title: nBM_Mature_S5

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

institute: Karolinska Institute

data_processing:
The data were geenerated on either Illumina NextSeq 500 via 50-cycle v2 sequencing run.
Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). All raw sequence reads available in FastQ format were mapped to the human genome (hg19) using Tophat2 combining with Bowtie2.
All mapped counts to each gene were further calculated by FeatureCounts function from Subread package installed in R. Genes with Reads Per Kilobase of transcript per Million mapped reads (RPKM) values more than 0.1 were considered as being actively transcribed and proceeded to the analysis of Differential Gene Expression (DGE).
The normalized read counts assigned to each sample were generated by Deseq2 and used for unsupervised clustering.
The differentially expressed genes between CML and healthy controls in each subset were identified by adjusted P value (padj < 0.05) using Benjamini-Hochberg correction for multiple testing, together with thresholds at log2fold changes >1 (up-regulated) or <-1 (down-regulated).
Assembly: hg19
Supplementary files format and content: xlsx file; Matrix table with normarized gene counts for every gene and every sample in each subset, together with multiple testing results with Benjamini-Hochberg correction

source_name: mature stromal cells

extract_protocol:
Total RNA from freshly sorted endothelial cells, mesenchymal stem cells and mature stromal cells were extracted with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
cDNA library was prepared by using the Ovation® Ultralow Library Systems (L2DR-BC1-16, NuGEN Technologies, San Calros, CA)

tag: developmental stage

value: Healthy

value: Bone Marrow

value: CD44+ mature stromal cells


title: CML_Mature_S3

status: Public on Oct 01 2023

type: SRA

country: Sweden

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: Chronical Myeloid Leukemia

tag: tissue

tag: cell type


title: CML_Mature_S1


title: CRA_WB_92

city: Boston

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

country: USA

institute: Mass General Brigham

data_processing:
Alignment and QC was done using the COMPSRA (Li et al. 2020) pipeline, which is similar to BCBio.
miRNAs with less than five mapped reads in at least 50% of subjects were removed prior to analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file with log normalized counts of miRNA x Sample, including sample batch.

source_name: whole blood

extract_protocol:
Total RNA was isolated from archival whole blood samples using the miRNeasy kit (Qiagen, Germantown, MD) according to the manufacturer's instructions
Blockers for miRs 451a, 486-5p, and 92a were added prior to library construction. Small RNA-seq libraries were prepared using the NEXTFLEX Small RNA-Seq Kit v3. First, adapters were ligated to the 3′ and 5′ ends of the RNA. Reverse transcription was then carried out to generate cDNA from the ligated RNA.
Detailed information is available in LaBelle et al, J Mol Diagnostics, 2021

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex

value: M


title: nBM_Mature_S3


title: CML_Mature_S2


title: CRA_WB_93

value: yes


title: CML_Mature_S4


title: nBM_Mature_S4


title: nBM_Mature_S2


title: CRA_WB_91


title: CRA_WB_90

value: F


title: CRA_WB_89


title: nBM_Mature_S1


title: CRA_WB_9


title: CRA_WB_88


title: CRA_WB_87


title: CML_MSC_S4

source_name: Mesenchymal Stem Cells

value: CD44- Mesenchymal Stem Cells(MSC)


title: CML_MSC_S5


title: CML_MSC_S3


title: CRA_WB_85


title: CML_MSC_S2


title: CRA_WB_83


title: CRA_WB_82


title: CML_MSC_S1


title: nBM_MSC_S5


title: nBM_MSC_S4


title: CRA_WB_81


title: nBM_MSC_S3


title: nBM_MSC_S1


title: CRA_WB_78


title: CRA_WB_8


title: CRA_WB_80


title: CRA_WB_79


title: nBM_MSC_S2


title: CML_EC_S5

source_name: Endothelial Cells

value: CD31+ Endothelial Cells (EC)


title: CRA_WB_77


title: CRA_WB_75


title: CRA_WB_76


title: CRA_WB_74


title: CML_EC_S4


title: CML_EC_S1


title: CRA_WB_73


title: nBM_EC_S6


title: CRA_WB_72


title: CRA_WB_84


title: CML_EC_S2


title: CRA_WB_71


title: nBM_EC_S5


title: nBM_MSC_S6


title: nBM_EC_S4


title: nBM_EC_S3


title: CRA_WB_7


title: CRA_WB_70


title: CML_EC_S3


title: nBM_EC_S1


title: CRA_WB_69


title: CRA_WB_68


title: CRA_WB_66


title: CRA_WB_65


title: CRA_WB_64


title: CRA_WB_67


title: CRA_WB_63


title: CRA_WB_61


title: MemoryB Basal

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell sequencing data was processed using the Cellranger v6.0.1 (10x Genomics) pipeline and aligned to customized germline V and J gene references.
Assembly: Customized germline V and J gene references
Supplementary files format and content: Cell Ranger Loupe-formatted output

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen and lymph nodes

extract_protocol:
Memory B-cell fractions were enriched by magnetic positive selection according to the manufacturer’s protocol (Miltenyi Biotec, 130-095-838). Briefly, spleen and lymph nodes were gently homogenized and red blood cells were lysed in ACK lysis buffer (Lonza). The remaining cells were washed by PBS with 2%FBS. Thereafter, B cells were labeled with memory B cell biotin-antibody cocktail combined with anti-biotin microbeads. The enriched memory B cells were eluted and mixed with 25ug of Omicron RBD recombinant protein or 25ug of recombinant CD22 extracellular domain with his tag and incubated for 30mins on ice. After incubation, the complex was washed and respectively incubated with anti-his-APC antibody and anti-APC microbeads. The final antigen-specific B cells were eluted in PBS and stored on ice until use. For GPRC5D, the memory B cells were labeled with APC anti-mouse IgG1 and anti-mouse IgG2ab and incubated for 30mins on ice. After incubation, the complex was washed and incubated with anti-APC microbeads. The final IgG1 or IgG2ab positive B cells were eluted in PBS and stored on ice until use. Plasma B cells were collected by fragmenting and rinsing bone marrows with PBS containing 2% FBS. Non-plasma cells were labeled with a biotin-conjugated antibody cocktail combined with anti-biotin microbeads and separated using a magnetic rack according to the manufacturer’s protocol (Miltenyi Biotec, 130-092-530). Purified plasma B cells were eluted and sequentially incubated with CD138 microbeads for an additional 15 minutes at 4℃. The final CD138+ plasma B cells were eluted in PBS and stored on ice until use. PBMC cells were isolated from fresh whole blood by using SepMate-15 tubes with Lymphoprep gradient medium (StemCell Technologies) after centrifugation at 1200g for 20 minutes. Poured top layer solution that contained PBMCs from SepMate tubes to a new falcon tube and washed once with PBS+2%FBS, resuspended with PBS and stored on ice until use.
Cell suspension were normalized to 1000 cells/ml and loaded to achieve targeted cell recovery to 10000 cells. The samples were subjected to 14 cycles of cDNA amplification. Following this, BCR-enriched libraries were prepared according to the manufacturer’s protocol (10x Genomics). All libraries were sequenced using a Miseq (Illumina) with 26X91 read length.
scVDJ-seq

value: Spleen and lymph nodes

value: Memory B cell

tag: genotype

value: human IgG and IgK knock-in

tag: treatment

value: Non-treatment


title: CRA_WB_62


title: MemoryB CD22

description: 10x Genomics

tag: agent

value: single transmembrane protein CD22

value: four dose of 10μg and one dose of 20 ug


title: PlasmaB Basal

description: 10x Genomics

source_name: Bone marrows

value: Bone marrows

value: Plasma B cell


title: PBMC  B.1.1.529 SARS-CoV-2

description: 10x Genomics

source_name: Peripheral Blood

value: Peripheral Blood

value: B.1.1.529 SARS-CoV-2 spike

value: Peripheral blood mononuclear cell


title: PlasmaB  B.1.1.529 SARS-CoV-2

description: 10x Genomics


title: CRA_WB_6

value: whole blood


title: MemoryB  B.1.1.529 SARS-CoV-2

description: 10x Genomics


title: CRA_WB_58

value: no

value: M


title: CRA_WB_60

value: yes


title: AC16_DDX41 KO_MEF2A_JD12

city: Columbus

first: Adriana

last: Forero

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence Partek Flow
Trimmed sequence reads were mapped to hg38  using Partek Flow
Read count extraction and normalization were performed using HT-seq on Partek Flow
Assembly: hg38
Supplementary files format and content: HT-seq derived count matrix

extract_protocol:
RNA was harvested using Nuclespin RNA
RNA libraries for RNA-seq were prepared by Genewiz.

tag: cell line

value: DDX41 KO


title: OCI-AML3 cells treated with SCCRI025044 2

type: RNA

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

label: biotin

source_name: OCI-AML3 cell line

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: cell were treated for 72hrs before extraction

tag: gender

value: MALE


title: OCI-AML3 cells treated with SCCRI025044 1

label_protocol: In accordance with manufacturer's protocols


title: OCI-AML3 cells treated with DMSO 2

value: DMSO


title: nBM_EC_S2

value: Healthy

value: Bone Marrow

value: CD31+ Endothelial Cells (EC)


title: OCI-AML3 cells treated with DMSO 1


title: AC16_DDX41 KO_MEF2A_JD10


title: CRA_WB_55


title: AC16_DDX41 KO_Mock_JD9

value: Mock


title: AC16_DDX41 KO_Mock_JD8


title: AC16_DDX41 KO_MEF2A_JD11


title: CRA_WB_53

value: F


title: CRA_WB_52


title: AC16_DDX41 KO_Mock_JD7


title: CRA_WB_59


title: MemoryB GPRC5D

description: 10x Genomics

value: Spleen and lymph nodes

value: single transmembrane protein GPCR GPRC5D

value: Memory B cell

value: human IgG and IgK knock-in

value: four dose of 10μg and one dose of 20 ug


title: CRA_WB_56

value: whole blood


title: AC16_WT_MEF2A_JD6

value: WT


title: CRA_WB_51

value: no

value: M


title: AC16_WT_Mock_JD2


title: AC16_WT_MEF2A_JD5


title: AC16_WT_Mock_JD3


title: CRA_WB_49

value: yes


title: CRA_WB_5


title: CRA_WB_48


title: CRA_WB_50


title: AC16_WT_MEF2A_JD4


title: CRA_WB_57


title: AC16_WT_Mock_JD1


title: ESCC cells, shYY1_2

city: Jinan

first: chunyan

last: zheng

address: Jiyan Road

country: China

institute: Shandong Cancer Hospital and Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: ESCC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in incubator with 5% CO2 at 37C

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Knocking down expression of YY1 using shRNA,and selected the stably cells using puromycin, and verifying the deficiency using RT-qPCR and WB.

value: Human-derived ESCC cells

value: YY1 knockdown


title: CRA_WB_47


title: CRA_WB_54


title: CRA_WB_46


title: ESCC cells, shYY1_1


title: ESCC cells, shNC_2

value: Negative control


title: CRA_WB_44


title: CRA_WB_45


title: ESCC cells, shNC_1


title: CRA_WB_43


title: CRA_WB_42


title: NC04_Cal33_JQ1_1uM_8_13

first: Srinivas Vinod

last: Saladi

state: Massachusetts

address: 20 Staniford St

institute: Harvard Medical School

data_processing:
Paired-end fastq files were trimmed of adapter sequence and aligned using Tophat v2.1.1
Reads were counted in each gene using htseq-count and normalized to each sample's total counts
RNA expression log2 fold change was calculated between JQ-treated sample and DMSO-treated sample.
Assembly: hg19 assembly
Supplementary files format and content: txt

source_name: Squamous cell carcinoma of the oral tongue

growth_protocol: CAL33 was maintained in RPMI 1640 with 10% fetal bovine serum (FBS) and 100 units/ml antibiotic antimycotic solution at 37 °C in the presence of 5% CO2

extract_protocol:
RNA was harvested by RNeasy Plus Mini Kit (Cat#74134, QIAGEN) according to the manufacturer’s instructions.
The library construction following the instructions of NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: CAL33 was treated by DMSO or JQ1 (1µM)(Sigma-Aldrich) for 24 hrs.

value: tongue squamous cell carcinoma

value: FAT1 mutant

value: JQ1 1uM


title: NC02_Cal33_1uM_JQ1_5_20

value: Squamous cell carcinoma of the oral tongue


title: CRA_WB_41


title: NC01_Cal33_con_5_20

value: DMSO


title: CRA_WB_40

value: F


title: CRA_WB_4


title: CRA_WB_38


title: CRA_WB_375


title: CRA_WB_39


title: CRA_WB_374


title: 18_CML56_24h_CTRL_S16

data_processing:
The data were generated on Illumina Illumina HiSeq 2000 via a 75-cycle v2 sequencing run.
Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). All raw sequence reads available in FastQ format were mapped to the human genome (hg19) using Tophat2 combining with Bowtie2.
All mapped counts to each gene were further calculated by FeatureCounts function from Subread package installed in R. Genes with Reads Per Kilobase of transcript per Million mapped reads (RPKM) values more than 0.1 were considered as being actively transcribed and proceeded to the analysis of Differential Gene Expression (DGE).
The normalized read counts assigned to each sample were generated by Deseq2 and used for unsupervised clustering.
The differentially expressed genes between CML and healthy controls in each subset were identified by adjusted P value (padj < 0.05) using Benjamini-Hochberg correction for multiple testing, together with thresholds at log2fold changes >1 (up-regulated) or <-1 (down-regulated).
Assembly: hg19
Supplementary files format and content: xlsx file; Matrix table with normarized gene counts for every gene and every sample in each subset, together with multiple testing results with Benjamini-Hochberg correction

source_name: CML CD34+CD38- cells

growth_protocol: CD34+CD38- cells were sorted from bone marrow of patients with CML at diagnosis and then stimulated with conditioned media derived from CXCL14-overexpressed NIH3 cells or control NIH3 cells for 6hours and 24hours. The cells were then collected into lysis buffer for RNA extraction

extract_protocol:
Total RNA from freshly sorted endothelial cells, mesenchymal stem cells and mature stromal cells were extracted with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio. Cat. No. 634898).
The cDNA quality was examined on Agilent TapeStation system using a High Sensitivity D5000 ScreenTape (Agilent, Cat. No. 5067-5592). One ng cDNA was used for library preparation using Nextera XT DNA Library Preparation Kit (Illumina, Cat. Nos. FC-131-1024 & FC-131-1096). ). The yield and quality of the amplified libraries were analyzed using Qubit by Thermo Fisher and the Agilent Tapestation System. The indexed cDNA libraries were sequenced on the Illumina 2000 or Nextseq 550 (Illumina, San Diego, CA) for a 75-cycle v2 sequencing run generating 75 bp single-end reads.

value: CML CD34+CD38- cells

tag: time point


title: CRA_WB_372


title: 15_CML56_6h_CXCL14_S14


title: CRA_WB_373


title: 17_CML56_6h_CTRL_S15


title: 13_CML62_24h_CTRL_S12


title: 14_CML56_0h_S13


title: 12_CML62_24h_CXCL14_S11


title: 11_CML62_0h_S10


title: CRA_WB_371


title: CRA_WB_369


title: 6_CML59_0h_S6


title: 9_CML59_6h_CTRL_S9


title: 7_CML59_6h_CXCL14_S7


title: NC03_Cal33_con_8_13


title: CRA_WB_368


title: 5_CML72_24h_CTRL_S5


title: CRA_WB_366


title: 4_CML72_6h_CTRL_S4


title: CRA_WB_365


title: 3_CML72_24h_CXCL14_S3


title: CRA_WB_364


title: 2_CML72_6h_CXCL14_S2


title: CRA_WB_362


title: CRA_WB_363


title: CRA_WB_360


title: CRA_WB_370


title: 8_CML59_24h_CXCL14_S8


title: CRA_WB_361


title: CRA_WB_36


title: CRA_WB_367


title: CRA_WB_359


title: 2nd_H11_39bx

first: Seungkyu

last: Lee

address: 3 Blackfan circle, CLS bldg. #12260

department: Neurobiology Dept.

institute: Boston Children's Hospital

description:
2nd_genes.count_table
2nd_genes.fpkm_table

data_processing:
The data was demultiplexed and aligned to the human genome (hg19) using Tophat version 2.0.10
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1
Raw counts of reads mapped per gene were extracted from aligned bam Feature Counts (subread-1.5.0-p1)
Genome_build: hg19
Supplementary_files_format_and_content: read count table, fpkm table, run information, sample table

source_name: iPSC-derived motor neurons

growth_protocol: iPSC were differentiated for 24 days with initial neuralization with SB431542 (10 μM, Sigma Aldrich) and Dorsomorphin (1 μM, Stemgent), and motor neuron patterning with retinoic acid (1 μM, Sigma) and a small smoothened Agonist 1.3 (1 μM, Calbiochem). Differentiated motor neuron were dissociated using accutase, then filtered with a 70 µm filter and motor neurons, subsequently, isolated by activated flow cell sorting using HB9::GFP expression. Motor neurons were plated in the presence of P0 mouse glial cells and were maintained in Neurobasal media, supplemented with N2 and B27 (Invitrogen), 10 ng/mL each of BDNF, GDNF, CNTF (R&D) and ascorbic acid (0.4 μg/ml, Sigma) and fed every 2-3 days.

extract_protocol:
Total RNA from single cells was purified using RNA-SPRI beads. Poly(A)+ mRNA was converted to cDNA and amplified.
Poly(A)+ mRNA was converted to cDNA and amplified. cDNA was subjected to transposon-based fragmentation using dual-indexing to barcode each transcript fragment with a combination of barcodes specific to a single cell. Barcoded cDNA fragments were then pooled for sequencing.

value: SOD1 A4V

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_H10_39bc

tag: genotype

value: SOD1 WT

tag: batch

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)


title: 2nd_H08_39bx

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)


title: 2nd_H09_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - freq1st5

tag: electrophysiology - serial resistance (mω)


title: 2nd_H07_39bx

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: 1_CML72_0h_S1

tag: cell type

tag: treatment

tag: time point


title: Day 28 - 2

city: Frankfurt am Main

first: Urs

last: Christen

address: Theodor-Stern Kai 7

department: Pharmacenter

country: Germany

institute: Goethe University Frankfurt

description: Gene expression data from islets of RIP-LCMV mice at day 28 after infection

hyb_protocol: Microarray hybridization to GeneChip Mouse Gene 1.0 ST V1 arrays (Affymetrix), washing steps, and scanning of the microarrays were performed according to the Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Applied Biosystems GeneChip™ Scanner 3000 7G.

data_processing:
Data were filtered with an intensity filter (above 100 in at least 0.5 percent of the samples, if the group size is equal) and a variance filter (interquartile range of log2 intensities of at least 0.3, if the group size is equal).
After intensity filtering p-values were calculated with the two-sample t-test (variance=equal) to identify differentially expressed genes between two groups.
For the multiple testing problems, a False Discovery Rate (FDR) was used. Also, Fold Changes (FC) between the two groups were calculated for each gene. The lists of differentially expressed genes were filtered with p-value and FC criteria

source_name: RIP-LCMV-GP mouse islets - Day 28 after infection

label_protocol: The total RNA (input: 20ng) amplification and cDNA labelling was done using standardized protocols (Ovation Pico WTA System V2 amplification kit and Encore Biotin Module labelling kit from NuGEN).

extract_protocol: Islet tissue was collected in 0.5 ml soft tubes (Biozym) containing RTL lysis buffer (Qiagen) containing 1% β-mercaptoethanol and RNA extraction was performed using a RNeasy Micro Kit (Qiagen)

treatment_protocol:
RIP-LCMV-GP mice were infected with 5x10e4 pfu LCMV stain Armstrong (i.p. in RPMI)
The islet microenvironment (islet and infiltrating immune cells) was isolated from pancreas sections using a laser-dissection microscope

tag: strain

tag: tissue

value: Laser-dissected islet microenvironment

tag: genotype

value: RIP-LCMV-GP


title: CRA_WB_357

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: 2nd_H12_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - freq1st5

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_358

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: M


title: Day 28 - 3

tag: strain

tag: genotype


title: Day 28 - 1


title: Day 28 - 4


title: 2nd_H06_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CRA_WB_356

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_355


title: Day 14 - 4

description: Gene expression data from islets of RIP-LCMV mice at day 14 after infection

source_name: RIP-LCMV-GP mouse islets - Day 14 after infection

tag: strain

tag: genotype


title: 2nd_H05_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Day 10 - 5

description: Gene expression data from islets of RIP-LCMV mice at day 10 after infection

source_name: RIP-LCMV-GP mouse islets - Day 10 after infection

tag: strain

tag: tissue

tag: genotype


title: Day 10 - 4


title: Day 10 - 3


title: CRA_WB_354

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex


title: 2nd_H03_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CRA_WB_353

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 2nd_H02_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_352

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Day 14 - 1

tag: strain

tag: genotype


title: 2nd_H01_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Day 7 - 3

description: Gene expression data from islets of RIP-LCMV mice at day 7 after infection

source_name: RIP-LCMV-GP mouse islets - Day 7 after infection

tag: strain

tag: tissue

tag: genotype


title: Day 7 - 4


title: Day 14 - 3


title: CRA_WB_351

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Day 10 - 2


title: 2nd_H04_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_350

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Day 14 - 2

tag: strain

tag: genotype


title: Day 3 - 2

description: Gene expression data from islets of RIP-LCMV mice at day 3 after infection

source_name: RIP-LCMV-GP mouse islets - Day 3 after infection


title: Day 7 - 1


title: Day 1 - 3

description: Gene expression data from islets of RIP-LCMV mice at day 1 after infection

source_name: RIP-LCMV-GP mouse islets - Day 1 after infection


title: 2nd_G12_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Day 3 - 3

tag: strain

tag: tissue

tag: genotype


title: Day 1 - 2


title: Day 3 - 1


title: Day 10 - 1


title: Day 7 - 2


title: 2nd_G11_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_35

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Day 0 - 6

description: Gene expression data from islets of uninfected RIP-LCMV mice

source_name: RIP-LCMV-GP mouse islets - Uninfected

tag: strain

tag: genotype


title: 2nd_G10_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Day 0 - 4

tag: strain

tag: tissue

tag: genotype


title: Day 0 - 5


title: CRA_WB_348

source_name: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 2nd_G08_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_G09_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Day 0 - 3

tag: strain

tag: tissue


title: Day 0 - 2

tag: genotype


title: 2nd_G07_39bx

tag: batch

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_346

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_347


title: CRA_WB_344


title: 2nd_G05_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Day 1 - 1

tag: strain

tag: tissue

tag: genotype


title: Day 0 - 1


title: 2nd_G04_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - freq1st5

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_345

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_349


title: CRA_WB_343


title: OFT-RV, mutant, biological rep4 (mRNA)

city: Bronx

first: Silvia

middle: Elisa

last: Racedo

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: Gene expression data from E9.5 OFT-RV

hyb_protocol: A total of 3.8 mg of cDNA from the last step was hybridized to the Affymetrix Mouse GeneST 1.0 or miRNA 4.0 chip. Hybridization, washing, staining and scanning were performed in the Genomics Core at Einstein (https://www.einstein.yu.edu/research/shared-facilities/cores/46/genomics/) according to the Affymetrix manual.

scan_protocol: Scanning were performed in the Genomics Core at Albert Einstein College using Genechip G7 scanner.

data_processing: Data analysis was performed in the R statistical package. GeneChip data were pre-processed by the ‘oligo’ package (PMID: 20688976), which implements Robust Multichip Average (RMA) algorithm with background correction, quantile normalization and gene level summarization (PMID: 12925520).

source_name: OFT-RV, mutant

label_protocol: The sense-strand cDNA was amplified and converted from 100 nanograms (ng) starting total RNA using Ambion WT Expression Kit.

growth_protocol: Embryos at E9.5 (19 - 21 somite pairs) were used for quentitative gene expression studies of microdissected anterior second heart field and outflow tract with the right ventricle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions-miRNeasy Mini Kit QIAGEN 217004.

treatment_protocol: Embryos were isolated on embryonic day E9.5 and immediate processed for microdissection of aSHF and OFT-RV tissues following by fast freezing at -80C. After multiple litter collections and genotyping, the tissues were pooled according to genotype for total RNA extraction.

value: OFT-RV

tag: genotype

value: Mef2c-AHF-Cre/+; Dgcr8 f/f

tag: developmental stage

value: embryonic day E9.5


title: OFT-RV, mutant, biological rep1 (mRNA)

description: Gene expression data from E9.5 OFT-RV


title: OFT-RV, mutant, biological rep2 (mRNA)

description: Gene expression data from E9.5 OFT-RV


title: OFT-RV, wild-type, biological rep4 (mRNA)

description: Gene expression data from E9.5 OFT-RV

source_name: OFT-RV, wild-type

value: Dgcr8 f/+


title: OFT-RV, mutant, biological rep3 (mRNA)

description: Gene expression data from E9.5 OFT-RV


title: aSHF, mutant, biological rep4 (mRNA)

description: Gene expression data from E9.5 aSHF

source_name: aSHF, mutant

value: aSHF


title: OFT-RV, wild-type, biological rep3 (mRNA)

description: Gene expression data from E9.5 OFT-RV


title: aSHF, mutant, biological rep2 (mRNA)

description: Gene expression data from E9.5 aSHF


title: 2nd_G06_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CRA_WB_342

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: F


title: OFT-RV, wild-type, biological rep1 (mRNA)

description: Gene expression data from E9.5 OFT-RV

tag: genotype

tag: developmental stage


title: aSHF, mutant, biological rep3 (mRNA)

description: Gene expression data from E9.5 aSHF


title: aSHF, mutant, biological rep1 (mRNA)

description: Gene expression data from E9.5 aSHF


title: 2nd_G03_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_G02_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: 2nd_G01_39bx

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3


title: CRA_WB_340

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_339


title: aSHF, wild-type, biological rep3 (mRNA)

description: Gene expression data from E9.5 aSHF

source_name: aSHF, wild-type

tag: genotype

tag: developmental stage


title: aSHF, wild-type, biological rep2 (mRNA)

description: Gene expression data from E9.5 aSHF


title: 2nd_F12_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_F11_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3


title: 2nd_F10_39bc

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CD4Cre_CD8_mouse5

city: Berlin

first: Francis

middle: G

last: Baumgartner

address: Hindenburgdamm 30

institute: Charité University Medicine Berlin

data_processing:
Illumina adapter clipping with cutadapt v3.4
Quality trimming with trimmomatic v0.39, mode MAXINFO, target read length 75, strictness 0.5
Transcript quantification with salmon v1.5.2, with gcBias correction, with seqBias correction
Generation of a gene count matrix with tximport v1.20.0, countsFromAbundace = lengthScaledTPM
Minimum expression filtering and normalization with edgeR v3.34.1, filtering with filterByExpr function, TMM normalization with calcNormFactors, conversion to counts per million with cpm function
Assembly: GRCm38, Ensembl release 97
Supplementary files format and content: Tab-delimited text file with isoform identifiers, raw counts and transcripts per million as output by salmon (“quant.sf” file)
Supplementary files format and content: Tab-delimited text file with raw gene counts for each gene per sample
Supplementary files format and content: Tab-delimited text file with normalized gene counts for each gene per sample (counts per million, TMM normalized)

source_name: Spleen

extract_protocol:
Splenocytes of Lgp and CD4Cre mice were collected by smashing the spleens through 100μM cell strainers, incubating in erythrolysis buffer, and passing through 40μM cell strainers for single cell suspension. CD4+ T-cells were isolated through a positive selection using CD4-directed magnetic beads (Miltenyi Biotec) according to the company’s protocols for open procedures. CD8+ T-cells were isolated by negative magnetic enrichment using the EasySep Mouse CD8+ T-cell isolation kit (STEMCELL Technologies) according to manufacturer’s instructions. . RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). RNA concentration was determined with a Nanodrop spectrophotometer. Only RNA samples with an RNA integrity number (RIN) > 7 were used for RNA sequencing. RNA quality was assessed with Agilent RNA 6000 Pico Kit according to the manufacturer’s instructions in the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
Library preparation and paired-end, unstranded, 150 bp sequencing for all samples was performed by Novogene (Cambridge, UK).

tag: strain

tag: tissue

value: Spleen

tag: age

value: post natal day 35

tag: genotype

tag: Sex

value: male

tag: cell type

value: Purified CD8+ T-cells


title: CD4Cre_CD8_mouse6

value: female


title: CD4Cre_CD8_mouse4


title: CRA_WB_337

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: 2nd_F09_39bc

value: SOD1 WT

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: aSHF, wild-type, biological rep1 (mRNA)

description: Gene expression data from E9.5 aSHF

tag: tissue

tag: genotype

tag: developmental stage


title: CD4Cre_CD8_mouse2

tag: strain

tag: age

tag: Sex

tag: cell type


title: CD4Cre_CD8_mouse3


title: CRA_WB_336

value: whole blood

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: 2nd_F08_39bx

value: SOD1 A4V

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Lgp_CD8_mouse3

tag: strain

tag: tissue

tag: age

tag: genotype

tag: Sex

tag: cell type


title: aSHF, wild-type, biological rep4 (mRNA)

description: Gene expression data from E9.5 aSHF

tag: developmental stage


title: 2nd_F07_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_335

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex

value: M


title: Lgp_CD8_mouse1

tag: strain

tag: genotype

tag: cell type


title: CRA_WB_34


title: CD4Cre_CD4_mouse6

value: Purified CD4+ T-cells


title: CRA_WB_338

value: yes


title: CRA_WB_341


title: CD4Cre_CD8_mouse1


title: CRA_WB_333


title: CD4Cre_CD4_mouse4


title: CD4Cre_CD4_mouse2


title: CRA_WB_332


title: 2nd_F04_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CD4Cre_CD4_mouse1

tag: strain

tag: tissue

tag: age

tag: genotype

tag: Sex

tag: cell type


title: Lgp_CD4_mouse6


title: CD4Cre_CD4_mouse3


title: CRA_WB_331

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: 2nd_F06_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Lgp_CD4_mouse4

tag: strain

tag: tissue

tag: age

tag: genotype

tag: Sex

tag: cell type


title: Lgp_CD4_mouse2


title: 2nd_F02_39bc

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CRA_WB_33

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Lgp_CD4_mouse1

tag: strain

tag: genotype

tag: cell type


title: Lgp_CD4_mouse5


title: Lgp_CD4_mouse3


title: 2nd_E12_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_F01_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CRA_WB_334

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex


title: CRA_WB_329

tag: batch


title: CD4Cre_CD4_mouse5

tag: strain

tag: genotype

tag: cell type


title: SM_HFSC_KO_4

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt with raw counts

source_name: skeletal muscle

extract_protocol:
Trizol (Invitrogen) was used for RNA isolation from white adipose tissue.
PolyA selection

treatment_protocol: RNA-sequencing on skeletal muscle of systemic miR-181a2b2 KO mice in response to chow and HFSC diet feeding and hindlimb ischemia

tag: diet

value: HFSC


title: 2nd_F05_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: SM_HFSC_KO_3

tag: genotype

tag: diet


title: 2nd_E11_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: SM_HFSC_KO_2

tag: genotype


title: 2nd_F03_39bc

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_327

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_328


title: SM_HFSC_WT_3

tag: genotype

value: miR-181a2b2flox/flox (flox)

tag: diet


title: SM_HFSC_WT_2


title: CRA_WB_330

value: F


title: Adultmarmoset_Per1CD90_S1

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: Callithrix jacchus-3.2
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

molecule: nuclear RNA

organism: Callithrix jacchus

source_name: Retina

extract_protocol:
Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. They were dissociated in papain, followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors.
Single cell libraries were generated using the Chromium 3’ V3 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single cells were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single cell RNA sequecning (10X Genomics)

value: Retina

tag: cell line

tag: cell type

value: Retinal neurons


title: 2nd_E09_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Adultmarmoset_Per1CD73dp_S2

tag: tissue

tag: cell line

tag: cell type


title: 2nd_E08_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: SM_HFSC_WT_1

tag: genotype

tag: diet


title: CRA_WB_325

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: SM_CHOW_KO_3

value: CHOW


title: CRA_WB_326


title: 2nd_E07_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Adultmarmoset_Per1CD73dp_S1

tag: tissue

tag: cell line

tag: cell type


title: SM_CHOW_KO_2

tag: genotype

tag: diet


title: SM_CHOW_KO_1


title: CRA_WB_323

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 2nd_E06_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_324

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Adultmarmoset_Fovea_2S1

tag: cell line

tag: cell type


title: 2nd_E05_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: Adultmarmoset_Fovea_2S2

tag: tissue

tag: cell line

tag: cell type


title: SM_HFSC_WT_4

tag: genotype

tag: diet


title: SM_CHOW_WT_4


title: CRA_WB_321

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_322


title: 2nd_E10_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Adultmarmoset_Fovea_1S3

tag: tissue

tag: cell line

tag: cell type


title: CRA_WB_320

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 2nd_E03_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: 2nd_E04_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: SM_CHOW_WT_3

tag: diet


title: 2nd_E02_39bc

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)


title: SM_CHOW_WT_2

tag: genotype


title: Adultmarmoset_Fovea_1S2

tag: tissue

tag: cell line

tag: cell type


title: 2nd_E01_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CHOW_KO_4

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: cvs with raw counts

source_name: bone marrow

treatment_protocol: RNA-sequencing on bone marrow cells after chow diet feeding and hindlimb ischemia

tag: genotype

tag: diet

value: chow


title: CRA_WB_32

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: SC19, Anaerobic, rep3

city: Wuhan,Hubei

first: Hao

last: Tang

address: Shizishan Street 1

institute: Huazhong Agriculture University

description: streptococcus suis serovar 2 str. SC19(firmicutes)

data_processing:
Quality control of the high-quality RNA-seq data, read mapping, and gene expression quantification were performed using the "fastp," "STAR," and "RSEM" packages, respectively.
Analysis of differentially expressed genes (DEGs) was conducted using the "DESeq2" R package (), considering genes with q-value < 0.05 and |Log2FC| > 1 as significantly differentially expressed genes (SDEGs).
Assembly: Streptococcus suis SC19 (ASM211140v1)
Supplementary files format and content: The txt files include the reads counts and TPM values for each sample

organism: Streptococcus suis

source_name: Bacteria

growth_protocol: Strain SC19 was cultured to late-log phase at 37°C in hypoxia or in normoxia.

extract_protocol:
Total RNA from the samples was extracted using the RNA Isolation Kit (Tianmo Biotech, China).
Illumina PE RNA libraries for RNA-seq were prepared using IlluminaTruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: Cultured in hypoxia or in normoxia.

value: Bacteria

tag: cell line

value: streptococcus suis serovar 2

tag: cell type

value: str. SC19

value: wild type

tag: treatment

value: cultured in hypoxia with shaking


title: Adultmarmoset_Fovea_1S1


title: CRA_WB_319

value: whole blood


title: SC19, Anaerobic, rep1


title: CHOW_KO_2


title: CRA_WB_318

value: no


title: SC19, Anaerobic, rep2


title: 2nd_D12_39bc

source_name: iPSC-derived motor neurons

value: SOD1 WT

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: 2nd_D11_39bx

tag: genotype

value: SOD1 A4V

tag: batch

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CHOW_KO_1

tag: diet


title: SC19, Aerobic, rep2

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: cultured in normoxia with shaking


title: 2nd_D10_39bc

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency


title: CRA_WB_316

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: F


title: CHOW_WT_2

tag: genotype

value: miR-181a2b2flox/flox (flox)

tag: diet


title: CHOW_WT_3


title: 2nd_D09_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: SC19, Aerobic, rep3

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 2nd_D08_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency


title: CRA_WB_313

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: CRA_WB_317


title: CRA_WB_315


title: 2nd_D07_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_314

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: SC19, Aerobic, rep1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 2nd_D06_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol


title: CHOW_WT_1

tag: genotype

tag: diet

value: chow


title: Niclosamide treated SARS CoV-2 Vero E6 infected samples at 48 hours rep2

city: Gainesville

first: Rhoel

last: Dinglasan

state: Florida

address: 2055 Mowry Rd

institute: University of Florida

data_processing:
Sequenced reads were trimmed for adaptor sequences, <20 nucleotide reads and low-quality reads. RNA STAR v2.7.7a  was used to map samples to the Chlorocebus sabaeus genome and associated annotation (GenBank accession # GCA_015252025.1). feature-Counts v 2.0.1  was used to sum reads for each gene. Read counts for each sample were input into DESeq2 v 1.22.1 to call differential gene ex-pression, analyzing the effect of time, drug, and virus on the samples.
Genome_build: GenBank accession # GCA_015252025.1
Supplementary_files_format_and_content: tab-delimited text files including read counts for each gene

organism: Chlorocebus sabaeus

source_name: Vero E6 cells

extract_protocol:
Cell pellets were resuspended in 1mL Trizol, 200 µL chloroform was added to each sample, and samples were mixed thoroughly by vortexing, then incubated at room temperature for 3 minutes. Samples were centrifuged at 12,000xg for 15 minutes at 4°C. The upper aqueous layer was transferred to a new tube and 500 µL isopropanol was added and mixed by vortex-ing, prior to incubation at room temperature for 10 minutes. RNA was pelleted by centrifuging at 12,000 xg for 10 minutes at 4°C, and supernatant was discarded. The pellet was rinsed in 75% ethanol and pelleted by centrifuging at 7,500xg for 5 minutes at 4°C. Ethanol wash and spin were repeated a second time. The pellet was air dried in an inverted tube. Genomic DNA was digested using the TURBO DNA-free™ Kit (Invitrogen #AM1907) according to manufac-turer instructions. Samples were mixed with 350 µL buffer RLT from the RNeasy® Mini kit (Qi-agen #74104) and 250 µL 100% ethanol, then transferred to a RNeasy® Mini kit spin column. Columns were centrifuged at 8,000xg for 15 seconds at room temperature, and flow-through was discarded. Buffer RPE (500 µL) was added to the column, which was centrifuged at the same conditions, and flow-through was discarded. The RPE wash was repeated a second time. The column was transferred to a fresh collection tube and centrifuged at 12,000 xg for 1 min to dry. RNA was eluted by adding 50 µL of nuclease free water and centrifuging for 1 mi-nute at 8,000xg.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Vero E6 cells

tag: treatment

value: Niclosamide

tag: time point

value: 48 hrs


title: Niclosamide treated SARS CoV-2 Vero E6 infected samples at 48 hours rep3


title: HFSC_KO_4

treatment_protocol: RNA-sequencing on bone marrow cells after HFSC diet feeding and hindlimb ischemia

tag: strain

value: HFSC


title: CHOW_KO_3


title: OFT-RV, wild-type, biological rep2 (mRNA)

description: Gene expression data from E9.5 OFT-RV

tag: tissue

value: OFT-RV

value: Dgcr8 f/+

tag: developmental stage

value: embryonic day E9.5


title: 2nd_D05_39bc

value: SOD1 WT

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_311

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: 2nd_D04_39bx

tag: genotype

value: SOD1 A4V

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - freq1st3


title: HFSC_WT_4

tag: strain

tag: diet


title: SARS CoV-2 Vero E6 infected samples at 48 hours rep3

tag: cell type

tag: treatment

tag: time point


title: HFSC_WT_1


title: Niclosamide treated SARS CoV-2 Vero E6 infected samples at 16 hours rep3

value: 16 hrs


title: CRA_WB_309

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: HFSC_KO_3


title: 2nd_D03_39bc

tag: genotype

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: HFSC_KO_2

tag: strain

tag: diet


title: 2nd_D01_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - freq1st3


title: CRA_WB_307

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex


title: Niclosamide treated SARS CoV-2 Vero E6 infected samples at 48 hours rep1

tag: cell type

tag: treatment

tag: time point


title: Niclosamide treated SARS CoV-2 Vero E6 infected samples at 16 hours rep2


title: CRA_WB_312

tag: batch


title: HFSC_WT_3

tag: strain

value: miR-181a2b2flox/flox (flox)

tag: diet


title: SARS CoV-2 Vero E6 infected samples at 48 hours rep2


title: 2nd_D02_39bx

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: SARS CoV-2 Vero E6 infected samples at 16 hours rep3

tag: cell type

tag: treatment

tag: time point


title: 2nd_C11_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol


title: 2nd_C10_39bc

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_C12_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5


title: CRA_WB_308

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex

value: F


title: CRA_WB_310

tag: batch

value: yes


title: CRA_WB_304

value: M


title: CRA_WB_305


title: 2nd_C09_39bx

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_302

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Niclosamide Vero E6 treated samples at 48 hours rep3

tag: cell type

value: Vero E6 cells

tag: treatment

value: E6 treated

tag: time point


title: SARS CoV-2 Vero E6 infected samples at 16 hours rep1


title: SARS CoV-2 Vero E6 infected samples at 16 hours rep2


title: Lgp_CD8_mouse2

tag: strain

value: Spleen

value: post natal day 35

tag: genotype

value: male

value: Purified CD8+ T-cells


title: CRA_WB_306


title: SARS CoV-2 Vero E6 infected samples at 48 hours rep1

value: 48 hrs


title: Niclosamide Vero E6 treated samples at 48 hours rep2


title: 2nd_C07_39bc

value: SOD1 WT

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5


title: CRA_WB_301

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 2nd_C06_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_C05_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency


title: Niclosamide Vero E6 treated samples at 48 hours rep1

tag: cell type

tag: treatment

tag: time point


title: Niclosamide Vero E6 treated samples at 16 hours rep3


title: CRA_WB_300

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

value: no

tag: Sex


title: CRA_WB_30

tag: batch


title: CRA_WB_303


title: CRA_WB_299


title: 2nd_C04_39bx

tag: genotype

value: SOD1 A4V

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_3

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Niclosamide Vero E6 treated samples at 16 hours rep2

tag: cell type

tag: treatment

tag: time point

value: 16 hrs


title: Niclosamide Vero E6 treated samples at 16 hours rep1


title: 2nd_C03_39bc

tag: genotype

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency


title: 2nd_C02_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Vero E6 vehicle samples at 48 hours rep3

tag: cell type

tag: treatment

value: vehicle

tag: time point


title: CRA_WB_297

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: F


title: CRA_WB_298


title: 2nd_C01_39bx

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency


title: Vero E6 vehicle samples at 48 hours rep1

tag: cell type

tag: treatment

tag: time point


title: Vero E6 vehicle samples at 48 hours rep2


title: Vero E6 vehicle samples at 16 hours rep3


title: 2nd_B12_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_B11_39bx

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency


title: Vero E6 vehicle samples at 16 hours rep2

tag: cell type

tag: treatment

tag: time point


title: CRA_WB_295

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex


title: 2nd_B10_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: CRA_WB_293

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_294

value: M


title: CRA_WB_296


title: Vero E6 vehicle samples at 16 hours rep1

tag: cell type

value: Vero E6 cells

tag: treatment

tag: time point


title: Vero E6 untreated samples at 0 hours rep3

value: untreated

value: 0 hr


title: 2nd_B09_39bx

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)