubit Broad Range Double Stranded DNA Assay (Thermo Fisher Scientific, Waltham, MA).

tag: patient id

tag: regimen

tag: tissue source

value: oral cavity

tag: time point

value: Baseline


title: 20070004a_202817030109_R05C01

source_name: oral cavity_regimen 2_Baseline


title: 20070006a_202817030119_R01C01


title: Oral apparatus post sucrose shock (T=120min) rep 1

type: SRA

city: San Francisco

first: Wallace

last: Marshall

state: CA

institute: UCSF

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Stentor genome (StentorDB), using tophat2 (-i 9 -I 101 --min-segment-intron 9 --min-coverage-intron 9 --max-segment-intron 101 --max-coverage-intron 101 -p 20). We used Trinity to build a transcriptome (--genome_guided_max_intron 1000). For quantification of transcript abundance, we aligned reads to the transcriptome using Kallisto (-t 15 -b 30). Transcriptome file is included here: SteCoe_Trinity_assembled_transcriptome_for_GEO.fasta
Genome_build: Stentor coeruleus (GCA_001970955.1)
Supplementary_files_format_and_content: For each Sample:
tsv file containing matrix of estimated counts, TPM, effective length for each gene.
HDF5 binary file containing run info, abundance estimates, bootstrap estimates, and transcript length information length.
json file containing information about the run
Trinity generated transcriptome (fasta)

molecule: total RNA

organism: Stentor coeruleus

source_name: Stentor coeruleus cell

extract_protocol:
At each time point, a sample of cells was lysed into RNA-stabilizing buffers specified by the extraction kit, and then stored on ice until the end of the experiment when the RNA purification was performed in parallel on all samples. RNA was extracted at each time point using the Nucleospin RNA XS kit from Clontech (cat. num. 740902.250).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

tag: treatment

value: sucrose shock

tag: genotype

value: wild type


title: ER-Hoxa9.WM1119.2

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Alignment-independent quantification using Salmon
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: TPM as txt file

organism: Mus musculus

growth_protocol: MOLM-13 cell line was cultured in RPMI (Corning, 10-041-CV) with 10% FBS (Life Technologies, 16000044) and 1% Penicillin Streptomycin (Gibco, 15-140-122). Mouse ER-Hoxa9 cells was cultured in RPMI (Corning, 10-041-CV) with 10% FBS (Life Technologies, 16000044), 1% Penicillin Streptomycin (Gibco, 15-140-122), 1% - 2% stem cell factor (SCF) conditioned media (generated from a Chinese hamster ovary (CHO) cell line that stably secretes SCF), and 0.5 µM β-estradiol (Fisher Scientific MP021016562).

extract_protocol:
RNA was extracted using Qiagen RNeasy  Kit.
RNA-seq libraries were build by a commercial company, Novogene, following standard protocols.

treatment_protocol: MOLM-13 cells were treated with 4uM WM-1119 for 4 days and ER-Hoxa9 cells were treated with 2uM WM-1119 for 4 days.

tag: cell line


title: 20310014a_202817030119_R03C01


title: Oral apparatus post sucrose shock (T=180min) rep 1


title: Oral apparatus post sucrose shock (T=30min) rep 1


title: control_1

type: RNA

city: Chiba City

first: Ryunosuke

last: Nozaki

state: Chiba Prefecture

address: 1-8-1 Inohana, Chuo-ku, Chiba, Japan

department: Depertment of Oral science

country: Japan

institute: Graduate School of Medecine, Chiba university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: LH2F/F CAG-Cre, tamoxifen (-) medium

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Mouse tails were skinned and minced into 1-cm pieces, which were then placed on 30-mm tissue culture dishes coated with collagen I and containing Dulbecco's Modified Eagle's Medium (DMEM without sodium pyruvate; Nacalai Tesque, Kyoto, Japan), 10% fetal bovine serum (FBS; Sigma-Aldrich, St. Louis, MO, USA), and 50 units/ml penicillin. The plates were maintained at 37 °C with 5% CO2.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Total RNA was extracted from cells with TRIzol Reagent (Invitrogen) and the SV Total RNA Isolation System (Promega), according to the manufacturer's instructions.

tag: strain

tag: cell type

value: tail tissue fibroblast (TTF)

value: LH2 cKO

value: tamoxifen (-) medium


title: Arabidopsis mkk4-5 Agro rep3

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

country: China

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Psojae v1.1 whole genome using hisat2 v2.1.0 with default parameters
FPKM were calculated using stringtie v1.3.3b with default parameters
Genome_build: GCF_000001735.4_TAIR10.1
Supplementary_files_format_and_content: gtf files include FPKM,TPM,and coverage values for each Sample

organism: Arabidopsis thaliana

source_name: 10-day old seedlings

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

tag: developmental stage

value: 10-day old seedlings

value: mkk4-5 double mutant

value: agrobacteria infection for 24h


title: 20290006b_202817030109_R04C01

source_name: oral cavity_regimen 2_Month 1

value: Month 1


title: 20070006b_202817030119_R02C01

source_name: oral cavity_regimen 1_Month 1


title: E24_rep1: nsPEF, 24 h, TM3, replicate 1

city: Warsaw

first: Alicja

last: Trebinska-Stryjewska

address: gen. S. Kaliskiego 2

department: Institute of Optoelectronics

country: Poland

institute: Military University of Technology

description: Gene expression in nanosecond pulsed electric field (nsPEF)-exposed TM3 Leydig cells 24 h after treatment

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented following the manufacturer's protocol at 60°C for 30 min; fragmentation reaction was stopped by adding 2 × Hi-RPM Hybridization buffer. Fragmented Cy3-labeled cRNA was hybridized to Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed following manufacturer's instructions with GE Wash Buffer 1 and 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing with the SureScan Microarray Scanner (Agilent) using the Agilent Microarray Scan Control program version 9.1 with the following settings: resolution, 3 µm; dye channel, green; green PMT sensitivity, 100%.

data_processing: Scanned images were analyzed with the Feature Extraction Software 12.0 using default parameters (protocol: GE1_1200_Jun14, grid: 074809_D_F_20190110) to obtain the background-subtracted and detrended Processed Signal intensities. Data were processed with GeneSpring version 14.9, and log2-transformed normalized signal intensities were obtained after normalization by a percentile shift (75th percentile). The baseline was set to the median of all samples. Normalized signal intensities were further used to create gene-level experiments (only genes detected in at least 2 out of 4 biological replicates in any condition were included). Differential gene expression was performed in GeneSpring using a two-way ANOVA with interaction (p <0.05) with Benjamini-Hochberg FDR multiple testing correction.

source_name: nsPEF, 24 h, TM3, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the Low Input Quick Amp Labeling Kit, One Color (Agilent) according to manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Addition of RNA Spike-In, One color (Agilent) served as an internal control. Cy3-labeled cRNA quality and quantity were assessed using 2100 Agilent Bioanalyzer (Agilent) and Agilent RNA 6000 Nano Reagent (Agilent).

growth_protocol: TM3 cell line (Leydig cells, Mus musculus, ATCC CRL-1714) was propagated in a medium composed of Ham's F12 and Dulbecco's modified Eagle’s medium (1:1) (DMEM/F12) supplemented with 5% horse serum, 2.5% fetal bovine serum, and antibiotic/antimycotic in 5% carbon dioxide at 37ºC until semi-confluent.

extract_protocol: After treatment, cells were washed twice with ice-cold PBS, centrifuged at 600xg for 5 min at 4ºC; cell pellets were frozen at -80ºC. Total RNA was isolated from the frozen pellets using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions (including on-column DNaseI treatment). RNA was quantified using the QuantiFluor RNA System and Quantus Fluorometer (Promega). RNA quality was assessed with 2100 Agilent Bioanalyzer and Agilent RNA 6000 Nano Reagent. RIN ranged from 8.9 to 10.0.

treatment_protocol: Before the exposure, TM3 cells were washed two times in cold BD-PBS, resuspended at the density of 2.E+06 cells/ml in 1×binding buffer, passed through a 40-µm nylon cell strainer filter, and aliquoted into electroporation cuvettes (0.4 cm gap size width) in a volume of 200 µl per sample. Cells were either sham-exposed or exposed to nanosecond pulsed electric field (nsPEF): 80 pulses of quasi-rectangular shape, 60 ns pulse width, 5.5 kV amplitude at the repetition rate 26.4 pulses per minute. The electric field was 14 kV/cm, and the duration of treatment was 180 s.

value: Leydig cell, epithelial


title: Oral apparatus post sucrose shock (T=240min) rep 1


title: S24_rep2: sham, 24 h, TM3, replicate 2

description: Gene expression in sham-exposed TM3 Leydig cells 24 h after treatment

source_name: sham, 24 h, TM3, replicate 2

value: sham-exposed


title: S24_rep3: sham, 24 h, TM3, replicate 3

source_name: sham, 24 h, TM3, replicate 3


title: E4_rep3: nsPEF, 4 h, TM3, replicate 3

description: Gene expression in nanosecond pulsed electric field (nsPEF)-exposed TM3 Leydig cells 4 h after treatment

source_name: nsPEF, 4 h, TM3, replicate 3

value: 4 h


title: oe rep2

city: harbin

first: Qi

last: Jiang

state: heilongjiang

address: baojian road 157

department: Department of histology and embryology

institute: Harbin Medical University

library_source: genomic

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse reference genome UCSC MM10 using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4. Then the peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: wig files were generated using MACS

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained from 13.5-dpc embryos collected from  C57BL/6 females which had been mated with DBA/2 males. 293T and MEFs were cultured in Dulbecco's modified eagle medium (DMEM) containing 15%(vol/vol) fetal bovine serum (FBS), 1X MEM NEAA, 1X L-Glutamine and 1X Penicillin-Streptomycin. (FBS from BI and others from Invitrogen). For iPSC reprogramming, infected or drug treated 4F2A MEFs were cultured in KnockOut DMEM with 15% KnockOut Serum Replacement, 1X MEM NEAA, 1X L-Glutamine, 1X Penicillin-Streptomycin, 1X Sodium Pyruvate, 1000U/ml LIF, 1X 2-Mercaptoethanol and 2 μg/ml doxycycline (LIF from Millipore, doxycycline from Sigma-Aldrich and others from Invitrogen), the medium were changed every day.

extract_protocol:
48 hrs after infection,The DNA was extracted using H3K27me3 antibody.
10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads.

value: Mouse embryonic fibroblasts (MEFs)

tag: genotype/variation

value: KDM6A overexpression

tag: chip antibody


title: S24_rep1: sham, 24 h, TM3, replicate 1

source_name: sham, 24 h, TM3, replicate 1


title: E24_rep2: nsPEF, 24 h, TM3, replicate 2

source_name: nsPEF, 24 h, TM3, replicate 2

value: nanosecond pulsed electric field (nsPEF)-exposed


title: E4_rep4: nsPEF, 4 h, TM3, replicate 4

source_name: nsPEF, 4 h, TM3, replicate 4


title: con input

value: control


title: oe rep1


title: Arabidopsis mkk4-5 Agro rep2


title: Oral apparatus post sucrose shock (T=90min) rep 1


title: 20290006a_202817030109_R03C01

value: oral cavity

value: Baseline


title: 20310012b_202817030088_R08C01


title: con rep2


title: con rep1


title: Arabidopsis mkk4-5 MOCK rep3

value: MOCK


title: E4_rep1: nsPEF, 4 h, TM3, replicate 1

source_name: nsPEF, 4 h, TM3, replicate 1


title: E4_rep2: nsPEF, 4 h, TM3, replicate 2

source_name: nsPEF, 4 h, TM3, replicate 2


title: Arabidopsis mkk4-5 MOCK rep2


title: 20310012a_202817030088_R07C01


title: 20070003a_202817030109_R01C01


title: 20310011a_202817030088_R05C01


title: Arabidopsis mkk4-5 MOCK rep1


title: 20310011b_202817030088_R06C01


title: Arabidopsis mkk4-5 Agro rep1


title: 20070003b_202817030109_R02C01


title: B16 tumor in CCRL2 WT mouse - replica 1

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic)
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR software to generate read alignments.
The annotation file Mus_musculus.GRCm38.84.gtf was obtained from the ftp.Ensembl.org server
Following transcript assembly, gene level counts were obtained using HTSeq
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: Excel xlsx file includes counts per 20 millions of aligned reads values for each sample.

source_name: B16 tumor

extract_protocol:
Tumors were lysed in TRIzol, and total RNA extracted with the RNAeasy micro kit (Qiagen) following the manufacturer's instructions.
TruSeq RNA sample preparation kit (Illumina)
RNA-Seq 2x100 bases Paired-End

tag: tumor stage

value: 5 days tumor graft in the back

value: syngeneic C57BL/6

value: CCRL2 WT


title: B16 tumor in CCRL2 WT mouse - replica 2


title: Arabidopsis WT Agro rep2

value: 10-day old seedlings

value: WT


title: B16 tumor in CCRL2 KO mouse - replica 2

value: CCRL2 KO


title: Arabidopsis WT Agro rep3

value: agrobacteria infection for 24h


title: B16 tumor in CCRL2 KO mouse - replica 1


title: Arabidopsis WT Agro rep1


title: LLC tumor in CCRL2 KO mouse - replica 2

source_name: LLC tumor


title: 20230004a_202817030088_R03C01

source_name: oral cavity_regimen 1_Baseline


title: Arabidopsis WT MOCK rep3


title: 20310009b_202817030088_R02C01

value: Month 1


title: Arabidopsis WT MOCK rep2


title: 20230004b_202817030088_R04C01


title: LLC tumor in CCRL2 WT mouse - replica 2


title: NH_FLI_zebrafish 190_skin_RNAseq

status: Public on Oct 19 2021

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

description:
sample_counts.xls
sample_rpkms.xls

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.8.2 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCz10, and respective gene annotation (GRCz10.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

organism: Danio rerio

source_name: skin

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.

value: AB JxTu

tag: tissue

value: skin

tag: age

value: 1 year

tag: Sex

value: male

tag: perturbation

value: Rotenone 3.75 nM


title: 20310009a_202817030088_R01C01

source_name: oral cavity_regimen 2_Baseline

tag: patient id

tag: regimen


title: NH_FLI_zebrafish 191_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 192_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: S4_rep1: sham, 4 h, TM3, replicate 1

description: Gene expression in sham-exposed TM3 Leydig cells 4 h after treatment

source_name: sham, 4 h, TM3, replicate 1

value: Leydig cell, epithelial

value: sham-exposed

value: 4 h


title: E0_rep3: nsPEF, 0 h, TM3, replicate 3

description: Gene expression in nanosecond pulsed electric field (nsPEF)-exposed TM3 Leydig cells 0 h after treatment

source_name: nsPEF, 0 h, TM3, replicate 3

value: 0 h


title: S4_rep3: sham, 4 h, TM3, replicate 3

source_name: sham, 4 h, TM3, replicate 3


title: NH_FLI_zebrafish 166_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 167_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: E0_rep1: nsPEF, 0 h, TM3, replicate 1

source_name: nsPEF, 0 h, TM3, replicate 1

value: nanosecond pulsed electric field (nsPEF)-exposed


title: E0_rep2: nsPEF, 0 h, TM3, replicate 2

source_name: nsPEF, 0 h, TM3, replicate 2


title: S4_rep2: sham, 4 h, TM3, replicate 2

source_name: sham, 4 h, TM3, replicate 2


title: S4_rep4: sham, 4 h, TM3, replicate 4

source_name: sham, 4 h, TM3, replicate 4


title: S0_rep3: sham, 0 h, TM3, replicate 3

description: Gene expression in sham-exposed TM3 Leydig cells 0 h after treatment

source_name: sham, 0 h, TM3, replicate 3


title: S0_rep4: sham, 0 h, TM3, replicate 4

source_name: sham, 0 h, TM3, replicate 4


title: S0_rep2: sham, 0 h, TM3, replicate 2

source_name: sham, 0 h, TM3, replicate 2


title: E0_rep4: nsPEF, 0 h, TM3, replicate 4

source_name: nsPEF, 0 h, TM3, replicate 4


title: NH_FLI_zebrafish 165_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 164_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 193_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 193_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

source_name: liver

value: liver


title: NH_FLI_zebrafish 189_skin_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 192_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 190_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 189_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Superior2_Left_Rep2-3

city: Pittsburgh

first: Leah

last: Byrne

state: PA

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

description:
Superior2_S4_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep2_results.csv
aav_barcode_key.txt

data_processing:
Sequencing data was demultiplexed into sample-level fastq files using Cell Ranger mkfastq (v3 10X Genomics).
Alignment and cell demultiplexing were run using STARsolo(14) (v2.7) with default parameters, creating raw count matrices.
GFP-barcodes were analyzed from the original scRNA-seq samples and PCR amplification of GFP from the 10x single cell prepped sample libraries. In both cases, the GFP-barcodes were identified using Salmon (Patro et al., 2017) (v0.9.1) transcript quantification. Only reads with 1 hit to a GFP barcode were kept. Using these reads, AAV variants were identified based on the GFP barcode (aav_barcode_key.txt). 10x barcodes in the reads from the PCR amplification analysis were corrected according to the 10x Cell Ranger count algorithm to mitigate any errors that may have been introduced by multiple rounds of PCR. Rarely, multiple AAV variants were found per UMI (unique molecular identifier), and in this case the AAV variant with the highest number of counts for that UMI was kept.
Genome_build: Cynomolgus macaque samples were aligned to the Macaca_fascicularis_5.0/macFas5 reference obtained from UCSC and marmoset samples were aligned to ASM275486v1 obtained from Ensembl.
Supplementary_files_format_and_content: Matrix tables with raw gene expression counts for every cell; Cell-by-GFP tables with raw GFP-barcode expression counts

molecule: polyA RNA

organism: Callithrix jacchus

extract_protocol:
The NHP retinas were dissected and regions of interest were isolated (macula, superior and inferior periphery). For cynomolgus macaque, superior and inferior periphery were pooled. Retinal tissue was placed in Hibernate solution (Hibernate A -Ca Solution, BrainBits LLC), and cells were then dissociated using Macs Miltenyi Biotec Neural Tissue Dissociation Kit for postnatal neurons (130-094-802) according to manufacturer’s recommendations. Dissected retina pieces were incubated with agitation at 37 °C and further mechanically dissociated. The dissociated neural retina was filtered using a 70 µm MACS Smart Strainer (Miltenyi Biotec) to ensure single-cell suspension. Cells were resuspended in 0.1% BSA in D-PBS and processed immediately for scRNA-seq.
Marmoset and cynomolgus macaque samples were prepared for single cell analysis using a 10x Chromium Single Cell 3’ v3 kit. Briefly, single cells from retina samples were captured using 10X Chromium system (10X Genomics), the cells were partitioned into Gel beads-in-emulsion (GEMS), mRNAs were reverse transcribed and cDNAs with 10X Genomics Barcodes were created with unique molecular identifiers (UMIs) for different transcripts. Purified cDNA was PCR amplified and further purified with SPRIselect reagent (Beckman Coulter, B23318). Final libraries were generated after fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR steps according to 10x Single Cell 3’ workflow. An additional targeted sequencing analysis was run on these 10x-prepped cDNA samples, using PCR amplification with Q5 High Fidelity DNA Polymerase to target the GFP sequence and its associated AAV barcode.

treatment_protocol: Marmosets, cynomolgus macaques and rhesus macaques between 3-10 years and retinas were injected intravitreally with AAV libraries. Monkeys used for K912-scCAG-GFP fluorophore expression received daily oral doses of cyclosporine at a dose of 6 mg/kg for the duration of the study. Marmosets received oral daily doses of meloxicam (0.2 mg/kg) for one week after injection.

value: Retina

tag: region

value: Retina superior region

tag: sorting strategy

value: unsorted


title: NH_FLI_zebrafish 191_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Superior2_Left_Rep2-4

description:
Superior2_S4_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 165_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Superior2_Left_Rep2-2

description:
Superior2_S4_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 166_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 193_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

source_name: brain

value: brain


title: Marmoset2_Superior1_Left_Rep1-4

description:
Superior1_S3_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep1_results.csv
aav_barcode_key.txt


title: Marmoset2_Superior1_Left_Rep1-3

description:
Superior1_S3_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 163_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 191_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Superior1_Left_Rep1-1

description:
Superior1_S3_L001
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep1_results.csv
aav_barcode_key.txt


title: Marmoset2_Inferior_Left_Rep2-4

description:
Inferior2_S6_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep2_results.csv
aav_barcode_key.txt

value: Retina inferior region


title: Marmoset2_Superior1_Left_Rep1-2

description:
Superior1_S3_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 192_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Inferior_Left_Rep2-3

description:
Inferior2_S6_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 189_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: S0_rep1: sham, 0 h, TM3, replicate 1

source_name: sham, 0 h, TM3, replicate 1

tag: treatment

tag: time


title: NH_FLI_zebrafish 167_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 190_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Inferior_Left_Rep2-2

description:
Inferior2_S6_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep2_results.csv
aav_barcode_key.txt


title: Marmoset2_Inferior_Left_Rep2-1

description:
Inferior2_S6_L001
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep2_results.csv
aav_barcode_key.txt


title: Marmoset2_Inferior_Left_Rep1-4

description:
Inferior1_S5_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep1_results.csv
aav_barcode_key.txt


title: Marmoset2_Superior2_Left_Rep2-1

description:
Superior2_S4_L001
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_superior_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 163_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Inferior_Left_Rep1-3

description:
Inferior1_S5_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 167_liver_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Marmoset2_Inferior_Left_Rep1-2

description:
Inferior1_S5_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep1_results.csv
aav_barcode_key.txt


title: Marmoset2_Macula_Left_Rep2-4

description:
Macula2_S2_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep2_results.csv
aav_barcode_key.txt

value: Retina macula region


title: Marmoset2_Inferior_Left_Rep1-1

description:
Inferior1_S5_L001
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_inferior_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 164_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: AB JxTu


title: Marmoset2_Macula_Left_Rep2-2

description:
Macula2_S2_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 202_skin_RNAseq

value: skin

value: Rotenone 37.5 nM


title: NH_FLI_zebrafish 200_skin_RNAseq

value: 1 year

value: male


title: NH_FLI_zebrafish 166_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: Rotenone 3.75 nM


title: NH_FLI_zebrafish 198_skin_RNAseq


title: NH_FLI_zebrafish 197_skin_RNAseq

value: AB JxTu Tg(flk:mCherry)

value: 3 years


title: NH_FLI_zebrafish 195_skin_RNAseq


title: NH_FLI_zebrafish 196_skin_RNAseq


title: Marmoset2_Macula_Left_Rep1-4

description:
Macula1_S1_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep1_results.csv
aav_barcode_key.txt


title: Marmoset2_Macula_Left_Rep1-3

description:
Macula1_S1_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep1_results.csv
aav_barcode_key.txt


title: Marmoset2_Macula_Left_Rep1-1

description:
Macula1_S1_L001
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 199_skin_RNAseq


title: NH_FLI_zebrafish 165_brain_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_zebrafish 194_skin_RNAseq


title: Marmoset2_Macula_Left_Rep2-1

description:
Macula2_S2_L001
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 201_skin_RNAseq


title: Marmoset2_Macula_Left_Rep1-2

description:
Macula1_S1_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep1_results.csv
aav_barcode_key.txt


title: Marmoset1_Superior_Left_Rep2-4

description:
left_superior_2_S11_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 181_skin_RNAseq


title: Marmoset1_Superior_Left_Rep2-2

description:
left_superior_2_S11_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 180_skin_RNAseq


title: Marmoset1_Superior_Left_Rep2-3

description:
left_superior_2_S11_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 179_skin_RNAseq


title: Marmoset1_Superior_Left_Rep1-4

description:
left_superior_1_S5_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_left_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 177_skin_RNAseq


title: NH_FLI_zebrafish 174_skin_RNAseq


title: Marmoset1_Superior_Left_Rep1-2

description:
left_superior_1_S5_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_left_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 173_skin_RNAseq


title: Marmoset1_Superior_Right_Rep2-3

description:
right_superior_2_S8_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_right_rep2_results.csv
aav_barcode_key.txt


title: Marmoset1_Superior_Right_Rep1-2

description:
right_superior_1_S2_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_right_rep1_results.csv
aav_barcode_key.txt


title: Marmoset1_Superior_Right_Rep1-3

description:
right_superior_1_S2_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_right_rep1_results.csv
aav_barcode_key.txt


title: Marmoset1_Superior_Right_Rep1-4

description:
right_superior_1_S2_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_right_rep1_results.csv
aav_barcode_key.txt


title: Marmoset1_Inferior_Left_Rep2-4

description:
left_inferior_2_S12_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 202_liver_RNAseq


title: NH_FLI_zebrafish 201_liver_RNAseq


title: NH_FLI_zebrafish 199_liver_RNAseq


title: Marmoset1_Inferior_Left_Rep2-3

description:
left_inferior_2_S12_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 200_liver_RNAseq


title: NH_FLI_zebrafish 198_liver_RNAseq


title: NH_FLI_zebrafish 197_liver_RNAseq


title: NH_FLI_zebrafish 196_liver_RNAseq


title: Marmoset1_Inferior_Left_Rep2-2

description:
left_inferior_2_S12_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 178_skin_RNAseq


title: Marmoset1_Inferior_Left_Rep1-4

description:
left_inferior_1_S6_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_left_rep1_results.csv
aav_barcode_key.txt


title: Marmoset1_Superior_Left_Rep1-3

description:
left_superior_1_S5_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_left_rep1_results.csv
aav_barcode_key.txt


title: Oral apparatus pre sucrose shock rep 1

source_name: Stentor coeruleus cell

value: baseline

value: no treatment

tag: genotype

value: wild type


title: NH_FLI_zebrafish 175_skin_RNAseq

source_name: skin

tag: strain


title: Marmoset1_Superior_Right_Rep2-4

description:
right_superior_2_S8_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_right_rep2_results.csv
aav_barcode_key.txt

value: Retina


title: NH_FLI_zebrafish 194_liver_RNAseq

value: liver


title: NH_FLI_zebrafish 181_liver_RNAseq


title: Marmoset1_Inferior_Left_Rep1-3

description:
left_inferior_1_S6_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_left_rep1_results.csv
aav_barcode_key.txt

value: unsorted


title: Marmoset1_Inferior_Left_Rep1-2

description:
left_inferior_1_S6_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_left_rep1_results.csv
aav_barcode_key.txt


title: Marmoset1_Inferior_Right_Rep2-4

description:
right_inferior_2_S9_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_right_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 177_liver_RNAseq


title: Marmoset1_Inferior_Right_Rep2-3

description:
right_inferior_2_S9_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_right_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 178_liver_RNAseq


title: Marmoset1_Inferior_Right_Rep1-4

description:
right_inferior_1_S3_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_right_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 174_liver_RNAseq


title: NH_FLI_zebrafish 175_liver_RNAseq


title: NH_FLI_zebrafish 173_liver_RNAseq


title: NH_FLI_zebrafish 195_liver_RNAseq


title: Marmoset1_Macula_Left_Rep2-4

description:
left_macula_2_S10_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 202_brain_RNAseq

value: brain


title: Marmoset1_Macula_Left_Rep2-3

description:
left_macula_2_S10_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_left_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 199_brain_RNAseq


title: Marmoset1_Inferior_Right_Rep1-2

description:
right_inferior_1_S3_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_right_rep1_results.csv
aav_barcode_key.txt

value: Retina inferior region


title: Marmoset1_Macula_Left_Rep2-2

description:
left_macula_2_S10_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_left_rep2_results.csv
aav_barcode_key.txt

value: Retina macula region


title: NH_FLI_zebrafish 200_brain_RNAseq

value: AB JxTu


title: Marmoset1_Macula_Left_Rep1-4

description:
left_macula_1_S4_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_left_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 198_brain_RNAseq


title: Marmoset1_Macula_Left_Rep1-3

description:
left_macula_1_S4_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_left_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 196_brain_RNAseq


title: NH_FLI_zebrafish 197_brain_RNAseq


title: Marmoset1_Macula_Left_Rep1-2

description:
left_macula_1_S4_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_left_rep1_results.csv
aav_barcode_key.txt


title: Marmoset1_Inferior_Right_Rep2-2

description:
right_inferior_2_S9_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_right_rep2_results.csv
aav_barcode_key.txt


title: Marmoset1_Macula_Right_Rep2-4

description:
right_macula_2_S7_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_right_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 194_brain_RNAseq


title: NH_FLI_zebrafish 195_brain_RNAseq


title: Marmoset1_Macula_Right_Rep2-3

description:
right_macula_2_S7_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_right_rep2_results.csv
aav_barcode_key.txt


title: Marmoset1_Macula_Right_Rep2-2

description:
right_macula_2_S7_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_right_rep2_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 181_brain_RNAseq


title: Marmoset1_Macula_Right_Rep1-4

description:
right_macula_1_S1_L004
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_right_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 201_brain_RNAseq


title: Marmoset1_Macula_Right_Rep1-3

description:
right_macula_1_S1_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_right_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 177_brain_RNAseq


title: Marmoset1_Macula_Right_Rep1-2

description:
right_macula_1_S1_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_macula_right_rep1_results.csv
aav_barcode_key.txt


title: NH_FLI_zebrafish 178_brain_RNAseq


title: LLC tumor in CCRL2 KO mouse - replica 1

source_name: LLC tumor

value: 5 days tumor graft in the back

value: syngeneic C57BL/6

value: CCRL2 KO


title: Marmoset1_Superior_Right_Rep2-2

description:
right_superior_2_S8_L002
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_superior_right_rep2_results.csv
aav_barcode_key.txt

value: Retina superior region


title: NH_FLI_zebrafish 174_brain_RNAseq

value: 1 year

value: male

value: Rotenone 37.5 nM


title: Sample_44: SCO18

city: Berlin

first: Simone

last: Schmid

address: Charitéplatz 1

department: Department of Neuropathology

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was done using the minfi package running on R version 3.6.1 (2019-07-05) -- "Action of the Toes".
Processed data: Average beta-Values after normalization using the Funnorm method and detection p values

label: Cy3, Cy5

source_name: Tumor

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

tag: histology

value: spindle cell oncocytoma (SCO)

tag: gender

value: m

tag: mutation


title: Sample_42: SCO16


title: NH_FLI_zebrafish 176_brain_RNAseq


title: Sample_41: SCO15


title: Sample_43: SCO17

value: f

value: EpiReg


title: Arabidopsis WT MOCK rep1

source_name: 10-day old seedlings

tag: developmental stage

value: 10-day old seedlings

value: WT

value: MOCK


title: NH_FLI_zebrafish 175_brain_RNAseq

value: brain


title: Marmoset1_Inferior_Right_Rep1-3

description:
right_inferior_1_S3_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset1_inferior_right_rep1_results.csv
aav_barcode_key.txt

value: Retina

value: Retina inferior region

value: unsorted


title: Sample_40: SCO14


title: LLC tumor in CCRL2 WT mouse - replica 1

tag: tumor stage

value: 5 days tumor graft in the back

value: syngeneic C57BL/6

value: CCRL2 WT


title: Sample_38: SCO12


title: Sample_39: SCO13


title: NH_FLI_zebrafish 179_brain_RNAseq

value: AB JxTu Tg(flk:mCherry)

tag: tissue

value: 3 years


title: SS_FSU_Celeg32_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step.
Reads were trimmed und filtered using trimmomatic (0.36) [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20].
Reads were mapped using BWA (0.7.12-r1039) [parameter: -n 0 -o 0 -e 0 -l 8 -k 0].
Reads per gene were counted using samtools (1.3.1-9-ge5dfb0a).
Genome_build: mirBase Release 21 (C. elegans sequences only)
Supplementary_files_format_and_content: The Excel file includes raw counts (sample_counts.xls) of all mirBase C. elegans sequences for each sample.

organism: Caenorhabditis elegans

source_name: N2_20 days_2-Deoxyglucose

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.

value: whole worms

tag: age

value: 20 days

value: hermaphrodite


title: SS_FSU_Celeg27_smallRNAseq

source_name: N2_10 days_2-Deoxyglucose

value: 10 days

tag: Sex


title: SS_FSU_Celeg30_smallRNAseq

source_name: N2_20 days_Rotenone 0.039441 µg/ml

tag: perturbation

value: Rotenone 0.039441 µg/ml


title: SS_FSU_Celeg26_smallRNAseq


title: SS_FSU_Celeg31_smallRNAseq


title: Sample_36: SCO10

value: spindle cell oncocytoma (SCO)

value: f


title: SS_FSU_Celeg25_smallRNAseq


title: Sample_35: SCO09

value: m


title: Sample_33: SCO07

value: EpiReg


title: Sample_32: SCO06


title: SS_FSU_Celeg33_smallRNAseq


title: Sample_34: SCO08


title: SS_FSU_Celeg23_smallRNAseq

source_name: N2_10 days_Rotenone 0.039441 µg/ml


title: SS_FSU_Celeg18_smallRNAseq

source_name: N2_5 days_2-Deoxyglucose

value: 5 days


title: SS_FSU_Celeg22_smallRNAseq


title: Sample_30: SCO04


title: Sample_29: SCO03

value: MAPK


title: Sample_31: SCO05


title: Sample_27: SCO01


title: SS_FSU_Celeg16_smallRNAseq


title: Marmoset2_Macula_Left_Rep2-3

description:
Macula2_S2_L003
supplementary or processed data file:
barcodes.tsv
marmoset_genes.tsv
cell_by_aav_marmoset2_macula_rep2_results.csv
aav_barcode_key.txt

value: Retina

value: Retina macula region

value: unsorted


title: Sample_37: SCO11


title: SS_FSU_Celeg15_smallRNAseq

source_name: N2_5 days_Rotenone 0.039441 µg/ml


title: SS_FSU_Celeg17_smallRNAseq


title: Sample_26: PITUI14

value: Pituicytoma (PITUI)


title: SS_FSU_Celeg14_smallRNAseq


title: SS_FSU_Celeg13_smallRNAseq


title: Sample_25: PITUI13


title: Sample_24: PITUI12


title: SS_FSU_Celeg09_smallRNAseq

source_name: N2_1 day_2-Deoxyglucose

value: 1 day


title: SS_FSU_Celeg08_smallRNAseq


title: SS_FSU_Celeg24_smallRNAseq


title: Sample_22: PITUI10


title: SS_FSU_Celeg06_smallRNAseq

source_name: N2_1 day_Rotenone 0.039441 µg/ml


title: Sample_21: PITUI09


title: SS_FSU_Celeg04_smallRNAseq


title: SS_FSU_Celeg29_smallRNAseq

source_name: N2_20 days


title: Sample_19: PITUI07


title: Sample_28: SCO02


title: Sample_18: PITUI06


title: Sample_20: PITUI08


title: Sample_16: PITUI04


title: SS_FSU_Celeg05_smallRNAseq


title: Sample_12: GCT12

value: granular cell tumor (GCT)


title: SS_FSU_Celeg20_smallRNAseq

source_name: N2_10 days

value: whole worms


title: SS_FSU_Celeg21_smallRNAseq


title: Sample_13: PITUI01


title: Sample_15: PITUI03


title: Sample_17: PITUI05


title: SS_FSU_Celeg28_smallRNAseq

value: 20 days


title: Sample_14: PITUI02


title: SS_FSU_Celeg19_smallRNAseq

value: hermaphrodite


title: SS_FSU_Celeg07_smallRNAseq


title: Sample_11: GCT11


title: SS_FSU_Celeg10_smallRNAseq

source_name: N2_5 days


title: SS_FSU_Celeg02_smallRNAseq

source_name: N2_1 day


title: SS_FSU_Celeg12_smallRNAseq


title: SS_FSU_Celeg11_smallRNAseq


title: Sample_23: PITUI11


title: Sample_10: GCT10


title: SS_FSU_Celeg03_smallRNAseq


title: Sample_9: GCT09


title: SS_FSU_Celeg01_smallRNAseq


title: Sample_6: GCT06


title: Sample_7: GCT07


title: Sample_8: GCT08


title: MB_FLI_MR6.1_brain_RNAseq

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.8.2 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome v20150522 and annotation v20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

organism: Nothobranchius furzeri

source_name: brain

value: brain

value: 9 weeks

value: male

value: Rotenone 0.1% LC50


title: MB_FLI_MR3.1_brain_RNAseq


title: MB_FLI_MR2.1_brain_RNAseq


title: MB_FLI_MR7.1_brain_RNAseq


title: Sample_2: GCT02

value: m


title: Sample_3: GCT03

value: f


title: MB_FLI_MR7.5_skin_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls

source_name: skin

value: skin


title: MB_FLI_MR10.1_brain_RNAseq


title: MB_FLI_MR10.5_skin_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls


title: MB_FLI_MR2.5_skin_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls


title: Sample_1: GCT01


title: MB_FLI_MR3.5_skin_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls


title: NH_FLI_111_ZF_skin_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step.
Reads were trimmed und filtered using trimmomatic (0.36) [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20].
Reads were mapped using BWA (0.7.12-r1039) [parameter: -n 0 -o 0 -e 0 -l 8 -k 0].
Reads per gene were counted using samtools (1.3.1-9-ge5dfb0a).
Genome_build: mirBase Release 21 (D. rerio sequences only)
Supplementary_files_format_and_content: The Excel file includes raw counts (sample_counts.xls) of all mirBase D. rerio sequences for each sample.

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.

value: AB JxT\xFC Tg(wt1a:GFP)

value: 3.5 years


title: NH_FLI_109_ZF_skin_smallRNAseq


title: MB_FLI_MR7.3_liver_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls

source_name: liver

value: liver


title: MB_FLI_MR6.3_liver_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls


title: MB_FLI_MR3.3_liver_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls


title: NH_FLI_106_ZF_skin_smallRNAseq


title: NH_FLI_150_ZF_skin_smallRNAseq

value: AB JxT\xFC Tg(pu.1:GFP)

value: 3 years


title: Sample_5: GCT05

source_name: Tumor


title: NH_FLI_147_ZF_skin_smallRNAseq


title: NH_FLI_146_ZF_skin_smallRNAseq


title: MB_FLI_MR6.5_skin_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls


title: MB_FLI_MR23.5_skin_RNAseq

source_name: 27 weeks_Rotenone 1% LC50_skin

value: 27 weeks

value: Rotenone 1% LC50


title: MB_FLI_MR24.5_skin_RNAseq


title: NH_FLI_145_ZF_skin_smallRNAseq


title: NH_FLI_108_ZF_skin_smallRNAseq


title: MB_FLI_MR21.5_skin_RNAseq


title: NH_FLI_137_ZF_skin_smallRNAseq

value: AB JxT\xFC

value: 2 years


title: NH_FLI_133_ZF_skin_smallRNAseq


title: NH_FLI_136_ZF_skin_smallRNAseq


title: NH_FLI_135_ZF_skin_smallRNAseq


title: MB_FLI_MR25.5_skin_RNAseq


title: Sample_4: GCT04

value: granular cell tumor (GCT)


title: NH_FLI_134_ZF_skin_smallRNAseq


title: MB_FLI_MR22.5_skin_RNAseq


title: MB_FLI_MR16.5_skin_RNAseq

source_name: 9 weeks_Rotenone 10% LC50_skin

value: Rotenone 10% LC50


title: MB_FLI_MR18.5_skin_RNAseq

value: 9 weeks


title: MB_FLI_MR20.5_skin_RNAseq

value: male


title: MB_FLI_MR17.5_skin_RNAseq


title: MB_FLI_MR2.3_liver_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls

value: Rotenone 0.1% LC50


title: MB_FLI_MR10.3_liver_RNAseq

description:
sample_counts_2.xls
sample_rpkms_2.xls


title: NH_FLI_125_ZF_skin_smallRNAseq

value: AB JxT\xFC Tg(flk:mCherry)

value: 1 year


title: NH_FLI_120_ZF_skin_smallRNAseq

value: skin


title: MB_FLI_MR15.5_skin_RNAseq

source_name: 9 weeks_Rotenone 1% LC50_skin


title: MB_FLI_MR14.5_skin_RNAseq


title: NH_FLI_121_ZF_skin_smallRNAseq


title: NH_FLI_98_ZF_skin_smallRNAseq

value: 6 months


title: MB_FLI_MR13.5_skin_RNAseq


title: MB_FLI_MR12.5_skin_RNAseq


title: NH_FLI_85_ZF_skin_smallRNAseq


title: MB_FLI_MR25.3_liver_RNAseq

source_name: 27 weeks_Rotenone 1% LC50_liver


title: NH_FLI_122_ZF_skin_smallRNAseq


title: NH_FLI_156_ZF_brain_smallRNAseq

value: brain


title: MB_FLI_MR21.3_liver_RNAseq

value: liver


title: MB_FLI_MR11.5_skin_RNAseq


title: NH_FLI_94_ZF_skin_smallRNAseq


title: MB_FLI_MR22.3_liver_RNAseq


title: NH_FLI_153_ZF_brain_smallRNAseq

value: AB JxT\xFC Tg(pu.1:GFP)


title: MB_FLI_MR23.3_liver_RNAseq


title: NH_FLI_154_ZF_brain_smallRNAseq

value: 3 years


title: MB_FLI_MR20.3_liver_RNAseq

source_name: 9 weeks_Rotenone 10% LC50_liver


title: NH_FLI_152_ZF_brain_smallRNAseq


title: MB_FLI_MR19.3_liver_RNAseq


title: MB_FLI_MR17.3_liver_RNAseq


title: MB_FLI_MR24.3_liver_RNAseq

value: 27 weeks


title: NH_FLI_140_ZF_brain_smallRNAseq


title: NH_FLI_150_ZF_brain_smallRNAseq


title: NH_FLI_107_ZF_skin_smallRNAseq

value: AB JxT\xFC Tg(wt1a:GFP)

value: 3.5 years


title: NH_FLI_96_ZF_skin_smallRNAseq

value: AB JxT\xFC


title: MB_FLI_MR18.3_liver_RNAseq


title: NH_FLI_143_ZF_brain_smallRNAseq

value: 2 years


title: MB_FLI_MR16.3_liver_RNAseq

value: Rotenone 10% LC50


title: MB_FLI_MR14.3_liver_RNAseq

source_name: 9 weeks_Rotenone 1% LC50_liver

value: 9 weeks

value: Rotenone 1% LC50


title: NH_FLI_100_ZF_skin_smallRNAseq

value: male


title: NH_FLI_139_ZF_brain_smallRNAseq


title: NH_FLI_142_ZF_brain_smallRNAseq


title: NH_FLI_125_ZF_brain_smallRNAseq

value: AB JxT\xFC Tg(flk:mCherry)


title: NH_FLI_119_ZF_skin_smallRNAseq

value: 1 year


title: MB_FLI_MR13.3_liver_RNAseq


title: NH_FLI_114_ZF_brain_smallRNAseq


title: NH_FLI_124_ZF_brain_smallRNAseq


title: NH_FLI_128_ZF_brain_smallRNAseq


title: MB_FLI_MR11.3_liver_RNAseq


title: NH_FLI_129_ZF_brain_smallRNAseq


title: NH_FLI_127_ZF_brain_smallRNAseq


title: MB_FLI_MR12.3_liver_RNAseq


title: NH_FLI_99_100_ZF_brain_smallRNAseq


title: MB_FLI_MR15.3_liver_RNAseq


title: NH_FLI_97_98_ZF_brain_smallRNAseq


title: MB_FLI_MR22.1_brain_RNAseq

source_name: 27 weeks_Rotenone 1% LC50_brain


title: NH_FLI_112_ZF_brain_smallRNAseq


title: MB_FLI_MR23.1_brain_RNAseq


title: NH_FLI_138_ZF_brain_smallRNAseq


title: MB_FLI_MR21.1_brain_RNAseq


title: MB_FLI_MR24.1_brain_RNAseq


title: NH_FLI_95_96_ZF_brain_smallRNAseq


title: MB_FLI_MR25.1_brain_RNAseq


title: MB_FLI_MR19.1_brain_RNAseq

source_name: 9 weeks_Rotenone 10% LC50_brain


title: NH_FLI_116_ZF_brain_smallRNAseq


title: NH_FLI_109_ZF_brain_smallRNAseq


title: MB_FLI_MR20.1_brain_RNAseq


title: MB_FLI_MR17.1_brain_RNAseq


title: MB_FLI_MR16.1_brain_RNAseq


title: MB_FLI_MR18.1_brain_RNAseq


title: NH_FLI_111_ZF_brain_smallRNAseq


title: MB_FLI_MR15.1_brain_RNAseq

source_name: 9 weeks_Rotenone 1% LC50_brain


title: NH_FLI_103_104_ZF_brain_smallRNAseq


title: MB_FLI_MR14.1_brain_RNAseq


title: NH_FLI_101_102_ZF_brain_smallRNAseq


title: MB_FLI_MR13.1_brain_RNAseq


title: MB_FLI_Dre_em_ctrl_4_all_RNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCz10, and respective gene annotation (GRCz10.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

value: wild type

value: whole organism

value: 2 days


title: MB_FLI_MR11.1_brain_RNAseq

value: brain


title: MB_FLI_Dre_em_29a_2_all_RNAseq

value: synthetic miR-29a  2 ng


title: MB_FLI_Dre_em_ctrl_2_all_RNAseq


title: MB_FLI_Dre_em_101a_2_all_RNAseq

value: synthetic miR-101a  2 ng


title: MB_FLI_Dre_em_29a_4_all_RNAseq


title: MB_FLI_Dre_em_ctrl_1_all_RNAseq


title: MB_FLI_Dre_em_101a_1_all_RNAseq


title: MB_FLI_Dre_em_101a_4_all_RNAseq


title: MB_FLI_GR11.5_skin_RNAseq

value: GRZ

value: skin

value: Rotenone 150 pM


title: MB_FLI_GR12.5_skin_RNAseq


title: MB_FLI_GR1.5_skin_RNAseq

value: Rotenone 15 pM


title: MB_FLI_MR12.1_brain_RNAseq


title: MB_FLI_GR8.5_skin_RNAseq


title: MB_FLI_GR10.5_skin_RNAseq


title: MB_FLI_GR5.5_skin_RNAseq


title: AC_FLI_RNA_40_brain_RNAseq

value: 6 months


title: MB_FLI_GR9.5_skin_RNAseq


title: MB_FLI_Dre_em_29a_3_all_RNAseq


title: MB_FLI_GC4.5_skin_RNAseq

value: DMSO


title: MB_FLI_GR4.5_skin_RNAseq

value: 9 weeks


title: AC_FLI_RNA_41_brain_RNAseq


title: MB_FLI_Dre_em_29a_1_all_RNAseq


title: MB_FLI_Dre_em_101a_3_all_RNAseq


title: MB_FLI_GR3.5_skin_RNAseq


title: AC_FLI_RNA_39_brain_RNAseq


title: AC_FLI_RNA_38_brain_RNAseq


title: AC_FLI_RNA_36_brain_RNAseq


title: MB_FLI_GC3.5_skin_RNAseq


title: MB_FLI_GR2.5_skin_RNAseq


title: AC_FLI_RNA_35_brain_RNAseq


title: AC_FLI_RNA_33_brain_RNAseq


title: MB_FLI_Dre_em_ctrl_3_all_RNAseq


title: MB_FLI_JG66.5_skin_RNAseq

value: 14 weeks


title: MB_FLI_GC5.5_skin_RNAseq

value: male


title: AC_FLI_RNA_31_brain_RNAseq


title: MB_FLI_GC2.5_skin_RNAseq


title: AC_FLI_RNA_30_brain_RNAseq


title: MB_FLI_JG61.5_skin_RNAseq

value: 10 weeks


title: AC_FLI_RNA_37_brain_RNAseq


title: MB_FLI_MR19.5_skin_RNAseq

value: Rotenone 10% LC50


title: MB_FLI_JG68.5_skin_RNAseq


title: NH_FLI_271_skin_RNAseq

value: AB tert(+/-)

value: 3 months


title: MB_FLI_JG69.5_skin_RNAseq


title: MB_FLI_GC1.5_skin_RNAseq


title: NH_FLI_270_skin_RNAseq

value: AB wildtype


title: MB_FLI_JG60.5_skin_RNAseq


title: AC_FLI_RNA_34_brain_RNAseq

value: brain


title: MB_FLI_JG70.5_skin_RNAseq


title: MB_FLI_JG64.5_skin_RNAseq

value: 7 weeks


title: NH_FLI_258_skin_RNAseq


title: MB_FLI_JG67.5_skin_RNAseq


title: MB_FLI_JG65.5_skin_RNAseq


title: NH_FLI_149_ZF_skin_smallRNAseq

value: AB JxT\xFC Tg(pu.1:GFP)

value: 3 years


title: MB_FLI_JG57.5_skin_RNAseq

value: GRZ

value: skin


title: NH_FLI_273_skin_RNAseq

value: AB tert(-/-)


title: NH_FLI_257_skin_RNAseq


title: NH_FLI_256_skin_RNAseq


title: MB_FLI_JG58.5_skin_RNAseq


title: MB_FLI_JG59.5_skin_RNAseq


title: MB_FLI_JG55.5_skin_RNAseq


title: MB_FLI_JG48.5_skin_RNAseq


title: NH_FLI_254_skin_RNAseq


title: MB_FLI_JG53.5_skin_RNAseq


title: MB_FLI_JG35.5_skin_RNAseq

value: 5 weeks


title: AC_FLI_RNA_32_brain_RNAseq

value: wild type

value: 6 months


title: MB_FLI_JG21.5_skin_RNAseq


title: NH_FLI_255_skin_RNAseq


title: NH_FLI_253_skin_RNAseq


title: MB_FLI_GR9.3_liver_RNAseq

value: liver

value: 9 weeks

value: Rotenone 150 pM


title: NH_FLI_235_skin_RNAseq

value: male


title: MB_FLI_JG19.5_skin_RNAseq


title: NH_FLI_251_skin_RNAseq

value: AB tert(+/-)


title: NH_FLI_264_skin_RNAseq

value: 3 months


title: NH_FLI_231_skin_RNAseq

value: AB JxTu

value: swim-tunnel


title: NH_FLI_228_skin_RNAseq


title: NH_FLI_234_skin_RNAseq

value: AB wildtype


title: NH_FLI_230_skin_RNAseq


title: MB_FLI_GR5.3_liver_RNAseq

value: Rotenone 15 pM


title: MB_FLI_GR8.3_liver_RNAseq


title: MB_FLI_JG18.5_skin_RNAseq


title: NH_FLI_227_skin_RNAseq

value: 3 years


title: MB_FLI_GR4.3_liver_RNAseq

value: GRZ


title: MB_FLI_JG25.5_skin_RNAseq

value: skin


title: MB_FLI_GR3.3_liver_RNAseq


title: MB_FLI_GR2.3_liver_RNAseq


title: NH_FLI_223_skin_RNAseq


title: NH_FLI_229_skin_RNAseq


title: NH_FLI_224_skin_RNAseq


title: MB_FLI_GR11.3_liver_RNAseq


title: NH_FLI_225_skin_RNAseq


title: MB_FLI_GR12.3_liver_RNAseq


title: NH_FLI_219_skin_RNAseq

value: 1 year


title: NH_FLI_217_skin_RNAseq


title: NH_FLI_218_skin_RNAseq


title: MB_FLI_GC5.3_liver_RNAseq

value: DMSO


title: MB_FLI_GR1.3_liver_RNAseq


title: NH_FLI_222_skin_RNAseq


title: NH_FLI_216_skin_RNAseq


title: MB_FLI_GC4.3_liver_RNAseq


title: MB_FLI_GC2.3_liver_RNAseq


title: NH_FLI_215_skin_RNAseq


title: MB_FLI_GC3.3_liver_RNAseq


title: MB_FLI_GC1.3_liver_RNAseq


title: MB_FLI_JG73.3_liver_RNAseq

value: 14 weeks


title: MB_FLI_JG71.3_liver_RNAseq


title: NH_FLI_212_skin_RNAseq


title: NH_FLI_211_skin_RNAseq


title: MB_FLI_JG65.3_liver_RNAseq

value: 7 weeks


title: MB_FLI_JG68.3_liver_RNAseq

value: liver


title: NH_FLI_221_skin_RNAseq


title: MB_FLI_GR10.3_liver_RNAseq

value: 9 weeks


title: NH_FLI_273_muscle_RNAseq

source_name: muscle

value: AB tert(-/-)

value: muscle


title: NH_FLI_210_skin_RNAseq

value: male


title: MB_FLI_JG67.3_liver_RNAseq


title: MB_FLI_JG70.3_liver_RNAseq


title: MB_FLI_JG64.3_liver_RNAseq


title: NH_FLI_258_muscle_RNAseq

value: AB tert(+/-)

value: 3 months


title: MB_FLI_JG60.3_liver_RNAseq

value: 10 weeks


title: NH_FLI_271_muscle_RNAseq


title: MB_FLI_JG59.3_liver_RNAseq


title: MB_FLI_JG58.3_liver_RNAseq


title: NH_FLI_264_muscle_RNAseq


title: NH_FLI_255_muscle_RNAseq

value: AB wildtype


title: NH_FLI_213_skin_RNAseq

value: AB JxTu


title: MB_FLI_JG55.3_liver_RNAseq


title: MB_FLI_JG53.3_liver_RNAseq


title: NH_FLI_256_muscle_RNAseq


title: MB_FLI_JG57.3_liver_RNAseq


title: NH_FLI_209_skin_RNAseq


title: NH_FLI_257_muscle_RNAseq


title: MB_FLI_JG25.3_liver_RNAseq

value: 5 weeks


title: MB_FLI_JG23.3_liver_RNAseq

value: GRZ


title: NH_FLI_230_muscle_RNAseq

value: 3 years

value: swim-tunnel


title: MB_FLI_JG22.3_liver_RNAseq


title: MB_FLI_JG48.3_liver_RNAseq


title: NH_FLI_228_muscle_RNAseq


title: NH_FLI_227_muscle_RNAseq


title: NH_FLI_226_muscle_RNAseq


title: NH_FLI_251_muscle_RNAseq


title: NH_FLI_235_muscle_RNAseq


title: MB_FLI_JG35.3_liver_RNAseq


title: NH_FLI_234_muscle_RNAseq


title: NH_FLI_223_muscle_RNAseq


title: MB_FLI_JG62.3_liver_RNAseq


title: MB_FLI_GR3.1_brain_RNAseq

value: brain

value: Rotenone 15 pM


title: NH_FLI_270_muscle_RNAseq


title: MB_FLI_GR12.1_brain_RNAseq

value: Rotenone 150 pM


title: MB_FLI_GR9.1_brain_RNAseq


title: NH_FLI_225_muscle_RNAseq


title: NH_FLI_221_muscle_RNAseq


title: MB_FLI_GR8.1_brain_RNAseq


title: NH_FLI_231_muscle_RNAseq


title: humanized rat liver 2

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
All sequencing reads from RNA-seq were mapped to the human reference genome (hg38) using hisat2-2.10.
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks v.2.2.1 using default parameters for gene expression levels.
We used htseq-count to count reads on genes. Differential expression analysis was performed using DESeq2 (R package).
Genome_build: hg38
Supplementary_files_format_and_content: excel files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: humanized rat liver

extract_protocol:
Total RNA was isolated from humanized rat liver by Trizol
Libraries were prepared with an Illumina TruSeq Stranded mRNA Library Preparation Kit

treatment_protocol: Human hepatocytes were transplanted to the rat livers

tag: organ

value: liver


title: MB_FLI_GR4.1_brain_RNAseq

value: 9 weeks


title: humanized rat liver 1


title: NH_FLI_229_muscle_RNAseq


title: MB_FLI_GR5.1_brain_RNAseq


title: MB_FLI_GR2.1_brain_RNAseq


title: NH_FLI_219_muscle_RNAseq

value: 1 year


title: MB_FLI_GR10.1_brain_RNAseq


title: NH_FLI_222_muscle_RNAseq

value: muscle


title: NH_FLI_254_muscle_RNAseq

value: AB tert(-/-)

value: male


title: MB_FLI_JG17.3_liver_RNAseq


title: NH_FLI_253_muscle_RNAseq

value: 3 months


title: NH_FLI_220_muscle_RNAseq


title: MB_FLI_GC5.1_brain_RNAseq

value: DMSO


title: NH_FLI_216_muscle_RNAseq


title: MB_FLI_GC4.1_brain_RNAseq


title: MB_FLI_GC3.1_brain_RNAseq


title: MB_FLI_GR11.1_brain_RNAseq


title: Lung_21

city: Tucson

first: Donata

last: Vercelli

state: Arizona

address: 1657 E. Helen St.

institute: University of Arizona

data_processing:
Adapter sequences were trimmed from RNA-seq reads (fastq files) and only reads >25bp long were included in the analysis
Reads were mapped to the BALB/cJ genome (version mm10) using STAR and genomic coordinates were shifted to the standard mm10 genome using MARGE
HOMER was used to select uniquely aligning reads and to generate gene counts. A maximum of 3 clones/read was included to minimize bias due to PCR amplification.
Expression data were estimated for 24,538 genes and were filtered to include only genes with at least one read in 20% of the samples, which retained a total of 19,613 genes.
RUVSeq was used to estimate latent factors of unwanted variation (3 RUVs) that were included as covariates in differential expression analysis.
Differential expression analysis was performed using DESeq2 and differentially expressed genes were defined as having an FDR-adjusted P-value <0.05 and a |log2 fold change| >0.5.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file including normalized counts (rlog transformation) for each sample

source_name: unfractionated lung tissue

extract_protocol:
total RNA was isolated using RNeasy mini kits (Qiagen) and mRNA capture (polyA enrichment) was achieved using oligo(dT)25 Dynabeads (ThermoFisher)
cDNA libraries were constructed using KAPA Biosystems kits (Roche)

treatment_protocol: Balb/c mice (7-8 weeks old) were sensitized intra-peritoneally (i.p.) with OVA (chicken egg white albumin, Sigma: 20 ug) + Alum (Imject Alum, Thermo Fisher: 50 ul) at day 0 and 14 and challenged i.n. with OVA (50 ug) 6 at day 28 and 38. OM-85 (1 mg in 0.9% saline/treatment x 14 treatments) was administered i.n, 25 ul/nostril, under light anesthesia (1-5% isoflurane) every 2-3 days from day 0. Control mice received PBS at the time of sensitization, challenge and treatment. Unfractionated lung tissue was collected at day 39 and processed for RNA-sequencing.

value: lung

value: BALB/cJ

value: OVA

value: Male

tag: bal eosinophils (percent)

tag: ahr slope (z-score)


title: Lung_23


title: NH_FLI_214_muscle_RNAseq

value: AB JxTu


title: Lung_18


title: Lung_26


title: MB_FLI_GC1.1_brain_RNAseq

value: GRZ


title: NH_FLI_212_muscle_RNAseq


title: Lung_16


title: Lung_25


title: NH_FLI_218_muscle_RNAseq

value: swim-tunnel


title: MIC B1KO

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Raw BCL files from the Illumina HiSeq were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10)  that included Cre and PyV mT, and transcript counts quantified for each annotated gene within every cell.
The resulting UMI count matrices (genes × cells) were then provided as input to Seurat suite (version 3.2.3). A minimum of 800 and a maximum of 8000 detected genes per cell was defined as acceptable range to exclude low-quality cells. Cells with more than 8% of the transcript counts derived from mitochondrial-encoded genes were further removed.
Single cell RNA Seq datasets were integrated using Seurat’s alignment procedure. Canonical correlation analysis (CCA) was performed to identify shared sources of variation to produce anchors across the datasets following SCTransform normalization.
Clustering and visualization of the integrated dataset were performed using Uniform Manifold Approximation and Projection (UMAP), based on the first 11 principal components with a resolution of 0.3 (FindClusters and RunUMAP functions in Seurat). Cluster-specific marker genes were identified using FindAllMarkers function with a cut-off of log fold-change > 0.5 and Bonferroni adjusted p value < 0.05, and cell-type annotation was performed using SCSA.
Differential gene expression analysis between β1 integrin-proficient and -deficient cells was performed using FindMarkers. Differentially expressed genes were identified using a cut-off of |log fold-change| > 0.25 and Bonferroni adjusted p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 binary data format

source_name: Mammary carcinoma

growth_protocol: Mice were given drinking water with doxycycline (2 mg/mL) at 10 weeks of age and monitored weekly by physical palpations for tumour formation.

extract_protocol:
Dormant lesions for each genotype were pooled, dissociated into single cell suspension,  blocked with TruStain FcX™, and stained with Viability Dye eFluor506. Negatively stained viable cells were collected back from Flow Cytometry and sent to Génome Québec Innovation Tumour for quality assessment and sequencing (Illumina HiSeq 4000).
10X Chromium Single Cell 3'

value: FVB

tag: tumour stage

value: Early invsive mammary carcinoma

tag: tissue type

value: Mammary carcinoma


title: MIC WT


title: NH_FLI_210_muscle_RNAseq


title: Lung_19

tag: treatment


title: MB_FLI_JG70.1_brain_RNAseq

source_name: brain

value: brain

value: 14 weeks


title: NH_FLI_215_muscle_RNAseq

value: muscle

value: 1 year


title: Lung_20


title: MB_FLI_JG69.1_brain_RNAseq

value: male


title: NH_FLI_213_muscle_RNAseq


title: Lung_22

value: PBS


title: Lung_27


title: Lung_10


title: Lung_17


title: Lung_15


title: Lung_13


title: MB_FLI_JG72.1_brain_RNAseq


title: NH_FLI_271_liver_RNAseq

value: AB tert(+/-)

value: liver

value: 3 months


title: Lung_24

value: lung

value: BALB/cJ


title: Lung_7

value: Male


title: MB_FLI_GR1.1_brain_RNAseq

value: GRZ

value: 9 weeks

value: Rotenone 150 pM


title: MB_FLI_GC2.1_brain_RNAseq

value: DMSO


title: Lung_12

value: OVA


title: Lung_8


title: NH_FLI_273_liver_RNAseq

value: AB tert(-/-)


title: MB_FLI_JG73.1_brain_RNAseq

value: brain

value: 14 weeks


title: Lung_5


title: MB_FLI_JG65.1_brain_RNAseq

value: 7 weeks


title: NH_FLI_270_liver_RNAseq

value: AB wildtype

value: male


title: Lung_14


title: NH_FLI_211_muscle_RNAseq

value: AB JxTu

value: muscle

value: 1 year


title: NH_FLI_264_liver_RNAseq

value: AB tert(+/-)

value: liver

value: 3 months


title: Lung_11

value: lung

value: BALB/cJ

value: Male


title: Lung_6


title: Lung_9

value: PBS


title: Lung_4


title: Lung_1


title: NH_FLI_258_liver_RNAseq


title: MB_FLI_JG62.1_brain_RNAseq

value: GRZ

value: 10 weeks


title: MB_FLI_JG66.1_brain_RNAseq

value: brain


title: MB_FLI_JG64.1_brain_RNAseq


title: SUM159 DMSO_WCE

city: singapore

first: Ser Yue

last: Loo

address: 60 biopolis street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using BWA aligner.
Aligned reads were deduplicated using Picard Markduplicates.jar.
Peak-calling was performed using MACS2 peak-caller with default parameters.
Differential binding was performed using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using MACS2 peak-caller.

source_name: Mammary  cells

growth_protocol: NAMEC8 is maintained in MEGM (Lonza) and split in a ratio of 1:10 every 2 days. SUM159 is maintained in Ham's F12 (Gibco) supplemented with 5%FBS, insulin, hydrocortisone and Pen/Strep and split in a ratio of 1:6 every 2 days.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was then inactivated by the addition of 125 mM glycine. Chromatin extracts containing DNA fragments with an average size of 200-500 bp were immunoprecipitated using anti-RARα, anti-RXRα, anti-H3K27ace or anti-p300 antibody. The ChIP-enriched DNA was then decrosslinked and used for library preparation.
Libraries were prepared according to Illumina's instructions. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were treated with Bexarotene (1uM) for 7 and 14 days. Media was changed with fresh drug every 2 days.

value: breast

tag: cell line

tag: cell type

value: Triple negative breast cancer cells

tag: agent

value: DMSO

tag: time

value: control

tag: chip antibody


title: MB_FLI_JG59.1_brain_RNAseq

tag: strain

value: male


title: SUM159 ST_WCE

value: Bexarotene

value: 7 days


title: SUM159 DMSO_Histone H3K27ac

value: Histone H3K27ac (Active Motif, 39135)


title: NH_FLI_257_liver_RNAseq

source_name: liver

value: AB wildtype

value: liver


title: SUM159 LT_Histone H3K27ac

value: 14 days


title: NH_FLI_256_liver_RNAseq

value: AB tert(-/-)

value: 3 months


title: Lung_3

value: lung

value: BALB/cJ

value: PBS

value: Male


title: SUM159 LT_WCE

value: breast


title: SUM159 ST_Histone H3K27ac

value: Triple negative breast cancer cells


title: SUM159 ST_p300

value: p300 (Santa Cruz, sc-585)


title: NH_FLI_254_liver_RNAseq


title: SUM159 LT_p300


title: NH_FLI_253_liver_RNAseq


title: Lung_2


title: NH_FLI_251_liver_RNAseq

value: AB tert(+/-)


title: SUM159 DMSO_p300

value: DMSO

value: control


title: MB_FLI_JG55.1_brain_RNAseq

value: GRZ

value: brain

value: 7 weeks

value: male


title: SUM159 LT_RARa

value: Bexarotene

value: 14 days

value: RARa (Diagenode, C15310155)


title: MB_FLI_JG53.1_brain_RNAseq


title: NH_FLI_235_liver_RNAseq

value: liver

value: 3 months


title: NH_FLI_255_liver_RNAseq

value: AB wildtype


title: SUM159 LT_RXRa

value: RXRa (Santa Cruz, sc-553)


title: MB_FLI_JG60.1_brain_RNAseq

value: 10 weeks


title: SUM159 DMSO_RARa

value: breast

value: Triple negative breast cancer cells


title: SUM159 ST_RXRa

value: 7 days


title: MB_FLI_JG58.1_brain_RNAseq


title: NAMEC8 DMSO_WCE none

source_name: Mammary epithelial cells

value: Derived from human mammary epitheilal cells

value: DMSO


title: NAMEC8 LT_WCE none


title: NH_FLI_231_liver_RNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome GRCz10 and respective gene annotation (GRCz10.84).
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

value: AB JxTu

value: 3 years

value: swim-tunnel


title: MB_FLI_JG48.1_brain_RNAseq

value: GRZ

value: brain

value: 7 weeks

value: male


title: NAMEC8 ST_WCE none

value: Bexarotene


title: NH_FLI_234_liver_RNAseq

value: liver

value: 3 months


title: MB_FLI_JG57.1_brain_RNAseq


title: NAMEC8 DMSO_Histone H3K27ac

value: control

value: Histone H3K27ac (Active Motif, 39135)


title: SUM159 ST_RARa

value: breast

value: RARa (Diagenode, C15310155)


title: MB_FLI_JG23.1_brain_RNAseq

value: 5 weeks


title: NH_FLI_230_liver_RNAseq


title: MB_FLI_JG25.1_brain_RNAseq


title: MB_FLI_JG35.1_brain_RNAseq


title: NAMEC8 LT_p300

value: Derived from human mammary epitheilal cells

value: 14 days

value: p300 (Santa Cruz, sc-585)


title: NAMEC8 ST_Histone H3K27ac

value: 7 days


title: NH_FLI_229_liver_RNAseq

value: AB JxTu

value: 3 years

value: swim-tunnel


title: NAMEC8 ST_p300


title: NAMEC8 DMSO_p300

value: DMSO


title: MB_FLI_JG21.1_brain_RNAseq

value: GRZ

value: brain

value: male


title: MB_FLI_JG20.1_brain_RNAseq


title: SUM159 DMSO_RXRa

value: Triple negative breast cancer cells

value: RXRa (Santa Cruz, sc-553)


title: NAMEC8 LT_RARa

value: Bexarotene


title: NH_FLI_227_liver_RNAseq

value: liver


title: NAMEC8 ST_RARa

value: breast

value: RARa (Diagenode, C15310155)


title: NAMEC8 LT_Histone H3K27ac

value: Derived from human mammary epitheilal cells

value: Histone H3K27ac (Active Motif, 39135)


title: NAMEC8 DMSO_RARa

value: control


title: F2: MCF7_KO#2_estrogen_4h

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: MCF7 CRISPR/Cas9 HSF1 knockout cells 2 - estrogen treated for 30 minutes (10nM)

data_processing:
Quality control of sequencing data was performed using FastQC and MultiQC
Raw sequencing data were aligned to human reference genome GRCh38 using hisat 2.0.5
Reads aligned in the regions of genes (GRCh38.p12) were counted using FeatureCounts
Read counts were normalized using DESeq2 in R
Genome_build: GRCh38 available at NCBI servers: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Supplementary_files_format_and_content: Processed files are in tab separated text format. They include raw counts and normalized expression per gene.

source_name: MCF7 cells

growth_protocol: The wild-type MCF7 cells were purchased from ATCC (HTB-22) and used as a primary model. Cells were grown in DMEM/F12 medium supplemented with 10% fetal bovine serum and antibiotic-antimycotic cocktail (penicillin, streptomycin, amphotericin) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from all MCF7 cell variants (untreated and treated with 10 nM E2 for 4 h or heat shocked for 1h at 43°C and recovered for 2 h) using the Direct-ZolTM RNA MiniPrep Kit (Zymo Research) and digested with DNase I (Worthington Biochemical Corporation). For each experimental point, RNAs from three biological replicates were first tested by RT-qPCR for the efficiency of treatments, then pooled and sequenced.
RNA libraries were prepared for sequencing according to the standard Illumina protocols

treatment_protocol: Cells were seeded on culture plates. Next day the medium was replaced into phenol-free DMEM/F12 medium supplemented with 5% dextran-activated charcoal-stripped FBS and 48 hours later 17β-estradiol was added to final concentration of 10nM for 4 hour or cells were subjected to hyperthermia (43°C) for 1 hour with 2 hours of recovery.

tag: tumor

value: adenocarcinoma

value: female

value: 69 years

tag: genotype

value: CRISPR/Cas9 HSF1 knockout 2


title: NH_FLI_225_liver_RNAseq

value: AB JxTu

tag: tissue

tag: age

value: 3 years


title: NAMEC8 LT_RXRa

value: 14 days


title: NAMEC8 ST_RXRa

value: 7 days


title: F1: MCF7_KO#2_control

description: MCF7 CRISPR/Cas9 HSF1 knockout cells 2 - untreated

tag: Sex


title: SSM_FLI_9_day_Quiescence_2_none_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCh38, and respective gene annotation (GRCh38.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

source_name: cell line MRC-5

value: MRC-5 fibroblasts

tag: population doublings

tag: perturbation

value: subjected to quiescence using 9 days contact inhibition


title: SSM_FLI_9_day_Quiescence_3_none_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: SSM_FLI_Shiva8_3_none_RNAseq

value: male

value: FLI06 10 uM


title: F3: MCF7_KO#2_HS_1h/2h_rec

description: MCF7 CRISPR/Cas9 HSF1 knockout cells 2 - hyperhermia (43°C) for 1hour & 2hours of recovery

value: breast


title: E2: MCF7_KO#1_estrogen_4h

description: MCF7 CRISPR/Cas9 KSF1 knockout cells 1 - estrogen treated for 30 minutes (10nM)

value: CRISPR/Cas9 KSF1 knockout 1


title: NH_FLI_223_liver_RNAseq

value: liver


title: SSM_FLI_Shiva8_2_none_RNAseq


title: SSM_FLI_9_day_Quiescence_1_none_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_228_liver_RNAseq

value: swim-tunnel


title: E3: MCF7_KO#1_HS_1h/2h_rec

description: MCF7 CRISPR/Cas9 HSF1 knockout cells 1 - hyperhermia (43°C) for 1hour & 2hours of recovery

value: CRISPR/Cas9 HSF1 knockout 1


title: NH_FLI_222_liver_RNAseq


title: NH_FLI_221_liver_RNAseq


title: NH_FLI_218_liver_RNAseq

value: 1 year


title: SSM_FLI_Shiva7_2_none_RNAseq

source_name: cell line HFF

value: HFF


title: SSM_FLI_Shiva8_1_none_RNAseq


title: NH_FLI_219_liver_RNAseq


title: D2: MCF7_MIX_estrogen_4h

description: MCF7 CRISPR/Cas9 control cells - estrogen treated for 30 minutes (10nM)

value: adenocarcinoma

value: female

value: 69 years

value: CRISPR/Cas9 control


title: SSM_FLI_Shiva7_3_none_RNAseq


title: E1: MCF7_KO#1_control

description: MCF7 CRISPR/Cas9 HSF1 knockout cells 1 - untreated


title: D3: MCF7_MIX_HS_1h/2h_rec

description: MCF7 CRISPR/Cas9 control cells - hyperhermia (43°C) for 1hour & 2hours of recovery


title: NH_FLI_224_liver_RNAseq

value: AB JxTu

value: 3 years


title: SSM_FLI_Shiva7_1_none_RNAseq


title: D1: MCF7_MIX_control

description: MCF7 CRISPR/Cas9 control cells - untreated


title: SSM_FLI_Shiva5_3_none_RNAseq

value: BFA 1 ug/ml


title: C3: MCF7_shHSF1_HS_1h/2h_rec

description: MCF7 shHSF1 cells - hyperhermia (43°C) for 1hour & 2hours of recovery


title: NH_FLI_216_liver_RNAseq


title: NH_FLI_217_liver_RNAseq


title: SSM_FLI_Shiva6_2_none_RNAseq


title: NAMEC8 DMSO_RXRa

value: Derived from human mammary epitheilal cells

value: DMSO

value: control

value: RXRa (Santa Cruz, sc-553)


title: C2: MCF7_shHSF1_estrogen_4h

description: MCF7 shHSF1 cells - estrogen treated for 30 minutes (10nM)

value: breast


title: SSM_FLI_Shiva4_2_none_RNAseq

value: male


title: SSM_FLI_Shiva4_1_none_RNAseq


title: SSM_FLI_Shiva4_3_none_RNAseq


title: SSM_FLI_Shiva5_1_none_RNAseq


title: NH_FLI_213_liver_RNAseq

value: liver


title: SSM_FLI_Shiva6_1_none_RNAseq


title: NH_FLI_215_liver_RNAseq

value: swim-tunnel


title: SSM_FLI_Shiva5_2_none_RNAseq


title: SSM_FLI_Shiva3_1_none_RNAseq

value: FLI06 10 uM


title: SSM_FLI_Shiva2_3_none_RNAseq

value: HFF


title: SSM_FLI_Shiva3_3_none_RNAseq


title: B1: MCF7_SCR_control

description: MCF7 shRNA control cells - untreated

value: adenocarcinoma

value: shRNA control


title: NH_FLI_210_liver_RNAseq

value: 1 year


title: NH_FLI_209_liver_RNAseq


title: B2: MCF7_SCR_estrogen_4h

description: MCF7 shRNA control cells - estrogen treated for 30 minutes (10nM)

value: female

value: 69 years


title: B3: MCF7_SCR_HS_1h/2h_rec

description: MCF7 shRNA control cells - hyperhermia (43°C) for 1hour & 2hours of recovery


title: SSM_FLI_Shiva12_3_none_RNAseq

source_name: cell line BJ

value: BJ


title: A2: MCF7_WT_estrogen_4h

description: MCF7 wild type - estrogen treated for 30 minutes (10nM)

value: wild type


title: NH_FLI_271_brain_RNAseq

value: AB tert(+/-)

value: brain

value: 3 months


title: SSM_FLI_Shiva6_3_none_RNAseq

value: BFA 1 ug/ml


title: SSM_FLI_Shiva2_2_none_RNAseq


title: SSM_FLI_Shiva12_1_none_RNAseq


title: NH_FLI_270_brain_RNAseq

value: AB wildtype


title: SSM_FLI_Shiva2_1_none_RNAseq

value: male


title: SSM_FLI_Shiva1_3_none_RNAseq


title: NH_FLI_211_liver_RNAseq

value: AB JxTu

value: liver


title: SSM_FLI_Shiva1_2_none_RNAseq

value: FLI06 10 uM


title: SSM_FLI_Shiva11_2_none_RNAseq


title: NH_FLI_273_brain_RNAseq

value: AB tert(-/-)


title: NH_FLI_264_brain_RNAseq


title: NH_FLI_212_liver_RNAseq


title: A3: MCF7_WT_HS_1h/2h_rec

description: MCF7 wild type - hyperhermia (43°C) for 1hour & 2hours of recovery

value: adenocarcinoma

value: breast


title: C1: MCF7_shHSF1_control

description: MCF7 shHSF1 cells - untreated


title: SSM_FLI_Shiva3_2_none_RNAseq


title: SSM_FLI_Shiva1_1_none_RNAseq

value: HFF


title: SSM_FLI_Shiva11_1_none_RNAseq


title: A1: MCF7_WT_control

description: MCF7 wild type - untreated

value: female


title: NH_FLI_258_brain_RNAseq


title: MG_UKJ_D7T_skin_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were trimmed und filtered using trimmomatic (0.36) [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20].
Reads per gene were counted using samtools (1.3.1-9-ge5dfb0a).
Genome_build: mirBase Release 21 (H. sapiens sequences only)
Supplementary_files_format_and_content: The text file includes raw counts (sample_counts.txt) of all mirBase H. sapiens sequences for each sample.

source_name: skin

value: skin

value: 75-80 years


title: SSM_FLI_Shiva11_3_none_RNAseq

value: BJ


title: MG_UKJ_D14T_skin_smallRNAseq


title: NH_FLI_257_brain_RNAseq


title: MG_UKJ_D13T_skin_smallRNAseq


title: MG_UKJ_D11T_skin_smallRNAseq


title: MG_UKJ_D12T_skin_smallRNAseq


title: MG_UKJ_D2T_skin_smallRNAseq


title: NH_FLI_255_brain_RNAseq


title: MG_UKJ_C9T_skin_smallRNAseq

value: 60-65 years


title: MG_UKJ_D1T_skin_smallRNAseq


title: MG_UKJ_C3T_skin_smallRNAseq


title: MG_UKJ_D10T_skin_smallRNAseq


title: NH_FLI_256_brain_RNAseq

value: brain


title: SSM_FLI_Shiva12_2_none_RNAseq


title: NH_FLI_235_brain_RNAseq

value: AB tert(+/-)

value: 3 months


title: MG_UKJ_C6T_skin_smallRNAseq


title: NH_FLI_254_brain_RNAseq


title: MG_UKJ_C2T_skin_smallRNAseq


title: MG_UKJ_C12T_skin_smallRNAseq


title: MG_UKJ_B8T_skin_smallRNAseq

value: 45-50 years


title: NH_FLI_253_brain_RNAseq

value: AB wildtype

value: male


title: MG_UKJ_C1T_skin_smallRNAseq


title: NH_FLI_251_brain_RNAseq


title: MG_UKJ_C13T_skin_smallRNAseq


title: MG_UKJ_B3T_skin_smallRNAseq


title: MG_UKJ_B9T_skin_smallRNAseq


title: NH_FLI_234_brain_RNAseq


title: MG_UKJ_B4T_skin_smallRNAseq


title: NH_FLI_232_brain_RNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCz10, and respective gene annotation (GRCz10.84).
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

value: AB JxTu

value: 3 years

value: swim-tunnel


title: MG_UKJ_B1T_skin_smallRNAseq


title: NH_FLI_231_brain_RNAseq


title: MG_UKJ_B14T_skin_smallRNAseq


title: MG_UKJ_B13T_skin_smallRNAseq


title: MG_UKJ_A9T_skin_smallRNAseq

value: 24-29 years


title: MG_UKJ_A8T_skin_smallRNAseq


title: MG_UKJ_B2T_skin_smallRNAseq


title: MG_UKJ_B12T_skin_smallRNAseq


title: NH_FLI_228_brain_RNAseq


title: NH_FLI_229_brain_RNAseq


title: MG_UKJ_A6T_skin_smallRNAseq


title: NH_FLI_227_brain_RNAseq


title: MG_UKJ_A13T_skin_smallRNAseq


title: MG_UKJ_A5T_skin_smallRNAseq


title: MG_UKJ_D7B_blood_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were trimmed und filtered using trimmomatic (0.36) [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20].
Reads per gene were counted using samtools (1.3.1-9-ge5dfb0a).
Genome_build: mirBase Release 21 (H. sapiens sequences only)
Supplementary_files_format_and_content: The text file includes raw counts (sample_counts.txt) of all mirBase H. sapienssequences for each sample.

source_name: blood

value: blood


title: MG_UKJ_D2B_blood_smallRNAseq


title: MG_UKJ_A7T_skin_smallRNAseq


title: NH_FLI_224_brain_RNAseq


title: MG_UKJ_D14B_blood_smallRNAseq


title: NH_FLI_223_brain_RNAseq


title: NH_FLI_226_brain_RNAseq


title: MG_UKJ_D12B_blood_smallRNAseq


title: MG_UKJ_D11B_blood_smallRNAseq


title: MG_UKJ_D13B_blood_smallRNAseq


title: MG_UKJ_D10B_blood_smallRNAseq


title: MG_UKJ_C8B_blood_smallRNAseq


title: NH_FLI_222_brain_RNAseq


title: NH_FLI_221_brain_RNAseq


title: MG_UKJ_C6B_blood_smallRNAseq


title: NH_FLI_220_brain_RNAseq

value: 1 year


title: MG_UKJ_C2B_blood_smallRNAseq


title: NH_FLI_219_brain_RNAseq


title: MG_UKJ_C13B_blood_smallRNAseq


title: NH_FLI_218_brain_RNAseq


title: MG_UKJ_B9B_blood_smallRNAseq


title: MG_UKJ_C3B_blood_smallRNAseq


title: MG_UKJ_C12B_blood_smallRNAseq


title: MG_UKJ_B8B_blood_smallRNAseq


title: NH_FLI_217_brain_RNAseq


title: MG_UKJ_B4B_blood_smallRNAseq


title: MG_UKJ_B3B_blood_smallRNAseq


title: MG_UKJ_B2B_blood_smallRNAseq


title: NH_FLI_215_brain_RNAseq


title: MG_UKJ_C1B_blood_smallRNAseq


title: FHRCC03Ca

city: Chengdu

first: Guangxi

last: Sun

address: No.37 Guoxue Alley, Wuhou District, Chengdu City, Sichuan Province, PR China

institute: West China hospital, sichuang university

description:
Hereditary leiomyomatosis and renal cell cancer patient No.03 derived tumor sample
204088090064_R06C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio and ChAMP with default settings

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor and normal tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

tag: individual

value: patient No.03

value: Tumor


title: FHRCC19Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.19 derived tumor sample
204088090064_R02C01

value: patient No.19


title: FHRCC25Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.25 derived tumor sample
204088090064_R01C01

value: patient No.25


title: NH_FLI_214_brain_RNAseq


title: FHRCC01Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.01 derived tumor sample
204088090064_R03C01

value: patient No.01


title: FHRCC04Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.04 derived tumor sample
204088090064_R07C01

value: patient No.04


title: MG_UKJ_B1B_1_blood_smallRNAseq


title: NH_FLI_212_brain_RNAseq

value: brain


title: MG_UKJ_B14B_blood_smallRNAseq


title: MG_UKJ_B13B_blood_smallRNAseq


title: FHRCC05Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.05 derived tumor sample
204088090082_R01C01

value: patient No.05


title: FHRCC08Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.08 derived tumor sample
204088090082_R05C01

value: patient No.08


title: FHRCC04N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.04 derived normal sample
204088090064_R08C01

value: Normal


title: MG_UKJ_A9B_blood_smallRNAseq

value: male


title: MG_UKJ_B12B_blood_smallRNAseq

value: 45-50 years


title: FHRCC09N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.09 derived normal sample
204088090082_R08C01

value: patient No.09


title: FHRCC10N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.10 derived normal sample
204088090084_R02C01

value: patient No.10


title: FHRCC02N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.02 derived normal sample
204088090064_R05C01

value: patient No.02


title: FHRCC07N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.07 derived normal sample
204088090082_R04C01

value: patient No.07


title: MG_UKJ_A7B_blood_smallRNAseq

value: blood

value: 24-29 years


title: MG_UKJ_A8B_blood_smallRNAseq


title: NH_FLI_211_brain_RNAseq

value: AB JxTu

value: 1 year


title: NH_FLI_210_brain_RNAseq


title: NH_FLI_209_brain_RNAseq


title: MG_UKJ_A5B_blood_smallRNAseq


title: MG_UKJ_A2B_3_blood_smallRNAseq


title: MG_UKJ_A6B_blood_smallRNAseq


title: FHRCC02Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.02 derived tumor sample
204088090064_R04C01

value: Tumor


title: FHRCC08N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.08 derived normal sample
204088090082_R06C01


title: MG_UKJ_A13B_blood_smallRNAseq


title: FHRCC10Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.10 derived tumor sample
204088090084_R01C01


title: FHRCC16N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.16 derived normal sample
204088090084_R07C01

value: patient No.16


title: FHRCC09Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.09 derived tumor sample
204088090082_R07C01


title: Liver, Ad-Inpolin-4

first: Yunchen

last: Luo

address: shanghai hongkou

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA.
Fold change>=2.0, that is, log(FC)>=1.0, p-value<=0.05, and FPKM value>=0.1 in at least one (or a group of) samples as the threshold for differential screening.
Genome_build: MM10
Supplementary_files_format_and_content: mRNA Expression Profiling.xls (FPKM Values)

source_name: Liver, Ad-Inpolin

growth_protocol: Male ob/ob mice aged 8-12 weeks were purchased from GemPharmatech Company (Nanjing, China).

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: The mice were administered with Ad-Inpolin or Ad-GFP (1×109 plaque-forming units) through the tail vein and sacrificed at 12th day of administration.

value: liver

value: ob/ob

value: Ad-Inpolin


title: Liver, Ad-Inpolin-3


title: SSM_FLI_BRHF6.1_none_RNAseq

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.7 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCh38, and respective gene annotation (GRCh38.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

source_name: cell ine Wi-38

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's mRNA Sample Preparation Singleplex Kit following the manufacturer's instruction.

value: female


title: AGD1289 replicate 1

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Standard Illumina Pipeline Processing
FASTQ reads quality trimmed with Trim Galore v0.4.4 using Cutadapt v1.15
Mapped with HISAT2 (v2.1.0)
Differential gene expression performed with SeqMonk and DESeq2.
Genome_build: WBCel235 / WBCel235.75 splice sites
Supplementary_files_format_and_content: Excel file comprising 2 worksheets:  DEgenes_per_replicate – output from SeqMonk giving a log10 normalised quantitation of each gene using the SeqMonk “RNA-Seq quantitation pipeline”.  The worksheet lists each gene, genomic location and quantitation value.  log2FC_average_AGD1289_vs_WT – gives the average log2-fold change of each gene between conditions and P-value as determined by DESeq2 and SeqMonk.  The table lists the gene name, genomic location and quantitation values for each gene.

source_name: 1000 young adult worms

growth_protocol: Worms were age-synchobized by treatment with alkaline hypochlorite solution, according to standard procedures. 1000 L1 worms were plated on 9 cm NGM plate per genotype. Nematodes were harvested at the young adult stage about 50h post L1 plating. £ biological replicates were collected for each genotype.

extract_protocol:
RNA was extracted by standard Trizol extraction techniques.
Libraries were made using either NEBNext mRNA Second Strand Synthesis Module (E6111) followed by NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB-E7645) or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NE7490) as per manufacturers protocols using half reactions. 13 Cycles of amplification was used for library enrichment; quality and size distribution of the the libraries was ascertained by running on a Bioanalyzer High Sensitivity DNA Chip (Agilent 5067-4626) and concentration was determined using KAPA Library Quantification Kit (KK4824). Libraries were sequenced on an Illumina HiSeq 2500 system by the Babraham Sequencing Facility.

treatment_protocol: Standard growth conditions. Temperature: 20 degrees Celsius.

tag: Stage

value: young adult


title: Liver, Ad-Inpolin-2

tag: treatment


title: FHRCC15N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.15 derived normal sample
204088090084_R05C01

value: patient No.15

value: Normal


title: N2 replicate 2


title: N2 replicate 1


title: SSM_FLI_BRHF6.0_none_RNAseq

tag: cell line


title: N2 replicate 3


title: FHRCC16Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.16 derived tumor sample
204088090084_R06C01


title: Liver, Ad-Inpolin-1