title: ZT18fed_r1

description:
SM4483_S25
Sample_4483
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT18fed_r2

status: Public on Sep 08 2021

type: SRA

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
SM4484_S26
Sample_4484
processed data file: RNAseq_RAW_CT_FED_FAST.txt

library_source: transcriptomic

data_processing:
RNA-seq and ChIP-seq sequencing data was aligned to mm10 or rn5 using STAR
RNAseq data was quantified by HOMER and normalised using DESeq2
GR ChIPseq peaks and bedgraph files were generated using HOMER
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text files with DESeq2 normalised RNAseq data

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were housed at 12 hour light/dark cycles and trained to night restricted feeding. Primary hepatocytes were isolated from Male Sprague Dawley rats and seeded on collagen coated plates in Gibo Medium 199 + GlutaMAX (Gibco life technologies, cat: 41150-020) supplemented with 100 nM.  Decadron (dex), 1 % P/S, 4 % FCS and 1 nM human insulin. 2-3 hours after isolation, the medium was changed to Gibo Medium 199 + GlutaMAX supplemented with 1 % P/S, 0.1 % FCS, 1 nM human Insulin and kept overnight.

extract_protocol:
RNA_seq: Primary hepatocytes: Cells were lysed in TRIzol-RNA lysis reagent  (ThermoFisher). Liver tissue: Approximately 5 mg of liver tissues were homogenized using Ultra-Thorax in TRIzol-RNA lysis reagent. RNA was purified using  EconoSpin columns (Epoc Life) according to manufacturer’s instructions.
ChIP-seq: Chromatin was prepared from 100-150mg formaldehyde crosslinked liver tissu. Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
Libraries from ChIP'ed DNA were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions. Total RNA (1000 ng) was prepared for sequencing using ribosome depletion followed by random primed cDNA synthesis or polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina.

treatment_protocol: Nr3c1fl/fl mice were injected with AAV-tbg-GFP or AAV-tbg-CRE ten days before sacrifice. The primary hepatocytes were serum depleted in Gibo Medium 199 + GlutaMAX supplemented with 1 % P/S and 0.1 % HAS for 4 hours before cells were stimulated with 500 nM dex for 2.5 hours, human insulin for 2 hours or in a combination and RNA was harvested.

tag: strain

tag: aav injection

value: non treated

tag: treatment

value: fed

tag: circadian timepoint

tag: tissue/cell type

value: Liver


title: R8-15101202_S13_E1-50

city: Seattle

first: Bosiljka

last: Tasic

state: WA

address: 615 Westlake Ave N.

department: Molecular Genetics

country: USA

institute: Allen Institute for Brain Science

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10, Mmul_10

source_name: Mouse LGN - Core

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia. The brain tissues of two adult M. nemestrina (southern pig-tailed macaque) and one M. fascicularis  (crab-eating macaque) were obtained through the Tissue Distribution Program of the Washington  National Primate Research Center and conformed to the guidelines provided by the US National  Institutes of Health. All procedures were approved by the Institutional Animal Care and Use Commit-  tee of the University of Washington under protocol number 4277-01.

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

tag: donor

tag: Sex

value: M

tag: genotype

value: dLGN - Core

tag: facs gating

value: RFP-positive

tag: sequencing batch

tag: cell class

value: GABA

tag: cell cluster


title: R8-15101202_S15_E1-50


title: R8-15101202_S12_E1-50


title: ZT14unfed_r3

description:
SM4476_S18
Sample_4476
processed data file: RNAseq_RAW_CT_FED_FAST.txt

value: unfed


title: R8-15101202_S16_E1-50


title: SM-GE67L_S144_E1-50

organism: Macaca nemestrina

source_name: Macaque LGN Parvocellular

tag: age

value: 2.3 yrs

value: PC

value: NeuN-positive

value: Glut

value: P


title: ZT18unfed_r2

description:
SM4481_S23
Sample_4481
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT14fed_r2

description:
SM4478_S20
Sample_4478
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: SM-GE67L_S142_E1-50


title: R8-15101202_S10_E1-50


title: ZT14fed_r3

description:
SM4479_S21
Sample_4479
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: SM-GE67L_S143_E1-50


title: ZT13fed_r1

description:
SM4471_S13
Sample_4471
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: R8-15101202_S11_E1-50


title: SM-GE67L_S141_E1-50


title: SM-GE67L_S139_E1-50


title: ZT14unfed_r1

description:
SM4474_S16
Sample_4474
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: SM-GE67L_S140_E1-50


title: ZT10_r3

description:
SM4467_S9
Sample_4467
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT13fed_r3

description:
SM4473_S15
Sample_4473
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT13fed_r2

description:
SM4472_S14
Sample_4472
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT10_r1

description:
SM4465_S7
Sample_4465
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: R8-15101201_S70_E1-50


title: SM-GE67L_S135_E1-50


title: CRE_ZT22_r2

description:
8063_S114
Sample_8063
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

molecule: total RNA

value: AAV-tbg-CRE

tag: molecule subtype

value: rRNA depleted RNA


title: SM-GE67L_S138_E1-50


title: ZT14fed_r1

description:
SM4477_S19
Sample_4477
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT13unfed_r3

description:
SM4470_S12
Sample_4470
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT13unfed_r2

description:
SM4469_S11
Sample_4469
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: GFP_ZT22_r3

description:
8061_S112
Sample_8061
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: AAV-tbg-GFP


title: ZT14unfed_r2

description:
SM4475_S17
Sample_4475
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: SM-GE67L_S137_E1-50


title: R8-15101201_S72_E1-50


title: R8-15101201_S69_E1-50


title: R8-15101202_S09_E1-50


title: R8-15101201_S68_E1-50


title: R8-15101201_S67_E1-50


title: GFP_ZT22_r2

description:
8060_S111
Sample_8060
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: GFP_ZT22_r1

description:
8059_S110
Sample_8059
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: R8-15101201_S66_E1-50


title: CRE_ZT22_r3

description:
8064_S115
Sample_8064
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: ZT10_r2

description:
SM4466_S8
Sample_4466
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: SM-GE67L_S136_E1-50

value: Low Quality


title: SM-GE67L_S134_E1-50


title: CRE_ZT22_r1

description:
8062_S113
Sample_8062
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: ZT13unfed_r1

description:
SM4468_S10
Sample_4468
processed data file: RNAseq_RAW_CT_FED_FAST.txt

value: non treated


title: R8-15101201_S71_E1-50


title: CRE_ZT18_r3

description:
8058_S109
Sample_8058
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: fed


title: SM-GE67L_S132_E1-50


title: CRE_ZT14_r3

description:
8052_S103
Sample_8052
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: Liver


title: SM-GE67L_S133_E1-50

value: M


title: CRE_ZT18_r2

description:
8057_S108
Sample_8057
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: CRE_ZT14_r2

description:
8051_S102
Sample_8051
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: CRE_ZT14_r1

description:
8050_S101
Sample_8050
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: R8-15101201_S52_E1-50

value: dLGN - Core


title: GFP_ZT14_r2

description:
8048_S99
Sample_8048
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: GFP_ZT14_r1

description:
8047_S98
Sample_8047
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: R8-15101201_S51_E1-50

value: RFP-positive


title: SM-GE67L_S131_E1-50


title: CRE_ZT18_r1

description:
8056_S107
Sample_8056
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: CRE_ZT13_r2

description:
8045_S96
Sample_8045
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: SM-GE67L_S126_E1-50


title: R8-15101201_S65_E1-50

value: GABA


title: R8-15101201_S50_E1-50


title: SM-GE67L_S130_E1-50


title: GFP_ZT13_r2

description:
8042_S93
Sample_8042
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: R8-15101201_S49_E1-50


title: GFP_ZT18_r2

description:
8054_S105
Sample_8054
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: GFP_ZT13_r1

description:
8041_S92
Sample_8041
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: SM-GE67L_S129_E1-50


title: CRE_ZT12_r3

description:
8040_S91
Sample_8040
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: unfed


title: R8-15101201_S54_E1-50


title: GFP_ZT14_r3

description:
8049_S100
Sample_8049
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: SM-GE67L_S128_E1-50

value: 2.3 yrs


title: SM-GE67L_S123_E1-50

value: PC


title: R8-15101201_S53_E1-50


title: R8-15101201_S31_E1-50


title: SM-GE67L_S122_E1-50

value: NeuN-positive


title: SM-GE67L_S121_E1-50

value: Glut


title: SM-GE67L_S124_E1-50

value: P


title: GFP_ZT18_r3

description:
8055_S106
Sample_8055
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: GFP_ZT12_r1

description:
8035_S86
Sample_8035
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: CRE_ZT13_r3

description:
8046_S97
Sample_8046
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: AAV-tbg-CRE


title: R8-15101201_S27_E1-50


title: CRE_ZT10_r3

description:
8034_S85
Sample_8034
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: rRNA depleted RNA


title: CRE_ZT10_r2

description:
8033_S84
Sample_8033
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: GFP_ZT18_r1

description:
8053_S104
Sample_8053
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: AAV-tbg-GFP


title: SM-GE67L_S125_E1-50


title: GFP_ZT10_r3

description:
8031_S82
Sample_8031
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: CRE_ZT13_r1

description:
8044_S95
Sample_8044
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: GFP_ZT10_r1

description:
8029_S80
Sample_8029
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: R8-15101201_S22_E1-50


title: GFP_ZT13_r3

description:
8043_S94
Sample_8043
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: SM-GE67L_S117_E1-50


title: Primary microglia-Chd8 siRNA 3

city: Tokyo

first: Shogo

last: Tanabe

address: 4-1-1 Ogawahigashicho

country: Japan

institute: National Center of Neurology and Psychiatry

data_processing:
Sequenced read counts were calculated with Salmon (v 0.14.1) based on mm10 reference.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts

source_name: Primary microglia

extract_protocol:
RNA from primary microglia was harvested using Trizol reagent. SMARTER stranded kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Primary micoglia

value: Chd8 siRNA


title: SM-GE67L_S127_E1-50


title: R8-15101201_S32_E1-50


title: CRE_ZT12_r1

description:
8038_S89
Sample_8038
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: CRE_ZT12_r2

description:
8039_S90
Sample_8039
processed data file: RNAseq_RAW_CT_GFP_CRE.txt


title: R8-15101201_S21_E1-50


title: Primary microglia-control siRNA 3

value: Control siRNA


title: Primary microglia-control siRNA 2


title: GFP_ZT12_r2

description:
8036_S87
Sample_8036
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: Liver


title: R8-15101201_S20_E1-50

value: M


title: R8-15101201_S30_E1-50

value: dLGN - Core


title: Primary microglia-Tsc2 siRNA 1

value: Tsc2 siRNA


title: R8-15101201_S24_E1-50

value: RFP-positive

value: GABA


title: CRE_ZT10_r1

description:
8032_S83
Sample_8032
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: unfed


title: SM-GE67L_S119_E1-50

value: 2.3 yrs

value: PC

value: Low Quality


title: SM-GE67L_S113_E1-50

value: NeuN-positive

value: Glut

value: P


title: Mouse cochlea lateral wall, noise 4

city: Boston

first: Gabriela

last: Pregernig

state: Massachusetts

address: 1325 Boylston Street, Suite 500

institute: Decibel Therapeutics

description: 3' polyA RNASeq reads

data_processing:
3' polyA RNA-Seq (10X Genomics, chemistry v2)
CellRanger 2.0.1 (reference genome: mm10)
The gene count matrices were loaded into Seurat v3. Cells with 1% or more reads from hemoglobin genes were filtered out, as well as cells with more than 10 or 25% mitochondrial transcript reads (for the neuronal and lateral wall datasets, respectively).
Dimensionality reduction and clustering were performed using Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are gene count matrices as output by CellRanger. The matrix.mtx file is the genes x cells matrix, the barcodes.tsv file contains column (cell) labels, and the genes.tsv file contains the row (gene) labels.

source_name: WT mouse lateral wall cells

extract_protocol:
Neuronal tissue: Temporal bones from naïve (n = 4) and noise exposed (n = 4) 9 wko, male CBA/CaJ mice were isolated in ice-cold Leibovitz’s L-15 medium. The overlying bone and lateral wall were extracted from apex to base, leaving just the modiolus, with the spiral ganglion, the spiral limbus, inner sulcus, and portions of the organ of Corti and outer sulcus remaining. Microdissected tissue from each mouse was pooled in a solution of Leibovitz containing 200 units/mL collagenase IV (Sigma) and 10 kunitz/ml DNase I (Stem Cell Technologies) and incubated for 30 min at 37 °C to digest extracellular matrix. The collagenase IV solution was replaced with EBSS containing 20 units of papain (Worthington Biochemical), 1 mM L-cysteine, 0.5 mM EDTA, 15 mM HEPES, and 10 kunitz/ml DNase I and incubated for an additional 30 min at 37 °C, triturating with a 1000 µL pipette at 10 min intervals to generate a single cell suspension. An equal volume of Leibovitz containing 20% ovomucoid protease inhibitor (Worthington Biochemical) was added, and the cell suspension passed through a 20 m filter (pluriSelect) to remove debris. The cells were pelleted at 300g for 5 min, washed twice with PBS containing 0.04% BSA, then pelleted and resuspended in PBS/BSA solution. Finally, a 9 µL sample of the cell suspension was counted on a Luna Fl automated counter using an AO/PI fluorescent cell viability assay (Logos Biosystems).   Lateral wall tissue: Temporal bones from naïve (n = 4) and noise exposed (n = 4) 7-8 wko, male CBA/CaJ mice were isolated in ice-cold Leibovitz’s L-15 medium. Using a #11 scalpel, the bony wall of the cochlea was removed to reveal the cochlear lateral wall.  The lateral wall with attached stria vascularis was extracted from apex to base and separated from the modiolus and other cochlear tissue. Microdissected tissue was then dissociated into single cells using the collagenase IV and papain enzyme mixtures as described for the dissociation of SGN tissue.  For the strial tissues, however, the total incubation time in papain was extended to 1 hr to ensure complete tissue dissociation.
After cell counting, the appropriate volume of cell suspension was added to target capture of 10,000 cells per sample using the high throughput, droplet microfluidics Gemcode platform from 10X Genomics with v2 chemistry (Zheng et al., 2017). Each droplet on the Gemcode co-encapsulates a cell and a gel bead that is hybridized with oligo(dT) primers encoding a unique cell barcode and unique molecular identifiers (UMIs) in lysis buffer. The capture process takes 6 min, after which the transcriptomes captured on gel beads are pooled and reverse transcribed to cDNA. RT, PCR amplification of cDNA, and preparation of a library from 3’ ends were conducted according to the manufacturer’s published protocol. We performed 15 cycles of PCR amplification of cDNA. The libraries were sequenced on an Illumina NovaSeq 6000 at the Broad Institute Sequencing Facility.

treatment_protocol: Mice were noise exposed in a custom acoustic delivery chamber. Within the acoustic delivery chamber animals were placed in individually compartmentalized wire cage and exposed to 105 dB SPL 8-16 kHz broadband noise for 2 hours.  Animals recovered for 24 hours post exposure before tissue dissection and dissociation.

value: CBA/CaJ

value: wild-type

value: Noise-exposed


title: Mouse cochlea lateral wall, noise 2

description: 3' polyA RNASeq reads


title: R8-15101201_S19_E1-50


title: GFP_ZT12_r3

description:
8037_S88
Sample_8037
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: AAV-tbg-GFP

value: rRNA depleted RNA


title: R8-15101201_S16_E1-50

value: M


title: SM-GE67L_S111_E1-50


title: Primary microglia-Tsc2 siRNA 3

value: Primary micoglia


title: R8-15101201_S15_E1-50

value: dLGN - Core


title: SM-GE67L_S116_E1-50


title: Primary microglia-Tsc2 siRNA 2

value: Tsc2 siRNA


title: Primary microglia-Chd8 siRNA 2

value: Chd8 siRNA


title: R8-15101201_S23_E1-50

value: RFP-positive

value: GABA


title: SM-GE67L_S118_E1-50

value: 2.3 yrs

value: PC


title: SM-GE67L_S115_E1-50

value: NeuN-positive


title: GFP_ZT10_r2

description:
8030_S81
Sample_8030
processed data file: RNAseq_RAW_CT_GFP_CRE.txt

value: unfed

value: Liver


title: Mouse cochlea lateral wall, naive 4

description: 3' polyA RNASeq reads

value: CBA/CaJ


title: SM-GE67L_S120_E1-50

value: Glut


title: R8-15101201_S14_E1-50


title: SM-GE67L_S112_E1-50

value: Low Quality


title: SM-GE67L_S114_E1-50


title: SM-GE67L_S109_E1-50

value: P


title: Primary microglia-Chd8 siRNA 1


title: R8-15101201_S18_E1-50


title: Mouse cochlea lateral wall, noise 1

description: 3' polyA RNASeq reads

value: wild-type

value: Noise-exposed


title: Mouse cochlea lateral wall, noise 3

description: 3' polyA RNASeq reads


title: Mouse cochlea lateral wall, naive 3

description: 3' polyA RNASeq reads


title: Mouse cochlea neurons, noise 2

description: 3' polyA RNASeq reads

source_name: WT mouse spiral ganglion cells


title: Mouse cochlea neurons, noise 3

description: 3' polyA RNASeq reads


title: Primary microglia-control siRNA 1

value: Primary micoglia

value: Control siRNA


title: SM-GE67L_S107_E1-50

value: M


title: Mouse cochlea neurons, naive 3

description: 3' polyA RNASeq reads


title: Mouse cochlea neurons, naive 2

description: 3' polyA RNASeq reads


title: SM-GE67L_S105_E1-50


title: SM-GE67L_S110_E1-50


title: Mouse cochlea lateral wall, naive 2

description: 3' polyA RNASeq reads


title: R8-15101201_S17_E1-50

value: dLGN - Core


title: Mouse cochlea lateral wall, naive 1

description: 3' polyA RNASeq reads


title: SM-GE67L_S108_E1-50


title: Mouse cochlea neurons, noise 4

description: 3' polyA RNASeq reads


title: R8-15101201_S13_E1-50

value: RFP-positive


title: SM-GE67L_S103_E1-50

value: GABA


title: R8-15101201_S12_E1-50


title: Mouse cochlea neurons, noise 1

description: 3' polyA RNASeq reads


title: SM-GE67L_S102_E1-50

value: 2.3 yrs


title: WT.G1, RF201

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

library_source: genomic

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step  with ratio relative to Input (IP) or relative to G1 (ADNg)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Wild type in G1 phase of the cell cycle

growth_protocol: Growth medium : SC + 2% glucose

extract_protocol:
Standard protocol for preparation of yeast genomic DNA
Libraries were constructed using standard Illumina kits (TruSeq SBS Kit v3) and protocols. Sequencer: HiSeq4000. Reads lenght: 50.

treatment_protocol: Samples were released from alpha-factor arrest in the presence of 200 mM HU (hydroxyurea) for 60 min.

value: WT

tag: cell-cycle phase


title: Mouse cochlea neurons, naive 4

description: 3' polyA RNASeq reads


title: R8-15101201_S11_E1-50


title: SM-GE67L_S106_E1-50

value: PC

value: NeuN-positive


title: R8-15101201_S10_E1-50


title: Mouse cochlea neurons, naive 1

description: 3' polyA RNASeq reads


title: ZT10_input

description:
SM1199
Sample_1103

value: non treated

value: unfed

value: Liver

tag: chip antibody

value: Cocktail:PA1-511A (Invitrogen), MA1-510 (Invitrogen), sc-1004 (Santa-Cruz)


title: RPE Control

city: Daejeon

first: Ho-yeon

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

data_processing:
raw data were aligned to mm10 genome assembly using 10X Genomics CellRanger count and filtered
Genome_build: mm10

source_name: Retinal Pigment Epithelium cells

extract_protocol:
After removing retina from dissected anterior eye cups, RPE/choroid/scleral complex tissues were dissociated using the papain dissociation system (Worthington, Lakewood, NJ, USA).  RPE/choroid/scleral complex tissues were triturated and collected the dissociated single RPE cell after centrifugation at 1200 RPM for 3 minutes. scRNA-seq libraries of collected live cells were prepared using the Chromium controller and Next Gem Single cell 5’ Reagent v2 kits (10x Genomics)
Chromium Next GEM Single Cell 5p RNA library v1.1
Single Cell RNA-Seq

treatment_protocol: For all experiments, mice were randomly assigned to control or treatment groups. One microliter of 100 ng/µl Dox was injected into the subretinal space of C57BL/6J mice, respectively.

tag: tissue

value: Retinal Pigment Epithelium cells

tag: strain

value: 3 months

value: Control


title: R8-15101201_S09_E1-50


title: SM-GE67L_S104_E1-50

value: Glut

value: P


title: mec1-S1991D.HU, JP214

source_name: mec1-S1991A 60' after release in S-Phase in presence of HU(200mM)

value: S phase + HU

tag: treatment

value: hydroxyurea 200mM


title: SM-GE8Z1_S096_E1-50

organism: Macaca fascicularis

source_name: Macaque Pulvinar - Inferior

value: 10 yrs

value: Pulv


title: R8-15101201_S08_E1-50

value: M

value: dLGN - Core

value: RFP-positive

value: GABA


title: mec1-S1991A.HU, JP213


title: SM-GE8Z1_S092_E1-50

value: NeuN-positive


title: WT.HU, JP210

source_name: Wild type 60' after release in S-Phase in presence of HU(200mM)

value: WT


title: SM-GE67L_S098_E1-50

value: 2.3 yrs

value: PC


title: R8-15101201_S07_E1-50


title: SM-GE67L_S101_E1-50

value: Low Quality


title: SM-GE8Z1_S090_E1-50


title: R8-15101201_S06_E1-50


title: R8-15101201_S05_E1-50


title: ZT10_GR

description:
SM1103
Sample_1199

tag: aav injection

value: non treated

value: unfed

tag: circadian timepoint

value: Liver

value: Cocktail:PA1-511A (Invitrogen), MA1-510 (Invitrogen), sc-1004 (Santa-Cruz)


title: R8-15101201_S01_E1-50

tag: donor


title: SM-GE8Z1_S088_E1-50

value: Glut


title: RPE Doxorubicin

value: Retinal Pigment Epithelium cells

value: 3 months

value: Dox


title: SM-GE8Z1_S095_E1-50

value: 10 yrs

value: Pulv


title: SM-GE8Z1_S085_E1-50


title: SM-GE67L_S095_E1-50

tag: Sex

value: M


title: SM-GE67L_S100_E1-50

value: P


title: R8-15101201_S04_E1-50

tag: genotype

value: dLGN - Core

value: RFP-positive

value: GABA


title: SM-GE8Z1_S094_E1-50

tag: facs gating

value: NeuN-positive


title: SM-GE67L_S099_E1-50

value: 2.3 yrs

value: PC

tag: sequencing batch


title: SM-GE67L_S094_E1-50

tag: cell class


title: SM-GE8Z1_S093_E1-50

tag: cell cluster


title: SM-GE8Z1_S091_E1-50

tag: age


title: SM-GE67L_S093_E1-50


title: LS-14659_S78_E1-50

source_name: Mouse LGN - Shell

value: dLGN - Shell

value: LGd


title: SM-GE8Z1_S083_E1-50


title: R8-15101201_S03_E1-50


title: SM-GE8Z1_S089_E1-50


title: SM-GE67L_S092_E1-50


title: SM-GE8Z1_S082_E1-50


title: SM-GE8Z1_S079_E1-50


title: SM-GE8Z1_S080_E1-50


title: R8-15101201_S02_E1-50


title: SM-GE67L_S097_E1-50


title: SM-GE67L_S096_E1-50


title: SM-GE8Z1_S086_E1-50


title: SM-GE8Z1_S087_E1-50


title: LS-14659_S79_E1-50


title: SM-GE8Z1_S084_E1-50


title: SM-GE8Z1_S075_E1-50


title: LS-14658_S88_E1-50


title: SM-GE67L_S088_E1-50


title: LS-14659_S77_E1-50

value: LP


title: SM-GE8Z1_S071_E1-50

value: Glut


title: SM-GE8Z1_S070_E1-50


title: LS-14659_S76_E1-50


title: LS-14658_S87_E1-50


title: SM-GE8Z1_S069_E1-50


title: LS-14658_S86_E1-50


title: SM-GE8Z1_S081_E1-50


title: SM-GE8Z1_S077_E1-50


title: SM-GE8Z1_S078_E1-50


title: LS-14659_S75_E1-50


title: SM-GE67L_S090_E1-50


title: LS-14659_S74_E1-50


title: SM-GE8Z1_S074_E1-50


title: LS-14659_S73_E1-50


title: SM-GE67L_S091_E1-50


title: SM-GE8Z1_S072_E1-50


title: SM-GE67L_S089_E1-50


title: SM-GE8Z1_S076_E1-50


title: SM-GE8Z1_S073_E1-50


title: SM-GE67L_S087_E1-50


title: SM-GE8Z1_S068_E1-50


title: SM-GE8Z1_S063_E1-50


title: SM-GE67L_S086_E1-50

value: Low Quality


title: LS-14658_S83_E1-50


title: SM-GE8Z1_S066_E1-50


title: SM-GE8Z1_S057_E1-50


title: LS-14658_S82_E1-50


title: LS-14658_S81_E1-50


title: SM-GE8Z1_S058_E1-50


title: SM-GE8Z1_S065_E1-50


title: SM-GE8Z1_S064_E1-50


title: SM-GE8Z1_S067_E1-50


title: SM-GE67L_S081_E1-50


title: LS-14658_S84_E1-50


title: SM-GE67L_S084_E1-50


title: LS-14658_S85_E1-50


title: SM-GE8Z1_S059_E1-50


title: SM-GE8Z1_S053_E1-50

source_name: Macaque LGN Magnocellular

value: MC


title: SM-GE8Z1_S062_E1-50


title: SM-GE8Z1_S061_E1-50


title: LS-14658_S80_E1-50


title: SM-GE8Z1_S056_E1-50


title: SM-GE8Z1_S055_E1-50


title: SM-GE8Z1_S060_E1-50


title: SM-GE67L_S082_E1-50


title: SM-GE67L_S085_E1-50


title: SM-GE67L_S080_E1-50


title: SM-GE67L_S078_E1-50


title: SM-GE67L_S077_E1-50


title: SM-GE8Z1_S049_E1-50


title: SM-GE67L_S076_E1-50


title: SM-GE8Z1_S046_E1-50


title: SM-GE67L_S083_E1-50


title: SM-GE8Z1_S047_E1-50


title: LS-14658_S76_E1-50


title: SM-GE8Z1_S054_E1-50


title: SM-GE67L_S079_E1-50


title: SM-GE8Z1_S052_E1-50


title: LS-14658_S79_E1-50


title: SM-GE8Z1_S045_E1-50


title: SM-GE8Z1_S042_E1-50


title: SM-GE67L_S074_E1-50


title: SM-GE8YW_S096_E1-50


title: LS-14658_S73_E1-50


title: SM-GE67L_S073_E1-50


title: SM-GE8Z1_S048_E1-50


title: SM-GE67L_S075_E1-50


title: LS-14658_S75_E1-50


title: SM-GE8YW_S095_E1-50


title: SM-GE8Z1_S051_E1-50


title: LS-14658_S77_E1-50


title: SM-GE67L_S064_E1-50


title: SM-GE8Z1_S044_E1-50


title: SM-GE8Z1_S041_E1-50


title: SM-GE67L_S063_E1-50


title: SM-GE8Z1_S050_E1-50


title: LS-14658_S68_E1-50


title: SM-GE8Z1_S043_E1-50


title: LS-14658_S71_E1-50


title: SM-GE8YW_S094_E1-50


title: LS-14658_S69_E1-50


title: SM-GE8YW_S092_E1-50


title: LS-14658_S67_E1-50


title: SM-GE8YW_S093_E1-50


title: SM-GE8YW_S090_E1-50


title: SM-GE8YW_S086_E1-50


title: LS-14658_S70_E1-50


title: SM-GE67L_S061_E1-50


title: LS-14658_S65_E1-50


title: SM-GE8YW_S091_E1-50


title: LS-14658_S78_E1-50


title: SM-GE8YW_S088_E1-50


title: SM-GE67L_S060_E1-50


title: LS-14658_S74_E1-50


title: SM-GE8YW_S089_E1-50


title: SM-GE67L_S059_E1-50


title: SM-GE8YW_S085_E1-50


title: SM-GE8YW_S083_E1-50


title: SM-GE8YW_S082_E1-50


title: SM-GE67L_S057_E1-50


title: SM-GE8YW_S084_E1-50


title: SM-GE8YW_S087_E1-50


title: SM-GE67L_S058_E1-50


title: LS-14658_S66_E1-50


title: SM-GE8YW_S081_E1-50


title: LS-14659_S95_E1-50


title: SM-GE67L_S062_E1-50


title: SM-GE67L_S056_E1-50


title: SM-GE8YW_S080_E1-50


title: SM-GE8YW_S079_E1-50


title: LS-14659_S94_E1-50


title: SM-GE8YW_S078_E1-50


title: SM-GE67L_S054_E1-50


title: SM-GE8YW_S077_E1-50


title: SM-GE67L_S055_E1-50


title: LS-14659_S93_E1-50

value: Non-Neuronal


title: LS-14659_S92_E1-50


title: SM-GE8YW_S074_E1-50

value: 10 yrs


title: SM-GE8YW_S075_E1-50

value: Pulv


title: SM-GE8YW_S076_E1-50


title: SM-GE67L_S053_E1-50

value: M


title: SM-GE67L_S052_E1-50

value: P


title: SM-GE67L_S051_E1-50


title: LS-14659_S90_E1-50

value: dLGN - Core


title: SM-GE67L_S048_E1-50


title: LS-14659_S91_E1-50

value: RFP-positive


title: SM-GE8YW_S066_E1-50

value: GABA


title: SM-GE8YW_S070_E1-50

value: NeuN-positive


title: SM-GE8YW_S072_E1-50


title: SM-GE8YW_S071_E1-50


title: SM-GE67L_S050_E1-50

value: 2.3 yrs


title: SM-GE8YW_S068_E1-50


title: SM-GE8YW_S067_E1-50


title: LS-14659_S88_E1-50


title: LS-14659_S89_E1-50


title: LS-14659_S86_E1-50


title: LS-14659_S87_E1-50


title: SM-GE8YW_S073_E1-50


title: SM-GE8YW_S053_E1-50


title: SM-GE8YW_S052_E1-50


title: SM-GE67L_S046_E1-50

value: PC


title: SM-GE8YW_S051_E1-50


title: SM-GE67L_S045_E1-50


title: SM-GE8YW_S054_E1-50


title: SM-GE8YW_S055_E1-50


title: SM-GE8YW_S056_E1-50


title: SM-GE8YW_S065_E1-50


title: LS-14659_S84_E1-50


title: SM-GE67L_S044_E1-50


title: SM-GE67L_S047_E1-50


title: SM-GE8YW_S069_E1-50


title: SM-GE67L_S043_E1-50


title: SM-GE67L_S042_E1-50


title: SM-GE67L_S041_E1-50


title: LS-14659_S81_E1-50


title: LS-14659_S72_E1-50


title: LS-14659_S83_E1-50


title: LS-14659_S82_E1-50


title: LS-14659_S85_E1-50


title: SM-GE67L_S039_E1-50


title: LS-14659_S70_E1-50


title: LS-14659_S69_E1-50


title: LS-14659_S71_E1-50


title: SM-GE8YW_S048_E1-50


title: LS-14659_S68_E1-50


title: SM-GE8YW_S037_E1-50


title: SM-GE67L_S040_E1-50


title: SM-GE8YW_S050_E1-50


title: SM-GE8YW_S049_E1-50


title: SM-GE67L_S038_E1-50


title: SM-GE67L_S037_E1-50


title: SM-GE8YW_S038_E1-50


title: SM-GE67L_S036_E1-50


title: SM-GE8YW_S036_E1-50


title: SM-GE8YW_S041_E1-50


title: SM-GE8YW_S042_E1-50


title: SM-GE8YW_S044_E1-50


title: SM-GE8YW_S045_E1-50


title: SM-GE8YW_S047_E1-50


title: SM-GE8YW_S039_E1-50


title: SM-GE8YW_S043_E1-50


title: SM-GE8YW_S046_E1-50


title: SM-GE8YW_S035_E1-50


title: SM-GE8YW_S040_E1-50


title: SM-GE8YW_S033_E1-50


title: LS-14659_S66_E1-50


title: SM-GE67L_S035_E1-50


title: SM-GE8YW_S032_E1-50


title: SM-GE8YW_S031_E1-50


title: LS-14659_S65_E1-50


title: SM-GE8YW_S029_E1-50


title: SM-GE8YW_S030_E1-50


title: SM-GE67L_S034_E1-50


title: LS-14659_S67_E1-50


title: SM-GE8YW_S028_E1-50


title: LS-14659_S64_E1-50


title: SM-GE67L_S033_E1-50


title: LS-14659_S63_E1-50


title: SM-GE8YW_S026_E1-50


title: SM-GE8YW_S027_E1-50


title: SM-GE8YW_S025_E1-50


title: SM-GE8YW_S024_E1-50


title: SM-GE8YW_S022_E1-50


title: SM-GE67L_S030_E1-50


title: LS-14659_S61_E1-50


title: SM-GE8YW_S021_E1-50


title: SM-GE8YW_S023_E1-50


title: SM-GE67L_S032_E1-50


title: SM-GE8YW_S017_E1-50


title: SM-GE8YW_S019_E1-50


title: SM-GE8YW_S018_E1-50


title: LS-14659_S60_E1-50


title: SM-GE67L_S031_E1-50


title: SM-GE67L_S029_E1-50


title: LS-14659_S58_E1-50


title: SM-GE67L_S028_E1-50


title: SM-GE67L_S027_E1-50


title: SM-GE8YW_S015_E1-50


title: SM-GE8YW_S016_E1-50


title: SM-GE8YW_S014_E1-50


title: SM-GE8YW_S020_E1-50


title: LS-14659_S56_E1-50


title: LS-14659_S62_E1-50


title: SM-GE67L_S026_E1-50


title: SM-GE67L_S025_E1-50


title: SM-GE8YW_S013_E1-50


title: SM-GE8YW_S011_E1-50


title: LS-14659_S55_E1-50


title: SM-GE67L_S024_E1-50


title: SM-GE8YW_S009_E1-50


title: LS-14659_S54_E1-50


title: SM-GE8YW_S010_E1-50


title: SM-GE8YW_S007_E1-50


title: SM-GE8YW_S006_E1-50


title: SM-GE67L_S022_E1-50


title: LS-14659_S57_E1-50


title: SM-GE8YW_S005_E1-50


title: SM-GE67L_S023_E1-50


title: SM-GE8YW_S002_E1-50


title: SM-GE8YV_S192_E1-50


title: LS-14659_S51_E1-50


title: SM-GE67L_S020_E1-50


title: SM-GE8YW_S001_E1-50


title: SM-GE8YV_S191_E1-50


title: SM-GE67L_S019_E1-50


title: SM-GE8YV_S190_E1-50


title: SM-GE8YW_S008_E1-50


title: LS-14659_S50_E1-50


title: LS-14659_S59_E1-50


title: LS-14659_S49_E1-50


title: LS-14659_S53_E1-50


title: SM-GE8YV_S189_E1-50


title: SM-GE8YW_S004_E1-50


title: SM-GE8YV_S187_E1-50


title: SM-GE8YV_S188_E1-50


title: LS-14659_S52_E1-50


title: SM-GE67L_S021_E1-50


title: SM-GE8YW_S003_E1-50


title: LS-14659_S32_E1-50


title: SM-GE67L_S017_E1-50


title: SM-GE8YV_S186_E1-50


title: LS-14659_S31_E1-50


title: SM-GE67L_S016_E1-50


title: SM-GE8YV_S185_E1-50


title: SM-GE8YV_S184_E1-50


title: SM-GE67L_S015_E1-50


title: LS-14659_S30_E1-50


title: LS-14659_S29_E1-50


title: SM-GE67L_S014_E1-50


title: LS-14659_S28_E1-50


title: SM-GE8YV_S183_E1-50


title: SM-GE8YV_S182_E1-50


title: SM-GE67L_S018_E1-50


title: SM-GE8YV_S180_E1-50


title: SM-GE8YV_S179_E1-50


title: SM-GE8YV_S181_E1-50


title: SM-GE67L_S013_E1-50


title: SM-GE8YV_S178_E1-50


title: SM-GE67L_S012_E1-50


title: SM-GE67L_S011_E1-50


title: LS-14659_S26_E1-50


title: SM-GE67L_S010_E1-50


title: SM-GE8YV_S175_E1-50


title: SM-GE8YV_S176_E1-50


title: SM-GE8YV_S177_E1-50


title: SM-GE67L_S009_E1-50


title: LS-14659_S24_E1-50


title: SM-GE8YV_S174_E1-50


title: LS-14659_S23_E1-50


title: SM-GE8YV_S172_E1-50


title: LS-14659_S25_E1-50


title: LS-14659_S22_E1-50


title: SM-GE8YV_S169_E1-50


title: SM-GE67L_S008_E1-50


title: SM-GE8YV_S170_E1-50


title: SM-GE8YV_S171_E1-50


title: SM-GE8YV_S168_E1-50


title: LS-14659_S21_E1-50


title: SM-GE8YV_S166_E1-50


title: SM-GE67L_S007_E1-50


title: SM-GE8YV_S167_E1-50


title: SM-GE8YV_S165_E1-50


title: SM-GE8YV_S173_E1-50


title: LS-14659_S19_E1-50


title: SM-GE67L_S006_E1-50


title: SM-GE8YV_S164_E1-50


title: LS-14659_S18_E1-50


title: SM-GE67L_S005_E1-50


title: SM-GE8YV_S163_E1-50


title: SM-GE8YV_S162_E1-50


title: SM-GE8YV_S161_E1-50


title: LS-14659_S17_E1-50


title: LS-14659_S16_E1-50


title: SM-GE8YV_S159_E1-50


title: SM-GE8YV_S158_E1-50


title: SM-GE67L_S004_E1-50


title: SM-GE67L_S003_E1-50


title: SM-GE8YV_S156_E1-50


title: SM-GE8YV_S155_E1-50


title: LS-14659_S15_E1-50


title: SM-GE67L_S002_E1-50


title: LS-14659_S12_E1-50


title: SM-GE8YV_S157_E1-50


title: SM-GE8YV_S153_E1-50


title: SM-GE67K_S191_E1-50


title: SM-GE67L_S001_E1-50


title: SM-GE67K_S192_E1-50


title: SM-GE8YV_S144_E1-50


title: SM-GE8YV_S141_E1-50


title: LS-14659_S13_E1-50


title: SM-GE8YV_S142_E1-50


title: LS-14659_S09_E1-50


title: SM-GE8YV_S143_E1-50


title: SM-GE67K_S190_E1-50


title: LS-14659_S10_E1-50


title: SM-GE8YW_S034_E1-50


title: SM-GE8YV_S140_E1-50


title: LS-14659_S07_E1-50


title: SM-GE8YV_S154_E1-50


title: SM-GE67K_S189_E1-50


title: SM-GE8YV_S139_E1-50


title: SM-GE8YV_S137_E1-50


title: SM-GE67K_S188_E1-50


title: SM-GE8YV_S138_E1-50


title: SM-GE8YV_S134_E1-50


title: LS-14659_S06_E1-50


title: SM-GE67K_S187_E1-50


title: SM-GE8YV_S133_E1-50


title: SM-GE8YV_S136_E1-50


title: LS-14659_S05_E1-50


title: SM-GE8YV_S132_E1-50


title: LS-14659_S04_E1-50


title: SM-GE8YV_S130_E1-50


title: LS-14659_S03_E1-50


title: SM-GE67K_S184_E1-50


title: SM-GE8YV_S135_E1-50


title: LS-14659_S02_E1-50


title: SM-GE8YV_S127_E1-50


title: SM-GE8YV_S128_E1-50


title: SM-GE67K_S183_E1-50


title: SM-GE67K_S186_E1-50


title: SM-GE8YV_S126_E1-50


title: SM-GE67K_S182_E1-50


title: SM-GE8YV_S124_E1-50


title: SM-GE8YV_S125_E1-50


title: SM-GE8YV_S129_E1-50


title: SM-GE67K_S185_E1-50


title: SM-GE67K_S181_E1-50


title: LS-14659_S01_E1-50


title: SM-GE8YV_S123_E1-50


title: SM-GE8YV_S122_E1-50


title: SM-GE8YV_S131_E1-50


title: LS-14659_S11_E1-50


title: SM-GE8YW_S012_E1-50


title: LS-14658_S63_E1-50


title: LS-14658_S61_E1-50


title: SM-GE8YV_S121_E1-50


title: SM-GE67K_S180_E1-50


title: SM-GE8YV_S119_E1-50


title: SM-GE67K_S179_E1-50


title: SM-GE8YV_S120_E1-50


title: LS-14658_S64_E1-50


title: LS-14658_S60_E1-50


title: SM-GE8YV_S118_E1-50


title: SM-GE67K_S178_E1-50


title: LS-14658_S59_E1-50


title: SM-GE8YV_S114_E1-50


title: SM-GE8YV_S113_E1-50


title: SM-GE67K_S175_E1-50


title: LS-14658_S58_E1-50


title: SM-GE8YV_S116_E1-50


title: SM-GE8YV_S112_E1-50


title: SM-GE67K_S177_E1-50


title: SM-GE67K_S176_E1-50


title: SM-GE8YV_S111_E1-50


title: SM-GE67K_S174_E1-50


title: SM-GE8YV_S117_E1-50


title: SM-GE8YV_S109_E1-50


title: SM-GE8YV_S115_E1-50


title: SM-GE8YV_S110_E1-50


title: LS-14658_S54_E1-50


title: LS-14658_S57_E1-50


title: SM-GE8YV_S108_E1-50


title: LS-14658_S56_E1-50


title: SM-GE8YV_S106_E1-50


title: SM-GE8YV_S107_E1-50


title: SM-GE8YV_S105_E1-50


title: SM-GE67K_S172_E1-50


title: SM-GE67K_S173_E1-50


title: LS-14658_S53_E1-50


title: SM-GE8YV_S104_E1-50


title: SM-GE67K_S171_E1-50


title: SM-GE8YV_S103_E1-50


title: LS-14658_S52_E1-50


title: LS-14658_S51_E1-50


title: SM-GE8YV_S102_E1-50


title: SM-GE67K_S170_E1-50


title: SM-GE67K_S169_E1-50


title: SM-GE8YV_S100_E1-50


title: LS-14658_S50_E1-50


title: SM-GE67K_S168_E1-50


title: SM-GE8YV_S099_E1-50


title: LS-14658_S48_E1-50


title: SM-GE8YV_S098_E1-50


title: SM-GE8YV_S097_E1-50


title: SM-GE8YV_S096_E1-50


title: LS-14658_S46_E1-50


title: LS-14658_S45_E1-50


title: SM-GE8YV_S092_E1-50


title: SM-GE8YV_S095_E1-50


title: SM-GE8YV_S093_E1-50


title: LS-14658_S44_E1-50


title: SM-GE8YV_S094_E1-50


title: SM-GE67K_S167_E1-50


title: SM-GE8YV_S089_E1-50


title: SM-GE8YV_S090_E1-50


title: SM-GE67K_S165_E1-50


title: SM-GE8YV_S101_E1-50


title: LS-14658_S43_E1-50


title: SM-GE67K_S164_E1-50


title: SM-GE8YV_S087_E1-50


title: SM-GE8YV_S086_E1-50


title: SM-GE67K_S163_E1-50


title: SM-GE8YV_S160_E1-50


title: LS-14658_S41_E1-50


title: SM-GE8YV_S082_E1-50


title: SM-GE67K_S166_E1-50


title: SM-GE8YV_S081_E1-50


title: LS-14658_S42_E1-50


title: SM-GE8YV_S088_E1-50


title: SM-GE67K_S152_E1-50


title: SM-GE8YV_S085_E1-50


title: SM-GE67K_S162_E1-50


title: SM-GE67K_S161_E1-50


title: SM-GE8YV_S080_E1-50


title: LS-14658_S39_E1-50


title: SM-GE8YV_S079_E1-50


title: SM-GE8YV_S091_E1-50


title: LS-14658_S38_E1-50


title: SM-GE67K_S151_E1-50


title: SM-GE67K_S150_E1-50


title: SM-GE8YV_S076_E1-50


title: LS-14658_S40_E1-50


title: SM-GE8YV_S078_E1-50


title: SM-GE8YV_S083_E1-50


title: SM-GE8YV_S084_E1-50


title: SM-GE67K_S148_E1-50


title: LS-14658_S35_E1-50


title: SM-GE8YV_S077_E1-50


title: LS-14658_S36_E1-50


title: LS-14658_S34_E1-50


title: SM-GE8YV_S072_E1-50


title: SM-GE67K_S146_E1-50


title: SM-GE67K_S145_E1-50


title: SM-GE8YV_S070_E1-50


title: LS-14658_S37_E1-50


title: SM-GE8YV_S071_E1-50


title: SM-GE8YV_S069_E1-50


title: SM-GE8YV_S073_E1-50


title: SM-GE67K_S149_E1-50


title: SM-GE8YV_S074_E1-50


title: SM-GE8YV_S066_E1-50


title: LS-14658_S32_E1-50


title: LS-14658_S29_E1-50


title: SM-GE67H_S136_E1-50


title: LS-14658_S30_E1-50


title: SM-GE67H_S135_E1-50


title: SM-GE8YV_S075_E1-50


title: SM-GE8YV_S062_E1-50


title: SM-GE8YV_S068_E1-50


title: LS-14658_S33_E1-50


title: LS-14658_S28_E1-50


title: SM-GE8YV_S064_E1-50


title: SM-GE8YV_S067_E1-50


title: SM-GE8YV_S065_E1-50


title: SM-GE67H_S133_E1-50


title: SM-GE8YV_S060_E1-50


title: SM-GE67H_S134_E1-50


title: SM-GE67K_S147_E1-50


title: SM-GE67H_S132_E1-50


title: SM-GE8YV_S061_E1-50


title: SM-GE8YV_S063_E1-50


title: LS-14658_S27_E1-50


title: SM-GE8YV_S058_E1-50


title: SM-GE67H_S131_E1-50


title: LS-14658_S26_E1-50


title: SM-GE8YV_S059_E1-50


title: LS-14658_S23_E1-50


title: SM-GE8YV_S056_E1-50


title: LS-14658_S25_E1-50


title: SM-GE8YV_S057_E1-50


title: SM-GE67H_S129_E1-50


title: SM-GE8YV_S050_E1-50


title: LS-14658_S21_E1-50


title: SM-GE8YV_S051_E1-50


title: SM-GE8YV_S053_E1-50


title: SM-GE8YV_S055_E1-50


title: LS-14658_S22_E1-50


title: SM-GE8YV_S052_E1-50


title: SM-GE67H_S130_E1-50


title: SM-GE8YV_S054_E1-50


title: SM-GE8YV_S049_E1-50


title: SM-GE67H_S128_E1-50


title: SM-GE8YV_S040_E1-50


title: LS-14658_S20_E1-50


title: SM-GE67H_S126_E1-50


title: SM-GE8YV_S036_E1-50


title: SM-GE8YV_S039_E1-50


title: SM-GE8YV_S035_E1-50


title: LS-14658_S18_E1-50


title: SM-GE8YV_S033_E1-50


title: LS-14658_S16_E1-50


title: SM-GE8YV_S031_E1-50


title: SM-GE67H_S127_E1-50


title: SM-GE8YV_S032_E1-50


title: LS-14658_S15_E1-50


title: LS-14658_S19_E1-50


title: SM-GE8YV_S037_E1-50


title: SM-GE8YV_S027_E1-50


title: SM-GE67H_S122_E1-50


title: SM-GE67H_S120_E1-50


title: LS-14658_S17_E1-50


title: SM-GE8YV_S034_E1-50


title: SM-GE8YV_S025_E1-50


title: SM-GE8YV_S024_E1-50


title: SM-GE67H_S124_E1-50


title: SM-GE67H_S125_E1-50


title: SM-GE8YV_S029_E1-50


title: SM-GE67H_S121_E1-50


title: SM-GE8YV_S028_E1-50


title: SM-GE8YV_S022_E1-50


title: SM-GE8YV_S030_E1-50


title: SM-GE67H_S123_E1-50


title: LS-14658_S14_E1-50


title: LS-14658_S13_E1-50


title: LS-14658_S12_E1-50


title: SM-GE8YV_S020_E1-50


title: SM-GE8YV_S019_E1-50


title: LS-14658_S10_E1-50


title: SM-GE8YV_S023_E1-50


title: SM-GE67H_S119_E1-50


title: SM-GE8YV_S016_E1-50


title: SM-GE67H_S118_E1-50


title: LS-14658_S07_E1-50


title: SM-GE67H_S115_E1-50


title: LS-14658_S11_E1-50


title: SM-GE67H_S117_E1-50


title: SM-GE8YV_S026_E1-50


title: SM-GE8YV_S013_E1-50


title: LS-14658_S06_E1-50


title: SM-GE8YV_S011_E1-50


title: SM-GE8YV_S038_E1-50


title: SM-GE8YV_S017_E1-50


title: SM-GE8YV_S018_E1-50


title: LS-14658_S04_E1-50


title: LS-14658_S05_E1-50


title: LS-14658_S08_E1-50


title: SM-GE8YV_S007_E1-50


title: SM-GE8YV_S008_E1-50


title: SM-GE8YV_S021_E1-50


title: SM-GE8YV_S015_E1-50


title: SM-GE67H_S114_E1-50


title: LS-14658_S03_E1-50


title: SM-GE8YV_S012_E1-50


title: SM-GE67H_S113_E1-50


title: SM-GE8YV_S004_E1-50


title: SM-GE8YV_S010_E1-50


title: LS-14658_S02_E1-50


title: SM-GE8YV_S003_E1-50


title: SM-GE8YV_S009_E1-50


title: LS-14658_S09_E1-50


title: SM-GE8YV_S002_E1-50


title: LS-14658_S01_E1-50


title: SM-GE67H_S112_E1-50


title: SM-GE67H_S108_E1-50


title: LS-14653_S72_E1-50

value: dLGN - Shell


title: SM-GE8YU_S192_E1-50


title: SM-GE8YV_S006_E1-50


title: SM-GE8YV_S014_E1-50


title: SM-GE67H_S116_E1-50


title: SM-GE67H_S111_E1-50


title: SM-GE8YU_S191_E1-50


title: SM-GE8YV_S005_E1-50


title: SM-GE67H_S107_E1-50


title: SM-GE67H_S110_E1-50


title: SM-GE8YV_S001_E1-50


title: SM-GE67H_S106_E1-50


title: SM-GE67H_S109_E1-50


title: LS-14653_S71_E1-50


title: SM-GE8YU_S190_E1-50


title: SM-GE8YU_S189_E1-50


title: LS-14653_S70_E1-50


title: SM-GE67H_S105_E1-50


title: SM-GE8YU_S186_E1-50


title: SM-GE8YU_S187_E1-50


title: LS-14653_S69_E1-50


title: SM-GE8YU_S185_E1-50


title: SM-GE8YU_S188_E1-50


title: LS-14653_S68_E1-50


title: SM-GE8YU_S181_E1-50


title: LS-14653_S67_E1-50


title: SM-GE8YU_S180_E1-50


title: SM-GE8YU_S182_E1-50


title: SM-GE67H_S104_E1-50


title: SM-GE67H_S102_E1-50


title: SM-GE8YU_S174_E1-50


title: SM-GE8YU_S178_E1-50


title: SM-GE8YU_S179_E1-50


title: LS-14653_S65_E1-50


title: SM-GE8YU_S177_E1-50


title: SM-GE8YU_S183_E1-50


title: LS-14653_S87_E1-50

value: LGd


title: SM-GE8YU_S173_E1-50


title: SM-GE67H_S103_E1-50


title: LS-14653_S66_E1-50


title: LS-14653_S88_E1-50


title: SM-GE8YU_S170_E1-50


title: SM-GE67H_S101_E1-50


title: LS-14653_S86_E1-50


title: LS-14653_S85_E1-50


title: SM-GE8YU_S175_E1-50


title: SM-GE67H_S099_E1-50


title: SM-GE8YU_S165_E1-50


title: SM-GE67H_S098_E1-50


title: SM-GE67H_S038_E1-50


title: SM-GE67H_S040_E1-50


title: SM-GE8YU_S171_E1-50


title: SM-GE67H_S100_E1-50


title: SM-GE8YU_S163_E1-50


title: SM-GE67H_S097_E1-50


title: SM-GE8YU_S176_E1-50


title: SM-GE8YU_S169_E1-50


title: LS-14653_S84_E1-50


title: SM-GE8YU_S167_E1-50


title: SM-GE8YU_S166_E1-50


title: SM-GE8YU_S172_E1-50


title: SM-GE67H_S039_E1-50


title: SM-GE8YU_S161_E1-50


title: SM-GE8YU_S164_E1-50


title: LS-14653_S82_E1-50


title: LS-14653_S83_E1-50


title: SM-GE8YU_S168_E1-50


title: SM-GE8YU_S162_E1-50


title: LS-14653_S81_E1-50


title: SM-GE67H_S036_E1-50


title: SM-GE8YU_S160_E1-50


title: LS-14653_S80_E1-50


title: SM-GE67H_S035_E1-50


title: SM-GE8YU_S158_E1-50


title: SM-GE8YU_S159_E1-50


title: SM-GE8YU_S157_E1-50


title: LS-14653_S79_E1-50


title: SM-GE67H_S037_E1-50


title: LS-14653_S78_E1-50


title: SM-GE8YU_S155_E1-50


title: SM-GE8YU_S150_E1-50


title: SM-GE67H_S031_E1-50


title: LS-14653_S76_E1-50


title: LS-14653_S77_E1-50


title: SM-GE67H_S033_E1-50


title: SM-GE8YU_S153_E1-50


title: SM-GE8YU_S154_E1-50


title: SM-GE8YU_S147_E1-50


title: SM-GE8YU_S151_E1-50


title: SM-GE8YU_S152_E1-50


title: SM-GE67H_S032_E1-50


title: SM-GE8YU_S145_E1-50


title: SM-GE8YU_S156_E1-50


title: SM-GE67H_S034_E1-50


title: SM-GE8YU_S149_E1-50


title: SM-GE67H_S030_E1-50


title: SM-GE67H_S027_E1-50


title: SM-GE8YU_S148_E1-50


title: LS-14653_S64_E1-50


title: SM-GE8YU_S142_E1-50


title: LS-14653_S74_E1-50


title: SM-GE8YU_S146_E1-50


title: LS-14653_S75_E1-50


title: SM-GE67H_S029_E1-50


title: SM-GE8YU_S140_E1-50


title: SM-GE8YU_S128_E1-50


title: SM-GE67H_S024_E1-50


title: LS-14653_S73_E1-50


title: SM-GE67H_S028_E1-50


title: SM-GE8YU_S127_E1-50


title: SM-GE8YU_S144_E1-50


title: SM-GE8YU_S126_E1-50


title: LS-14653_S63_E1-50


title: SM-GE67H_S026_E1-50


title: SM-GE67H_S023_E1-50


title: SM-GE8YU_S138_E1-50


title: SM-GE8YU_S143_E1-50


title: SM-GE67H_S022_E1-50


title: SM-GE8YU_S137_E1-50


title: LS-14653_S62_E1-50


title: SM-GE8YU_S123_E1-50


title: SM-GE67H_S021_E1-50


title: SM-GE67H_S025_E1-50


title: SM-GE8YU_S125_E1-50


title: LS-14653_S60_E1-50


title: SM-GE8YU_S124_E1-50


title: LS-14653_S59_E1-50


title: SM-GE8YU_S121_E1-50


title: SM-GE8YU_S141_E1-50


title: LS-14653_S58_E1-50


title: SM-GE67H_S020_E1-50


title: SM-GE8YU_S122_E1-50


title: SM-GE8YU_S119_E1-50


title: LS-14653_S56_E1-50


title: LS-14653_S57_E1-50


title: SM-GE8YU_S120_E1-50


title: SM-GE8YU_S117_E1-50


title: SM-GE8YU_S118_E1-50


title: SM-GE8YU_S116_E1-50


title: LS-14653_S61_E1-50


title: SM-GE67H_S019_E1-50


title: SM-GE8YU_S115_E1-50


title: LS-14653_S54_E1-50


title: SM-GE67H_S018_E1-50


title: SM-GE8YU_S113_E1-50


title: SM-GE67H_S017_E1-50


title: SM-GE8YU_S114_E1-50


title: LS-14653_S53_E1-50


title: SM-GE8YU_S111_E1-50


title: SM-GE67H_S016_E1-50


title: SM-GE8YU_S110_E1-50


title: LS-14653_S52_E1-50


title: SM-GE8YU_S109_E1-50


title: SM-GE67H_S015_E1-50


title: LS-14653_S55_E1-50


title: LS-14653_S51_E1-50


title: LS-14653_S50_E1-50


title: SM-GE8YU_S106_E1-50


title: SM-GE8YU_S104_E1-50


title: SM-GE67H_S013_E1-50


title: SM-GE67H_S012_E1-50


title: SM-GE8YU_S107_E1-50


title: SM-GE8YU_S103_E1-50


title: SM-GE8YU_S112_E1-50


title: LS-14653_S49_E1-50


title: SM-GE8YU_S108_E1-50


title: SM-GE8YU_S102_E1-50


title: SM-GE8YU_S100_E1-50


title: LS-14653_S45_E1-50


title: LS-14653_S46_E1-50


title: SM-GE8YU_S099_E1-50


title: SM-GE8YU_S098_E1-50


title: SM-GE67H_S010_E1-50


title: LS-14653_S44_E1-50


title: SM-GE8YU_S097_E1-50


title: SM-GE67H_S009_E1-50


title: SM-GE8YR_S144_E1-50


title: SM-GE67H_S014_E1-50


title: SM-GE8YR_S143_E1-50


title: SM-GE8YR_S142_E1-50


title: SM-GE8YU_S105_E1-50


title: SM-GE67H_S011_E1-50


title: SM-GE67H_S008_E1-50


title: SM-GE8YU_S101_E1-50


title: LS-14653_S43_E1-50


title: SM-GE8YR_S138_E1-50


title: SM-GE8YR_S137_E1-50


title: SM-GE8YR_S140_E1-50


title: SM-GE67H_S006_E1-50


title: LS-14653_S39_E1-50


title: SM-GE67H_S007_E1-50


title: SM-GE8YR_S136_E1-50


title: LS-14653_S42_E1-50


title: SM-GE8YR_S135_E1-50


title: SM-GE67H_S005_E1-50


title: SM-GE67H_S004_E1-50


title: LS-14653_S40_E1-50


title: LS-14653_S38_E1-50


title: SM-GE8YR_S134_E1-50


title: SM-GE8YR_S141_E1-50


title: SM-GE67H_S003_E1-50


title: LS-14653_S41_E1-50


title: LS-14653_S37_E1-50


title: SM-GE8YR_S139_E1-50


title: SM-GE8YR_S133_E1-50


title: SM-GE67H_S002_E1-50


title: SM-GE8YR_S131_E1-50


title: SM-GE8YR_S132_E1-50


title: LS-14653_S36_E1-50


title: SM-GE67H_S001_E1-50


title: SM-GE8YR_S129_E1-50


title: SM-GE8YR_S128_E1-50


title: SM-GE8YR_S127_E1-50


title: SM-GE67G_S167_E1-50


title: SM-GE8YR_S125_E1-50


title: LS-14653_S35_E1-50


title: SM-GE67G_S168_E1-50


title: SM-GE8YR_S130_E1-50


title: SM-GE8YR_S124_E1-50


title: LS-14653_S32_E1-50


title: SM-GE8YR_S126_E1-50


title: SM-GE67G_S166_E1-50


title: SM-GE8YR_S123_E1-50


title: LS-14653_S33_E1-50


title: LS-14653_S31_E1-50


title: SM-GE8YR_S122_E1-50


title: SM-GE67G_S165_E1-50


title: SM-GE8YR_S120_E1-50


title: SM-GE8YR_S118_E1-50


title: SM-GE8YR_S121_E1-50


title: SM-GE67G_S164_E1-50


title: LS-14653_S30_E1-50


title: LS-14653_S29_E1-50


title: SM-GE67G_S163_E1-50


title: SM-GE67G_S162_E1-50


title: SM-GE8YR_S119_E1-50


title: LS-14653_S28_E1-50


title: SM-GE8YR_S115_E1-50


title: LS-14653_S27_E1-50


title: SM-GE67G_S161_E1-50


title: SM-GE8YR_S117_E1-50


title: SM-GE8YR_S114_E1-50


title: SM-GE8YR_S109_E1-50


title: SM-GE8YR_S116_E1-50


title: LS-14653_S26_E1-50


title: SM-GE8YR_S112_E1-50


title: SM-GE67G_S152_E1-50


title: SM-GE8YR_S111_E1-50


title: SM-GE8YR_S110_E1-50


title: LS-14653_S25_E1-50


title: SM-GE8YR_S107_E1-50


title: LS-14653_S24_E1-50


title: SM-GE8YR_S108_E1-50


title: SM-GE8YR_S104_E1-50


title: SM-GE8YR_S105_E1-50


title: SM-GE8YR_S113_E1-50


title: SM-GE67G_S149_E1-50


title: LS-14653_S21_E1-50


title: SM-GE8YR_S103_E1-50


title: SM-GE67G_S150_E1-50


title: LS-14653_S23_E1-50


title: LS-14653_S22_E1-50


title: SM-GE67G_S151_E1-50


title: SM-GE8YR_S101_E1-50


title: SM-GE67G_S148_E1-50


title: SM-GE8YR_S106_E1-50


title: SM-GE8YR_S102_E1-50


title: SM-GE8YR_S097_E1-50


title: SM-GE8YR_S098_E1-50


title: SM-GE67G_S146_E1-50


title: LS-14653_S18_E1-50


title: SM-GE67G_S145_E1-50


title: LS-14653_S19_E1-50


title: SM-GE67G_S147_E1-50


title: SM-GE8YR_S099_E1-50


title: SM-GE8YR_S092_E1-50


title: SM-GE8YR_S091_E1-50


title: SM-GE67G_S144_E1-50


title: LS-14653_S16_E1-50


title: SM-GE8YR_S095_E1-50


title: SM-GE67G_S143_E1-50


title: SM-GE8YR_S093_E1-50


title: SM-GE8YR_S089_E1-50


title: SM-GE8YR_S090_E1-50


title: SM-GE8YR_S096_E1-50


title: SM-GE8YR_S088_E1-50


title: SM-GE67G_S141_E1-50


title: SM-GE8YR_S100_E1-50


title: SM-GE8YR_S087_E1-50


title: LS-14653_S15_E1-50


title: SM-GE8YR_S086_E1-50


title: LS-14653_S20_E1-50


title: SM-GE67G_S140_E1-50


title: LS-14653_S13_E1-50


title: LS-14653_S14_E1-50


title: LS-14653_S17_E1-50


title: SM-GE8YR_S084_E1-50


title: SM-GE67G_S139_E1-50


title: SM-GE67G_S138_E1-50


title: SM-GE8YR_S081_E1-50


title: SM-GE8YR_S082_E1-50


title: SM-GE67G_S142_E1-50


title: SM-GE67G_S136_E1-50


title: SM-GE8YR_S071_E1-50


title: LS-14653_S10_E1-50


title: SM-GE8YR_S085_E1-50


title: SM-GE8YR_S070_E1-50


title: SM-GE67G_S134_E1-50


title: SM-GE67G_S135_E1-50


title: SM-GE8YR_S069_E1-50


title: SM-GE8YR_S067_E1-50


title: SM-GE8YR_S066_E1-50


title: SM-GE8YR_S065_E1-50


title: SM-GE8YR_S068_E1-50


title: LS-14653_S09_E1-50


title: LS-14653_S08_E1-50


title: LS-14653_S07_E1-50


title: LS-14653_S12_E1-50


title: LS-14653_S06_E1-50


title: SM-GE8YR_S064_E1-50


title: SM-GE8YR_S083_E1-50


title: LS-14653_S11_E1-50


title: SM-GE8YR_S063_E1-50


title: SM-GE67G_S133_E1-50


title: SM-GE67G_S132_E1-50


title: SM-GE8YR_S062_E1-50


title: SM-GE8YR_S072_E1-50


title: SM-GE67G_S137_E1-50


title: SM-GE8YR_S060_E1-50


title: SM-GE8YR_S061_E1-50


title: SM-GE67G_S131_E1-50


title: LS-14653_S05_E1-50


title: SM-GE8YR_S059_E1-50


title: SM-GE8YR_S058_E1-50


title: LS-14653_S04_E1-50


title: SM-GE67G_S130_E1-50


title: SM-GE67G_S129_E1-50


title: SM-GE8YR_S057_E1-50


title: SM-GE8YR_S056_E1-50


title: SM-GE8YR_S055_E1-50


title: SM-GE67G_S024_E1-50


title: SM-GE8YR_S053_E1-50


title: SM-GE8YR_S054_E1-50


title: LS-14653_S01_E1-50


title: LS-14653_S02_E1-50


title: SM-GE67G_S023_E1-50


title: SM-GE8YR_S052_E1-50


title: SM-GE8YR_S051_E1-50


title: SM-GE8YR_S050_E1-50


title: SM-GE8YR_S049_E1-50


title: SM-GE67G_S021_E1-50


title: SM-GE8YR_S048_E1-50


title: SM-GE8YR_S047_E1-50


title: SM-GE67G_S022_E1-50


title: T9_3370_63_CM_CHW_M_G3_21065

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

description:
microRNA
MicroRNAseq library prep.
training_mature_normalized_CPM.tsv
training_mature_mirTOPcounts.tsv

data_processing:
Cutadapt preprocesssing was performed to remove the first three bases and adapter sequences with the parameters "cutadapt -a TCTGGAATTCTCGGGTGCCAAGGAACTCC -m 16 -u 3"; fastqs in this submission from validation cohort timepoint 5 have already been trimmed.
Cutadapt trimmed reads were processed with the nf-core smRNASeq pipeline version 1.0 using the GRCm38 genome reference (with the parameter --genome GRCm38) and adapters for the Illumina small RNA protocol (by setting --protocol Illumina). Briefly, trimmed reads were mapped using bowtie to miRBase mature miRNAs (using the parameters -k 50 --best --strata), and the number of reads mapping to each was counted using samtools stats and miRTOP. Each library was also subjected to extensive quality control, including estimation of library complexity, contamination, sequence quality, read length and depth, among other metrics detailed in the pipeline repository. Mapped reads were merged into a matrix of counts per gene for each sample at each timepoint and normalized to counts per million (CPM) reads mapped, as implemented in edgeR. Surrogate variable analysis was used to check for confounding experimental effects and none were apparent.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.tsv: Expression matrices of miRNAs in rows and samples in columns.

source_name: PBMC

growth_protocol: The expression of the leukemogenic fusion gene Cbfb-MYH11 (CM) in conditional CM knock-in mice (Cbfb56M/+/Mx1-Cre) leads to development of AML with a median survival of approximately 4 months after induction of CM. This model recapitulates the human inv(16) AML, one of the common subsets of AML characterized by the rearrangement of chromosome 16 at bands p13 and q22, which at the molecular level creates the chimeric fusion gene CBFB-MYH11. To induce CM expression, 6-8 weeks old CM knock-in mice were injected intraperitoneally with polyinosinic–polycytidylic acid [poly (I:C)] (InvivoGen, tlrl-picw-250) at 14 mg/kg/dose every other day for a total of 7 doses. Age-matched littermates lacking the transgene were similarly treated and used as control. All mice were maintained in an Association for Assessment and Accreditation of Laboratory Animal Care–accredited animal facility and all experimental procedures were performed in accordance with federal and state government guidelines and established institutional guidelines and protocols approved by the Institutional Animal Care and Use Committee at City of Hope.

extract_protocol:
Total RNA was isolated from PBMC using AllPrep DNA/RNA Kit (Qiagen).
Testing cohort samples were allocated to randomized batches for library preparation, such that samples from each timepoint were distributed evenly over all sequencing runs. Validation cohort samples were processed in batches as collected. All libraries were prepared using the Illumina TruSeq Small RNA protocol with minor modification following the manufacturer’s instructions. Briefly, for each sample, 280 ng of total RNA was ligated to the sRNA 3′ adaptor (5’-TCTGGAATTCTCGGGTGCCAAGGAACTCC-3’) with T4 RNA Ligase 2, truncated (New England BioLabs) for 1 h at 22°C, and subsequently ligated to a 5′ adaptor: 5’-GUUCAGAGUUCUACAGUCCGACGAUCNNN-3’) with T4 RNA ligase 1 (New England BioLabs) for 1 h at 20°C. The constructed small RNA library was first reverse-transcribed using GX1 (5′- GGAGTTCCTTGGCACCCGAGA) as the RT primer then subjected to PCR amplification for 13 cycles, using the primers GX1 (5′-CAAGCAGAAGACGGCATACGAGAT[NNNNNN]GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’) and GX2 (5′- AATGATACGGCGACCACCGAGATCTACAC[NNNNNNNN]CGACAGGTTCAGAGTTCTACAGTCCGA-3’), followed by 6% TBE PAGE gel purification with size selection (for targeted small RNAs of 17–35 nt). Individual libraries were prepared using a unique index primer (NNNNNNNN in the GX1 and GX2 primer) in order to allow for pooling of multiple samples prior to sequencing.

value: PBMC

tag: timepoint

value: CM

value: CHW

value: Male


title: T9_3368_52_CM_CHW_M_G1_21024


title: T9_3350_139_CTL_WT_F_G3_21076

value: CTL

value: WT

value: Female


title: SM-GE67G_S020_E1-50

value: M

value: MC

value: Low Quality


title: SM-GE8YR_S046_E1-50

value: 10 yrs

value: Glut

value: P


title: LS-14653_S03_E1-50

value: dLGN - Core

value: RFP-positive

value: GABA


title: T9_3349_106_CTL_CW_F_G6_21130

value: CW


title: SM-GE8YR_S045_E1-50

value: PC

value: NeuN-positive


title: SM-GE8YR_S044_E1-50


title: SM-GE8YR_S043_E1-50


title: T9_3346_95_CTL_CW_M_G7_21150

value: PBMC


title: SM-GE67G_S018_E1-50

value: 2.3 yrs


title: T9_3342_84_CTL_CW_M_G2_21048

value: CTL

value: Male


title: SM-GE8YR_S039_E1-50


title: SM-GE8YR_S040_E1-50


title: T9_3340_128_CTL_HW_M_G5_21114

value: HW


title: SM-GE8YR_S038_E1-50


title: SM-GE67G_S016_E1-50

value: M


title: SM-GE67G_S017_E1-50

value: MC


title: SM-GE8YR_S042_E1-50


title: SM-GE8YR_S041_E1-50


title: SM-GE8YR_S035_E1-50


title: SM-GE67G_S014_E1-50


title: SM-GE8YR_S036_E1-50


title: SM-GE8YR_S034_E1-50


title: SM-GE67G_S013_E1-50

value: Low Quality


title: SM-GE8YR_S032_E1-50

value: 10 yrs


title: SM-GE8YR_S031_E1-50

value: Glut


title: T9_3339_73_CTL_CW_M_G3_21067


title: SM-GE8YR_S037_E1-50

value: P


title: SM-GE8YR_S030_E1-50


title: T8_3370_62_CM_CHW_M_G7_21144

value: CM

value: CHW


title: SM-GE8YR_S033_E1-50


title: T8_3368_51_CM_CHW_M_G4_21084


title: SM-GE8YR_S028_E1-50

value: GABA


title: T9_3335_117_CTL_HW_M_G7_21153


title: SM-GE67G_S011_E1-50


title: SM-GE8YR_S029_E1-50


title: SM-GE67G_S019_E1-50


title: SM-GE67G_S012_E1-50


title: SM-GE67G_S010_E1-50


title: SM-GE8YR_S027_E1-50


title: SM-GE8YR_S026_E1-50


title: T8_3350_138_CTL_WT_F_G1_21036

value: WT

value: Female


title: SM-GE8YR_S025_E1-50

value: PC

value: NeuN-positive


title: SM-GE67G_S015_E1-50

value: 2.3 yrs


title: SM-GE8YR_S023_E1-50


title: SM-GE67G_S008_E1-50


title: T8_3349_105_CTL_CW_F_G2_21052

value: PBMC

value: CTL

value: CW


title: SM-GE8YR_S024_E1-50


title: SM-GE8YR_S022_E1-50


title: SM-GE8YR_S021_E1-50


title: SM-GE67G_S006_E1-50

value: M


title: SM-GE67G_S007_E1-50

value: MC


title: T8_3339_72_CTL_CW_M_G2_21046

value: Male


title: SM-GE8YR_S020_E1-50

value: 10 yrs


title: T8_3340_127_CTL_HW_M_G4_21093

value: HW


title: SM-GE8YR_S018_E1-50

value: Glut


title: SM-GE8YR_S019_E1-50


title: SM-GE8YR_S016_E1-50


title: T8_3335_116_CTL_HW_M_G3_21074


title: SM-GE8YR_S015_E1-50


title: SM-GE67G_S005_E1-50


title: T7_3370_61_CM_CHW_M_G6_21125

value: CM


title: SM-GE8YR_S013_E1-50


title: SM-GE8YR_S014_E1-50


title: SM-GE67G_S004_E1-50

value: P


title: T7_3368_50_CM_CHW_M_G7_21141

value: CHW


title: T8_3342_83_CTL_CW_M_G6_21128


title: SM-GE8YR_S012_E1-50

value: GABA


title: SM-GE67G_S009_E1-50

value: Low Quality


title: SM-GE8YR_S017_E1-50


title: SM-GE8YR_S011_E1-50


title: T7_3350_137_CTL_WT_F_G4_21096

value: WT

value: Female


title: SM-GE8YR_S010_E1-50

value: NeuN-positive


title: SM-GE67G_S001_E1-50

value: 2.3 yrs


title: SM-GE8YR_S009_E1-50


title: SM-GE67G_S002_E1-50


title: T7_3349_104_CTL_CW_F_G5_21111

value: PBMC

value: CTL


title: SM-GE8YR_S006_E1-50


title: T7_3346_93_CTL_CW_M_G2_21050

value: CW


title: SM-GE8YR_S007_E1-50

value: MC


title: SM-GE8YR_S008_E1-50


title: SM-GE8YR_S002_E1-50

value: M


title: SM-GE67G_S003_E1-50


title: SM-GE67F_S120_E1-50


title: SM-GE8YR_S005_E1-50

value: 10 yrs


title: T7_3342_82_CTL_CW_M_G7_21148

value: Male


title: SM-GE8YR_S001_E1-50

value: Glut


title: SM-GE8YR_S004_E1-50


title: SM-GE67F_S119_E1-50


title: SM-GE8YQ_S192_E1-50

value: Pulv


title: SM-GE8YQ_S191_E1-50


title: SM-GE8YR_S003_E1-50


title: T7_3340_126_CTL_HW_M_G2_21055

value: HW


title: T7_3336_17_CM_CHW_F_G3_21059

value: CM

value: CHW


title: SM-GE8YQ_S186_E1-50


title: T6p5_3336_16_CM_CHW_F_G4_21079


title: SM-GE8YQ_S185_E1-50


title: T6p5_3334_8_CM_CHW_M_G6_21117


title: SM-GE67F_S117_E1-50


title: SM-GE8YQ_S190_E1-50


title: T7_3339_71_CTL_CW_M_G6_21126


title: T7_3335_115_CTL_HW_M_G6_21133


title: SM-GE67F_S116_E1-50


title: SM-GE8YQ_S187_E1-50


title: SM-GE67F_S115_E1-50

value: Low Quality


title: SM-GE8YQ_S188_E1-50

value: GABA


title: SM-GE67F_S112_E1-50


title: SM-GE8YQ_S189_E1-50


title: SM-GE67F_S114_E1-50


title: T6_3368_49_CM_CHW_M_G6_21122


title: SM-GE67F_S109_E1-50


title: SM-GE67F_S111_E1-50


title: SM-GE67F_S118_E1-50


title: T6_3349_103_CTL_CW_F_G4_21090

value: Female


title: SM-GE8YQ_S180_E1-50

value: NeuN-positive


title: T6_3370_60_CM_CHW_M_G5_21105


title: SM-GE8YQ_S183_E1-50


title: SM-GE8YQ_S175_E1-50


title: SM-GE8YQ_S184_E1-50


title: SM-GE8YQ_S181_E1-50


title: SM-GE8YQ_S178_E1-50


title: SM-GE8YQ_S179_E1-50


title: T6_3350_136_CTL_WT_F_G2_21056

value: WT


title: SM-GE67F_S110_E1-50

value: 2.3 yrs


title: T6_3341_31_CM_CHW_F_G3_21062

value: PBMC


title: SM-GE8YQ_S176_E1-50


title: SM-GE8YQ_S174_E1-50


title: SM-GE8YQ_S182_E1-50


title: T6_3346_92_CTL_CW_M_G5_21110

value: CTL

value: CW


title: SM-GE8YQ_S159_E1-50


title: SM-GE67F_S106_E1-50

value: M

value: MC


title: SM-GE67F_S107_E1-50


title: SM-GE67F_S105_E1-50


title: SM-GE8YQ_S158_E1-50

value: 10 yrs


title: SM-GE8YQ_S177_E1-50


title: SM-GE8YQ_S173_E1-50

value: Glut


title: SM-GE67F_S108_E1-50


title: SM-GE8YQ_S171_E1-50

value: Pulv


title: T6_3339_70_CTL_CW_M_G7_21146

value: Male


title: SM-GE8YQ_S160_E1-50


title: SM-GE67F_S104_E1-50


title: SM-GE8YQ_S172_E1-50


title: SM-GE8YQ_S170_E1-50


title: T6_3342_81_CTL_CW_M_G2_21047


title: SM-GE67F_S103_E1-50


title: SM-GE8YQ_S157_E1-50


title: T6_3335_114_CTL_HW_M_G2_21112

value: HW


title: SM-GE8YQ_S155_E1-50


title: SM-GE67F_S101_E1-50


title: SM-GE8YQ_S154_E1-50


title: SM-GE8YQ_S152_E1-50


title: SM-GE8YQ_S151_E1-50


title: T6_3336_15_CM_CHW_F_G6_21118

value: CM

value: CHW


title: T6_3334_7_CM_CHW_M_G5_21038


title: SM-GE8YQ_S156_E1-50


title: SM-GE8YQ_S149_E1-50


title: T5_3370_59_CM_CHW_M_G1_21025


title: T8_3346_94_CTL_CW_M_G3_21070


title: SM-GE67F_S100_E1-50

value: GABA


title: SM-GE8YQ_S153_E1-50


title: SM-GE8YQ_S150_E1-50


title: SM-GE8YQ_S146_E1-50


title: T5_3350_135_CTL_WT_F_G6_21136

value: Female


title: SM-GE8YQ_S148_E1-50

value: NeuN-positive


title: SM-GE67F_S099_E1-50


title: SM-GE67F_S102_E1-50

value: Low Quality


title: SM-GE67F_S097_E1-50

value: 2.3 yrs


title: T5_3368_48_CM_CHW_M_G7_21142

value: PBMC


title: SM-GE8YQ_S144_E1-50

value: PC

value: P


title: SM-GE8YQ_S147_E1-50


title: SM-GE8YQ_S140_E1-50


title: T5_3346_91_CTL_CW_M_G7_21149

value: CTL

value: CW


title: SM-GE8YQ_S141_E1-50

value: 10 yrs


title: SM-GE67F_S098_E1-50

value: M

value: MC

value: Glut


title: T5_3341_29_CM_CHW_F_G3_21061


title: SM-GE67F_S024_E1-50


title: SM-GE8YQ_S143_E1-50


title: T5_3349_102_CTL_CW_F_G3_21072


title: SM-GE67F_S021_E1-50


title: SM-GE8YQ_S145_E1-50

value: Pulv


title: SM-GE67F_S023_E1-50


title: SM-GE67F_S022_E1-50


title: SM-GE8YQ_S139_E1-50


title: SM-GE8YQ_S142_E1-50


title: SM-GE8YQ_S137_E1-50


title: SM-GE8YQ_S138_E1-50


title: SM-GE8YQ_S134_E1-50


title: SM-GE8YQ_S136_E1-50


title: T5_3336_14_CM_CHW_F_G2_21039

value: CM


title: T5_3339_69_CTL_CW_M_G1_21027

value: Male


title: SM-GE8YQ_S133_E1-50


title: T5_3342_80_CTL_CW_M_G4_21087


title: SM-GE8YQ_S135_E1-50


title: SM-GE8YQ_S132_E1-50


title: SM-GE8YQ_S130_E1-50


title: T5_3340_124_CTL_HW_M_G7_21154

value: HW


title: SM-GE67F_S017_E1-50


title: SM-GE8YQ_S129_E1-50


title: SM-GE67F_S019_E1-50


title: SM-GE8YQ_S131_E1-50

value: GABA


title: SM-GE8YQ_S128_E1-50

value: NeuN-positive


title: T4_3370_58_CM_CHW_M_G6_21124

value: CHW


title: SM-GE8YQ_S125_E1-50


title: T5_3334_113_CM_CHW_M_G4_21092


title: T4_3368_47_CM_CHW_M_G2_21044


title: SM-GE67F_S016_E1-50

value: 2.3 yrs

value: Low Quality


title: SM-GE67F_S020_E1-50


title: SM-GE8YQ_S122_E1-50

value: PC


title: SM-GE8YQ_S123_E1-50

value: P


title: SM-GE8YQ_S127_E1-50


title: T5_3335_6_CTL_HW_M_G7_21137

value: PBMC

value: CTL


title: SM-GE67F_S013_E1-50


title: SM-GE67F_S018_E1-50


title: SM-GE67F_S015_E1-50


title: SM-GE8YQ_S117_E1-50

value: 10 yrs


title: SM-GE8YQ_S115_E1-50


title: T4_3342_79_CTL_CW_M_G3_21068

value: CW


title: T4_3341_28_CM_CHW_F_G2_21041

value: Female


title: SM-GE8YQ_S116_E1-50

value: MC

value: Glut


title: SM-GE67F_S009_E1-50

value: M


title: SM-GE8YQ_S126_E1-50


title: SM-GE67F_S014_E1-50


title: SM-GE8YQ_S120_E1-50


title: SM-GE8YQ_S124_E1-50


title: SM-GE8YQ_S109_E1-50


title: SM-GE8YQ_S111_E1-50


title: T4_3350_134_CTL_WT_F_G5_21116

value: WT


title: SM-GE8YQ_S110_E1-50


title: SM-GE67F_S007_E1-50


title: T4_3339_68_CTL_CW_M_G4_21086

value: Male


title: SM-GE8YQ_S119_E1-50


title: T4_3357_36_CM_CHW_F_G1_21021

value: CM


title: SM-GE8YQ_S121_E1-50

value: NeuN-positive


title: SM-GE67F_S012_E1-50


title: SM-GE8YQ_S107_E1-50


title: SM-GE67F_S006_E1-50


title: SM-GE8YQ_S118_E1-50


title: SM-GE8YQ_S104_E1-50


title: T4_3349_101_CTL_CW_F_G7_21151


title: SM-GE8YQ_S102_E1-50


title: SM-GE8YQ_S100_E1-50

value: GABA


title: SM-GE67F_S010_E1-50

value: 2.3 yrs


title: SM-GE8YQ_S114_E1-50


title: T4_3346_90_CTL_CW_M_G4_21088


title: SM-GE8YQ_S112_E1-50


title: SM-GE67F_S008_E1-50


title: T4_3340_123_CTL_HW_M_G3_21075

value: HW


title: SM-GE8YQ_S099_E1-50


title: SM-GE8YQ_S098_E1-50


title: T4_3335_5_CTL_HW_M_G4_21077


title: SM-GE8YQ_S113_E1-50


title: T4_3334_112_CM_CHW_M_G2_21053

value: CHW


title: SM-GE8YQ_S095_E1-50

value: Pulv


title: SM-GE8YQ_S093_E1-50


title: SM-GE67F_S011_E1-50

value: P


title: T3_3350_133_CTL_WT_F_G1_21035

value: PBMC

value: CTL


title: SM-GE8YQ_S091_E1-50

value: 10 yrs


title: T4_3338_23_CM_CHW_F_G1_21019

value: Female


title: T3_3349_100_CTL_CW_F_G1_21031

value: CW


title: SM-GE8YQ_S106_E1-50

value: MC

value: Glut


title: SM-GE8YQ_S090_E1-50


title: SM-GE67B_S141_E1-50

value: M

value: PC


title: SM-GE8YQ_S108_E1-50


title: SM-GE8YQ_S089_E1-50


title: T3_3346_89_CTL_CW_M_G2_21049

value: Male


title: SM-GE8YQ_S088_E1-50

value: NeuN-positive


title: SM-GE67F_S004_E1-50


title: SM-GE67B_S140_E1-50


title: SM-GE67F_S003_E1-50

value: Low Quality


title: SM-GE8YQ_S105_E1-50


title: SM-GE8YQ_S101_E1-50

value: GABA


title: SM-GE8YQ_S092_E1-50


title: T3_3368_46_CM_CHW_M_G5_21103

value: CM


title: SM-GE8YQ_S086_E1-50


title: SM-GE8YQ_S084_E1-50


title: T3_3370_57_CM_CHW_M_G4_21085

value: CHW


title: SM-GE8YQ_S096_E1-50

value: Pulv


title: SM-GE67F_S002_E1-50

value: 2.3 yrs


title: SM-GE67B_S144_E1-50

value: P


title: T3_3341_27_CM_CHW_F_G4_21081

value: PBMC


title: SM-GE67B_S138_E1-50


title: SM-GE8YQ_S085_E1-50

value: 10 yrs


title: SM-GE67F_S001_E1-50


title: SM-GE8YQ_S082_E1-50


title: SM-GE67B_S137_E1-50


title: SM-GE8YQ_S097_E1-50


title: SM-GE8YQ_S078_E1-50


title: T3_3357_35_CM_CHW_F_G5_21101

value: Female


title: SM-GE8YQ_S079_E1-50


title: SM-GE67B_S139_E1-50


title: SM-GE67B_S143_E1-50


title: SM-GE67B_S142_E1-50


title: SM-GE8YQ_S094_E1-50


title: SM-GE8YQ_S076_E1-50


title: SM-GE67B_S132_E1-50


title: T3_3334_111_CM_CHW_M_G3_21073


title: T3_3342_78_CTL_CW_M_G1_21029

value: CTL

value: CW


title: SM-GE8YQ_S083_E1-50

value: Glut


title: SM-GE8YQ_S077_E1-50


title: SM-GE67B_S131_E1-50

value: M


title: SM-GE8YQ_S087_E1-50


title: SM-GE67B_S136_E1-50

value: PC


title: T3_3340_122_CTL_HW_M_G2_21054

value: HW

value: Male


title: SM-GE8YQ_S080_E1-50

value: NeuN-positive


title: SM-GE8YQ_S075_E1-50


title: SM-GE67B_S135_E1-50


title: T3_3339_67_CTL_CW_M_G3_21066


title: SM-GE8YQ_S081_E1-50

value: GABA


title: T3_3338_22_CM_CHW_F_G4_21080

value: CM


title: SM-GE8YQ_S071_E1-50


title: SM-GE67B_S133_E1-50

value: Low Quality


title: SM-GE8YQ_S067_E1-50

value: Pulv


title: SM-GE8YQ_S074_E1-50


title: SM-GE8YQ_S072_E1-50


title: SM-GE8YQ_S065_E1-50


title: T3_3336_12_CM_CHW_F_G5_21098

value: CHW


title: T3_3335_4_CTL_HW_M_G2_21037


title: SM-GE67B_S120_E1-50

value: 2.3 yrs

value: MC


title: SM-GE8YQ_S069_E1-50

value: 10 yrs


title: SM-GE8YQ_S070_E1-50


title: SM-GE67B_S134_E1-50

value: P


title: SM-GE8YQ_S056_E1-50


title: SM-GE67B_S118_E1-50


title: SM-GE8YQ_S073_E1-50


title: SM-GE8YQ_S053_E1-50


title: SM-GE8YQ_S055_E1-50


title: SM-GE8YQ_S052_E1-50


title: T2_3370_56_CM_CHW_M_G2_21045

value: PBMC


title: T2_3342_77_CTL_CW_M_G7_21147

value: CTL

value: CW


title: T2_3341_26_CM_CHW_F_G1_21020

value: Female


title: T2_3368_45_CM_CHW_M_G1_21023


title: SM-GE8YQ_S068_E1-50


title: SM-GE67B_S117_E1-50

value: M

value: Glut


title: SM-GE67B_S116_E1-50


title: SM-GE8YQ_S054_E1-50


title: SM-GE8YQ_S066_E1-50


title: SM-GE8YQ_S048_E1-50

value: PC


title: T2_3340_121_CTL_HW_M_G6_21134

value: HW

value: Male


title: SM-GE67B_S129_E1-50

value: NeuN-positive


title: SM-GE67B_S130_E1-50

value: Low Quality


title: SM-GE67B_S119_E1-50


title: T2_3350_132_CTL_WT_F_G6_21135

value: WT


title: SM-GE8YQ_S042_E1-50


title: SM-GE67B_S113_E1-50


title: T2_3346_88_CTL_CW_M_G5_21109


title: SM-GE8YQ_S049_E1-50

value: Pulv

value: GABA


title: T2_3357_34_CM_CHW_F_G2_21042

value: CM

value: CHW


title: SM-GE67B_S111_E1-50

value: 2.3 yrs

value: MC


title: SM-GE8YQ_S047_E1-50

value: 10 yrs

value: P


title: SM-GE8YQ_S037_E1-50


title: T1_3370_55_CM_CHW_M_G5_21104

value: PBMC


title: SM-GE8YQ_S044_E1-50


title: SM-GE8YQ_S045_E1-50


title: SM-GE8YQ_S043_E1-50


title: SM-GE67B_S114_E1-50

value: M


title: SM-GE8YQ_S035_E1-50

value: Glut


title: T2_3349_99_CTL_CW_F_G4_21089

value: CTL

value: CW

value: Female


title: SM-GE8YQ_S051_E1-50

value: NeuN-positive


title: SM-GE67B_S110_E1-50


title: T1_3368_44_CM_CHW_M_G3_21064

value: Male


title: SM-GE67B_S115_E1-50


title: SM-GE67B_S109_E1-50


title: SM-GE8YQ_S041_E1-50

value: PC


title: T2_3336_11_CM_CHW_F_G7_21138


title: T1_3357_33_CM_CHW_F_G4_21082


title: SM-GE8YQ_S050_E1-50

value: Pulv


title: SM-GE8YQ_S046_E1-50


title: T1_3350_131_CTL_WT_F_G5_21115

value: WT


title: T2_3338_21_CM_CHW_F_G3_21060

value: CM


title: SM-GE8YQ_S039_E1-50


title: SM-GE8YQ_S040_E1-50

value: GABA


title: SM-GE67B_S107_E1-50

value: 2.3 yrs


title: SM-GE8YQ_S026_E1-50


title: SM-GE8YQ_S027_E1-50


title: SM-GE67B_S106_E1-50

value: MC


title: SM-GE8YQ_S028_E1-50

value: 10 yrs


title: T2_3335_3_CTL_HW_M_G3_21057

value: HW


title: T1_3346_87_CTL_CW_M_G6_21129

value: PBMC


title: SM-GE8YQ_S038_E1-50

value: P


title: SM-GE8YQ_S024_E1-50


title: T2_3339_66_CTL_CW_M_G7_21145


title: SM-GE8YQ_S033_E1-50

value: Glut


title: SM-GE8YQ_S036_E1-50


title: SM-GE8YQ_S021_E1-50


title: SM-GE8YQ_S034_E1-50


title: SM-GE67B_S094_E1-50

value: M


title: SM-GE8YQ_S017_E1-50


title: SM-GE67B_S112_E1-50


title: T1_3340_120_CTL_HW_M_G1_21033

value: CTL


title: SM-GE8YQ_S032_E1-50


title: SM-GE8YQ_S025_E1-50


title: SM-GE8YQ_S030_E1-50


title: SM-GE8YQ_S031_E1-50


title: T1_3349_98_CTL_CW_F_G3_21071

value: CW

value: Female


title: SM-GE67B_S105_E1-50

value: NeuN-positive


title: SM-GE67B_S108_E1-50


title: SM-GE67B_S096_E1-50

value: PC


title: T1_3339_65_CTL_CW_M_G5_21106

value: Male


title: SM-GE8YQ_S029_E1-50


title: T1_3338_20_CM_CHW_F_G7_21139

value: CHW


title: T1_3342_76_CTL_CW_M_G6_21127


title: SM-GE8YQ_S023_E1-50


title: T1_3341_25_CM_CHW_F_G5_21100

value: CM


title: SM-GE8YQ_S022_E1-50

value: GABA


title: SM-GE67B_S095_E1-50

value: 2.3 yrs


title: T1_3336_10_CM_CHW_F_G4_21078


title: SM-GE8YQ_S019_E1-50

value: MC


title: SM-GE67B_S093_E1-50


title: SM-GE8YQ_S018_E1-50

value: 10 yrs


title: T1_3335_2_CTL_HW_M_G5_21097

value: HW


title: SM-GE67B_S092_E1-50

value: Low Quality


title: SM-GE8YQ_S013_E1-50


title: SM-GE67B_S091_E1-50


title: SM-GE8YQ_S014_E1-50


title: SM-GE8YQ_S016_E1-50


title: SM-GE8YQ_S015_E1-50


title: SM-GE8YQ_S011_E1-50


title: SM-GE8YQ_S010_E1-50


title: SM-GE8YQ_S020_E1-50

value: P


title: SM-GE67B_S088_E1-50

value: Glut


title: T10_3368_53_CM_CHW_M_G6_21123

value: PBMC


title: SM-GE8YQ_S008_E1-50


title: SM-GE67B_S089_E1-50

value: M


title: T1_3334_109_CM_CHW_M_G6_21132


title: SM-GE67B_S090_E1-50


title: SM-GE8YQ_S007_E1-50


title: SM-GE8YQ_S012_E1-50


title: SM-GE8YQ_S004_E1-50


title: T10_3346_96_CTL_CW_M_G1_21028

value: CTL

value: CW


title: SM-GE8YQ_S009_E1-50

value: NeuN-positive


title: SM-GE8YQ_S001_E1-50


title: SM-GE67B_S085_E1-50

value: PC


title: SM-GE8YQ_S002_E1-50


title: SM-GE8YQ_S003_E1-50


title: SM-GE8YP_S192_E1-50

value: Pulv


title: SM-GE67B_S087_E1-50


title: T10_3340_129_CTL_HW_M_G4_21094

value: Male


title: SM-GE67B_S086_E1-50


title: T10_3342_85_CTL_CW_M_G1_21030


title: SM-GE8YP_S190_E1-50


title: SM-GE8YP_S191_E1-50


title: T10_3339_74_CTL_CW_M_G5_21107


title: SM-GE8YP_S188_E1-50


title: T10_3349_107_CTL_CW_F_G6_21131

value: Female


title: SM-GE8YP_S185_E1-50


title: SM-GE8YP_S183_E1-50

value: GABA


title: SM-GE67B_S083_E1-50

value: 2.3 yrs


title: SM-GE8YP_S189_E1-50


title: SM-GE8YP_S184_E1-50


title: SM-GE8YQ_S005_E1-50

value: MC


title: SM-GE8YP_S186_E1-50

value: 10 yrs


title: SM-GE67B_S084_E1-50


title: SM-GE67B_S079_E1-50


title: T10_3335_118_CTL_HW_M_G1_21032

value: HW


title: SM-GE67B_S082_E1-50


title: SM-GE67B_S081_E1-50


title: T0_3368_43_CM_CHW_M_G5_21102

value: CM

value: CHW


title: SM-GE8YP_S179_E1-50

value: Glut


title: SM-GE8YP_S178_E1-50


title: SM-GE67B_S077_E1-50

value: P


title: T0_3370_54_CM_CHW_M_G7_21143

value: PBMC


title: Human skeletal muscle biopsy collected after 14 consecutive days of endurance exercise training_Subject 3

city: Copenhagen

first: Christian

last: Garde

address: Blegdamsvej 3

institute: University of Copenhagen

data_processing:
Short RNA sequencing reads were trimmed using FastX.
Trimmed reads were mapped to hg38 with Bowtie2.
miRNA coverages were computed using featureCounts with miRBase v21 annotations.
Differentially expressed genes were determined using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

organism: Homo sapiens

source_name: Vastus lateralis skeletal muscle

extract_protocol:
Muscle samples were taken using the percutaneous muscle biopsy technique, snap frozen in liquid nitrogen, and stored at -80°C until total RNA was extracted using TRIzol. Small RNA molecules 18-24 nucleotides long were purified using mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific) followed by fractionantion of small RNAs by  15% PAGE/7 M urea.
3’- and 5’-adaptors were ligated, cDNA was synthetized and amplified as described (PMID: 19800275)

tag: phenotype

value: After 14 consecutive days of endurance exercise training

tag: vo2peak (ml/kg/min)


title: Human skeletal muscle biopsy collected before endurance exercise training_Subject 3

value: Baseline


title: SM-GE8YP_S181_E1-50

value: NeuN-positive


title: T0_3349_97_CTL_CW_F_G2_21051

value: CTL

value: CW


title: Human skeletal muscle biopsy collected after 14 consecutive days of endurance exercise training_Subject 2


title: T0_3357_32_CM_CHW_F_G6_21120


title: SM-GE8YP_S187_E1-50

value: Pulv


title: SM-GE8YP_S174_E1-50


title: SM-GE8YP_S180_E1-50


title: SM-GE67B_S078_E1-50

value: M

value: PC

value: Low Quality


title: T0_3346_86_CTL_CW_M_G3_21069

value: Male


title: SM-GE8YP_S175_E1-50

value: 10 yrs


title: T0_3350_130_CTL_WT_F_G4_21095

value: WT

value: Female


title: Human skeletal muscle biopsy collected after 14 consecutive days of endurance exercise training_Subject 1


title: SM-GE67B_S080_E1-50

value: 2.3 yrs


title: SM-GE8YP_S182_E1-50

value: Glut


title: SM-GE8YP_S176_E1-50


title: T0_3339_64_CTL_CW_M_G1_21026


title: SM-GE8YP_S177_E1-50


title: Human skeletal muscle biopsy collected before endurance exercise training_Subject 2


title: T0_3341_24_CM_CHW_F_G2_21040

value: CM

value: CHW


title: T0_3340_119_CTL_HW_M_G5_21113

value: PBMC

value: HW


title: SM-GE8YP_S172_E1-50

value: NeuN-positive


title: SM-GE67B_S074_E1-50

value: P


title: SM-GE67B_S073_E1-50

value: GABA


title: SM-GE67B_S076_E1-50


title: SM-GE67B_S075_E1-50


title: SM-GE67B_S070_E1-50

value: MC


title: SM-GE8YP_S173_E1-50

value: Pulv


title: T0_3342_75_CTL_CW_M_G5_21108

value: CTL

value: CW


title: SM-GE67B_S069_E1-50

value: M


title: SM-GE67B_S072_E1-50


title: Human skeletal muscle biopsy collected before endurance exercise training_Subject 1

value: Baseline


title: SM-GE8YP_S167_E1-50

value: 10 yrs


title: SM-GE67B_S071_E1-50


title: T0_3335_1_CTL_HW_M_G1_21017

value: Male


title: T0_3334_108_CM_CHW_M_G4_21091


title: T0_3336_9_CM_CHW_F_G3_21058

value: Female


title: T0_3338_19_CM_CHW_F_G6_21119


title: 2720-1

description:
microRNA
MicroRNAseq library prep.
validation_mature_normalized_CPM.tsv

value: Ctrl


title: SM-GE8YP_S170_E1-50

value: Glut


title: SM-GE8YP_S169_E1-50


title: SM-GE8YP_S168_E1-50


title: SM-GE67B_S066_E1-50

value: 2.3 yrs


title: SM-GE67B_S067_E1-50


title: SM-GE67B_S068_E1-50


title: SM-GE8YP_S164_E1-50


title: SM-GE67B_S065_E1-50


title: 2718-1

value: PBMC

value: CM

value: CHW


title: SM-GE8YP_S163_E1-50

value: NeuN-positive


title: SM-GE8YP_S166_E1-50


title: 2719-1


title: SM-GE8YP_S165_E1-50


title: SM-GE67B_S064_E1-50

value: P


title: SM-GE67B_S063_E1-50

value: MC

value: Low Quality


title: 2709-1


title: 2731-1


title: SM-GE8YP_S160_E1-50

value: Pulv

value: GABA


title: SM-GE67B_S061_E1-50

value: M


title: SM-GE67B_S062_E1-50


title: 2705-1

value: HW


title: Commercial_hCMECs_line_knock_out_RNF213_proliferation_001_clone1_rep1

type: RNA

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

description: Gene expression of hCMECs line proliferating knock out for RNF213 in passage 33

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Commercial human cerebral microvascular endothelial cells line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: hCMECs were purchased from Cedarlane Laboratories and were maintained in a gelatin-coated tissue culture flask in EBM-2 basal medium supplemented with 5% foetal bovine serum , 1.4 mM hydrocortisone, 5 mg/ml ascorbic acid, 1% chemically defined lipid concentrate, 1 ng/ml human basic fibroblast growth factor, 10 mM HEPES and the antibiotics, 100 IU/ml penicillin G and 25 μg/ml gentamicin and grown in an incubator at 37°C, 8% CO2 and 95% relative humidity. The culture medium was changed 3 times a week

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: we generated RNF213 hCMECs knockout cells using CRISPR/Cas9 genome editing technology. Two sgRNAs were designed and cloned into expressing vector. csgRNAa cleavage efficiencies were calculated using mismatch assays (sgRNA-A, 41%; sgRNA-B, 40%). Both sgRNAs were cloned in a home-made lentiviral vector co-expressing the SpCas9and a puromycin N-acetyltransferase gene conferring resistance to puromycin antibiotics exposure. A negligible amount of RNF213 protein expression was observed in hCMECs RNF213-/- cells. Gene expression profiling analysis also revealed that transduced hCMECs preserved key endothelial markers. The sgRNAs used to produce the invalidation of RNF213 were specific for their designed RNF213 target and that the effects of knockout were not the result of unintended genomic alteration.

tag: cell type

tag: transfection

value: Knock out RNF213 (Cas9 with guide RNA)

tag: culture

value: Proliferating cells

value: Adult

value: F


title: SM-GE8YP_S161_E1-50

value: 10 yrs

value: Glut


title: Commercial_hCMECs_line_transfection_control_proliferation_001_rep1

description: Gene expression of hCMECs line proliferating transfected with Cas9 without guide RNA in passage 33

value: cerebral microvascular endothelial cells

value: Transfection control (Cas9 without guide RNA)


title: 2702-1

tag: strain

tag: tissue

value: PBMC

tag: treatment

value: Ctrl

value: CW

value: Female


title: SM-GE67B_S059_E1-50

tag: donor

value: 2.3 yrs

value: MC

value: NeuN-positive


title: Commercial_hCMECs_line_knock_out_RNF213_confluency_001_clone2_rep2

description: Gene expression of hCMECs line at confluency knock out for RNF213 in passage 33

value: Confluent cells

tag: Sex


title: Commercial_hCMECs_line_knock_out_RNF213_proliferation_001_clone1_rep2


title: Commercial_hCMECs_line_knock_out_RNF213_proliferation_001_clone2_rep2


title: SM-GE67B_S060_E1-50

value: M


title: SM-GE8YP_S159_E1-50

value: Pulv

value: GABA


title: Commercial_hCMECs_line_knock_out_RNF213_proliferation_001_clone2_rep1

value: Knock out RNF213 (Cas9 with guide RNA)

value: Proliferating cells

value: Adult


title: 2708-1

value: CM

tag: genotype

value: CHW


title: SM-GE8YP_S157_E1-50

value: 10 yrs

tag: facs gating


title: SM-GE8YP_S156_E1-50

tag: sequencing batch

value: Glut


title: 2690-1

value: PBMC


title: Commercial_hCMECs_line_wild_type_proliferation_001_rep1

description: Gene expression of hCMECs line proliferating in passage 33

value: cerebral microvascular endothelial cells

value: No transfection

value: F


title: Commercial_hCMECs_line_wild_type_proliferation_001_rep2


title: 2700-1

value: Female


title: Commercial_hCMECs_line_knock_out_RNF213_confluency_001_clone2_rep1


title: Commercial_hCMECs_line_knock_out_RNF213_confluency_001_clone1_rep1


title: Commercial_hCMECs_line_transfection_control_confluency_001_rep1

description: Gene expression of hCMECs line at confluency transfected with Cas9 without guide RNA in passage 33

value: Transfection control (Cas9 without guide RNA)


title: Commercial_hCMECs_line_transfection_control_confluency_001_rep2

value: Confluent cells


title: SM-GE8YP_S158_E1-50

value: NeuN-positive

tag: cell class


title: 2689-1

value: Ctrl

value: CW


title: Commercial_hCMECs_line_knock_out_RNF213_confluency_001_clone1_rep2

value: Knock out RNF213 (Cas9 with guide RNA)


title: SM-GE67B_S056_E1-50

value: M

value: 2.3 yrs

value: MC

tag: cell cluster


title: Commercial_hCMECs_line_wild_type_confluency_001_rep2

description: Gene expression of hCMECs line at confluency in passage 33

tag: age

value: Adult


title: 2692-1

tag: timepoint


title: SM-GE67B_S058_E1-50

value: P


title: EyeBank_cultured_human_corneal_epithelial_cells_Wnk_inhibitor_003_rep1

description: Gene expression of passage 3 cells until they reached near-confluence in culture with Wnk inhibitor (1 μM)

source_name: Primary human corneal epithelial cell population

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: Human corneal epithelial cells were isolated from the limbal area of normal eyes of 52-, 70-, and 71  year-old donors. Briefly, the limbus was incubated in 2 mg/ml dispase II in HEPES buffer overnight at 4 °C. The epithelium of the limbal region was removed and digested in trypsin for 15 min at 37 °C. Cells were then transferred to tissue culture flasks containing a lethally irradiated human fibroblasts feeder layer seeded 7 days before. Human corneal epithelial cells were cultured with Dulbecco-Vogt modified Eagle medium: Ham's F12, ratio 3:1, 24.3 μg/mL adenine, 5 μg/mL insulin, 0.4 μg/mL hydrocortison, 0.212 μg/mL isoproterenol hydrochloride, 5% bovine HyClone FetalClone II serum, 10 ng/mL human epidermal growth factor, 100 U/mL penicillin and 25 μg/mL gentamicin. Cells were maintained in 37°C and 8% CO2 incubators and culture medium was changed after 2 days.

treatment_protocol: Human corneal epithelial cells were grown either in the presence of Wnk inhibitor (1 μM) or vehicle alone (DMSO; controls) until they reached near-confluence.

value: corneal epithelial cells

tag: inhibitor

value: Wnk inhibitor used


title: SM-GE8YP_S155_E1-50

value: 10 yrs

value: Pulv

value: GABA


title: SM-GE8YP_S154_E1-50


title: 2685-1

value: PBMC

value: CM

value: CHW

value: Male


title: 2686-1


title: SM-GE67B_S054_E1-50

value: NeuN-positive

value: Low Quality


title: SM-GE67B_S053_E1-50

value: Glut


title: 2683-1

value: Ctrl

value: WT


title: SM-GE8YP_S143_E1-50

value: PC


title: 2684-1


title: SM-GE67B_S055_E1-50

value: M

value: 2.3 yrs

value: MC


title: SM-GE8YP_S144_E1-50

value: P


title: EyeBank_cultured_human_corneal_epithelial_cells_Wnk_inhibitor_002_rep1

value: corneal epithelial cells

value: Wnk inhibitor used

value: F


title: SM-GE8YP_S153_E1-50

value: 10 yrs

value: Pulv


title: SM-GE67B_S057_E1-50


title: SM-GE8YP_S142_E1-50

value: GABA


title: EyeBank_cultured_human_corneal_epithelial_cells_002_rep1

description: Gene expression of passage 3 cells until they reached near-confluence in culture with vehicle alone (DMSO; controls)

value: no Wnk inhibitor used


title: SM-GE8YP_S141_E1-50

value: NeuN-positive


title: SM-GE67B_S052_E1-50


title: SM-GE8YP_S162_E1-50


title: SM-GE67B_S049_E1-50


title: EyeBank_cultured_human_corneal_epithelial_cells_001_rep1


title: 2731-L

value: PBMC

value: L

value: CM

value: CHW

value: Female


title: EyeBank_cultured_human_corneal_epithelial_cells_Wnk_inhibitor_001_rep1


title: SM-GE8YP_S139_E1-50

value: PC

value: Glut


title: SM-GE67B_S050_E1-50

value: M

value: 2.3 yrs

value: MC


title: SM-GE67B_S048_E1-50


title: 2719-L

value: Male


title: SM-GE67B_S047_E1-50


title: SM-GE8YP_S138_E1-50

value: P


title: 2718-L


title: 2720-7

value: Ctrl

value: HW


title: 2690-L


title: SM-GE8YP_S137_E1-50

value: 10 yrs


title: 2709-7


title: Cell_Bank_cultured_human_keratinocytes_serum-free-medium_004_rep1

description: Gene expression of keratinocytes in passage 2, cultivated in serum-free medium until they reached near-confluence in culture

source_name: Primary human keratocytes (foreskin)

growth_protocol: Skin biopsies were washed in antibiotics-containing PBS, cut into 3 mm × 100 to 150 mm strips, and incubated overnight at 4°C in a 500 μg/mL thermolysin-HEPES solution. The epithelium was subsequently peeled from the dermis with sterile tweezers. Epidermal strips were then incubated for 30 minutes in a trypsin-ethylenediaminetretraacetic acid (EDTA) solution (0.05% w/v of porcine trypsin 1-250, 0.01% w/v of EDTA, 2.8 mM of D-glucose, 100 IU/mL of penicillin G, 25 μg/mL of gentamicin, and phenol red) in PBS at 37°C on a stirring plate. A 0.44 mg/mL soybean trypsin inhibitor (STI)/Surge SFM Light mixture was used to neutralize trypsin activity. Surge SFM Light was used to wash and resuspend the cell pellets. Keratinocytes were seeded at 1.4 × 104 cells/cm2 on iHFL in either Surge SFM or DME-Ham. Cells were kept in incubators at 37°C, 8% CO2, and 95 ± 5% humidity. Medium was changed three times per week. When cells attained 75-95% confluence, they were passaged.

treatment_protocol: Keratinocytes were seeded at 1.4 × 104 cells/cm2 on iHFL in either Surge SFM (Patent pending) or ckDME-Ham (Dulbecco-Vogt modified Eagle medium: Ham's F12, ratio 3:1, 24.3 μg/mL adenine, 5 μg/mL insulin, 0.4 μg/mL hydrocortison, 0.212 μg/mL isoproterenol hydrochloride, 5% bovine HyClone FetalClone II serum, 10 ng/mL human epidermal growth factor, 100 U/mL penicillin and 25 μg/mL gentamicin). Cells were kept in incubators at 37°C, 8% CO2, and 95 ± 5% humidity. Medium was changed three times per week. When cells attained 75-95% confluence, they were passaged

value: keratinocytes

tag: medium culture

value: Free-serum (Surge SFM medium)

tag: donor age

tag: donor sex


title: SM-GE67B_S045_E1-50

value: NeuN-positive

value: GABA


title: SM-GE8YP_S140_E1-50


title: Cell_Bank_cultured_human_keratinocytes_serum-free-medium_003_rep1

source_name: Primary human keratocytes (liposuction)

tag: cell type

value: F


title: SM-GE8YP_S135_E1-50

source_name: Macaque LGN Parvocellular


title: Dex+Ins_r2

description:
SM3039
Sample_3039
processed data file: RNAseq_RAW_CT_rat_hepa.txt

organism: Rattus norvegicus

source_name: primary hepatocyte

tag: strain

value: Sprague Dawley

tag: aav injection

value: non treated

value: Dexamethasone+insulin

tag: tissue/cell type

value: primary hepatocyte


title: Cell_Bank_cultured_human_keratinocytes_serum-medium_004_rep1

description: Gene expression of keratinocytes in passage 2, cultivated in medium with serum until they reached near-confluence in culture

value: With serum (DME-Ham medium)

value: M


title: SM-GE8YP_S134_E1-50

tag: donor

value: PC

value: Glut


title: 2705-7

tag: tissue

value: PBMC

tag: treatment

tag: Sex

value: Male


title: Dex+Ins_r3

description:
SM3040
Sample_3040
processed data file: RNAseq_RAW_CT_rat_hepa.txt


title: SM-GE67B_S046_E1-50

value: 2.3 yrs

value: MC

tag: facs gating

tag: sequencing batch


title: Cell_Bank_cultured_human_keratinocytes_serum-medium_001_rep1

source_name: Primary human keratocytes (mammary)

value: keratinocytes


title: 2702-7

value: Ctrl

tag: genotype

value: CW

value: Female


title: Ins_r3

description:
SM3037
Sample_3037
processed data file: RNAseq_RAW_CT_rat_hepa.txt

value: Insulin


title: Cell_Bank_cultured_human_keratinocytes_serum-medium_003_rep1

value: F


title: Cell_Bank_cultured_human_keratinocytes_serum-free-medium_001_rep1

value: Free-serum (Surge SFM medium)


title: Cell_Bank_cultured_human_keratinocytes_serum-medium_002_rep1

source_name: Primary human keratocytes (face-lift)


title: Ins_r1

description:
SM3035
Sample_3035
processed data file: RNAseq_RAW_CT_rat_hepa.txt

value: Sprague Dawley

value: non treated


title: SM-GE8YP_S132_E1-50

tag: age

value: 10 yrs

value: NeuN-positive

tag: cell class

tag: cell cluster

value: P


title: SM-GE8YP_S131_E1-50

value: PC

value: GABA


title: Dex+Ins_r1

description:
SM3038
Sample_3038
processed data file: RNAseq_RAW_CT_rat_hepa.txt

value: Dexamethasone+insulin

value: primary hepatocyte


title: 2708-L

value: PBMC

tag: timepoint

value: L

value: CM

value: CHW


title: 2685-7

value: Male


title: 2700-7

value: Female


title: 2692-7

value: Ctrl

value: CW


title: SM-GE8YP_S128_E1-50

value: Glut


title: 2683-7

value: WT


title: 2689-7


title: 2686-7


title: Ins_r2

description:
SM3036
Sample_3036
processed data file: RNAseq_RAW_CT_rat_hepa.txt

value: Sprague Dawley

value: non treated

value: Insulin


title: SM-GE8YP_S130_E1-50

value: 10 yrs

value: PC

value: NeuN-positive

value: P


title: Dex_r3

description:
SM3034
Sample_3034
processed data file: RNAseq_RAW_CT_rat_hepa.txt

value: Dexamethasone

value: primary hepatocyte


title: Dex_r2

description:
SM3033
Sample_3033
processed data file: RNAseq_RAW_CT_rat_hepa.txt


title: SM-GE8YP_S133_E1-50


title: Dex_r1

description:
SM3032
Sample_3032
processed data file: RNAseq_RAW_CT_rat_hepa.txt


title: SM-GE8YP_S127_E1-50

value: GABA


title: 2720-6

description:
microRNA
MicroRNAseq library prep.
validation_mature_normalized_CPM.tsv

value: PBMC

value: HW


title: 2718-6

value: CM

value: CHW

value: Male


title: 2705-6

value: Ctrl


title: SM-GE8YP_S124_E1-50

value: Glut


title: 2709-6

value: Female


title: SM-GE8YP_S125_E1-50


title: SM-GE8YP_S126_E1-50


title: SM-GE8YP_S129_E1-50

value: Low Quality


title: Veh_r1

description:
SM3029
Sample_3029
processed data file: RNAseq_RAW_CT_rat_hepa.txt

value: Sprague Dawley

value: non treated

value: vehicle


title: Veh_r3

description:
SM3031
Sample_3031
processed data file: RNAseq_RAW_CT_rat_hepa.txt


title: Cell_Bank_cultured_human_keratinocytes_serum-free-medium_002_rep1

value: keratinocytes

tag: medium culture

value: Free-serum (Surge SFM medium)

tag: donor age

value: F


title: 2700-6


title: SM-GE8YP_S123_E1-50

value: 10 yrs

value: PC

value: NeuN-positive


title: 2692-6

value: PBMC

value: CW


title: SM-GE8YP_S121_E1-50

value: P