title: C1-SF18101215-24h


title: C11-SF18101224-24h

status: Public on Nov 21 2023

type: SRA

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

country: USA

institute: VUMC

library_source: transcriptomic single cell

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

molecule: total RNA

organism: Gallus gallus

source_name: basilar papilla

extract_protocol:
FACS sorted into 96-well plates containing RNA lysis buffer
smartseq2

treatment_protocol: in vivo administration of sisomicin with harvesting of cells at indicated timepoints

tag: tissue

value: basilar papilla

tag: treatment


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title: G3-SF18103107-p11control


title: G4-SF18103106-p11control


title: G2-SF18103107-p11control


title: G3-SF18103106-p11control


title: G7-SF18103107-p11control


title: G2-SF18103106-p11control


title: G2-SF18103105-p11control


title: G12-SF18103110-p11control


title: G3-SF18103105-p11control


title: G12-SF18103109-p11control


title: G12-SF18103107-p11control


title: G12-SF18103106-p11control


title: G11-SF18103107-p11control


title: G11-SF18103110-p11control


title: G5-SF18103106-p11control


title: G11-SF18103106-p11control


title: G12-SF18103105-p11control


title: G10-SF18103107-p11control


title: G11-SF18103105-p11control


title: G10-SF18103110-p11control


title: G10-SF18103106-p11control


title: G10-SF18103105-p11control


title: G1-SF18103107-p11control


title: G1-SF18103108-p11control


title: G1-SF18103105-p11control


title: F9-SF18103108-p11control


title: F9-SF18103107-p11control


title: F9-SF18103106-p11control


title: F9-SF18103105-p11control


title: F8-SF18103110-p11control


title: F8-SF18103108-p11control


title: F8-SF18103107-p11control


title: F8-SF18103106-p11control


title: F8-SF18103105-p11control


title: F7-SF18103108-p11control


title: F7-SF18103107-p11control


title: G1-SF18103106-p11control


title: F7-SF18103105-p11control


title: F7-SF18103106-p11control


title: F6-SF18103110-p11control


title: F6-SF18103107-p11control


title: F6-SF18103106-p11control


title: F6-SF18103105-p11control


title: F5-SF18103110-p11control


title: F5-SF18103107-p11control


title: F4-SF18103110-p11control


title: F5-SF18103105-p11control


title: F4-SF18103108-p11control


title: F4-SF18103107-p11control


title: F4-SF18103105-p11control


title: F3-SF18103109-p11control


title: F3-SF18103108-p11control


title: F3-SF18103107-p11control


title: F3-SF18103105-p11control


title: F2-SF18103105-p11control


title: F2-SF18103107-p11control


title: F11-SF18103107-p11control


title: F4-SF18103109-p11control


title: F11-SF18103105-p11control


title: F2-SF18103109-p11control


title: F10-SF18103109-p11control


title: F4-SF18103106-p11control


title: F10-SF18103107-p11control


title: F5-SF18103106-p11control


title: F10-SF18103105-p11control


title: F12-SF18103105-p11control


title: F1-SF18103108-p11control


title: F10-SF18103106-p11control


title: F11-SF18103106-p11control


title: F1-SF18103107-p11control


title: E9-SF18103107-p11control


title: E9-SF18103108-p11control


title: E9-SF18103106-p11control


title: F1-SF18103106-p11control


title: E8-SF18103107-p11control


title: E9-SF18103105-p11control


title: E8-SF18103108-p11control


title: E8-SF18103109-p11control


title: E8-SF18103105-p11control


title: E7-SF18103109-p11control


title: E7-SF18103107-p11control


title: E7-SF18103105-p11control


title: F1-SF18103109-p11control


title: E7-SF18103106-p11control


title: F1-SF18103105-p11control


title: E6-SF18103110-p11control


title: E6-SF18103107-p11control


title: E5-SF18103110-p11control


title: E5-SF18103106-p11control


title: E5-SF18103107-p11control


title: E5-SF18103109-p11control


title: E6-SF18103106-p11control


title: E5-SF18103105-p11control


title: E4-SF18103110-p11control


title: E4-SF18103106-p11control


title: E4-SF18103109-p11control


title: E4-SF18103107-p11control


title: E3-SF18103110-p11control


title: E3-SF18103109-p11control


title: E3-SF18103108-p11control


title: E12-SF18103105-p11control


title: E11-SF18103108-p11control


title: E2-SF18103105-p11control


title: E3-SF18103106-p11control


title: E2-SF18103108-p11control


title: E3-SF18103107-p11control


title: E3-SF18103105-p11control


title: E6-SF18103105-p11control


title: E11-SF18103106-p11control


title: E10-SF18103109-p11control


title: E4-SF18103105-p11control


title: E1-SF18103109-p11control


title: E10-SF18103106-p11control


title: E1-SF18103107-p11control


title: D9-SF18103110-p11control


title: E1-SF18103105-p11control


title: E1-SF18103106-p11control


title: E2-SF18103107-p11control


title: D9-SF18103106-p11control


title: D9-SF18103107-p11control


title: D9-SF18103105-p11control


title: E11-SF18103105-p11control


title: D8-SF18103105-p11control


title: D7-SF18103109-p11control


title: D7-SF18103107-p11control


title: D8-SF18103108-p11control


title: D5-SF18103106-p11control


title: D8-SF18103107-p11control


title: D5-SF18103105-p11control


title: D7-SF18103108-p11control


title: D8-SF18103106-p11control


title: D6-SF18103105-p11control


title: E10-SF18103105-p11control


title: D6-SF18103107-p11control


title: D4-SF18103105-p11control


title: D3-SF18103107-p11control


title: D3-SF18103105-p11control


title: D5-SF18103110-p11control


title: D12-SF18103105-p11control


title: D11-SF18103106-p11control


title: D11-SF18103107-p11control


title: D4-SF18103106-p11control


title: E1-SF18103108-p11control


title: D4-SF18103108-p11control


title: D3-SF18103106-p11control


title: D10-SF18103107-p11control


title: D2-SF18103105-p11control


title: D10-SF18103105-p11control


title: D2-SF18103107-p11control


title: Control-Blood-3

city: Bern

first: Aref

last: Hosseini

state: Switzerland

address: Inselspital, INO-F

country: Switzerland

institute: Institute of Pharmacology

library_source: transcriptomic

data_processing:
The quality of the RNA-seq data was assessed usingfastqc v. 0.11.9.
The reads were mapped to the reference genome using HISAT2 v. 2.2.1
FeatureCounts v. 2.0.1was used to count the number of reads overlapping with each gene as specified in the genome annotation (Mus_musculus.GRCm39.104)
Subsequent data analysis was performed in R v. 4.1.0. The Bioconductor package DESeq2 v. 1.32.0 was used to analyze differentially expressed genes with default parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count reads for each gene for each sample

organism: Mus musculus

source_name: Eosinophil

extract_protocol:
RNA from the samples was extracted using the RNeasy Plus Mini Kit (74134, Qiagen, Hilden Germany), following the manufacturer’s instructions. The quantity and quality of the purified total RNA was assessed using a Thermo Fisher Scientific Qubit 3.0 fluorometer with the Qubit RNA BR Assay Kit (Q10211, Thermo Fisher Scientific, distributed by LuBioScience GmbH, Lucerne, Switzerland) and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer RNA Kit (DNF-471, Agilent Technologies, Santa Clara, USA), respectively.
Sequencing libraries were constructed using an illumina TruSeq Stranded mRNA Library Prep kit (20020595, illumina, San Diego, USA) in combination with TruSeq RNA UD Indexes (20022371, illumina) according to illumina’s guidelines. The cDNA libraries were evaluated using a Thermo Fisher Scientific Qubit 3.0 fluorometer with the Qubit dsDNA HS Assay Kit (Q32854, Thermo Fisher Scientific) and an Agilent Fragment Analyzer (Agilent) with an HS NGS Fragment Kit (DNF-474, Agilent), respectively.

tag: cell type

value: Eosinophil


title: D7-SF18103106-p11control


title: Control-Blood-1


title: D10-SF18103106-p11control


title: Control-BoneMarrow-2


title: D1-SF18103110-p11control


title: D7-SF18103105-p11control


title: D1-SF18103106-p11control


title: D6-SF18103108-p11control


title: Atg5-Knockout-BoneMarrow-2


title: D11-SF18103105-p11control


title: D10-SF18103110-p11control


title: Atg5-Knockout-BoneMarrow-1


title: Control-BoneMarrow-1


title: C9-SF18103108-p11control


title: D1-SF18103107-p11control


title: Atg5-Knockout-Blood-2


title: Control-Blood-2


title: C9-SF18103106-p11control


title: Atg5-Knockout-Blood-1


title: D2-SF18103108-p11control


title: E9-SF18103109-p11control


title: C9-SF18103109-p11control


title: Atg5-Knockout-BoneMarrow-3


title: Atg5-Knockout-Blood-3


title: LNCaP_Control_R1

city: Los Angeles

first: Qian

last: Yang

state: CA

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC version 0.9.0 was applied to do Quality Control.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome using Bowtie2.
Combat package was applied to remove batch effect.
Assembly: hg38

organism: Homo sapiens

growth_protocol: LNCaP cells were grown in RPMI-1640 media (Gibco) supplemented with 10% FBS and penicillin/streptomycin. LAPC4 cells were grown in IMDM (Gibco)supplemented with 10% FBS and 1nM R1881 plus penicillin/streptomycin.

extract_protocol:
Total RNA was extracted by RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions
Standard Illumina library preparation protocol

treatment_protocol: Combined treatment: LNCaP was treated with 7 days of vehicle control, enzalutamide treatment (10uM), and combination treatment (Enzalutamide (10uM) + OC2 inhibitor (10uM)).

tag: cell line

value: LNCaP

value: vehicle control


title: C9-SF18103107-p11control


title: C8-SF18103106-p11control


title: C9-SF18103105-p11control


title: LNCaP_Control_R3


title: C8-SF18103109-p11control


title: C8-SF18103107-p11control


title: LNCaP_Combine_R3

value: combination treatment (Enzalutamide (10uM) + OC2 inhibitor (10uM))


title: Control-BoneMarrow-3


title: C8-SF18103105-p11control


title: LNCaP_Combine_R1


title: D1-SF18103105-p11control


title: LNCaP_Combine_R2


title: C7-SF18103109-p11control


title: LNCaP_Enza_7D_2

value: enzalutamide treatment (10uM)


title: LNCaP_Enza_7D_3


title: C7-SF18103108-p11control


title: C7-SF18103107-p11control


title: LNCaP_Enza_7D_1


title: LNCaP_Control_R2


title: LAPC4_OC2OE_3

value: OC2 OE


title: C7-SF18103105-p11control


title: LAPC4_OC2OE_2


title: LAPC4_OC2OE_1


title: C6-SF18103106-p11control


title: C7-SF18103106-p11control


title: LAPC4_Vec_3

value: Vec


title: C6-SF18103105-p11control


title: C5-SF18103110-p11control


title: LAPC4_Vec_2


title: LAPC4_Vec_1


title: Lncap cell line-shOC2_2


title: C5-SF18103107-p11control


title: Lncap cell line-shOC2_1


title: C5-SF18103105-p11control


title: C5-SF18103106-p11control


title: C4-SF18103110-p11control


title: C4-SF18103107-p11control


title: Lncap cell line-OC2_OE_1


title: C4-SF18103106-p11control


title: Lncap cell line-shCon_1

value: shCon


title: Lncap cell line-OC2_OE_2


title: C4-SF18103105-p11control


title: Lncap cell line-Control_2

value: Control


title: Lncap cell line-Control_1


title: C3-SF18103107-p11control


title: C3-SF18103110-p11control


title: C6-SF18103110-p11control


title: Combine_FOXA1_2-CutRun

library_source: genomic

data_processing:
Pair-end 150bp reads were aligned to the hg38 reference genome using Bowtie2. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome using Bowtie2.
Adaptors were removed using Trim galore software. Each replicate, the raw reads were aligned to masked version of the reference human genome hg19 in 4C analysis.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
hg38 Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using SEACR method with top 1% peaks and simultaneously generating bedgraph files in Reads Per Million scale
Assembly: hg38
Supplementary files format and content: bigwig files  were generated by deeptools with corresponding scale in each sample, which representing signal normalized to per million reads

molecule: genomic DNA

extract_protocol:
The DNA extractions were performed according to the manufacturer’s protocol from cell signaling technology (CST, #86652)
The CUT & RUN library wasgenerated with the DNA Library Prep Kit for Illumina (CST, #56795) combined with Multiplex Oligos for Illumina®(Dual Index Primers) (CST, # 47538). The adaptor was diluted 1:25 to avoid contamination.  The PCR enrichment step run 15 cycles to amplify the adaptor-ligated CUT&RUN DNA.

value: combination treatment (Enzalutamide (10uM) + OC2 inhibitor (10uM)


title: Combine_FOXA1_1-CutRun


title: Enza_FOXA1-CutRun


title: Veh_Con_FOXA1_L2-CutRun


title: C3-SF18103105-p11control


title: C4-SF18103109-p11control


title: Veh_Con_FOXA1_L1-CutRun


title: Lncap cell line-shCon_2


title: C2-SF18103107-p11control


title: C2-SF18103109-p11control


title: OE_GR_L2-CutRun


title: C2-SF18103106-p11control


title: C2-SF18103105-p11control


title: OE_GR_L1-CutRun


title: C11-SF18103110-p11control


title: Vec_Con_GR_L2-CutRun

value: Vector control


title: C11-SF18103109-p11control


title: OE_AR_L2-CutRun


title: C11-SF18103108-p11control


title: OE_AR_L1-CutRun


title: Vec_Con_AR_L2-CutRun


title: Vec_Con_AR_L1-CutRun


title: C11-SF18103106-p11control


title: C3-SF18103106-p11control


title: C11-SF18103107-p11control


title: C11-SF18103105-p11control


title: OE_H3K4me1_L2-CutRun


title: OE_H3K4me1_L1-CutRun


title: C10-SF18103109-p11control


title: Vec_Con_H3K4me1_L2-CutRun


title: Vec_Con_H3K4me1_L1-CutRun


title: C10-SF18103107-p11control


title: C12-SF18103105-p11control


title: Vec_Con_H3K27Ac_L2-CutRun


title: OE_H3K27Ac_L2-CutRun


title: C1-SF18103110-p11control


title: C1-SF18103106-p11control


title: OE_H3K27Ac_L1-CutRun


title: Vec_Con_GR_L1-CutRun


title: B9-SF18103110-p11control


title: C1-SF18103105-p11control


title: Vec_Con_H3K27Ac_L1-CutRun


title: OE_H3K4me3_L2-CutRun


title: OE_H3K4me3_L1-CutRun


title: Vec_Con_H3K4me3_L1-CutRun


title: B9-SF18103106-p11control


title: Vec_Con_H3K4me3_L2-CutRun


title: B9-SF18103109-p11control


title: B9-SF18103107-p11control


title: OE_H3K27me3_L2-CutRun


title: B8-SF18103107-p11control


title: OE_H3K27me3_L1-CutRun


title: B9-SF18103105-p11control


title: B8-SF18103106-p11control


title: C10-SF18103105-p11control


title: B8-SF18103105-p11control


title: Vec_Con_H3K27me3_L2-CutRun


title: Vec_Con_H3K27me3_L1-CutRun


title: C1-SF18103107-p11control


title: B7-SF18103110-p11control


title: B7-SF18103109-p11control


title: OE_OC2_L1-CutRun


title: Vec_Con_OC2_L1-CutRun


title: B7-SF18103107-p11control


title: B7-SF18103105-p11control


title: B7-SF18103106-p11control


title: Lncap cell line-Combine_2-ATAC-Seq

data_processing:
Pair-end 150bp reads were aligned to the hg38 reference genome using Bowtie2 in Vec Con, Enza and combine ATAC-Seq data. Hg19 reference genome was used in Control and OE OC2 ATAC-Seq data.
Adaptors were removed using Trim galore software.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale
Assembly: hg38 in Vec Con, Enza and combine ATAC-Seq data; hg19 in Control and OE OC2 ATAC-Seq data.
Supplementary files format and content: bigwig files representing signal normalized to per million reads

extract_protocol:
50,000 viable cells were precipitated and kept on ice and subsequently resuspended ATAC Resuspension Buffer (RSB) (49.25mL nuclease-free water, 500uL 1M PH7.5 Tris-HCL, 100uL 5M NaCl, and 150uL 1M MgCl2). 50uL of Transposition Master mix (25uL 2xTD buffer, 1uL Tagment DNA enzyme, 16.5uL of PBS, 0.5uL 1% Digitonin, 0.5uL 10% Tween-20 and 6.5uL Nuclease-free water) for 30min reaction at 37C with 1000 rpm mixing. DNA was then purified using Zymo DNA clean and Concentrator-5 kit.
Libraries were prepared following the Buenrostro protocol (Buenrostro, Wu et al. 2015).


title: Lncap cell line-Combine_1-ATAC-Seq


title: B6-SF18103110-p11control


title: B6-SF18103108-p11control


title: Lncap cell line-Enza_2-ATAC-Seq


title: Lncap cell line-Enza_1-ATAC-Seq


title: Lncap cell line-Veh Con_1-ATAC-Seq


title: Lncap cell line-Veh Con_2-ATAC-Seq


title: Lncap cell line-OE-OC2_2-ATAC-Seq

value: OE OC2


title: B6-SF18103105-p11control


title: OE_OC2_L2-CutRun


title: B6-SF18103106-p11control


title: Lncap cell line-OE-OC2_1-ATAC-Seq


title: B6-SF18103107-p11control


title: B5-SF18103107-p11control


title: B5-SF18103108-p11control


title: B5-SF18103106-p11control


title: Lncap cell line-vector-Control-1-ATAC-Seq

value: vector control


title: B5-SF18103105-p11control


title: Vec_Con_OC2_L2-CutRun


title: Lncap cell line-vector-Control-2-ATAC-Seq


title: Hi-ChIP_H3K27ac_GI-MEN_ASCL1_pos

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
Hi-ChIP data were aligned and processed using HiC-Pro pipeline version 2.11.1, and the reads in the fastq files were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 version 2.4.1.
The restriction sites ^GATC and G^ANTC across the human genome were cut and utilized by HiC-Pro using the HiC-Pro Utilities Python script “digest genome”.
HiC-Pro configuration on ligation site were set to be ^GATC and G^ANTC optimize for ARIMA kit data. The aligned data were further processed using hichipper to call interactions.
Hichipper version 2.7.9 was used to extract the valid interactions from the HiC-Pro data and generate the bedpe interaction file by utilizing anchors from peaks called by MACS2 broadPeak using the dangling-end and self-cycle Hi-ChIP read pairs with the following parameters: --keep-dup all -p 1e-9 --extsize 147 --nomodel -f bed.
Hichipper used to process interactions using the following parameters: -l 50 -mi 5000 -ma 2000000.
Assembly: hg19
Supplementary files format and content: txt file output from HiC-Pro
Supplementary files format and content: bedpe file output from hichipper
Supplementary files format and content: anchor used by hichipper
Library strategy: HiChIP

source_name: GI-MEN cells

growth_protocol: GI-MEN DOX-ASCL1 cells cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from the H3K27ac HiChIP-seq samples and sequencing of paired-end 100-bp-long reads by the DNBseq were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Paired-end HiChIP

treatment_protocol: Cells were cross-linked with formaldehyde, lysed with Hi-C buffer and then sonicated. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. Post-ChIP DNA was tagmented with Tn5 enzyme follwed by PCR amplification library synthesis

value: GI-MEN cells

value: Neuroblastoma

value: ASCL1 overexpression

tag: chip antibody

value: H3K27ac Antibody (abcam; ab4729)


title: B4-SF18103109-p11control

value: basilar papilla


title: B4-SF18103110-p11control


title: CEN.PK113-7D mtRNA Glucose replicate 2

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

country: Netherlands

institute: Delft University of Technology

library_source: other

data_processing:
RNA-seq reads were aligned to the CEN.PK113-7D reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
raw counts normalized with CPM from edgeR
Assembly: CEN.PK113-7D ASM257140v2
Supplementary files format and content: Comma delimited file, normalized transcript counts

molecule: other

organism: Saccharomyces cerevisiae

source_name: Isolated mitochondria of S. cerevisiae cell culture

growth_protocol: Cells were grown in shake flasks containing 100 mL synthetic medium supplied with either glucose r ethanol-glycerol as carbon source, and harvested in mid-exponential phase

extract_protocol:
RNA was extracted using the miRNeasy Mini kit (Qiagen) with on-column DNA digestion
Samples were poly(A) tailed enzymatically using using E. coli Poly(A) Polymerase (New England Biolabs #M0276), then purified using the miRNeasy Mini kit (Qiagen). Poly(A)-tailed RNA samples were used for library preparation using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies [ONT], Oxford, UK), following manufacturer’s instructions.

treatment_protocol: Mitochondria were isolated from whole cells by a process of spheroplasting, homogenization and differential centrifugation

tag: replicate

value: Replicate 2

tag: strain

tag: carbon source

value: Glucose


title: CEN.PK113-7D mtRNA Glucose replicate 3

value: Replicate 3


title: B4-SF18103106-p11control


title: CEN.PK113-7D mtRNA Glucose replicate 1

value: Replicate 1


title: B4-SF18103107-p11control


title: CEN.PK113-7D mtRNA Ethanol replicate 3

value: Ethanol


title: B5-SF18103109-p11control


title: B4-SF18103105-p11control


title: CEN.PK113-7D mtRNA Ethanol replicate 2


title: Rat 9 76

type: RNA

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

country: China

institute: School of Pharmaceutical Sciences, Jilin University

hyb_protocol: Then the Hy3-labelled samples were hybridised on the miRCURYTMLNA Array (v.18.0) (Exiqon, Vedbaek, Denmark) according to the array manual

scan_protocol: The slides were scanned using an Axon GenePix 4000 B microarray scanner (Axon Instruments, Foster City, CA, USA)

data_processing:
The scanned images were imported into GenePix Pro 6.0 software for grid alignment and data extraction.
Normalized signal intensity

organism: Rattus norvegicus

source_name: Nonalcoholic fatty liver

label_protocol: the miRCURY™ Hy3™/Hy5™ Power labelling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

growth_protocol: After one week of adaptive feeding, rats were were fed with a basic diet or high-fat diet for 12 weeks.

extract_protocol: Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Mini Kit (Qiagen, Carlsbad, USA) according to the manufacturer’s instructions

treatment_protocol: 1,4,8 normal diet feeding, 11,12,19 high-fat diet feeding, 74,75,76 high-fat diet feeding plus HTG treatment.

value: Nonalcoholic fatty liver

value: high-fat diet + HCG treatment

value: Wistar

tag: age

tag: Sex

value: Male

tag: Stage

value: Early and middle stage


title: Hi-ChIP_H3K27ac_GI-MEN_ASCL1_neg

value: control


title: CEN.PK113-7D mtRNA Ethanol replicate 1


title: B3-SF18103109-p11control


title: B3-SF18103107-p11control


title: Rat 8 75


title: Rat 6 8

source_name: Normal liver tissue

value: Normal liver tissue

value: normal diet

value: normal


title: B3-SF18103106-p11control


title: Rat 7 74


title: Rat 5 4


title: Rat 4 1


title: Rat 3 19

value: high-fat diet


title: B2-SF18103110-p11control


title: B3-SF18103105-p11control


title: B2-SF18103107-p11control


title: B2-SF18103109-p11control


title: Rat 2 12


title: B3-SF18103110-p11control


title: B2-SF18103106-p11control


title: B2-SF18103105-p11control


title: Rat 1 11


title: B12-SF18103105-p11control


title: B3-SF18103108-p11control


title: B11-SF18103109-p11control


title: B11-SF18103107-p11control


title: B11-SF18103106-p11control


title: B11-SF18103105-p11control


title: B10-SF18103110-p11control


title: B10-SF18103107-p11control


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 4

city: Vancouver

first: Ryan

middle: Thomas

last: McCallum

state: BC

address: 938 W 28th Ave

department: Faculty of Medicine

country: Canada

institute: University of British Columbia

hyb_protocol: Whole-genome microarray analyses were performed with the Affymetrix GeneChip Rat Gene 2.0 ST microarray at SickKids (Toronto).

data_processing: The data were analyzed with GeneSpring GX software v. 14.9.1 using default Affymetrix settings.

label: biotin

source_name: Female, CUS + Dimethyl Fumarate

growth_protocol: Male and female Wistar rats weighing approximately 200-250 grams at the beginning of the study were used. Following arrival, rodents were housed in same sex groups of three in ventilated cages with access to water and food ad libitum. Rodents were housed in a temperature-controlled colony room (temperature 21°C, humidity 30%–45%), maintained on a 12-hour reverse light–dark cycle (08:00hr lights off; 20:00hr lights on) unless otherwise noted. On the first day of the chronic unpredictable stress (CUS) protocol rodents were relocated to non-ventilated, wire-roofed, opaque individual cages for the remainder of the study. No enrichment was provided, and animals were food restricted to 15-20 grams of 18% rodent chow daily. All behavioural experiments were conducted in a red light illuminated room during the dark phase of the day-night cycle when rodents were active. All experimental procedures and protocols were approved by the Animal Care Committee of the University of Guelph and carried out in accordance with the recommendations of the Canadian Council on Animal Care.  Developed to last a total of 8 weeks, the current CUS protocol consisted of various uncontrollable, non-debilitating, and inescapable physical, psychological, and circadian stressors. Stressors varied daily and included: cage tilt (30–45°, 8 hours), cold swim (10–13°C, 5 minutes), cold exposure (4°C, 1 hour), damp bedding (500 mL water, 12–14 hours), food and water deprivation (24 hours), lights on and off intermittently (8 hours), and reverse light cycle (24 hours). Each stressor was only administered once in any given week, with each weekly schedule generated randomly to prevent predictability. Stressors were continued throughout the behavioural testing period to maintain the depression-like phenotype.

extract_protocol: Total RNA was isolated from hippocampal tissue of male and female animals and purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) (N = 4/group) and the RNA quality was assessed by NanoDrop (ThermoScientific). Samples were then sent to the TCAG Microarray Facility at Sick Kids Hospital (Toronto) for microarray processing.

treatment_protocol: Rodents were randomly assigned to one of six experimental groups (N = 10 subjects) and included: male vehicle (VEH)-treated non-stressed control (male VEH); male VEH-treated CUS (CUS-VEH); male dimethyl fumarate (DMF)-treated CUS (CUS-DMF); female VEH-treated non-stressed control (female VEH); female CUS-VEH; female CUS-DMF. Rodent weights were collected twice per week to monitor rodent health and adjust DMF dosage accordingly.

value: Female

tag: condition

value: CUS

tag: drug

value: Dimethyl Fumarate

value: Dorsal Hippocampus


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 2

scan_protocol: Whole-genome microarray analyses were performed with the Affymetrix GeneChip Rat Gene 2.0 ST microarray at SickKids (Toronto).


title: B10-SF18103105-p11control

value: basilar papilla


title: B1-SF18103110-p11control


title: B1-SF18103109-p11control


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Vehicle Biological Rep 4

source_name: Female, CUS + Vehicle

label_protocol: Whole-genome microarray analyses were performed with the Affymetrix GeneChip Rat Gene 2.0 ST microarray at SickKids (Toronto).

value: Vehicle


title: B1-SF18103107-p11control


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 1


title: B1-SF18103105-p11control


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 3


title: B1-SF18103106-p11control


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Vehicle Biological Rep 1


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Vehicle Biological Rep 3


title: B10-SF18103108-p11control


title: A9-SF18103109-p11control


title: Dorsal Hippocampus Female Control Vehicle Biological Rep 3

source_name: Female, Control + Vehicle

value: Control


title: Dorsal Hippocampus Female Control Vehicle Biological Rep 4


title: B10-SF18103106-p11control


title: Dorsal Hippocampus Female Chronic Unpredictable Stress Vehicle Biological Rep 2


title: Dorsal Hippocampus Female Control Vehicle Biological Rep 2


title: A9-SF18103106-p11control


title: Dorsal Hippocampus Female Control Vehicle Biological Rep 1


title: A9-SF18103108-p11control


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 4

source_name: Male, CUS + Dimethyl Fumarate


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 1


title: A9-SF18103105-p11control


title: A8-SF18103110-p11control


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 2


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Vehicle Biological Rep 3

source_name: Male, CUS + Vehicle


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Dimethyl Fumarate Biological Replicate 3


title: A8-SF18103106-p11control


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Vehicle Biological Rep 4


title: A8-SF18103107-p11control


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Vehicle Biological Rep 2


title: A8-SF18103105-p11control


title: A7-SF18103110-p11control


title: A7-SF18103109-p11control


title: A7-SF18103107-p11control


title: Dorsal Hippocampus Male Chronic Unpredictable Stress Vehicle Biological Rep 1


title: Fpt1KO_4_ethanol

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

data_processing:
Reads were mapped to the budding yeast reference genome (SacCer3) using STAR (version 2.7.1a). Count tables were generated using the bioconda package eXpress. Reads that could be mapped to multiple locations were excluded in further analysis.
Assembly: SacCer3
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 fpt1::KanMX

growth_protocol: Cells were grown to mid-log phase in YEPD and subsequently switched to ethanol for 2 hours at 30°C.

extract_protocol:
mRNA was extracted from exponentially growing cells using a RNeasy kit (Qiagen) and treated with DNaseI.
Sequencing libraries of cDNA were made using the TruSeq stranded mRNA kit (Illumina) according to the manufacturer’s protocol. The libraries were analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 fpt1::KanMX


title: A7-SF18103105-p11control


title: A7-SF18103106-p11control


title: Dorsal Hippocampus Male Control Vehicle Biological Rep 3

source_name: Male, Control + Vehicle


title: Fpt1KO_2_ethanol


title: Fpt1KO_3_ethanol


title: Fpt1KO_1_ethanol


title: Dorsal Hippocampus Male Control Vehicle Biological Rep 4


title: WT_3_ethanol

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: A6-SF18103109-p11control


title: A6-SF18103107-p11control


title: WT_2_ethanol


title: WT_1_ethanol


title: A6-SF18103106-p11control


title: A5-SF18103110-p11control


title: Dorsal Hippocampus Male Control Vehicle Biological Rep 2

value: Wistar


title: HCVmi

city: Wuhan

first: Haoran

last: Qu

state: Hubei

address: Wuhan University School of Basic Medical Sciences, Donghu Road 185#, Wuhan 430071, Hubei Province, P. R. China

institute: Wuhan University

description: Gene expression in uninfected Huh7.5.1 cells

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl 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 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Huh7.5.1 cells

label_protocol: Each RNA 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/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: HCVcc (JFH1)-containing virus supernatant was directly inoculated into Huh7.5.1 cells and cultured for 6 h. The cell culture medium was replaced with fresh 10% fetal bovine serum DMEM and cultured for another 3 days at 37 °C in a CO2 biochemical incubator.

value: hepatocellular carcinoma cells


title: Fpt1KO_4_YEPD


title: A6-SF18103105-p11control


title: A5-SF18103109-p11control


title: A5-SF18103107-p11control


title: HCVpl

description: Gene expression in Huh7.5.1 cells at 6 h post-infection with HCVcc

source_name: Huh7.5.1 cells infected with HCVcc for 6 h


title: Fpt1KO_3_YEPD


title: A6-SF18103110-p11control


title: A5-SF18103105-p11control


title: Fpt1KO_2_YEPD


title: Fpt1KO_1_YEPD


title: Dorsal Hippocampus Male Control Vehicle Biological Rep 1

value: Male


title: WT_3_YEPD


title: WT_2_YEPD


title: input_4

data_processing:
Reads were mapped to the sacCer3 reference genome downloaded from UCSC using the BWA-MEM program version 0.7.17-r1188 using the option ‘-M’. No filtering for mapping quality was performed. Coverage tracks were created using the GenomicRanges and rtracklayer R/Bioconductor packages. Specifically, unduplicated reads were extended 200 basepairs from their 5’ end and inversely weighted by the number of (multi-)mapping positions. Coverage was scaled to integrate to 1x genome size (reads per genomic content, RPGC). R version 4.2.1 and Bioconductor release 3.15 were used.
Assembly: SacCer3
Supplementary files format and content: Peak file with quantitative data (bigwig)

source_name: MAT⍺ can1::HphMX lyp1::STE3pr-LEU2 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 RPO31-TAP-His3MX6

growth_protocol: Cells were grown to mid-log phase in YEPD at 30°C.

extract_protocol:
Exponentially growing cells were cross-linked with 1% formaldehyde for 15 minutes and chromatin lysated were prepared. Pulldown of cross-linked proteins was done using a TAP antibody.
Sequencing libraries were made using the KAPA Hyper Prep Kit (KAPA Biosystems). Libraries were amplified by PCR and size selection (200-450 bp) was performed using AMPure XP beads (Beckman Coultier). DNA concentration was measured using a Qubit dsDNA HS Assay Kit (Invitrogen) and size-distribution of DNA fragments was visualized using an Agilent 2100 Bioanalyzer. Purified DNA was sequenced (single read, 65 bp) on a HiSeq2500 platform (Illumina).

value: MATalpha can1::HphMX lyp1::STE3pr-LEU2 his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 RPO31-TAP-His3MX6

value: TAP Tag (CAB1001)


title: A4-SF18103110-p11control

source_name: basilar papilla


title: A4-SF18103107-p11control


title: A4-SF18103105-p11control


title: WT_1_YEPD


title: A3-SF18103110-p11control


title: A3-SF18103109-p11control


title: RPB2_rep3

source_name: MAT⍺ can1::HphMX lyp1::STE3pr-LEU2 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 RPB2-TAP-His3MX6

value: MATalpha can1::HphMX lyp1::STE3pr-LEU2 his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 RPB2-TAP-His3MX6


title: RPB2_rep2


title: A3-SF18103105-p11control


title: A3-SF18103106-p11control


title: RPB2_rep1


title: A2-SF18103110-p11control


title: A2-SF18103108-p11control


title: RPL13A_rep3

source_name: MAT⍺ can1::HphMX lyp1::STE3pr-LEU2 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 RPL13A-TAP-His3MX6

value: MATalpha can1::HphMX lyp1::STE3pr-LEU2 his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 RPL13A-TAP-His3MX6


title: RPL13A_rep1


title: RPL13A_rep2


title: A2-SF18103107-p11control


title: A12-SF18103105-p11control


title: RPO31_rep3


title: A11-SF18103110-p11control


title: input_1

source_name: MAT⍺ can1::HphMX lyp1::STE3pr-LEU2 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 FPT1-TAP-His3MX6

value: MATalpha can1::HphMX lyp1::STE3pr-LEU2 his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 FPT1-TAP-His3MX6


title: RPO31_rep1


title: A11-SF18103107-p11control


title: YKR011C_rep2


title: RPO31_rep2


title: YKR011C_rep3


title: A3-SF18103107-p11control


title: A10-SF18103110-p11control


title: A10-SF18103108-p11control


title: A10-SF18103107-p11control


title: A11-SF18103106-p11control


title: A11-SF18103105-p11control


title: A10-SF18103106-p11control


title: A10-SF18103105-p11control


title: A2-SF18103106-p11control


title: A1-SF18103109-p11control


title: A1-SF18103107-p11control


title: A1-SF18103108-p11control


title: YKR011C_rep1


title: H6-SF18103137-96h


title: A1-SF18103105-p11control


title: A1-SF18103106-p11control


title: H6-SF18103133-96h


title: H5-SF18103133-96h


title: whole embryo, at stage 10.5, injected with Fam46a-MO2+MO3 biological rep2

city: Kyoto

first: Toshiyasu

last: Suzuki

address: Sakyo-ku

department: Department of Cell and Developmental Biology, Graduate school of Biostudies

country: Japan

institute: Kyoto University

description: Fam46a-MO2 (7 ng/cell) plus Fam46-MO3 (7 ng/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Embryos were collected at stage 10.5 for microarray analysis.

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Xenopus laevis Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The CEL files were analyzed with RMA algorithm on GeneSpring GX with default analysis settings.

organism: Xenopus laevis

source_name: whole embryo, stage 10.5, Fam46a-MO2+3-injected

label_protocol: Biotinylated cRNA was prepared from 100 ng total RNA using the GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix) according to the manufacturer’s instruction.

growth_protocol: Xenopus laevis embryos were obtained by in vitro fertilization and cultured in 0.1× MBS at 22°C.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and then purified by RNeasy Mini Kit (QIAGEN).
The quality of total RNA was assessed using the Agilent 2100 BioAnalyser.

treatment_protocol:
Morpholino oligonucleotides (MOs) were injected into the animal pole of all blastomeres at the four-cell stage.
Embryos were collected at stages 8 and 10.5 for microarray analysis.

value: whole embryo

value: stage 10.5


title: whole embryo, at stage 10.5, injected with Fam46a-MO2+MO3 biological rep1


title: whole embryo, at stage 10.5, injected with Fam46a-MO1 biological rep1

description: Fam46a-MO1 (10 ng/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Embryos were collected at stage 10.5 for microarray analysis.

source_name: whole embryo, stage 10.5, Fam46a-MO1-injected


title: whole embryo, at stage 10.5, injected with Fam46a-MO1 biological rep2


title: whole embryo, at stage 10.5, injected with CoMO biological rep2

description: CoMO (10 ng/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Embryos were collected at stage 10.5 for microarray analysis.

source_name: whole embryo, stage 10.5, CoMO-injected

value: CoMO-injected


title: whole embryo, at stage 8, injected with Fam46a-MO1 biological rep1

description: Fam46a-MO1 (10 ng/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Embryos were collected at stage 8 for microarray analysis.

source_name: whole embryo, stage 8, Fam46a-MO1-injected

value: stage 8


title: whole embryo, at stage 8, injected with Fam46a-MO2+MO3 biological rep2

description: Fam46a-MO2 (7 ng/cell) plus Fam46-MO3 (7 ng/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Embryos were collected at stage 8 for microarray analysis.

source_name: whole embryo, stage 8, Fam46a-MO2+3-injected


title: whole embryo, at stage 8, injected with Fam46a-MO1 biological rep2


title: whole embryo, at stage 8, injected with CoMO biological rep1

description: CoMO (10 ng/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Embryos were collected at stage 8 for microarray analysis.

source_name: whole embryo, stage 8, CoMO-injected


title: whole embryo, at stage 8, injected with Fam46a-MO2+MO3 biological rep1


title: H4-SF18103137-96h

value: basilar papilla


title: CAL-27sphere, IgG, rep1

first: Yuantong

last: Liu

address: Luoyu road

description: IgG control

data_processing:
*library strategy: CUT&Tag
Using Bowtie2 (2.3.5.1) to map the raw reads against the genome with the options.
Read redundancy was removed by the rmdup command of SAMtools.
using macs2 (2.2.7.1) to call peaks and selected peaks with -log10 p values larger than 8
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for IgG sample)

extract_protocol:
TCF4-DNA complexes were isolated with antibody.
The libraries were amplified by mixing the DNA with 2μL of a universal i5 and uniquely barcoded i7 primer. DNA was purified using the phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.

value: IgG antibody


title: CAL-27sphere, TCF4, rep1

description: TCF4-DNA complexes were isolated with antibody.

value: TCF4 antibody


title: H4-SF18103133-96h


title: H3-SF18103137-96h


title: H5-SF18103137-96h


title: whole embryo, at stage 10.5, injected with CoMO biological rep1


title: Animal cap explants of uninjected embryos biological rep1

description: Uninjected embryos were cultured until stage 8. Animal cap explants were prepared at stage 8 and incubated for 3 hours followed by collection for microarray analysis.

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on Affymetrix GeneChip Xenopus laevis Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

data_processing: The CEL files were analyzed with RMA algorithm on GeneSpring X8 with default analysis settings.

source_name: Animal cap explants, uninjected

label_protocol: Biotinylated cRNA was prepared from 250 ng total RNA using the GeneChip 3’ IVT Express Kit (Affymetrix) according to the manufacturer’s instruction.

growth_protocol: Xenopus laevis embryos were obtained by in vitro fertilization and cultured in 0.1× MBS at 22°C. Embryos at stage 4 were transferred into 4% Ficoll in 0.1×MBS and cultured overnight at 15°C in 4% Ficoll in 0.1x MBS until stage 8 (mid-blastula).

extract_protocol: Total RNA was extracted using TRIzol reagent.

treatment_protocol: chordin mRNA (25 pg/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Animal cap explants were prepared at stage 8 and incubated in 1x Steinberg's solution for 3 hours followed by collection for microarray analysis. For uninjected embryos, embryos were cultured and treated in the same way except injection.

value: Animal cap explant

value: Uninjected

value: dissected at stage 8 and incubated for 3 hours


title: H3-SF18103133-96h


title: H2-SF18103137-96h


title: H2-SF18103133-96h


title: Animal cap explants of chordin-injected embryos biological rep1

description: chordin mRNA (25 pg/cell) was injected into the animal pole of all blastomeres at the four-cell stage. Animal cap explants were prepared at stage 8 and incubated for 3 hours followed by collection for microarray analysis.

source_name: Animal cap explants, chordin-injected

value: chordin-injected


title: organoid D2, scRNA-seq

first: Giorgia

last: Quadrato

address: 1425 San Pablo Street, Rm 405

institute: Broad Institute, USC Stem Cell & Regenerative Medicine

description: 10X Genomics

data_processing:
Cell Ranger 6.0 pipeline (10x Genomics) was used to align reads from RNA-seq to the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: The filtered barcode, feature, and count matrix was used for subsequent bioinformatic analysis

source_name: cerebellar brain organoid

extract_protocol:
Individual brain organoids were dissociated to single cells, resuspended in PBS-BSA, and loaded into the Chromium Single Cell 3' platform.
Single-cell RNA-Seq libraries were prepared with the Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (10X Genomics,PN-1000128).  Libraries from different samples were pooled based on molar concentrations and sequenced on NovSeq S1(Illumina) with 29 bases for read 1, 91 bases for read 2 and 10 bases for Index 1 & 2.

value: cerebellar brain organoid

value: D2 hiPSC


title: organoid D1, scRNA-seq

description: 10X Genomics


title: organoid D3, scRNA-seq

description: 10X Genomics


title: H1-SF18103133-96h


title: Animal cap explants of uninjected embryos biological rep2


title: G9-SF18103133-96h


title: Animal cap explants of chordin-injected embryos biological rep2


title: whole embryo, at stage 8, injected with CoMO biological rep2


title: H1-SF18103137-96h


title: G8-SF18103134-96h


title: G8-SF18103137-96h


title: G8-SF18103133-96h


title: HC, TCRab

city: New York

first: Ellie

last: Ivanova

state: NY

address: 550 First Ave

department: Pathology

institute: NYU Langone

description:
Enriched TCRab fragment
TCRab: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment (abT cell receptor)

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: hc_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq

source_name: PBMCs

extract_protocol:
PBMCs were isolated form whole blood using ficoll gradient. Cells were encapsulated in Gel-Beads-in emulsion (GEMs) using 10x Controller with a Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1
Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)
The CITE-seq and hashing protocol described by Stoeckius et. al. was used to generate an antibody-derived tag (ADT) sequencing library and hashtag oligo (HTO) library (Stoeckius et. al., 2017). Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)

value: PBMCs

value: healthy control

tag: library type

value: TCRab


title: HC, TCRgd

description:
Enriched TCRgd fragment
TCRgd: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment (gdT cell receptor)

value: TCRgd


title: HC, ADT

description:
Antibody-derived tags (ADT)
ADT: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag

molecule: protein

value: ADT


title: G7-SF18103133-96h

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

extract_protocol:
FACS sorted into 96-well plates containing RNA lysis buffer
smartseq2


title: G6-SF18103137-96h


title: CV15, GEX

description:
Gene expression (GEX)
GEX (5' mRNA): Read 1 contains cell barcode and UMI, Read 2 contains transcript, I1 contains library index

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv15_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq

value: SARS-CoV-2 vaccine

value: GEX


title: HC, BCR

description:
Enriched BCR fragment
BCR: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment

value: BCR


title: HC, GEX


title: CV15, TCRab


title: CV15, TCRgd


title: CV15, ADT


title: HC, HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO: Read 1 contains cell barcode and UMI, Read 2 contains hashtag-derived tag

value: HTO


title: G6-SF18103134-96h

value: basilar papilla


title: G9-SF18103137-96h


title: G6-SF18103133-96h