description:
S54
Whole-blood RNA-seq from ACLF with septic shock treated (S54).
mRNAseq


status: Public on Apr 08 2025

type: SRA

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

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

country: Spain

institute: EF-CLIF

description:
S36
Whole-blood RNA-seq from ACLF with septic shock treated (S36).
mRNAseq

library_source: transcriptomic

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability.
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: *.tsv: RSEM expected counts.

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 4380204, Applied Biosystems). RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855).
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 40 million paired-end 100nt reads.

tag: group

value: ACLF with septic shock treated

tag: tissue

value: Whole blood


title: Whole-blood RNA-seq from preACLF with sepsis shock (S02)

description:
S02
Whole-blood RNA-seq from preACLF with septic shock (S02).
mRNAseq

value: preACLF with septic shock


title: Whole-blood RNA-seq from preACLF with sepsis shock (S63)

description:
S63
Whole-blood RNA-seq from preACLF with septic shock (S63).
mRNAseq


title: PBMC from sample HV3_1

description: PBMC from sample HV3_1

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
RNA wa extracted from PBMCs using the tryzol reagent.RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 40 million paired-end 100nt reads

treatment_protocol: PBMC were seeded at a density of 1.5x106 cells/ml and incubated with either albumin (Albutein®), recombinant albumin expressed in Oryza sativa (rHSA) (Sigma) (both at 15 mg/ml) or vehicle control for twenty-four hours at 37ºC in a 5% CO2 incubator. In some experiments, PBMCs were incubated with the FcRn blocking antibody, ADM31 (Aldevron) (10 g/ml) before the addition of albumin. Isolation of total RNA from cells was performed by TRIzol. RNA concentration and integrity, library preparation and RNA-Seq analysis was performed as already described for whole-blood RNA-seq.

tag: disease group

value: HV

tag: treatment

value: Veh


title: Whole-blood RNA-seq from preACLF with sepsis shock (S35)

description:
S35
Whole-blood RNA-seq from preACLF with septic shock (S35).
mRNAseq


title: PBMC from sample HV3_5

description: PBMC from sample HV3_5


title: PBMC from sample HV3_4

description: PBMC from sample HV3_4


title: PBMC from sample HV3_2

description: PBMC from sample HV3_2

value: HSA


title: PBMC from sample HV2_2

description: PBMC from sample HV2_2


title: PBMC from sample HV2_5

description: PBMC from sample HV2_5


title: PBMC from sample HV2_1

description: PBMC from sample HV2_1


title: PBMC from sample HV2_4

description: PBMC from sample HV2_4


title: PBMC from sample HV1_1

description: PBMC from sample HV1_1


title: PBMC from sample HV1_4

description: PBMC from sample HV1_4


title: PBMC from sample HV2_3

description: PBMC from sample HV2_3

value: rHSA


title: PBMC from sample HV1_3

description: PBMC from sample HV1_3


title: PBMC from sample AD5_5

description: PBMC from sample AD5_5

value: AD


title: PBMC from sample HV1_5

description: PBMC from sample HV1_5


title: PBMC from sample HV1_2

description: PBMC from sample HV1_2


title: PBMC from sample AD5_2

description: PBMC from sample AD5_2


title: PBMC from sample AD4_5

description: PBMC from sample AD4_5


title: PBMC from sample AD5_4

description: PBMC from sample AD5_4


description:
S39
Whole-blood RNA-seq from ACLF treated (S39).
mRNAseq

value: ACLF treated


title: PBMC from sample AD4_4

description: PBMC from sample AD4_4


title: PBMC from sample AD5_1

description: PBMC from sample AD5_1


title: PBMC from sample AD4_1

description: PBMC from sample AD4_1


title: PBMC from sample AD4_3

description: PBMC from sample AD4_3


title: PBMC from sample AD3_3

description: PBMC from sample AD3_3


title: PBMC from sample AD2_2

description: PBMC from sample AD2_2


title: PBMC from sample AD3_1

description: PBMC from sample AD3_1


title: PBMC from sample AD1_2

description: PBMC from sample AD1_2


title: PBMC from sample AD1_3

description: PBMC from sample AD1_3


title: PBMC from sample AD2_3

description: PBMC from sample AD2_3


title: PBMC from sample AD2_1

description: PBMC from sample AD2_1


title: PBMC from sample AD3_2

description: PBMC from sample AD3_2


title: PBMC from sample AD4_2

description: PBMC from sample AD4_2


title: PBMC from sample AD5_3

description: PBMC from sample AD5_3


title: PBMC from sample HV3_3

description: PBMC from sample HV3_3


title: Control Cortex replica 2 snRNAseq

status: Public on Apr 01 2025

city: Boston

first: Kris

last: Kahle

address: 55 Fruit Street

country: USA

institute: MGH

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)"
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Cortex

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

value: Cortex

value: Control


title: PTEN knockout Svz replica 2 snRNAseq

description: 10x Genomics

source_name: Subventricular zone

value: Subventricular zone

value: PTEN knockout


title: PTEN knockout Svz replica 3 snRNAseq

description: 10x Genomics


title: PTEN knockout Svz replica 1 snRNAseq

description: 10x Genomics


title: PTEN knockout Cortex replica 3 snRNAseq

description: 10x Genomics


title: Control Svz replica 3 snRNAseq

description: 10x Genomics


title: Control Cortex replica 1 snRNAseq

description: 10x Genomics


title: Control Choroid replica  scRNAseq

description: 10x Genomics

source_name: Choroid plexus

value: Choroid plexus


title: Control Svz replica 2 snRNAseq

description: 10x Genomics


title: Control Svz replica 1 snRNAseq

description: 10x Genomics


title: D52S_SAE_d14

status: Public on Mar 26 2025

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

description: 10x Genomics

data_processing:
cellranger v6.1.2
SoupX
scDblFinder
Seurat v4
Minimal gene count>400, Percent mitochondrial genes<20%
Assembly: GRCh38, GENCODE v39
Supplementary files format and content: R data serialization (RDS) file, containing gene x cell (barcode) data matrices, dimension reduction embeddings, and cell meta-data.

source_name: Airway

growth_protocol: LAE, SAE, and PCLS were placed on a media-soaked Gelfoam® sponge with the lumen exposed to air and maintained in a high humidity incubator.

extract_protocol:
LAE, SAE, and PCLS tissues were cryopreserved in CryoStor freezing medium after 0 (fresh), 2, and 14 days in culture. Cryovials were thawed, rinsed in PBS, placed into a 15 mL tube containing 5 mL of Accutase solution (Sigma-Aldrich, #A6964-100ML) with EDTA (invitrogen, #15575-038) (5 mM) and pronase (Roche, #10165921001) (1 mg/mL), and incubated on a shaker for 30 min at 37°C. Following incubation, the tube was centrifuged (600 g, 2 min, 4 oC), the supernatant was discarded, and 5 mL of Hank’s Balanced Salt Solution (Ca-, Mg-) (gibco) buffer containing liberase (Roche, #05401119001) (50 mg/mL) and DNase (Roche, #10104159001) (25 ug/mL) was added to the tube. The sample was then incubated on the shaker for 10 min at 37°C. After incubation, the cell suspension was gently pipetted 20 times using a wide-orifice pipette tip. To neutralize enzymes, 500 mL of fetal bovine serum was added to the cell suspension, and the neutralized mixture was filtered through a 100 um filter, followed by centrifugation (600 g, 2 min, 4 oC). After removing supernatant, dissociated cells were resuspended in PBS (Ca-, Mg-) containing 0.01% Ultrapure BSA (Invitrogen, #AM2616), filtered through a 40-μm cell strainer (Bel-Art, H13680-0040), and centrifuged (600 g, 2 min, 4 oC). Cell count and viability was assessed using trypan blue dye exclusion with a Countess 3 automated cell counter (Thermo Fisher Scientific), and the cell concentration was adjusted to approximately 1000 cells/uL. The dissociated cells were used for 10X Genomics scRNA-seq library preparation.
Single-cell suspensions targeting approximately 6,000 cells were loaded onto a 10x Genomics Chromium Next GEM Chip G (10x Genomics) device following the manufacturer’s instructions. After GEM generation, the library preparation was performed following the instructions for the 10x Chromium Next GEM Single Cell 3’ GEM Library kit v3.1 (10x Genomics).

treatment_protocol: LAE, SAE, and PCLS were used for scRNA-seq at 0 (fresh), 2, and 14 days after culture.

value: Airway

tag: cell line

value: Small airway explants

tag: cell type

value: lung cells

tag: genotype/donor

tag: time (day)


title: Control Cortex replica 3 snRNAseq

description: 10x Genomics


title: PTEN knockout Cortex replica 2 snRNAseq

description: 10x Genomics


title: D52S_SAE_Fresh

description: 10x Genomics


title: PBMC from sample AD1_1

description: PBMC from sample AD1_1


title: PTEN knockout Choroid replica  scRNAseq

description: 10x Genomics


title: D52S_PCLS_Fresh

description: 10x Genomics

source_name: Lung parenchyma

value: Lung parenchyma

value: Precision cut lung slices


title: D52S_PCLS_d14

description: 10x Genomics


title: D52S_LAE_Fresh

description: 10x Genomics

value: Large airway explants


title: PTEN knockout Cortex replica 1 snRNAseq

description: 10x Genomics


title: D51S_PCLS_d14

description: 10x Genomics


title: D52S_LAE_d2

description: 10x Genomics


title: D51S_SAE_Fresh

description: 10x Genomics


title: D52S_SAE_d2

description: 10x Genomics


title: D51S_SAE_d14

description: 10x Genomics


title: D51S_LAE_d2

description: 10x Genomics


title: D51S_LAE_d14

description: 10x Genomics


title: D42S_PCLS_Fresh

description: 10x Genomics


title: D51S_PCLS_Fresh

description: 10x Genomics


title: D51S_SAE_d2

description: 10x Genomics


title: D42S_SAE_d2

description: 10x Genomics


title: D42S_SAE_d14

description: 10x Genomics


title: D52S_LAE_d14

description: 10x Genomics


title: D42S_LAE_Fresh

description: 10x Genomics


title: D42S_SAE_Fresh

description: 10x Genomics


title: Moc2 cells, Control 3

status: Public on Mar 03 2025

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

description:
Bulk RNA-seq
8457-MR-1_3

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: tab-delimited text file for count data

growth_protocol: MOC2 cells cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a 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 HUR Crispr/cas9 were used to treat the cells for 18 hrs. A single clone isolated and cultured for the loss of HuR. 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: HNSCC cell line


title: CNS-1, Siglec-1+ FSChi AM

status: Public on Mar 24 2025

city: Sendai

first: Takuya

last: Saito

state: Miyagi

address: 1-1 Seiryomachi, Aobaku

department: Department of Respiratory Medicine

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
The FASTQ reads of each sample were aligned to the GENCODE human reference genome GRCh38, and the expression levels for each gene were calculated.
The calculated gene expression data were incorporated into Subio Platform (Subio inc., Japan) and analyzed with Basic and Advanced Plug-ins.
Assembly: hg38
Supplementary files format and content: Text files include normalized processed signals for each Sample

source_name: alveolar macrophages obtained from lung tissue

extract_protocol:
total RNA was extracted with RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
After quality control on an Agilent TapeStation, total RNA with RNA integrity number of 7.0-9.3 was subjected to amplification with the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (CloneTech). cDNA library was prepared with the Nextera XT DNA Library Prep Kit (illumina). Samples were analyzed on NovaSeq 6000 (illumina) in 2 × 150-bp paired-end mode, which generated 40 million paired reads per sample.

value: alveolar macrophages

tag: phenotype

value: CNS

tag: age

tag: gender

value: F

tag: ethnicity

value: Japanese


title: CNS-3, Siglec-1+ FSChi AM


title: Moc2 cells, HUR KD1

description:
Bulk RNA-seq
8457-MR-1_4

value: Knockout


title: D42S_PCLS_d14

description: 10x Genomics


title: D42S_LAE_d2

description: 10x Genomics


title: MOC2 cells, Control 2

description:
Bulk RNA-seq
8457-MR-1_2


title: AAH-13: Dac51-SK-UT-1 RNA

status: Public on Feb 01 2025

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: GRCh38, transcriptome mapped to Gencode V34 gene annotations
Supplementary files format and content: matrix of raw counts with genes in rows and samples in columns

source_name: uterine leiomyosarcoma cell line

growth_protocol: The uterine leiomyosarcoma cell line (SK-UT-1) was cultured and maintained in ATCC-formulated Eagle’s Minimum Essential Medium with 10% of fetal bovine serum

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

treatment_protocol: The SK-UT-1 cell line was treated with  Dac51 (5 uM) for 48 hours or vehicle control.

value: uterus

tag: disease state

value: leiomyosarcoma

value: FTO inhibitor


title: AAH-15: Dac51-SK-UT-1 RNA


title: CNS-2, Siglec-1+ FSChi AM

value: M


title: D42S_LAE_d14

description: 10x Genomics


title: AAH-11: VEH-SK-UT-1 RNA

value: DMSO (VEH)


title: MOC2 cells, Control 1

description:
Bulk RNA-seq
8457-MR-1_1

value: Control


title: Moc2 cells,HUR KD3

description:
Bulk RNA-seq
8457-MR-1_6


title: AAH-16: Dac51-SK-UT-1 RNA


title: Bpool, scRNAseq

status: Public on Feb 26 2025

description: 10x Genomics

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.1.2) (PMID: 28091601). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Mouse genome mm10 was used for the alignment and gencode vM25 was used for gene annotation and coordinates (PMID: 33270111).Downstream analysis was performed in R with Seurat (v4.1.0) (PMID: 34062119) and customized R scripts.
Assembly: mm10
Supplementary files format and content: .h5

source_name: Lung

extract_protocol:
Wild type C57Bl/6 mice (10 weeks old) were treated systemically for seven days with bleomycin (100 U/kg) using subcutaneously implanted osmotic minipumps (ALZET 1007D; DURECT Corporation, Cupertino, CA; containing 100 µl, designed to deliver contents at 0.5 µl/h for 7 days). Control mice were treated with saline vehicle. Pumps were removed on day 7 per manufacturer’s instructions. On day 21, mice were sacrificed by isoflurane overdose and the lungs harvested. The rib cage was opened to expose the lungs. Mice were systemically perfused via the left ventricle with PBS. The left lobe was then tied and cut off. Lung tissue was washed in cold DMEM and minced into small pieces using fine surgical scissors. The tissue from each mouse was resuspended in 5 ml of collagenase (1 mg/ml, Roche #10103578001) and shaken at low speed for 45 min at 37°C. Digestion was stopped by addition of 10 ml of DMEM/10% FBS. The sample was passed through a 40 μm cell strainer to prepare a monodisperse cell suspension. Cells were collected by centrifugation (1200 rpm, 10 min, 4°C, Beckman GS-6R centrifuge) and the cell pellets resuspended in 1 ml ACK lysing buffer (LONZA #10-548E) for 5 min to remove red blood cells. Lung cells were then collected by centrifugation, washed with PBS, and collected again. Single-cell suspensions from six control saline-treated mice and six bleomycin-treated mice were each pooled in equal numbers prior to loading onto a 10X Genomics Next GEM Chip B and emulsified with Single Cell 3’ GEM beads using a Chromium™ Controller (10x Genomics).
Library was performed according to the manufacter's instruction.(single cell 3' protocol, 10x Genomics). Cells collected were counted; 50,000 cells from each sample were labeled in 200uL of PDB +1% BSA. Mixed well by repeated gentle pipetting. Incubated on ice for 30mins. Labeled cells washed 2X w/1.5ml PBS +1% BSA(pelleted between washes at 500 tcf x 5 min @RT). After final wash,labeled cells resuspended in ~50uL PBS + 1%BSA and counted. Processing on 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) and sequenced at Vanderbilt’s Next Gen Sequencing Core (Illumina NovaSeq 6000).

value: Lung

tag: strain

value: 10 weeks old

value: Wildtype

value: Bleomycin


title: Moc2 cells, HUR KD2

description:
Bulk RNA-seq
8457-MR-1_5


title: AAH-09: VEH-SK-UT-1 RNA


title: Spool, scRNAseq

description: 10x Genomics

value: Saline


title: AAH-12: VEH-SK-UT-1 RNA


title: AAH-10: VEH-SK-UT-1 RNA


title: C26pos_s2

status: Public on Jan 15 2025

description:
10x Genomics
Protocol 2

data_processing:
human
Raw sequencing data were processed with CellRanger pipeline (v7.0.0) (PMID: 28091601). 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(v0.2.0)with standard parameters. Human Genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates(PMID: 33270111).   Downstream analysis was performed in R with Seurat (v4.3.0) (PMID: 34062119) and customized R scripts. Data from Negative samples ((Neg_C_PDAC, Neg_Control, Neg_WS_PDAC) and positive samples (Pos_C_PDAC, Pos_Control, Pos_WS_PDAC) were merged into a unique single cell object. Both Negative and Positive samples were analyzed individually.   Positive Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 20017 genes and 5796 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).  Negative Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 20017 genes and 11527 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9). Differential expression analysis: To identify differentially expressed genes in Negatives and Positive samples. 1. Neg Control vs Neg Cachetic PDAC (Neg_Control  vs Neg_C_PDAC)  2. Neg Control vs Neg Weight Stable PDAC (Neg_Control  vs Neg_WS_PDAC)  3.  Neg Cachetic PDAC  vs Neg Weight Stable PDAC (Neg_C_PDAC  vs Neg_WS_PDAC) 4. Pos Control vs Pos Cachetic PDAC (Pos_Control  vs Pos_C_PDAC)  5. Pos Control vs Pos Weight Stable PDAC (Pos_Control  vs Pos_WS_PDAC)  6.  Pos Cachetic PDAC  vs Pos Weight Stable PDAC (Pos_C_PDAC  vs Pos_WS_PDAC) in each defined cell types, the R package LIBRA (v1.0.0) with option wilcox was used to perform zero-inflated regression analysis (PMID: 34584091). Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2.
Assembly: Homo Sapiens hg38
Supplementary files format and content: HDF5 Feature-Barcode Matrix
mouse
Raw sequencing data were processed with CellRanger pipeline (v7.0.0) (PMID: 28091601). 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(v0.2.0)with standard parameters. Mouse Genome mm10 was used for the alignment and gencode vM25 was used for gene annotation and coordinates (PMID: 33270111).   Downstream analysis was performed in R with Seurat (v4.3.0) (PMID: 34062119) and customized R scripts. Data from Negative samples (CtrlNeg and KppNeg) were merged into a unique single cell object and positive samples (CtrlPos and KppPos) were merged into a unique single cell object. Both Negative and Positive samples were analyzed individually.   Positive Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 21850 genes and 17462 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).   Negative Samples: Cells with <10000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 21850 genes and 35352 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: Skeletal Muscle

extract_protocol: Dual-indexed libraries were pooled to and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 25 million paired-end 150 bp reads per library.

value: Skeletal Muscle

value: Mononuclear cells

value: 14 weeks


title: C26neg_s2

description:
10x Genomics
Protocol 2


title: posControl_s2

description:
10x Genomics
Protocol 2


title: Kpp_Neg

description:
10x Genomics
Protocol 2

value: 5 months


title: Kpp_Pos

description:
10x Genomics
Protocol 2


title: posControl_s1

description:
10x Genomics
Protocol 2


title: C26neg_s1

description:
10x Genomics
Protocol 2


title: C26pos_s1

description:
10x Genomics
Protocol 2


title: negControl_s1

description:
10x Genomics
Protocol 2


title: Ctrl_Pos

description:
10x Genomics
Protocol 2


title: Ctrl_Neg

description:
10x Genomics
Protocol 2


title: D51S_LAE_Fresh

description: 10x Genomics

value: Airway

value: Large airway explants

value: lung cells


title: Neg_WS_PDAC

description:
10x Genomics
Protocol 1


title: Neg_Control

description:
10x Genomics
Protocol 1


title: Treg_NoAct_donor12

status: Public on Nov 30 2024

description:
Library name: Sample 17
8457-MR-64_1_S1_L005_

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 v42). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Human GRCh38
Supplementary files format and content: Input tables are included as tab separated files.

source_name: Treg Tcell

extract_protocol:
Cells were immediately pelleted by centrifugation at 4°C and resuspended in Homogenization Buffer containing thioglycerol provided in the purification kit.  RNA was extracted with a Promega Maxwell RSC 16 using the Maxwell RSC simplyRNA Cells kit (Cat# AS1390) according to the manufacturer’s instructions and RNA concentration was measured using a NanoDrop 8000.  RNA quality was assessed using an Agilent 4200 TapeStation and RINe values ranged from 9.9 to10.
Total RNA (50 ng) was used the construction of libraries with the New England Biolabs NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# 7490L) and Ultra II Directional RNA Library Prep Kit for Illumina (Cat# 7760L) according to the manufacturer’s instructions.  Dual-indexed libraries were pooled to and sequenced at VANTAGE (Vanderbilt University) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 25 million paired-end 150 bp reads per library.

value: Treg Tcell


title: Teff_CAR_donor12

description:
Library name: Sample 22
8457-MR-64_6_S1_L005_

source_name: Teff Tcell

value: Teff Tcell


title: Treg_TCR_donor18

description:
Library name: Sample 16
8457-MR-32_0006_S1_L005_


title: Pos_WS_PDAC

description:
10x Genomics
Protocol 1


title: Teff_NoAct_donor12

description:
Library name: Sample 18
8457-MR-64_2_S1_L005_


title: Neg_C_PDAC

description:
10x Genomics
Protocol 1


title: Treg_CAR_donor12

description:
Library name: Sample 21
8457-MR-64_5_S1_L005_


title: Pos_Control

description:
10x Genomics
Protocol 1


title: Treg_CAR_donor18

description:
Library name: Sample 15
8457-MR-32_0005_S1_L005_


title: Teff_TCR_donor18

description:
Library name: Sample 13
8457-MR-32_0003_S1_L005_


title: Pos_C_PDAC

description:
10x Genomics
Protocol 1


title: Teff_TCR_donor12

description:
Library name: Sample 20
8457-MR-64_4_S1_L005_


title: Treg_TCR_donor12

description:
Library name: Sample 19
8457-MR-64_3_S1_L005_


title: Treg_CAR_CD19_donor33

description:
Library name: Sample 8
10282-MR-0016_03_S1_L005_


title: Treg_NoAct_donor18

description:
Library name: Sample 14
8457-MR-32_0004_S1_L005_


title: Teff_CAR_donor18

description:
Library name: Sample 12
8457-MR-32_0002_S1_L005_


title: Treg_NoAct_donor33

description:
Library name: Sample 6
10282-MR-0016_01_S1_L005_


title: Treg_TCR_donor33

description:
Library name: Sample 7
10282-MR-0016_02_S1_L005_


title: Treg_CAR_P2Y3_donor33

description:
Library name: Sample 10
10282-MR-0016_05_S1_L005_


title: Teff_TCR_donor31

description:
Library name: Sample 2
10282-MR-0014_2_S1_L005_


title: Teff_NoAct_donor18

description:
Library name: Sample 11
8457-MR-32_0001_S1_L005_


title: NAc_Ctrl2

status: Public on Nov 27 2024

description:
Nac
Staying Homecage
NAc_Counts.txt

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text files raw counts for each sample

source_name: C57Bl6J male mice, Nucleus Accumbens

extract_protocol:
RNAs were isolated with QIAGEN miRNseasy Kits.
Total RNA library

value: Nucleus Accumbens

tag: Sex

value: male

value: Homecage


title: Treg_CAR_P2Y3_donor31

description:
Library name: Sample 5
10282-MR-0014_5_S1_L005_


title: Treg_CAR_CAT_donor31

description:
Library name: Sample 3
10282-MR-0014_3_S1_L005_


title: Treg_CAR_CAT_donor33

description:
Library name: Sample 9
10282-MR-0016_04_S1_L005_


title: 7166.MR.144_6

status: Public on Nov 20 2024

source_name: Spleen

growth_protocol: T cells were stimulated with gp100 antigen (1ug/mL) and cultured in IMDM media supplemented with 10% FBS + 100 IU IL2/mL

extract_protocol:
mRNA was extracted using TRIzol reagent, per the manufacturer's protocol
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep following manufacturer's protocols.Libraries and sequencing were performed at the Translational Sequencing Core at MUSC. RNA was harvested using RNeasy Mini Kit (Qiagen). 500 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: T cells were treated with either vehicle control or 0.5 mM GYY4137 (H2S donor)

value: Spleen

value: CD8+ T lymphocytes

value: WT

value: H2S treatment


title: Treg_NoAct_donor31

description:
Library name: Sample 1
10282-MR-0014_1_S1_L005_


title: PFC_WT4

description:
PFC
Experinced Socail defeat stress
PFC_Counts.txt

source_name: C57Bl6J male mice, medial Prefrontal cortex

value: medial Prefrontal cortex

value: SocialDefeat


title: PFC_WT3


title: 7166.MR.144_2

value: vehicle control


title: AAH-14: Dac51-SK-UT-1 RNA

value: uterus

value: leiomyosarcoma

value: FTO inhibitor


title: 7166.MR.144_4


title: PFC_WT2

description:
PFC
Staying Homecage
PFC_Counts.txt


title: PFC_WT1

description:
PFC
Staying Homecage
PFC_Counts.txt


title: 7166.MR.144_5


title: TSVZ_MIS1B

description: 10x Genomics

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v7.0.0) (PMID: 28091601). The “mkfastq” command was used to generate FASTQ files and the “count” command was used to generate raw gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters. Mouse genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates (PMID: 33270111).  The data from 3 area (N_SVZ, T_SVZ and T_Mass) were analyzed individually. Samples from patients were combined in R using the Read10X() function from Seurat package(v4.3.0) (PMID: 34062119) and an integrated Seurat object was generated. Filtering was conducted by retaining cells that had unique molecular identifiers (UMIs) less than 25000 and had mitochondrial content less than 5 percent. Doublets were removed using scDblFinder (v1.12.0) (PMID: 35814628). The SCTransform workflow was used for count normalization and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony (v0.1.1)( PMID: 31740819). Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers (PMID: 26430063). Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. N_SVZ is from two patients HNS1 and HNS2 with a total of 19988 genes and 8772 cells. T_SVZ is from 12 patients GBM7B, GBM8B, GBM9B, GBM10B, GBM12B, GBM16B, GBM17B, GBM20B, GBM22B, MIS1B, MIS2B, MIS3B with a total of 19988 genes and 37360 cells. T_Mass is from 14 patients GBM7A, GBM8A, GBM9A, GBM10A, GBM12A, GBM14A, GBM16A, GBM17A, GBM18A, GBM20A, GBM22A, MIS1A, MIS2A, MIS3A with a total of 19988 genes and 67801 cells. For N_SVZ Cell annotation was performed using two different approaches: 1) scType an ultrafast unsupervised method for cell type annotations (PMID: 35273156) 2) Manual curation by gene markers to reflect the prediction results.  Cell type annotation for T_SVZ and T_Mass: Tumor cells were identified using InferCNV analysis (PMID: 31980621) with the following parameters - denoise TRUE, default hidden markov model (HMM) settings, and a value of 0.1 for “cutoff” and the N_SVZ clusters were used are reference. Each resulted CNV was annotated to be either a gain or a loss. Tumor cell clusters were classified based on Neftel GBM cell state (PMID: 31327527) using the their meta module gene markers, SCpubr(V2.0.1) was used to visualize the resultant enrichment. The Clusters that showed an enrichment for that a cell state were labelled as GBMopc(OPClike), GBMac(AClike), GBMmes(MESlike), GBMnpc(NPClike), other clusters that either showed enrichment for two or more cell states or no enrichment for any cell state were labelled as GBMcc(Cancer Cells). Healthy cells were manually curated by using canonical gene markers:. Astrocytes - "GFAP","AQP4", Microglia - "MEF2C","P2RY12", Neurons - "SYNPR","CNR1", "SYT1”, Oligodendrocytes - "MOG","MBP", OPC - "VCAN","SOX5", Endothelial - "VWF","ABCB1", Ependymal  - "SPARCL1","S100B".  All 3 area N_SVZ, T_SVZ and T_Mass were integrated with Harmony (v0.1.1)( PMID: 31740819), 30 PCA and a resolution of 0.3 was chosen.  Genes differentially expressed were calculated between N_SVZ vs T_SVZ, N_SVZ vs T_Mass, and T_SVZ vs T_Mass as a whole area. The R package LIBRA (v1.0.0) was used to perform zero-inflated regression analysis (PMID: 34584091). Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.3.
Assembly: hg38
Supplementary files format and content: Matrix files

molecule: nuclear RNA

source_name: tumor svz sample of glioblastoma patient mis1

extract_protocol:
Nuclei were isolated from frozen human brain tumor and non-tumor tissues. Briefly, frozen human tissue samples were homogenized and lysed with Triton X-100 in RNase-free water for nuclei isolation. The isolated nuclei were purified, centrifuged, and resuspended in PBS with BSA and RNAse Inhibitor. The nuclei were diluted to 700 nuclei/ul and loaded to 10x Genomics Chromium Controller to encapsulate single nuclei into droplet emulsions following the manufacturer’s recommendations.
3’ single nucleus gene expression libraries (Next GEM v3.1, dual index) were constructed using the 10x Genomics Chromium system. Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay and quality assessed by BioAnalyzer.
Each library was sequenced on Illumina NovaSeq 6000 (PE150). Reads were subsequently processed using 10x Genomics Cell Ranger analytical pipeline and human GRCh38 reference genome.

tag: disease

value: glioblastoma


title: TSVZ_MIS3B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient mis3


title: NAc_Coca1

description:
Nac
Exploration in conditioned place preference chamber with cocaine (7.5 mg/kg, i.p.) administraion
NAc_Counts.txt

value: Cocaine CPP


title: TSVZ_GBM17B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 17


title: NAc_Coca2


title: 7166.MR.144_3


title: Treg_CAR_CD19_donor31

description:
Library name: Sample 4
10282-MR-0014_4_S1_L005_

value: Treg Tcell


title: TSVZ_GBM9B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 9


title: 7166.MR.144_1


title: NAc_Ctrl1

description:
Nac
Staying Homecage
NAc_Counts.txt


title: TSVZ_GBM16B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 16


title: TSVZ_GBM8B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 8


title: TSVZ_GBM10B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 10


title: TSVZ_GBM7B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 7


title: TSVZ_GBM22B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 22


title: TSVZ_MIS2B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient mis2


title: TSVZ_GBM20B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 20


title: TMASS_GBM8A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 8


title: TMASS_GBM9A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 9


title: TSVZ_GBM12B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 12


title: TMASS_GBM14A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 14


title: TMASS_MIS3A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient mis3


title: TMASS_MIS2A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient mis2


title: Nsvz_HNS2

description: 10x Genomics

source_name: histologically normal human brain sample

value: normal


title: TMASS_MIS1A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient mis1


title: TMASS_GBM18A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 18


title: Nsvz_HNS1

description: 10x Genomics

value: histologically normal human brain sample


title: Colon Tumour AK Rep3

status: Public on Nov 05 2024

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

description: 10X Genomics

data_processing:
Sequence alignment of single-cell data to the mm10 genome was performed using the count tool from the Cell Ranger package version 6.1.2 according to the developer’s instructions, generating barcodes, features and matrix output files for each sample. Subsequent analysis was done using R version 4.1.1 using Seurat version 4.0.4.
Assembly: mm10
Supplementary files format and content: h5 matrix files

source_name: Colon

growth_protocol: Genetic alterations were induced by Tamoxifen, delivered intraperitoneally to produce tumours from ageing mice and intracolonically in mice with 'intracolonic induction tumours'. Organoids from intestinal tumours of the specified genotypes were injected into wild type mice to generate intracolonic transplant tumours. Tumours were collected at clinical end point.

extract_protocol:
Segments of colon from mice with the noted genetic mutations were homogenised and digested using a Mcllwain Tissue Chopper and the GentleMACS Octo Dissociator (Miltenyi Biotec, 130-096-427) in combination with the mouse tumour dissociation kit (Miltenyi Biotec, 130-096-730). Cells were then sorted using a FACSAria sorter (BD Biosciences) and DAPI (Invitrogen, D1306) to remove dead cells.
Libraries were prepared using reagents from the 10x Chromium Single-Cell 3′ v3 Gel Bead Kit and Library (10x Genomics) according to the manufacturer’s protocol, then analysed using the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).

value: Colon

value: Female

tag: sample type

value: Intracolonic Induction Tumour

value: VilCreER Apcfl/fl KRasG12D/+


title: Colon Tumour Apc Rep4

description: 10X Genomics

tag: tissue

value: Male

value: VilCreER Apcfl/fl


title: TMASS_GBM12A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 12


title: Colon Tumour Apc Rep3

description: 10X Genomics


title: TMASS_GBM7A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 7


title: TMASS_GBM22A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 22


title: TMASS_GBM20A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 20


title: Colon Tumour Apc Rep1

description: 10X Genomics


title: TMASS_GBM17A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 17


title: p74-myc-PAK1

status: Public on Sep 25 2024

city: Duarte

first: Debbie

middle: C.

last: Thurmond

state: California

address: 1500 E Duarte Rd

institute: City of Hope

library_source: genomic

data_processing:
The 75-nt single-end (SE75) sequence reads were mapped to the genome using the BWA algorithm (“bwa aln/samse” with default settings). Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
The tags were extended in silico (using Active Motif software) at their 3 ́- ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library. The fragment density was determined in 32-nt bins along the genome and stored in bigWig (.bw) files.
Peaks were called using MACS2.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: Excel file with peak intensities and genomic annotations.

molecule: genomic DNA

extract_protocol:
Cells were treated with 1% paraformadehyde at room temperature for 20 mins. Quenched cell lysate was sonicated to generate DNA fragments using Bioruptor (Diagenode).
Genomic DNA was prepared by treating aliquots of chromatin with Rnase, proteinase K and heat (overnight, 65 degrees C), followed by SPR1 bead clean up and quantified using a CLARIOstar microplate reader. An aliquot of chromatin was precleared with protein agarose beads. Genomic DNA regions of interest were isolated using antibody against myc-tag. Illumina sequencing libraries were prepared from the input DNA using standard enzymatic steps of end-polishing, dA-addition, and adapter ligation using an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: Human EndoC-H1 cells

tag: chip antibody

value: MygTag antibody (Abcam, Cat# ab9132, Lot# GR3235624-5)


title: TMASS_GBM16A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 16


title: TMASS_GBM10A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 10


title: Colon Tumour AK Rep1

description: 10X Genomics


title: Donor 15, PAK1

data_processing:
RNA-seq raw fastq reads were aligned to the human hg19 genome using TopHat2.
Gene counts were obtained using htseq-count, with UCSC known gene annotations (TxDb.Hsapiens.UCSC.hg19.knownGene), and converted into counts per million (CPM) using edgeR.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with columns containing raw gene counts from each sample.

source_name: Pancreatic islets

extract_protocol:
RNA extraction was performed using QIAGEN RNase kit.
250ng of total RNA from each samples was used for sequencing library preperation with KAPA mRNA Hyperp Kit according to user manual. The library QC was checked with Agilent bioanalyzer DNA high sensitivity chip, and qubit was used for library quantification. The final libries were sequenced on Illumina Hiseq2500 wtih single read mode of 51 cyles, plus 7 cycles of index sequencing with V4 kit.

value: Pancreatic islets

tag: individual

value: Donor 15

value: ND


title: p84-myc-PAK1

tag: cell line


title: Colon Tumour AK Rep2

description: 10X Genomics


title: Donor 15, Ctrl

value: Ctrl


title: Donor 16, PAK1

value: Donor 16

value: Type 2 diabetes


title: Donor 14, PAK1

value: Donor 14


title: Donor10, Ctrl


title: Donor 16, Ctrl


title: Donor9, PAK1


title: Donor10, PAK1


title: Donor 14, Ctrl


title: Donor9, Ctrl


title: Donor 13, Ctrl

value: Donor 13


title: Donor5, PAK1


title: Donor8, Ctrl


title: Donor5, Ctrl


title: Donor4, PAK1


title: Donor3, PAK1


title: Donor3, Ctrl


title: WT_plus - replicate 2

status: Public on Sep 15 2024

city: Praha

first: Blanka

last: Holendova

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology, CAS

data_processing:
Low quality reads and adaptor sequence were filtered out using TrimmomaticSE (v. 0.36) with the parameters “HEADCROP:10 ILLUMINACLIP:~/TruSeq-PE3.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”. Ribosomal RNA reads were filtered out using Sortmerna (v. 2.1b)  (default parameters) and the cleaned reads were then aligned using STAR (v. 2.7.3a) to the Mus musculus genome version GRCm38 and annotation version vM8. A count table was then generated using the python script htseq-count (v. 0.6.1p1) with the parameter “–m union”.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files raw read count values for each Sample

source_name: pancreas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Libraries were prepared from 500 ng of tal RUNA using SureSelect XT HS2 mRNA Library prepration System (Agilent) according to manufacture protocol (Version A1, September 2020). It utilize using Poly-A Selection Module (Cat.No 5190-6411), cDNA Module (Cat.No 5500-0149) and XT HS2 Index Primer Pairs (Cat.No 5191-5688). Adaptor-ligated cDNA libraries were amplified using 9 PCR cycles.

value: pancreas

tag: cell type

value: Beta cells/pancreatic islets

value: Wild Type

tag: treatment

value: High glucose


title: Donor4, Ctrl


title: WT_plus - replicate 3


title: Donor 13, PAK1


title: Donor8, PAK1


title: WT - replicate 1

value: Low glucose


title: hCiLB-0618,RNA-seq

status: Public on Sep 01 2024

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

country: China

institute: Peking University

data_processing:
Raw sequencing data were performed quality control using FastQC.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (parameter- ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Trimmed sequence reads were mapped to hg19 using STAR (parameters- --readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
Read count extraction were calculated using program featureCounts of Subread package
The gene count matrix was normalized for visualization using R package DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: induced from hADSC

extract_protocol:
The Direct-zol RNA MiniPrep Kit (Zymo Research, R2053) was used to extract total RNA.
The NEBNext Ultra RNA Library Prep Kit was used for RNA sequencing library construction. Fragmented and randomly primed 2 × 150 bp paired-end libraries were sequenced using the Illumina HiSeq X Ten system.

value: induced from hADSC


title: WT - replicate 3


title: WT_plus - replicate 1


title: hCiLB-0325,RNA-seq


title: hCiLB-1013,RNA-seq


title: WT - replicate 2


title: hADSC-0618,RNA-seq

source_name: Adipose tissue

value: Adipose tissue

value: hADSC


title: hADSC-1013,RNA-seq


title: hCiLB-0721,RNA-seq

source_name: induced from skin fibroblats

value: induced from skin fibroblats


title: hASF-0721,RNA-seq

source_name: Skin

value: Skin

value: dermal fibrobalsts


title: hCiLB-0721,scRNA-seq

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: hg19
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cells were harvested and resuspended at 1 x 106 cells per milliliter in PBS supplemented with 0.04% BSA.
Using Single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension containing 300-600 living cells per microliter was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. On an S1000TM Touch Thermal Cycler (Bio Rad), captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEM. These steps were carried out at 53 °C for 45 minutes, followed by 85 °C for 5 minutes, and held at 4 °C. Single-cell RNA sequencing libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics) and sequenced by IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150).


title: 1e11_5months_mouse_3

status: Public on Jul 12 2024

city: Urbana

first: Pablo

last: Perez-Pinera

state: il

address: 1406 West Green Street

institute: University of Illinois Urbana-Champaign

data_processing:
Supplementary files format and content: Excel sheet containing editing data sorted by figure number
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
RNAstar utilized for exon junction analysis, creating bam and SJ outputs to visualize and quantify RNA splicing. 2-pass mapping was used with a MAPQ quality score of 60
Assembly: chr38

source_name: striatum

extract_protocol:
Striatum extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: striatum

value: neuron

value: transgenic

value: AAV9 injection with SpRY-ABE-HTT-4 sgRNA

value: male


title: hASFs-0721,scRNA-seq

description: 10x Genomics

value: dermal fibroblats


title: hADSC-0325,RNA-seq


title: 1e11_5months_mouse_1

value: female


title: 1e11_5months_mouse_4


title: 1e10_5months_mouse_2


title: 1e10_5months_mouse_1


title: 1e9_5months_mouse_1


title: 1e11_mouse_2months_mouse_2


title: 1e10_mouse_2months_mouse_2


title: 1e11_mouse_2months_mouse_1


title: 1e9_5months_mouse_2


title: 1e9_mouse_2months_mouse_2


title: hADSCs-1013,scRNA-seq

description: 10x Genomics


title: SpRY-ABE-HTT-3_cDNA_mouse_5

extract_protocol:
Striatum extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment, splice junction quantification, sashimi plot analysis on IGV
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers


title: 1e10_mouse_2months_mouse_1


title: 1e11_5months_mouse_2


title: SpRY-ABE-HTT-3_cDNA_mouse_4


title: SpRY-ABE-HTT-3_cDNA_mouse_2


title: SpRY-ABE-HTT-3_cDNA_mouse_3


title: hCiLB-1013,scRNA-seq

description: 10x Genomics


title: SpRY-ABE-HTT-3_cDNA_mouse_1


title: Colon Tumour Apc Rep2

description: 10X Genomics

value: Colon

value: Male

value: Intracolonic Induction Tumour

value: VilCreER Apcfl/fl


title: 1e9_mouse_2months_mouse_1


title: SpRY-ABE-HTT-3_gDNA_mouse_5


title: SpRY-ABE-mRosa26_cDNA_mouse_7

value: AAV9 control injection with SpRY-ABE-mRosa26 sgRNA


title: SpRY-ABE-mRosa26_cDNA_mouse_5


title: SpRY-ABE-mRosa26_cDNA_mouse_6


title: SpRY-ABE-HTT-3_gDNA_mouse_2


title: SpRY-ABE-HTT-3_gDNA_mouse_1


title: SpRY-ABE-mRosa26_cDNA_mouse_3


title: SpRY-ABE-mRosa26_cDNA_mouse_4


title: SpRY-ABE-mRosa26_cDNA_mouse_1


title: SpRY-ABE-mRosa26_gDNA_mouse_4


title: SpRY-ABE-HTT-3_gDNA_mouse_4


title: SpRY-ABE-mRosa26_gDNA_mouse_5


title: SpRY-ABE-HTT-3_gDNA_mouse_3


title: CBE-HTT-4_cDNA_mouse_9

value: AAV9 injection with CBE-HTT-4 sgRNA


title: CBE-HTT-4_cDNA_mouse_8


title: SpRY-ABE-mRosa26_gDNA_mouse_7


title: SpRY-ABE-mRosa26_gDNA_mouse_3


title: SpRY-ABE-mRosa26_gDNA_mouse_6


title: SpRY-ABE-mRosa26_cDNA_mouse_2


title: CBE-HTT-4_cDNA_mouse_7


title: CBE-HTT-4_cDNA_mouse_2


title: SpRY-ABE-mRosa26_gDNA_mouse_1


title: CBE-HTT-4_cDNA_mouse_5


title: SpRY-ABE-mRosa26_gDNA_mouse_2


title: CBE-HTT-4_cDNA_mouse_3


title: CBE-HTT-4_cDNA_mouse_6


title: CBE-HTT-4_cDNA_mouse_4


title: CBE-mRosa26_cDNA_mouse 3

value: AAV9 control injection with CBE-mRosa26 sgRNA


title: CBE-mRosa26_cDNA_mouse 5


title: CBE-mRosa26_cDNA_mouse 6


title: CBE-HTT-4_cDNA_mouse_1


title: CBE-mRosa26_cDNA_mouse 2


title: CBE-HTT-4_gDNA_mouse_7


title: CBE-HTT-4_gDNA_mouse_10


title: CBE-mRosa26_cDNA_mouse 1


title: CBE-mRosa26_cDNA_mouse 4


title: CBE-HTT-4_gDNA_mouse_8


title: CBE-HTT-4_gDNA_mouse_6


title: CBE-HTT-4_gDNA_mouse_5


title: CBE-HTT-4_gDNA_mouse_1


title: CBE-HTT-4_gDNA_mouse_4


title: CBE-HTT-4_gDNA_mouse_9


title: CBE-HTT-4_gDNA_mouse_3


title: CBE-HTT-4_gDNA_mouse_2


title: CBE-mRosa26_gDNA_mouse 6


title: CBE-mRosa26_gDNA_mouse 5


title: CBE-mRosa26_gDNA_mouse 3


title: CBE-mRosa26_gDNA_mouse 1


title: CBE-mRosa26_gDNA_mouse 4


title: CBE-mRosa26_gDNA_mouse 2


title: SpRY-ABE-HTT-3_OT5_biorep_1

source_name: kidney

extract_protocol:
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: kidney

value: epithelial

value: Lipofectamine 2000 transfected split_SpRY-ABE-HTT-3 plasmid


title: SpRY-ABE-HTT-3_OT5_biorep_3


title: SpRY-ABE-HTT-3_OT5_biorep_2


title: SpRY-ABE-HTT-3_OT4_biorep_3


title: SpRY-ABE-HTT-3_OT4_biorep_2


title: SpRY-ABE-HTT-3_OT3_biorep_3


title: SpRY-ABE-HTT-3_OT3_biorep_1


title: SpRY-ABE-HTT-3_OT2_biorep_3


title: SpRY-ABE-HTT-3_OT3_biorep_2


title: SpRY-ABE-HTT-3_OT4_biorep_1


title: SpRY-ABE-HTT-3_OT2_biorep_2


title: SpRY-ABE-HTT-3_OT1_biorep_2


title: SpRY-ABE-HTT-3_OT1_biorep_3


title: CBE-HTT-4_OT8_biorep_3

value: Lipofectamine 2000 transfected split_CBE-HTT-4 plasmid


title: CBE-HTT-4_OT8_biorep_1


title: CBE-HTT-4_OT7_biorep_3


title: SpRY-ABE-HTT-3_OT2_biorep_1


title: CBE-HTT-4_OT8_biorep_2


title: SpRY-ABE-HTT-3_OT1_biorep_1


title: CBE-HTT-4_OT5_biorep_3


title: CBE-HTT-4_OT6_biorep_3


title: CBE-HTT-4_OT5_biorep_2


title: CBE-HTT-4_OT6_biorep_1


title: CBE-HTT-4_OT5_biorep_1


title: CBE-HTT-4_OT7_biorep_1


title: CBE-HTT-4_OT4_biorep_3


title: CBE-HTT-4_OT6_biorep_2


title: CBE-HTT-4_OT4_biorep_2


title: CBE-HTT-4_OT7_biorep_2


title: CBE-HTT-4_OT3_biorep_2


title: CBE-HTT-4_OT4_biorep_1


title: CBE-HTT-4_OT3_biorep_1


title: CBE-HTT-4_cDNA_mouse_10

value: striatum

value: neuron


title: CBE-HTT-4_OT1_biorep_2


title: CBE-HTT-4_OT2_biorep_2


title: CBE-HTT-4_OT2_biorep_1


title: CBE-HTT-4_OT1_biorep_1


title: CBE-HTT-4_OT2_biorep_3


title: CBE-HTT-4_OT3_biorep_3


title: CBE-HTT-4_OT1_biorep_3


title: full-length_SpRY-ABE-HTT-3_cDNA_biorep_2

extract_protocol:
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment, splice junction quantification, sashimi plot analysis on IGV
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: Lipofectamine 2000 transfected full length_SpRY-ABE-HTT-3 plasmid


title: split_SpRY-ABE-HTT-3_cDNA_biorep_4


title: split_SpRY-ABE-HTT-3_cDNA_biorep_3


title: full-length_SpRY-ABE-HTT-3_cDNA_biorep_1


title: split_SpRY-ABE-HTT-3_gDNA_biorep_1


title: split_SpRY-ABE-HTT-3_gDNA_biorep_2


title: split_SpRY-ABE-HTT-3_cDNA_biorep_2


title: SpRY-ABE_GFP_gDNA_biorep_2

value: Lipofectamine 2000 transfected GFP plasmid


title: split_SpRY-ABE-HTT-3_cDNA_biorep_1


title: SpRY-ABE_GFP_cDNA_biorep_2


title: full-length_SpRY-ABE-HTT-3_gDNA_biorep_2


title: SpRY-ABE_GFP_cDNA_biorep_1


title: split_SpRY-ABE-HTT-3_gDNA_biorep_3


title: WT293T_cDNA_biorep_1

value: native HEK293T cells


title: Clone_CBE-HTT-4_cDNA_biorep_2

value: Lipofectamine 2000 transfected and puromycin selected  clone of CBE-HTT-4 plasmid


title: Clone_CBE-HTT-4_cDNA_biorep_1


title: SpRY-ABE_GFP_gDNA_biorep_1


title: WT293T_cDNA_biorep_2


title: full-length_CBE-HTT-4_cDNA-biorep_1

value: Lipofectamine 2000 transfected full length_CBE-HTT-4 plasmid


title: full-length_CBE-HTT-4_cDNA-biorep_2


title: CBE_GFP control_ cDNA_biorep_2


title: full-length_CBE-HTT-4_gDNA_biorep_3


title: full-length_CBE-HTT-4_cDNA-biorep_3


title: split_CBE-HTT-4_cDNA_biorep_2


title: split_CBE-HTT-4_gDNA_biorep_3


title: CBE_GFP control_ cDNA_biorep_1


title: split_CBE-HTT-4_gDNA_biorep_1


title: split_CBE-HTT-4_gDNA_biorep_2


title: CBE_GFP control_ gDNA_biorep_3


title: CBE_GFP control_ gDNA_biorep_2


title: split_CBE-HTT-4_cDNA_biorep_3


title: split_CBE-HTT-4_cDNA_biorep_1


title: motor cortex, stim on PD, rat3

status: Public on Jul 11 2024

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

data_processing:
Low-quality adapter sequences were trimmed using TrimGalore.
The STAR 2-pass method was used to align the raw sequencing data to the rat reference genome (mRatBN7.2) using the STAR aligner.
Read count was extracted using featureCounts.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample.

organism: Rattus norvegicus

source_name: Motor cortex

extract_protocol:
A library was independently prepared with 1ug of total RNA from each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA).
Libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms (KAPA BIOSYSTEMS).

value: Motor cortex

value: stim on PD


title: full-length_CBE-HTT-4_gDNA_biorep_1


title: CBE_GFP control_ gDNA_biorep_1


title: motor cortex, stim on PD, rat1


title: motor cortex, stim on PD, rat2


title: motor cortex, PD, rat3

value: PD


title: full-length_SpRY-ABE-HTT-3_gDNA_biorep_1


title: motor cortex, stim on ctrl, rat2

value: stim on ctrl


title: full-length_CBE-HTT-4_gDNA_biorep_2


title: motor cortex, stim on ctrl, rat1


title: motor cortex, ctrl, rat2

value: ctrl


title: motor cortex, stim on ctrl, rat3


title: motor cortex, PD, rat1


title: Prg4-tdTomato+ cells isolated from Fsk-treated condition Rep5

status: Public on Jun 13 2024

first: April

middle: M

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
Novogene
Assembly: mm10
Supplementary files format and content: gene counts in xls file

source_name: 3xR mESC

extract_protocol:
Trizol
Novogene

value: 3xR mESC

tag: time

value: day 14

value: Fsk


title: motor cortex, ctrl, rat1


title: motor cortex, ctrl, rat3


title: motor cortex, PD, rat2


title: Prg4-tdTomato+ cells isolated from DMSO-treated condition Rep1

value: DMSO


title: Prg4-tdTomato+ cells isolated from Fsk-treated condition Rep1


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep1


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep5


title: Tumor bearing KPC with Metastasis B

status: Public on Apr 10 2024

source_name: Skeletal Muscle

extract_protocol:
Cells were  homogenized in 1mL of Trizol and RNA extracted as per manufacters protocol
Libraries were prepared by MUSC Translational Core using the New England Biolabs NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat# 7490L) and Ultra II Directional RNA Library Prep Kit from Illumina (Cat# 7760L). Dual indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 to a depth of approximately 25 million paired-end 150 bp reads per library.

value: Skeletal Muscle

tag: genotype

value: WT

value: tumor bearing


title: Tumor bearing KPC with no Metastasis B


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep4


title: Prg4-tdTomato+ cells isolated from DMSO-treated condition Rep3


title: Prg4-tdTomato+ cells isolated from Fsk-treated condition Rep4


title: Tumor bearing KPC with Metastasis A


title: Prg4-tdTomato+ cells isolated from DMSO-treated condition Rep5


title: Ctrl KPC_B

value: Control


title: Ctrl KPC_A


title: Control for KPP B


title: Tumor bearing KPP B


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep3


title: ATAC AGS_r2

status: Public on Apr 22 2024

city: Baltimore

first: Michael

middle: A

last: Beer

state: MD

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

data_processing:
Sequenced reads were mapped to the human genome assembly (hg38) using Bowtie2. Mitochondrial and viral reads were removed.
Peaks were called on each sample using MACS2 callpeak function.
Assembly: hg38
Supplementary files format and content: bigwig, bed

source_name: AGS

extract_protocol:
ATAC-seq was performed as described in Corces MR et al Nat Methods 2017. Cells were lysed in ATAC-resuspension buffer containing 0.5% NP40, 0.5 % Tween-20 and 0.01% Digitonin. Nuclei were then resuspended in 50 μl transposition mixture containing 25 μl of 2x TD buffer, 16.5 μl of PBS, 5 μl nuclease free water, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween-20 and 2.5 μl of transposase (Illumina Tagment DNA enzyme 1, #20034198) and incubated at 37°C for 30 minutes with agitation. DNA was extracted using the NEB Monarch® PCR & DNA cleanup kit (#T1030L) and used for PCR using the Illumina/Nextera primers. Library clean-up was performed using Ampure XP beads.
ATAC-seq: Libraries were sequenced on a NextSeq platform (Illumina).

value: AGS

value: Gastric cancer cell line


title: Tumor Bearing KPP A


title: Tumor bearing C26 B


title: Control for C26 A


title: Control for C26 B


title: Control for KPP A


title: Tumor bearing LLC A


title: KPCML1 B

source_name: Pancreatic Tumor Derived Cells

value: Pancreatic Tumor Derived Cells

value: KPC

value: Pancreatic Cancer Cell Line

value: metastatic line


title: Control for LLC A


title: Tumor bearing KPC with no Metastasis A


title: Tumor bearing LLC B


title: KPC A

value: parental cell line


title: KPC B


title: Day6 Wild-type(N2) feed with E. coli HT115

status: Public on Mar 21 2024

city: Ashburn

first: Shihong

middle: Max

last: Gao

address: 19700 Helix Dr

department: 4D Cellular Physiology

institute: Janelia Research Campus

description: 10x Genomics

data_processing:
We used Cell ranger (6.0, 10x Genomics) to align Raw base call (BCL) sequence files or FASTQ files to the C. elegans genome (WS282, Wormbase), and generated feature-barcode matrices. Doublets were removed based on the recommended ratio provided by the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 user guide (CG000204 Rev D), with a score calculated by Doubletfinder (Github/chris-mcginnis-ucsf). The feature-barcode matrices for each sample were constructed into a Seurat (R package, 4.0.5) object for downstream analysis. Cells were filtered by requiring a minimum of 100 genes to be expressed, and genes were filtered by being expressed in at least 3 cells. Integration of samples was performed with Seurat canonical correlation analysis (CCA) method to remove the batch effects. We tested CCA, reciprocal principal component analysis (PCA) and Harmony (0.1) for integration and chose the method with the best performance. The top 2,000 variable features were used for integration anchor identification. UMAP and tSNE dimension reduction were performed with the first 50 dimensions from PCA. Clustering was performed at multiple Leiden resolutions.
Assembly: WS282
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: cawa_neuronsubclusterlabel.rds (This file contains neuron subcluster identity labels for the Cell Atlas of Worm Aging (CAWA) dataset. Neuron nuclei were subsetted from the integrated Seurat object, re-integrated using Seurat CCA, and clustered at multiple Leiden resolutions to resolve 77 subclusters corresponding to 104 of 118 known adult C. elegans neuron classes. Subcluster annotation was performed using a combination of marker gene identification (via COSG) cross-referenced with known expression profiles, and reference-based mapping(SingleR) with SingleR using the Taylor et al. (2021) C. elegans neuronal transcriptome atlas as the primary reference.)

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
Worms were washed three times with PBS and collected in a 1.5 mL tube. We then added 100 μl of homogenization buffer {10.1126/science.abk2432} and grind the worms with a pestle motor for 30 seconds on ice. To minimize nuclei adhesion on the surface, all the pestles, tubes and filters were pre-coated with a homogenization buffer or 1x PBS. 900 μl of homogenization buffer was added to wash the pestle, and the total 1mL homogenized sample was transferred into a 1mL Dounce tissue grinder (Wheaton 357538). The grinder was autoclaved overnight in a 220℃ oven to deactivate ribonuclease. After placing the grinder on ice, 20 strokes were applied using a loose pestle, followed by another 20 strokes using a tight pestle, while avoiding generating foams. The 1000μl samples were filtered through a cell strainer (35 μm) and then through a Flowmi cell strainer (BelArt, H13680-0040) into a new 1.5 mL tube. The tubes were centrifuged for 10 minutes at 1000 g at 4°C, and the supernatant was removed while not disturbing the pellet, which was hardly visible. The pellet was resuspended with 500 μl 1x PBS with 0.5% BSA and RNAase inhibitor and filtered with a Flowmi cell strainer (BelArt, H13680-0040) again into a 5 mL flow cytometer tube. A total of 20 μl was transferred into another flow cytometer tube and diluted with 180 μl 1x PBS with 0.5% BSA and RNAase inhibitor as an unstained control. Hoechst (Invitrogen 33342) was used to stain the nuclei in 1:1000 working concentration. We coated the 1.5 mL sorting collection tube with 1x PBS with 0.5% BSA and RNAase inhibitor and ~300,000 nuclei were sorted with Hoechst 33342 positive gating, which indicates DNA content, and forward scatter area (FSC-A) gating, representing the particle size above threshold. The intestinal nuclei, which are polypoid (32N), usually form an obvious cluster separating from the other 2N somatic nuclei, and these were also included in our collection. The collection tube was centrifuged at 800g for 8 minutes at 4℃ and the sheath buffer supernatant was carefully removed before resuspending the sorted nuclei with 40-50 μl 1x PBS with 0.5% BSA and RNAase inhibitor. The concentration and morphology of the nuclei were checked under a microscope to ensure high-quality nuclei isolation. If the results were desirable, we proceeded to generate gel emulsion with 10X Chromium Controller.  For sorting the nuclei, we used either DB LSR II or Sony MA800 sorter. To obtain the best nuclei morphology and the least RNA degradation, it is recommended to minimize the sorting time. Two researchers could simultaneously set up the sorter and perform nuclei processing.
Library preparation was carried out using the published 10X Chromium Single Cell 3’ v2/v3 Solution protocol (Single/dual index). The resulting libraries were sequenced on the NextSeq550 or NovaSeq6000 platforms, with a depth ranging from 6,306 to 29,862 reads/cell, with the recommended cycle numbers: 26 cycles for Read 1, 8 cycles for i7 index, and 98 cycles for Read 2.

value: whole body


title: Day6 rsks-1 mutant feed with E. coli OP50

description: 10x Genomics


title: Day1 Wild-type(N2) feed with E. coli HT115

description: 10x Genomics


title: Tumor bearing C26 A


title: Day14 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: KPCML1 A


title: Day6 Wild-type(N2) feed with E. coli delta lon(Keio collection)

description: 10x Genomics


title: Day1 Wild-type(N2) feed with E. coli delta lon(Keio collection)

description: 10x Genomics


title: Early Day1 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics

value: day1(48h after L1)


title: Day6 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: Day12 daf-2 mutant feed with E. coli OP50

description: 10x Genomics

extract_protocol:
Worms were washed three times with PBS and collected in a 1.5 mL tube. We then added 100 μl of homogenization buffer {10.1126/science.abk2432} and grind the worms with a pestle motor for 30 seconds on ice. To minimize nuclei adhesion on the surface, all the pestles, tubes and filters were pre-coated with a homogenization buffer or 1x PBS. 900 μl of homogenization buffer was added to wash the pestle, and the total 1mL homogenized sample was transferred into a 1mL Dounce tissue grinder (Wheaton 357538). The grinder was autoclaved overnight in a 220℃ oven to deactivate ribonuclease. After placing the grinder on ice, 20 strokes were applied using a loose pestle, followed by another 20 strokes using a tight pestle, while avoiding generating foams. The 1000μl samples were filtered through a cell strainer (35 μm) and then through a Flowmi cell strainer (BelArt, H13680-0040) into a new 1.5 mL tube. The tubes were centrifuged for 10 minutes at 1000 g at 4°C, and the supernatant was removed while not disturbing the pellet, which was hardly visible. The pellet was resuspended with 500 μl 1x PBS with 0.5% BSA and RNAase inhibitor and filtered with a Flowmi cell strainer (BelArt, H13680-0040) again into a 5 mL flow cytometer tube. A total of 20 μl was transferred into another flow cytometer tube and diluted with 180 μl 1x PBS with 0.5% BSA and RNAase inhibitor as an unstained control. Hoechst (Invitrogen 33342) was used to stain the nuclei in 1:1000 working concentration. We coated the 1.5 mL sorting collection tube with 1x PBS with 0.5% BSA and RNAase inhibitor and ~300,000 nuclei were sorted with Hoechst 33342 positive gating, which indicates DNA content, and forward scatter area (FSC-A) gating, representing the particle size above threshold. The intestinal nuclei, which are polypoid (32N), usually form an obvious cluster separating from the other 2N somatic nuclei, and these were also included in our collection. The collection tube was centrifuged at 800g for 8 minutes at 4℃ and the sheath buffer supernatant was carefully removed before resuspending the sorted nuclei with 40-50 μl 1x PBS with 0.5% BSA and RNAase inhibitor. The concentration and morphology of the nuclei were checked under a microscope to ensure high-quality nuclei isolation. If the results were desirable, we proceeded to generate gel emulsion with 10X Chromium Controller. For sorting the nuclei, we used either DB LSR II or Sony MA800 sorter. To obtain the best nuclei morphology and the least RNA degradation, it is recommended to minimize the sorting time. Two researchers could simultaneously set up the sorter and perform nuclei processing.
Library preparation was carried out using the published 10X Chromium Single Cell 3’ v2/v3 Solution protocol (Single/dual index). The resulting libraries were sequenced on the NextSeq550 or NovaSeq6000 or NextSeq 2000 platforms, with a depth ranging from 6,306 to 29,862 reads/cell, with the recommended cycle numbers: 26 cycles for Read 1, 8 cycles for i7 index, and 98 cycles for Read 2.


title: Control for LLC B


title: Day12 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: Day1 Wild-type(N2) feed with E. coli K-12 BW25113

description: 10x Genomics


title: Day1 Wild-type(N2) feed with OP50 bacteria, replicate 3

description: 10x Genomics

value: day1(55~60h after L1)


title: Day14 Wild-type(N2) feed with E. coli OP50, replicate 3

description: 10x Genomics


title: Day1 lipl-4 intestinal overexpression line  feed with E. coli OP50

description: 10x Genomics

value: MCW14 raxIs3 [ges-1p::lipl-4::SL2GFP]


title: Day1 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: Day1 rsks-1 mutant feed with E. coli OP50

description: 10x Genomics


title: Day6 daf-2 mutant feed with E. coli OP50

description: 10x Genomics


title: Day1 Wild-type(N2) feed with E. coli OP50, replicate 2

description: 10x Genomics


title: Day6 Wild-type(N2) feed with E. coli K-12 BW25113

description: 10x Genomics


title: Day12 lipl-4 intestinal overexpression line feed with E. coli OP50

description: 10x Genomics


title: Heart, young, antibody-derived tags

status: Public on Feb 07 2024

data_processing:
Raw sequencing data were processed with Cell Ranger (v7.0.0). Cellranger mkfastq command was used to demultiplex the different samples and cellranger multi command was used to generate gene – cell expression, ADT - cell expression, and HTO - 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 gencode vM10 (GRCm38.p4)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 (young and aged) were merged into a unique single cell object. Nuclei with > 250 genes, < 20000 UMIs, and < 20% 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 16,418 genes and 15,826 cells. The SCTransform workflow was used for count normalization and data integration using 30 principal components and resolution of 0.6 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 manually curated using markers from literature. To identify differentially expressed genes between conditions (young vs aged) 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.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: heart

extract_protocol:
Myocardial infarction as induced in C57Bl6/J female mice by permanent occlusion of the left anterior descending artery ligation. At post-MI Day 5, cells were isolated from the infarct zone of young (3-5 months) and old (15-17 months old) and run for scRNA sequencing.
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. Antibody-derived tag (ADT) libraries were constructed using TotalSeq-A anti-mouse for CD8a, CD44, CD62L, NK1.1, TCRgd, and CD3. Three biological replicates were used for each category (young and aged); these replicates were each tagged with TotalSeq B anti-mouse hashtags 2, 3, and 4 and multiplexed.

value: heart

value: young (3-5 months)


title: Day6 Wild-type(N2) feed with E. coli OP50, replicate 2

description: 10x Genomics


title: Day6 Wild-type(N2) feed with E. coli OP50, replicate 3

description: 10x Genomics


title: Day14 Wild-type(N2) feed with E. coli OP50, replicate 2

description: 10x Genomics


title: Day12 Wild-type(N2) feed with E. coli OP50 , replicate 3

description: 10x Genomics


title: Day12 Wild-type(N2) feed with E. coli OP50 , replicate 2

description: 10x Genomics


title: Heart, aged, hashtag oligos

value: old (15-17 months)


title: Heart, young, hashtag oligos


title: Day6 lipl-4 intestinal overexpression line feed with E. coli OP50

description: 10x Genomics


title: Sorted renal cells, KO, Late, Male, tdTomato Positive, Rep 4

status: Public on Jan 16 2024

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

description:
10x Genomics
OY615_pos

data_processing:
Single-cell libraries were sequenced on Illumina NextSeq 2000 sequencing system with P3 200 cycle (Illumina 20040560) reagents. Equimolar pools of up to six sample libraries were prepared and diluted to 650 pM and mixed with 1% PhiX Control v3 DNA (Illumina FC-110-3001) in RSB buffer to a final volume of 25 μl. Sequencing was performed and preliminary sequencing results (bcl files) and FASTQ files were generated with the DRAGEN FASTQ Generation 3.8.4 or the DRAGEN BCL convert workflow optimized for Single Cell RNA Library Kit 1 library prep kit, and the Single Cell RNA Index Adaptors 1-B index adaptor kit, with 28 and 152 Read 1 and 2 cycles respectively
The mm10 reference genome was customized and the starting reference fastq files and GTF files came from refdata-gex-mm10-2020-A.tar.gz and are available for download at https://support.10xgenomics.com/single-cell-gene-expression/software/downloads or https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz. The transcript sequence for Vhlpjr.KO that included the tdTomato sequence was then added manually to the fasta reference genome file and annotation for tdTomato transcript was added manually to the gtf file. The cellranger 6.0.1 mkref function was used to build the custom reference genome and reads taken from FASTQ files generated for each sample were aligned to the custom reference genome by CellRanger (version 6.1.1; https://support.10xgenomics.com/single-cell-gene-expression/ software/pipelines/latest/what-is-cell-ranger) using default parameter sample by sample. After aligning, for each read pair, cell barcodes and unique molecular identifiers (UMIs) were obtained from Read 1 and read counts per feature were obtained from Read 2. Only those UMIs that could be linked to a valid cell barcode and a gene exon region were included to create the cell by gene count matrix. Reads from Vhl exon 1 were excluded from analysis to prevent ambiguous alignment. Cells were subjected to the following filters: detected genes > 200, fraction of mitochondrially-encoded reads < 0.5, and detected genes < 3 x median for each sample. The threshold for mitochondrially encoded reads was set to this value in line with published kidney scRNA-seq studies to account for the high mitochondrial content in RTE cells19. Information and quality control metrics for all sequenced samples are provided in Supplementary Table S1. Cells from different samples and sequencing runs were then aggregated, which sometimes required manual renaming of duplicate cell ‘names’. Downstream analysis was conducted using the R package Seurat 4.0.3: Read counts were log-normalized and scaled, PCA was run using the scaled data and UMAP was generated using the top 30 PCs.
Assembly: mm10
Supplementary files format and content: Seurat objects containing information from all the samples and positive samples were provided. They contain the information for all the cells after quality control, for example, raw counts and normalised counts for all the features, dimension reduction information and all the meta information.

source_name: Kidney

growth_protocol: All experimental procedures were conducted in line with AACR guidelines following approval by the Medical Science Ethical Review Committee of the University of Oxford and authorization under UK Home Office regulations of Animals (Scientific Procedures) Act 1986. Mice were housed in individually ventilated cages on a 13 h light/ 11 h dark cycle with food and water provided ad libitum.

extract_protocol:
Kidneys were dissociated using the Multi-Tissue Dissociation Kit 2 (Miltenyi 130-110-203). Briefly, the renal capsule was removed, and the tissue macerated for 5 min on a bed of ice. The macerated kidney was then transferred to 1.45 ml Buffer X, 30µl of Enzyme D, 15 µl of Enzyme P, 15 μl of Buffer Y, and 6 µl of Enzyme A, all prepared according to the manufacturer’s instructions. The tube was then agitated under water at 37˚C in a shaking incubator at 150 rpm for 30 min. Dissociation was stopped by the addition of 150 µl Fetal Bovine Serum (FBS; Sigma F7524), and resuspension in 9 ml of RPMI-1460 medium (Merck R0883). Undigested tissue was removed using a 40 µm cell strainer and the filtrate centrifuged (300g for 10 min at 4˚C). Erythrocytes were eliminated by resuspending dissociated cells in 3 ml of 1x RBC Lysis Buffer (Miltenyi 130-094-183) prepared in deionized water for 2 min at RT. Cells were centrifuged (300g for 5 min at 4˚C) and resuspended in ice-cold D-PBS before being counted on a Thermo Scientific Countess II machine for total yield and viability. Dissociated cells were resuspended in 10% FBS 2 mM EDTA in D-PBS (Thermo 14190144) to a concentration of 5 million live cells per ml. 10 μl of 10 μg/ml DAPI (Sigma D9542) was added to stain for viability. Cells were sorted using a BD Aria Fusion Cell Sorter. tdTomato was excited with a 561 nm laser and fluorescence detected with a 582/15 band pass filter. DAPI was excited with a 405 nm laser and fluorescence detected with a 450/40 band pass filter. Live, single, tdTomato-positive and -negative cells were collected in FBS-coated polypropylene tubes and pelleted by centrifugation at 300g for 10 min. Cells were counted again for yield and viability and processed for single-cell sequencing.
Sorted cells were prepared into single-cell droplets using the Chromium Next GEM Single-cell kit. 20,000 live cells were loaded per sample on separate Chromium Next GEM Chip G (10X Genomics PN-1000127) channels. cDNA clean-up, amplification and adaptor ligation were performed with the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics PN-1000268). Twelve reaction cycles were used for cDNA amplification. cDNA yield was quantified using the High Sensitivity D1000 ScreenTape Assay (Agilent 5067-5584 and 5067-5585) to optimize the number of reaction cycles for library preparation. Single cell sequencing libraries were prepared using Dual Index Kit TT Set A (10X Genomics PN-1000215) sequence indices. Prepared libraries were quantified with KAPA Library Quantification Kit (Roche KK4824) following the manufacturer’s protocol.

treatment_protocol: Five consecutive daily doses of 2 mg tamoxifen were administered to Control and KO mice >20 g by oral gavage using sterile, disposable plastic feeding tubes (Instech FTP-20-38).

value: Kidney

tag: cells

value: FAC-sorted cells

tag: facs tdtomato_status

value: Positive

tag: mouse genotype

value: Vhl(KO/flox) (KO)

tag: cellular vhl_status

value: Vhl(KO/KO)

tag: timepoint

value: Late (4-12 months)


title: Heart, aged, gene expression

tag: strain

tag: age


title: Day12 rsks-1 mutant feed with E. coli OP50

description: 10x Genomics


title: Sorted renal cells, KO, Early, Male, tdTomato Positive, Rep 3

description:
10x Genomics
OY1021_pos

value: Early (1-3 weeks)


title: Sorted renal cells, Control, Late, Female, tdTomato Positive, Rep 2

description:
10x Genomics
OY611_pos

value: Vhl(wt/flox) (Control)

value: Vhl(wt/KO)


title: Sorted renal cells, KO, Late, Female, tdTomato Positive, Rep 1

description:
10x Genomics
OY606_pos


title: Sorted renal cells, Control, Late, Female, tdTomato Positive, Rep 3

description:
10x Genomics
OY545_pos


title: Sorted renal cells, KO, Early, Male, tdTomato Positive, Rep 4

description:
10x Genomics
OY1166_pos


title: EARLI_50681_Hypo

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: Hypo

tag: gender

value: Male


title: EARLI_50660_Hypo

tag: tissue

value: Female


title: EARLI_50650_Hypo


title: Sorted renal cells, KO, Late, Female, tdTomato Positive, Rep 2

description:
10x Genomics
OY626_pos


title: Sorted renal cells, Control, Late, Male, tdTomato Positive, Rep 4

description:
10x Genomics
OY622_pos


title: Sorted renal cells, Control, Late, Female, tdTomato Positive, Rep 1

description:
10x Genomics
OY552_pos


title: EARLI_50634_Hypo


title: EARLI_50624_Hypo


title: EARLI_50626_Hypo


title: Sorted renal cells, KO, Early, Female, tdTomato Positive, Rep 2

description:
10x Genomics
OY978_pos


title: EARLI_50594_Hypo


title: EARLI_50593_Hyper

value: Hyper


title: EARLI_50600_Hypo


title: EARLI_50586_Hyper


title: Sorted renal cells, Control, Early, Male, tdTomato Positive, Rep 4

description:
10x Genomics
OY1004_pos


title: EARLI_50540_Hyper


title: EARLI_50552_Hypo


title: Sorted renal cells, Control, Early, Female, tdTomato Positive, Rep 3

description:
10x Genomics
OY954_pos


title: EARLI_50511_Hyper


title: Sorted renal cells, Control, Early, Female, tdTomato Positive, Rep 2

description:
10x Genomics
OY955_pos


title: Sorted renal cells, Control, Early, Female, tdTomato Positive, Rep 1

description:
10x Genomics
OY725_pos


title: EARLI_50537_Hypo


title: EARLI_50452_Hyper


title: EARLI_50435_Hyper


title: EARLI_50437_Hyper


title: EARLI_50447_Hypo


title: Heart, young, gene expression

value: heart


title: EARLI_50661_Hypo


title: Sorted renal cells, KO, Late, Male, tdTomato Positive, Rep 3

description:
10x Genomics
OY1023_pos


title: EARLI_50642_Hypo


title: EARLI_50418_Hyper


title: EARLI_50635_Hypo


title: EARLI_50618_Hyper


title: EARLI_50400_Hypo


title: EARLI_50647_Hypo


title: EARLI_50377_Hyper


title: EARLI_50631_Hypo


title: EARLI_50575_Hypo


title: EARLI_50515_Hypo


title: EARLI_50356_Hyper


title: EARLI_50471_Hypo


title: EARLI_50498_Hypo


title: EARLI_50371_Hypo


title: Heart, aged, antibody-derived tags


title: EARLI_50428_Hyper


title: EARLI_50292_Hypo


title: EARLI_50316_Hyper


title: EARLI_50445_Hypo


title: EARLI_50413_Hypo


title: EARLI_50398_Hyper


title: EARLI_50182_Hypo


title: EARLI_50366_Hyper


title: EARLI_50375_Hypo


title: EARLI_50417_Hyper


title: EARLI_50172_Hyper


title: EARLI_50383_Hypo


title: EARLI_50169_Hypo


title: EARLI_12110_Hyper


title: EARLI_50390_Hypo


title: EARLI_50348_Hypo


title: EARLI_12045_Hypo


title: EARLI_50302_Hyper


title: Sorted renal cells, KO, Early, Female, tdTomato Positive, Rep 1

description:
10x Genomics
OY733_pos


title: EARLI_50297_Hypo


title: EARLI_50291_Hypo


title: EARLI_50228_Hypo


title: EARLI_50367_Hypo


title: EARLI_50216_Hypo


title: EARLI_50222_Hypo


title: EARLI_50185_Hypo


title: EARLI_12012_Hypo


title: EARLI_12005_Hyper


title: EARLI_12003_Hyper


title: EARLI_12004_Hyper


title: EARLI_11956_Hyper


title: EARLI_50288_Hypo


title: EARLI_50178_Hypo


title: EARLI_12113_Hyper


title: EARLI_11945_Hypo


title: EARLI_11930_Hypo


title: EARLI_11848_Hyper


title: EARLI_11831_Hypo


title: EARLI_12013_Hypo


title: EARLI_12087_Hyper


title: EARLI_12018_Hyper


title: EARLI_11807_Hyper


title: EARLI_11990_Hypo


title: EARLI_11827_Hyper


title: EARLI_11814_Hyper


title: EARLI_11774_Hypo


title: EARLI_11959_Hypo


title: EARLI_11943_Hypo


title: EARLI_11942_Hypo


title: EARLI_11841_Hypo


title: EARLI_11742_Hyper


title: EARLI_11970_Hypo


title: EARLI_11734_Hyper


title: EARLI_11707_Hyper


title: EARLI_11795_Hyper


title: EARLI_11727_Hypo


title: EARLI_11796_Hypo


title: EARLI_11773_Hypo


title: EARLI_11781_Hyper


title: EARLI_11690_Hypo


title: EARLI_11766_Hypo


title: EARLI_11780_Hypo


title: EARLI_11636_Hyper


title: EARLI_11568_Hypo


title: EARLI_11764_Hyper


title: EARLI_11737_Hyper


title: EARLI_11752_Hypo


title: EARLI_11556_Hypo


title: EARLI_11544_Hyper


title: EARLI_11704_Hypo


title: EARLI_11724_Hypo


title: EARLI_11642_Hypo


title: EARLI_11586_Hyper


title: EARLI_11530_Hypo


title: EARLI_11555_Hypo


title: EARLI_11533_Hyper


title: EARLI_11599_Hypo


title: EARLI_11550_Hyper


title: EARLI_11526_Hypo


title: EARLI_11489_Hypo


title: EARLI_11521_Hypo


title: EARLI_11539_Hyper


title: EARLI_11503_Hypo


title: EARLI_11510_Hyper


title: EARLI_11498_Hyper


title: EARLI_11463_Hyper


title: EARLI_11486_Hyper


title: EARLI_11515_Hypo


title: EARLI_11456_Hypo


title: EARLI_11445_Hypo


title: EARLI_11430_Hypo


title: EARLI_50184_Hyper


title: EARLI_11428_Hypo


title: EARLI_11424_Hyper


title: EARLI_11422_Hyper


title: EARLI_11412_Hyper


title: EARLI_11479_Hypo


title: EARLI_11417_Hyper


title: EARLI_11353_Hypo


title: EARLI_11403_Hyper


title: EARLI_11344_Hypo


title: EARLI_11411_Hypo


title: EARLI_11329_Hypo


title: EARLI_11343_Hyper


title: EARLI_11321_Hyper


title: EARLI_11404_Hyper


title: EARLI_11320_Hypo


title: EARLI_11290_Hyper


title: EARLI_11308_Hypo


title: EARLI_11299_Hyper


title: EARLI_11221_Hypo


title: EARLI_11310_Hypo


title: EARLI_11300_Hyper


title: EARLI_11182_Hyper


title: EARLI_11180_Hyper


title: EARLI_11140_Hypo


title: EARLI_11203_Hyper


title: EARLI_11317_Hypo


title: EARLI_11139_Hypo


title: EARLI_11122_Hyper


title: EARLI_11168_Hyper


title: EARLI_11097_Hypo


title: EARLI_11086_Hypo


title: EARLI_11093_Hypo


title: EARLI_11175_Hypo


title: EARLI_11062_Hypo


title: EARLI_11137_Hyper


title: EARLI_11053_Hypo


title: EARLI_11035_Hyper


title: EARLI_11052_Hypo


title: EARLI_11079_Hypo


title: EARLI_11038_Hypo


title: EARLI_11046_Hypo


title: EARLI_10993_Hyper


title: EARLI_10958_Hyper


title: EARLI_10957_Hyper


title: EARLI_11043_Hypo


title: EARLI_10963_Hypo


title: EARLI_10956_Hypo


title: EARLI_11080_Hypo


title: EARLI_10971_Hyper


title: EARLI_10981_Hyper


title: EARLI_10929_Hyper


title: EARLI_10825_Hypo


title: EARLI_10846_Hyper


title: EARLI_10991_Hypo


title: EARLI_10820_Hypo


title: EARLI_10741_Hypo


title: EARLI_10819_Hypo


title: EARLI_10757_Hypo


title: EARLI_10755_Hyper


title: EARLI_10740_Hypo


title: EARLI_10691_Hypo


title: EARLI_10584_Hypo


title: EARLI_10456_Hypo