title: 2nd_B08_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

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 - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes


title: 2nd_B07_39bc

status: Public on Oct 01 2023

type: SRA

city: Boston

first: Seungkyu

last: Lee

state: MA

address: 3 Blackfan circle, CLS bldg. #12260

department: Neurobiology Dept.

country: USA

institute: Boston Children's Hospital

description:
2nd_genes.count_table
2nd_genes.fpkm_table

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

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 WT

value: Control

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 - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Vero E6 untreated samples at 0 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

molecule: total RNA

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: untreated

tag: time point

value: 0 hr


title: CRA_WB_29

first: Joanne

last: Sordillo

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

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

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: 2nd_B06_39bc

tag: genotype

tag: date

tag: div

tag: disease


title: Vero E6 untreated samples at 0 hours rep1


title: Exosc3_EpiLC_cKO_isoseq_Rep2

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads were imported into SMRTlink and IsoSeq3 software was used to obtain circular consensus sequences (CCS) for error correction, yielding highly accurate reads. Lima (v2.0.0) was subsequently used to remove barcodes, SMART-Seq primers and template-switching oligonucleotide sequences, further orienting isoforms in the correct 5’ to 3’ direction. Next, the refine command was used to remove poly(A) tails and concatamers. Reads were subsequently mapped to the mouse mm10 genome using minimap2 (v2.17) (Li, 2018) using the following parameters: -ax splice -uf -secondary=no -C5 –MD. Aligned reads were further filtered using sambamba (v0.5.7) (Tarasov et al., 2015), removing reads that are unmapped and have MAPQ < 50. Next, TranscriptClean (v.2.0.2) (Wyman and Mortazavi, 2019) as applied to correct long reads with mismatches, indels and noncanonical splice junctions not supported by spliced Illumina short reads identified from the STAR alignment described above. TALON (v5.0) (Wyman et al., 2020) was subsequently use to collapse the long reads into a novel reference transcriptome by using the talon_label_reads, talon_initialize_database, talon and talon_create_GTF commands, requiring isoforms to be at least 200bp long, and merging transcript models with matching internal splice sites but differing up to 1000bp at their 5’ or 3’ ends. Isoforms in the novel reference transcriptome were further required to have a minimum alignment threshold of 99%, a minimum sequence identity of 95%, a fraction of As ≤0.6 (removing internal priming artifacts), at least two supporting long reads, and at least one spliced short read overlapping each of the isoform’s junction in at least one short-read RNA-Seq sample. To produce a high quality reference transcriptome, isoform models classified as “incomplete splice match” or “genomic” by TALON were further discarded, as they are often products of transcript degradation or sequencing artifacts (Wyman et al., 2020).
Assembly: mm10
Supplementary files format and content: Reference transcriptome GTF; isoform counts TSV

organism: Mus musculus

source_name: EpiLC

extract_protocol:
For RNA extraction, cells were washed 3x with DPBS and lysed directly on the plate with 1mL of TRIzol reagent (Invitrogen, 15596026). Subsequently, RNA was purified using Direct-zol RNA Miniprep Plus Kits (Zymo, R2072) following manufacturer instructions. In brief, lysed cells in TRIzol were mixed 1:1 with 100% ethanol. Mixed lysates were added to the Zymo-spin columns, treated with DNase I, and washed with provided buffers. RNA was eluted with UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015). For complementary DNA synthesis, 100-200 µg of DNase I treated RNA was reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814). Random hexamers were used to capture total RNA.
Purified RNA was submitted to the Icahn School of Medicine Genomic Core facility for sequencing. Sequencing libraries were prepared using SMARTer PCR cDNA Synthesis Kit (Clontech, 634926) per manufacturer recommendations. OligodT primers were used to capture full-length polyadenylated transcripts. cDNA was then size selected and sorted into two bins of greater or less than 4kb. These bins were pooled together at equimolar concentrations using SMRTbell Template Preparation Kit v1.0. End repaired and purified libraries were loaded onto a SMRTcell 1M, which was then sequenced on a Sequel I system with a 10-hour movie.


title: CRA_WB_288

value: no

value: F


title: 2nd_B04_39bx

value: SOD1 A4V

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 - step_threshold (mv)

tag: electrophysiology - step_spikes


title: 2nd_C08_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_B05_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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - step_threshold (mv)


title: CRA_WB_292

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_287


title: Exosc3_EpiLC_cKO_isoseq_Rep1

tag: genotype


title: CRA_WB_286


title: 2nd_B03_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 - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Exosc3_EpiLC_CTRL_isoseq_Rep2

tag: genotype

value: CTRL


title: Exosc3_EpiLC_CTRL_isoseq_Rep1


title: CRA_WB_289

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 293FT_DOX-treated_10w

type: genomic

city: Tsukiji, Chuo-ku

first: Chihiro

last: Takeuchi

state: Tokyo

department: Division of Epigenomics

country: Japan

institute: National Cancer Center Research Institute

description:
Normal cells
293FT_DOX-treated_10w

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the standard phenol/chloroform method.

tag: cell line

tag: treatment

value: DOX

tag: timepoint


title: Exosc3_mESC_cKO_isoseq_Rep2

source_name: mESC


title: CRA_WB_285


title: HGEC6B_DOX-treated_10w

description:
Normal cells
HGEC6B_DOX-treated_10w


title: CRA_WB_284


title: 293FT_untreated_20w

description:
Normal cells
293FT_untreated_20w


title: 2nd_B01_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 - frequency

tag: electrophysiology - step_threshold (mv)


title: 2nd_B02_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 - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Gastric non-IM crypts_11

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_11

tag: Sex

value: Female

tag: age

tag: disease state

value: Gastric cancer


title: Gastric normal crypts

description:
Isolated gastric crypts without intestinal metaplasia
Normal

source_name: Normal

value: Gastrointestinal stromal tumor


title: HGEC6B_untreated_ 20w

description:
Normal cells
HGEC6B_untreated_ 20w

source_name: HGEC6B_untreated_ 20w

tag: cell line

tag: genotype

tag: treatment

tag: timepoint


title: 293FT_DOX-treated_20w

description:
Normal cells
293FT_DOX-treated_20w


title: CRA_WB_283

tag: tissue

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: Gastric non-IM crypts_8

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_8

value: Male


title: Exosc3_mESC_CTRL_isoseq_Rep2


title: Gastric non-IM crypts_9

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_9


title: 2nd_A12_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 - 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_A11_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: HGEC6B_untreated_0w

description:
Normal cells
HGEC6B_untreated_0w

tag: cell line

tag: treatment

tag: timepoint


title: 293FT_untreated_0w

description:
Normal cells
293FT_untreated_0w

tag: genotype


title: HGEC6B_DOX-treated_20w

description:
Normal cells
HGEC6B_DOX-treated_20w


title: Gastric non-IM crypts_10

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_10

tag: Sex

tag: age

tag: disease state


title: CRA_WB_281

tag: tissue

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: CRA_WB_282


title: 293FT_untreated_10w

description:
Normal cells
293FT_untreated_10w


title: Gastric non-IM crypts_4

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_4


title: Gastric non-IM crypts_2

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_2


title: Exosc3_mESC_cKO_isoseq_Rep1


title: 2nd_A09_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 - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)


title: CRA_WB_28

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Exosc3_mESC_CTRL_isoseq_Rep1

tag: genotype


title: 2nd_A10_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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_280

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 2nd_A08_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 - 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 - step_threshold (mv)


title: 2nd_A06_39bc

tag: genotype

tag: batch

tag: date

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_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Pig_NucNeunNChx10P_S3

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

description:
200207_H72KKCCX2_snSeq/pigNucNeunNChx10PS3
Pig_count_mat.csv

library_source: transcriptomic single cell

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: Sscrofa11.1
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: Sus scrofa domesticus

source_name: Retina

extract_protocol:
Frozen retinal tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with NEUN/RBFOX3 and/or CHX10/VSX2, washed once, pelleted at 500g for 5min, resuspended in PBS/BSA and stained with DAPI. NEUN+ and/or CHX10+ DAPI+ single nuclei were collected using a flow cytometer. The sorted nuclei were pelleted again, resuspended in PBS/BSA solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei 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 nucleus RNA sequecning (10X Genomics)

tag: tissue

value: Retina

tag: cell line

tag: cell type

value: Retinal neurons


title: 2nd_A07_39bc

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 - step_threshold (mv)


title: Gastric IM crypts_6

description:
Isolated gastric crypts with intestinal metaplasia
IM_6

tag: Sex

tag: age

tag: disease state


title: Small intestinal crypts

description:
Isolated gastric normal crypts
Small intestine

source_name: Small intestine

value: Neuroendocrine tumor


title: Pig_NucNeunP_S3

description:
200207_H72KKCCX2_snSeq/pigNucNeunPS3
Pig_count_mat.csv

tag: tissue

tag: cell line

tag: cell type


title: CRA_WB_277

value: whole blood

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes


title: HGEC6B_untreated_10w

description:
Normal cells
HGEC6B_untreated_10w

tag: genotype

tag: treatment

tag: timepoint


title: CRA_WB_278

value: M


title: 2nd_A05_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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_276

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Gastric non-IM crypts_3

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_3

tag: disease state


title: 2nd_A04_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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)


title: Pig_NucNeunPChx10N

description:
191216_H72LCCCX2/pigNucNeunPChx10N
Pig_count_mat.csv

tag: tissue

tag: cell line

tag: cell type


title: Pig_NucNeunP_S2

description:
200207_H72KKCCX2_snSeq/pigNucNeunPS2
Pig_count_mat.csv


title: CRA_WB_275

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: CRA_WB_274


title: Pig_NucNeunNChx10N

description:
191216_H72LCCCX2/pigNucNeunNChx10N
Pig_count_mat.csv


title: CRA_WB_273


title: Pig1_CD90_S2

description:
190503_HY25MCCXY/Pig1CD90S2
Pig_count_mat.csv


title: Gastric non-IM crypts_1

description:
Isolated gastric crypts without intestinal metaplasia
Non-IM_1

tag: disease state


title: 2nd_A01_39bx

description:
2nd_genes.count_table
2nd_genes.fpkm_table

tag: genotype

value: SOD1 A4V

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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Pig1_CD90_S1

description:
190503_HY25MCCXY/Pig1CD90S1
Pig_count_mat.csv

tag: tissue

tag: cell line

tag: cell type


title: CRA_WB_272

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 1st_H12_39bx

description:
1st_genes.count_table
1st_genes.fpkm_table

tag: genotype

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 - 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)


title: Pig1_CD73_dpS2

description:
190503_HY25MCCXY/Pig1CD73dpS2
Pig_count_mat.csv

tag: tissue

tag: cell line

tag: cell type


title: Pig_NucNeunNChx10P_S2

description:
200207_H72KKCCX2_snSeq/pigNucNeunNChx10PS2
Pig_count_mat.csv


title: 1st_H11_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Pig_NucNeunNChx10P

description:
191216_H72LCCCX2/pigNucNeunNChx10P
Pig_count_mat.csv

tag: tissue

tag: cell line

tag: cell type


title: Pig1_CD73_dpS1

description:
190503_HY25MCCXY/Pig1CD73dpS1
Pig_count_mat.csv


title: CRA_WB_270

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: F


title: CHIR99021+MTX-treated M-MØ macrophage donor3 rep3

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 5 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 5 days in RPMI 10% FBS containing M-CSF. 5 days later, fully-differentiated macrophages were exposed to DMSO, DMSO+MTX,  CHIR99021 and CHIR99021+MTX for 48 hours and total RNA was extracted.

tag: cell

value: Monocyte-derived M-CSF macrophages


title: CRA_WB_27


title: CRA_WB_271


title: 1st_H9_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 - 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)


title: CHIR99021+MTX-treated M-MØ macrophage donor2 rep2

tag: cell


title: 1st_H8_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 - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Gastric IM crypts_4

description:
Isolated gastric crypts with intestinal metaplasia
IM_4

tag: Sex

tag: age

tag: disease state


title: CRA_WB_269

tag: tissue

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: CRA_WB_268


title: CHIR99021+MTX-treated M-MØ macrophage donor1 rep1

tag: cell


title: 2nd_A03_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)


title: Gastric IM crypts_5

description:
Isolated gastric crypts with intestinal metaplasia
IM_5

tag: Sex

tag: age

tag: disease state


title: 1st_H7_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 - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CHIR99021-treated M-MØ macrophage donor3 rep3

tag: cell


title: CRA_WB_267

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 1st_H6_39bc

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)


title: CHIR99021-treated M-MØ macrophage donor2 rep2

tag: cell


title: CRA_WB_266

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CHIR99021-treated M-MØ macrophage donor1 rep1


title: 1st_H5_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 - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Gastric IM crypts_2

description:
Isolated gastric crypts with intestinal metaplasia
IM_2

tag: Sex

value: Female

tag: age

tag: disease state


title: CRA_WB_265

tag: tissue

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: 1st_H10_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 - halfwidth (ms)

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)


title: 1st_H4_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

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 - freq1st3

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 2nd_A02_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 - vupstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol


title: CRA_WB_264

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 1st_H3_39bx

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

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- 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: DMSO+MTX-treated M-MØ macrophage donor2 rep2

tag: cell


title: CRA_WB_263

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 1st_H2_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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - freq1st3


title: Gastric IM crypts_1

description:
Isolated gastric crypts with intestinal metaplasia
IM_1

tag: Sex

tag: age

tag: disease state

value: Gastric cancer


title: DMSO+MTX-treated M-MØ macrophage donor1 rep1

tag: cell


title: CRA_WB_262

tag: tissue

tag: height (cm)

tag: batch

tag: ics use_prior_year


title: 1st_H1_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 - voltage threshold (mv)

tag: electrophysiology - time to treshold (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: DMSO-treated M-MØ macrophage donor3 rep3

tag: cell


title: Proximal advanced adenomas cfDNA pool V

city: Vigo

first: María

last: Gallardo-Gómez

address: Campus As Lagoas Marcosende

institute: Universidad de Vigo

description:
Proximal advanced adenomas (P-AA) cfDNA pool V
P-AA_V

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Normalized beta values (ssNoob, single-sample normalization out-of-band method)

label: Cy3, Cy5

molecule: other

source_name: serum

label_protocol: Standard Illumina labelling protocol

extract_protocol: Circulating cell-free DNA was isolated from serum samples by a phenol-chloroform protocol

tag: pathology

value: P-AA

tag: sample type

value: serum

tag: molecule type

value: circulating cell-free DNA


title: Gastric IM crypts_3

description:
Isolated gastric crypts with intestinal metaplasia
IM_3

tag: Sex

value: Male

tag: age

tag: disease state


title: 1st_G12_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol


title: CRA_WB_260

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: DMSO-treated M-MØ macrophage donor2 rep2

tag: cell


title: Proximal advanced adenomas cfDNA pool X

description:
Proximal advanced adenomas (P-AA) cfDNA pool X
P-AA_X

tag: pathology

tag: sample type

tag: molecule type


title: DMSO+MTX-treated M-MØ macrophage donor3 rep3


title: DMSO-treated M-MØ macrophage donor1 rep1


title: CRA_WB_26


title: CRA_WB_261


title: 1st_G10_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 - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

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: Pgympsum_2

city: Athens

first: He

last: Fu

state: GA

address: 120 Cedar St

department: Microbiology

institute: University of Georgia

data_processing:
https://github.com/twbattaglia/RNAseq-workflow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore/0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4
Trimmed sequence reads were mapped to the genome of Cupriavidus using STAR/2.7.10a-GCC-8.3.0
Feature counts were performed using HTSeq/0.13.5-foss-2019b-Python-3.7.4
Supplementary files format and content: tab-delimited text files include transcript count values for each Sample

organism: Cupriavidus basilensis

source_name: not applicable

extract_protocol:
RNA was extracted using a phenol-chlorform method. Briefly, 500 µL culture and 1 ml PBS are centrifuged at 5000 g for 5 min. Lysozyme and Superase-IN RNase inhibitor are used. This is followed by bead-beating with RNASolv reagent (Omega Bio-tek). Chloroform is added and the samples sit at room temperature for 3 min. The samples are then centrifuged at >12000 g for 15 min at 4 ºC. The top aqueous layer is removed and an equal volume of 70% ethanol is added. The samples are then processed using the EZNA Total RNA Kit according to the manufacturer's instructions (Omega Bio-Tek).
5 µl of each sample (concentration 2-10 ng/µl) was used for library preparation with the NEBNext Ultra II Directional RNA library Prep kit following the manufacturer's instructions.
NovaSeq platform for paired-end 150bp

tag: strain

value: SRS

tag: cell line

value: not applicable

tag: cell type

tag: genotype

value: WT

tag: treatment

value: Pgympsum


title: Distal advanced adenomas cfDNA pool S

description:
Distal advanced adenomas (D-AA) cfDNA pool S
D-AA_S

tag: pathology

value: D-AA

tag: sample type

tag: molecule type


title: Distal advanced adenomas cfDNA pool T

description:
Distal advanced adenomas (D-AA) cfDNA pool T
D-AA_T


title: CRA_WB_259

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: CRA_WB_258


title: 1st_G8_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 - 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 - step_threshold (mv)

tag: electrophysiology - step_spikes


title: NoAddition_1

tag: strain

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Control (no addition)


title: 1st_G11_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 - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_257

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: Distal advanced adenomas cfDNA pool R

description:
Distal advanced adenomas (D-AA) cfDNA pool R
D-AA_R

tag: pathology

tag: sample type

tag: molecule type


title: Distal advanced adenomas cfDNA pool Q

description:
Distal advanced adenomas (D-AA) cfDNA pool Q
D-AA_Q


title: Cu_2

tag: strain

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Copper


title: CRA_WB_256

value: F


title: 1st_G6_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 - 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


title: Cu_1

tag: strain

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Chronic Asymptomatic HBV [L44]

city: Ede

first: Oluwadamilola

middle: Gideon

last: Osasona

state: Osun

address: Akoda

department: Biological Sciences

country: Nigeria

institute: Redeemer's University

data_processing:
Galaxy RNAseq Analysis Pipeline was used for analysis
Sequenced reads were trimmed for adapter/ low-quality sequence using trimmomatic
Read were aligned against human reference genome - GrCh38 using HISAT2
Sequence reads were quantified using stringtie
Differential Expression Analysis was conducted using DESEQ2

source_name: Blood

extract_protocol:
RNA was extracted from the peripheral blood moonuclear cells using RNeasy mini plus extraction kit. 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq of Peripheral blood mononuclear cells were prepared via Truseq RNA sample preparation v2 kit (low sample preparation protocol)

tag: tissue

value: Blood

value: Peripheral Blood mononuclear Cell

tag: disease state

value: Chronic Asymptomatic HBV


title: Proximal advanced adenomas cfDNA pool U

description:
Proximal advanced adenomas (P-AA) cfDNA pool U
P-AA_U

tag: pathology

value: P-AA

tag: sample type

value: serum

tag: molecule type

value: circulating cell-free DNA


title: Proximal advanced adenomas cfDNA pool W

description:
Proximal advanced adenomas (P-AA) cfDNA pool W
P-AA_W


title: CRA_WB_255

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Non-advanced adenomas cfDNA pool O

description:
Non-advanced adenomas (NAA) cfDNA pool O
NAA_O

value: NAA


title: Non-advanced adenomas cfDNA pool N

description:
Non-advanced adenomas (NAA) cfDNA pool N
NAA_N


title: 1st_G9_39bx

description:
1st_genes.count_table
1st_genes.fpkm_table

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 - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: NoAddition_2

tag: strain

value: SRS

tag: cell line

value: not applicable

tag: cell type

tag: genotype

value: WT

tag: treatment


title: 1st_G5_39bc

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)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes


title: Chronic Asymptomatic HBV [L41]

tag: tissue

tag: cell type

tag: disease state


title: Benign pathologies cfDNA pool K

description:
Benign pathologies (BEN) cfDNA pool K
BEN_K

tag: pathology

value: BEN

tag: sample type

tag: molecule type


title: 1st_G4_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 - 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 - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Colorectal cancer stages I and II cfDNA pool Y

description:
Colorectal cancer (CRC) stages I and II cfDNA pool Y
CRC-I/II_Y

tag: pathology

value: CRC-I/II

tag: sample type

tag: molecule type


title: CRA_WB_254

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: Benign pathologies cfDNA pool L

description:
Benign pathologies (BEN) cfDNA pool L
BEN_L


title: La_2

tag: strain

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Lanthanum


title: Benign pathologies cfDNA pool J

description:
Benign pathologies (BEN) cfDNA pool J
BEN_J


title: Chronic Asymptomatic HBV [L42]

value: Blood

value: Peripheral Blood mononuclear Cell

tag: disease state

value: Chronic Asymptomatic HBV


title: La_1


title: Chronic Asymptomatic HBV [FET2]


title: Colorectal cancer stages I and II cfDNA pool Z

description:
Colorectal cancer (CRC) stages I and II cfDNA pool Z
CRC-I/II_Z

value: serum

value: circulating cell-free DNA


title: Benign pathologies cfDNA pool I

description:
Benign pathologies (BEN) cfDNA pool I
BEN_I


title: Healthy Control [L46]

value: Healthy Control


title: 1st_G2_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 - 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)


title: Ce_1

tag: strain

value: SRS

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Cerium


title: CRA_WB_253

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: CRA_WB_252

value: F


title: Healthy Control [HC7]

tag: disease state


title: 1st_G3_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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - serial resistance (mω)


title: 1st_G1_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 - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)


title: CRA_WB_251

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex


title: Apatite_2

tag: strain

tag: cell line

value: not applicable

tag: cell type

tag: genotype

value: WT

tag: treatment

value: Apatite


title: 1st_G7_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_250

tag: tissue

value: whole blood

tag: age

value: yes


title: 1st_F12_39bx

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- 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)


title: Non-advanced adenomas cfDNA pool M

description:
Non-advanced adenomas (NAA) cfDNA pool M
NAA_M

tag: pathology

value: NAA

tag: sample type

tag: molecule type


title: No colorectal findings  cfDNA pool G

description:
No colorectal findings (NCF) cfDNA pool G
NCF_G

value: NCF


title: Healthy Control [HC5]

tag: tissue

value: Blood

tag: cell type

value: Peripheral Blood mononuclear Cell

tag: disease state


title: CRA_WB_249

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Non-advanced adenomas cfDNA pool P

description:
Non-advanced adenomas (NAA) cfDNA pool P
NAA_P

value: serum

value: circulating cell-free DNA


title: Proximal advanced adenomas cfDNA pool A5

description:
Proximal advanced adenomas (P-AA) cfDNA pool A5
P-AA_A5

value: P-AA


title: 1st_F11_39bc

tag: genotype

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- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - serial resistance (mω)


title: HBV Induced Hepatocellular Carcinoma [L43]

tag: tissue

tag: cell type

tag: disease state

value: HBV Induced Hepatocellular Carcinoma


title: 1st_F10_39bx

tag: genotype

value: SOD1 A4V

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 - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)


title: 1st_F9_39bx

tag: genotype

value: ALS

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 - serial resistance (mω)


title: CRA_WB_247

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: M


title: CRA_WB_248

value: no


title: HBV Induced Hepatocellular Carcinoma [EK23]

tag: cell type

tag: disease state


title: No colorectal findings  cfDNA pool H

description:
No colorectal findings (NCF) cfDNA pool H
NCF_H

tag: pathology

tag: sample type

tag: molecule type


title: Colorectal cancer stages I and II cfDNA pool A6

description:
Colorectal cancer (CRC) stages I and II cfDNA pool A6
CRC-I/II_A6

value: CRC-I/II


title: HBV Induced Hepatocellular Carcinoma [EK22]


title: Ce_2

tag: strain

value: SRS

tag: cell line

value: not applicable

tag: genotype

value: WT

tag: treatment

value: Cerium


title: 1st_F8_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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)


title: rosettes, Sid2.2_S-_C3

type: RNA

city: Versailles

first: Celine

last: Masclaux-Daubresse

address: Route de Saint Cyr

country: France

institute: IJPB INRAE

description: Gene expression data from sid2.2 rosette, in low sulfate at 60 days after sowing in short days

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45oC, 60 rpm on GeneChip® Arabidopsis ATH1 Genome arrays (Affymetrix) interrogating over 24,000 genes.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) using the FS450_0004 script and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 2.5 µm. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

organism: Arabidopsis thaliana

source_name: sid2 60 days growth under Low S culture

label_protocol: Biotinylated cRNA targets were prepared from 200 ng of total RNA using the “MessageAmp™ Premier RNA Amplification Kit from Ambion, according to the Instruction Manual # 4386269 Revision B, 18 september 2007.

growth_protocol: Plants were grown under low sulfate (0.016 mM sulfate)  for 60 days after sowing in short days (160 micromol.m-2.s-1; 8 h light, 16 h dark)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Low sulfate condition

tag: genotype

value: sid2.2 mutant

tag: tissue

value: whole rosette

tag: growth protocol

value: low sulfate


title: CRA_WB_246

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: F


title: rosettes, Sid2.2_S-_C2


title: CRA_WB_245


title: CRA_WB_244


title: 1st_F6_39bc

value: SOD1 WT

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - serial resistance (mω)


title: RNAseq_4month_tet2_wt_rep2

city: Charlottesville

first: Francine

last: Garrett-Bakelman

state: Virginia

address: 1340 Jefferson Park Avenue , Pinn hall 6054

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Fastq files were checked for quality using FASTQC (v 0.10.1). Reads were then aligned using STAR aligner (v 2.3.0) in single end mode.
After sorting and indexing, the aligned files were used with bedtools (v 2.16.1) and Ensembl zebrafish transcriptome (Zv9) to generate read counts for genes for all samples.
Assembly: Zv9 Ensemble
Supplementary files format and content: text file containing read counts per gene

organism: Danio rerio

source_name: Kidney

extract_protocol:
RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation
RNA-seq libraries were prepared using TruSeq RNA-Seq by poly(A) enrichment (Illumina) and sequenced on HiSeq2000 (Illumina) using a 50-bp single-end approach per the manufacturer's recommendations

value: Kidney

tag: cell type

value: marrow cells


title: ERRBS_4month_tet2_wt_rep2

description: HSPCs,WT ,4months,replicate2

library_source: genomic

data_processing:
The sequencing data was aligned with Zv9 as the reference genome using our in-house processing pipeline (Garrett-Bakelman/Sheridan et al , JovE ,2015)
Data was filtered for 10X coverage per CpG site
Assembly: Zv9 Ensemble v70
Supplementary files format and content: text file containing CpG chromosomal coordinates , strand , read coverage and percent of C vs T detected

extract_protocol:
DNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation
ERRBS was performed as previously described. Briefly, high molecular weight DNA isolated from the progenitor cells was digested with the MspI restriction enzyme. Fragments were purified and subjected to end repair, A-tailing and ligation of methylated Illumina adapters. This was followed by bisulfite conversion and PCR amplification. Libraries were sequenced on an Illumina 2500 using a 50bp single end read approach per manufacturer’s recommendations.


title: rosettes, Col_S-_C2

description: Gene expression data from wild type rosette, in low sulfate at 60 days after sowing in short days

source_name: Col-0 60 days growth under Low S culture

value: Col-0 wild type


title: rosettes, Sid2.2_S-_C1


title: 1st_F5_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 - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: Distal advanced adenomas cfDNA pool A4

description:
Distal advanced adenomas (D-AA) cfDNA pool A4
D-AA_A4

tag: pathology

value: D-AA

tag: sample type

value: serum

tag: molecule type

value: circulating cell-free DNA


title: CRA_WB_243

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: RNAseq_4month_tet2_wt_rep1

tag: cell type

tag: genotype

value: WT


title: HBV Induced Hepatocellular Carcinoma [EK21]

value: Blood

value: Peripheral Blood mononuclear Cell

tag: disease state

value: HBV Induced Hepatocellular Carcinoma


title: ERRBS_4month_tet2_wt_rep1

description: HSPCs,WT ,4months,replicate1


title: 1st_F7_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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: rosettes, Col_S-_C1

tag: genotype

tag: tissue

value: whole rosette

tag: growth protocol

value: low sulfate


title: CRA_WB_242

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: M


title: RNAseq_4month_tet2_mut_rep2

description: HSPCs,TET2 mutant ,15months,replicate2

value: Kidney

tag: cell type

value: TET2 mutant


title: CRA_WB_241

value: yes

value: F


title: ERRBS_4month_tet2_mut_rep2

description: HSPCs,TET2 mutant,4months,replicate2

value: marrow cells


title: 1st_F4_39bc

value: SOD1 WT

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: RNAseq_4month_tet2_mut_rep1

description: HSPCs,TET2 mutant ,15months,replicate1

tag: tissue

tag: genotype


title: 1st_F3_39bx

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- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: ERRBS_4month_tet2_mut_rep1

description: HSPCs,TET2 mutant,4months,replicate1

tag: tissue

tag: cell type


title: Benign pathologies cfDNA pool A2

description:
Benign pathologies (BEN) cfDNA pool A2
BEN_A2

tag: pathology

value: BEN

tag: sample type

value: serum

tag: molecule type

value: circulating cell-free DNA


title: Healthy Control [HC6]

value: Blood

value: Peripheral Blood mononuclear Cell

tag: disease state

value: Healthy Control


title: 1st_F2_39bc

description:
1st_genes.count_table
1st_genes.fpkm_table

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 - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: CRA_WB_24

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: Non-advanced adenomas cfDNA pool A3

description:
Non-advanced adenomas (NAA) cfDNA pool A3
NAA_A3

tag: pathology

value: NAA

tag: sample type

tag: molecule type


title: rosettes, Col_S-_C3

tag: genotype

value: Col-0 wild type

value: whole rosette

tag: growth protocol

value: low sulfate


title: ERRBS_15month_tet2_wt_rep1

description: HSPCs,WT ,15months,replicate1

value: Kidney

tag: cell type


title: ERRBS_15month_tet2_wt_rep2

description: HSPCs,WT ,15months,replicate2


title: CRA_WB_239

value: whole blood

value: yes


title: 1st_F1_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- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: ERRBS_15month_tet2_mut_rep2

description: HSPCs,TET2 mutant,15months,replicate2

tag: tissue

tag: cell type

value: marrow cells


title: 1st_E12_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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: CRA_WB_237

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex

value: M


title: 1st_E11_39bc

tag: genotype

value: SOD1 WT

tag: batch

tag: date

tag: div

value: Control

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- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Colorectal cancer stages III and IV cfDNA pool B1

description:
Colorectal cancer (CRC) stages III and IV cfDNA pool B1
CRC-III/IV_B1

tag: pathology

value: CRC-III/IV

tag: sample type

value: serum

tag: molecule type

value: circulating cell-free DNA


title: CRA_WB_240

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: F


title: ERRBS_15month_tet2_mut_rep1

description: HSPCs,TET2 mutant,15months,replicate1

tag: cell type


title: Colorectal cancer stages III and IV cfDNA pool A9

description:
Colorectal cancer (CRC) stages III and IV cfDNA pool A9
CRC-III/IV_A9


title: CRA_WB_235


title: 1st_E10_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

tag: electrophysiology - step_threshold (mv)


title: Roots, protoplasted, rep 3

city: Davis

first: Siobhan

last: Brady

state: California

address: One Shields

department: Plant Biology and Genome Center

institute: UC Davis

data_processing:
Only read 1 was used in the analyses, since Read2 contained mostly sequencing of the poly A tail of transcripts. Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.6.6). R1 Trimmed reads were pseudo-aligned to ITAG4.1 transcriptome (cDNA) using Kallisto (v0.46.2), with the parameter -b 100, to obtain count estimates.
Assembly: ITAG4.1 transcriptome (cDNA)
Supplementary files format and content: Column based data frame containing estimated raw pseudo-counts by Kallisto (v0.46.2)

organism: Solanum lycopersicum

source_name: 7 days-after sowing seedling 3 cm roots tips

growth_protocol: Solanum lycopersicum cv. M82 (LA3475) seeds were surface sterilized in 70% (v/v) ethanol for 5 min followed by 50% (v/v) commercial bleach for 20 min and three washes with sterile deionized water. Seeds were plated on 12cmx12cm plates (without sucrose) containing 4.3 g L−1 Murashige and Skoog (MS) medium (Caisson; catalog no. MSP09-50LT), 0.5 g L−1 MES, pH 5.8, and 10 g L−1 agar (Difco; catalog no. 214530) and maintained in a 23°C incubator with 16/8h light/dark periods.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit (ZYMO).
Bulk RNAseq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen).
Barcoded libraries were then pooled together, and PE 150-bp reads were sequenced on the NovaSeq 6000 instrument (Illumina) at the UC Davis DNA Technologies Core.

treatment_protocol: In summary, seven days after sowing, 50-100 primary roots per sample were cut ∼3 cm from the root tip. For protoplasted samples, roots were placed in a 35 mm-diameter dish containing a 70 μm cell strainer and 4.5 mL enzyme solution (1.25% [w/v] Cellulase R10, 1.25% Cellulase RS, 0.3% Macerozyme R10, 0.12% Pectolyase, 0.6 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol). Cellulase Onozuka R10, Cellulase Onozuka RS, and Macerozyme R10 were obtained from Yakoult Pharmaceutical Industries. Pectolyase was obtained from Sigma-Aldrich (P3026). After digestion at 25°C for 2 hours at 85 rpm on an orbital shaker with occasional stirring, the cell solution was filtered twice through 40 μm cell strainers and centrifuged for 5 minutes at 500 x g in a swinging bucket centrifuge with the acceleration set to minimal. Subsequently, the pellet was resuspended with 1 mL washing solution (0.6 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol) and centrifuged for 3 minutes at 500 x g. The pellet was resuspended with 1mL of washing solution and transferred to a 1.7mL microcentrifuge tube.

tag: cultivar

tag: tissue

value: Whole root tip

tag: genotype

value: wild type

tag: treatment

value: Protoplasted


title: Roots, whole, rep 3


title: Gene expression of CD64 treated BMSCs _rep2

first: Inyoul

address: 401 Terry Ave. North

institute: Institute for Systems Biology

description:
CD64 treated BMSCs
BMSC_p64_cell_rep2

hyb_protocol: The purified antisense cRNAs were hybridized to Agilent’s 8 × 60,000 microarrays (SurePrint G3 Human CGH Microarray 8x60K V2 ) at 45 °C for 16 hrs.

scan_protocol: Hybridized microarray slides were washed and scanned on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides

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

source_name: BMSCs

label_protocol: For each experiment, 100 ng RNAs were reverse treanscribed and followed by generation of cDNAs. The resulting cDNAs were transcribed and labled with cyanine 3-CTP and the labeled antisense cRNAs were purified using  RNAeasy columns (QIAGEN).

extract_protocol: Total RNA was prepared from cells or cell derived extracellular vesicles using miRNeasy Serum/Plasma advanced kit (Qiagen).

tag: cell type

value: Bone Marrow Stem Cells (BMSCs)

value: CD64 treated


title: CRA_WB_234

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Gene expression of PBS treated BMSCs

description:
PBS treated BMSCs
BMSC_PBS_cell

value: PBS treated


title: CRA_WB_238

value: no


title: Roots, protoplasted, rep 2


title: Gene expression of CD64 treated BMSCs _rep1

description:
CD64 treated BMSCs
BMSC_p64_cell_rep1


title: CRA_WB_232

value: yes


title: Roots, whole, rep 2


title: CRA_WB_233


title: 1st_E6_39bc

source_name: iPSC-derived motor neurons

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 - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Roots, whole, rep 1

tag: cultivar

tag: tissue

tag: genotype

tag: treatment


title: Gene expression of Contol BMSCs

description:
Contol BMSCs
BMSC_ctrl_cell

tag: cell type

value: Contol


title: 1st_E5_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 - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st5

tag: electrophysiology - step_threshold (mv)


title: Roots, protoplasted, rep 1

tag: cultivar

tag: tissue

tag: genotype

tag: treatment


title: 1st_E9_39bx

value: SOD1 A4V

tag: batch

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - trough (mv)

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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_230

source_name: whole blood

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex

value: M


title: Gene expression of TP53 treated BMSCs _rep2

description:
TP53 treated BMSCs
BMSC_p53_cell_rep2

tag: cell type

tag: treatment

value: TP53 treated


title: No colorectal findings cfDNA pool A1

description:
No colorectal findings (NCF) cfDNA pool A1
NCF_A1

tag: pathology

value: NCF

tag: sample type

value: serum

tag: molecule type


title: Gene expression of Plasmids CD64 and TP53 sequentially treated BMSC-derived EV

description:
Plasmids CD64 and TP53 sequentially treated BMSC-derived EV
BMSC_64+53_EV

source_name: extracellular vesicles (EVs)

value: extracellular vesicles (EVs)


title: Gene expression of TP53 treated BMSCs _rep1

description:
TP53 treated BMSCs
BMSC_p53_cell_rep1


title: 1st_E4_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)

tag: electrophysiology - time to peak (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)


title: M82 root, replicate 2, scRNAseq

description: 10x Genomics

data_processing:
FASTQ files were mapped using cellranger (10X Genomics). Reads were aligned to the tomato genome (SL4.0) with the ITAG4.1 gene annotation file. Organellar (mitochondria and plastid) sequences and gene annotation were appended to the main genome and annotation files.
Assembly: Tomato genome (SL4.0) with the ITAG4.1 gene annotation file; with organellar (mitochondria and plastid) sequences and gene annotation were appended to the main genome and annotation files.
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single cell libraries were then prepared by the UC Davis DNA Technologies Core. The protoplast suspension was then loaded onto microfluidic chips (10X Genomics) with v3 chemistry to capture 10,000 cells/sample. Cells were barcoded with a Chromium Controller (10X Genomics).
mRNA was reverse transcribed and Illumina libraries were constructed for sequencing with reagents from a 3’ Gene Expression v3 kit (10X Genomics) according to the manufacturer’s instructions.
Sequencing was performed with a NovaSeq 6000 instrument (Illumina) to produce 100bp paired end reads.

treatment_protocol: In summary, seven days after sowing, 50-100 primary roots per sample were cut ∼3 cm from the root tip. Roots were placed in a 35 mm-diameter dish containing a 70 μm cell strainer and 4.5 mL enzyme solution (1.25% [w/v] Cellulase R10, 1.25% Cellulase RS, 0.3% Macerozyme R10, 0.12% Pectolyase, 0.6 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol). Cellulase Onozuka R10, Cellulase Onozuka RS, and Macerozyme R10 were obtained from Yakoult Pharmaceutical Industries. Pectolyase was obtained from Sigma-Aldrich (P3026). After digestion at 25°C for 2 hours at 85 rpm on an orbital shaker with occasional stirring, the cell solution was filtered twice through 40 μm cell strainers and centrifuged for 5 minutes at 500 x g in a swinging bucket centrifuge with the acceleration set to minimal. Subsequently, the pellet was resuspended with 1 mL washing solution (0.6 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol) and centrifuged for 3 minutes at 500 x g. The pellet was resuspended with 1mL of washing solution and transferred to a 1.7mL microcentrifuge tube. Samples were centrifuged for 3 minutes at 500 x g and resuspended to a final concentration of ∼1000 cells/μL.

tag: tissue

value: Whole root tip

tag: cultivar

tag: genotype

value: wild type

tag: treatment

value: Protoplasted


title: CRA_WB_23

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex

value: F


title: 1st_E8_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 - freq1st5

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 1st_E3_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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)


title: Gene expression of Control BMSC-derived EV _rep1

description:
Control BMSC-derived EV
BMSC_Ctrl_EV_rep1

tag: cell type

value: Bone Marrow Stem Cells (BMSCs)

tag: tissue

tag: treatment


title: M82 root, replicate 1, scRNAseq

description: 10x Genomics

tag: cultivar

tag: genotype


title: Gene expression of PBS treated BMSC-derived EV _rep1

description:
PBS treated BMSC-derived EV
BMSC_PBS_EV_rep1

value: PBS treated


title: 1st_E2_39bc

tag: batch

tag: date

tag: div

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 - freq1st5

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Gene expression of PBS treated BMSC-derived EV _rep3

description:
PBS treated BMSC-derived EV
BMSC_PBS_EV_rep3

tag: cell type

tag: tissue

tag: treatment


title: 1st_E7_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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)


title: CRA_WB_231

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

value: no

tag: Sex


title: CRA_WB_228

tag: batch

value: yes


title: CRA_WB_229


title: HFD feed mice isolated immune cells from Adipose tissue-2

city: Memphis

first: Udai

middle: P

last: Singh

state: TN

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

description:
UPD0109-HFD-2
RNAseq data from adipose tissue immune cells fed on HFD

data_processing:
Sequence reads were trimmed using Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm10 using STAR v2.6.1e.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Adipose tissue

growth_protocol: Adipose tissue immune cells were isolated from both ND as well as HFD treated mice by standard protocol in our laboratory.

extract_protocol:
Trizol extraction of total RNA was performed according to manufacturer's instruction from Qiagen
RNA libraries for RNA-seq were prepared using Illumina stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: At 8 weeks of age, one group of ND fed animals that will serve as the control group, while the other half were fed with HFD for 12 weeks.

value: Adipose tissue

tag: cell type

value: Adipose tissue derived immune cells

tag: genotype

value: HFD


title: Gene expression of Plasmids cd64_TP53 treated BMSC-derived EV _rep2

description:
Plasmids cd64_TP53 treated BMSC-derived EV
BMSC_64_53_EV_rep2

tag: treatment

value: Plasmids cd64_TP53 treated


title: HFD feed mice isolated immune cells from Adipose tissue-1

description:
UPD0111-HFD-1
RNAseq data from adipose tissue immune cells fed on HFD


title: CRA_WB_227


title: CRA_WB_226

value: M


title: ND feed mice isolated immune cells from Adipose tissue-2

description:
UPD0110-ND-2
RNAseq data from adipose tissue immune cells fed on ND

value: ND (Control)


title: 1st_D12_39bx

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

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 - 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 - freq1st3

tag: electrophysiology - freq1st5

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)