title: SS_FSU_L_all_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 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.

source_name: N2_15 days_Rotenone, only for 24 hours starting at L4  100 nM

value: whole worms

value: 15 days

value: hermaphrodite


title: SSM_FLI_BRHF5.1_none_RNAseq

status: Public on Oct 19 2021

type: SRA

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

library_source: transcriptomic

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.

molecule: total RNA

organism: Homo sapiens

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.

tag: cell line

tag: population doublings

tag: Sex

value: female


title: FHRCC15Ca

type: genomic

city: Chengdu

first: Guangxi

last: Sun

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

country: China

institute: West China hospital, sichuang university

description:
Hereditary leiomyomatosis and renal cell cancer patient No.15 derived tumor sample
204088090084_R04C01

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

molecule: genomic DNA

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.15

tag: tissue

value: Tumor


title: FHRCC06Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.06 derived tumor sample
204088090082_R02C01

value: patient No.06


title: Liver, Ad-GFP-4

city: Shanghai

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)

organism: Mus musculus

source_name: Liver, Ad-GFP

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

tag: strain

value: ob/ob

tag: treatment

value: Ad-GFP


title: AGD1289 replicate 2

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.

molecule: polyA RNA

organism: Caenorhabditis elegans

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: SS_FSU_J_all_smallRNAseq

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.

tag: age

tag: perturbation

value: Rotenone, only for 24 hours starting at L4  100 nM


title: SSM_FLI_BRHF5.0_none_RNAseq


title: Liver, Ad-GFP-3


title: SS_FSU_I_all_smallRNAseq

source_name: N2_15 days_DMSO 0.1 %

value: DMSO 0.1 %


title: FHRCC07Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.07 derived tumor sample
204088090082_R03C01

value: patient No.07


title: SS_FSU_46_none_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: 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 HepG2

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: HepG2 human liver carcinoma cell

value: Arsenite 24 h 5 nM


title: Liver, Ad-GFP-2


title: FHRCC22Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.22 derived tumor sample
204088090084_R08C01

value: patient No.22


title: SS_FSU_G_all_smallRNAseq

value: whole worms


title: FHRCC22N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.22 derived normal sample
204088090086_R01C01

value: Normal


title: FHRCC13Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.13 derived tumor sample
204088090084_R03C01

value: patient No.13


title: SS_FSU_45_none_RNAseq


title: SS_FSU_H_all_smallRNAseq

value: 15 days

value: hermaphrodite


title: SS_FSU_44_none_RNAseq

value: H2O 24 h 5 nM


title: SS_FSU_E_all_smallRNAseq

source_name: N2_5 days_Rotenone, only for 24 hours starting at L4  100 nM

value: 5 days


title: Liver, Ad-GFP-1

value: liver


title: SS_FSU_C_all_smallRNAseq

source_name: N2_5 days_DMSO 0.1 %


title: SS_FSU_F_all_smallRNAseq


title: SS_FSU_B_all_smallRNAseq


title: FHRCC21N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.21 derived normal sample
204088090086_R03C01

value: patient No.21


title: NU_FSU_X3_all_smallRNAseq

source_name: N2_5 days_Rotenone 100 nM

value: Rotenone 100 nM


title: SSM_FLI_BRHF4.1_none_RNAseq

source_name: cell line MRC-5

value: male


title: NU_FSU_W3_all_smallRNAseq


title: FHRCC21Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.21 derived tumor sample
204088090086_R02C01

value: Tumor


title: SS_FSU_A_all_smallRNAseq

value: DMSO 0.1 %


title: NU_FSU_W2_all_smallRNAseq


title: SSM_FLI_BRHF3.1_none_RNAseq


title: NU_FSU_W1_all_smallRNAseq


title: SS_FSU_K_all_smallRNAseq

value: Rotenone, only for 24 hours starting at L4  100 nM


title: FHRCC23N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.23 derived normal sample
204088090086_R05C01

value: patient No.23


title: SS_FSU_43_none_RNAseq

value: HepG2 human liver carcinoma cell


title: NU_FSU_X2_all_smallRNAseq


title: NU_FSU_X1_all_smallRNAseq


title: NU_FSU_V3_all_smallRNAseq


title: ITK KO noncanonical Treg Rep1

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

country: USA

institute: Suny Upstate Medical University

data_processing:
All data were processed and analyzed using the R programming language (Version 4.0.4), the RStudio interface (Version 1.4.1106), and Bioconductor
The first six samples (2 per group) were library prepped using the Bio-Rad SEQ-uoia library prep kit, and the last three samples (1 sample for each group, named "MM_13","MM_14", "MM_15") were library prepped using the SMART-Seq HT kit (Takara Bio). These nine samples were all sequenced in the same run. Still, the six samples (2 samples in each group) library prepped using the SEQ-uioa kit resulted in an insufficient number of reads, making a comparison between groups impossible.
We had to re-prep and sequence the first six samples again (named "WT_CD25posFOXP3pos_1","WT_CD25posFOXP3pos_2", "ITKCD25posFOXP3pos_1", "ITKCD25posFOXP3pos_2", "ITKCD25negFOXP3pos_1",”ITKCD25negFOXP3pos_2") using the SMART-seq HT kit. The batch effect from sequencing runs between the six samples re-prepped, and the three original samples were later removed.
Three groups were created: WT canonical, Itk-/- canonical, and Itk-/- noncanonical Tregs. Pseudoalignment with Kallisto (version 0.46.2) 26 was used to determine the transcript abundance of samples. Transcript per million (TPM) values were normalized, and the batch effect was removed by fitting to a linear model by empirical Bayes method with the Voom and Limma R packages 27. Bonferroni and Hochberg 28 adjusted p-value - False Discovery Rate (FDR) of ≤  0.05 or FDR≤0.1 were used to describe the differential gene expression.
G:Profiler toolset, and g:GOSt tool was used for GO annotation analysis. C2 and C7 pathways collection from the Molecular Signatures Database (MSigDB) was utilized to perform Gene Set Enrichment Analysis (GSEA).
Genome_build: mm9
Supplementary_files_format_and_content: .tsv file, raw counts

source_name: Sorted CD25- FOXP3+ CD4+ CD3+ Tregs

extract_protocol:
Total RNA was extracted with the Qiagen miRNeasy Mini kit. RNA quality and quantity were assessed with the Agilent 2100 Bioanalyzer. cDNA was prepared with the SMARTseq HT Kit (Takara Bio), using 1ng total RNA. Dual indexed sequencing libraries were prepared using the Nextera XT DNA Library Prep kit (Illumina), using 250pg cDNA.
Illumina TruSeq

tag: background strain

tag: genotype

value: ITK KO

value: spleen


title: NU_FSU_V1_all_smallRNAseq

value: whole worms


title: ITK KO noncanonical Treg Rep2


title: 14837 CM

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

institute: Peking Univ.

data_processing:
Normal sequence Illumina Novaseq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with parameters hisat2 -p 8 --dta -x  -1  -2 -S.
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each Sample ...

source_name: PDAC Tumor

growth_protocol: 14837 PDAC cells were maintained at 37℃ and 5% CO2 in DMEM with 10% (v/v) FBS and 100U/ml penicillin.

extract_protocol:
RNA was harvested using Trizol reagent.2 ug of total RNA is used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standrad Illumina protocols.

treatment_protocol: 14837 PDAC cells were treated with conditional medium for 48h.

tag: cell type

value: mouse PDAC 14837

value: treated with 14837 conditional medium


title: ITK KO noncanonical Treg Rep3


title: FHRCC23Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.23 derived tumor sample
204088090086_R04C01


title: NU_FSU_U2_all_smallRNAseq

source_name: N2_3 days_Rotenone 100 nM

value: 3 days

value: hermaphrodite


title: SSM_FLI_BRHF3.0_none_RNAseq


title: SSM_FLI_BRHF8.1_none_RNAseq

source_name: cell line IMR-90

value: female


title: NU_FSU_U3_all_smallRNAseq


title: SS_FSU_D_all_smallRNAseq

value: 5 days


title: NU_FSU_V2_all_smallRNAseq


title: NU_FSU_T3_all_smallRNAseq

source_name: N2_3 days_DMSO 0.1 %


title: NU_FSU_U1_all_smallRNAseq


title: ITK KO canonical Treg Rep3

source_name: Sorted CD25+ FOXP3+ CD4+ CD3+ Tregs


title: AGD1289 replicate 3

value: young adult


title: mCAF CM

value: treated with CAF conditional medium


title: NU_FSU_S3_all_smallRNAseq

source_name: N2_2 days_Rotenone 100 nM

value: 2 days

value: Rotenone 100 nM


title: SSM_FLI_BRHF10.1_none_RNAseq

source_name: cell line HFF

value: HFF

value: male


title: NU_FSU_R3_all_smallRNAseq

source_name: N2_2 days_DMSO 0.1 %

value: DMSO 0.1 %


title: FHRCC12N

description:
Hereditary leiomyomatosis and renal cell cancer patient No.12 derived normal sample
204088090086_R08C01

value: patient No.12

value: Normal


title: NU_FSU_R2_all_smallRNAseq


title: NU_FSU_R1_all_smallRNAseq


title: NU_FSU_Q2_all_smallRNAseq

source_name: N2_1 day_Rotenone 100 nM

value: 1 day


title: ITK KO canonical Treg Rep1

value: ITK KO

value: spleen


title: SSM_FLI_BRHF8.0_none_RNAseq


title: NU_FSU_T1_all_smallRNAseq

value: whole worms


title: WT canonical Treg Rep3

value: WT


title: WT canonical Treg Rep1


title: NU_FSU_P3_all_smallRNAseq

value: hermaphrodite


title: FHRCC20Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.20 derived tumor sample
204088090086_R06C01

value: patient No.20

value: Tumor


title: NU_FSU_Q3_all_smallRNAseq


title: SSM_FLI_BRHF10.0_none_RNAseq


title: SSM_FLI_BRHF9.1_none_RNAseq


title: NU_FSU_P2_all_smallRNAseq


title: PC3-BTN1A1, IFNg, 48 h

type: RNA

city: Gaithersburg

first: Ezra

middle: Myung Chul

last: Chung

state: MD

address: 401 Professional Dr. Suite 250

department: R&D

institute: STCube Pharmaceuticals

hyb_protocol: All samples were run targeting 100 ng of total RNA prior to being processed on the nCounter FLEX Analysis System.

scan_protocol: Samples were run on the nCounter Prep Station with high sensitivity settings followed by imaging on the Digital Anlyzer with FOV (Field of view) data resolution set to 555.

data_processing: Raw data files were uploaded (RCC files) to the NanoString nSolver Analysis 4.0 software. According to nSolver Advanced Analysis Module (version 2.0.115) specifications, the geNorm algorithm (pairwise variation statistics) was used to choose an ideal set of housekeeping genes (from a total set of 30) with minimal pairwise variation for normalization. Based on NanoString cancer pathway score analysis [indicating expression changes relevant to EMT (epithelial to mesenchymal transition)], a select number of genes (23 in total) displaying statistically significant expression changes was included in our manuscript, substantiating the specific role of NRAS-driven EMT changes in malignant melanoma.

label: Biotin

source_name: prostate cancer cell line PC3

label_protocol: Reporter probe; fluorescent barcode; capture biotin

growth_protocol: Both empty vector transfected and BTN1A1 expression vector transfectted PC3 cells were grwon in DMEM/F12 medium supplemented with 10% FBS at 37ºC, 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted from cell lysates using a combination of Trizol and Rneasy mini kit.

treatment_protocol: The cells were plated in a 6-well plate, ncubated overnignt, and treated with 100 ng/ml IFN-gamma.

value: transfected with BTN1A1 expression  vector with IFN-gamma treatment for 48 h


title: FHRCC12Ca

description:
Hereditary leiomyomatosis and renal cell cancer patient No.12 derived tumor sample
204088090086_R07C01


title: PC3-BTN1A1, 48 h

value: transfected with BTN1A1 expression vector without IFN-gamma treatment


title: ITK KO canonical Treg Rep2


title: WT canonical Treg Rep2


title: NU_FSU_T2_all_smallRNAseq

value: 3 days


title: NU_FSU_O1_all_smallRNAseq

source_name: N2_1 day_DMSO 0.1 %


title: SSM_FLI_BRHF7.1_none_RNAseq

value: female


title: NU_FSU_S2_all_smallRNAseq

value: 2 days

value: Rotenone 100 nM


title: NU_FSU_N3_all_smallRNAseq

source_name: N2_6 hours_Rotenone 100 nM

value: 6 hours


title: NU_FSU_S1_all_smallRNAseq


title: MB_FLI_JM46.5_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 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.

organism: Nothobranchius furzeri

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 smallRNA Library Preparation Kit following the manufacturer's instruction.

value: skin

value: 39 weeks

value: male


title: NU_FSU_N2_all_smallRNAseq


title: NU_FSU_N1_all_smallRNAseq


title: mCaPS_ESC_RING1B_CUT&RUN_group3

city: Boston

first: Robert

last: Kingston

state: MA

address: 185 Cambridge Street, 7th Floor

department: Molecular Biology

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Adapter sequences were removed from reads usinng Cutadapt v.1.14 with "--minimumLength 30"
Reads were aligned to the mm10 and dm6 genomes using Bowtie 2 v.2.3.4.3 with one mismatch permitted per seed, a maximum insert of 2kb, and the "--no-discordant" option specified
PCR duplicates were removed using Samtools v1.9
To normalize ChIP-Seq data, mm10 reads were randomly downsampled using Samtools. The downsampling factor reflected the total number of dm6 reads in the sample, and was corrected with the ratio of dm6:mm10 reads to account for variation in spike-in mixing.
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.4
Supplementary_files_format_and_content: Peak files were generated using Homer v4.10.4. Peaks were filtered to those within 10kb of their associated TSS, and to a minimum tag density that was determined by examination of IGV browser tracks.

source_name: Embryonic stem cells

growth_protocol: Embryonic stem cells (ESCs) were cultured on 1% gelatin with a feeder layer of MEFs in DMEM supplemented with 15% Hyclone FBS (GE Healthcare), GlutaMax (Invitrogen), penicillin/streptomycin, non-essential amino acids, 1000U/mL LIF, and 2-betamercatoethanol. To form embryoid bodies (EBs), ESCs were de-MEFed and resuspended in differentiation media (IMDM supplemented with 15% HyClone FBS , GlutaMax, and penicillin/streptomycin) at a concentration of 8,400 cells/mL. Drops were set at 50uL per drop on the bottom of a non-adherent tissue culture plate, and plates were storeed upside down. After 4 days, EBs were pooled together and grown in suspension in non-adherent plates, changing media every day. EBs were collected for analysis on days 6 and 10 of differentiation.

extract_protocol:
CUT&RUN was performed as previously described in Skene et al., 2018 (Nat. Protoc.), in native conditions and with modifications for high-calcium/low-salt condititions as described in Meers et al., 2019 (eLife).
Libraries were prepared as described in Bowman et al., 2013 (BMC Genomics). In brief, this protocol includes end repair, A-tailing, adapter ligation, and real-time PCR amplification, with SPRI cleanup of samples between each step.

value: J1 cells

value: 0 days


title: SSM_FLI_BRHF7.0_none_RNAseq


title: SSM_FLI_BRHF9.0_none_RNAseq

value: HFF


title: MB_FLI_JM41.5_skin_smallRNAseq


title: SSM_FLI_BRHF2.1_none_RNAseq

source_name: cell line BJ

value: BJ


title: SS_FSU_L_all_RNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.3 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: WBcel235, and respective gene annotation (WBcel235.84)
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: N2_15 days_Rotenone, only for 24 hours starting at L4  100 nM

value: whole worms

value: 15 days

value: hermaphrodite


title: NU_FSU_Q1_all_smallRNAseq

value: 1 day


title: NU_FSU_O3_all_smallRNAseq

value: DMSO 0.1 %


title: SS_FSU_K_all_RNAseq

value: Rotenone, only for 24 hours starting at L4  100 nM


title: PC3-EV, INFg, 24 h

value: transfected with empty vector with IFN-gamma treatment for 24 h


title: NU_FSU_O2_all_smallRNAseq


title: SSM_FLI_BRHF1.1_none_RNAseq


title: SSM_FLI_BRHF4.0_none_RNAseq

source_name: cell line MRC-5


title: PC3-EV, 48 h

value: transfected with empty vector without IFN-gamma treatment


title: SS_FSU_H_all_RNAseq

source_name: N2_15 days_DMSO 0.1 %


title: MB_FLI_22_III_brain_smallRNAseq

source_name: brain

value: brain

value: 26 weeks


title: WT_ESC_RING1B_CUT&RUN_group3

value: WT


title: SSM_FLI_BRHF1.0_none_RNAseq


title: CaPS_ESC_IgG_CUT&RUN_group3


title: SS_FSU_F_all_RNAseq

source_name: N2_5 days_Rotenone, only for 24 hours starting at L4  100 nM

value: 5 days


title: MB_FLI_22_II_brain_smallRNAseq

value: male


title: PC3-BTN1A1, IFNg, 24 h

value: transfected with BTN1A1 expression  vector with IFN-gamma treatment for 24 h


title: SSM_FLI_BRHF2.0_none_RNAseq


title: SS_FSU_E_all_RNAseq


title: NU_FSU_M2_all_smallRNAseq

source_name: N2_6 hours_DMSO 0.1 %

value: 6 hours


title: SS_FSU_I_all_RNAseq


title: PC3-EV, IFNg, 48 h

value: transfected with empty vector with IFN-gamma treatment for 48 h


title: SS_FSU_D_all_RNAseq


title: MB_FLI_JM38.5_skin_smallRNAseq

value: skin

value: 39 weeks


title: CaPS_NPC8_RING1B_ChIP_group5

data_processing:
Adapter sequences were removed from reads usinng Cutadapt v.1.14 with "--minimumLength 30"
Reads were aligned to the mm10 and dm6 genomes using Bowtie 2 v.2.3.4.3 with one mismatch permitted per seed, a maximum insert of 2kb, and the "--no-discordant" option specified
PCR duplicates were removed using Samtools v1.9
To normalize ChIP-Seq data, mm10 reads were randomly downsampled using Samtools. The downsampling factor reflected the total number of dm6 reads in the sample, and was corrected with the ratio of dm6:mm10 reads to account for variation in spike-in mixing.
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.4
Supplementary_files_format_and_content: Peak files were generated using Homer v4.10.4. Peaks were filtered to those within 10kb of their associated TSS, and to a minimum tag density that was determined by examination of IGV browser tracks.

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells were formed as described in Bibel et al., 2007 (Nature Protocols). In brief, embryonic stem cells were de-MEFed and grown in suspension for 4 days without LIF to form cellular aggregates. After 4 days, retinoic acid was added to a final concentration of 5uM for neural differentiation. NPCs were collected for analysis on days 6 and 8 of differentiation.

extract_protocol:
Ten to twenty million harvested cells were crosslinked in 1% formaldehyde-PBS for 10 minutes at room temperature. Crosslinking was quenched with glycine, and cells were pelleted by centrifugation at 4°C and washed once in cold PBS. Cells were resuspended in cold lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA pH 8.0, 1% SDS, PIC, 1mM DTT) and incubated for 10 minutes on ice prior to sonication using a QSonica Q800R3 Sonicator. Insoluble chromatin was pelleted by centrifugation, and supernatant was diluted 1:10 with IP Dilution Buffer (20mM Tris-HCl pH 8.1, 150mM NaCl, 2mM EDTA pH 8.0, 0.1% Triton X-100, PIC, 1mM DTT). Sonicated Drosophila chromatin was added at a known ratio to experimental chromatin to serve as a spike-in as previously described (Egan et al., 2016). Triton X-100 was added to a final concentration of 1%, input was collected and diluted to 200mL, and chromatin was added to Protein A Dyanbeads (Invitrogen) that had been previously incubated with experimental and spike-in antibodies. Samples were rotated at 4°C overnight. Beads were washed with IP Dilution Buffer with 1% Triton X-100, followed by Wash Buffer A (50mM HEPES pH 7.9, 500mM NaCl, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, PIC, DTT), followed by Wash Buffer B (20mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA pH 8.0, 0.1% Na-deoxycholate, 1% Igepal, PIC, DTT), followed by a quick TE wash. Beads were incubated at 37°C in 200mL Extraction Buffer (1% SDS, 0.1M NaHCO3) for 15 minutes with shaking. Supernatant was collected, and 12mL 2M TrisHCl, 2mL RNase A (500mg/mL, Roche), and 12mL 5M NaCl were added to ChIP samples and inputs. Crosslinks were reversed overnight at 65°C, followed by 1 hour incubation at 55°C with Proteinase K. DNA was isolated by phenol:chloroform extraction and ethanol precipitation.
Libraries were prepared as described in Bowman et al., 2013 (BMC Genomics). In brief, this protocol includes end repair, A-tailing, adapter ligation, and real-time PCR amplification, with SPRI cleanup of samples between each step.

value: J1 cells

value: 8 days


title: mCaPS_ESC_IgG_CUT&RUN_group3

value: 0 days


title: SS_FSU_G_all_RNAseq

value: whole worms

value: 15 days

value: hermaphrodite

value: DMSO 0.1 %


title: SS_FSU_B_all_RNAseq

source_name: N2_5 days_DMSO 0.1 %


title: NU_FSU_M1_all_smallRNAseq


title: NU_FSU_P1_all_smallRNAseq

value: 1 day


title: MB_FLI_22_IV_brain_smallRNAseq

value: brain

value: 26 weeks


title: SS_FSU_J_all_RNAseq

value: Rotenone, only for 24 hours starting at L4  100 nM


title: CaPS_NPC6_RING1B_ChIP_group5

value: 6 days


title: CaPS_NPC6_input_TF_group5


title: ZK_FSU_RNA1407-32_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: WBcel235, and respective gene annotation (WBcel235.84)
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: 5 days


title: WT_ESC_IgG_CUT&RUN_group3

value: WT


title: CaPS_NPC8_input_TF_group5


title: ZK_FSU_RNA1407-30_all_RNAseq


title: CaPS_ESC_RING1B_CUT&RUN_group3


title: MB_FLI_6_III_brain_smallRNAseq

value: 6 weeks

value: male


title: SS_FSU_A_all_RNAseq


title: MB_FLI_6_IV_brain_smallRNAseq


title: SS_FSU_C_all_RNAseq


title: ZK_FSU_RNA1407-33_all_RNAseq


title: MB_FLI_JM46.1_brain_smallRNAseq

value: 39 weeks


title: MB_FLI_JM8.1_brain_smallRNAseq


title: MB_FLI_22_I_brain_smallRNAseq


title: ZK_FSU_RNA1407-28_all_RNAseq

source_name: N2_5 days


title: CaPS_ESC_RING1B_ChIP_group5

value: J1 cells


title: WT_NPC8_RING1B_ChIP_group5

value: 8 days


title: ZK_FSU_RNA1407-29_all_RNAseq


title: ZK_FSU_RNA1407-35_all_RNAseq


title: WT_NPC8_input_TF_group5


title: ZK_FSU_RNA1407-31_all_RNAseq


title: ZK_FSU_RNA1407-36_all_RNAseq


title: MB_FLI_6_I_brain_smallRNAseq


title: ZK_FSU_RNA1407-34_all_RNAseq


title: MB_FLI_JM6.1_brain_smallRNAseq


title: MB_FLI_JM41.1_brain_smallRNAseq


title: MB_FLI_6_II_brain_smallRNAseq


title: WT_NPC6_RING1B_ChIP_group5


title: RM_FSU_RNA1407-22_all_RNAseq

value: 2 days


title: ZK_FSU_RNA1407-27_all_RNAseq

value: whole worms


title: ZK_FSU_RNA1407-26_all_RNAseq


title: RM_FSU_RNA1407-18_all_RNAseq


title: MB_FLI_JM24.1_brain_smallRNAseq


title: RM_FSU_RNA1407-17_all_RNAseq


title: RM_FSU_RNA1407-21_all_RNAseq


title: RM_FSU_RNA1407-14_all_RNAseq


title: MB_FLI_JM38.1_brain_smallRNAseq


title: MB_FLI_JM144.5_skin_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 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.

source_name: 27 weeks_swim-tunnel_skin

value: 27 weeks

value: swim-tunnel

value: skin


title: JM_FSU_RNA1407-7_all_RNAseq

source_name: TU3311 (sid-1 tg; neuronal RNAi)_5 days_L4440

value: TU3311 (sid-1 tg; neuronal RNAi)

value: hermaphrodite


title: MB_FLI_JM142.5_skin_RNAseq


title: JM_FSU_RNA1307-5_all_RNSseq


title: WT_ESC_input_TF_group5

value: 0 days


title: WT_NPC6_input_TF_group5


title: CaPS_ESC_input_TF_group5


title: NU_FSU_M3_all_smallRNAseq

value: 6 hours

value: DMSO 0.1 %


title: ZK_FSU_RNA1407-25_all_RNAseq

value: 5 days


title: RM_FSU_RNA1407-13_all_RNAseq


title: JM_FSU_RNA1407-9_all_RNAseq


title: CaPS_ESC_H3K27me3_ChIP_group5


title: JM_FSU_RNA1407-10_all_RNAseq

source_name: TU3311 (sid-1 tg; neuronal RNAi)_5 days_daf-7


title: JM_FSU_RNA1407-11_all_RNAseq


title: CaPS_ESC_input_histone_group5


title: JM_FSU_RNA1407-8_all_RNAseq


title: JM_FSU_RNA1307-3_all_RNSseq


title: MB_FLI_JM141.5_skin_RNAseq


title: JM_FSU_RNA1307-6_all_RNSseq


title: CaPS_NPC8_H3K27me3_ChIP_group5


title: LG_FSU_RNAseq1410-6_all_RNAseq


title: JM_FSU_RNA1307-2_all_RNSseq


title: JM_FSU_RNA1307-4_all_RNSseq


title: WT_NPC8_input_histone_group5

value: WT


title: MB_FLI_JM143.5_skin_RNAseq


title: MB_FLI_JM136.5_skin_RNAseq


title: LG_FSU_RNAseq1410-3_all_RNAseq

source_name: N2_5 days_Y6B3B.9


title: JM_FSU_RNA1307-1_all_RNSseq


title: WT_ESC_RING1B_ChIP_group5


title: MB_FLI_JM133.5_skin_RNAseq


title: JM_FSU_RNA1407-12_all_RNAseq


title: LG_FSU_RNAseq1410-4_all_RNAseq


title: CaPS_NPC8_input_histone_group5


title: RM_FSU_RNA150424-29_all_RNAseq


title: WT_NPC8_H3K27me3_ChIP_group5


title: MB_FLI_JM135.5_skin_RNAseq


title: RNA_NPC_Day8_CaPS_R_Rep3

data_processing:
Adapter sequences were removed from reads usinng Cutadapt v.1.14 with "--minimumLength 30"
Reads were aligned to the mm10 genome using STAR v2.7.0
Reads in gene exons were counted using featureCounts v1.6.3
Gene annotations were obtained from ncbi refseq
EdgeR was used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.4

extract_protocol:
RNA was isolated from pelleted cells using the PureLink RNA Mini Kit (Invitrogen) according to manufacturer's instructions. Samples were treated with DNase using the TURBO DNA-free Kit (Invitrogen). rRNA was depleted using the NEBNext rRNA Depletion Kit, and cDNA was generated using the NEBNext Ultra II Directional RNA First and Second Strand Synthesis Modules (New England Biolabs).
Libraries were prepared as described in Bowman et al., 2013 (BMC Genomics). In brief, this protocol includes end repair, A-tailing, adapter ligation, and real-time PCR amplification, with SPRI cleanup of samples between each step.


title: MB_FLI_JM140.5_skin_RNAseq


title: MB_FLI_JM126.5_skin_RNAseq

source_name: 9 weeks_none_skin

value: 9 weeks


title: RM_FSU_RNA150424-26_all_RNAseq


title: RM_FSU_RNA150424-25_all_RNAseq


title: RM_FSU_RNA150424-24_all_RNAseq


title: LG_FSU_RNAseq1410-1_all_RNAseq


title: MB_FLI_JM125.5_skin_RNAseq

value: male


title: MB_FLI_JM134.5_skin_RNAseq


title: RM_FSU_RNA150424-30_all_RNAseq


title: LG_FSU_RNAseq1410-5_all_RNAseq


title: RM_FSU_RNA150424-21_all_RNAseq


title: WT_ESC_H3K27me3_ChIP_group5


title: WT_ESC_input_histone_group5


title: LG_FSU_RNAseq1410-2_all_RNAseq


title: RM_FSU_RNA150424-28_all_RNAseq


title: MB_FLI_JM124.5_skin_RNAseq


title: RNA_NPC_Day6_CaPS_R_Rep3

value: 6 days


title: RNA_NPC_Day8_CaPS_R_Rep2

value: J1 cells


title: RM_FSU_RNA150424-27_all_RNAseq


title: MB_FLI_JM132.5_skin_RNAseq


title: RNA_NPC_Day8_CaPS_R_Rep1

value: 8 days


title: RM_FSU_RNA150424-22_all_RNAseq


title: MB_FLI_JM127.5_skin_RNAseq


title: MB_FLI_JM121.5_skin_RNAseq

source_name: 9 weeks_swim-tunnel_skin


title: RM_FSU_RNA150424-18_all_RNAseq


title: RNA_NPC_Day6_CaPS_R_Rep2


title: MB_FLI_JM128.5_skin_RNAseq


title: RM_FSU_RNA150424-17_all_RNAseq


title: MB_FLI_JM119.5_skin_RNAseq


title: RNA_NPC_Day0_CaPS_R_Rep2

source_name: Embryonic stem cells


title: RM_FSU_RNA150424-23_all_RNAseq


title: RM_FSU_RNA150424-16_all_RNAseq


title: ZK_FSU_RNA150424-13_all_RNAseq


title: RNA_NPC_Day0_CaPS_R_Rep1


title: ZK_FSU_RNA150424-14_all_RNAseq


title: MB_FLI_JM118.5_skin_RNAseq


title: RNA_NPC_Day6_CaPS_R_Rep1


title: ZK_FSU_RNA150424-12_all_RNAseq


title: RNA_EB_Day10_CaPS_R_Rep2

source_name: Embryoid bodies

value: 10 days


title: RNA_NPC_Day0_CaPS_R_Rep3


title: ZK_FSU_RNA150424-8_all_RNAseq

value: whole worms


title: MB_FLI_JG83.5_skin_RNAseq

source_name: GRZ_w/ physical exercise_skin

value: GRZ

value: 10 weeks


title: MB_FLI_JM120.5_skin_RNAseq

value: swim-tunnel

value: skin


title: MB_FLI_JG82.5_skin_RNAseq


title: RM_FSU_RNA150424-20_all_RNAseq

value: hermaphrodite


title: RM_FSU_RNA150424-19_all_RNAseq


title: Marmoset2_Superior_Left_Rep2_PCR_GFP

city: Pittsburgh

first: Leah

last: Byrne

state: PA

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

description:
PCR_GFP_Superior2_S4_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
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

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: RNA_EB_Day6_CaPS_R_Rep1


title: MB_FLI_JG80.5_skin_RNAseq


title: RNA_EB_Day10_CaPS_R_Rep3


title: Marmoset2_Inferior_Left_Rep2_PCR_GFP

description:
PCR_GFP_Inferior2_S6_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina inferior region


title: RNA_EB_Day6_CaPS_R_Rep3


title: ZK_FSU_RNA150424-10_all_RNAseq

value: 5 days


title: RNA_EB_Day6_CaPS_R_Rep2


title: Adar1-deficient_BMDMs_rep1

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Clariom S Mouse GeneChip array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: BMDMs from Adar1fl/flLysMcre mouse

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip™ WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

growth_protocol: Primary mouse bone marrow-derived macrophages (BMDMs) were generated from the bone marrow of wild type and the indicated mutant mice. Cells were grown for 5–6 days in IMDM (Thermo Fisher Scientific, 12440053) supplemented with 1% non-essential amino acids (Thermo Fisher Scientific, 11140-050), 10% FBS (Biowest, S1620), 30% L929 conditioned media, and 1% penicillin and streptomycin (Thermo Fisher Scientific, 15070-063). BMDMs were then seeded into the growth media at a concentration of 1 x 10^6 cells into 12-well plates and incubated overnight.

extract_protocol: RNA was extracted from BMDMs using TRIzol™ Reagent (ThermoFisher P/N 15596026)

tag: genotype/variation

value: Adar1fl/flLysMcre genotype back-crossed against C57/BL6 background

value: Bone marrow derived macrophages (BMDMs)


title: MB_FLI_JG84.5_skin_RNAseq

value: male


title: Adar1-deficient_BMDMs_rep2


title: ZK_FSU_RNA150424-9_all_RNAseq


title: MB_FLI_JG81.5_skin_RNAseq


title: MB_FLI_JG78.5_skin_RNAseq


title: RNA_EB_Day10_CaPS_R_Rep1

value: J1 cells


title: ZK_FSU_RNA150424-11_all_RNAseq


title: Marmoset2_Inferior_Left_Rep1_PCR_GFP

description:
PCR_GFP_Inferior1_S5_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: Marmoset2_Superior_Left_Rep1_PCR_GFP

description:
PCR_GFP_Superior1_S3_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: MB_FLI_JM117.5_skin_RNAseq

value: 9 weeks


title: RNA_EB_Day0_CaPS_R_Rep3

value: 0 days


title: WT_BMDMs_rep2

source_name: BMDMs from Adar1fl/+LysMcre mouse

value: Adar1fl/+LysMcre genotype back-crossed against C57/BL6 background


title: MB_FLI_JG77.5_skin_RNAseq

value: GRZ


title: ZK_FSU_RNA150424-15_all_RNAseq

value: whole worms


title: RNA_EB_Day0_CaPS_R_Rep2


title: WT_BMDMs_rep3


title: MB_FLI_JG75.5_skin_RNAseq

value: 10 weeks

value: swim-tunnel


title: MB_FLI_JG76.5_skin_RNAseq

value: skin


title: Adar1-deficient_BMDMs_rep3


title: Marmoset2_Macula_Left_Rep1_PCR_GFP

description:
PCR_GFP_Macula1_S1_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina

value: Retina macula region


title: Marmoset2_Macula_Left_Rep2_PCR_GFP

description:
PCR_GFP_Macula2_S2_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: unsorted


title: MG_UKJ_24_1050_skin_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: GRCm38, and respective gene annotation (GRCm38.84)
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: skin

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

value: 24 months


title: MG_UKJ_24_1049_skin_RNAseq


title: CHD8KO#2_hNPC_rep2

city: WuHan

first: Song

last: Ding

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: Wuhan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to GRC38 whole genome using HISAT2 version 2.1.1.
Raw reads were performed with FeatureCounts using human gencode.v29.annotation.gtf
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2.
Genome_build: GRCh38

source_name: CHD8KO_hESC-derived neurol progenitor cells

growth_protocol: human embryonic stem cells (ESCs) H9 and CHD8KO_H9 were maintained in mTeSR1 on Matrigel-coated cell culture plate at 37℃ with 5% CO2. To induce neural differentiation, wildtype or CHD8 knockout human ESCs were seeded onto Matrigel-coated 24-well plates. After 3 days’ culture with mTeRS1 medium, the neuroectoderm differentiation was initiated by neural induction medium (DMEM/F12 , 0.5 × N2 , 0.5 × B27 , 1% Gluta-max, 1% NEAA, 1x penicillin/streptomycin, 0.1%β-mercaptoethanol) plus 10μM SB431542and 0.1μM LDN . After 5 days of neural induction, the TGF-β inhibitor SB431542 was withdrawn from the neural induction medium for another 2 days’ culture.

extract_protocol:
RNA was extracted with  RNAiso Plus (Takara, Cat#9109)
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: MB_FLI_JG74.5_skin_RNAseq


title: NH_FLI_nf_12_skin_RNAseq

source_name: skin w/o physical exercise

value: line 4010; Tg(mylz2:egfp,tfam)


title: CHD8KO#2_hNPC_rep1


title: RNA_EB_Day0_CaPS_R_Rep1


title: CHD8KO#2_ESC_rep1

source_name: CHD8KO_embryonic stem cells


title: GT02S3

city: Philadelphia

first: Qunzhou

last: Zhang

address: Levy Building 545, 240 S 40th Street, Philadelphia

institute: University of Pennsylvania School of Dental Medicine

data_processing:
Base quality value and base distribution of raw data were detected to control quality of initial RNA-seq data by Fastp.
In the trimming process, the sequencing adapters, 3 leading and 3 trailing bases were first trimmed. The reads were then scanned from both ends, using a 4bp-wide sliding window, within which the low quality (lower than Q30) bases were trimmed. Finally, the resulting reads of length at least 50 bases were selected for further analysis.
The read alignment is done using HISAT2 v.2.0.5 software with Ensembl GRCm38.91 genome as reference genome. Transcripts Assembly  is done using StringTie v.1.3.3b software. Significant DE genes or transcripts (q-value < 0.05) were extracted by edgeR (R package) for each comparison groups. DEGs were analyzed with gene ontology enrichment analysis and KEGG by R software with clusterProfiler package. Significant GO or KEGG terms (FDR-value < 0.05) were extracted using hypergeometric distribution.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 3D cultured GMSC2 rep3

extract_protocol:
RNA was harvested from 2D- and 3D-cultured GMSCs using Trizol reagent. RNA sequencing libraries were generated using the NEBNext, Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, U.S.A.) with multiplexing primers, according to the manufacturer protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gingiva

value: Gingival derived MSCs

tag: passage

value: passage 4

tag: culture method

value: 3D cultured for 48h


title: CHD8KO#2_ESC_rep2


title: Marmoset1_Superior_Left_Rep1_PCR_GFP

description:
PCR_GFP_G_S7_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina superior region


title: Marmoset1_Superior_Right_Rep2_PCR_GFP

description:
PCR_GFP_J_S10_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: MG_UKJ_24_1047_skin_RNAseq

tag: Sex

value: male


title: GT02S2

source_name: 3D cultured GMSC2 rep2


title: MG_UKJ_24_1046_skin_RNAseq


title: Marmoset1_Superior_Left_Rep2_PCR_GFP

description:
PCR_GFP_M_S13_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: WT_BMDMs_rep1

value: Adar1fl/+LysMcre genotype back-crossed against C57/BL6 background

value: Bone marrow derived macrophages (BMDMs)


title: GT02S1

source_name: 3D cultured GMSC2 rep1


title: MG_UKJ_24_1048_skin_RNAseq


title: NH_FLI_nf_11_skin_RNAseq


title: NH_FLI_nf_10_skin_RNAseq


title: G54-2S1

source_name: 3D cultured GMSC1 rep1


title: G54-2S3

source_name: 3D cultured GMSC1 rep3


title: Marmoset1_Inferior_Right_Rep2_PCR_GFP

description:
PCR_GFP_K_S11_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina inferior region


title: NH_FLI_nf_6_skin_RNAseq

source_name: skin w/ physical exercise

value: 10 weeks


title: G54-2S2

source_name: 3D cultured GMSC1 rep2


title: Marmoset1_Inferior_Left_Rep2_PCR_GFP

description:
PCR_GFP_N_S14_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: NH_FLI_nf_8_skin_RNAseq


title: MG_UKJ_9_330_skin_RNAseq

value: 9 months


title: MG_UKJ_9_329_skin_RNAseq

value: skin


title: GT0-S3

source_name: 2D cultured GMSC2 rep3


title: NH_FLI_nf_9_skin_RNAseq


title: Marmoset1_Superior_Right_Rep1_PCR_GFP

description:
PCR_GFP_D_S4_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina


title: MG_UKJ_9_326_skin_RNAseq


title: GT0-S1

source_name: 2D cultured GMSC2 rep1


title: Marmoset1_Inferior_Right_Rep1_PCR_GFP

description:
PCR_GFP_E_S5_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: Marmoset1_Macula_Left_Rep1_PCR_GFP

description:
PCR_GFP_F_S6_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina macula region


title: NH_FLI_nf_3_skin_RNAseq

value: swim-tunnel


title: NH_FLI_nf_5_skin_RNAseq


title: Marmoset1_Macula_Left_Rep2_PCR_GFP

description:
PCR_GFP_L_S12_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: unsorted


title: MG_UKJ_24_974_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq 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: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The text files include raw counts (sample_counts.txt) and RPKM values (sample_rpkms.txt) of all genes for each sample.

source_name: brain

value: brain, hemisphere

value: 24 months


title: NH_FLI_nf_4_skin_RNAseq

value: line 4010; Tg(mylz2:egfp,tfam)


title: Marmoset1_Inferior_Left_Rep1_PCR_GFP

description:
PCR_GFP_H_S8_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: MG_UKJ_9_328_skin_RNAseq


title: Marmoset1_Macula_Right_Rep2_PCR_GFP

description:
PCR_GFP_I_S9_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: GT0-S2

source_name: 2D cultured GMSC2 rep2

value: gingiva

value: Gingival derived MSCs

value: passage 4


title: NH_FLI_nf_2_skin_RNAseq

value: male


title: G540-S3

source_name: 2D cultured GMSC1 rep3


title: G540-S2

source_name: 2D cultured GMSC1 rep2


title: MG_UKJ_9_327_skin_RNAseq

source_name: skin


title: MG_UKJ_24_972_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM143.4_muscle_RNAseq

source_name: 27 weeks_swim-tunnel_muscle

value: 27 weeks

value: muscle


title: MG_UKJ_24_973_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: CHD8KO_hNPC_rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to GRC38 whole genome using HISAT2 version 2.1.1.
Raw reads were performed with FeatureCounts using human gencode.v29.annotation.gtf.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: featureCount.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: genes_fpkm_expression.txt: Tab-delimited text file includes FPKM values.

source_name: CHD8KO_hESC-derived neural progenitor cells

growth_protocol: Human embryonic stem cells (ESCs) H9 and CHD8KO_H9 were maintained in mTeSR1 on Matrigel-coated cell culture plate at 37℃ with 5% CO2. To induce neural differentiation, wildtype or CHD8 knockout human ESCs were seeded onto Matrigel-coated 24-well plates. After 3 days’ culture with mTeRS1 medium, the neuroectoderm differentiation was initiated by neural induction medium (DMEM/F12 , 0.5 × N2 , 0.5 × B27 , 1% Gluta-max, 1% NEAA, 1x penicillin/streptomycin, 0.1%β-mercaptoethanol) plus 10μM SB431542and 0.1μM LDN . After 5 days of neural induction, the TGF-β inhibitor SB431542 was withdrawn from the neural induction medium for another 2 days’ culture.

extract_protocol:
RNA was extracted with RNAiso Plus (Takara, Cat#9109).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: type

value: hESC-derived neural progenitor cells

value: CHD8 KO


title: ZK_FSU_RNA150424-5_all_RNAseq

tag: tissue

value: whole worms

value: 5 days

value: hermaphrodite


title: MG_UKJ_24_970_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

tag: strain


title: MG_UKJ_24_969_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM142.4_muscle_RNAseq


title: ZK_FSU_RNA150424-6_all_RNAseq


title: ZK_FSU_RNA150424-4_all_RNAseq


title: G540-S1

source_name: 2D cultured GMSC1 rep1


title: CHD8KO_hNPC_rep1


title: MG_UKJ_24_968_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: enriched environment


title: Marmoset1_Macula_Right_Rep1_PCR_GFP

description:
PCR_GFP_C_S3_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina

value: Retina macula region


title: MB_FLI_JM140.4_muscle_RNAseq

value: swim-tunnel


title: MB_FLI_JM137.4_muscle_RNAseq


title: MB_FLI_JM139.4_muscle_RNAseq


title: LG_FSU_RNA1409-9_all_RNAseq


title: ES_rep4

source_name: embryonic stem cells

value: embryonic stem cells

value: WT


title: MB_FLI_JM141.4_muscle_RNAseq


title: MG_UKJ_24_964_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hemisphere

value: 24 months


title: MB_FLI_JM133.4_muscle_RNAseq


title: ES_rep3


title: MB_FLI_JM132.4_muscle_RNAseq


title: hNPC_rep1

source_name: hESC-derived neural progenitor cells


title: MB_FLI_JM136.4_muscle_RNAseq


title: LG_FSU_RNA1409-7_all_RNAseq


title: MG_UKJ_24_967_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: hNPC_rep2


title: ZK_FSU_RNA150424-3_all_RNAseq


title: CHD8KO_ESC_rep2

source_name: CHD8KO_embryonic stem cells


title: MG_UKJ_24_965_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_966_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: ZK_FSU_RNA150424-2_all_RNAseq


title: LG_FSU_RNA1409-8_all_RNAseq


title: ES_rep1


title: MB_FLI_JM127.4_muscle_RNAseq

source_name: 9 weeks_none_muscle

value: 9 weeks


title: MG_UKJ_5_25_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months

value: male


title: MG_UKJ_24_971_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: ZK_FSU_RNA150424-1_all_RNAseq


title: LG_FSU_RNA1409-3_all_RNAseq


title: MG_UKJ_5_27_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: ZK_FSU_RNA150424-7_all_RNAseq


title: MG_UKJ_5_23_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SS_FSU_40_none_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: 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 NIH 3T3

value: NIH 3T3 mouse fibroblasts

tag: population doublings

value: H2O 24 h 5 nM


title: LG_FSU_RNA1409-2_all_RNAseq


title: CHD8KO_ESC_rep1

value: CHD8 KO


title: MB_FLI_JM120.4_muscle_RNAseq

source_name: 9 weeks_swim-tunnel_muscle

value: muscle


title: MG_UKJ_5_20_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: ES_rep2


title: MG_UKJ_5_19_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM128.4_muscle_RNAseq


title: MG_UKJ_24_963_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM117.4_muscle_RNAseq


title: MB_FLI_JM121.4_muscle_RNAseq


title: MB_FLI_JM134.4_muscle_RNAseq

value: 27 weeks


title: MG_UKJ_2_500_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

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: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The text files include raw counts (sample_counts.txt) and RPKM values (sample_rpkms.txt) of all genes for each sample.

value: brain, right hemisphere


title: MG_UKJ_5_17_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: LG_FSU_RNA1409-6_all_RNAseq

value: whole worms

value: 5 days

value: hermaphrodite


title: MB_FLI_JM126.4_muscle_RNAseq


title: MB_FLI_JG84.4_muscle_RNAseq

source_name: GRZ_muscle w/ physical exercise

value: GRZ

value: 10 weeks

value: swim-tunnel


title: LG_FSU_RNA1409-5_all_RNAseq


title: MG_UKJ_5_22_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hemisphere


title: SS_FSU_42_none_RNAseq

value: Arsenite 24 h 5 nM


title: SS_FSU_41_none_RNAseq


title: MB_FLI_JM125.4_muscle_RNAseq

value: 9 weeks


title: MG_UKJ_5_24_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months

value: enriched environment


title: MB_FLI_JM119.4_muscle_RNAseq

value: male


title: MG_UKJ_30_10_brain_RNAseq 2

description:
sample_counts.txt
sample_rpkms.txt

value: brain

value: 30 months


title: LG_FSU_RNA1409-4_all_RNAseq


title: MG_UKJ_24_974_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: 24 months


title: LG_FSU_RNA1409-1_all_RNAseq


title: MG_UKJ_5_26_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_30_8_brain_RNAseq 2

description:
sample_counts.txt
sample_rpkms.txt


title: SS_FSU_39_none_RNAseq

value: NIH 3T3 mouse fibroblasts

value: H2O 24 h 5 nM


title: MG_UKJ_24_969_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_2_502_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, right hemisphere


title: MG_UKJ_5_18_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_968_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_2_499_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_2_498_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG80.4_muscle_RNAseq

value: muscle


title: MB_FLI_JM118.4_muscle_RNAseq


title: JM_FSU_RNA1307-43_all_RNAseq

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

value: whole worms

value: 10 days

value: hermaphrodite


title: MB_FLI_JM124.4_muscle_RNAseq


title: MG_UKJ_24_973_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG83.4_muscle_RNAseq

value: GRZ

value: 10 weeks

value: swim-tunnel


title: MG_UKJ_30_9_brain_RNAseq 2

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG78.4_muscle_RNAseq


title: MG_UKJ_24_971_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG77.4_muscle_RNAseq


title: MG_UKJ_5_21_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hemisphere

value: 5 months


title: MB_FLI_JG74.4_muscle_RNAseq

value: male


title: MG_UKJ_30_11_brain_RNAseq 2

description:
sample_counts.txt
sample_rpkms.txt

value: brain


title: NH_FLI_31_ZF_skin_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: 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

value: AB JxTu

value: skin


title: MB_FLI_JG81.4_muscle_RNAseq


title: NH_FLI_nf_12_muscle_RNAseq

source_name: muscle w/o physical exercise

value: line 4010; Tg(mylz2:egfp,tfam)


title: MG_UKJ_2_501_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: JM_FSU_RNA1307-45_all_RNAseq

source_name: N2_10 days_prp-19


title: MG_UKJ_24_964_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

source_name: brain

value: brain, hippocampus

value: 24 months

value: enriched environment


title: JM_FSU_RNA1307-40_all_RNAseq


title: MG_UKJ_24_963_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG82.4_muscle_RNAseq

value: muscle


title: MG_UKJ_24_970_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: JM_FSU_RNA1307-44_all_RNAseq

source_name: N2_10 days_skp-1

value: whole worms


title: JM_FSU_RNA1307-39_all_RNAseq

value: 10 days


title: JM_FSU_RNA1307-42_all_RNAseq

value: hermaphrodite


title: JM_FSU_RNA1307-38_all_RNAseq


title: MG_UKJ_5_15_brain_hemispheare_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: JM_FSU_RNA1307-37_all_RNAseq


title: NH_FLI_nf_9_muscle_RNAseq


title: MG_UKJ_5_27_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NH_FLI_68_ZF_skin_RNAseq

value: AB JxTu Tg(wt1b:GFP)


title: JM_FSU_RNA1307-36_all_RNAseq

source_name: N2_5 days_prp-19

value: 5 days


title: MB_FLI_JG76.4_muscle_RNAseq

value: GRZ

value: 10 weeks

value: swim-tunnel


title: NH_FLI_69_ZF_skin_RNAseq

value: male


title: zno-3

city: Guangzhou

first: Yan

last: Yu

address: Huangpu street

institute: Jinan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool, in which TopHat can generate a database of splice junctions based on the gene model annotation file, so that a better mapping result can be obtained compared to other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: whole chicken embryos

extract_protocol:
Chicken embryos were removed and using a Trizol kit to hsrvest the RNA. Illumina TruSeq sample prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

value: whole chicken embryos

tag: Stage

value: HH10 stage (34 hours-44 hours)

tag: group

value: Zinc oxide Nanoparticles-treated


title: NH_FLI_nf_8_muscle_RNAseq

value: line 4010; Tg(mylz2:egfp,tfam)

tag: age

tag: perturbation


title: NH_FLI_9_ZF_skin_RNAseq

source_name: skin

value: AB JxTu

value: skin

value: 30 months


title: MB_FLI_JG75.4_muscle_RNAseq

value: muscle


title: JM_FSU_RNA1307-35_all_RNAseq

source_name: N2_5 days_skp-1

value: whole worms


title: MG_UKJ_24_966_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: 24 months

value: enriched environment


title: JM_FSU_RNA1307-41_all_RNAseq

value: 10 days

value: hermaphrodite


title: MG_UKJ_5_26_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months


title: SS_FSU_34_all_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: WBcel235, and respective gene annotation (WBcel235.84)
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: N2_1 day_Arsenite 100nM

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: 1 day

value: Arsenite 100 nM


title: JM_FSU_RNA1307-31_all_RNAseq

value: 5 days


title: NH_FLI_nf_5_muscle_RNAseq

source_name: muscle w/ physical exercise

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: 10 weeks

value: male

value: swim-tunnel


title: zno-2

value: whole chicken embryos

value: HH10 stage (34 hours-43 hours)

value: Zinc oxide Nanoparticles-treated


title: absence-2

value: HH10 stage (34 hours-40 hours)

value: control


title: JM_FSU_RNA1307-23_all_RNAseq

value: whole worms


title: MG_UKJ_5_20_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: MG_UKJ_24_967_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 24 months

value: enriched environment


title: zno-1

value: HH10 stage (34 hours-42 hours)


title: NH_FLI_nf_6_muscle_RNAseq

value: line 4010; Tg(mylz2:egfp,tfam)

value: muscle


title: MG_UKJ_5_18_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months


title: SS_FSU_26_all_RNAseq

source_name: N2_5 days_Arsenite 100nM

value: 5 days

value: hermaphrodite

value: Arsenite 100 nM


title: NH_FLI_nf_10_muscle_RNAseq

value: 10 weeks

value: male


title: SS_FSU_32_all_RNAseq

value: 1 day


title: absence-1

value: whole chicken embryos

value: HH10 stage (34 hours-39 hours)


title: JM_FSU_RNA1307-20_all_RNAseq


title: JM_FSU_RNA1307-19_all_RNAseq


title: MG_UKJ_5_25_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SS_FSU_31_all_RNAseq

source_name: N2_1 day_H2O 100nM

value: H2O 100 nM


title: absence-3

value: HH10 stage (34 hours-41 hours)

value: control


title: NH_FLI_nf_3_muscle_RNAseq

value: swim-tunnel


title: MG_UKJ_5_23_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: enriched environment


title: NH_FLI_nf_4_muscle_RNAseq

value: line 4010; Tg(mylz2:egfp,tfam)


title: JM_FSU_RNA1307-13_all_RNAseq

value: whole worms


title: SS_FSU_33_all_RNAseq


title: MG_UKJ_5_21_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months


title: MB_FLI_JM143.3_liver_RNAseq

source_name: 27 weeks_swim-tunnel_liver

value: 27 weeks

value: liver


title: MG_UKJ_5_22_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NH_FLI_nf_11_muscle_RNAseq

value: muscle


title: MB_FLI_JM144.3_liver_RNAseq


title: ZK_FSU_N2_Nr22_all_RNAseq

data_processing:
Sequence information was extracted in FastQ format using NA NA 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: WBcel235, and respective gene annotation (WBcel235.84)
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: wild type_5 days_OP50 heat inactivated

value: wild type (unspecified)

value: 5 days

value: hermaphrodite

value: OP50 heat inactivated


title: MG_UKJ_5_24_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: male


title: SS_FSU_24_all_RNAseq

value: Arsenite 100 nM


title: SS_FSU_23_all_RNAseq

source_name: N2_5 days_H2O 100nM

value: H2O 100 nM


title: MB_FLI_JM140.3_liver_RNAseq


title: JM_FSU_RNA1307-21_all_RNAseq


title: MB_FLI_JM141.3_liver_RNAseq


title: JM_FSU_RNA1307-27_all_RNAseq


title: SS_FSU_25_all_RNAseq


title: NH_FLI_nf_1_muscle_RNAseq

value: 10 weeks


title: JM_FSU_RNA1307-22_all_RNAseq


title: JM_FSU_RNA1307-8_all_RNAseq

source_name: N2_1 day_skp-1

value: 1 day


title: ZK_FSU_N2_Nr19_all_RNAseq


title: JM_FSU_RNA1307-9_all_RNAseq

source_name: N2_1 day_prp-19


title: MG_UKJ_5_17_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: MB_FLI_JM142.3_liver_RNAseq

value: swim-tunnel


title: MB_FLI_JM135.3_liver_RNAseq


title: MB_FLI_JM134.3_liver_RNAseq


title: MRC_5_PD32_2 (reanalysis of GSM1492878)

description:
sample_counts.xls
sample_rpkms.xls
reanalysis of GSM1492878

source_name: cell line MRC-5

value: MRC-5 fibroblasts

value: control


title: MB_FLI_JM136.3_liver_RNAseq


title: MG_UKJ_24_1012_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

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: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The text files include raw counts (sample_counts.txt) and RPKM values (sample_rpkms.txt) of all genes for each sample.

value: 24 months


title: MG_UKJ_24_1014_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_1015_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: JM_FSU_RNA1307-5_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: WBcel235, and respective gene annotation (WBcel235.84)
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: whole worms


title: MG_UKJ_24_1029_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: enriched environment


title: MG_UKJ_24_1034_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM133.3_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 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.

value: 27 weeks

value: liver


title: MG_UKJ_24_1035_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF5.2_none_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.8.2 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 (H. sapiens sequences only)
Supplementary_files_format_and_content: The Excel file includes raw counts (sample_counts.xls) of all mirBase H. sapiens sequences for each sample.


title: JM_FSU_RNA1307-4_all_RNAseq


title: MG_UKJ_24_1020_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF5.1_none_smallRNAseq


title: JM_FSU_RNA1307-3_all_RNAseq


title: MG_UKJ_24_1030_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_1028_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MRC_5_PD32_1 (reanalysis of GSM1492877)

description:
sample_counts.xls
sample_rpkms.xls
reanalysis of GSM1492877


title: MB_FLI_JM128.3_liver_RNAseq

source_name: 9 weeks_none_liver

value: 9 weeks


title: MB_FLI_JM132.3_liver_RNAseq


title: MRC_5_PD32_3 (reanalysis of GSM1492879)

description:
sample_counts.xls
sample_rpkms.xls
reanalysis of GSM1492879


title: SSM_FLI_TRHF5.0_none_smallRNAseq


title: JM_FSU_RNA1307-6_all_RNAseq

value: hermaphrodite


title: JM_FSU_RNA1307-2_all_RNAseq


title: MG_UKJ_5_63_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

source_name: brain

value: 5 months


title: MG_UKJ_24_1018_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: male


title: SSM_FLI_TRHF4.2_none_smallRNAseq


title: MB_FLI_JM127.3_liver_RNAseq


title: MB_FLI_JM126.3_liver_RNAseq


title: SSM_FLI_TRHF4.1_none_smallRNAseq


title: JM_FSU_RNA1307-1_all_RNAseq


title: RL_FSU_RNA150427-47_all_RNAseq

value: whole worm

value: 5 days


title: MG_UKJ_5_60_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_5_59_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: RL_FSU_RNA150427-45_all_RNAseq


title: RL_FSU_RNA150427-46_all_RNAseq


title: RL_FSU_RNA150427-48_all_RNAseq


title: MG_UKJ_5_61_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF3.0_none_smallRNAseq


title: SSM_FLI_TRHF3.2_none_smallRNAseq


title: RL_FSU_RNA150427-44_all_RNAseq


title: RL_FSU_RNA150427-43_all_RNAseq


title: MG_UKJ_5_67_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM124.3_liver_RNAseq


title: SSM_FLI_TRHF2.2_none_smallRNAseq


title: SSM_FLI_TRHF4.0_none_smallRNAseq


title: MG_UKJ_5_58_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: RL_FSU_RNA150427-42_all_RNAseq


title: MB_FLI_JM120.3_liver_RNAseq

source_name: 9 weeks_swim-tunnel_liver


title: MB_FLI_JM119.3_liver_RNAseq


title: MB_FLI_JG84.3_liver_RNAseq

value: GRZ

value: 10 weeks


title: RL_FSU_RNA150427-40_all_RNAseq


title: SSM_FLI_TRHF3.1_none_smallRNAseq


title: RL_FSU_RNA150427-39_all_RNAseq

value: 1 day


title: MB_FLI_JM118.3_liver_RNAseq

value: swim-tunnel


title: SSM_FLI_TRHF1.1_none_smallRNAseq


title: MG_UKJ_5_66_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: MB_FLI_JM125.3_liver_RNAseq


title: SSM_FLI_TRHF2.1_none_smallRNAseq


title: MB_FLI_JM117.3_liver_RNAseq


title: RL_FSU_RNA150427-38_all_RNAseq


title: SSM_FLI_TRHF2.0_none_smallRNAseq


title: RL_FSU_RNA150427-37_all_RNAseq


title: MG_UKJ_5_50_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_956_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hemisphaere

value: 20 months


title: MB_FLI_JM121.3_liver_RNAseq


title: MB_FLI_JG78.3_liver_RNAseq


title: MG_UKJ_5_49_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: RL_FSU_RNA150427-35_all_RNAseq


title: SSM_FLI_TRHF1.2_none_smallRNAseq


title: MG_UKJ_24_955_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG83.3_liver_RNAseq


title: MG_UKJ_24_954_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: treadmill


title: RL_FSU_RNA150427-41_all_RNAseq


title: MG_UKJ_24_958_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG80.3_liver_RNAseq


title: RL_FSU_RNA150427-36_all_RNAseq


title: MG_UKJ_24_959_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG76.3_liver_RNAseq


title: SSM_FLI_TRHF10.2_none_smallRNAseq

source_name: cell line HFF

value: HFF


title: RL_FSU_RNA150427-33_all_RNAseq


title: SSM_FLI_TRHF1.0_none_smallRNAseq


title: MB_FLI_JG77.3_liver_RNAseq


title: SSM_FLI_TRHF9.0_none_smallRNAseq


title: RL_FSU_RNA150427-32_all_RNAseq


title: SSM_FLI_TRHF10.1_none_smallRNAseq


title: RL_FSU_RNA150427-34_all_RNAseq


title: MG_UKJ_24_957_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF10.0_none_smallRNAseq


title: NH_FLI_nf_12_liver_RNAseq

source_name: no exercise control_liver

value: line 4010; Tg(mylz2:egfp,tfam)


title: MG_UKJ_5_51_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NH_FLI_nf_11_liver_RNAseq

value: liver


title: SSM_FLI_TRHF8.1_none_smallRNAseq


title: MB_FLI_JG75.3_liver_RNAseq


title: MB_FLI_JG82.3_liver_RNAseq


title: NU_FSU_X1_all_RNAseq

source_name: N2_5 days_Rotenone 100 nM

value: Rotenone 100 nM


title: MG_UKJ_24_952_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_5_12_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF9.2_none_smallRNAseq


title: MB_FLI_JG81.3_liver_RNAseq


title: MG_UKJ_24_953_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG74.3_liver_RNAseq


title: MG_UKJ_24_947_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF8.2_none_smallRNAseq


title: MG_UKJ_5_10_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NU_FSU_W2_all_RNAseq

value: hermaphrodite


title: NU_FSU_X2_all_RNAseq


title: SSM_FLI_TRHF7.0_none_smallRNAseq


title: SSM_FLI_TRHF9.1_none_smallRNAseq


title: NH_FLI_nf_10_liver_RNAseq


title: NU_FSU_X3_all_RNAseq


title: NU_FSU_W1_all_RNAseq


title: NH_FLI_nf_6_liver_RNAseq


title: MG_UKJ_5_13_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months


title: RL_FSU_RNA150427-31_all_RNAseq


title: MG_UKJ_5_9_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: male


title: NU_FSU_W3_all_RNAseq

value: whole worm


title: SSM_FLI_TRHF6.1_none_smallRNAseq


title: NH_FLI_nf_5_liver_RNAseq


title: SSM_FLI_TRHF7.2_none_smallRNAseq


title: SSM_FLI_TRHF7.1_none_smallRNAseq


title: SSM_FLI_TRHF6.2_none_smallRNAseq


title: NU_FSU_V3_all_RNAseq

source_name: N2_5 days_DMSO 0.1 %

value: 5 days

value: DMSO 0.1 %


title: MG_UKJ_5_11_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF8.0_none_smallRNAseq


title: NH_FLI_nf_8_liver_RNAseq

value: 10 weeks


title: MG_UKJ_24_950_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NH_FLI_nf_9_liver_RNAseq


title: MG_UKJ_5_5_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NH_FLI_nf_4_liver_RNAseq


title: MG_UKJ_5_7_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NH_FLI_nf_3_liver_RNAseq


title: MG_UKJ_5_4_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NU_FSU_V1_all_RNAseq


title: NU_FSU_U3_all_RNAseq

source_name: N2_3 days_Rotenone 100 nM

value: 3 days


title: MG_UKJ_5_3_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: SSM_FLI_TRHF6.0_none_smallRNAseq


title: NH_FLI_nf_2_liver_RNAseq

value: swim-tunnel


title: MCF7-3xFlag-KI-CTR9: Flag-Sigma-Rep2

city: Madison

first: NGAI TING

last: CHAN

state: WI

address: 4849 Sheboygan Ave

department: Oncology

institute: University of Wisconsin -- Madison

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP sequencing reads that passed quality score were aligned to the human reference genome (hg38) using Bowtie2 (v2.4.1)
Only unique alignments that passed high mapping quality (MAPQ>30) were retained for downstream analysis. Duplicated reads and reads resides in hg38 blacklist regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) were eliminated by sambamba tools (v0.7.1). Sequencing reads were also aligned to the Drosophila genome (dm6) and normalization factors (Rx factor) were calculated after removing multi-mapping and duplicated reads.
Bigwig files were generated at a resolution of 20bp using the bamCoverage utility from the deepTools (v3.4.3) suits and data were subsequently visualized as ChIP-Rx normalized tracks using IGV genome browser (v2.8.9).
Peaks were called using MACS2 (v2.1.4) with FDR<0.01 for narrow beaks and FDR<0.05 for broad peaks. Peaks intersection was performed by bedtools (v2.29.2). Overlapped peaks that shorter than sequencing tag (100bp) will be discarded.
Genome_build: hg38
Supplementary_files_format_and_content: format: bigwig  content: a continous track representing the normalized ChIP-seq signal

growth_protocol: Cells are maintained in Dulbecco’s modified medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS) (VWR) and 1% Penicillin-Streptomycin (P/S) (Gibco) and cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with corresponding antibodies.
Libraries were prepared according to manufacturer’s protocol of  the Ovation Ultralow System V2 1-16 Kit (NuGEN Technologies).  Briefly, the DNA was end-repaired and ligated to Illumina sequencing adaptors. The ligated DNA was purified using Agencourt RNAClean XP beads (Beckman Coulter). A subsequent PCR amplification step (8-15 cycles) was performed to add linker sequence to the purified fragments for annealing to the Genome Analyzer flow-cell. Following PCR amplification, the library was separated on a 2% agarose gel (120 V, 1.5 hours) to select a narrow range of fragment sizes, and bands between 200-500 bp were excised. The library was purified from the excised agarose gel using the Qiagen MiniElute PCR Purification Kit following the manufacturer’s protocol.

treatment_protocol: Doxcycline (Clonetech,Cat# NC0424034) were directly added to cell culture medium to a final concentration of 500ng/ml. Cells were treated up to 7 days.

value: human luminal breast cancer

value: 3xFlag Knock in at TSS of CTR9 gene

tag: chip antibody

value: Anti-Flag (Sigma-Aldrich, Cat# F7425, RRID:AB_439687)

tag: treatment


title: MG_UKJ_5_1_brain_hemisphaere_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hemisphaere

value: treadmill


title: NU_FSU_U1_all_RNAseq


title: MB_FLI_JM144.1_brain_RNAseq

source_name: 27 weeks_swim-tunnel_brain

value: 27 weeks

value: brain


title: MB_FLI_JM143.1_brain_RNAseq


title: MCF7-3xFlag-KI-CTR9: Flag-Sigma-Rep1

tag: cell type


title: MCF7-3xFlag-KI-CTR9: Flag-CST-Rep2

value: Anti-DYKDDDDK Tag (Cell signaling technology, Cat# 14793, RRID:AB_2572291)


title: MB_FLI_JM141.1_brain_RNAseq


title: MCF7-3xFlag-KI-CTR9: Flag-CST-Rep1


title: MG_UKJ_24_959_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: 20 months


title: NU_FSU_U2_all_RNAseq

value: hermaphrodite

value: Rotenone 100 nM


title: NU_FSU_T3_all_RNAseq

source_name: N2_3 days_DMSO 0.1 %

value: whole worm


title: MB_FLI_JM140.1_brain_RNAseq

value: male


title: MB_FLI_JM139.1_brain_RNAseq


title: MG_UKJ_24_957_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NU_FSU_T2_all_RNAseq

value: DMSO 0.1 %


title: NU_FSU_T1_all_RNAseq

value: 3 days


title: Atoh1_Ascl1_2wk

city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

description: Sorted retinal cells from Glast-CreER:LNL-tTA:tetO-mAscl1-tetO-Atoh1-ires-GFP mice

data_processing:
Data were demultiplexed and fastqs were generated using cellranger mkfastq (v 3.0)
Fastqs were aligned to the mm10 genome and gene x cell matrices were constructed using cellranger count (v 3.0)
Downstream analysis was preformed in R and Seurat
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger pipeline feature matrix directory

source_name: retinal cells

growth_protocol: Details of sample treatments are outlined in the linked manuscript.

extract_protocol:
Extraction protocol is outlined in the linked manuscript.
Libraries were constucted using 10x genomics 3’ single cell RNA v3 and v3.1 protocols

value: in vivo retina


title: MG_UKJ_24_956_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: Ascl1 5day in vitro

description: Sorted cultured glia  infected with pLOC-hAscl1-IRES-turboGFP virus

source_name: Cultured Muller glia

value: in vitro primary Muller glia


title: MB_FLI_JM136.1_brain_RNAseq

value: swim-tunnel


title: NU_FSU_S3_all_RNAseq

source_name: N2_2 days_Rotenone 100 nM

value: 2 days


title: Control cultured glia

description: Sorted cultured mouse glia treated infected with a lentivirus containing RFP


title: MG_UKJ_24_954_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM135.1_brain_RNAseq


title: MG_UKJ_24_958_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NU_FSU_S1_all_RNAseq


title: MG_UKJ_24_953_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM134.1_brain_RNAseq


title: Non.CM4

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads were mapped to mm10 using STAR (“--runMode alignReads --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMismatchNmax 2 --quantMode GeneCounts –outSAMty”)
Read counts were normalized and analyzed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Read Count and Differential expression

source_name: Adult Cardiac Interstitual Cells

extract_protocol:
Total RNA extraction
Bulk RNA sequencing

value: Heart

tag: genotype

value: MCM/+ Wls fl/fl


title: MB_FLI_JM133.1_brain_RNAseq

value: 27 weeks


title: Atoh7 5day in vitro

description: Sorted cultured mouse glia infected with pLOC-hATOH7-IRES-copGFP virus

tag: genotype/variation


title: Non.CM7


title: MB_FLI_JM132.1_brain_RNAseq

value: brain


title: MG_UKJ_24_952_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: treadmill


title: Non.CM3


title: NU_FSU_S2_all_RNAseq


title: NU_FSU_R2_all_RNAseq

source_name: N2_2 days_DMSO 0.1 %


title: Non.CM8

value: MCM/+


title: MG_UKJ_24_950_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: 20 months


title: MB_FLI_JM130.1_brain_RNAseq

source_name: 9 weeks_none_brain

value: 9 weeks


title: MG_UKJ_24_947_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_5_13_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months


title: MG_UKJ_24_955_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: male


title: NU_FSU_Q3_all_RNAseq

source_name: N2_1 day_Rotenone 100 nM

value: whole worm

value: 1 day

value: hermaphrodite

value: Rotenone 100 nM


title: NU_FSU_R1_all_RNAseq

value: DMSO 0.1 %


title: MB_FLI_JM129.1_brain_RNAseq


title: NU_FSU_Q2_all_RNAseq


title: Non.CM5


title: MB_FLI_JM125.1_brain_RNAseq


title: CM13

source_name: Adult Cardiomyocytes


title: MG_UKJ_5_12_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

source_name: brain


title: MG_UKJ_5_11_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NU_FSU_R3_all_RNAseq

value: 2 days


title: NU_FSU_Q1_all_RNAseq


title: CM10

value: Heart


title: MG_UKJ_5_10_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM124.1_brain_RNAseq


title: Non.CM6


title: CM9

value: MCM/+ Wls fl/fl


title: NU_FSU_P2_all_RNAseq


title: NU_FSU_P1_all_RNAseq


title: NU_FSU_P3_all_RNAseq


title: MB_FLI_JM121.1_brain_RNAseq

source_name: 9 weeks_swim-tunnel_brain

value: swim-tunnel


title: MG_UKJ_5_7_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_5_5_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JM120.1_brain_RNAseq

value: brain


title: MB_FLI_JM118.1_brain_RNAseq


title: MB_FLI_JM119.1_brain_RNAseq


title: MB_FLI_JM126.1_brain_RNAseq


title: CM12


title: MG_UKJ_5_4_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: treadmill


title: NU_FSU_O1_all_RNAseq

source_name: N2_1 day_DMSO 0.1 %


title: NU_FSU_O2_all_RNAseq


title: NU_FSU_N3_all_RNAseq

source_name: N2_6 hours_Rotenone 100 nM

value: 6 hours


title: MB_FLI_MR49.1_brain_RNAseq

source_name: MZM-04/10p_9 weeks_Rotenone 1% LC50

value: Rotenone 1% LC50


title: MG_UKJ_9_337_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 (M. musculus sequences only)
Supplementary_files_format_and_content: The txt file includes raw counts (sample_counts.txt) of all mirBase M. musculus sequences for each sample.

source_name: skin

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: skin

value: 9 months


title: MB_FLI_JM117.1_brain_RNAseq

value: 9 weeks


title: CM14

value: MCM/+


title: NU_FSU_N2_all_RNAseq

value: whole worm


title: MB_FLI_MR50.1_brain_RNAseq

value: male


title: CM11


title: NU_FSU_V2_all_RNAseq

source_name: N2_5 days_DMSO 0.1 %

value: 5 days

value: hermaphrodite


title: MG_UKJ_5_9_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: 5 months


title: MG_UKJ_9_336_skin_smallRNAseq


title: NU_FSU_N1_all_RNAseq

value: Rotenone 100 nM


title: MG_UKJ_9_335_skin_smallRNAseq


title: MB_FLI_MR48.1_brain_RNAseq


title: MG_UKJ_5_3_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NU_FSU_O3_all_RNAseq

value: 1 day

value: DMSO 0.1 %


title: MG_UKJ_9_334_skin_smallRNAseq


title: MG_UKJ_9_338_skin_smallRNAseq


title: MG_UKJ_5_1_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: NU_FSU_M3_all_RNAseq

source_name: N2_6 hours_DMSO 0.1 %


title: MG_UKJ_30_73_skin_smallRNAseq

value: 30 months


title: MB_FLI_MR46.1_brain_RNAseq

value: brain


title: MB_FLI_MR47.1_brain_RNAseq


title: NU_FSU_M2_all_RNAseq

value: 6 hours


title: MG_UKJ_30_9_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

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 following the manufacturer's instruction.

value: brain, hemisphere


title: MB_FLI_MR45.1_brain_RNAseq

source_name: MZM-04/10p_27 weeks_Rotenone 1% LC50

value: 27 weeks

value: Rotenone 1% LC50


title: MG_UKJ_30_10_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_30_72_skin_smallRNAseq

value: skin


title: NU_FSU_M1_all_RNAseq


title: JM_FSU_RNA1404-11_all_RNAseq

value: 2 days


title: JM_FSU_RNA1404-12_all_RNAseq

source_name: N2_2 days_bcat-1

value: whole worm


title: MB_FLI_MR44.1_brain_RNAseq

value: male


title: MG_UKJ_30_8_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: JM_FSU_RNA1404-9_all_RNAseq


title: MG_UKJ_24_253_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 24 months


title: MG_UKJ_30_7_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MR42.1_brain_RNAseq


title: MG_UKJ_24_256_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_1057_skin_smallRNAseq


title: MG_UKJ_24_1059_skin_smallRNAseq


title: MG_UKJ_30_70_skin_smallRNAseq


title: JM_FSU_RNA1404-7_all_RNAseq

value: hermaphrodite


title: MG_UKJ_15_222_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 15 months


title: MG_UKJ_24_1056_skin_smallRNAseq


title: JM_FSU_RNA1404-10_all_RNAseq


title: MG_UKJ_24_255_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_30_71_skin_smallRNAseq


title: MG_UKJ_24_252_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_254_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MR41.1_brain_RNAseq


title: MB_FLI_MR43.1_brain_RNAseq


title: MG_UKJ_30_11_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MC27.1_brain_RNAseq

source_name: MZM-04/10p_9 weeks_DMSO

value: 9 weeks

value: DMSO


title: JM_FSU_RNA1404-5_all_RNAseq

value: 1 day


title: MB_FLI_MC29.1_brain_RNAseq


title: MG_UKJ_2_1156_skin_smallRNAseq

value: 2 months


title: MG_UKJ_24_1058_skin_smallRNAseq


title: MB_FLI_MC28.1_brain_RNAseq


title: JM_FSU_RNA1404-8_all_RNAseq


title: MG_UKJ_30_69_skin_smallRNAseq

value: 30 months


title: MG_UKJ_15_220_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: JM_FSU_RNA1404-6_all_RNAseq

source_name: N2_1 day_bcat-1


title: MB_FLI_MC24.1_brain_RNAseq

source_name: MZM-04/10p_27 weeks_DMSO

value: brain


title: MG_UKJ_15_221_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: JM_FSU_RNA1404-4_all_RNAseq


title: MB_FLI_MC30.1_brain_RNAseq


title: MG_UKJ_2_1153_skin_smallRNAseq


title: MG_UKJ_24_1055_skin_smallRNAseq


title: MB_FLI_MC25.1_brain_RNAseq


title: MG_UKJ_2_1154_skin_smallRNAseq


title: MB_FLI_MC26.1_brain_RNAseq


title: MG_UKJ_2_1155_skin_smallRNAseq


title: JM_FSU_RNA1404-3_all_RNAseq


title: JM_FSU_RNA1404-2_all_RNAseq


title: MG_UKJ_15_219_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MC23.1_brain_RNAseq


title: MG_UKJ_9_325_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 9 months