title: Pt16_Z1, scRNAseq

status: Public on Jan 05 2024

city: Guangzhou

first: Lixia

last: Xu

address: 58 Zhongshan Road 2

institute: Sun Yat-sen University First Affiliated Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver adjacent tissue

extract_protocol:
Tissue samples were processed with mechanical chopping with blades, followed by Tumor Dissociation Kit (Miltenyi Biotec) and DNaseI (DN25-100MG, Sigma Aldrich) digestion in medium (RPMI1640 with 5% FBS) for 30 min at 37°C. The cell suspension was passed through a 70-um filter (Miiltenyi Biotec), followed by 1×RBC lysis buffer (eBioscience) treatment.
Single cells were processed with the GemCode Single Cell Platform using the Gemcode Gel Bead, Chip and Libraray Kits (10x Genomics, Pleasanton, CA) following the manufacturer’s protocol with modifications. Briefly, samples were processed using kits pertaining to the Chromium 5' immune profling v2 barcoding chemistry of 10x Genomics. Libraries were constructed according to the standard 10x Genomics protocol (Single Cell 5’Reagent Kits v5.2 User Guide) with modifications and performed the paired-end 2×150bp (PE150) sequencing on Novaseq 6000 (llumina, San Diego, CA).

value: liver adjacent tissue


title: Pt18_Z2, scRNAseq

type: SRA

country: China

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: 1_siSTAU1_0hr

status: Public on Dec 18 2023

city: Bethesda

first: Ashish

last: Lal

state: MD

address: 37 Convent Drive, Bldg 3, Room 6134

department: Genetics Branch

country: USA

institute: NCI, NIH

library_source: transcriptomic

data_processing:
RTA 3.10.30 software used for basecalling.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt
Reads were aligned with the reference genome (hg38) and the annotated transcripts using STAR 2.7
Gene expression was quantified using RSEM 1.3.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

molecule: polyA RNA

extract_protocol:
Samples had their RNA extracted with RNeasy Plus Mini Kit.
RNA libraries were prepared using Illumina® Stranded mRNA Prep

tag: cell line

tag: cell type

value: Colorectal cancer cell line

tag: treatment

value: 72 hours + 72 hours siSTAU1


title: 2_siCTRL_0hr

value: 72 hours + 72 hours siCTRL


title: 1_siCTRL_0hr


title: HCT116_ActD_2hr_3

data_processing:
RTA 3.4.4. software used for basecalling.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt
Reads were aligned with the reference genome (hg19) and the annotated transcripts using STAR 2.7
Gene expression was quantified using RSEM 1.3.1
Assembly: hg19
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

extract_protocol:
Samples had their RNA extracted with RNeasy Plus Mini Kit.
RNA libraries were prepared using Illumina® Stranded Total RNA

value: 5 ug/ml Actinomycin D treatment_ 2 hour


title: HCT116_ActD_2hr_2


title: HCT116_0hr_2

value: 5 ug/ml Actinomycin D treatment_ 0 hour


title: HCT116_ActD_2hr_1


title: EARLI_10447_Hyper

status: Public on Jan 08 2024

city: San Francisco

first: Lucile

middle: P A

last: Neyton

state: CA

address: 505 Parnassus Ave

institute: UCSF

data_processing:
Alignment against human genome with kallisto v0.46.1
Gene-level aggregation using tximport v1.14
Genes with less than 16 counts in more than 10% of the samples were filtered
Assembly: ENSEMBL v99
Supplementary files format and content: CSV files with gene counts

source_name: whole blood

growth_protocol: PAXgene tubes

extract_protocol:
rRNA depletion with FastSelect from QIAGEN
NEBnext Ultra II RNAseq from New England Biolabs

value: whole blood

tag: lca

value: Hyper

tag: gender

value: Male

tag: age


title: EARLI_11309_Hyper


title: HCT116_0hr_3


title: HCT116_0hr_1


title: LS180_ActD_4hr_3

value: 5 ug/ml Actinomycin D treatment_ 4 hour


title: 2_siSTAU1_0hr


title: LS180_ActD_4hr_2


title: HCT116_ActD_4hr_1


title: LS180_ActD_4hr_1


title: LS180_ActD_2hr_1


title: LS180_ActD_2hr_3


title: HCT116_ActD_4hr_3


title: LS180_0hr_3


title: LS180_ActD_2hr_2


title: LS180_0hr_2


title: LS180_0hr_1


title: UMSCC74B cells, FXR1 KD2

status: Public on Sep 30 2023

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_5

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Human hg38
Supplementary files format and content: Input tables are included as tab separated files.

growth_protocol: UMSCC74B mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 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.

treatment_protocol: 25 MOI of lentiviral particles containing the control and FXR1 shRNAs were used to treat the cells for 18 hrs. Cells were washed after 18 hrs, kept for 72hrs more in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

tag: genotype

value: Knockdown

value: mesenchymal cells

value: shRNA

tag: time

value: 72 hrs


title: HCT116_ActD_4hr_2


title: UMSCC74B cells, FXR1 KD1

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_4


title: UMSCC74B cells, FXR1 KD3

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_6


title: UMSCC74B cells, Control 3

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_3

value: Control


title: UMSCC74B cells, Control 2

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_2


title: L11N

status: Public on Sep 25 2023

city: Houston

first: Kangyu

last: Lin

address: 1515 Holcombe Blvd

department: Department of Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver normal

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue source

value: colorectal cancer (CRC) patient

value: Liver normal


title: L9N

description: 10x Genomics


title: UMSCC74B cells, Control 1

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_1


title: L5N

description: 10x Genomics


title: C-shNPAS4

status: Public on Aug 31 2023

description:
10X single-nuclei RNA-seq
10x Genomics
Protocol 1

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.1.2). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.232) with standard parameters. Mouse genome mm10 was used for the alignment and genecode vM25 was used for gene annotation and coordinates. We used the R package Seurat (v4.1.0) and customized R scripts for data analyses Data from different samples (SalineCPP, CocaineCPP, SalineNPAS4, CocaineNPAS4) were merged into a unique single cell object. Nuclei with > 250 genes, < 10000 UMIs, and < 5% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) for a resultant expression matrix with 21,516 genes and 52,743 cells. The SCTransform workflow was used for count normalization and data integration using 30 principal components and resolution of 0.5 for Louvain clustering and UMAP. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. After removing 4 clusters showing high expression of glutamatergic neuronal markers and subsequent re-clustering, we identified 20 final distinct clusters. Cell annotation was performed using two different approaches: 1) markers enrichment using a Nucleus Accumbens independent data by Fisher’s exact test and 2) a predictive machine learning model based on a Nucleus Accumbens atlas reference data using the R package scPred. Cell annotation then was manually curated to reflect both analyses. To identify differentially expressed genes between conditions (SalCPP vs CocCPP, CocCPP vs CocNPAS4) in each defined cell types, the R package LIBRA with option MAST was used to perform zero-inflated regression analysis. Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2. We further confirmed these results using a Wilcoxon’s rank sum test.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

molecule: nuclear RNA

organism: Mus musculus

source_name: nucleus accumbens

extract_protocol:
Wild-type C57BL/6J mice received bilateral NAc infusion of AAV-NPAS4 shRNA-GFP or scrambled-GFP control and underwent conditioned place preference for cocaine or saline (total of 4 groups with 4 animals/group). Mice were then rapidly decapitated at 12 weeks of age, and the brains extracted into 4˚C Hibernate A medium with the GlutaMAX, B27 supplement, and NxGen RNase inhibitor (0.2U/uL; Lucigen). NAc tissues were dissected rapidly, flash frozen, and stored at -80˚C until the day of dissociation. These specific steps were modified from Savell et al., 2020 by Hughes, B.W. The following day (when all samples were prepped), frozen tissues were slowly thawed on ice, then chopped with a razor blade ~75-100 times in 2 orthogonal directions. Chopped NAc tissue was lysed with hypotonic lysis buffer (10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) IGEPAL), then supplemented Hibernate-A medium was added, tissue triturated 15-20 times/sample using 3 glass capillaries with decreasing diameters, then 40-micron filtered. Nuclei were isolated by 500xg centrifugation, washed with 1X PBS + 1% BSA and 0.2U/uL RNase inhibitor. Nuclei were then incubated in 7AAD and underwent FACS to remove clumps and whole cells. Samples were then counted and diluted to 1500 nuclei/ul before immediate processing using the 10x Genomics Single-Cell Protocol by the MUSC Translation Science Lab. Libraries were constructed using the Chromium Single Cell 3’ Library Construction Kit (10x Genomics, v3.1), sequenced at Vanderbilt’s Next Gen Sequencing Core (Illumina NovaSeq 6000).
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 according to the manufacturer’s protocol. Libraries and sequencing were performed at the Translational Sequencing Core at MUSC.

value: nucleus accumbens

tag: knockdown

value: cocaine

tag: strain

value: 12 weeks old


title: 12wTi

status: Public on Aug 24 2023

city: Boston

first: April

middle: M

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
the Cell Ranger pipeline v3 was used to process the fastq files and generate the count matrix
Assembly: hg19

source_name: in vitro derived cartilage chrondrocytes, TGFb-treated, 12-weeks

growth_protocol: A detailed description of the protocol for generating chondrogenic cells and tissues from human pluripotent stem cells has been published (PMID: 25961409).

extract_protocol: RNA libraries were prepared using the 10x Chromium v2 3' kit following the manufacturer's protocols

tag: Sex

value: F

value: 12 weeks


title: L7N

description: 10x Genomics


title: S-shNPAS4

value: saline


title: L1N

description: 10x Genomics


title: 06wTi

source_name: in vitro derived cartilage chrondrocytes, TGFb-treated, 6-weeks

value: 6 weeks


title: L3N

description: 10x Genomics


title: C-shScram

value: scScram


title: PPAC4_T_rep3

description: WISP3 KO

data_processing:
alignment to hg19: Star align version 2.7.3, default parameters for hg19 alignment
RNA-seq read mapping: Salmon version 1.2.1, salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization: DESeq2 version 1.36.0
Assembly: hg19
Supplementary files format and content: Batch1-4_normalized_counts.xlsx : Normalized abundance counts across primary RNA-seq datasets generated

source_name: PPAC iPSC line

extract_protocol: TruSeq RNA Library Prep Kit v2 (Illumina)

value: human iPSC-derived articular cartilage treated with TGFB3 for 12 weeks

value: male

value: treated with TGFB3 for 12 weeks


title: S-shScram


title: WISP3ko12wT


title: PPAC4_T_rep1

description: WISP3 KO


title: H9_KO_T_rep1

description: H9WISP3KO hESC-derived articular chondrocytes, female

source_name: In-vitro TGF-beta treated sample

treatment_protocol: Collagenase digestion

value: HESC-derived chondrocytes

value: female


title: L4N

description: 10x Genomics


title: H9_KO_T_rep3


title: H9_KO_T_rep2


title: WISP3ko6wT


title: PPAC1C_T_rep3

description: WISP3 WT


title: PPAC1_T_rep3

description: WISP3 KO


title: PPAC1_T_rep1

description: WISP3 KO


title: L2N

description: 10x Genomics


title: PPAC4_T_rep2

description: WISP3 KO


title: PPAC1C_T_rep2

description: WISP3 WT


title: PPAC1C_T_rep1

description: WISP3 WT


title: PPAC1_T_rep2

description: WISP3 KO


title: In-vitro TGF-beta treated sample [H9_T_30_rep1]

source_name: HESC-derived chondrocytes

value: chondrocytes

value: In-vitro TGF-beta treated sample


title: In-vitro TGF-beta treated sample [H9_T_28_rep1]


title: In-vitro TGF-beta treated sample [H9_T_44_rep2]


title: In-vitro TGF-beta treated sample [H9_T_44_rep3]


title: VEH-MMSCs + TGFβ1 biol rep 2

status: Public on Aug 07 2023

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

data_processing:
Base calling was performed using the Illumina NovaSeq 6000 platform
Adapters were trimmed using Trim Galore! (0.6.7)
Trimmed sequences were aligned to the reference genome and projected to the transcriptome using STAR (4.0.2)
Raw gene counts were quantified using Salmon (1.5.2)
Assembly: Rnor_6.0, mapped to Ensembl version 102 transcriptome
Supplementary files format and content: matrix of raw counts with genes in rows and samples in columns

organism: Rattus norvegicus

source_name: Rat myometrial stem cells (MMSCs) isolated from Eker rat treated with vehicle (sesame oil)

growth_protocol: Isolated VEH- and EDC-MMSCs were plated in coated flasks (Attachment factor #S006100, Thermo Fisher Scientific, Waltham, MA) and cultured separately in Smooth Muscle Growth Medium-2 BulletKit (complete SmGm media) (CC-3182, Lonza, Walkersville, MD) under hypoxic conditions (37°C, 5% CO2, 2% O2).

extract_protocol:
Total cellular RNA was isolated from frozen MMSCs pellets using TRIzol Reagent (#15596026, Invitrogen, Waltham, MA, USA) following manufacturer instructions.
RNA quality and quantity were assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ mRNA-SEQ library protocol (Illumina provided). Library quality and quantity were assessed using the Agilent bio-analyzer, and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).

treatment_protocol: Once VEH- or EDC-MMSCs reached 80% confluence, they were treated with human recombinant TGF-β1 (10 ng/ml, 7754-BH, R&D Systems,) for 48 h or with TGF-β Receptor I inhibitor (2µM, LY-364947, L6293, Sigma, St. Louis, MO, USA) for 24 h, respectively. The vehicle used to dissolve TGF-β1 was 4 mM HCl (SA49, Thermo Fisher Scientific, Waltham, MA, USA) containing 0.1% bovine serum albumin (BSA, A3294, Sigma, St. Louis, MO, USA). Mature human TGF-β1 shares 99% amino acid identity with rat TGF-β1, and it demonstrated cross-species activity [35]. Dimethyl sulfoxide (DMSO, 472301, Sigma, St. Louis, MO, USA) was used as a VEH to dissolve the TGF-β Receptor I inhibitor (final concentration <0.1%). VEH- and EDC-treated MMSCs were washed with PBS, trypsinized, and centrifuged at 500 × g for 5 min. The supernatant was discarded, and the pellets were snap-frozen and stored at -80°C for RNA isolation.

value: MMSCs

value: Eker (Tsc2/wt)

tag: in vivo treatment

value: vehicle (sesame oil)

tag: in vitro treatment

value: TGFβ1 treatment:10 ng/ml - serum-free media (SmBm) (TGFb R&D system cat#7754-BH)


title: PPAC1C-12wT


title: In-vitro TGF-beta treated sample [H9_T_25_rep1]


title: EDC-MMSCs + LY-364947 biol rep 3

source_name: Rat myometrial stem cells (MMSCs) isolated from Eker rat treated with Diethylstilbestrol (an EDCs)

value: Diethylstilbestrol (an EDCs)

value: TGFβ Receptor I INHIBITOR treatment (LY-364947):2 uM - serum-free media (SmBm) (Sigma cat#L6293)


title: EDC-MMSCs + LY-364947 biol rep 2


title: In-vitro TGF-beta treated sample [H9_T_44_rep1]


title: EDC-MMSCs + veh biol rep 1

value: veh:DMSO <0.1% - serum-free media (SmBm)


title: VEH-MMSCs + veh biol rep 2

value: veh: 4mM HCl 0.1 BSA- serum-free media (SmBm)


title: VEH-MMSCs + veh biol rep 3


title: PPAC1-12wT

value: F

value: 12 weeks


title: EDC-MMSCs + veh biol rep 2


title: polyA siMatrin3 rep3

status: Public on Mar 17 2023

data_processing:
RTA 1.18.64 software used for basecalling.
Sequenced reads were trimmed for low-quality bases using Cutadapt, then mapped to hg19 genome using STAR 2.5.1
Gene expression was quantified using RSEM
Assembly: hg19
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

extract_protocol:
Samples had their RNA extracted with RNeasy Plus Mini Kit.
RNA libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep

value: Colorectal cancer cell line

value: 72 hours + 48 hours siMatrin3


title: polyA siMatrin3 rep2


title: VEH-MMSCs + TGFβ1 biol rep 3


title: polyA siMatrin3 rep1


title: polyA siCTRL rep2

value: 72 hours + 48 hours siCTRL


title: VEH-MMSCs + TGFβ1 biol rep 1


title: EDC-MMSCs + veh biol rep 3


title: HCT116 Iso-seq

description: PacBio IsoSeq

data_processing:
PacBio SMRTlink generated raw subreads were converted into HiFi circular consensus sequences (CCS)
PacBio IsoSeq v3 pipeline was used to demultiplex the barcodes and remove primers. Additional refine steps included trimming polyA tails and removing concatemers to generate Full Length Non-Concatemer (FLNC) reads.
Hierarchical clustering,  iterative clustering and merging steps were performed to obtain consensus isoforms and the full-length (FL) consensus sequences
The high-quality FL transcripts were mapped to the reference genome by using the minimap2
Isoform classification and quality control were done using SQANTI3 software
Assembly: hg38
Supplementary files format and content: tab-delimited text files include SQUANT3 annotated isoforms for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for PacBio sequencing  were prepared using PacBio Iso-seq  Library Prep Kit following manufacturer's protocols.

value: WT


title: VEH-MMSCs + veh biol rep 1


title: PAR-CLIP Matrin3_rep2

data_processing:
Illumina software used for basecalling.
The analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Assembly: hg19
Supplementary files format and content: csv files including binding sites positions

extract_protocol:
Matrin-3 PAR-CLIP method was performed in three biological replicates as described previously (Benhalevy et al., 2017; Hafner et al., 2010). We used anti-Matrin3 antibody (Bethyl Laboratories, Catalog No. A300-591A) for the immunoprecipitation of RNPs.
Small RNA cDNA library preparation protocol was performed as described in Benhalevy et al., (2017).

value: anti-Matrin3 antibody


title: Radiation Control

status: Public on Jul 19 2023

city: Albany

first: Katherine

middle: C

last: MacNamara

state: NY

address: 47 New Scotland Avenue

department: Immunology and Microbial Disease

institute: Albany Medical College

description: 10x Genomics

data_processing:
Barcode processing, gene counting, and aggregation were done using Cell Ranger software v6.0.1.
Assembly: mm10

source_name: Bone marrow

extract_protocol:
Whole BM was flushed from femus and tibias into HBSS. After RBC lysis, cells suspensions were stained and 7-AAD- CD11b+ Ly6C+ Ly6G- cells were sorted on a BD FACSAria Cell Sorter. Cells from each experimental group (radiation and SAA, n = 3 mice per group) were pooled together.
Library construction was performed according to the manufacter's instructions (single cell 5' v2 protocol, 10x Genomics). Briefly, BM cells were resuspended in the master mix and loaded into the chromium chip with partioninig oil to generate the gel bead-in-emulsion (GEM). Reverse transcription was then performed and cDNA cleaned up with Silane DynaBeads and amplified by PCR. Library construction and sequencing was next performed by the Center for Functional Genomics at SUNY Albany.

value: Bone marrow

value: 300 rads


title: PAR-CLIP Matrin3_rep3


title: SAA

description: 10x Genomics

value: 300 rads + 6.5e7 B6 splenocytes


title: polyA siCTRL rep1


title: polyA siCTRL rep3


title: siCTRL rep1

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for low-quality bases using Cutadapt, then mapped to hg19 genome using TopHat.
Gene expression was quantified using RSEM
Assembly: hg19
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

extract_protocol:
Samples had their RNA extracted with TRIzol™ Reagent
RNA libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep

value: 48 hours siCTRL


title: siMatrin3  rep1

value: 48 hours siMatrin3


title: siCTRL  rep2


title: siMatrin3  rep3


title: PAR-CLIP Matrin3_rep1


title: WT_D1_5

status: Public on Mar 01 2023

type: RNA

hyb_protocol: Hybridizations overnight to Mouse Clariom D microarrays (ThermoFisher) and post-hybridization washing, and staining were done with GeneChip™ Hybridization, Wash, and Stain Kit, Fluidics Station 450.

scan_protocol: Scans were done on 7G scanner according to manufacturer protocols

data_processing: Microarray data were analyzed with custom codes in R.

label: biotin

source_name: Nucleus accumbens

label_protocol: biotin-labeled cDNA using 90 ng of total RNA and the GeneChip™ WT PLUS Reagent Kit

extract_protocol: RNA from the Ribo-TRAP assay were submitted to the Medical University of South Carolina Proteogenomics Facility for DNA microarray analysis

treatment_protocol: Rats were injected in the NAc with either AAV-DIO-L10aGFP or a 50-50 mixture of AAV-HDAC5-3SA and AAV-L10aGFP. After about 4 weeks of expression, NAc tissue was harvested using native GFP fluorescence as a guide

tag: batch

value: m


title: WT_D1_4


title: WT_D1_6

value: f


title: WT_D2_2


title: WT_D2_3


title: WT_D1_3


title: siMatrin3  rep2


title: siCTRL  rep3


title: WT_D1_1


title: HDAC5_D2_2


title: WT_D2_4


title: HDAC5_D2_4


title: WT_D2_1


title: HDAC5_D2_3


title: HDAC5_D1_6


title: HDAC5_D1_5


title: WT_D1_2


title: HDAC5_D1_4


title: HDAC5_D2_1


title: HDAC5_D1_3


title: HDAC5_D1_2


title: HDAC5_D1_1


title: center_pog_3

status: Public on Feb 15 2023

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
RNA-seq counts were generated by Salmon (Patro et al., 2017)
Assembly: hg19
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample

source_name: FACS sorted MUC16-positive cells

extract_protocol:
Human donor whole globes were obtained from eye banks. Cornea was dissected from the other parts of the eyes, the central cornea was separated by an 8mm disposable biopsy punch and the corneal endothelium was removed mechanically. After 1 h incubation with PluriSTEM Dispase II Solution at 37 °C, limbal epithelial cells and central corneal epithelial cells were scraped and incubated with TrypLE Express Enzyme at 37 °C for 30 min to dissociate. (1) Dissociated limbal epithelial cells were cultured and treated with siRNAs (Control, TET2 knockdown #1 and TET2 knockdown #2). siRNAs were transfected on day 0, 2 and 4 and the cells were harvested on day 7 for RNA extraction. (2) Dissociated central corneal epithelial cells were stained with fluorescence conjugated antibodies for 30 min on ice (mouse anti-MUC16 monoclonal antibody (mAb) conjugated with Alexa Fluor 647 and  0.125μg/ml PE-conjugated anti-CD45 mAb. The cells were incubated with 30nM SYTOX Green Dead Cell Stain to exclude nonviable cells. Cell sorting was performed using FACSAria II cell sorter (BD Biosciences, San Jose, CA) using a 100 mm nozzle. RNA was extracted from sorted MUC16-positive cells and MUC-negatibe cells.
mRNA libraries were generated by SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech, Mountain View, CA) and sequencing was carried out by the Illumina NextSeq 500 Platform (Single-end 75 bp) (Illumina, San Diego, CA) at the Molecular Biology Core Facility (MBCF) of Dana-Farber Cancer Institute.

value: FACS sorted MUC16-positive cells

value: In vivo human corneal epithelial cells

value: Sample 6, MUC16-positive cells


title: center_pog_4

value: Sample 7, MUC16-positive cells


title: center_neg_4

source_name: FACS sorted MUC16-negative cells

value: FACS sorted MUC16-negative cells

value: Sample 7, MUC16-negative cells


title: center_neg_3

value: Sample 6, MUC16-negative cells


title: center_pog_2

value: Sample 5, MUC16-positive cells


title: LPS

status: Public on Feb 17 2023

first: Kris

last: Kahle

address: 55 Fruit Street

institute: MGH

data_processing: The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger.

source_name: choroid plexus (ChP)

extract_protocol:
Animals were anesthetized with Ketamine/Xylazine and transcardially perfused with ice cold TBS before brain removal. Choroid plexi from bilateral lateral ventricles were microdissected in ice cold HBSS with 30uM Actinomycin D (ActD, Sigma, cat#A1410 ) and digested at 37oC for 20 min with Collagenases-I and -IV (10 U/mL, 400 U/mL final, Worthington, Cat# LS004194, and LS004184) and DNase I (30 U/mL, Roche, cat# 04716728001) and ActD (3uM). For Flow sorting, the cell suspension was blocked with CD16-CD32 antibodies (1:100, biolegend, cat#101302) and stained 30 min at 4oC with anti-rat CD45-PE/cy7 (1:100, biolegend, cat#202207) to and DAPI (50ug/mL). Cells were subsequently washed in FACS staining buffer (0.5% BSA, 2mM EDTA in PBS without Calcium/Magnesium) and centrifuged at 350 rcf for 5 minutes. Cells were resuspended in 300ul of FACS buffer and sorted by CD45 positivity on a BD ARIA instrument. CD45 positive and CD45 negative cells were collected in 0.4% BSA/PBS and 3uM ActD and sent for 10X 3prime library preparation and sequencing at Yale Center for Genome Analysis
Sequencing libraries were loaded on an Illumina HiSeq4000 flow cell with sequencing settings following the recommendations of 10x Genomics (read 1: 26 cycles; read 2: 98 cycles; index i7: eight cycles; index i5: no cycles; 2.1 pM loading concentration). The Cell Ranger pipeline was designed to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index. Read 2, containing the cDNA, was mapped to the reference genome (mouse mm10) using STAR

treatment_protocol: LPS/IVH 48 hhs ICV

value: LPS-Treated


title: center_neg_1

value: Sample 4, MUC16-negative cells


title: S3_siRNA1

source_name: Cultured corneal epithelial cells

value: Cultured corneal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 3, TET2 knockdown #1


title: S2_siRNA2

value: Sample 2, TET2 knockdown #2


title: S3_control

value: Sample 3, Control for TET2 knockdown


title: center_pog_1

value: Sample 4, MUC16-positive cells


title: S2_control

value: Sample 2, Control for TET2 knockdown


title: S1_siRNA2

value: Sample 1, TET2 knockdown #2


title: Control

value: Untreated


title: colorectal cancer, immune cells

status: Public on Feb 22 2023

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

data_processing:
For scRNA-seq, the BD Genomics Rhapsody Targeted Analysis pipeline was used to demultiplex cellular barcodes, map reads to the reference genome.
For ST-seq, raw sequencing reads were processed with CellRanger V3 and aligned to human genome
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw UMI counts and metadata for every cells
Supplementary files format and content: H&E staining images for ST-seq tissues

source_name: colorectal and liver tissues

extract_protocol:
For scRNA-seq, freshly resected tumors were rinsed with 1×PBS for three times, cut into small pieces and transferred to 15 mL digestion medium containing collagenase IV (1 mg/mL, C5138, Sigma-Aldrich) in DME/F-12 1:1 (70100300, Biosharp). Tissues were digested for 45 minutes at 37 ℃ under agitation at 120 rpm, afterwards, the samples were filtered using a 150 μm nylon mesh. Following the centrifugation at 450 g for 5 minutes, the supernatants were discarded and the cell pellets were resuspended in 3 mL red blood cell lysis buffer (C3702, Beyotime) at 4 ℃ for 10 minutes. After washing with 1×PBS, the cell pellets were suspended in 1×PBS containing 0.2% bovine serum albumin (4240GR500, BioFroxx) and filtered using a 74 μm nylon mesh. Single cell suspensions were stained with APC/Cy7-CD45 (HI30, BioLegend) and 7-aminoactinomycin D (7-AAD, B226396, BioLegend) for fluorescence-activated cell sorting using BD Aria ⅡI (BD Biosciences). Non-immune cells were sorted as 7-AAD-CD45-, and immune cells as 7-AAD-CD45+. For spatial transcriptome sequencing (ST-seq), The tissues were obtained from patients after resection, fixed by formalin and embedded in the paraffin. 10x FFPE gene expression slide (PN-1000185, 10x Genomics) was used for ST. Slide with 5μm FFPE section was dewaxed with xylene (214736, Sigma-Aldrich) and stained with hematoxylin (51275, Sigma-Aldrich) and eosin (HT110116, Sigma-Aldrich). After visualizing and scanning the whole slide, decrosslinking was performed using the TE buffer (10-0046, GeneMed) to release the RNA. Forward and reverse human transcriptome probes (PN-1000364, 10x Genomics) were used for probe hybridization overnight.
Single-cell library preparation was carried out according to the BD Rhapsody™ Single-Cell Whole transcriptome analysis alpha protocol (https://www.bdbiosciences.com/) and ST library were constructed according to the 10x protocol (CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevA)

value: colorectal and liver tissues


title: 1 uM RG7112 treated A549 cells rep 3

status: Public on Dec 31 2022

city: New York

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing reads were pseudoaligned to the human reference transcriptome GRCh38.95
Transcript abundance was estimated using kallisto (v0.45.0)
Genome_build: GRCh38.95
Supplementary_files_format_and_content: A549_H1792_counts.txt

source_name: lung adenocaricnoma

growth_protocol: H1792 and A549 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.

treatment_protocol: A549 and H1792 cells were treated with DMSO or 1μM RG7112 for 48hr.

tag: treatment condition


title: S3_siRNA2

tag: tissue

value: Sample 3, TET2 knockdown #2


title: S1_siRNA1

value: Sample 1, TET2 knockdown #1


title: center_neg_2

value: FACS sorted MUC16-negative cells

value: In vivo human corneal epithelial cells

value: Sample 5, MUC16-negative cells


title: S2_siRNA1

value: Sample 2, TET2 knockdown #1


title: DMSO treated A549 cells rep 3

tag: cell line

value: DMSO


title: S1_control

value: Cultured corneal epithelial cells

tag: cell type

value: Sample 1, Control for TET2 knockdown


title: DMSO treated A549 cells rep 2


title: 1 uM RG7112 treated A549 cells rep 1


title: 1 uM RG7112 treated A549 cells rep 2


title: DMSO treated H1792 cells rep 2


title: DMSO treated H1792 cells rep 3


title: 1 uM RG7112 treated H1792 cells rep 3


title: DMSO treated H1792 cells rep 1


title: DMSO treated A549 cells rep 1


title: 1 uM RG7112 treated H1792 cells rep 2


title: 2_HepG2

status: Public on Oct 18 2022

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt.
Trimmed reads were aligned to the human genome (hg19) using the STAR aligner
Gene expression quantification analysis was performed for all samples using the RSEM tool
Sample specific scaling factors were calculated using DESeq2.
Normalized bigwig files were generated using BAMscale with the calculated size factors
Assembly: hg19
Supplementary files format and content: bw: normalized bigwig file
Supplementary files format and content: rsem.genes.results: raw counts quantified by RSEM

growth_protocol: HepG2 and SKHEP1 liver cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% PenStrep in a 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was harvested using RNeasy Plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Prep following manufacturer's protocols.

value: hepatocellular carcinoma

value: WT


title: 23_SKHEP1_PURPL_sgRNA_5_Nutlin_3

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt.
Trimmed reads were aligned to the human genome (hg38) using the STAR aligner
Gene expression quantification analysis was performed for all samples using the RSEM tool
Differentlial expression analysis was performed using DESeq2, including calculating the size factor for each sample.
Normalized bigwig files were generated with BAMscale, using the scaling factors obtained from DESeq2.
Assembly: hg38
Supplementary files format and content: bw: bigwig files  for each sample
Supplementary files format and content: Supplementary file: combined raw read counts ("RawCountFile_rsemgenes.txt")

growth_protocol: SKHEP1 CRISPRi established cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% PenStrep in a 5% CO2 atmosphere at 37°C.

treatment_protocol:
p53 induction was achieved in SKHEP1 cells with 10 μM Nutlin-3a treatment for 6 hr. DMSO was used as vehicle control.
SKEHP1 CRISPRi cells were established using two different Non-Targeting sgRNAs (NTC) or 4 sgRNAs targeting PURPL. Two biological replicates were harvested for each RNA sample.

value: endothelial cells

value: CRISPRi PURPL sgRNA-5

tag: treatment

value: 6 hr


title: 20_SKHEP1_NTC2_Nutlin_3

value: CRISPRi Non-Targeting sgRNA-2


title: 16_SKHEP1_PURPL_sgRNA_4_Nutlin_1

value: CRISPRi PURPL sgRNA-4


title: 12_SKHEP1_PURPL_sgRNA_6_DMSO_3

value: CRISPRi PURPL sgRNA-6


title: 15_SKHEP1_PURPL_sgRNA_2_Nutlin_1

value: CRISPRi PURPL sgRNA-2


title: 13_SKHEP1_NTC1_Nutlin_1

value: CRISPRi Non-Targeting sgRNA-1


title: 11_SKHEP1_PURPL_sgRNA_5_DMSO_3


title: IVH

value: IVH-Treated


title: 1_SKHEP1


title: 24_SKHEP1_PURPL_sgRNA_6_Nutlin_3


title: EDC-MMSCs + LY-364947 biol rep 1

value: MMSCs

value: Eker (Tsc2/wt)

value: Diethylstilbestrol (an EDCs)

value: TGFβ Receptor I INHIBITOR treatment (LY-364947):2 uM - serum-free media (SmBm) (Sigma cat#L6293)


title: 17_SKHEP1_PURPL_sgRNA_5_Nutlin_1


title: 21_SKHEP1_PURPL_sgRNA_2_Nutlin_3


title: 4_SKHEP1_PURPL_sgRNA_4_DMSO_1

value: DMSO


title: 1_SKHEP1 Iso-Seq

description: PacBio IsoSeq

data_processing:
PacBio SMRTlink generated raw subreads were converted into HiFi circular consensus sequences (CCS)
PacBio IsoSeq v3 pipeline was used to demultiplex the barcodes and remove primers. Additional refine steps included trimming polyA tails and removing concatemers to generate Full Length Non-Concatemer (FLNC) reads.
Hierarchical clustering,  iterative clustering and merging steps were performed to obtain consensus isoforms and the full-length (FL) consensus sequences
The high-quality FL transcripts were mapped to the reference genome by using the minimap2
Isoform classification and quality control were done using SQANTI3 software
Assembly: hg38
Supplementary files format and content: xlsx: tab-delimited text files include SQUANTI annotated isoforms for each Sample

growth_protocol: SKHEP1 and HepG2 liver cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% PenStrep in a 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was harvested using RNeasy Plus kit (Qiagen).
RNA libraries for PacBio sequencing  were prepared using PacBio Iso-seq  Library Prep Kit following manufacturer's protocols.


title: 14_SKHEP1_NTC2_Nutlin_1


title: 22_SKHEP1_PURPL_sgRNA_4_Nutlin_3


title: 18_SKHEP1_PURPL_sgRNA_6_Nutlin_1


title: 9_SKHEP1_PURPL_sgRNA_2_DMSO_3


title: 19_SKHEP1_NTC1_Nutlin_3


title: Pre patient 30 [Sample 61]

status: Public on Sep 28 2022

city: Providence

first: Jennifer

middle: Renee

last: Ribeiro

state: RI

address: 200 Chestnut St.

institute: Women and Infants Hospital of Rhode Island

description: low count genes were filtered out for a total of 750 genes detected on the panel

hyb_protocol: The reporter code set and capture probe set tubes were removed from -80C and thawed on ice, prior to mixing by tapping and pulse centrifugation. 70 µl hybridization buffer was added to the tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 8 µl of the diluted reporter probe was added to a PCR tube. Each RNA sample was diluted in water to 25 ng/µl and 2 µl final volume for 50 ng total input per sample. 5 µl RNA sample was added to each tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 2 µl Capture Probe Set was added to each tube, mixed by tapping, and the sample was collected by pulse centrifugation and then immediately placed in a pre-heated PCR machine, with the lid set to 70 °C and the block set to 65 °C. The hybridization was performed for 18 h at 65 °C. Samples were cooled to 4 °C and any condensation was collected by pulse centrifugation. Each sample was diluted with 18 µl hybridization buffer.

scan_protocol: An nCounter Sprint cartridge was calibrated to room temperature for 15 min prior to injection of 33 µl of each sample into one of the 12 injection ports of the cartridge, followed by the introduction of an air seal. The sample injection cartridge was sealed with provided tape and the reagent supply ports were unsealed prior to loading on the nCounter Sprint profiler. The analysis run was started immediately after loading.

data_processing: The resulting data file in RCC format was used for data analysis in the nCounter Advanced Analysis Software. Raw data in RCC format was uploaded to nSolver for automated normalization, background subtraction, and quality control (QC) check.

label: fluorescent barcode

extract_protocol: Pre-treatment and post-treatment cases were reviewed to select an optimal formalin-fixed, paraffin-embedded tissue block for each case. An optimal pre-treatment block contained maximum tumor cellularity (minimum of 20%) with no lymph node tissue present.   An optimal post-treatment block contained maximum tumor cellularity (minimum of 20%) with no lymph node tissue present, and with evidence of a lymphocytic response. For each block, ten unstained sections of 4-5 micron thickness were cut and placed on Avantix uncharged slides. An eleventh slide was cut at 4-5 microns, stained with hematoxylin and eosin, cover-slipped and reviewed to confirm the appropriate tissue was still present. FFPE sections were scraped into tubes for RNA isolation using an RNeasy FFPE Kit (Qiagen, 73504) according to manufacturer’s instructions. RNA concentration and quality was measured by NanoDrop

treatment_protocol: patients samples were obtained from naïve tumors during biopsy, or during interval debulking sugery after neoadjuvant treatment with carboplatin and paclitaxel chemotherapy

value: primary high grade serous ovarian cancer biopsy

tag: histology

value: high grade serous ovarian cancer

tag: Stage

value: IIIB

value: female

tag: platinum-free interval

tag: progression status as of 4/25/22

value: yes


title: Pre patient 31 [Sample 62]

source_name: primary high grade serous ovarian cancer

value: IIIC

tag: age


title: 7_SKHEP1_NTC1_DMSO_3

value: endothelial cells

tag: genotype

tag: time

value: 6 hr


title: 6_SKHEP1_PURPL_sgRNA_6_DMSO_1

value: CRISPRi PURPL sgRNA-6


title: 8_SKHEP1_NTC2_DMSO_3

value: CRISPRi Non-Targeting sgRNA-2


title: 10_SKHEP1_PURPL_sgRNA_4_DMSO_3

value: CRISPRi PURPL sgRNA-4


title: 5_SKHEP1_PURPL_sgRNA_5_DMSO_1

value: CRISPRi PURPL sgRNA-5


title: 1_SKHEP1_NTC1_DMSO_1

value: CRISPRi Non-Targeting sgRNA-1


title: Pre patient 25 [Sample 56]


title: Pre patient 27 [Sample 58]


title: 2_HepG2 Iso-Seq

description: PacBio IsoSeq

value: hepatocellular carcinoma

value: WT


title: Pre patient 22 [Sample 53]

value: IIIA


title: 3_SKHEP1_PURPL_sgRNA_2_DMSO_1

value: CRISPRi PURPL sgRNA-2

value: DMSO


title: 2_SKHEP1_NTC2_DMSO_1


title: Pre patient 16 [Sample 47]

value: primary high grade serous ovarian cancer biopsy

value: high grade serous ovarian cancer


title: Pre patient 29 [Sample 60]

value: female


title: Pre patient 15 [Sample 46]

value: yes


title: Pre patient 28 [Sample 59]

value: IIIC


title: Pre patient 24 [Sample 55]


title: Pre patient 13 [Sample 44]


title: Pre patient 11 [Sample 42]


title: Pre patient 14 [Sample 45]


title: Pre patient 23 [Sample 54]

value: IIIB


title: Pre patient 18 [Sample 49]

value: IV


title: Pre patient 21 [Sample 52]

value: no


title: Pre patient 20 [Sample 51]


title: Pre patient 26 [Sample 57]


title: Pre patient 1 [Sample 32]


title: Pre patient 19 [Sample 50]


title: Pre patient 2 [Sample 33]


title: Post patient 31 [Sample 31]

value: primary high grade serous ovarian cancer


title: Pre patient 17 [Sample 48]


title: Pre patient 12 [Sample 43]


title: Post patient 28 [Sample 28]


title: Pre patient 9 [Sample 40]


title: Post patient 26 [Sample 26]


title: Pre patient 6 [Sample 37]


title: Pre patient 5 [Sample 36]


title: Post patient 20 [Sample 20]


title: Pre patient 8 [Sample 39]


title: Pre patient 4 [Sample 35]


title: Post patient 18 [Sample 18]


title: Post patient 17 [Sample 17]


title: Pre patient 3 [Sample 34]


title: Pre patient 10 [Sample 41]


title: Post patient 30 [Sample 30]


title: Post patient 13 [Sample 13]


title: Post patient 9 [Sample 9]


title: Post patient 23 [Sample 23]


title: Post patient 24 [Sample 24]


title: Post patient 27 [Sample 27]


title: Post patient 25 [Sample 25]


title: Post patient 6 [Sample 6]


title: SOX1 gRNA 3 NCI-H187 cells

status: Public on Sep 12 2022

data_processing:
Sequencing reads were pseudoaligned to the human reference transcriptome GRCh38.95
Transcript abundance was estimated using kallisto (v0.45.0)
Genome_build: GRCh38.95
Supplementary_files_format_and_content: Text files

source_name: small cell lung cancer

growth_protocol: NCI-H187 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

value: cell line

tag: crispr-cas9 vector

tag: grna vector

value: pLenti-GFP-SOX1 sRNA3


title: Post patient 22 [Sample 22]

tag: Sex


title: Post patient 29 [Sample 29]


title: Post patient 21 [Sample 21]


title: Post patient 2 [Sample 2]


title: Post patient 19 [Sample 19]


title: Post patient 3 [Sample 3]


title: NKX2-1 gRNA 3 NCI-H187 cells

value: pLenti-GFP-NKX2-1 sRNA3


title: Post patient 16 [Sample 16]


title: non-target gRNA 1 NCI-H187 cells

value: pLenti-GFP-NT sRNA1


title: NKX2-1 gRNA 1 NCI-H187 cells

value: pLenti-GFP-NKX2-1 sRNA1


title: non-target gRNA 2 NCI-H187 cells

value: pLenti-GFP-NT sRNA2


title: Post patient 15 [Sample 15]


title: Parental H187 cells


title: Post patient 10 [Sample 10]


title: Post patient 14 [Sample 14]


title: Post patient 11 [Sample 11]


title: SOX1 ChIP for H345

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS2
Bedgraph was converted to bigwig
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: Small cell lung cancer

growth_protocol: NCI-H345 was maintained in HITES medium (serum free) with 1% P/S. NCI-H1436 was maintained in HITES medium with 5% FBS and 1% P/S, the others Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin,

extract_protocol:
For SOX1, NKX2-1 and H3K27ac ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

value: Cell line

tag: antibody


title: Post patient 12 [Sample 12]


title: Post patient 8 [Sample 8]


title: SOX1 ChIP for DMS 79


title: SOX1 gRNA 2 NCI-H187 cells

value: pLenti-GFP-SOX1 sRNA2


title: Post patient 5 [Sample 5]


title: NKX2-1 ChIP for COR-L88

value: NKX2-1 (Bethyl Laboratories, A300-BL4000)


title: NKX2-1 ChIP for DMS 79


title: Post patient 4 [Sample 4]

value: high grade serous ovarian cancer


title: Post patient 7 [Sample 7]

value: female


title: Post patient 1 [Sample 1]

value: yes


title: SOX1 gRNA 1 NCI-H187 cells

value: pLenti-GFP-SOX1 sRNA1


title: NKX2-1 gRNA 2 NCI-H187 cells

value: pLenti-GFP-NKX2-1 sRNA2


title: NKX2-1 ChIP for H345


title: NKX2-1 ChIP for H209


title: NKX2-1 ChIP for H2087

source_name: Lung adenocarcinoma


title: ChIP input for H2171

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS
wig file was depth normalized and converted to bigwig
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig

extract_protocol:
For H3K27ac, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.


title: ChIP input for DMS 79


title: ChIP input for SHP-77


title: ChIP input for H196


title: SOX1 ChIP for H209


title: ChIP input for HCC33


title: ChIP input for H526


title: ChIP input for H209


title: ChIP input for H2081_2


title: ChIP input for H1963


title: H3K27ac ChIP for H69

value: acetyl-histone H3K27  (Abcam, ab4729)


title: ChIP input for H2081_1


title: ChIP input for H187


title: ChIP input for H345


title: ChIP input for H841


title: H3K27ac ChIP for H82


title: ChIP input for COR-L88


title: ChIP input for H1436_1


title: ChIP input for H1436_2


title: FiTAc-seq for Input of Human SCLC Tumor_27812

source_name: Human primary SCLC tumor

extract_protocol:
FiTAc-seq has been previously described, briefly, two sections of 50um thickness for full sections of human FFPE tumors were used for ChIP profiling. Samples were treated with xylene to remove paraffin and then rehydrated with 100% ethanol for 10 min, 70% ethanol for 10 min, and water for another 10 min. Hydrated tissues were resuspended in 200ul of 1% SDS lysis buffer with 4ul of 50× EDTA-free protease inhibitor cocktail (PIC) and 1ul of 1 M sodium butyrate, then incubated overnight at 65°C with constant agitation at 1,000 r.p.m. The homogenized tissues were sonicated with Bioruptor for 12 cycles of 30 second on and 30 second off at 4°C. The soluble chromatins were subject to ChIP assay as described above. Library preparation and sequencing were done as described above.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

value: formalin-fixed, paraffin-embedded (FFPE) tissues


title: H3K27ac ChIP for H2081_1


title: 1 uM RG7112 treated H1792 cells rep 1


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27810


title: ChIP input for H82


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27812


title: ChIP input for H69


title: H3K27ac ChIP for H1436_1


title: H3K27ac ChIP for H526


title: H3K27ac ChIP for H1436_2


title: NKX2-1 ChIP for H187_NT gRNA2


title: H3K27ac ChIP for H2081_2


title: NKX2-1 ChIP for H187_NT gRNA1


title: NKX2-1 ChIP for H187_SOX1 gRNA3


title: Pre patient 7 [Sample 38]

value: primary high grade serous ovarian cancer biopsy

value: IIIB


title: NKX2-1 ChIP for H187_SOX1 gRNA2


title: H3K27ac ChIP for H196


title: H3K27ac ChIP for H2171


title: NKX2-1 ChIP for H187_SOX1 gRNA1


title: H3K27ac ChIP for H187


title: H3K27ac ChIP for H841


title: FiTAc-seq for Input of Human SCLC Tumor_27810


title: H3K27ac ChIP for HCC33


title: H3K27ac ChIP for SHP-77


title: H3K27ac ChIP for H187_NT gRNA2


title: H3K27ac ChIP for H209


title: H3K27ac ChIP for H1963


title: NKX2-1 ChIP for H187_Parental


title: H3K27ac ChIP for H187_SOX1 gRNA2


title: H3K27ac ChIP for H187_Parental


title: H3K27ac ChIP for H187_NT gRNA1


title: H3K27ac ChIP for H187_SOX1 gRNA3


title: H3K27ac ChIP for H345


title: H3K27ac ChIP for H187_SOX1 gRNA1


title: FiTAc-seq for Input of Human SCLC Tumor_27818


title: FiTAc-seq for Input of Human SCLC Tumor_27187


title: NKX2-1 ChIP for H187


title: SOX1 ChIP for H187


title: FiTAc-seq for Input of Human SCLC Tumor_27622


title: NKX2-1 ChIP for H3122


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27814


title: ChIP input for H3122


title: ChIP input for H2087


title: ABCB5-positive LSCs from donor 2

status: Public on Aug 09 2022

data_processing:
The reads were pre-processed with Cell Ranger v2.1.0, which demultiplexed cells from different samples and quantified transcript counts per putative cell (3,768 cells total).
Quantification was performed using the STAR aligner against the hg19 transcriptome. Cell Ranger aggr was used to combine the three libraries, normalizing based on mapped sequencing depth.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file includes differentially expressed genes.

source_name: ABCB5-positive LSCs

extract_protocol:
Human donor whole globes were obtained from eye banks. Cornea was dissected from the other parts of the eyes, the central cornea was separated by an 8mm disposable biopsy punch and the corneal endothelium was removed mechanically. After 1 h incubation with PluriSTEM Dispase II Solution at 37 °C, limbal/central corneal epithelial cells were scraped and incubated with TrypLE Express Enzyme at 37 °C for 30 min to dissociate. Dissociated limbal epithelial cells were stained with fluorescence conjugated antibodies for 30 min on ice (2.5μg/ml mouse anti-ABCB5 monoclonal antibody (mAb) (clone 3C2-1D12) conjugated with Alexa Fluor 647, 0.125μg/ml PE-conjugated anti-CD45 mAb). The cells were incubated with 30nM SYTOX Green Dead Cell Stain to exclude nonviable cells. Cell sorting was performed using FACSAria II cell sorter (BD Biosciences, San Jose, CA) using a 100 mm nozzle. The cells were loaded onto a Chromium chip (10X Genomics) followed by encapsulation in lipid droplets.
cDNA libraries were prepared per manufacturer's protocol (10X Genomics). cDNA libraries were sequenced using an Illumina NextSeq 500.

value: FACS sorted ABCB5-positive LSCs

value: LSCs


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27818


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27187


title: hCS at day 227 of differentation

status: Public on Jul 23 2022

city: Stanford

first: Kevin

last: Kelley

address: 318 Campus Drive, W200

institute: Stanford University

data_processing:
Gene expression levels were quantified for each putative nuclei barcode using the 10x Genomics CellRanger analysis software suite (version 6.1.2).
CellRanger count command with –include-introns=TRUE to include reads mapping to intronic regions.
For t-hCS samples, human nuclei were identified based on a conservative requirement of at least 95% of total mapped reads aligning to the human genome.
Raw count matrices outputted from CellRanger were further processed using the R  (version 4.1.2) package Seurat (version 4.1.1) (Stuart et al., 2019). Low quality nuclei with less than 1,000 unique genes detected and with mitochondrial counts accounting for greater than 20% of the total counts were identified and removed. Gene normalization (sctransform), PCA anaylsis (top 30 PCs), clustering (FindNeighbors/FindClusters, dataset dimension = 30, resolution=0.5) were performed using Seurat with default paramaters.
An initial round of clustering was performed with a high-resolution parameter (resolution = 2) to identify subpopulations of low-quality cells based on outlier low gene count detection, predominantly mitochondrial marker genes , and/or high proportions of putative doublets using the DoubletFinder package (McGinnis et al., 2019). Following low quality nuclei removal, each sample was reanalyzed using the above Seurat workflow with a clustering resolution = 0.5. We identified and categorized major cell classes through marker gene expression and comparisons with published literature.
Assembly: human (GRCh38, Ensemble release 98) and rat (Rnor_6.0, Ensemble release 100)
Supplementary files format and content: tsv files with feature  and nuclei barcode  information corresponding to row and column indices of gene count data for each sample
Supplementary files format and content: matrix exchange format for sparse matrices of gene count data for each sample
Supplementary files format and content: csv file with annotated cell classes of high-quality nuclei for each sample
Supplementary_files_format_and_content: rds files are processed seurat objects in RDS format

source_name: hCS day 227

growth_protocol: To initiate the generation of hCS from hiPS cells cultured on feeders, intact hiPS cell colonies were lifted from the plates using dispase (0.35 mg ml−1) and transferred to ultra-low-attachment plastic dishes (Corning) in hiPS cell medium supplemented with the two SMAD inhibitors dorsomorphin (5 μM, Sigma-Aldrich, P5499) and SB-431542 (10 μM, Tocris, 1614) and the ROCK inhibitor Y-27632 (10 μM, Selleckchem, S1049). For the first five days, the hiPS cell medium was changed every day and supplemented with dorsomorphin and SB-431542. On the sixth day in suspension, neural spheroids were transferred to neural medium containing neurobasal-A (Life Technologies, 10888), B-27 supplement without vitamin A (Life Technologies, 12587), GlutaMax (1:100, Life Technologies), penicillin and streptomycin (1:100, Life Technologies) and supplemented with the epidermal growth factor (EGF, 20 ng ml−1; R&D Systems) and fibroblast growth factor 2 (FGF2, 20 ng ml−1; R&D Systems) until day 24. From day 25 to day 42, the medium was supplemented with brain-derived neurotrophic factor (BDNF, 20 ng ml−1, Peprotech) and neurotrophin 3 (NT3, 20 ng ml−1, Peprotech) with medium changes every other day. From day 43 onward, hCSs were maintained in unsupplemented neurobasal-A medium (NM, Thermo Fisher, 1088022) with medium changes every 4–6 days.

extract_protocol:
Nuclei isolation was performed as described in (Matson et al., 2018) with some modifications. Briefly, t-hCS and hCS were disrupted using the detergent-mechanical cell lysis method with a 2 ml glass tissue grinder (Sigma-Aldrich/KIMBLE, D8938). Crude nuclei were then filtered using a 40 μm filter and centrifuged at 320 x g for 10 minutes at 4°C before performing a sucrose density gradient to separate them from cellular debris. After a centrifugation step (320 x g, 20 minutes at 4°C), samples were resuspended in 0.04% BSA/PBS supplemented with 0.2 U/μl RNAse inhibitor (Ambion 40U/μl, AM2682) and passed through a 40 μm flowmi filter.
Dissociated nuclei were then resuspended in PBS containing 0.02% BSA and loaded onto a Chromium Single cell 3’ chip (with an estimated recovery of 10,000 cells per channel). snRNA-seq libraries were prepared with the Chromium Single cell 3’ GEM, Library & Gel Bead Kit v3 (10x Genomics).

value: cell type:hiPS-derived cortical spheroids (hCS)

tag: differentiation day

value: in vitro


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27622


title: ABCB5-positive LSCs from donor 3


title: H661_TVB

status: Public on Jun 29 2022

data_processing:
Reads were aligned to the human hg38 reference genome using STAR (v2.7.3a)
Gencode annotation for human (version v37) was used as reference alignment annotation and downstream quantification
Gene level expression was calculated using featureCounts (v2.0.1) with intersection-strict mode by exon. Counts were calculated based on protein-coding genes from the annotation file.
Low expressed genes were filtered using a per time-point approach with Reads Per Kilobase of exon per Megabase of library size (RPKM) >= 0.5 in all samples in one or the other group.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung cancer

growth_protocol: Cell lines were maintained in RPMI (GE, SH30027) supplemented with 5% heat-inactivated FBS (SIGMA ALDRICH, F6178)

extract_protocol:
Total RNA was extracted with TRIzol Residual genomic DNA was removed with the Turbo DNA-free kit (AM1907, ThermoFisher).
NEBNext Ultra II Directional RNA Library Prep kit

treatment_protocol: Cell lines were treated with  0.2 μM TVB-3664 or 0.2% DMSO, in RPMI (GE, SH30027) supplemented with 5% dialyzed FBS (SIGMA-ALDRICH, F0394) for 4 days

tag: kras status

value: wild-type KRAS

value: 0.2 microM TVB-3664 in 0.2percent DMSO, for 4 days


title: ABCB5-positive LSCs from donor 1

tag: tissue


title: H522_vehicle

tag: cell line

value: 0.2percent DMSO, for 4 days


title: transplanted hCS at day 227 of differentiation

source_name: t-hCS day 227

tag: cell type

value: transplanted into rat


title: H522_TVB

tag: treatment


title: transplanted hCS at day 224 of differentiation

data_processing:
Gene expression levels were quantified for each putative nuclei barcode using the 10x Genomics CellRanger analysis software suite (version 6.1.2).
CellRanger count command with –include-introns=TRUE to include reads mapping to intronic regions.
For t-hCS samples, human nuclei were identified based on a conservative requirement of at least 95% of total mapped reads aligning to the human genome.
Raw count matrices outputted from CellRanger were further processed using the R  (version 4.1.2) package Seurat (version 4.1.1) (Stuart et al., 2019). Low quality nuclei with less than 1,000 unique genes detected and with mitochondrial counts accounting for greater than 20% of the total counts were identified and removed. Gene normalization (sctransform), PCA anaylsis (top 30 PCs), clustering (FindNeighbors/FindClusters, dataset dimension = 30, resolution=0.5) were performed using Seurat with default paramaters.
An initial round of clustering was performed with a high-resolution parameter (resolution = 2) to identify subpopulations of low-quality cells based on outlier low gene count detection, predominantly mitochondrial marker genes , and/or high proportions of putative doublets using the DoubletFinder package (McGinnis et al., 2019). Following low quality nuclei removal, each sample was reanalyzed using the above Seurat workflow with a clustering resolution = 0.5. We identified and categorized major cell classes through marker gene expression and comparisons with published literature.
Genome_build: human (GRCh38, Ensemble release 98) and rat (Rnor_6.0, Ensemble release 100)
Supplementary_files_format_and_content: tsv files with feature  and nuclei barcode  information corresponding to row and column indices of gene count data for each sample
Supplementary_files_format_and_content: matrix exchange format for sparse matrices of gene count data for each sample
Supplementary_files_format_and_content: csv file with annotated cell classes of high-quality nuclei for each sample
Supplementary_files_format_and_content: rds files are processed seurat objects in RDS format

source_name: t-hCS day 224

value: hiPS-derived cortical spheroids (hCS)


title: A549_TVB

value: mutant KRAS


title: A549_vehicle


title: hCS at day 236-251 of differentation


title: H3K27ac ChIP for DMS 79

value: Cell line


title: transplanted hCS at day 276 of differentiation

source_name: t-hCS day 276


title: CITE_RNA

status: Public on Jun 13 2022

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

description: RNA data of the CITE dataset

data_processing:
Standard 10X Genomics Cell Ranger and Cell Ranger ARC pipelines, as well as kallisto | bustools workflow for ADT and HTO libraries.
Assembly: GRCh38
Supplementary files format and content: For each sample, the filtered UMI count matrix and filtered peak count matrix from 10X Genomics pipelines are stored in a h5 file, with atac_fragments.tsv.gz provided. HTO and ADT count matrices from kallisto | bustools workflow are stored in csv files, with non-singlets filtered out.
Library strategy: CITE-seq

source_name: Peripheral blood T cells

extract_protocol:
T cells were enriched from 30 ml of whole blood from healthy human subjects, ages 18-35, following the MACSxpress® Whole Blood Pan T Cell Isolation Kit, human (Miltenyi Biotec) protocol. Four aliquots of one million cells each per study subject were stimulated overnight for 12 hours in 1 ml X-VIVO™ 15 Serum-free Hematopoietic Cell Medium (Lonza) with 10 ul ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies), 50 ng/ml IL-1B (R&D Systems), and 50 ng/ml IL-23 (R&D Systems), and either 1 uM Prostaglandin E2 (PGE2) (Sigma) or 3 ng/ml TGFB (R&D Systems), or both, for a total of four stimulation conditions per subject. After the overnight incubation, the cells were collected into 15 ml conical tubes through a 30-um strainer and washed with up to 14 ml of PBS/0.2% BSA, centrifuged at 400g for 5 minutes at 4°C, and resuspended in 50 ul Pharmingen Stain Buffer (BSA) (BD Biosciences).
For CITE-seq, a total of 30,000 cells were loaded into each of two wells of a Chromium Next GEM Chip G and run on the Chromium Controller (10X Genomics) for Gel Bead-in-emulsion (GEM) generation. The samples were processed according to the CG000204 Chromium Next GEM Single Cell 3’ v3.1 Rev. D protocol (10X Genomics) for RNA library construction while modifications for CITE-seq ADT and cell hashing HTO library preparation were performed according to the TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 or v3.1 single index protocol (BioLegend). The modifications include the addition of ADT and HTO additive primers to a final concentration of 0.2 uM in the cDNA amplification reaction (step 2.2), and using Illumina TruSeq™ Small RNA RPIX (with custom indexes) and Illumina TruSeq™ D70X_short primers, respectively, together with the SI-PCR primer, in ADT and HTO sample index PCRs. The ADT and HTO sample index PCRs were performed on the purified fraction of the supernatant recovered from cDNA amplification cleanup.  For DOGMA-seq, the cells were processed according to the CG000338 Chromium Next GEM Multiome ATAC + Gene Expression Rev. D protocol (10X Genomics) for Gene Expression and ATAC library construction while modifications for DOGMA-seq were performed following the “Cell permeabilization with DIG” section of the DOGMA-seq protocol (NYGC Innovation Lab).  We first optimized the concentration of DIG that we would use for the DIG cell permeabilization step. We tested 0.0025%, 0.005%, 0.0075% and 0.01% DIG with about 230,000 cells each, and a DIG concentration of 0.0075% was chosen.  Approximately 600,000 cells were centrifuged at 400g for 5 minutes at 4°C and permeabilized in 100 ul chilled DIG lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.0075% DIG and 2 U/ul Protector RNase inhibitor (Roche)) for 1 min on ice, followed by the addition of 1 ml of chilled DIG wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2 and 1 U/ul RNase inhibitor) and pipette mixing, before centrifugation at 500g for 5 minutes at 4°C. The supernatant was discarded, the pellet was resuspended in a very small volume of about 17 ul of diluted Nuclei Buffer (10X Genomics) and 5 ul were used for cell counting.  In a separate experiment, we compared DOGMA-seq’s DIG and LLL protocols. Approximately 600,000 cells were permeabilized with DIG as described above and resuspended in 7.5 ul of Nuclei Buffer. Approximately 300,000 cells were fixed with 0.1% formaldehyde for 5 minutes at room temperature. Glycine was added as a quencher at 0.125M. The cells were washed twice with PBS/1% BSA/RNase inhibitor, centrifuged at 400g for 5 minutes at 4°C and permeabilized in 100 ul chilled LLL lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 1% BSA, 1 mM DTT and 2 U/ul RNase inhibitor) for 3 min on ice followed by the addition of 1 ml of chilled LLL wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT and 1 U/ul RNase inhibitor) and pipette mixing, before centrifugation at 500g for 5 minutes at 4°C. The cells were resuspended in 7.5 ul of Nuclei Buffer. DIG and LLL-treated cells were also processed as described below. The cell recovery after DIG permeabilization was approximately 25-30 %, while the cell recovery after LLL permeabilization was approximately 50%.   Following the CG000338 Chromium Next GEM Multiome ATAC + Gene Expression Rev. D protocol, 30,000 cells were processed for each of two transposition reactions, which were then loaded into each of two wells of a Chromium Next GEM Chip J and run on the Chromium Controller (10X Genomics) for GEM generation.  During sample pre-amplification (step 4.2), ADT and HTO additive primers were added to a final concentration of 0.2 uM. After cleanup and elution in 100 ul, 30 ul were set aside for ADT and 10 ul were set aside for HTO sample index PCR reactions, that were performed using Illumina TruSeq™ Small RNA RPIX (with custom indexes) and Illumina TruSeq™ D70X_short primers, respectively, and the SI-PCR primer.  When generating the RNA library in the Chromium Next GEM Multiome ATAC + Gene Expression protocol, we chose to use the Single Index Plate T Set A instead of the Dual Index Plate TT Set A.

tag: molecule

value: RNA


title: H661_vehicle


title: hCS at day 257 of differentation

source_name: hCS day 257


title: CITE_ADT

description: ADT data of the CITE dataset

library_source: other

molecule: other

value: ADT


title: CITE_HTO

description: HTO data of the CITE dataset

value: HTO


title: H460_vehicle


title: LLL_RNA

description: RNA data of the LLL dataset

data_processing:
Standard 10X Genomics Cell Ranger and Cell Ranger ARC pipelines, as well as kallisto | bustools workflow for ADT and HTO libraries.
Assembly: GRCh38
Supplementary files format and content: For each sample, the filtered UMI count matrix and filtered peak count matrix from 10X Genomics pipelines are stored in a h5 file, with atac_fragments.tsv.gz provided. HTO and ADT count matrices from kallisto | bustools workflow are stored in csv files, with non-singlets filtered out.
Library strategy: DOGMA-seq

tag: condition

value: LLL


title: FiTAc-seq for Input of Human SCLC Tumor_27814

value: formalin-fixed, paraffin-embedded (FFPE) tissues


title: LLL_ATAC

description: ATAC data of the LLL dataset

value: ATAC


title: DIG_RNA

description: RNA data of the DIG dataset

value: DIG


title: LLL_HTO

description: HTO data of the LLL dataset


title: LLL_ADT

description: ADT data of the LLL dataset


title: DOGMA_RNA

description: RNA data of the DOGMA dataset


title: DOGMA_ADT

description: ADT data of the DOGMA dataset


title: DIG_HTO

description: HTO data of the DIG dataset


title: DOGMA_HTO

description: HTO data of the DOGMA dataset


title: DIG_ATAC

description: ATAC data of the DIG dataset


title: DIG_ADT

description: ADT data of the DIG dataset


title: 5.non_smoker.do.ma_NGS19.K310

status: Public on May 23 2022

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

data_processing:
Sequence alignment with the human genome, sequence counting and quality control were performed using the nf-core/rnaseq pipeline. RNA-seq data were analyzed using R Bioconductor (3.5.1) and DESeq2 package (version 1.26.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Text gene counts: counts of genes for each sample

source_name: Sorted AFhi CD206+ CD45+ macrophages from BALF

extract_protocol:
For bulk mRNA-sequencing (RNA-seq), CD14+ monocytes were isolated from the blood and AFlo and AFhi CD45+CD206+ cells were FACS-sorted from the BALF of the same patients. Total RNA was extracted and concentrated from the different samples with the RNA Clean & Concentrator 5 (Zymo Research). Possible DNA contaminant were removed with DNAse I. RNA quality and quantity were evaluated using a 2100 bioanalyzer (Agilent) and the Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher). The RNA Integrity Number (RIN) was greater than 7 for all samples.
One hundred nano-grams of RNA was used to generate the libraries using the Truseq stranded mRNA kit (Illumina). These libraries were sequenced on an Illumina Novaseq sequencer on a SP flow cell in single read 100 bp.

tag: patient group


title: 14.non_smoker.ld.ma_NGS19.K319

value: Sorted AFhi CD206+ CD45+ macrophages from BALF


title: DOGMA_ATAC

description: ATAC data of the DOGMA dataset


title: Sample_14983 [Control]

status: Public on Apr 20 2022

type: genomic

city: Royal Oak

first: Stewart

middle: F

last: Graham

state: Michigan

address: 3811 West 13 Mile Road, Suite 415

department: OBGYN

institute: Corewell Health - Research Institute

description: Normal Brain tissue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC-8+ v1.0 Kit (32 samples) 20020531 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R package based
Normalized (Noob normalization)

label: Cy3, Cy5

source_name: Brain

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from the lyophilized and milled brain tissue using the QIAamp DNA Mini Kit (Qiagen)

treatment_protocol: lyophilized and milled brain tissue

value: Normal Brain tissue

value: M

tag: pmi

tag: repository

value: Mount Sinai

tag: race

value: Hispanic

tag: group

value: Control


title: Sample_14981 [Control]

description: Normal Brain tissue

tag: age

value: Asian


title: Sample_14982 [Control]

description: Normal Brain tissue

value: White


title: Sample_14979 [Control]

description: Normal Brain tissue

value: F

value: Black


title: Sample_14975 [PD]

description: Parkinson's disease Affected Brain tissue

value: Harvard

value: Parkinson's disease (PD)


title: Sample_14973 [Control]

description: Normal Brain tissue

value: Unknown


title: Sample_14974 [Control]

description: Normal Brain tissue


title: Sample_14980 [Control]

description: Normal Brain tissue


title: 17.non_smoker.pk.ma_NGS19.K322


title: H460_TVB

value: mutant KRAS

value: 0.2 microM TVB-3664 in 0.2percent DMSO, for 4 days


title: H3K27ac ChIP for COR-L88

value: Cell line

value: acetyl-histone H3K27  (Abcam, ab4729)


title: Sample_14972 [Control]

description: Normal Brain tissue


title: Sample_14970 [PD]

value: Parkinson's disease Affected Brain tissue


title: Sample_14969 [PD]


title: Sample_14967 [PD]


title: Sample_14971 [Control]

description: Normal Brain tissue

value: Normal Brain tissue


title: Sample_14977 [Control]

description: Normal Brain tissue


title: Sample_14968 [Control]

description: Normal Brain tissue

value: M


title: Sample_14966 [PD]


title: Sample_14958 [Control]

description: Normal Brain tissue


title: Sample_14959 [PD]


title: Sample_14962 [Control]

description: Normal Brain tissue


title: Sample_14960 [PD]


title: Sample_14956 [PD]


title: Sample_14949 [PD]


title: Sample_14964 [PD]


title: Sample_14952 [PD]


title: Sample_14946 [Control]

description: Normal Brain tissue


title: Sample_14961 [PD]


title: Sample_14955 [PD]


title: Sample_14965 [PD]


title: Sample_14942 [PD]


title: Sample_14957 [PD]


title: Sample_14954 [PD]


title: Sample_14940 [PD]


title: Sample_14941 [PD]


title: Sample_14953 [PD]


title: Sample_14948 [Control]

description: Normal Brain tissue


title: Sample_14951 [PD]


title: Sample_14950 [PD]


title: Sample_14947 [PD]


title: Sample_14976 [PD]


title: Sample_14937 [Control]

description: Normal Brain tissue


title: Sample_14945 [PD]


title: Sample_14944 [Control]

description: Normal Brain tissue


title: Sample_14931 [Control]

description: Normal Brain tissue


title: Sample_14939 [PD]


title: Sample_14938 [Control]

description: Normal Brain tissue


title: Sample_14936 [Control]

description: Normal Brain tissue


title: Sample_14928 [PD]


title: Sample_14929 [Control]

description: Normal Brain tissue


title: Sample_14943 [PD]


title: Sample_14934 [PD]


title: Sample_14935 [PD]


title: Sample_14933 [PD]


title: Sample_14923 [Control]

description: Normal Brain tissue


title: Sample_14930 [Control]

description: Normal Brain tissue


title: Sample_14932 [Control]

description: Normal Brain tissue


title: Sample_14921 [PD]


title: Sample_14925 [PD]


title: Sample_14922 [PD]


title: Sample_14927 [PD]


title: Sample_14917 [Control]

description: Normal Brain tissue


title: Sample_14916 [PD]


title: Sample_14920 [Control]

description: Normal Brain tissue


title: Sample_14910 [Control]

description: Normal Brain tissue

value: Miami


title: Sample_14926 [PD]


title: Sample_14914 [PD]


title: Sample_14911 [Control]

description: Normal Brain tissue


title: Sample_14912 [Control]

description: Normal Brain tissue


title: Sample_14918 [PD]


title: Sample_14915 [PD]


title: Sample_14908 [Control]

description: Normal Brain tissue


title: Sample_14909 [Control]

description: Normal Brain tissue


title: Sample_14901 [Control]

description: Normal Brain tissue


title: Sample_14902 [Control]

description: Normal Brain tissue


title: Sample_14904 [Control]

description: Normal Brain tissue


title: M604

status: Public on Feb 08 2022

city: Duarte

first: Debbie

middle: C.

last: Thurmond

state: California

address: 1500 E Duarte Rd

institute: City of Hope

description: RNA-Seq data, Pak1Loxp-Dox, replicate 1

data_processing:
Real Time Analysis (RTA, v1.18.64) was used for base calling, and bcl2fastq v2.18 was used to generate FASTQ files
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search --library-type fr-firststrand
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Mmusculus.UCSC.mm10.knownGene (Bioconductor annotations, downloaded 12/22/2016).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM normalized expression (using aligned reads and TxDb annotations in R) and read counts (calculated using htseq-count)

source_name: mouse skeletal muscle

growth_protocol: Inducible skeletal muscle specific PAK1 knock out and over expression mouse were driven by doxycyclin

extract_protocol:
RNAs were isolated by TRIZol method
KAPA Stranded RNA-Seq Kit
stranded polyA RNA-Seq

treatment_protocol: 2 mg/mL of doxycyclin conferring skeletal muscle specific over expression or knocking out of PAK1

tag: strain

tag: genotype

tag: dox

value: -Dox

tag: pak1 status


title: M182

description: RNA-Seq data, dTg-Dox, replicate 2

value: dTg-Dox

value: dTg


title: Sample_14905 [Control]

description: Normal Brain tissue

tag: Sex

value: White

value: Control


title: M592

description: RNA-Seq data, Pak1Loxp+Dox, replicate 2

value: +Dox


title: Sample_14907 [Control]

description: Normal Brain tissue

tag: tissue

value: F


title: Sample_14903 [Control]

description: Normal Brain tissue


title: M107

description: RNA-Seq data, dTg-Dox, replicate 1


title: M605

description: RNA-Seq data, Pak1Loxp-Dox, replicate 3


title: M183

description: RNA-Seq data, dTg+Dox, replicate 3


title: M13

description: RNA-Seq data, dTg+Dox, replicate 1


title: M14

description: RNA-Seq data, dTg-Dox, replicate 3


title: M500

description: RNA-Seq data, Pak1Loxp+Dox, replicate 3


title: M595

description: RNA-Seq data, Pak1Loxp-Dox, replicate 2


title: M109

description: RNA-Seq data, dTg+Dox, replicate 2


title: M593

description: RNA-Seq data, Pak1Loxp+Dox, replicate 1


title: M92

description: RNA-Seq data, WT+Dox, replicate 2

value: WT+Dox

value: WT


title: M82

description: RNA-Seq data, WT+Dox, replicate 1


title: M22

description: RNA-Seq data, WT+Dox, replicate 3


title: Biopsy_before_NACT_11

status: Public on Jan 27 2022

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

description: Paired with surgery sample 11

hyb_protocol: Hybridization was performed according to manufacturer's instructions. nCounter uses a molecular barcode technology, where the RNA is directly tagged with a target-specific capture probe and target-specific reporter probe containing a labeled barcode. We used the PanCancer IO 360 gene expression panel which includes 770 immune-related genes and associated controls.

scan_protocol: Scanning and image acquisition using the nanoString Digital Analyzer.

data_processing: nanoString data were analyzed and normalized in nSolver software, correcting for the expression of technical controls and 30 housekeeping genes included in the panel.

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_11

label_protocol: Labeling was performed according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from cells using RNeasy FFPE Kit (Qiagen) according to the manufacturer's instructions and DNA was eliminated by means of Rnase-Free Dnase Set (Qiagen).

treatment_protocol: Biopsy samples were collected from primary lesions before EOC patients underwent carboplatin/paclitaxel-based neoadjuvant chemotherapy, according to availability. Surgery samples were extracted from residual lesions after treatment with chemotherapy, according to availability.

value: Epithelial Ovarian Cancer

tag: sample type

value: Biopsy sample

tag: response to nact

value: Non-responder

tag: crs score


title: Biopsy_before_NACT_12

description: Paired with surgery sample 12

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_12


title: Biopsy_before_NACT_7

description: Paired with surgery sample 6

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_7


title: Biopsy_before_NACT_9

description: Paired with surgery sample 9

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_9

value: Responder


title: Biopsy_before_NACT_5

description: Paired with surgery sample 4

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_5


title: Surgery_after_NACT_17

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_17

value: Surgery sample


title: Biopsy_before_NACT_6

description: Paired with surgery sample 5

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_6


title: Surgery_after_NACT_19

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_19


title: Biopsy_before_NACT_8

description: Paired with surgery sample 8

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_8


title: Biopsy_before_NACT_1

description: Paired with surgery sample 1

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_1


title: Surgery_after_NACT_16

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_16


title: Surgery_after_NACT_13

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_13


title: Surgery_after_NACT_9

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_9


title: Surgery_after_NACT_11

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_11


title: Biopsy_before_NACT_4

description: Paired with surgery sample 3

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_4


title: Surgery_after_NACT_15

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_15


title: Surgery_after_NACT_14

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_14


title: Surgery_after_NACT_12

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_12


title: Biopsy_before_NACT_10

description: Paired with surgery sample 10

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_10


title: Surgery_after_NACT_18

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_18


title: Surgery_after_NACT_6

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_6


title: Surgery_after_NACT_10

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_10


title: Surgery_after_NACT_5

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_5


title: Surgery_after_NACT_4

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_4


title: Surgery_after_NACT_1

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_1


title: Biopsy_before_NACT_23

description: Paired with surgery sample 17

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_23


title: Biopsy_before_NACT_25

description: Paired with surgery sample 19

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_25


title: RNAseq_Nvitripennis_uninjected_rep3

status: Public on Dec 21 2021

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research (Netherlands)

data_processing:
Reads from whole embryos were mapped to Nvit_psr_1.1 N. vitripennis genome version with RefSeq annotation GCF_009193385.1 using STAR version 2.6.1b with --quantMode geneCounts
Genome_build: Nvit_psr_1.1
Supplementary_files_format_and_content: Raw gene counts (.tab)

organism: Nasonia vitripennis

source_name: whole white larvae

growth_protocol: The N. vitripennis lab strain AsymCX cured with Wolbachia infection (Werren et al., 2010) was used throughout the experiments. Wasps were reared on Calliphora sp. hosts and cultured at 25 °C at a L16:D8 cycle.

extract_protocol:
Total RNA of larvae pools was extracted with Quick-RNA Tissue/Insect Kit coupled with on column DNase treatment (ZymoResearch - R2030) according to manufacturer's protocol. RNA was resuspended in 10 µl DNase RNase free water and RNA concentration was measured on fluorometer (Qubit 2.0 – Life Technologies).
Absence of RNA degradation was checked on a bioanalyzer (Agilent 2000 - Agilent). Then, mRNA was enriched using ology (dT) primers and randomly fragmented using a fragmentation buffer. First strand cDNA synthesis was performed using random hexamers and followed by second strand synthesis by nick-translation using a customized synthesis buffer (containing dNTP, RNase H, Esccherichia coli DNA polymerase I). Double-stranded DNA was subsequently purified, end-repaired, A-tailed and ligated to Illumina sequencing adapters. Size selection was then performed and library was amplified by PCR. Library concentration was quantify on a fluorometer (Qubit 2.0 – Life Technologies) and insert size was analyzed on a bioanalyzer (Agilent 2100 – Agilent). Sequencing libraries were paired-end sequenced (150 bp read-length) on an Illumina NovoSeq platform.  For more details, please contact Novogen (HK) company limited.on a bioanalyzer (Agilent 2000 - Agilent).

treatment_protocol: Larval RNAi knockdown was induced in AsymCX males in second instar larval stage (approximately 3 days after egg laying) (Werren, 2009, Cold Spring Harb Protoc). Gfp dsRNA was generated from the vector pOPINEneo-3C-GFP (Addgene plasmid # 53534; http://n2t.net/addgene: 53534; RRID: Addgene_53534, gift from Ray Owens).Full length GFP CDS was amplified by PCR with GFP_RNAi_F (5’-GTGACCACCTTGACCTACG-3’) and GFP_RNAi_R (5’-TCTCGTTGGGGTCTTTGCT-3’) primers. The 5′ and 3′ ends of those amplicons were provided with a T7 promotor sequence for dsRNA production using the MEGAscript RNAi kit (Ambion, Austin, Texas, USA) according to the manufacturer's protocol. Before injection, 2nd instar male larvae were placed on a petri-dish covered with 1% agarose in 1x PBS. Larvae were injected in the posterior part with 4 μg/μl GFP dsRNA diluted in milliQ water mixed with red food dye in the ratio 9:1, milliQ water with red food dye, or non-injected as control. Injections were performed using custom made needles and a IM300 Microinjecctor (Narishige). After injection, 2nd instar larvae were transferred back to host (6-8 per host) and sealed with the host shell. After 5 to 6 days post-injection, three samples (five individuals per sample) of white pupa stage males per category were collected, snap-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction.

value: AsymCX

value: whole larvae

value: white pupae

tag: treatment

value: uninjected


title: Biopsy_before_NACT_20

description: Paired with surgery sample 15

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_20


title: RNAseq_Nvitripennis_uninjected_rep2


title: Biopsy_before_NACT_24

description: Paired with surgery sample 18

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_24


title: Sample_14906 [Control]

description: Normal Brain tissue

source_name: Brain

value: Normal Brain tissue

value: Miami


title: Biopsy_before_NACT_21

description: Paired with surgery sample 16

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_21


title: Biopsy_before_NACT_15

description: Paired with surgery sample 13

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_15


title: Biopsy_before_NACT_18

description: Paired with surgery sample 14

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_18


title: RNAseq_Nvitripennis_uninjected_rep1


title: RNAseq_Nvitripennis_water_rep2

value: water


title: Surgery_after_NACT_3

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_3


title: RNAseq_Nvitripennis_water_rep3


title: RNAseq_Nvitripennis_dsGFP_RNA_rep3


title: RNAseq_Nvitripennis_dsGFP_RNA_rep1


title: RNAseq_Nvitripennis_dsGFP_RNA_rep2


title: RNAseq_Nvitripennis_water_rep1


title: Old adult CBA/CaJ mouse AN-3

status: Public on Dec 10 2021

first: Jeremy

last: Barth

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out using Partek Flow. Alignment was conducted with TopHat2 using mouse genome (mm10) and the default option set
Aligned reads were quantified to annotation model (Partek E/M) using mm10 and RefSeq transcripts 83 (2017-11-01) with the settings: a) strict paired-end compatibility, b) require junction reads to match introns, c) min read overlap with feature 100% of read length, d) min reads 10
Gene counts were analyzed using DESeq2 to determine normalized expression measures and signficant differences (p-adjusted) for all pairwise comparisons among the postnatal samples
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of normalized counts and comparison measures

source_name: Isolated auditory nerves

extract_protocol:
Microdissections were performed to isolate the auditory nerve from mouse cochlear structures. Two cochleas from each mouse were pooled for individual samples. Total RNA was purified from each sample using the miRNeasy Mini Kit per the manufacturer’s instructions. Quality of each total RNA isolation was assessed using the Agilent 2100 Bioanalyzer and low-quality samples showing degradation or contamination were excluded.
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq RNA Library Prep Kit

tag: cell type

value: Auditory nerve cells

value: Isolated auditory nerves

value: CBA/CaJ


title: Old adult CBA/CaJ mouse AN-2


title: Old adult CBA/CaJ mouse AN-1


title: Young adult CBA/CaJ mouse AN-3

value: 2 mo


title: Young adult CBA/CaJ mouse AN-2


title: Young adult CBA/CaJ mouse AN-1


title: Surgery_after_NACT_8

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_8


title: PBMC from sample HB250

status: Public on Nov 03 2021

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

institute: EF-CLIF

description: PBMC from sample HB250

data_processing:
enumerated and resuspended in RPMI 1640 medium containing penicillin (100 U/ml),
streptomycin (100 U/ml) and L-glutamine (4 mM) without fetal bovine serum (FBS).
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

source_name: PBMC

extract_protocol:
PBMCs and PMNs were isolated from 20 ml of EDTA blood. Blood samples were centrifuged at
200 g for 10 min to collect plasma and sedimented cells were diluted with DPBS -/- up to a volume
of 20 ml. Diluted blood was layered over 13.3 ml of Ficoll-Hypaque and centrifuged at 500 g for
25 min with the break off. PBMCs were obtained from the mononuclear cell layer, washed with
Dulbecco’s PBS -/- and centrifuged again at 400 g for 5 min. Pelleted PMNs were incubated with

value: PBMC

tag: disease state

value: HV


title: PBMC from sample HB249

description: PBMC from sample HB249


title: PBMC from sample AD6

description: PBMC from sample AD6

value: AD


title: PBMC from sample HB20

description: PBMC from sample HB20


title: PBMC from sample AD7

description: PBMC from sample AD7


title: PBMC from sample AD9

description: PBMC from sample AD9


title: PBMC from sample ACLF9

description: PBMC from sample ACLF9

value: ACLF


title: PBMC from sample HB222

description: PBMC from sample HB222


title: PBMC from sample AD11

description: PBMC from sample AD11


title: PBMC from sample HB246

description: PBMC from sample HB246


title: PBMC from sample AD14

description: PBMC from sample AD14


title: PBMC from sample ACLF24

description: PBMC from sample ACLF24


title: PBMC from sample ACLF11

description: PBMC from sample ACLF11


title: PBMC from sample ACLF23

description: PBMC from sample ACLF23


title: PBMC from sample ACLF25

description: PBMC from sample ACLF25


title: PBMC from sample ACLF32

description: PBMC from sample ACLF32