title: 1st_E1_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 - 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: 1st_D11_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:
1st_genes.count_table
1st_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 - 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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_225

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.

molecule: total RNA

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: ND feed mice isolated immune cells from Adipose tissue-1

city: Memphis

first: Udai

middle: P

last: Singh

state: TN

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

description:
UPD0112_ND-1
RNAseq data from adipose tissue immune cells fed on ND

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

organism: Mus musculus

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: ND (Control)


title: 1st_D10_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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: CRA_WB_224

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex

value: F


title: kidney, M92KO rep2

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

country: China

institute: shenzhen people's hospital

description:
92b-UUO-K-2
raw_counts kidney.txt

data_processing:
Clc Geromics Workbench y 11.0.1
Secuence reads were trimmed for adaptor secuencelow-auality seouence usina ClC oenomic benchwork (parameter- Quality limit: 0.05)
Timmed seuence reads were mapped to GrCM38/mm10 using CLC genomic benchwok (parameters-msmath cost 2 insertion ost-3 deleton cost 3 length fector: 0.8 simlarity facton:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: kidney

growth_protocol: MiR-92b global knockout mice (miR-92b-/-) (C57BL/6JGpt- Mir-92bem22Cd549/Gpt; Strain ID: T050823) were purchased from Gempharmatech Co. Ltd (Jiangsu, Nanjing, China).These conditions included a 12-hour light cycle (from 8 a.m. to 8 p.m.) at a temperature of 23 ± 1°C and 60-70 % humidity.The mice had ad libitum access to a standard rodent diet and water provided in plastic bottles.Before the experiments, the mice were given a minimum of 7 days to acclimate to their housing environment. In each plastic cage, up to five mice were housed together with corn cob bedding material for comfort. Throughout the study, the mice were treated in a blinded manner, and randomization was performed prior to treatment administration.

extract_protocol:
RNA was havested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manutacturer's protocols

treatment_protocol: Eight-week-old male C57BL/6J or miR-92b-/- mice were randomly assigned to either the sham surgery group or the unilateral ureteral obstruction (UUO) surgery group. The surgery was performed following a well-established protocol. Briefly, the mice were given general anesthesia via intraperitoneal administration of pentobarbital (50 mg/kg) prior to surgery. A left-sided incision was made to expose the left ureter, which was then double ligated with 6-0 silk. Kidneys subjected to ureter ligation, serving as nonfibrotic controls, were collected at the designated time points (10 days) after surgery.

value: kidney

tag: genotype

value: miR-92b knockout

tag: treatment

value: 8 weeks-old mice underwent UUO surgery


title: CRA_WB_223


title: 1st_D9_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 - 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 - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Gene expression of PBS treated BMSC-derived EV _rep2

type: RNA

city: Seattle

first: Inyoul

state: WA

address: 401 Terry Ave. North

institute: Institute for Systems Biology

description:
PBS treated BMSC-derived EV
BMSC_PBS_EV_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: extracellular vesicles (EVs)

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)

tag: tissue

value: extracellular vesicles (EVs)

tag: treatment

value: PBS treated


title: Gene expression of Plasmids cd64_TP53 treated BMSC-derived EV _rep1

description:
Plasmids cd64_TP53 treated BMSC-derived EV
BMSC_64_53_EV_rep1

value: Plasmids cd64_TP53 treated


title: Gene expression of Plasmids cd64_TP53 treated BMSC-derived EV _rep3

description:
Plasmids cd64_TP53 treated BMSC-derived EV
BMSC_64_53_EV_rep3


title: 1st_D8_39bc

tag: genotype

value: SOD1 WT

tag: batch

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: kidney, M92KO rep1

description:
92b-UUO-K-1
raw_counts kidney.txt


title: CRA_WB_222

value: whole blood

tag: age

tag: height (cm)

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: 1st_D7_39bx

tag: genotype

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (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 - latency

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: CRA_WB_220

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 1st_D6_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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)


title: kidney, M92KO rep3

description:
92b-UUO-K-3
raw_counts kidney.txt

tag: tissue

tag: genotype

tag: treatment


title: kidney, WT rep2

description:
NC_UUO_K_2
raw_counts kidney.txt

value: WT


title: CRA_WB_22

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CuO_rep3

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_3.txt
Gene expression in the placenta after 6 hours of perfusion with 10 µg/ml of CuO nanoparticles

hyb_protocol: Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's instructions (Agilent).

scan_protocol: Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V11.5.1.1)

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were log2 transformed and normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.

source_name: Human placenta perfused with CuO nanoparticles, replicate 3

label_protocol: Samples (100 ng) were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).

growth_protocol: Human placentas were obtained from uncomplicated full term pregnancies after caeserean section. The donors provided written informed consent prior to delivery.

extract_protocol: Total RNA was extracted from tissue lysates with miRNeasy Mini Kit (Qiagen, GmbH, Hilden, Germany) following the instructions of the manufacturer. RNA quantity and quality were assessed with NanoDrop (ND-1000, Thermo Fisher Scientific Inc., Wilmington, NC, USA) and Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), respectively. Samples with RNA integrity number > 7.5 were used for the analysis.

treatment_protocol: The perfusions of the placentas were performed using an ex vivo dual recirculating perfusion system described e.g. in Wick, P., et al., Barrier capacity of human placenta for nanosized materials. Environ Health Perspect, 2010. 118(3): p. 432-6. The perfusion medium consisted of M199 tissue culture medium, diluted 1:2 with Earl’s buffer and supplemented with glucose (1 g/L), bovine serum albumin (BSA; 10 g/L), dextran 40 (10 g/L), sodium heparin (2500 IU/L), amoxicillin (250 mg/L) and sodium bicarbonate (2.2 g/L). For the nanoparticle exposures, CuO or PS nanoparticles were added to the maternal chamber to reach a final concentration of 10 µg/mL (CuO, primary particle size 20 nm) and 25 µg/mL (PS, primary particle size 70 nm). Control samples were perfused with perfusion medium only. Tissue samples were collected from the villous region after 6 hours of exposure. Samples were stored in RNAlater (Thermo Fisher Scientific, Zurich, Switzerland) at -20 C.

tag: donor

tag: dose

value: 10 µg/ml

tag: exposure time

value: 6 hours

value: CuO

tag: tissue type

value: human placenta derived from an uncomplicated pregnancy

tag: slide position


title: 1st_D5_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- 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: kidney, WT rep3

description:
NC_UUO_K_3
raw_counts kidney.txt

tag: tissue

value: kidney

tag: genotype

tag: treatment

value: 8 weeks-old mice underwent UUO surgery


title: PS_rep3

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_2.txt
Gene expression in the placenta after 6 hours of perfusion with 25 µg/ml of PS nanoparticles

source_name: Human placenta perfused with PS nanoparticles, replicate 3

tag: donor

tag: dose

value: 25 µg/ml

tag: exposure time

value: PS

tag: tissue type

tag: slide position


title: 1st_D4_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 - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)


title: Gas muscles, M92KO muscle rep3

description:
92b-8W-GAS-3
raw_counts GAS.txt

source_name: gastrocnemius muscle

growth_protocol: MiR-92b global knockout mice (miR-92b-/-) (C57BL/6JGpt- Mir-92bem22Cd549/Gpt; Strain ID: T050823) were purchased from Gempharmatech Co. Ltd (Jiangsu, Nanjing, China).These conditions included a 12-hour light cycle (from 8 a.m. to 8 p.m.) at a temperature of 23 ± 1°C and 60-70 % humidity.The mice had ad libitum access to a standard rodent diet and water provided in plastic bottles.

tag: tissue

value: gastrocnemius muscle

tag: genotype

value: miR-92b knockout

tag: treatment

value: 8 weeks-old mice without treatment


title: Donor_S88_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_4.txt
Gene expression in the placenta from donor S88 prior to perfusion

source_name: Human placenta prior to perfusion, donor S88

tag: donor

tag: dose

value: 0 µg/ml

tag: exposure time

value: 0 hours

value: untreated

tag: tissue type

tag: slide position


title: CRA_WB_221

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex

value: M


title: CRA_WB_219


title: kidney, WT rep1

description:
NC_UUO_K_1
raw_counts kidney.txt

value: WT


title: Gene expression of Control BMSC-derived EV _rep2

description:
Control BMSC-derived EV
BMSC_Ctrl_EV_rep2

tag: cell type

value: Bone Marrow Stem Cells (BMSCs)

value: extracellular vesicles (EVs)

value: Control


title: CRA_WB_218

value: yes

value: F


title: Gas muscles, M92KO muscle rep2

description:
92b-8W-GAS-2
raw_counts GAS.txt


title: Control_rep2

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_1.txt
Gene expression in the placenta after 6 hours of perfusion with the medium only

source_name: Human placenta perfused with perfusion medium only, replicate 2

value: 6 hours

value: perfusion medium

value: human placenta derived from an uncomplicated pregnancy


title: Donor_S86_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_1.txt
Gene expression in the placenta from donor S86 prior to perfusion

source_name: Human placenta prior to perfusion, donor S86


title: Donor_S90_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_3.txt
Gene expression in the placenta from donor S90 prior to perfusion

source_name: Human placenta prior to perfusion, donor S90


title: PS_rep2

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_4.txt
Gene expression in the placenta after 6 hours of perfusion with 25 µg/ml of PS nanoparticles

source_name: Human placenta perfused with PS nanoparticles, replicate 2

value: 25 µg/ml

value: PS


title: 1st_D2_39bc

value: SOD1 WT

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Gas muscles, M92KO muscle rep1

description:
92b-8W-GAS-1
raw_counts GAS.txt

tag: tissue

value: gastrocnemius muscle

tag: genotype

value: miR-92b knockout

tag: treatment

value: 8 weeks-old mice without treatment


title: 1st_D3_39bx

value: SOD1 A4V

tag: batch

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- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - step_threshold (mv)


title: CRA_WB_217

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: ics use_prior_year

value: no

tag: Sex


title: Gas muscles, WT muscles rep3

description:
C57-8W-GAS-3
raw_counts GAS.txt

tag: genotype

value: WT

tag: treatment


title: CRA_WB_216

tag: batch


title: 1st_C12_39bx

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_215

tag: tissue

value: M


title: 1st_D1_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 - step_threshold (mv)


title: 1st_C11_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

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_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_214

tag: tissue

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex

value: F


title: 1st_C10_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

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 - step_threshold (mv)


title: Donor_S93_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_2.txt
Gene expression in the placenta from donor S93 prior to perfusion

source_name: Human placenta prior to perfusion, donor S93

tag: donor

tag: dose

value: 0 µg/ml

tag: exposure time

value: 0 hours

tag: treatment

value: untreated

tag: tissue type

tag: slide position


title: CuO_rep2

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_4.txt
Gene expression in the placenta after 6 hours of perfusion with 10 µg/ml of CuO nanoparticles

source_name: Human placenta perfused with CuO nanoparticles, replicate 2

value: 10 µg/ml

value: 6 hours

value: CuO

value: human placenta derived from an uncomplicated pregnancy


title: PS_rep1

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_3.txt
Gene expression in the placenta after 6 hours of perfusion with 25 µg/ml of PS nanoparticles

source_name: Human placenta perfused with PS nanoparticles, replicate 1

value: 25 µg/ml

value: PS


title: Donor_S92_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_2.txt
Gene expression in the placenta from donor S92 prior to perfusion

source_name: Human placenta prior to perfusion, donor S92


title: CRA_WB_212

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_210


title: C57WT48hPostONCRep1

city: Baltimore

first: Ying

last: Xin

state: MD

address: 400 N Broadway (Smith Building)

institute: Johns Hopkins University

description: S2 100

library_source: transcriptomic single cell

data_processing:
Feature-barcode matrices were generated using the Cell Ranger software v3.0.2
Assembly: mm10
Supplementary files format and content: Tab-saparated values files and matrix files

source_name: mouse retina

extract_protocol:
The eyeballs were enucleated and kept in ice-cold PBS. The retinas were quickly and carefully dissected, and whole retinal cells were dissociated using the Papain enzyme system (LK003150, Worthington). 30mM actinomycin-D was added to the Papain system to prevent post-enucleation transcription. The tissues then underwent manual trituration in neurobasal medium supplemented with 3% BSA, 10 mg/mL Ovomucoid, 1U/uL RNase inhibitor, and 3mM actinomycin D. Cells were filtered through a 40-μm strainer and centrifuged under 500´g. For scRNA-seq, the cell concentration was kept at ~1000 cells/uL.
The scRNA-seq libraries were prepared using the 10X Genomics Chromium 3’ Single-Cell Gene Expression V3 Kit following the standard protocol by the manufacturer. Approximately 8,000-12,000 cells were loaded onto the platform. Libraries were sequenced with the NovaSeq S2 100 platform.

treatment_protocol: mice optic nerve crush surgery

value: mouse retina

tag: genotype


title: Donor_S89_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_2_1.txt
Gene expression in the placenta from donor S89 prior to perfusion

source_name: Human placenta prior to perfusion, donor S89


title: CRA_WB_21

source_name: whole blood


title: KOS_UT_3

city: Bengaluru

first: Amit

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description: Replicate 3

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) was used to filter out multiply mapped reads (-q 1)
BEDTOOLS(2.25.0) -S was used to calculate the read counts per gene in strand specific manner
Normalisation and differential gene expression analysis was done using edgeR
Assembly: Reference genome used : Mycobacterium tuberculosis H37Rv, accession number : NC_000962.3
Supplementary files format and content: tab delimited .csv files containing raw reads count (raw_read_coverage_all_samples.csv), normalised read counts per million(CPM) reads and comparison of genes’ expression for sample pairs

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria grown in 7H9 media

growth_protocol: Mycobacterium tuberculosis H37Rv strains were grown in 7H9-ADS till log phase ~0.4 OD600 at 37 degrees Celcius at 180 rpm.

extract_protocol:
Total RNA was extracted from bacteria and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for 15 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads and a 1% PhiX spike-in control.

value: bacteria grown in 7H9 media

value: iscS-knockout + sufS knockdown strain


title: 1st_C8_39bc

description:
1st_genes.count_table
1st_genes.fpkm_table

source_name: iPSC-derived motor neurons

value: SOD1 WT

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

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: Control_rep1

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_2.txt
Gene expression in the placenta after 6 hours of perfusion with the medium only

source_name: Human placenta perfused with perfusion medium only, replicate 1

tag: donor

tag: dose

tag: exposure time

tag: treatment

value: perfusion medium

tag: tissue type

tag: slide position


title: CRA_WB_209

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: 1st_C9_39bc

tag: genotype

tag: date

tag: div

tag: disease

value: Control

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)


title: KOS_UT_2

description: Replicate 2

tag: tissue

tag: genotype


title: Gas muscles, WT muscles rep1

description:
C57-8W-GAS-1
raw_counts GAS.txt

value: gastrocnemius muscle

value: WT

tag: treatment

value: 8 weeks-old mice without treatment


title: C57WT12hPostONCRep1

description: S2 100


title: CRA_WB_208

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex

value: F


title: Gas muscles, WT muscles rep2

description:
C57-8W-GAS-2
raw_counts GAS.txt


title: 1st_C6_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 1st_C7_39bx

tag: genotype

value: SOD1 A4V

tag: batch

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)


title: 1st_C5_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 - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - step_spikes


title: C57WT48hPostONCRep2

description: S2 100

tag: tissue

tag: genotype

tag: treatment


title: C57WTShamRep2

description: S2 100

value: sham


title: Donor_S87_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_4.txt
Gene expression in the placenta from donor S87 prior to perfusion

source_name: Human placenta prior to perfusion, donor S87

tag: donor

tag: dose

value: 0 µg/ml

tag: exposure time

value: 0 hours

value: untreated

tag: tissue type

value: human placenta derived from an uncomplicated pregnancy

tag: slide position


title: C57WT24hPostONCRep2

description: S2 100

value: mouse retina


title: CuO_rep1

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_3.txt
Gene expression in the placenta after 6 hours of perfusion with 10 µg/ml of CuO nanoparticles

source_name: Human placenta perfused with CuO nanoparticles, replicate 1

value: 10 µg/ml

value: 6 hours

value: CuO


title: C57WT24hPostONCRep1

description: S2 100


title: 1st_C4_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 - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: RvS_UT_3

description: Replicate 3

tag: tissue

value: bacteria grown in 7H9 media

tag: genotype

value: sufS- knockdown strain


title: CRA_WB_206

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex

value: M


title: C57WTShamRep1

description: S2 100

tag: treatment


title: RvS_UT_2

description: Replicate 2


title: CRA_WB_207


title: 1st_C3_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 - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes


title: RvS_UT_1

description: Replicate 1

tag: tissue

tag: genotype


title: CRA_WB_205

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 1st_C2_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: KOS_UT_1

description: Replicate 1

tag: tissue

tag: genotype

value: iscS-knockout + sufS knockdown strain


title: CRA_WB_204

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: nCo_UT_3

description: Replicate 3

value: Native-complimented strain


title: CRA_WB_203


title: vlPAG nuclus, NFD

city: HangZhou

first: hao

last: wu

address: YuHang street

institute: Zhejiang University

description: 10x Genomics

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version5.01). Sample demultiplexing, barcode processing and single-cell 3'gene counting was conducted using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger, version 3.1.0) and snRNA-seq data were aligned to the Ensembl genome GRCm38 reference genome. The R package Seurat (version 3.1.1) was used for Dimensional reduction, clustering, and analysis of snRNA-seq data. Transcriptomes with more than 500 total counts and less than 20% of counts coming from mitochondrial genes, were retained for subsequent analysis.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: brain

extract_protocol:
C57/BL6J mice (8 weeks old at the start of diet manipulation) were fed with on either NFD (n = 18 mice) or HFD (n = 18 mice) for 7 weeks. Mice were then deeply anesthetized with pentobarbital and sacrificed, followed by transcardial perfusion with ice-cold cutting solution containing (in mM): 110 Choline chloride, 2.5 KCl, 1.3 NaH2PO4, 7 MgCl2·6H2O, 0.5 CaCl2·2H2O, 25 NaHCO3, 20 D-glucose. Brains were quickly removed, and coronal sections of 300 μm covering the whole vlPAG were obtained using a Leica VT1200S vibratome. Then the sections were placed under a dissecting microscope (Olympus, SZ61) and dissected with surgical instruments for retinal operation. Afterwards tissues were stored at -80℃ until further processing. Nuclei were isolated using Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies).
Single-nuclei suspensions were loaded to 10X Chromium to capture 8000 single cells using a 10X Genomics Chromium Single-Cell 3' kit (V3) according to the manufacturer's instructions.The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150 bp) by LC-Bio Technology co.ltd., (HangZhou, China).

value: brain

value: WT

tag: treatment

value: normal food diet


title: vlPAG nuclus, HFD 7W

description: 10x Genomics

value: high-fat diet 7 weeks


title: nCo_UT_2

description: Replicate 2


title: 1st_B11_39bc

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)


title: 1st_B12_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 - 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_spikes


title: GW95, RNAseq

city: BOSTON

first: Gongwei

last: Wu

address: 450 Brookline Ave, SM1022, Dana-Farber Cancer Institute

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
For RNAseq, paired end RNAseq samples were mapped to the mouse genome reference assembly (mm10) with STAR 2.4.2a. Transcript expressions were estimated with Cufflinks 2.2.1 without transcript assembly.
Assembly: mm10
Supplementary files format and content: For RNAseq, Tab-delimited text files includes raw counts

source_name: lymphoma

growth_protocol: All mice were maintained under a 12 h light/12 h dark cycle at constant temperature (23 °C), with free access to food and water.

extract_protocol:
For RNAseq  for tumor cells, the spleen cells bearing lymphoma were collected, red blood cells were lysed by ACK lysis buffer on ice, washed with cold PBS, passed through a 70-μm cell strainer and used for RNA extraction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: tissue

value: lymphoma

tag: cell type

value: Mouse spleen cells

tag: genotype

value: transgenic mouse

tag: treatment

value: enlarged spleen with tumor


title: 1st_C1_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: GW328, RNAseq


title: GW255, RNAseq


title: nCo_UT_1

description: Replicate 1

value: bacteria grown in 7H9 media


title: CRA_WB_201

tag: age

tag: height (cm)

tag: ics use_prior_year

value: yes

tag: Sex

value: F


title: CRA_WB_200

value: whole blood


title: hCo_UT_2

description: Replicate 2

value: iscS-complemented strain


title: CRA_WB_20


title: HFD; scRNAseq

city: Changsha

first: Limin

last: Xie

state: Hunan

address: No.139，Renmin Road Central Changsha, Hunan, China

institute: The second xiangya hospital of central south university

description: 10X Genomics

data_processing:
The Cell Ranger software was obtained from 10× Genomics website.  Alignment, filtering, barcode counting, and UMI counting were performed with cell ranger count module on the raw sequencing data to generate a gene-barcode matrix for subsequent analysis.
The output of Cell Ranger filtered gene expression matrix were analyzed by R software with the Seurat package.
Before the downstream analysis, low-quality cells were excluded and retained the high-quality single-cell data that met the following criterial: Briefly, cells with a detected gene count less than 300 or exceeding 4000, or mitochondrial gene ratio was more than 10%, or an nCount exceeding 15000 were filtered out. Additionally, genes expressed in fewer than 5 cells were removed.
After removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function in Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Epididymal white adipose tissue

extract_protocol:
Samples were washed by PBS to remove the remaining blood cells and then cut into small pieces.These small pieces were digested with Type II collagenase at 1 mg ml-1 for 30 min at 37 ℃ while shaking at 120 rpm. The samples were prepared into single-cell suspensions, Cell counts and cell viability were measured with the Countess® II Automated Cell Counter with cell activity above 80%, and cell concentrations were adjusted to the ideal concentration of 1000 /μL.
scRNA-seq libraries were generated using the Chromium Single Cell 3' Library and Gel Bead Kit V3 (10X Genomics, 1000075), Chromium Single Cell B Chip kit (10X Genomics, 1000074), and Chromium i7 Multiplex Kit (10X Genomics, 120262). Cells were resuspended in reverse transcription enzyme mix and loaded onto the Chromium Single Cell B Chip to generate gel beads-in-emulsion of 6,000 cells per channel. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio-Rad). The cDNA was generated and then amplified, and quality was assessed using an Agilent 4200. ScRNA-seq libraries were constructed using Single Cell 3' Library and Gel Bead Kit V3 and finally sequenced using an Illumina NovaSeq 6000 instrument with a sequencing depth of at least 50,000 reads per cell with paired-end 150-bp reading strategy.

value: Epididymal white adipose tissue

value: male

value: stromal vascular fraction

value: 18 weeks old

tag: strain

value: C57BL/6J wild type

value: high fat diet (HFD)


title: 1st_B8_39bc

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 - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes


title: 1st_B9_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: hCo_UT_1

description: Replicate 1

tag: tissue


title: KO_UT_3

description: Replicate 3

value: iscS- knockout strain


title: CRA_WB_2

tag: age

tag: height (cm)

tag: ics use_prior_year

tag: Sex

value: M


title: NCD; scRNAseq

description: 10X Genomics

tag: cell type

tag: strain

tag: treatment

value: normal chow diet (NCD)


title: 1st_B7_39bx

tag: genotype

value: SOD1 A4V

tag: batch

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_spikes


title: CRA_WB_202

tag: tissue

tag: age

value: no


title: Heart, KO3 input

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction:
Read count extraction and normalization were performed using CC genomic benchwork
Assembly: GRCm38.p6
Supplementary files format and content: bigwig files for each sample

source_name: Heart

growth_protocol: Myocardial tissues of WT mice and ALKBH5-KO mice were methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Oiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR

treatment_protocol: Mice were subjected to permanent left anterior descending artery ligation

value: Heart

tag: rip antibody

value: input

value: Myocardial infarction


title: CRA_WB_199

value: whole blood

tag: height (cm)

tag: ics use_prior_year

value: yes

tag: Sex


title: KO_UT_2

description: Replicate 2

value: bacteria grown in 7H9 media


title: 1st_B6_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- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Heart, KO2 input

tag: tissue

tag: rip antibody

tag: genotype

tag: treatment


title: 1st_B5_39bx

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology - step_spikes


title: Heart, WT3 input

tag: tissue

tag: rip antibody

tag: genotype

value: WT

tag: treatment


title: 1st_B4_39bc

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

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_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_197

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_198

value: F


title: Heart, KO1 input

tag: rip antibody

tag: genotype

tag: treatment


title: hCo_UT_3

description: Replicate 3

value: iscS-complemented strain


title: KO_UT_1

description: Replicate 1


title: CRA_WB_196


title: Rv_UT_3

description: Replicate 3

value: Wild type Mtb


title: 1st_B10_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 - step_spikes


title: CRA_WB_195

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: Rv_UT_2

description: Replicate 2

tag: genotype


title: Heart, WT2 input

tag: rip antibody

tag: treatment


title: 1st_B3_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 - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Heart, WT1 input

tag: tissue

tag: rip antibody

tag: genotype

tag: treatment


title: CRA_WB_194

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: KD_NO2

description: Replicate 2

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) was used to filter out multiply mapped reads (-q 1)
BEDTOOLS(2.25.0) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using edgeR for genes with >= 0.5 cpm in all samples for the comparison
Assembly: Reference genome used : Mycobacterium tuberculosis H37Rv, accession number : NC_000962.3
Supplementary files format and content: tab delimited .cov.txt files containing raw reads count for every sample, csv files with ‘cpm_’ prefix containing normalised read counts per million(CPM) reads and csv files with prefix ‘diffexpr-results_’ containing comparison of genes’ expression for sample pairs

growth_protocol: Mycobacterium tuberculosis H37Rv strains were grown in 7H9-ADS till log phase at 37 degrees Celcius at 180 rpm.

treatment_protocol: Treated with DETA-NO for NO stress

value: whiB1-knockdown strain + NO treatment


title: Heart, KO3 IP

value: Anti-m6A (Synaptic Systems, Cat. No 202 003)


title: CRA_WB_193


title: 1st_B1_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 - 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_spikes


title: 1st_A12_39bx

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: KD_NO1

description: Replicate 1

tag: tissue


title: GW19, RNAseq

value: lymphoma

tag: cell type

value: Mouse spleen cells

value: transgenic mouse

tag: treatment

value: enlarged spleen with tumor


title: WT_NO2

description: Replicate 2

value: Wild type Mtb + NO treatment


title: Heart, KO1 IP

value: Heart

tag: rip antibody


title: 1st_A10_39bx

tag: genotype

value: SOD1 A4V

value: ALS

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 trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes


title: CRA_WB_190

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: CRA_WB_192

value: M


title: Heart, WT3 IP

tag: rip antibody

tag: genotype

value: WT

tag: treatment

value: Myocardial infarction


title: WT_NO1

description: Replicate 1

value: bacteria grown in 7H9 media


title: Heart, WT2 IP


title: KD2

description: Replicate 2

value: whiB1-knockdown strain


title: 1st_A11_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 - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_19

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: 1st_A9_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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_spikes


title: 1st_B2_39bc

tag: genotype

tag: batch

tag: date

tag: div

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 - step_threshold (mv)

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Rv_UT_1

description: Replicate 1

tag: tissue

value: Wild type Mtb


title: 1st_A8_39bc

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 - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - freq1st5


title: KD1

description: Replicate 1

tag: tissue

tag: genotype


title: CRA_WB_189

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex


title: CRA_WB_188

value: F


title: WT1

description: Replicate 1


title: WT2

description: Replicate 2


title: Heart, KO2 IP

tag: rip antibody

value: Anti-m6A (Synaptic Systems, Cat. No 202 003)

tag: treatment


title: HSPC_GW4869_120h_rep3

city: philadelphia

first: Stephanie

middle: N

last: Hurwitz

address: 3400 Spruce St

institute: University of Pennsylvania

description:
10X genomics
filtered_counts.csv.gz
metadata_percell.csv

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using  Cell Ranger software.
The data from all samples were loaded in R (version 4.2.2) and processed using the Seurat package (version 4.3.0 – Hao et al. Cell 2021). Cells with low UMI counts and low number of detected genes were filtered out. The filtering thresholds were determined independently for each condition (DMSO-24h: 3000 UMIs/cell, 1500 genes/cell; DMSO-120h: 2700 UMIs/cell, 700 UMIs/cell; GW4869-24h: 2700 UMIs/cell, 1500 genes/cell; GW4869-120h: 3700 UMIs/cell, 700 genes/cell). The dataset was normalized for sequencing depth per cell and log-transformed using a scaling factor of 10,000. Principal component analysis (PCA) was performed on the 2,000 most variable features. The first 33 PCs were used to generate the UMAP.
We used marker genes Slamf1, Cd48, and Flt3 to sort cells in silico into Long-term HSCs (LT-HSC) (Flt3- Slamf1+ Cd48-), Short-term HSC (ST-HSC) (Flt3- Slamf1- Cd48-), Multipotent Progenitors 2 (MPP2) (Flt3- Slamf1+ Cd48+), MPP3 (Flt3- Slamf1- Cd48+) and MPP4 (Flt3+ Slamf1-). Flt3+ Slamf1+ cells were labelled as “Unknown”.
Assembly: mm10
Supplementary files format and content: Comma-separated values files and matrix files

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
Ex vivo expanded murine HSPCs were stained with a viability stain and live cells were sorted using a FACS Jazz (Becton Dickinson) into PBS for downstream processing.
Library was performed according to the manufacter’s instructions (single cell 3’ protocol, 10x Genomics)

tag: cell type

value: Hematopoietic stem and progenitor cells


title: 1st_A6_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 - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: CRA_WB_187

tag: tissue

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: HSPC_GW4869_120h_rep2

tag: cell type

tag: treatment


title: Ferret2_All_S6

first: Joshua

middle: William

last: Hahn

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: MusPutFur1.0
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.

organism: Mustela putorius furo

source_name: Retina

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

value: Retina

value: Retinal neurons


title: CRA_WB_191


title: CRA_WB_186


title: 1st_A5_39bx

tag: genotype

value: SOD1 A4V

tag: date

tag: div

tag: disease

value: ALS

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3


title: Ferret2_All_S5

tag: tissue

tag: cell type


title: HSPC_GW4869_120h_rep1

tag: treatment


title: CRA_WB_185

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: HSPC_DMSO_120h_rep3

value: DMSO


title: CRA_WB_184


title: HSPC_DMSO_120h_rep1


title: Ferret2_CD73dp_S4


title: Heart, WT1 IP

value: Heart

tag: rip antibody

tag: genotype

value: WT

value: Myocardial infarction


title: Donor_S94_before_perfusion

description:
US11263921_253949437527_S01_GE2_1105_Oct12_1_1.txt
Gene expression in the placenta from donor S94 prior to perfusion

source_name: Human placenta prior to perfusion, donor S94

tag: donor

tag: dose

value: 0 µg/ml

tag: exposure time

value: 0 hours

value: untreated

tag: tissue type

value: human placenta derived from an uncomplicated pregnancy

tag: slide position


title: CRA_WB_183

value: yes

value: F


title: 1st_A2_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 - freq1st5

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: Ferret2_CD90_S2

tag: tissue

value: Retina

tag: cell type

value: Retinal neurons


title: HSPC_DMSO_120h_rep2

value: Hematopoietic stem and progenitor cells

tag: treatment


title: 1st_A4_39bc

tag: genotype

tag: batch

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - peak (mv)

tag: electrophysiology - height (mv)

tag: electrophysiology - upstroke (mv)

tag: electrophysiology - downstroke (mv)

tag: electrophysiology - vupstr

tag: electrophysiology - vdnstr

tag: electrophysiology - halfwidth (ms)

tag: electrophysiology - time to peak (ms)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - freq1st3


title: 1st_A1_39bx

description:
processed file
1st_genes.fpkm_table

tag: genotype

value: SOD1 A4V

tag: batch

value: ALS

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

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: 1st_A3_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)


title: HSPC_GW4869_24h_rep3

tag: cell type

tag: treatment


title: CRA_WB_181

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: no

tag: Sex


title: CRA_WB_182

value: M


title: HSPC_GW4869_24h_rep1


title: CRA_WB_180


title: HSPC_GW4869_24h_rep2


title: Ferret2_CD90_S1


title: Ferret2_CD90CD73dp_S3


title: Ferret1_All_S1


title: Ferret1_CD90_S1


title: CRA_WB_18


title: HSPC_DMSO_24h_rep3

value: DMSO


title: CRA_WB_179


title: HSPC_DMSO_24h_rep2


title: 1st_A7_39bx

tag: genotype

tag: date

tag: div

tag: disease

tag: electrophysiology - spikes

tag: electrophysiology - input resistance (gω)

tag: electrophysiology - trough (mv)

tag: electrophysiology - time to trough (ms)

tag: electrophysiology - voltage threshold (mv)

tag: electrophysiology - time to treshold (ms)

tag: electrophysiology - latency

tag: electrophysiology - avgvm

tag: electrophysiology - prevol

tag: electrophysiology- interspike interval (ms)

tag: electrophysiology - frequency

tag: electrophysiology - instant frequency

tag: electrophysiology - freq1st3

tag: electrophysiology - step_threshold (mv)

tag: electrophysiology - step_spikes

tag: electrophysiology - membrane capacitance (pf)

tag: electrophysiology - serial resistance (mω)


title: HSPC_DMSO_24h_rep1

tag: cell type

tag: treatment


title: Gene expression of Control MEF-derived EV_rep4

description:
Control MEF-derived EV
MEF_Ctrl_EV_rep4

hyb_protocol: The purified antisense cRNAs were hybridized to Agilent’s 8 × 60,000 microarrays at 45 °C for 16 hrs.

source_name: extracellular vesicles (EVs)

value: Mouse Embryonic Fibroblast (MEF)

tag: tissue

value: extracellular vesicles (EVs)


title: CRA_WB_178

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

tag: Sex


title: CRA_WB_177


title: CNOT7&8 KO, GV stage, R4

city: Kunigami-gun

first: Tadashi

last: Yamamoto

state: Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology

data_processing:
nf-core/rnaseq pipeline v2.0
Sequence reads were mapped to GRCm38/mm10 using STAR aligner (v2.6.1d).
Read count extraction and normalization were performed using EdgeR (v3.11) and a cut-off of at least 0.2 counts per million (CPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: CNOT7&8 KO, GV stage

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). 100 oocytes were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumine TrueSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (illumina) following manufacturer's protocols.

value: GV stage oocytes

tag: genotype

value: CNOT7&8 KO


title: Gene expression of Plasmids cd64_TP53 treated BMSC-derived EV_rep2

description:
Plasmids cd64_TP53 treated BMSC-derived EV
MEF_64.53_EV_rep2

value: Bone Marrow Stem Cells (BMSCs)

value: Plasmids cd64_TP53 treated


title: Cnt3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Rattus norvegicus

source_name: normal lung

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: control

value: normal lung


title: Cnt1


title: Cnt2


title: CNOT7&8 KO, GV stage, R3


title: DEX4

source_name: implanted fetal lung

value: Dexamethasone administration

value: implanted fetal lung


title: CRA_WB_175

source_name: whole blood

value: yes

value: F


title: Gene expression of Plasmids cd64_TP53 treated BMSC-derived EV_rep1

description:
Plasmids cd64_TP53 treated BMSC-derived EV
MEF_64.53_EV_rep1


title: CNOT7&8 KO, GV stage, R2


title: CRA_WB_174


title: Gene expression of Control MEF-derived EV_rep1

description:
Control MEF-derived EV
MEF_Ctrl_EV_rep1

value: Control


title: Gene expression of PBS treated MEF-derived EV_rep4

description:
PBS treated MEF-derived EV
MEF_PBS_EV_rep4

value: PBS treated


title: Gene expression of Control MEF-derived EV_rep3

description:
Control MEF-derived EV
MEF_Ctrl_EV_rep3


title: CRA_WB_176

value: whole blood


title: DEX3


title: CRA_WB_173

value: no


title: Zp3-Cre, GV stage, R3

source_name: Zp3-Cre, GV stage


title: DEX2


title: Zp3-Cre, GV stage, R4


title: CRA_WB_172

value: M


title: Gene expression of PBS treated MEF-derived EV_rep1

description:
PBS treated MEF-derived EV
MEF_PBS_EV_rep1

value: Mouse Embryonic Fibroblast (MEF)


title: DEX1


title: Gene expression of Plasmids cd64_TP53 treated MEF-derived EV_rep2

description:
Plasmids cd64_TP53 treated MEF-derived EV
MEF_64_53_rep2

value: extracellular vesicles (EVs)


title: Gene expression of PBS treated MEF-derived EV_rep3

description:
PBS treated MEF-derived EV
MEF_PBS_EV_rep3


title: Zp3-Cre, GV stage, R2

value: GV stage oocytes


title: CRA_WB_171


title: MS+3

value: mechanical strech+


title: CNOT7&8 KO, GV stage, R1

value: CNOT7&8 KO


title: THY1 + spermatogonia,Ddx20 knockout, 3

city: beijing

first: dingfeng

last: zou

state: 北京

address: Beijing, Dong Dan San Tiao 5

institute: Institute of Basic Medical Sciences  Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
The original RNA-seq reads used Trimmomatic (v0.39) to filter low-quality reads and trim the adaptor sequence.
Reads then were aligned to the mm10 reference genome using STAR (2.7.5c).
After comparing with the reference genome, use StringTie (v2.1.7) for gene quantification, and get the standardized gene level FPKM value. Use DEseq2 to analyze the difference of the gene count matrix. Use edgeR to perform difference analysis on the grouping of no duplicate samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: THY1 spermatogonia

extract_protocol:
About 1000 cells were collected in tubes and lysed in the lysis buffer containing ribonuclease inhibitor. Reverse transcription was carried out using anchored oligo-dT primer, followed by PCR amplification and magnetic AMPure bead (Beckman Coulter) purification to clean up the cDNA products. Subsequently, cDNA concentration and quality were performed on a few samples using Qubit 3.0 Fluorometer (Thermo) and BioAnalyzer (Agilent) to ensure the expected production with a length longer than1000 bp.
The library was finally generated by DNA fragmentation, end repair, adapter ligation, PCR amplification, and AMPure XP bead purification. Then, the qualified libraries were sequenced on the Illumina HiSeq-PE150 platform with paired-end 150 bp read length.
SMART-seq2

value: THY1 spermatogonia

value: Ddx20 knockout

tag: time

value: Day 4


title: Gene expression of PBS treated MEF-derived EV_rep2

description:
PBS treated MEF-derived EV
MEF_PBS_EV_rep2


title: CRA_WB_167

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.


title: THY1 + spermatogonia,Ddx20 knockout, 2


title: Gene expression of PBS treated MEF-derived EV_rep5

description:
PBS treated MEF-derived EV
MEF_PBS_EV_rep5


title: Gene expression of Control MEF-derived EV_rep2

description:
Control MEF-derived EV
MEF_Ctrl_EV_rep2


title: Zp3-Cre, GV stage, R1


title: Gene expression of Plasmids cd64_TP53 treated MEF-derived EV_rep3

description:
Plasmids cd64_TP53 treated MEF-derived EV
MEF_64_53_rep3

value: Plasmids cd64_TP53 treated


title: Gene expression of Plasmids cd64_TP53 treated MEF-derived EV_rep1

description:
Plasmids cd64_TP53 treated MEF-derived EV
MEF_64_53_rep1


title: CRA_WB_166


title: THY1 + spermatogonia,Ddx20 knockout, 1


title: MS+4

value: implanted fetal lung


title: THY1 + spermatogonia, control, 3


title: MS-2

value: mechanical strech-


title: MS-4


title: CRA_WB_169

value: yes

value: F


title: MS-1


title: CRA_WB_164


title: CRA_WB_168


title: MS+1


title: THY1 + spermatogonia, control, 1

value: Control


title: breast cancer cell derived exosome RNA expression from HR+/HER2- breast cancer patient 3

city: Shenyang

first: qi

last: zhou

address: No.155, Nanjing North Street, Heping District,

institute: CMU

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5μl 10 × Blocking Agent and 1μlof 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: HR+/HER2- Breast Cancer Cell Derived Exosome

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured by NanoDrop ND-1000.

growth_protocol: The samples of carcinomas and the normal tissues were obtained from surgical specimens which were collected immediately after surgery. Fresh tissues were dissociated mechanically and enzymatically to preparation of single cell suspensions and subsequent primary culture. When 80% confluence was reached, the Cells were passaged, and seeded into T175 flasks and expanded over several passages until sufficient cell numbers had been achieved, and then were frozen in −80 °C, stored in −80 °C for subsequent analysis.

extract_protocol: Total RNA from exosomes were extracted by Trizol Reagent (Incitrogen,USA). 1ug RNA was reversely transcribed using a PrimeScript™ RT Master Mix kit (Takara,China)

value: breast cancer

tag: rna population

value: exosome

tag: maximum tumor diameter

tag: number of lymph node metastases

tag: er

tag: pr


title: CRA_WB_163

first: Joanne

address: 181 Longwood Avenue

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

value: whole blood

value: no


title: breast cancer cell derived exosome RNA expression from HR+/HER2- breast cancer patient 2


title: AND2 hCOs scRNAseq

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

description: 10x Genomics

data_processing:
Raw scRNA-seq output was processed in order to generate a count matrix with CellRanger Count (version 6.1.2. 10X Genomics)
Assembly: GRCh38 human reference genome
Supplementary files format and content: Tab-separated values files and Matrix files

source_name: hCOs from Human Embryonic Stem Cell (hESCs)

extract_protocol:
hCOs were collected with the aid of a pipette and treated with HBSS (Hank's Balanced Salt Solution; 1X, Gibco, #14180046) for 15 minutes. The organoid were centrifuged (3 minutes at 600 rpm) and digested with trypsin (0.025%, Gibco) for 20 minutes at 37°C and trypsin inhibition with 1:1 DMEM:F12 + 10% FBS. Subsequently, the dissociated and individual cells were centrifuged (3 minutes at 600 rpm) and resuspended in a buffered solution of BSA (0.04%, Sigma) in PBS at 4°C.
The single cell library was prepared according to manufacturer’s instructions using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics) workflow by the Genomics Unit of the Instituto de Salud Carlos III

tag: cell line

value: AND-2 cell line

value: 4 weeks of maintenance


title: CRA_WB_162

city: Boston

institute: Mass General Brigham

value: M


title: siCsde_TGF_3

city: Mannheim

first: Joerg

last: Heineke

address: Ludolf-Krehlstr. 7-11 Tridomus B

department: Cardiovascular Physiology

country: Germany

institute: Medical Faculty of Mannheim Heidelberg University

data_processing:
Allignment, Hisat2
Mapping, feature counts
Diff analysis, Deseq2
Splicing, rMATs
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: Excel files from differentially expressed genes

source_name: MCEC

extract_protocol:
RNA was extracted using a commertial RNA extraction kit
Novogene

treatment_protocol: NS vs. TGF-β

value: MCEC

value: Endothelial Cells

tag: knockdown

value: 10 ng/ml TGF-Beta


title: CRA_WB_165

last: Sordillo


title: CRA_WB_161


title: breast epithelial cell derived exosome RNA expression from HR+/HER2- breast cancer patient 3

source_name: Normal Breast Epithelial Cell  Derived Exosome

value: Breast Epithelial Cell


title: siCsde_TGF_2

tag: cell type


title: Detached cells sgRNAs

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

description:
This sample represents the sgRNAs enriched within the cells that detached from the plate following CSF1 stimulation.
Unstim.count.txt

library_source: other

data_processing:
20 base sgRNA reads were trimmed using Cutadapt 2.3, where 20bp sequence flanked by cgaaacaccg...gttttagagc was identifed from all fastq files. Cutadapt arguments= -g cgaaacaccg...gttttagagc, -o, --minimum-length 15, --discard-untrimmed, -e 0.2, --cores=8
Counts of sgRNA reads generated and mapped to Brie library sgRNAs using MAGeCK 0.5.9. arguments= count, -l BrieGuideLibwithNonTarg.csv, --sample-label, --fastq, -n, --unmapped-to-file, --pdf-report
We used the MAGeCK test command to identify enriched sgRNAs within the high and low populations. Arguments= test, -k, -c low, -t high, -n, --control-sgrna nontargets.txt --keep-tmp --pdf-reports
Assembly: Brie Library
Supplementary files format and content: .txt and .csv files contain the data files used to process the data.  The BrieGuideLibwithNonTarg.csv file contains the Brie library file used by MAGeCK to map the trimmed reads back to the library.  The readmapping step generated the "CSF1stim.count.txt" and "unstim.count.txt" files used for the MAGeCK test functions.  The MAGeCK test step used one of the count tables and the "nontargets.txt" file to identify sgRNAs enriched in the low and high fluroescence populations.  The MAGeCK test output includes the "CSF1_dexuptake_highlow.gene_summary.txt" and "unstim_dexuptake.gene_summary.txt" files.  The MAGeCK out files were used to identify genes regulating  dextran uptake.
Library strategy: CRISPR screen

molecule: other

source_name: Bone Marrow Derived Macrophages

growth_protocol: BMDM were cultured in bone-marrow medium (BMM) containing Dulbecco’s Modified Eagle Medium (4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate), 20% heat-inactivated fetal bovine serum and 30% L-cell supernatant (a source of colony-stimulating factor-1), 10,000 IU penicillin and 10 mg/mL streptomycin, and 5.7 mM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was extracted from cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher) and the sgRNA library was amplified by a single-step PCR protocol (Broad Institute) for NGS using barcoded primers with staggered sequences. PCR product from multiple PCR reactions was pooled and gel purified and quantified by Qubit Fluorometer and subjected to sequencing on Illumina Nextseq 500 with 75 reads.
Mouse Brie CRISPR knockout pooled library developed by David Root and John Doench was obtained from Addgene (Addgene #73633) was amplified in Stable 3 competent E. coli (Thermofisher) and subjected to next-generation-sequencing (NGS) to determine the distribution of sgRNAs in the library. To produce Lentivirus, 1.8 x 106 NIH 293T cells were seeded in six 10-cm plates and transfected the following day with 6 μg sgRNA pooled library in lentiGuide-Puro (Addgene# 73633), 6 μg psPAX2 plasmid, 1 μg pVSVG plasmid, and 0.024 mg polyethyleneimine (PEI). After 48 h, the lentivirus was harvested, centrifuged, and aliquoted into multiple 15 mL tubes and stored at -80o C or - 150o C. The functional titer of the lentivirus was determined by live-cell counting after puromycin selection.
The parameters for how the library sequenced - chip: 75 high fidelity read

treatment_protocol: Primary Macrophages expressing Cas9-GFP were transduced with the Brie Library at low multiplicity of infection (MOI) (0.3) to achieve 50 fold representation of each sgRNA in the Brie Mouse library.  After 48 h, transduced cells were selected with 5 ug/ml puromycin for 2 days and cultured another 8 before sorting.  To identify genes regulating dextran uptake, cells were starved of CSF1 overnight in DMEM plus 10% FBS.  Then, cells were exposed to 300 ug/ml 40 kDa fluorescent dextran for 15 minutes in the presence or absence of CSF1.  Cells were then sorted based on their ability to internalize dextran using a BD FACs jazz flow cytometer.  We sorted the top (high fluorescence) and bottom (low fluorescence) quintiles based on dextran fluorescence and sequenced both samples to idenfity sgRNAs enriched in each sample.

tag: strain

value: Primary Macrophage


title: hBMSC

city: Hong Kong

first: Hongfei

last: Wang

address: Pok Fu Lam

country: Hong Kong

institute: The University of Hong Kong

description: BMSC

data_processing:
Illumina base call files (BCL) of cultured BMSCs and BMSC-derived neurospheres were demultiplexed and converted to FASTQ files with the bcl2fastq2 program (version 2.20).
The FASTQ files were then aligned to the human genome reference sequence (GRCh38) for filtering, barcode counting, as well as UMI counting by the Cell Ranger (v7.1) count pipeline. A barcode table, gene table, and gene expression matrix were generated for downstream analyses.
Assembly: GRCh38/hg38
Supplementary files format and content: barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: bone marrow

extract_protocol:
P5 BMSCs and Day 8 BMSCs-derived neurospheres (both generated from the 41-year-old female donor) were dissociated into single cells by treatment with papain at 37℃ for 30 min. Dissociated cells were filtered through a 40 μm cell strainer with determination of cell concentration and viability (>98%) upon chamber slides following trypan blue staining. Cells were resuspended in ice-cold PBS and 0.04% bovine serum albumin at a density of 1,000 cells / μl.
Resuspended BMSCs and BMSC-derived neurospheres were loaded onto the 10x Genomics Chromium platform according to the manufacturer’s protocol, whilst scRNAseq libraries were prepared using the Chromium Single Cell 3ʹ GEM Library and Gel Bead Kit v3.

tag: tissue

value: bone marrow

value: female

value: Bone marrow stromal cells

tag: cell culture

value: Passage 5


title: MS-3

tag: treatment

value: mechanical strech-

value: implanted fetal lung


title: THY1 + spermatogonia, control, 2

value: THY1 spermatogonia

value: Control

value: Day 4


title: Human_PRet887mc869fc

city: Seattle

description:
Human_count_mat_1.csv
Human_count_mat_2.csv
Human_count_mat_3.csv
Human_count_mat_4.csv

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: GRCh38.p13
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. This GEM has been split into four separate csv files.

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)

value: Retina

value: Retinal neurons


title: breast epithelial cell derived exosome RNA expression from HR+/HER2- breast cancer patient 2

value: exosome

tag: age


title: siCsde_TGF_1

value: MCEC


title: Unstimulated high dextran uptake sgRNAs

description:
This sample represents the sgRNAs enriched within the unstimulated high dextran uptake sample.  These sgRNAs induced a loss of function that increased dextran uptake.
Unstim.count.txt


title: breast cancer cell derived exosome RNA expression from HR+/HER2- breast cancer patient 1

value: breast cancer


title: CRA_WB_160

value: whole blood

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

value: F


title: Human_PRet563mc


title: Unstimulated low dextran uptake sgRNAs

description:
This sample represents the sgRNAs enriched within the unstimulated low dextran uptake sample.  These sgRNAs induced a loss of function that decreased dextran uptake.
Unstim.count.txt

tag: genotype

value: Primary Macrophage


title: siCsde_NS_3

value: Endothelial Cells

value: 0 ng/ml TGF-Beta


title: breast epithelial cell derived exosome RNA expression from HR+/HER2- breast cancer patient 1

value: Breast Epithelial Cell

tag: rna population


title: CRA_WB_16

tag: Sex

value: M


title: Human_PRet326mc355fc


title: hBM-NS

description: Neurosphere

value: bone marrow

value: female

value: BMSC-derived neurosphere

value: Day 8


title: Unstimulated Presort sgRNAs

description:
This sample represents the sgRNAs present in the cell populations on sorting day for the unstimulated dextran uptake screen
Unstim.count.txt


title: siCsde_NS_2


title: CSF1 stimulated high dextran uptake sgRNAs

description:
This samples represents the sgRNAs present in the high dextran uptake sample and induced a gain of function that increased dextran uptake in response to CSF1 stimulation.
CSF1stim.count.txt


title: CRA_WB_158

value: no


title: Human_CMixS2

value: Retina

value: Retinal neurons


title: Human_PRet1059fc564mc


title: CSF1 stimulated low dextran uptake sgRNAs

description:
This sample represents the sgRNAs enriched within the low dextran uptake samples.  These sgRNAs induced a loss of function that reduced dextran uptake in response to CSF1 stimulation.
CSF1stim.count.txt


title: siCsde_NS_1

value: MCEC


title: CSF1 stimulated Presort sgRNAs

description:
This sample represents the sgRNAs present in the cell populations on sorting day for the CSF1 stimulated dextran uptake screen
CSF1stim.count.txt


title: CRA_WB_156


title: CRA_WB_157


title: Human_CMixS1


title: Human_235OS_PeriRetina


title: si_H_TGF_2

value: sihnRNP H1

value: 10 ng/ml TGF-Beta


title: si_H_TGF_3