title: CRISPR screen, biol rep 1


title: mNPC, V2, 2D, Day22, biol rep 2

status: Public on Mar 14 2024

type: SRA

city: Los Angeles

first: Zhongwei

last: Li

state: CA

address: 1425 San Pablo St

department: Keck medicine

country: USA

institute: University of Southern California

description:
mNPC DESeq2 Medium ratio
2D NPC (D22) #2

library_source: transcriptomic

data_processing:
For Bulk RNA-Seq
Partek Flow Genomic Analysis Software
FASTQ files were trimmed from both ends based on a minimum read length of 25 bps and an end mininum quality score (Phred) of 20 or higher
For mouse samples, reads were aligned to mm39 - GENCODE Genes - release M28 GENCODE mm10 (release M24) using STAR 2.7.8a.
For human samples, reads were aligned to hg38 - GENCODE Genes - release 40 using STAR 2.7.8a.
Aligned reads were quantified to the Partek E/M annotation model. Gene counts were normalized using DESeq2 Median ratio.
For CRISPR Screen
MAGeCKFlute
1798 genes from CRISPR screen replicate #1, and 1627 genes from CRISPR screen replicate #2, with beta scores > 1.5 or < -1.5, and p-values < 0.05, were identified as potential hits
These hits were further analysed using Canonical Pathway Analysis tools of the Ingenuity Pathway Analysis (IPA) platform
Assembly: mm39 and hg38
Supplementary files format and content: Tab-delimited excel files include DESeq2 Median ratio for each Sample
Supplementary files format and content: Tab-delimited excel files include beta scores for each genes
Supplementary files format and content: Tab-delimited excel files include read counts for each genes

molecule: total RNA

organism: Mus musculus

source_name: Embryonic Kidney

growth_protocol: Nephron progenitor cells cultured in NPSR V1 or V2 medium, 37C, 5% CO2

extract_protocol:
Total RNA was extract using the Zymo Research Quick-RNA Microprep kit, 200-400 ug total RNA was used for the construction of sequencing library
All the single-end data library were prepared using Roche KAPA Standed mRNA-seq Kit. All the paired-end data library were constructed by NovoGene with total RNA we provided.

tag: tissue

value: Embryonic Kidney

tag: cell line

value: 2D mNPC

tag: cell type

value: Nephron Progenitor Cell

tag: genotype

tag: treatment

value: mNPSR-v2 culture

tag: time

value: Clonal mNPC line was derived from one single NPC of mNPC lines cultured for 22 days with mNPSR-v2 medium


title: mNPC, V2, 2D, Day22, biol rep 1

description:
mNPC DESeq2 Medium ratio
2D NPC (D22) #1

treatment_protocol: Nephron progenitor cells cultured in NPSR V1 or V2 medium, 37C, 5% CO2


title: mNPC, V2, 3D-2D, biol rep 1

description:
mNPC DESeq2 Medium ratio
3D-to-2D NPC #1

value: 3D-to-2D mNPC

value: 28 days


title: mNPC, V2, 2D, Day44, biol rep 2

description:
mNPC DESeq2 Medium ratio
2D NPC (D44) #2

value: Clonal mNPC line was derived from one single NPC of mNPC lines cultured for 44 days with mNPSR-v2 medium


title: D16 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D16_2

data_processing:
Partek Flow Genomic Analysis Software
FASTQ files were trimmed from both ends based on a minimum read length of 25 bps and an end mininum quality score (Phred) of 20 or higher
For mouse samples, reads were aligned to mm39 - GENCODE Genes - release M28 GENCODE mm10 (release M24) using STAR 2.7.8a.
For human samples, reads were aligned to hg38 - GENCODE Genes - release 40 using STAR 2.7.8a.
Aligned reads were quantified to the Partek E/M annotation model. Gene counts were normalized using DESeq2 Median ratio or TMM.
Assembly: mm39 and hg38
Supplementary files format and content: Tab-delimited excel file include TMM for each Sample

organism: Homo sapiens

source_name: hPSC-derived cells

growth_protocol: SIX2- cells or SIX2-/PODXL+ podocytes isolated iNPC-derived nephron organoids were cultured with hNPSR-v2 medium. Kidney organoids were cultured with Stage II medium (STEMdiffTM APELTM2 medium with 50 ng/mL FGF9 and 1 μg/mL heparin) or Stage III medium (Advanced RPMI 1640 medium with 1X B27 and 200nM A83-01), 37C, 5% CO2

extract_protocol:
Total RNA was extracted using Direct-zol RNA MicroPrep Kit (Zymo) or Quick-RNA Microprep Kit (Zymo) following the kit instruction.
RNA-Seq library were constructed by NovoGene with total RNA we provided.

value: H1 hESC

value: Kidney cells

value: iNPCLCs were cultured with hNPSR-v2 medium


title: D9 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D9_2

treatment_protocol: SIX2- cells or SIX2-/PODXL+ podocytes isolated iNPC-derived nephron organoids were cultured with hNPSR-v2 medium. Kidney organoids were cultured with Stage II medium (STEMdiffTM APELTM2 medium with 50 ng/mL FGF9 and 1 μg/mL heparin) or Stage III medium (Advanced RPMI 1640 medium with 1X B27 and 200nM A83-01), 37C, 5% CO2


title: SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 6 days, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D6_2

value: SIX2-/PODXL+ podocytes were cultured with hNPSR-v2 medium


title: SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 6 days, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D6_1


title: SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 4 days, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D4_2


title: D9 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D9_1


title: SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 4 days, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D4_1


title: SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 2 days, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D2_2


title: SIX2-/PODXL+ podocytes, cultured with hNPSR-v2 for 2 days, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D2_1


title: SIX2-/PODXL+ podocytes, isolated from D7 iNPC-derived nephron organoids, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D0_2


title: D21 iNPC-derived nephron organoid, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D21_2

value: Kidney organoids were cultured with Stage III medium


title: SIX2-/PODXL+ podocytes, isolated from D7 iNPC-derived nephron organoids, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D0_1


title: D21 iNPC-derived nephron organoid, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D21_1


title: D14 iNPC-derived nephron organoid, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D14_2


title: D10 iNPC-derived nephron organoid, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D10_2


title: D14 iNPC-derived nephron organoid, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D14_1


title: D10 iNPC-derived nephron organoid, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D10_1


title: D4 iNPC-derived nephron organoid, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D4_2

value: Kidney organoids were cultured with Stage II medium


title: D7 iNPC-derived nephron organoid, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D7_2


title: D4 iNPC-derived nephron organoid, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D4_1


title: D24 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D24_1


title: D16 iNPCLCs, reprogrammed from SIX2-/PODXL+ podocytes, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7PX_D16_1


title: D19 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7OG_D19_1


title: D2 iNPC-derived nephron organoid, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D2_2


title: D7 iNPC-derived nephron organoid, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D7_1


title: D2 iNPC-derived nephron organoid, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
OG_D2_1


title: D13 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7OG_D13_2


title: D13 iNPCLCs, reprogrammed from SIX2- cells of D5 iNPC-derived nephron organoids, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
iNPC_D5_OG_2


title: D13 iNPCLCs, reprogrammed from SIX2- cells of D5 iNPC-derived nephron organoids, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
iNPC_D5_OG_1


title: SIX2- cells, isolated from D7 iNPC-derived nephron organoids, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7OG_D0_2


title: D13 iNPCLCs, reprogrammed from SIX2- cells of D3 iNPC-derived nephron organoids, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
iNPC_D3_OG_2


title: SIX2- cells, isolated from D7 iNPC-derived nephron organoids, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7OG_D0_1


title: iNPC, SIX2+/PAX2+, Day0, biol rep 2

description:
hNPC DESeq2 Medium ratio
D0-iNPC-SIX2/PAX2-2

value: hPSC-derived cells

value: iNPC

value: 0 day


title: iNPC, V2, 2D, Day80

description:
hNPC DESeq2 Medium ratio
iNPC-v2-D80

value: 2D iNPC

value: hNPSR-v2 culture

value: 80 days


title: iNPC, SIX2+/PAX2+, Day0, biol rep 1

description:
hNPC DESeq2 Medium ratio
D0-iNPC-SIX2/PAX2-1

value: Nephron Progenitor Cell


title: D13 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7OG_D13_1


title: iNPC, SIX2+, Day0, biol rep 2

description:
hNPC DESeq2 Medium ratio
D0-iNPC-SIX2-2


title: hNPC, V2, 2D, Day52

description:
hNPC DESeq2 Medium ratio
hNPC-v2-D52

source_name: Human Fetal Kidney

value: Human Fetal Kidney

value: 2D hNPC

value: WT

value: 52 days


title: iNPC, V2, 2D, Day55

description:
hNPC DESeq2 Medium ratio
iNPC-v2-D55

value: 55 days


title: hNPC, V2, 2D, Day80

description:
hNPC DESeq2 Medium ratio
hNPC-v2-D80


title: iNPC, SIX2+, Day0, biol rep 1

description:
hNPC DESeq2 Medium ratio
D0-iNPC-SIX2-1


title: iNPC, V2, 2D, Day30

description:
hNPC DESeq2 Medium ratio
iNPC-v2-D30

value: 30 days


title: hNPC, V2, 2D, Day30

description:
hNPC DESeq2 Medium ratio
hNPC-v2-D30


title: iNPC, V2, 2D, Day17

description:
hNPC DESeq2 Medium ratio
iNPC-v2-D17

value: 17 days


title: D19 iNPCLCs, reprogrammed from SIX2- cells of D7 iNPC-derived nephron organoids, replicate 2

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
D7OG_D19_2

value: H1 hESC

value: Kidney cells

value: iNPCLCs were cultured with hNPSR-v2 medium


title: hNPC, V2, 2D, Day16

description:
hNPC DESeq2 Medium ratio
hNPC-v2-D16

value: 16 days


title: hNPC, V1, 2D, Day15, Biol rep 3

description:
hNPC DESeq2 Medium ratio
hNPC-v1-3-D15

value: hNPSR-v1 culture

value: 15 days


title: iNPC, V1, 2D, Day15, Biol rep 3

description:
hNPC DESeq2 Medium ratio
iNPC-v1-3-D15

value: hPSC-derived cells

value: 2D iNPC


title: iNPC, V1, 2D, Day15, Biol rep 2

description:
hNPC DESeq2 Medium ratio
iNPC-v1-2-D15


title: hNPC, V1, 2D, Day15, Biol rep 1

description:
hNPC DESeq2 Medium ratio
hNPC-v1-1-D15


title: Otud7b_retina_WT-LD

status: Public on Mar 12 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: retina

extract_protocol:
Total RNAs were harvested using TRIzol RNA extraction reagent (Invitrogen).
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: retina

value: exposuretolight


title: Skeletal muscle, Ope

status: Public on Mar 11 2024

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Generated reads were input into the cellranger count pipeline (Cell Ranger v.4.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: comma-delimited text files include filtered counts for cells detected

source_name: skeletal muscle

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
Single-cell RNA library construction was processed according to the protocol outlined in the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide.

value: skeletal muscle

tag: Sex

value: male

tag: strain

tag: age

value: 12 weeks

value: Tenotomy 4 days


title: D13 iNPCLCs, reprogrammed from SIX2- cells of D3 iNPC-derived nephron organoids, replicate 1

description:
Bulk RNA-Seq conducted by Novogene Co
Partek_iNPCs_Normalized_TMM.xlsx
iNPC_D3_OG_1


title: CRISPR screen plasmid Lib

description:
CRISPR screen beta scores (All genes)
Normalized sgRNA read counts in CRISPR screen

library_source: genomic

molecule: genomic DNA

organism: synthetic construct


title: hNPC, V1, 2D, Day15, Biol rep 2

description:
hNPC DESeq2 Medium ratio
hNPC-v1-2-D15

value: Human Fetal Kidney

value: 2D hNPC

value: Nephron Progenitor Cell

value: WT


title: iNPC, V1, 2D, Day15, Biol rep 1

description:
hNPC DESeq2 Medium ratio
iNPC-v1-1-D15


title: Skeletal muscle, Sham

value: sham control


title: Healthy mouse liver CV-2

status: Public on Mar 06 2024

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger count pipeline (cellranger-4.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: mm10
Supplementary files format and content: comma-delimited text files include raw counts for all cells detected

molecule: polyA RNA

source_name: Liver

extract_protocol:
Single cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
Single-cell RNA library construction was processed through the 10x Genomics Chromium Controller following the protocol outlined in the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide.

value: Liver

tag: tissue zone

value: CV

value: CD45+ cells

value: PA-GFP C57BL/6

value: Photoactivation


title: Crispr Mouse with ReDeeM, Batch1, ATAC (enriched mito included), sample 14

status: Public on Feb 26 2024

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

description: Combined ATAC library and enriched mtDNA library(Cell barcodes are matchable with mRNA, TargetSite, and CellHash lib in sample 14): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

library_source: genomic single cell

data_processing:
Standard ReDeeM pipeline was used for pre-processing mtDNA data as described above. The Target Site data was pre-processed using Python package Cassiopeia. Briefly, reads with identical cellBC and UMI were collapsed into a single, error-corrected consensus sequence representing a single-expressed transcript. Consensus sequences were identified within a cell based on a maximum of 10 high-quality mismatches (PHRED score greater than 30) and an edit distance less than 2 (default pipeline parameters). UMIs within a cell reporting more than one consensus sequence were resolved by selecting the consensus sequence with more reads. Each consensus sequence was aligned to the wild-type reference Target Site sequence using a local alignment strategy, and the intBC and indel alleles were called from the alignment. Cells with fewer than 2 reads per UMI on average or fewer than 10 UMIs overall were filtered out. These data were summarized in a molecule table which records the cellBC, UMI, intBC, indel allele, read depth, and other relevant information. Then, character matrices were formed summarizing indel information across the N cells in a population and their M cut-sites. Characters (i.e., cut-sites) with more than 80% missing information or containing a mutation that was reported in greater than 98% of cells were filtered out for downstream analysis
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: Analyzed Indels per cell by Cassiopeia:  indel_alleles.tar.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv

source_name: Lung cancer

extract_protocol:
Mouse experiments were approved by the Massachusetts Institute of Technology Institutional Animal Care and Use Committee (IACUC) (institutional animal welfare assurance no. A-3125-01). A male mouse embryonic stem cell (mESC) line harbouring the conditional alleles KrasLSL-G12D/+ and Trp53fl/fl (KP) was engineered with the lineage tracer cassettes. The detailed engineering process, including vector information, tumour harvest and single-cell suspension were prepared as described in Yang et al.  Two independent mESC lines were used for batch-1 and batch-2 experiments.
The single cells of batch-1 from multiple tumors were labelled with Cell Hash and were profiled using ReDeeM except the following modification. Additional Target Site libraries were needed. The amplified cDNA libraries were further amplified with Target Site-specific primers containing Illumina-compatible adapters and sample indices (oDYT023-oDYT038, forward:5′CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATCCAGCTAGCTGTGCAGC; reverse:5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCTTTCCCTACACGACGCTCTTCCGATCT; “N” denotes sample indices) using Kapa HiFi ReadyMix (Roche), as described.
For sequencing scRNA, scATAC, mtDNA libraries, the same strategy as described for ReDeeM were used, except that four sets of mouse specific probes were designed to enrich mitochondrial fragments. For sequencing Target Site libraries, 15,000 total reads per cell were expected, and the following read lengths were used: Read1: 26 cycles, i7: 8 cycles, Read2: 290 cycles).

value: Lung cancer

tag: library type

value: ATAC


title: Healthy mouse liver CV-1


title: Healthy mouse liver PV-2

value: PV


title: Skeletal muscle, S 20

status: Public on Feb 22 2024

city: Chengdu

first: Tao

address: No. 88, Keyuan South Road, High-tech Zone, Chengdu

department: Department of Anesthesiology

country: China

institute: Sichuan Universiy West China Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skeletal muscle

growth_protocol: After being cleaned of excess blood, connective and fat tissue, muscle biopsies were was promptly frozen in liquid nitrogen and stored at -80°C.

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

value: Skeletal muscle

tag: bmi

tag: disease state

value: sarcopenia


title: Healthy mouse liver PV-1


title: Skeletal muscle, S 18

value: male


title: Skeletal muscle, S 17


title: Skeletal muscle, S 16


title: Skeletal muscle, S 15


title: Skeletal muscle, S 13


title: Skeletal muscle, S 12


title: Skeletal muscle, S 14


title: Skeletal muscle, S 10

value: female


title: Skeletal muscle, S 11


title: Skeletal muscle, S 09


title: Otud7b_retina_KO-LD

value: retina

value: exposuretolight


title: Skeletal muscle, S 08


title: Skeletal muscle, S 07


title: Skeletal muscle, S 05


title: Skeletal muscle, S 06


title: Skeletal muscle, S 04


title: Skeletal muscle, S 01


title: Skeletal muscle, PS 19

value: pre-sarcopenia


title: Skeletal muscle, PS 18


title: Skeletal muscle, PS 17


title: Skeletal muscle, PS 20


title: Skeletal muscle, S 19


title: Skeletal muscle, S 03


title: Skeletal muscle, PS 15


title: Skeletal muscle, PS 14


title: Skeletal muscle, PS 16


title: Skeletal muscle, PS 13


title: Skeletal muscle, PS 12


title: Skeletal muscle, PS 11


title: Skeletal muscle, PS 10


title: Skeletal muscle, PS 08


title: Skeletal muscle, PS 09


title: Skeletal muscle, PS 06


title: Skeletal muscle, HA 20

value: healthy aged


title: Skeletal muscle, PS 02


title: Skeletal muscle, PS 01


title: Skeletal muscle, PS 03


title: Skeletal muscle, HA 18


title: Skeletal muscle, HA 19


title: Skeletal muscle, HA 17


title: Skeletal muscle, HA 16


title: Skeletal muscle, S 02


title: Skeletal muscle, HA 15


title: Skeletal muscle, HA 14


title: Skeletal muscle, HA 12


title: Skeletal muscle, HA 11


title: Skeletal muscle, HA 08


title: Skeletal muscle, HA 09


title: Skeletal muscle, HA 10


title: Skeletal muscle, HA 13


title: Skeletal muscle, HA 06


title: Skeletal muscle, HA 07


title: Skeletal muscle, HA 05


title: Skeletal muscle, PS 04


title: Skeletal muscle, HA 01


title: Skeletal muscle, PS 07


title: Skeletal muscle, HA 02


title: Roxa_APN_2

status: Public on Feb 21 2024

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mapped read counts for each sample

source_name: UV-F2 cells stably expressing T-cadherin

growth_protocol: F2T cells were generated by transfecting full length murine T-cadherin genes on pMX-puro vector into UV-F2 cells, murine endotherial cell line. F2T cells were routinely cultured in DMEM high glucose(nacalai tesque) with 10% fetal bovine serum and ABX.

extract_protocol:
RNA was hervested using QIAzol Lysis Reagent(QIAGEN) and purified by miRNeasy Mini Kit(QIAGEN).
TruSeq stranded mRNA Library Prep Kit (Illumina) was used with 1μg of total RNA for the construction of sequencing libraries according to standard Illumina protocols.

treatment_protocol: F2T cells were treated in DMEM high glucose containing 5% Adiponectin knockout mouse serum and ABX with or without Roxadustat 50μM or Adiponectin 10μg/mL.

value: endotherial cell line stably overexpressed T-cadherin

value: treated with Roxadustat 50uM and Adiponectin 10ug/mL for 48hours


title: Roxa_APN_3

value: UV-F2 cells stably expressing T-cadherin


title: Skeletal muscle, HA 03


title: Skeletal muscle, PS 05


title: Skeletal muscle, HA 04


title: APN_3

value: treated with Adiponectin 10ug/mL for 48hours


title: APN_2


title: Roxa_3

value: treated with Roxadustat 50uM for 48hours


title: Roxa_APN_1


title: APN_1


title: Roxa_1


title: Roxa_2


title: Cont_3

value: untreated


title: Cont_2


title: Cont_1


title: 4_T_1ketsu [GA43152]

status: Public on Feb 19 2024

data_processing:
Sequencing was performed on a NovaSeq6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: hg19
Supplementary files format and content: COUNT.txt: Tab-delimited text files including mapped read counts for each gene and sample.

source_name: tumors

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent (Qiagen).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: tumors

value: HT29;Human Colon Cancer

value: after rearing on food without methionine


title: 3_T_1ketsu [GA43151]


title: ZEN [GA43149]

value: after rearing on normal food


title: zen [miRNA-seq]

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 101-base single-end mode.
Before analysis of the micro RNA-Seq data, reads were trimmed the 3' adapter sequence (AGATCGGAAGAGCACACGTCT) using the software Cutadapt 3.2.
Trimmed reads were mapped to the miRBase human miRNA dataset (https://mirbase.org/download/ ) using the software miRDeep2.
Quantification of mapped read counts was performed with the software quantifier.pl of miRDeep2.
Assembly: miRBase human miRNA dataset
Supplementary files format and content: miRNA_raw_count.tsv: Tab-delimited text files include count data for each combination of mature miRNA and sample.

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent (Qiagen).
Each library was prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).


title: zen

data_processing:
Sequencing was performed on a NovaSeq6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

source_name: tumor

value: tumor

value: HT29; Human Colon Cancer


title: Dnmt3a mutant sample 6, OSM treated 2022

status: Public on Feb 18 2024

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
150bp paired-end
D3a_LTHSC_6_OSM_GT22

data_processing:
For 2021 the samples were run twice and the fastq's were concatenated
FASTQ files were adapter trimmed, and had leading and trailing low quality (below 3) or N bases and reads below 36 bases removed using Trimmomatic v0.35.
Trimmed FASTQ files were used to generate read counts using RSEMv1.3.3.
Expected read counts per gene produced by RSEM were rounded to integer values, filtered to include only genes that had at least two samples within a sample group having a counts per million reads >1, and passed to R (v4.1.3)and edgeR (v3.36.0) for differential expression analysis.A negative binomial generalized log-linear model was fit to the read counts for each gene.The dispersion trend was estimated by Cox-Reid approximate profile likelihood followed by empirical Bayes estimate of the negative binomial dispersion parameter for each tag, with expression levels specified by a log-linear model.
Likelihood ratio tests for coefficient contrasts in the linear model were evaluated producing a p-value per contrast. The Benjamini and Hochberg's algorithm (P value adjustment) was used to control the false discovery rate (FDR). Features with FDR-adjusted P < 0.05 were declared significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file

source_name: Bone Marrow

growth_protocol: whole bone marrow was collect from adult mice and sorted for HSCs based on cell surface markers (Lin- Sca-1+ c-Kit+ Flt3- CD150+ CD48-) 2000 per sample

extract_protocol:
Total RNA was isolated from cells using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the RNA 6000 Pico Assay (Agilent Technologies).
Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2-Pico (Takara), according to the manufacturer’s protocol.  Briefly, the protocol entails RNA fragmentation and cDNA synthesis, addition of Illumina-specific adapters containing a unique barcode sequence for each library, cleavage of ribosomal cDNA with Takara’s ZapR v2 and R-Probes v2, and PCR amplification of uncleaved fragments.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.
2021:Libraries were sequenced 75 bp paired-end on an Illumina NextSeq 500 using the High Output Reagent Kit v2.5. 2022: Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5.

treatment_protocol: HSCs were stimulated for 1hour with PBS (vehicle) or OSM (500ng/ml) following stimulation cells were flash frozen in liquid nitrogen

value: Bone Marrow

tag: cell number

value: 2000 cells

value: HSCs

value: Dnmt3a-mutant (R878H/+)

value: OSM


title: 5_T_2ketsu [GA43153]

value: after rearing on food without tryptophan/niacin


title: sanketsu [miRNA-seq]

value: after rearing on food without methionine/tryptophan/niacin


title: sanketsu


title: Dnmt3a mutant sample 4, OSM treated 2022

description:
150bp paired-end
D3a_LTHSC_4_OSM_GT22


title: Dnmt3a mutant sample 2, vehicle treated 2022

description:
150bp paired-end
D3a_LTHSC_2_vehicle_GT22

value: Vehicle


title: Dnmt3a mutant sample 6, vehicle treated 2022

description:
150bp paired-end
D3a_LTHSC_6_vehicle_GT22


title: Dnmt3a mutant sample 2, OSM treated 2022

description:
150bp paired-end
D3a_LTHSC_2_OSM_GT22


title: Dnmt3a mutant sample 4, vehicle treated 2022

description:
150bp paired-end
D3a_LTHSC_4_vehicle_GT22


title: Control sample 3, OSM treated 2022

description:
150bp paired-end
CNT_LTHSC_3_OSM_GT22

value: Control


title: Control sample 5, vehicle treated 2022

description:
150bp paired-end
CNT_LTHSC_5_vehicle_GT22


title: Control sample 5, OSM treated 2022

description:
150bp paired-end
CNT_LTHSC_5_OSM_GT22


title: Dnmt3a mutant sample 6, OSM treated 2021

description:
76bp-paired end
D3a_LTHSC_6_OSM_GT21


title: Dnmt3a mutant sample 4, OSM treated 2021

description:
76bp-paired end
D3a_LTHSC_4_OSM_GT21


title: Control sample 3, vehicle treated 2022

description:
150bp paired-end
CNT_LTHSC_3_vehicle_GT22


title: Control sample 1, vehicle treated 2022

description:
150bp paired-end
CNT_LTHSC_1_vehicle_GT22


title: Control sample 1, OSM treated 2022

description:
150bp paired-end
CNT_LTHSC_1_OSM_GT22


title: Dnmt3a mutant sample 6, vehicle treated 2021

description:
76bp-paired end
D3a_LTHSC_6_vehicle_GT21


title: 3K [GA43150]


title: Dnmt3a mutant sample 2, vehicle treated 2021

description:
76bp-paired end
D3a_LTHSC_2_vehicle_GT21


title: Dnmt3a mutant sample 2, OSM treated 2021

description:
76bp-paired end
D3a_LTHSC_2_OSM_GT21


title: Control sample 5, OSM treated 2021

description:
76bp-paired end
CNT_LTHSC_5_OSM_GT21


title: Dnmt3a mutant sample 4, vehicle treated 2021

description:
76bp-paired end
D3a_LTHSC_4_vehicle_GT21


title: Control sample 1, OSM treated 2021

description:
76bp-paired end
CNT_LTHSC_1_OSM_GT21


title: Control sample 3, vehicle treated 2021

description:
76bp-paired end
CNT_LTHSC_3_vehicle_GT21


title: Control sample 5, vehicle treated 2021

description:
76bp-paired end
CNT_LTHSC_5_vehicle_GT21


title: Control sample 1, vehicle treated 2021

description:
76bp-paired end
CNT_LTHSC_1_vehicle_GT21


title: [scRNA-Seq] AD3_D90

status: Public on Feb 15 2024

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

data_processing:
The BCL files were de-multiplexed using CellRanger mkfastq version 3.01 and then aligned and quan-tify them against the human reference genome GRCh38 using Cellranger count
We performed quality control checks for each sample in R for each sample and removed any cells with fewer than 1000 reads or 500 genes or greater than 10% mitochondrial reads. Any cells which expressed haemoglobin genes were also removed from the analysis. Doublets were predicted using DoubletFinder and filtered from the data.
The Seurat R package (version 4.3.0) was then used to process the data prior to integration. Firstly the raw data was normalised using the standard parameters.
Supplementary files format and content: csvFile containing filtered count matrix for each cell
Supplementary files format and content: csv with metadata for each cell, contains cell identifcation

source_name: organoid

extract_protocol:
All samples were isolated and dissociated to single cells using a neurosphere dissociation kit (Miltenyi Biotech).
Libraries generated using the Chromium Single Cell 3’ Library & Gel Bead Kit (version 3, 10x Genomics)
Single cell RNA-Seq libraries were sequenced to 50,000 reads per cell on an Illumina NovaSeq 6000

value: organoid

tag: developmental stage


title: [scRNA-Seq] AD3_D45


title: [scRNA-Seq] AD3_D60


title: [scRNA-Seq] AD3_D35


title: [scRNA-Seq] AD3_D20


title: [scRNA-Seq] AD3_D150


title: [scRNA-Seq] AD3_D10


title: AD3_D90

data_processing:
CellRanger version 1.2  was used to process the ATACseq data.  Cellranger-atac agrr module was used to create a set of shared peaks present across all four samples.
Signac used to further process the data. The as filtered using thresholds to remove cells where the number of fragments within peaks was less than 1000 or greater than 50000
or with a blacklist ration of greater than 5% or a nucleosome signal of greater than 10 and a TTS enrichment of  , greater than 2
GRCh38
The filtered peak accessibilty matrix and metadata containing cell type assignements are provided as a csv file.
Supplementary files format and content: csv file containing peak accessibilty matrix
Supplementary files format and content: csv with metadata for each cell, contains cell identifcation

extract_protocol:
All samples were isolated and dissociated to single cells using a neurosphere dissociation kit (Miltenyi Biotech). 10,000 of the subsequent nuclei were captured sample were captured.
Sequencing libraries generated using the Chromium Single Cell ATAC Library & Gel Bead Kit (version 1, 10x Genomics)
scATAC-Seq libraries were sequenced to 25,000 reads per nucleus on an Illumina NovaSeq 6000


title: AD3_D210


title: AD3_D45


title: AD3_D60


title: AD3_D35


title: AD3_D150


title: [scRNA-Seq] AD3_D210


title: AD3_D10


title: Control sample 3, OSM treated 2021

description:
76bp-paired end
CNT_LTHSC_3_OSM_GT21


title: HEK 293T, RPB1_S7E_sp, replicate 1

status: Public on Feb 09 2024

city: Austin

first: Qian

last: Zhang

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

data_processing:
Base-calling was performed by Novogene Inc. with the latest Illumina software.
Quality of raw reads was assessed using FastQC read quality reports (Galaxy).
Adapter Illumina sequences (--illumina) were trimmed off by TrimGalore! v.0.6.7 with default parameters.
Reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.5.0. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS v2.2.7.1 with the default significance cut-off q-value <=0.1 for broad peaks, bigWig files were generated using the bedGraph files of scores outputted from MACS2.
Assembly: hg38
Supplementary files format and content: bigWig files outputted from MACS2 (except for input files).

source_name: HEK 293T

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s media, supplemented with 10% fetal bovine serum at 37 °C in humidified atmosphere with 5% CO2.

extract_protocol:
Cells were fixed by 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorupter UCD-200, and then GFP antibody was used for immunoprecipitation (IP).
ChIP-seq libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina with barcode primers from NEBNext® Multiplex Oligos. 5 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 11 cycles on the thermocycler. Post amplification libraries were size selected at 300-500bp in length using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: We transfected RPB1_52xCTD, RPB1_26xCTD or RPB1_26xCTD T4E/S7E mutants with YFP tag  plasmids in HEK 293T cells separately, after 24 h of transfection, cells were collected for Chip experiment.

value: HEK 293T

value: embryonic kidney cells

value: WT


title: PanIN low grade6 R

status: Public on Feb 06 2024

city: Baltimore

first: Luciane

middle: Tsukamoto

last: Kagohara

state: MD

address: 1650 Orleans St - Rm 485

department: Oncology

institute: Johns Hopkins University

data_processing:
Sequencing alignment and demultiplexing with Space Ranger (10x Genomics).
Quality check and filtering with Seurat.
Normalization using SCTransform in Seurat.
Dimensional reduction using PCA in Seurat.
Gene expression analysis using Seurat.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv: spatial barcodes
Supplementary files format and content: features.tsv: genes
Supplementary files format and content: matrix.mtx: sequencing counts
Supplementary files format and content: excluded_spots.tar: list of Visium barcodes filtered out from the analysis
Supplementary files format and content: grade_assignment_correction.tar: PanIN grade assigned to each Visium barcode by pathology examination
Library strategy: Spatial transcriptomics.

source_name: pancreas

extract_protocol:
There was no extraction protocol used.
Libraries were constructed using the Visium FFPE Spatial Gene Expression Reagent Kits (10x Genomics).

value: pancreas

tag: disease

value: pancreatic intraepithelial neoplasia

tag: group

value: low grade


title: PanIN low grade3 R

tag: tissue


title: PanIN low grade5 R


title: PanIN low grade2 R


title: PanIN low grade4 R


title: PanIN low grade3


title: PanIN high grade 3

value: high grade


title: PanIN low grade1 R


title: PanIN high grade 1


title: PanIN high grade4


title: PanIN low grade2


title: AD3_D20


title: HEK 293T, RPB1_S7E_sp, replicate 2

tag: cell line


title: DXR_D16_1

status: Public on Jan 24 2024

city: Onna-son, Kunigami-gun

first: Nurhanani

last: Razali

state: Okinawa

address: 1919-1 Tancha

department: Membranology

institute: Okinawa Institute of Science and Technology Graduate University (OIST)

data_processing:
All samples were sequenced by Novaseq6000. Paired-end cDNA libraries were sequenced with a 2×150-bp configuration.
Each sample was sequenced at a depth of more than 20 million paired-end reads.
Trim_galore, HISAT2 to the human GRCh38 reference genome
htseq-count, featureCount, DEseq2
Assembly: Human GRCh38 reference genome, hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: WI-38 cells DXR-treated, Day 16

growth_protocol: The human embryonic fibroblast WI-38 was acquired from RIKEN Bioresource Research Center (BRC) and cultured in a humidified incubator at 37 °C and 5% CO2 with high-glucose DMEM (FUJIFILM Wako Pure Chemical) supplemented with 10% fetal bovine serum (FBS, Sigma), 2mM L-Alanyl-L-Glutamine (FUJIFILM Wako Pure Chemical), and 100U/mL penicillin-streptomycin (Gibco).

extract_protocol: Total RNA was extracted and purified according to the manufacturer’s instructions using TRIzol (Thermo Fisher Scientific) and RNA Clean and Concentrator-5 kit (Zymo Research). The concentrations of extracted RNA were determined by using a NanoDrop OneC spectrophotometer (Thermo Fisher Scientific) and Qubit fluorometer (Thermo Fisher Scientific). The integrity of RNA was checked using an automated electrophoresis system, 4200 Agilent TapeStation (Agilent).

treatment_protocol: Young cells (population doubling level: PDL 32-46) were used as controls. For replicative senescence, WI-38 cells were passaged until they lost the ability to proliferate and became senescent around PDL 52. For the plasma membrane damage-induced senescence (PMDS), DNA damage response-induced senescence (DDRS), and calcium influx-induced senescence (CIS), WI-38 cells were treated with 0.0090% sodium dodecyl sulfate (SDS), 250 nM doxorubicin (DXR) (Cayman Chemical), or 75 mM KCl-containing medium, respectively, for 24 hr. The day after treatment, cells were washed twice with fresh medium, then cultured up to 16 days with medium change for every four days. Samples were then collected from the non-treated cells and the treated cells at 0 day (24 hr of treatment), and 1, 2, 3, 4, 5, 6, 8, and 16 days after  treatment for PMDS, CIS and DDRS.

tag: cell type

value: lung fibroblast cells

value: DXR-treated

value: DNA damage response-induced senescence


title: DXR_D8_2

source_name: WI-38 cells DXR-treated, Day 8

tag: genotype


title: PanIN high grade1 R


title: DXR_D4_1

source_name: WI-38 cells DXR-treated, Day 4

tag: treatment


title: DXR_D6_1

source_name: WI-38 cells DXR-treated, Day 6


title: DXR_D4_2


title: DXR_D2_2

source_name: WI-38 cells DXR-treated, Day 2


title: DXR_D2_1


title: DXR_D1_2

source_name: WI-38 cells DXR-treated, Day 1


title: PanIN high grade 2


title: KCl_D16_2

source_name: WI-38 cells KCl-treated, Day 16

value: KCl-treated

value: Calcium influx-induced senescence


title: DXR_D0_2

source_name: WI-38 cells DXR-treated, Day 0


title: DXR_D1_1


title: KCl_D16_1


title: PanIN low grade1


title: KCl_D8_2

source_name: WI-38 cells KCl-treated, Day 8


title: KCl_D8_1


title: DXR_D8_1


title: DXR_D16_2


title: KCl_D6_1

source_name: WI-38 cells KCl-treated, Day 6


title: DXR_D6_2


title: KCl_D4_2

source_name: WI-38 cells KCl-treated, Day 4


title: KCl_D6_2


title: KCl_D4_1


title: KCl_D3_2

source_name: WI-38 cells KCl-treated, Day 3


title: DXR_D3_1

source_name: WI-38 cells DXR-treated, Day 3


title: KCl_D2_2

source_name: WI-38 cells KCl-treated, Day 2


title: DXR_D3_2


title: KCl_D1_2

source_name: WI-38 cells KCl-treated, Day 1


title: KCl_D2_1


title: KCl_D3_1


title: KCl_D0_2

source_name: WI-38 cells KCl-treated, Day 0


title: DXR_D0_1


title: SDS_D16_1

source_name: WI-38 cells, SDS-treated, Day 16

value: SDS-treated

value: Plasma membrane damage-induced senescence


title: KCl_D0_1


title: SDS_D8_2

source_name: WI-38 cells, SDS-treated, Day 8


title: SDS_D16_2


title: SDS_D8_1


title: SDS_D6_2

source_name: WI-38 cells, SDS-treated, Day 6


title: SDS_D6_1


title: SDS_D4_1

source_name: WI-38 cells, SDS-treated, Day 4


title: SDS_D4_2


title: SDS_D3_1

source_name: WI-38 cells, SDS-treated, Day 3


title: SDS_D2_2

source_name: WI-38 cells, SDS-treated, Day 2


title: SDS_D2_1


title: SDS_D1_2

source_name: WI-38 cells, SDS-treated, Day 1


title: SDS_D1_1


title: SDS_D0_1

source_name: WI-38 cells, SDS-treated, Day 0


title: Untreated-control_2

source_name: WI-38 cells, Untreated

value: Untreated


title: Replicative Sen_2

source_name: WI-38 cells, Replicative senescence

value: Telomere shortening

value: Telomere shortening-induced senescence


title: Untreated-control_1


title: PSC011_B1_VISIUM

status: Public on Jan 18 2024

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

description: Spatial transcriptomics on OCT-embedded tissue

data_processing:
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: GRCh38-2020-A transcriptome
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hires image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.cv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: metrix_summary.csv: summary of key sample metrics
Supplementary files format and content: Merged.tif.gz: high-resolution image
Library strategy: Spatial transcriptomics

molecule: cytoplasmic RNA

source_name: Adult Liver

extract_protocol:
Tissue was prepared for Visium Spatial transcriptomics as previously described (https://doi.org/10.1002/hep4.1854)]. Briefly, liver tissue was embedded in OCT media, frozen, and cryosectioned with 16-um thickness at −10ºC (cryostar NX70 HOMP). Sections were placed on a chilled Visium Tissue Optimization Slide (10x Genomics) and processed following the Visium Spatial Gene Expression User Guide. Tissue was permeabilized for 12 minutes, based on an initial optimizations trial. Libraries were prepared according to the Visium Spatial Gene Expression User Guide and samples sequenced on a NovaSeq 6000.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Adult Liver

value: Primary sclerosing cholangitis (PSC)


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

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
OY626_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: Sorted renal cells, KO, Late, Female, tdTomato Positive, Rep 1

description:
10x Genomics
OY606_pos


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

description:
10x Genomics
OY615_pos


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

description:
10x Genomics
OY626_neg

value: Negative

value: Vhl(KO/wt)


title: PSC011_D1_VISIUM


title: PSC011_C1_VISIUM


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

description:
10x Genomics
OY1023_pos


title: SDS_D3_2

value: lung fibroblast cells


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

description:
10x Genomics
OY545_pos

value: Vhl(wt/flox) (Control)

value: Vhl(wt/KO)


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

description:
10x Genomics
OY1023_neg


title: PSC011_A1_VISIUM


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

description:
10x Genomics
OY622_pos


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

description:
10x Genomics
OY615_neg


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

description:
10x Genomics
OY611_pos


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

description:
10x Genomics
OY606_neg


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

description:
10x Genomics
OY611_neg

value: Vhl(wt/wt)


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

description:
10x Genomics
OY622_neg


title: SDS_D0_2

value: SDS-treated

value: Plasma membrane damage-induced senescence


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

description:
10x Genomics
OY545_neg


title: Replicative Sen_1

value: Telomere shortening

value: Telomere shortening-induced senescence


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, KO, Early, Male, tdTomato Positive, Rep 4

description:
10x Genomics
OY1166_pos

value: Kidney


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

description:
10x Genomics
OY733_pos

value: FAC-sorted cells


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

description:
10x Genomics
OY1166_neg


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

description:
10x Genomics
OY978_pos

value: Positive


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

description:
10x Genomics
OY978_neg

value: Vhl(KO/flox) (KO)


title: KCl_D1_1

value: KCl-treated

value: Calcium influx-induced senescence


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

description:
10x Genomics
OY954_pos


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

description:
10x Genomics
OY1004_neg

value: Negative


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

description:
10x Genomics
OY955_pos


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

description:
10x Genomics
OY955_neg


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

description:
10x Genomics
OY552_pos

value: Late (4-12 months)


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

description:
10x Genomics
OY725_pos


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

description:
10x Genomics
OY725_neg


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

description:
10x Genomics
OY551_neg


title: RIP1

status: Public on Jan 12 2024

description:
GA59726
Sequencing of RNAs bound by variant1 of SRP9 with nuclear translocation signals

data_processing:
Sequencing was performed on a NovaSeq6000 platform in a 101+101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using HISAT2 (v2.1.0).
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: GRCh38_p13
Supplementary files format and content: RawCount.tsv: tab-delimited text file including mapped read counts for each gene and sample

source_name: MiaPaCa

extract_protocol:
10 million pancreatic cancer MiaPaCa cells were cultured in 15cm plastic culture dish (nunc) in RPMI1640 (Nacalai Tesque, Kyoto, Japan) with 10 % FBS under 5% CO2 at 37℃ condition.  V1SRP9V1-3xFLAG and SRP9V2-3xFLAG gene were prepared by DNA synthesis (Eurofins), of which sequences were confirmed by Sanger sequencer (ABI). pIRES2-acGFP1-NLS-SRP9V1-3xFLAG vector and pIRES2-acGFP1-NLS-SRP9V2-3xFLAG vector were designed to express exogeneous SRP9V1-3xFLAG or SRP9V2-3xFLAG genes in the split protein by the internal ribosome entry site signal (IRES, an RNA element that enables cap-independent initiation of translation as part of the process of protein synthesis) from acGFP1 under NLS, which is fused with exogeneous SRP9V1-3xFLAG or SRP9V2-3xFLAG. The SRP9V1 or SRP9V2 peptide is translated in frame with 3xFLAG peptide (MDYKDHDGDYKDHDIDYKDDDDK), respectively. Transfection of pIRES2-acGFP1-NSL-SRP9V1 vector or pIRES2-acGFP1-NSL-SRP9V2 vector plasmid performed by electroporation with Nepagene system (Nepagene), which can allow the preservation of membrane damages during transfection, with compared to lipofectamine methods (Takara). The cells were grown in the RPMI1640 with 10% FBS and 200mg/ml Geneticin (Nacalai) for two weeks to select gene transfected cells. The expression of protein was confirmed by acGFP signal under observation with fluorescent All-In-One microscope (Keyence). The 5x106 of acGFP expressing cells were collected by fluorescence-activated cell sorting (FACS; BD) and cultured in RPMI1640 with 10% FBS for 24 hours and subjected to protein extraction. For protein extraction, adherent cells were washed with PBS(-) (Nacalai) for three times in 15cm plastic culture dish, to exclude amino acids in the medium, which can interfere potentially with cross-linker. Cells were harvested with plastic cell-scrapers, and collected in 2ml tubes. Samples were centrifuged at 1200 rpm at 4oC for 5 min. Collected cell pellets were lysed in the 1ml HEPES-RIPA (150 mM KCl, 50 mM HEPES-NaOH (pH7.4), 1% NP-40, and 1xRoche cOmplete, proteinase inhibitor, prepared from 50x stock reagent (catalog number 04693116001; Roche. Samples were centrifuged at 1200 rpm at 4℃ for 5 min. Collected cell lysates were incubated for 30 min at room temperature with crosslinking agent, BS3 (bis(sulfosuccinimidyl)suberate) (Thermo Fisher Scientific), which do not permeate cell membranes, so we permeabilized with the treatment of a surfactant, NP-40, as mentioned above. We used a newly purchased BS3 (Lot. YB351210), considering it absorbs moisture from the atmosphere and becomes inactive. After the cross-linking reaction, 1/50 (final concentration 20 mM) of 1 M Tris-HCl, pH 7.5 was added to quench the excess cross-linking agent and gently mix by inverting for 15 minutes. For purification of target SRP9V1-3xFLAG or SRP9V2-3xFLAG proteins, samples were subjected to the immunoprecipitation. To this end, 20ul of anti-DDDDK antibody, which binds to FLAG tag sequence was added to each sample, and incubated at 4℃ for overnight (16 hr), and then purified with protein A and G conjugated magnetic beads ( Bio-Rad). The immunoprecipitated SRP9V1-3xFLAG or SRP9V2-3xFLAG protein, which crosslinked with endogenous RNA was wash with 1ml HEPES-RIPA (150 mM KCl, 50 mM HEPES-NaOH (pH7.4), 1% NP-40）; then, 1ml high salt HEPES-RIPA (300 mM KCl, 50 mM HEPES-NaOH (pH7.4), 1% NP-40); and once again 1ml HEPES-RIPA (150 mM KCl, 50 mM HEPES-NaOH (pH7.4), 1% NP-40, which were to exclude non-specific bound substances to protein A and G conjugated magnetic beads. Finally, samples were treated with 100 mg of 3xDYKDDDDK peptide (FP-1; Sigma), to elute endogenous RNA bound SRP9V1-3xFLAG or SRP9V2-3xFLAG proteins (hereinafter referred to as "RIP1" and "RIP2" respectively). RNA was extracted from samples by RNeasy extraction kit (Qiagen). 100 ng of RNAs were subjected to high-speed sequencing system of NovaSeq6000 (Illumina). As controls, input RNAs were prepared and used from geneticin-selected transfected cells with SRP9V1-3xFLAG or SRP9V2-3xFLAG (hereinafter referred to as "INPUT1" and "INPUT2" respectively).
Each Illumina sequencing library was prepared using SMARTer Stranded Total RNA-seq Kit v2 -Pico Input Mammalian (Takara Bio).

value: MiaPaCa

value: Pancreatic cancer cell line

value: transfected with SRP9 v1 with nuclear translocation signals


title: INPUT2

description:
GA59729
Whole cell RNA sequencing in RIP2 experiments

value: transfected with SRP9 v2 with nuclear translocation signals


title: 08_T_zen

data_processing:
Sequencing was performed on a NovaSeq6000 platform in a 101+101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using HISAT2 (v2.1.0).
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: GRCh38_p13
Supplementary files format and content: RawCount: tab-delimited text file including mapped read counts for each gene and sample

source_name: RNA sequencing of tumor sites that were reared on normal food for 7 days, then reared on food without methionine/tryptophan/niacin for 11 days, and then reared again on normal food for 3 days

value: HT29;Human Colon Cancer

value: after rearings on normal food for 7 days, then on food without methionine/tryptophan/niacin for 11 days, and then again on normal food for 3 days


title: 07_T_3ketsu

source_name: RNA sequencing of tumor sites after rearing on food without methionine/tryptophan/niacin


title: 09_T_3ketsu

source_name: RNA sequencing of tumor sites that were reared on normal food for 7 days, and then reared on food without methionine/tryptophan/niacin for 11 days

value: after rearings on normal food for 7 days, and then on food without methionine/tryptophan/niacin for 11 days


title: 04_T_1ketsu

source_name: RNA sequencing of tumor sites after rearing on food without methionine


title: 05_T_2ketsu

source_name: RNA sequencing of tumor sites after rearing on food without tryptophan/niacin


title: 06_T_3ketsu

value: after rearing on food without methionine/tryptophan/niacin


title: INPUT1

description:
GA59728
Whole cell RNA sequencing in RIP1 experiments


title: 03_T_1ketsu

value: after rearing on food without methionine


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

description:
10x Genomics
OY733_neg

value: Kidney

value: Vhl(KO/wt)

value: Early (1-3 weeks)


title: 01_T_zen

source_name: RNA sequencing of tumor sites after rearing on normal food

value: after rearing on normal food


title: 7T


title: 5T

value: after rearing on food without tryptophan/niacin


title: 4T


title: 02_T_zen


title: 3T


title: 6T


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

description:
10x Genomics
OY1004_pos

value: FAC-sorted cells

value: Positive

value: Vhl(wt/flox) (Control)

value: Vhl(wt/KO)


title: 2T


title: 1T


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

description:
10x Genomics
OY954_neg

value: Negative

value: Vhl(wt/wt)


title: Parent, replicate 2, BRD1, ChIP

status: Public on Jan 11 2024

first: Sarah

middle: J.

last: Hill

state: MA

address: 450 Brookline Ave., Dana Building, Room 1410C

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-Seq reads were filtered and trimmed using Atropos.
High-quality reads were mapped to hg38 using Bowtie2 and multi-mapping reads were excluded.
Normalization factors were calculated by comparing the reads mapped to the Drosophila genome with the reads mapped to the human genome.
The fewest number of spike-in reads was used to normalize the reads mapped to Drosophila across samples and then the reads mapped to the human genome were normalized using the same ratio. Normalization factors were calculated using a custom script.
bigWig files were generated using the bamCoverage function from deeptools and the calculated normalization factors.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: UWB1.289 parent line

growth_protocol: UWB1.289 cells were grown in 50% ATCC-formulated RPMI-1640 Medium (ATCC Cat. # 30-2001)/50% MEGM (Lonza Cat. # CC-3150) made of MEBM basal medium and additives (without gentamycin-amphotericin B) with 3% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Chromatin was prepared using the Cell Signaling SimpleChIP Enzymatic Chromatin IP Kit following the manufacturer's protocol (Catalog #9003)
ChIPseq libraries were prepared using IDT xGen DNA library prep reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA with 14cycles of PCRamplificationaccording to manufacturer’s protocol. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on an Illumina NovaSeq6000 targeting 40 million 150bp read pairs by the Molecular Biology Core facilities at Dana-Farber Cancer Institute.

value: UWB1.289 parent line

tag: chip antibody


title: Parent, replicate 1, Input


title: Parent, replicate 2, Input


title: RIP2

description:
GA59727
Sequencing of RNAs bound by variant2 of SRP9 with nuclear translocation signals

value: MiaPaCa

value: Pancreatic cancer cell line

value: transfected with SRP9 v2 with nuclear translocation signals


title: Parent, replicate 2, HBO1, ChIP


title: Parent, replicate 1, HBO1, ChIP


title: Parent, replicate 1, BRD1, ChIP


title: 2month_cauda

status: Public on Jan 05 2024

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff v2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: cauda epididymis

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: cauda epididymis

tag: age

tag: Sex

value: male

value: WT

tag: strain


title: 24month_cauda


title: 18month_cauda


title: 2month_testis

source_name: testis

value: testis


title: 18month_testis


title: 24month_testis


title: fc45a7eb-6bd4-4b9d-aee5-83e2e5c09dd1

status: Public on Jan 04 2024

city: La Jolla

first: Kelly

middle: Ann

last: Frazer

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San Diego

data_processing:
ATAC-seq reads were aligned with STAR (2.7.3) {Dobin, 2013} to the hg19 reference using Gencode v34lift37 {Harrow, 2021} with default alignment parameters and the following adjustments: --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMax 1  --seedSearchStartLmax 20 --outFilterScoreMinOverLread 0.1 --outFilterMatchNminOverLread 0.1. Using Samtools (1.9.0) {Danecek, 2021}, bam files were sorted by coordinates, and duplicate reads were marked. To remove reads that were not from captured nucleosomes, we removed reads with fragment length less than 38 bp or more than 2,000 bp. Reads that were duplicate, not uniquely mapped, not properly mapped, and with mapping quality less than 20 were removed.
Assembly: hg19
Supplementary files format and content: broadPeak

source_name: iPSC

extract_protocol:
Bulk ATAC-seq: ATAC-seq was performed using the protocol from Buenrostro et al., 2013 with small modifications. Frozen nuclear pellets at 5x10^4 iPSCs were thawed on ice and tagmented in 25ul of permeabilization buffer containing digitonin and 2.5ul of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 30-75min at 37C, 500 RPM.
Bulk ATAC-seq:  Libraries within a pool were indexed with unique i7 and i5 barcodes. Libraries were amplified for 12 cycles using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and custom barcoded primers from Integrated DNA Technologies (IDT), and then sequenced on Illumina HiSeq 4000 using paired-end 100bp reads or 150bp reads.

value: iPSC


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title: 25f35d46-05bc-49b3-8c89-6e92422bc1ba


title: 2fea0513-186c-4cb4-8ad5-6fbc980be86c


title: 2498178b-08b6-4918-bfbf-fcd0aaf3a183


title: 11ba0e5a-046a-491a-aa52-b46f12f3fbf6


title: 1b8b4b2a-25e3-49d3-a05d-1037c7961cb0


title: 03d4046a-bbf9-4c2b-9dbe-8e8a768af016


title: 05d25e86-a228-446f-ba66-1b998e0406ed


title: 02040edd-0972-460e-9696-41835ae8df28


title: 00855a45-d18d-4c45-b114-48ceda592e7c


title: 018ebad1-43c5-4658-8ae3-652f05ce51c6


title: Müller glial cells, 7983f_f

status: Public on Dec 20 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10 with exogenous_genes) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10 with exogenous_genes (Cre, mTFP1)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: retina

extract_protocol:
RNA was harvested from cells using miRNeasy Micro Kit (Qiagen).
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: retina

value: mTFP positive cells

value: Rax iCKO  (Raxflox/flox; Rlbp1-CreERT2; R26-CAG-LoxP-mTFP1)

value: tamoxifen induced


title: Müller glial cells, 3911f_w

value: control  (Raxflox/WT; Rlbp1-CreERT2; R26-CAG-LoxP-mTFP1)


title: Müller glial cells, 7984f_w


title: Müller glial cells, 3914f_f


title: 6h_control_2

status: Public on Dec 18 2023

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: HUVEC

extract_protocol:
Total RNA was isolated from HUVECs using an RNeasy Mini Kit (Qiagen K.K., Tokyo, Japan).
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a Nextera DNA Library Preparation Kit (Illumina).

value: HUVEC

value: LPS plus sIL-6R, 6 hours


title: 081d2d2f-aa37-4f8e-a114-4dd19bc271f0


title: non_2

value: non-treated


title: non_1


title: 15278_Eye_8PCW

status: Public on Nov 29 2023

data_processing:
The BCL files were de-multiplexed using CellRanger mkfastq version 3.01 and then aligned and quan-tify them against the human reference genome GRCh38 using Cellranger count
We performed quality control checks for each sample in R for each sample and removed any cells with fewer than 1000 reads or 500 genes or greater than 10% mitochondrial reads. Any cells which expressed haemoglobin genes were also removed from the analysis. Doublets were predicted using DoubletFinder and filtered from the data.
The Seurat R package (version 4.3.0) was then used to process the data prior to integration. Firstly the raw data was normalised using the standard parameters.

source_name: Whole Eye

value: Whole Eye

tag: developmental stage


title: 14Ret_08102020_Retina_14PCW

source_name: Retina

value: Retina


title: 6h_control_1


title: 15220_Eye_8PCW


title: 15046_Eye_7.5PCW


title: 15700_Retina_18PCW


title: 15222_Eye_7.7PCW


title: 15189.2_Eye_8.5PCW


title: 15232_Retina_16PCW


title: 15189.1_Eye_8.5PCW


title: 14817_Eye_8PCW


title: 10PCW_232020_Retina_10PCW


title: 15221_Retina_17PCW


title: 15183_Retina_20PCW


title: 14611_Retina_15PCW


title: 14680_Retina_12PCW


title: 14849_Eye_10PCW


title: 14713.2_Eye_16PCW


title: 14713.1_Retina_16PCW


title: 14601_Eye_10PCW


title: 14149.2_Retina_16PCW


title: 15184_Retina_21PCW


title: 14601.fixed_Eye_10PCW


title: 15183_20PCW

data_processing:
CellRanger version 1.2  was used to process the ATACseq data.  Cellranger-atac agrr module was used to create a set of shared peaks present across all four samples.
Signac used to further process the data. The as filtered using thresholds to remove cells where the number of fragments within peaks was less than 1000 or greater than 50000
or with a blacklist ration of greater than 5% or a nucleosome signal of greater than 10 and a TTS enrichment of  , greater than 2
GRCh38
The filtered peak accessibilty matrix and metadata containing cell type assignements are provided as a csv file.
Supplementary files format and content: 15761_multiome_counts.csv
Supplementary files format and content: 14680_counts.csv
Supplementary files format and content: 14713_counts.csv
Supplementary files format and content: 14556_counts.csv
Supplementary files format and content: 15221_counts.csv
Supplementary files format and content: 15700_counts.csv
Supplementary files format and content: 15189.1_counts.csv
Supplementary files format and content: 15189.2_counts.csv
Supplementary files format and content: 14601_counts.csv
Supplementary files format and content: 15232_counts.csv
Supplementary files format and content: 15183_counts.csv
Supplementary files format and content: 15184_counts.csv
Supplementary files format and content: 15761_multiome_md.csv
Supplementary files format and content: 14680_md.csv
Supplementary files format and content: 14713_md.csv
Supplementary files format and content: 14556_md.csv
Supplementary files format and content: 15221_md.csv
Supplementary files format and content: 15700_md.csv
Supplementary files format and content: 15189.1_md.csv
Supplementary files format and content: 15189.2_md.csv
Supplementary files format and content: 14601_md.csv
Supplementary files format and content: 15232_md.csv
Supplementary files format and content: 15183_md.csv
Supplementary files format and content: 15184_md.csv

extract_protocol:
All samples were isolated and dissociated to single cells using a neurosphere dissociation kit (Miltenyi Biotech). 10,000 of the subsequent nuclei were captured sample were captured.
Sequencing libraries generated using the Chromium Single Cell ATAC Library & Gel Bead Kit (version 1, 10x Genomics)


title: 14556_Retina_20PCW


title: 15184_21PCW


title: 15189.2_8PCW-Late.2

source_name: Eye

value: Eye


title: 15232_16PCW


title: 15700_18PCW


title: 15189.1_8PCW-Late.1


title: 15221_17PCW


title: 14713_16PCW


title: 14556_20PCW


title: DU-145 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 3 replicate [DU-145 cells]

status: Public on Nov 17 2023

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

data_processing:
The quality of RNA-Seq FASTQ files was assessed with FastQC v0.11.9.
Adapter sequences were removed with the use of cutadapt v2.10: AGATCGGAAGAGCACACGTCT -- miRNA-Seq 3'-adapter.
IsomiR read count matrices were obtained using IsomiRMap with miRBase v22 annotation.
The standard isomiR notation was utilized: A number after the first ``|'' character denotes the shift from the canonical 5'-end in 5'-3' direction (5'-isomiR notation); an additional ``|'' symbol followed by a number denoted 3'-end shifts (3'-isomiR notation); finally, symbols inside ``(.)'' denoted other nucleotides added to the shifted 3'-end.
Assembly: miRBase v22
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: prostate cancer

growth_protocol: The human prostate adenocarcinoma cell lines DU-145 were grown in DMEM medium containing 4.5g/L glucose (PanEco, Russia) supplemented with 4 mM L-Glutamine (PanEco, Russia), 10% fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and cultured under the standard cell culture conditions (37◦C, saturated humidity, 5% CO2).

extract_protocol:
According to the manufacturer's instructions, the total RNA was isolated from about $1 \times 10^6$ cells using miRNeasy Mini Kit (Qiagen, Germany).
All RNA samples were treated with DNase I during the isolation procedure.
The RNA yield was determined by UV absorbance using a NanoDrop 1000 spectrophotometer (Peqlab, Germany).
The RNA quality was assessed by analyzing the ribosomal RNA integrity number (RIN) on an Agilent 2000 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, USA).
The RIN values of the isolated RNA samples were 9.5 and higher.
Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit (Illumina, USA).

treatment_protocol:
Stable overexpression of hsa-miR-93-5p isoforms was achieved by a shRNA-mediated approach.
In particular, each of the three double-stranded DNA fragments (in length 65 bp, 68 bp, and 67 bp) containing a 23 base hsa-miR-93-5p sequence (5'-CAAAGTGCTGTTCGTGCAGGTAG) was cloned into the BsmBI restriction sites of the LentiGuide-Hygro lentiviral vector (Addgene #139462, UK) without sgRNA scaffold.
The shRNAs coding by these DNA oligomers differed in the loop sequence only (5'-CTCGAG, 5'-TTCAAGAGA, and 5'-TTCTAGAA).
The same vector containing a short sequence of sgRNA (5'-TTCTCTTGCTGAAAGCTCGA) was used to generate a transduced control cell line (``Control'').
Nucleotide compositions of the obtained lentiviral vectors were confirmed by Sanger sequencing.
Lentiviral particles were obtained as cell-free supernatants by transient transfection of HEK-293T and using GenJect-39 transfection reagent (Molecta, Russia).
Briefly, lentiviral vectors based on pLentiGuide-Hygro were packaged using the second-generation packaging plasmid pCMV-dR8.2 dvpr (Addgene #8455, UK) and pCMV-VSV-G (Addgene #8454, UK) expressing the envelope protein of vesicular stomatitis virus.
The supernatant was harvested 24h and 48h after transfection, 0.45 $\mu$m filtered and was immediately used for transduction or stored at -80C
Target DU-145 cells were plated at 8 x 104 cells in 2 mL medium in each well of a 6-well plate 24 hours before transduction.
After viral particles containing supernatant were added to the cells, the medium was replaced in 3 days, cells were seeded into a 25 cm^2 flask, and hygromycin was added at a concentration of 150 $\mu$g/mL.
The hygromycin selection was carried out for at least two weeks.

value: prostate cancer

value: shRNA with 5'-UUCAAGAGA-3' loop


title: DU-145 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 2 replicate [DU-145 cells]

value: shRNA with 5'-UUCUAAAA-3' loop


title: 14680_12PCW


title: DU-145 cells, (Control) shControl, 2 replicate [DU-145 cells]

value: shControl


title: DU-145 cells, (Control) shControl, 3 replicate [DU-145 cells]


title: DU-145 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 3 replicate [DU-145 cells]


title: DU-145 cells, (Control) shControl, 1 replicate [DU-145 cells]


title: 15761_13PCW


title: DU-145 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 2 replicate [DU-145 cells]


title: DU-145 cells, (sh-miR93#2) shRNA with 5'-UUCAAGAGA-3' loop, 1 replicate [DU-145 cells]


title: DU-145 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 3 replicate [DU-145 cells]

value: shRNA with 5'-CUCGAG-3' loop


title: 14601_10PCW


title: 14149.1_Retina_16PCW


title: SMARCB1-Rescue 3

status: Public on Nov 15 2023

city: Houston

first: Wenbo

last: Chen

address: 7000 Fannin Street

institute: The University of Texas Health Science Center at Houston

data_processing:
Quality control and adapter trimming were conducted on the raw sequencing reads using Trim-galore.
Competitive method: the human reference transcripts (GENCODE GRCh38) and the mouse reference transcripts (GENCODE GRCm39) were concatenating together for evaluating transcript expression levels from trimmed sequences using Salmon.
Competitive method: the estimated human transcript-level expression was further summarized to gene-level expression using the R package Tximport.
Non-competitive method: trimmed sequences were mapped to both the human reference genome (GENCODE GRCh38) and the mouse reference genome (GENCODE GRCm39) using STAR.
Non-competitive method: the mouse sequences were then filtered using the R package XenofilteR.
Non-competitive method: the raw counts were generated by HTSeq-count.
The R package DESeq2 was used to normalize the raw counts and conduct differential analysis of gene expression for both competitive method and non-competitive method.
Assembly: GRCh38 and GRCm39
Supplementary files format and content: comma-delimited text files include raw count for each Sample from Salmon
Supplementary files format and content: comma-delimited text files include raw count for each Sample from XenofilteR

source_name: Xenograft (Bladder)

growth_protocol: T24 bladder cancer cells were cultured in McCoy's media supplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
NA was harvested using Rneasy mini plus kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA HyperPrep Kit with RiboErase (HMR) kit

treatment_protocol: 200,000 cells were implanted orthotopically into the bladder wall of immune deficient NOD-SCID mice for a period of 22 days. Next, day mice were euthanized and tumors were isolated. Small junks of tumors were then subjected to RNA isolation and RNA-sequencing.

value: Xenograft (Bladder)

value: Bladder cancer cell line

value: Cells implanted into mouse bladder, intiated tumors were isolated for RNA-seq profiling.


title: SMARCB1-Rescue 1


title: DU-145 cells, (sh-miR93#3) shRNA with 5'-UUCUAAAA-3' loop, 1 replicate [DU-145 cells]


title: SMARCB1-KO 4


title: SMARCB1-KO 3


title: SMARCB1-KO 1


title: SMARCB1-KO 2


title: Control 1

value: Control


title: Control 3


title: Control 4


title: Control 2


title: PPC024

status: Public on Oct 03 2023

description: Cells were collected at day 15 of differentiation for sequencing

data_processing:
RNA-seq reads were aligned with STAR (2.7.3) 101 to the hg19 reference using GENCODE version 34 hg1996 splice junctions with default alignment parameters and the following adjustments: -outFilterMultimapNmax 20, -outFilterMismatchNmax 999, -alignIntronMin 20, -alignIntronMax 1000000, -alignMatesGapMax.
We obtained common bi-allelic and exonic variants from the 1000 Genomes Phase 3 panel 103 with minor allele frequencies between 45% and 55% and predicted their genotypes in the 107 bulk RNA-seq samples using mpileup and call functions in BCFtools (1.9.0). Then, we used the genome command in plink to estimate the identity-by-state (IBS) between each pair of bulk RNA-seq and WGS samples. VCF containing WGS results for IPSCORE subjects were downloaded from dbGaP phs001325.v3.
TPM and relative isoform usage was estimated for each gene in each RNA-seq sample using RSEM (version 1.2.20) with the following options –seed 3272015 –estimate-rspd –paired-end –forward-prob.
Assembly: GENCODE hg39 version 34
Supplementary files format and content: rsem.genes.results - gene expression quantification
Supplementary files format and content: rsem.isoforms.results - isoform expression quantification
Supplementary files format and content: plink.genome - sample identity results from plink. Each sample is matched to the WGS sample with PI_HAT > 0.95.

source_name: iPSC-derived pancreatic progenitor cells

growth_protocol: The iPSC lines were differentiated into PPCs using the STEMdiffTM Pancreatic Progenitor Kit (StemCell Technologies) protocol with minor modifications. Briefly, iPSC lines were thawed into mTeSR1 medium containing 10 µM Y-27632 ROCK Inhibitor (Selleckchem) and plated onto one well of a 6-well plate coated with Matrigel. iPSCs were grown until they reached 80% confluency 95 and then passaged using 2mg/ml solution of Dispase II (ThermoFisher Scientific) onto three wells of a 6-well plate (ratio 1:3). To expand the iPSC cells for differentiation, iPSCs were passaged a second time onto six wells of a 6-well plate (ratio 1:2). When the iPSCs reached 80% confluency, cells were dissociated into single cells using Accutase (Innovative Cell Technologies Inc.) and resuspended at a concentration of 1.85 x 106 cells/ml in mTeSR medium containing 10 µM Y-27632 ROCK inhibitor. Cells were then plated onto six wells of a 6-well plate and grown for approximately 16 to 20 hours to achieve a uniform monolayer of 90-95% confluence (3.7 x 106 cells/well; about 3.9 x 105 cells/cm2). Differentiation of the iPSC monolayers was initiated by the addition of the STEMdiffTM Stage Endoderm Basal medium supplemented with Supplement MR and Supplement CJ (2 ml/well) (Day 1, D1). The following media changes were performed every 24 hours following initiation of differentiation (2 ml/well). On D2 and D3, the medium was changed to fresh STEMdiffTM Stage Endoderm Basal medium supplemented with Supplement CJ. On D4, the medium was changed to STEMdiffTM Pancreatic Stage 2-4 Basal medium supplemented with Supplement 2A and Supplement 2B. On D5 and D6, the medium was changed to STEMdiffTM Pancreatic Stage 2-4 Basal medium supplemented with Supplement 2B. From D7 to D9, the medium was changed to STEMdiffTM Pancreatic Stage 2-4 Basal medium supplemented with Supplement 3. From D10 to D14, the medium was changed to STEMdiffTM Pancreatic Stage 2-4 Basal medium supplemented with Supplement 4. On D15, cells were dissociated with Accutase and then collected, counted, and processed for data generation. iPSC-PPC cells were cryopreserved in CryoStor® CS10 (StemCell Technologies) until sequencing.

extract_protocol:
RNA was isolated from total-cell lysates using the Quick-RNATM MiniPrep Kit (Zymo Research) with on-column DNAse treatments. RNA was eluted in 48 µl RNAse-free water and analyzed on a TapeStation (Agilent) to determine sample integrity. All iPSC-PPC samples had RNA integrity number (RIN) values over 9.
Illumina TruSeq Stranded mRNA libraries were prepared according to the manufacturer’s instructions and sequenced on NovaSeq6000 for 101bp paired-end sequencing.

tag: library name

tag: time


title: PPC106

value: iPSC-derived pancreatic progenitor cells


title: PPC037


title: PPC035


title: PPC161


title: DU-145 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 2 replicate [DU-145 cells]

tag: tissue


title: DU-145 cells, (sh-miR93#1) shRNA with 5'-CUCGAG-3' loop, 1 replicate [DU-145 cells]

tag: cell line


title: PPC117

tag: cell type


title: PPC102


title: PPC042


title: PPC083


title: SMARCB1-Rescue 4

tag: genotype


title: PPC118


title: PPC070


title: SMARCB1-Rescue 2

tag: treatment


title: PPC068


title: PPC058


title: PPC025


title: PPC076


title: PPC030


title: PPC012


title: PPC095


title: PPC055


title: PPC054


title: PPC018


title: PPC013


title: PPC114


title: PPC016


title: PPC040


title: PPC028


title: PPC098


title: PPC130


title: PPC049


title: PPC051


title: PPC067


title: PPC123


title: PPC113


title: PPC034


title: PPC111


title: PPC094


title: PPC005


title: PPC159


title: PPC127


title: PPC006


title: PPC002


title: PPC039


title: PPC038


title: PPC027


title: PPC133


title: PPC158


title: PPC112


title: PPC063


title: PPC056


title: PPC163


title: PPC057


title: PPC060


title: PPC021


title: PPC059


title: PPC036


title: PPC120


title: PPC010


title: PPC137


title: PPC043


title: PPC074


title: PPC110


title: PPC014


title: PPC089


title: PPC107


title: PPC032


title: PPC160


title: PPC003


title: PPC029


title: PPC092


title: PPC061


title: PPC115


title: PPC100


title: PPC157


title: PPC073


title: PPC086


title: PPC082


title: PPC116


title: 20189536-379f-48a7-a4e7-96697e6ede11

value: iPSC


title: PPC023


title: PPC031


title: PPC128


title: PPC022


title: PPC150


title: PPC079


title: PPC103


title: PPC050


title: PPC084


title: PPC085


title: PPC104


title: PPC071


title: PPC066


title: PPC080


title: PPC101


title: PPC093


title: PPC019


title: PPC134


title: PPC062


title: PPC017


title: PPC087


title: PPC126


title: PPC007


title: PPC033


title: PPC064


title: PPC153


title: PPC047


title: PPC147


title: PPC041


title: PPC072