title: Episomal_MPRA_RNA1

description:
RNA
RNA1_GEN00141102_S04
Episomal_MPRA_readcounts.csv


title: PRO_dTAG-3h_SRSF1-201A-OE_PNUTS-dTAG_DLD-1_Rep2

status: Public on Dec 02 2024

type: SRA

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

country: China

institute: Fudan University

description: SRSF1-201A overexpressed and treated with dTAG13 for 3h

library_source: transcriptomic

data_processing:
The paired PRO-seq reads were subjected to trimming using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a read length threshold of >15 bp.
After removal of molecular barcode (UMI) with fastp v0.21.0,100 ribosomal RNA reads were discarded using Bowtie v2.3.5.1 with ‘‘--un-conc-gz’’.
Then the remaining reads were aligned to the hg19 or mm10 genome using Bowtie v2.3.5.1 with ‘‘--local --sensitive-local’’.
The mapped data were next deduplicated with UMI-tools to remove PCR duplicates based on the UMI sequences.
The normalization factor was generated following the approach used in ChIP-Rx, and strand-specific coverage tracks were created using deeptools v3.5.0.
Assembly: hg19
Supplementary files format and content: bigWig files
Library strategy: PRO-Seq

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: Human DLD-1 cells were grown in DMEM (Gibco) supplemented with 10% FBS (Yeasen) and 1 × Penicillin-Streptomycin (Thermo) at 37 °C, 5% CO2.

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.  Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG13 for corresponding time.

tag: cell line

tag: cell type

value: colorectal adenocarcinoma cell line

tag: genotype

value: PNUTS-dTAG

tag: treatment


title: Integrated_MPRA_RNA2

city: Indianapolis

first: Nathan

middle: J

last: VanDusen

state: IN

department: Pediatrics

country: USA

institute: Indiana University School of Medicine

description:
RNA
LIB040097_GEN00149944_S11
HDR_MPRA_readcounts.csv

data_processing:
Reads were trimmed down to the barcode-containing region using Trimmomatic
The shell tool Grep was used to count the number of reads containing each barcode.
Supplementary files format and content: HDR_MPRA_readcounts.csv: Table containing the raw number of reads for each enhancer, for the Tnni1 integrated MPRA.
Supplementary files format and content: Episomal_MPRA_readcounts.csv: Table containing the raw number of reads for each enhancer-promoter pair, for the episomal MPRA.

molecule: total RNA

organism: Mus musculus

source_name: P28 CMs

growth_protocol: Mouse in vivo

extract_protocol:
DNA: Proteinase K digestion followed by isopropanol precipitation. RNA: extracted by Trizol and purified by Zymo RNA Clean and Concentrator column with DNAse digestion.
RNA was reverse transcribed with Oligo-dT, reporter transcripts were selectively amplfied, and NGS adapters added during two rounds of PCR.
NGS adapter addition by two sequential rounds of PCR

treatment_protocol: AAV injection at birth

tag: tissue

value: P28 CMs

value: cTnnt2-Cre(+); R26fsCas9-P2A-GFP/+

value: AAV


title: PRO_dTAG-3h_SRSF1-201A-OE_PNUTS-dTAG_DLD-1_Rep1

value: SRSF1-201A overexpressed and treated with dTAG13 for 3h


title: Episomal_MPRA_RNA3

description:
RNA
RNA3_GEN00141104_S06
Episomal_MPRA_readcounts.csv

source_name: P28 ventricles

value: P28 ventricles

value: wildtype


title: Integrated_MPRA_RNA1

description:
RNA
LIB040097_GEN00149943_S10
HDR_MPRA_readcounts.csv


title: Integrated_MPRA_DNA2

description:
DNA
LIB040097_GEN00149941_S08
HDR_MPRA_readcounts.csv

library_source: other

molecule: other


title: PRO_dTAG-3h_MYBL1-5A-OE_PNUTS-dTAG_DLD-1_Rep1

description: MYBL1-5A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPU-59D-OE_PNUTS-dTAG_DLD-1_Rep2

description: HNRNPU-59D overexpressed and treated with dTAG13 for 3h


title: Integrated_MPRA_DNA1

description:
DNA
LIB040097_GEN00149940_S07
HDR_MPRA_readcounts.csv


title: PRO_dTAG-3h_HNRNPU-59D-OE_PNUTS-dTAG_DLD-1_Rep1

value: HNRNPU-59D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPU-59A-OE_PNUTS-dTAG_DLD-1_Rep2

description: HNRNPU-59A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_CC2D1A-120D-OE_PNUTS-dTAG_DLD-1_Rep1

description: CC2D1A-120D overexpressed and treated with dTAG13 for 3h


title: DR_BMT_host_Microglia_3

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl Street, Wolfson Building 321

department: Immunology and Regenerative Biology

country: Israel

institute: Weizmann Institute Of Science

description:
MARSseq
JS_NHS_DR_BMT_DN_Microglia_3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation is done with MARSseq pipeline and UTAP analysis reported in https://doi.org/10.1186/s12859-019-2728-2.
Assembly: mm10
Supplementary files format and content: comma separated values file includes raw count and RPKM for each sample

molecule: polyA RNA

source_name: brain

extract_protocol:
Mice were anesthetized with Pental (1:1 in PBS) and perfused with cold PBS. Whole mouse brains were isolated in intact condition and incubated for 40 min at 37 °C with gentle shaking in the digestion solution (3 ml HBSS /per brain containing 2% BSA, 5 mM EDTA, and 0.2 mg/ml Collagenase type 2 (Worthington)). After the incubation leptomeningeal cells were washed out from the surface of mouse brains with pipetting of digestion solution on the surface and collected in tubes with cold PBS after passing a 100-µm mesh filter. Collected cells were centrifuged at 400 g at 4 °C for 5 min and re-suspended with cold FACS buffer containing 2% FBS and 1 mM EDTA based on PBS w/o Ca2+ and Mg2+ for antibody staining. Intact brains were further digested for parenchymal cell isolation. Brains were dissected in 1 ml of digestion solution containing 2% BSA, 1 mg/ml collagenase D (Sigma) and 1 mg/ml DNase1 (Sigma), and incubated for 20 min at 37 °C. In the middle of incubation, brains were homogenized by pipetting. After the incubation, the homogenate was filtered through a 100-µm mesh and centrifuged at 970 g at 4 °C for 5 min. To enrich brain cells, the cell pellet was re-suspended with 3 ml of 40% Percoll solution and centrifuged at 970 g, w/o acceleration and brake, at room temperature for 15 min. After the centrifugation, the myelin layer was removed, and the rest of the supernatant and cell pellets were washed in cold PBS. Cells were re-suspended with cold FACS buffer for antibody staining for sorting. Cells were kept on ice during all steps, except for the enzymatic digestion and cells for bulk-RNAseq and scRNAseq were processed always with actinomycin D (ActD) to prevent transcriptomic changes, as reported.
100000 or less (when isolated cell number was insufficient) microglia and leptomeningeal macrophages were sorted into 40 µL of lysis/binding buffer (Life Technologies) and stored at -80 C degree  until mRNA isolation. mRNA was captured with Dynabeads oligo(dT) (Life Technologies) according to the manufacturer’s guidelines. A derivation of MARSseq protocol was used to prepare libraries for RNAseq reported in https://doi.org/10.1038/s41596-019-0164-4.

value: brain

value: microglia

value: BMT 32w


title: PRO_dTAG-3h_HNRNPU-59A-OE_PNUTS-dTAG_DLD-1_Rep1

value: HNRNPU-59A overexpressed and treated with dTAG13 for 3h


title: ICF16.1e H (passage 26)

city: Glasgow

first: Holly

last: Hall

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: Cancer Research UK Scotland Institute

description:
TC10
ICF_16_1e_H_P26_S10

data_processing:
MultiQC version 1.11, and FastQ Screen version 0.14.0. RNA-Seq paired-end reads were mapped to the GRCm39.109 version of the Mus musculus genome and annotationusing HiSat2 version 2.2.1 . Expression levels were determined by FeatureCounts from the Subread package version 2.0.1.
Assembly: GRCm39.109
Supplementary files format and content: Raw counts table

source_name: Liver

extract_protocol:
RNA extracted from HCCO (Trizol)
RNA quality and quantity was analysed on a Nanodrop 2000 (Thermo Fisher Scientific) and an Agilent 2200 TapeStation (D1000 screentape). Only samples with a RIN value >7 were used for library preparation. Libraries were prepared using Illumina Stranded mRNA Prep kit

value: Liver

value: ICF16.1e H (passage 26)

value: Organoids

value: Ctnnb1tm1Mmt (Ctnnb1ex3) [HETEROZYGOUS]; Gt(ROSA)26Sortm1(MYC)Djmy (R26LSL-MYC) [HOMOZYGOUS]; Trp53tm2Tyj (Trp53R172H) [HETEROZYGOUS]; Cdkn2atm1.1Brn (Cdkn2aKO) [HOMOZYGOUS]; Ptentm2Mak (Ptenfl)  [HOMOZYGOUS]; AAV8.TBG.PI.Cre.rBG [1.28*10^8 GC/mouse]

tag: Sex

value: Male


title: ICF16.1e H (passage 19)

description:
TC9
ICF_16_1e_H_P19_S9

value: ICF16.1e H (passage 19)


title: PRO_dTAG-3h_GATAD2A-340D-OE_PNUTS-dTAG_DLD-1_Rep2

description: GATAD2A-340D overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG


title: ICF17.3b H (passage p22)

description:
TC8
ICF_17_3b_H_P22_S8

value: ICF17.3b H (passage p22)


title: PRO_dTAG-3h_GATAD2A-340D-OE_PNUTS-dTAG_DLD-1_Rep1

value: GATAD2A-340D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_MYBL1-5D-OE_PNUTS-dTAG_DLD-1_Rep1

description: MYBL1-5D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_GATAD2A-340A-OE_PNUTS-dTAG_DLD-1_Rep2

description: GATAD2A-340A overexpressed and treated with dTAG13 for 3h


title: ICF17.3b H (passage p15)

description:
TC7
ICF_17_3b_H_P15_S7

value: ICF17.3b H (passage p15)


title: ICO3.5g (passage 15)

description:
TC6
ICO_3_5g_P15_S6

value: ICO3.5g (passage 15)

value: Ctnnb1tm1Mmt (Ctnnb1ex3) [HETEROZYGOUS]; Gt(ROSA)26Sortm1(MYC)Djmy (R26LSL-MYC) [HOMOZYGOUS]; Trp53tm2Tyj (Trp53R172H) [HETEROZYGOUS]; Cdkn2atm1.1Brn (Cdkn2aKO) [HOMOZYGOUS]; AAV8.TBG.PI.Cre.rBG [6.4*10^8 GC/mouse]


title: ICZ8.4a (passage 12)

description:
TC5
ICZ_8_4a_P12_S5

value: ICZ8.4a (passage 12)

value: Ctnnb1tm1Mmt (Ctnnb1ex3) [HETEROZYGOUS]; Gt(ROSA)26Sortm1(MYC)Djmy (R26LSL-MYC) [HOMOZYGOUS]; Trp53tm2Tyj (Trp53R172H) [HETEROZYGOUS];AAV8.TBG.PI.Cre.rBG [6.4*10^8 GC/mouse]


title: PRO_dTAG-3h_GATAD2A-340A-OE_PNUTS-dTAG_DLD-1_Rep1

value: GATAD2A-340A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HDGFL2-137D-OE_PNUTS-dTAG_DLD-1_Rep2

description: HDGFL2-137D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HDGFL2-137D-OE_PNUTS-dTAG_DLD-1_Rep1

value: HDGFL2-137D overexpressed and treated with dTAG13 for 3h


title: ICZ5.3d (passage 13)

description:
TC4
ICZ_5_3d_P13_S4

value: Liver

value: ICZ5.3d (passage 13)


title: PRO_dTAG-3h_HDGFL2-137A-OE_PNUTS-dTAG_DLD-1_Rep2

description: HDGFL2-137A overexpressed and treated with dTAG13 for 3h


title: RMH115.2d (passage 13)

description:
TC2
RMH_115_2d_P13_S2

value: RMH115.2d (passage 13)

value: Organoids

value: Ctnnb1tm1Mmt (Ctnnb1ex3) [HETEROZYGOUS]; Gt(ROSA)26Sortm1(MYC)Djmy (R26LSL-MYC) [HOMOZYGOUS]; AAV8.TBG.PI.Cre.rBG [6.4*10^8 GC/mouse]


title: PRO_dTAG-3h_HDGFL2-137A-OE_PNUTS-dTAG_DLD-1_Rep1

value: HDGFL2-137A overexpressed and treated with dTAG13 for 3h


title: RMH115.2d (passage 20)

description:
TC3
RMH_115_2d_P20_S3

value: RMH115.2d (passage 20)

value: Male


title: RMH47.1b (passage 41)

description:
TC1
RMH_47_1b_P41_S1

value: RMH47.1b (passage 41)


title: PRO_dTAG-3h_SMARCC1-573D-OE_PNUTS-dTAG_DLD-1_Rep2

description: SMARCC1-573D overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG


title: PRO_dTAG-3h_SMARCC1-573A-OE_PNUTS-dTAG_DLD-1_Rep1

description: SMARCC1-573A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_SMARCC1-573D-OE_PNUTS-dTAG_DLD-1_Rep1

value: SMARCC1-573D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_SMARCC1-573A-OE_PNUTS-dTAG_DLD-1_Rep2

value: SMARCC1-573A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPC-241D-OE_PNUTS-dTAG_DLD-1_Rep1

description: HNRNPC-241D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPC-241D-OE_PNUTS-dTAG_DLD-1_Rep2

value: HNRNPC-241D overexpressed and treated with dTAG13 for 3h


title: R26myc HOM, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP196

data_processing:
MultiQC version 1.954, and FastQ Screen version 0.14.055. RNA-Seq paired-end reads were mapped to the GRCm39.103 version of the Mus musculus genome and annotation56using STAR version 2.7.8a57. Expression levels were determined by FeatureCounts from the Subread package version 2.0.158.
Assembly: GRCm39.103
Supplementary files format and content: Raw counts table

extract_protocol:
Tissue was homogenized using the Precellys Evolution homogenizer and bulk RNA was isolated using a Trizol (Invitrogen) extraction protocol according to the manufacturer’s instructions.
RNA quality and quantity was analysed on a Nanodrop 2000 (Thermo Fisher Scientific) and an Agilent 2200 TapeStation (D1000 screentape). Only samples with a RIN value >7 were used for library preparation. Libraries were prepared using a Lexogen QuantSeq FWD Kit

value: male

tag: disease

value: Hepatocellular carcinoma (HCC)

tag: group


title: R26myc HOM, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP197


title: R26myc HOM, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP195


title: R26myc HOM, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP200


title: R26myc HOM, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP198


title: PRO_dTAG-3h_HNRNPC-241A-OE_PNUTS-dTAG_DLD-1_Rep1

description: HNRNPC-241A overexpressed and treated with dTAG13 for 3h


title: R26myc HOM, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP199


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; MWD + CCl4; liver; Male; DP193


title: PRO_dTAG-3h_SRSF7-192D-OE_PNUTS-dTAG_DLD-1_Rep2

description: SRSF7-192D overexpressed and treated with dTAG13 for 3h


title: R26myc HOM, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP194


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; MWD + CCl4; liver; Male; DP192


title: PRO_dTAG-3h_SRSF7-192D-OE_PNUTS-dTAG_DLD-1_Rep1

value: SRSF7-192D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_SRSF7-192A-OE_PNUTS-dTAG_DLD-1_Rep2

description: SRSF7-192A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; MWD + CCl4; liver; Male; DP191

value: Liver


title: PRO_dTAG-3h_SRSF7-192A-OE_PNUTS-dTAG_DLD-1_Rep1

value: SRSF7-192A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; MWD + CCl4; liver; Male; DP189


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; MWD + CCl4; liver; Male; DP190


title: PRO_dTAG-3h_PTPN11-562D-OE_PNUTS-dTAG_DLD-1_Rep2

description: PTPN11-562D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_PTPN11-562A-OE_PNUTS-dTAG_DLD-1_Rep2

description: PTPN11-562A overexpressed and treated with dTAG13 for 3h


title: Orthotopic Cell Transplant; liver; ; DP182

value: Orthotopic Cell Transplant


title: Orthotopic Cell Transplant; liver; ; DP181


title: PRO_dTAG-3h_PTPN11-562A-OE_PNUTS-dTAG_DLD-1_Rep1

value: PTPN11-562A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPA1-360-363D-OE_PNUTS-dTAG_DLD-1_Rep2

description: HNRNPA1-360-363D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPC-241A-OE_PNUTS-dTAG_DLD-1_Rep2

value: HNRNPC-241A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPA1-360-363D-OE_PNUTS-dTAG_DLD-1_Rep1

value: HNRNPA1-360-363D overexpressed and treated with dTAG13 for 3h


title: Orthotopic Cell Transplant; liver; ; DP179


title: PRO_dTAG-3h_HNRNPA1-360-363A-OE_PNUTS-dTAG_DLD-1_Rep2

description: HNRNPA1-360-363A overexpressed and treated with dTAG13 for 3h


title: DEN + ALIOS; liver; Male; DP177

value: DEN + ALIOS

tag: date


title: PRO_dTAG-3h_HNRNPA1-360-363A-OE_PNUTS-dTAG_DLD-1_Rep1

value: HNRNPA1-360-363A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ASH2L-101D-OE_PNUTS-dTAG_DLD-1_Rep2

description: ASH2L-101D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ASH2L-101D-OE_PNUTS-dTAG_DLD-1_Rep1

value: ASH2L-101D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ASH2L-101A-OE_PNUTS-dTAG_DLD-1_Rep2

description: ASH2L-101A overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line


title: DEN + ALIOS; liver; Male; DP176


title: DEN + ALIOS; liver; Male; DP174


title: DEN + ALIOS; liver; Male; DP175


title: PRO_dTAG-3h_ASH2L-101A-OE_PNUTS-dTAG_DLD-1_Rep1

value: PNUTS-dTAG

value: ASH2L-101A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ZNF446-137D-OE_PNUTS-dTAG_DLD-1_Rep2

description: ZNF446-137D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_PTPN11-562D-OE_PNUTS-dTAG_DLD-1_Rep1

value: PTPN11-562D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; MWD + CCl4; liver; Male; DP188


title: DEN + ALIOS; liver; Male; DP171


title: PRO_dTAG-3h_ZNF446-137A-OE_PNUTS-dTAG_DLD-1_Rep2

description: ZNF446-137A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ZNF446-137D-OE_PNUTS-dTAG_DLD-1_Rep1

value: ZNF446-137D overexpressed and treated with dTAG13 for 3h


title: DEN + ALIOS; liver; Male; DP173

value: male


title: DEN + ALIOS; liver; Male; DP170

value: Hepatocellular carcinoma (HCC)


title: DEN + ALIOS; liver; Male; DP169


title: PRO_dTAG-3h_ZNF446-137A-OE_PNUTS-dTAG_DLD-1_Rep1

value: ZNF446-137A overexpressed and treated with dTAG13 for 3h


title: Orthotopic Cell Transplant; liver; ; DP180

value: Liver


title: PRO_dTAG-3h_NUCKS1-177-181D-OE_PNUTS-dTAG_DLD-1_Rep2

description: NUCKS1-177-181D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_NUCKS1-177-181D-OE_PNUTS-dTAG_DLD-1_Rep1

value: NUCKS1-177-181D overexpressed and treated with dTAG13 for 3h


title: MWD + CCl4; liver; Male; DP168

value: MWD + CCl4


title: MWD + CCl4; liver; Male; DP167


title: MWD + CCl4; liver; Male; DP166


title: PRO_dTAG-3h_NUCKS1-177-181A-OE_PNUTS-dTAG_DLD-1_Rep2

description: NUCKS1-177-181A overexpressed and treated with dTAG13 for 3h


title: Orthotopic Cell Transplant; liver; ; DP178

value: Orthotopic Cell Transplant


title: MWD + CCl4; liver; Male; DP165


title: MWD + CCl4; liver; Male; DP163


title: PRO_dTAG-3h_HNRNPA1-199D-OE_PNUTS-dTAG_DLD-1_Rep2

description: HNRNPA1-199D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPA1-199D-OE_PNUTS-dTAG_DLD-1_Rep1

value: HNRNPA1-199D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_NUCKS1-177-181A-OE_PNUTS-dTAG_DLD-1_Rep1

value: NUCKS1-177-181A overexpressed and treated with dTAG13 for 3h


title: STZ + HFD; liver; Female; DP162

value: female

value: STZ + HFD


title: DEN + ALIOS; liver; Male; DP172

value: DEN + ALIOS


title: PRO_dTAG-3h_HNRNPA1-199A-OE_PNUTS-dTAG_DLD-1_Rep1

description: HNRNPA1-199A overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line


title: STZ + HFD; liver; Female; DP160


title: STZ + HFD; liver; Female; DP161


title: PRO_dTAG-3h_MAPK1-183D-OE_PNUTS-dTAG_DLD-1_Rep2

description: MAPK1-183D overexpressed and treated with dTAG13 for 3h

value: PNUTS-dTAG


title: STZ + HFD; liver; Male; DP159


title: PRO_dTAG-3h_HNRNPA1-199A-OE_PNUTS-dTAG_DLD-1_Rep2

value: HNRNPA1-199A overexpressed and treated with dTAG13 for 3h


title: STZ + HFD; liver; Male; DP158


title: STZ + HFD; liver; Female; DP157


title: PRO_dTAG-3h_MAPK1-183A-OE_PNUTS-dTAG_DLD-1_Rep1

description: MAPK1-183A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_MAPK1-183A-OE_PNUTS-dTAG_DLD-1_Rep2

value: MAPK1-183A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_MAPK1-183D-OE_PNUTS-dTAG_DLD-1_Rep1

value: MAPK1-183D overexpressed and treated with dTAG13 for 3h


title: STZ + HFD; liver; Female; DP155


title: PRO_dTAG-3h_AFF4-549A-OE_PNUTS-dTAG_DLD-1_Rep1

description: AFF4-549A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Female; DP154


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Female; DP153


title: PRO_dTAG-3h_AFF4-549A-OE_PNUTS-dTAG_DLD-1_Rep2

value: AFF4-549A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_AFF4-549D-OE_PNUTS-dTAG_DLD-1_Rep1

description: AFF4-549D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Female; DP151

value: Hepatocellular carcinoma (HCC)


title: PRO_dTAG-3h_AFF4-549D-OE_PNUTS-dTAG_DLD-1_Rep2

value: AFF4-549D overexpressed and treated with dTAG13 for 3h


title: N1N1 2 DPA epidermis and fiber protoplasts

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Library name: N1-2DPA

library_source: transcriptomic single cell

data_processing:
Initial mapping and processing was carried out using the Cellranger pipeline. Detailed analysis was carried out in R using the Seurat package. Cells were filtered to include only those with a minimum of 200 distinct features, with >80% of features mapping to the parent genome.
Assembly: Gossypium hirsutum v2.1 VKGJ00000000
Assembly: Gossypium barbadense v1.1 VKDL01000000
Supplementary files format and content: Processed ouput from the 10x cellranger pipeline  with default setting for each sample with the peaks.bed barcodes.tsv and matrix.mtx files readable by Seurat packge in R.

organism: Gossypium hirsutum

source_name: Cotton Ovule

growth_protocol: All plants were grown under a natural sunlight a greenhouse at The University of Texas at Austin

extract_protocol:
Ovules were digested in a enzyme mix of cellulase and macerase in 450 mM mannitol for 15 minutes to release protoplasts from the epidermal layers. The ovules were then strained out and the protoplasts were allowed to continue digesting for an additional hour to remove any remaining cell wall debris. To recover the protoplasts, we used density gradient flotation: samples were centrifuged for 2 minutes at 200 g at 4°C to gently pellet the protoplasts, after which all but ~100 ul of the protoplasting buffer was removed, which was mixed with 0.25 volumes chilled Iodixanol (OptiPrep, Sigma-Aldritch, St. Louis, MO) and used to gently resuspend the pellet. 100 ul of chilled 450 mM mannitol was layered atop the denser layer containing iodixanol, and the samples were centrifuged at 200g and 4°C, followed by collecting protoplasts from the top layer.
Libraries were constructed acording to the manufacturer's instructions using the single cell 3' v2 kit (10x Genomics) the the Genome Sequencing and Analysis Facility at UT Austin.

value: Cotton Ovule

tag: age

value: 2 DPA


title: PRO_dTAG-3h_INTS12-128A-OE_PNUTS-dTAG_DLD-1_Rep1

description: INTS12-128A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Female; DP148

value: Liver


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Female; DP149


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Female; DP152


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Female; DP147


title: N1N1 0 DPA epidermis and fiber protoplasts

description: Library name: N1-0DPA

value: 0 DPA


title: PRO_dTAG-3h_INTS12-128D-OE_PNUTS-dTAG_DLD-1_Rep2

description: INTS12-128D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Female; DP150


title: TM-1 2 DPA epidermis and fiber protoplasts

description: Library name: Gh-2DPA


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Female; DP145


title: TM-1 1 DPA epidermis and fiber protoplasts

description: Library name: Gh-1DPA

value: 1 DPA


title: PRO_dTAG-3h_INTS12-128D-OE_PNUTS-dTAG_DLD-1_Rep1

value: INTS12-128D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Female; DP143

value: female


title: PRO_dTAG-3h_Gdown1-270A-OE_PNUTS-dTAG_DLD-1_Rep1

description: Gdown1-270A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Female; DP142


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Female; DP141


title: PRO_dTAG-3h_Gdown1-270A-OE_PNUTS-dTAG_DLD-1_Rep2

value: Gdown1-270A overexpressed and treated with dTAG13 for 3h


title: TM-1 0 DPA epidermis and fiber protoplasts

description: Library name: Gh-0DPA


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Female; DP144


title: Bcatex3 HET, R26Notch.ICD HOM; AAV-Cre low dose; liver; Male; DP140

value: male


title: PRO_dTAG-3h_Gdown1-270D-OE_PNUTS-dTAG_DLD-1_Rep2

description: Gdown1-270D overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line


title: Bcatex3 HET, R26Notch.ICD HOM; AAV-Cre low dose; liver; Male; DP139


title: STZ + HFD; liver; Female; DP156

value: STZ + HFD


title: PRO_dTAG-3h_INTS12-128A-OE_PNUTS-dTAG_DLD-1_Rep2

value: PNUTS-dTAG

value: INTS12-128A overexpressed and treated with dTAG13 for 3h


title: snATAC, Mouse, OIR Model, retina, P17

city: Tianjin

first: Xueming

last: Yao

address: No.94 Weijin Road, Nankai District

institute: Nankai University

description: Library name: OIR_P17_ATAC

library_source: genomic

data_processing:
The demultiplexed fastq files for snRNA-seq and snATAC-seq were processed through the Cell Ranger ARC pipeline (version 2.0.2) from 10x Genomics, yielding barcoded count matrices for gene expression and ATAC data.
Assembly: mm10
Supplementary files format and content: snRNA cellranger-arc output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: snATAC cellranger-arc output: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

molecule: genomic DNA

source_name: retina

extract_protocol:
Retinas from P17 mice under the OIR model were digested using 1 mg/mL Collagenase/Dispase (10269638001; Roche, Basel, Switzerland) and 60 U/mL DNase I (4716728001; Roche) in cell culture medium at 37°C for 15 minutes. The resulting single-cell suspension was filtered through a 40-µm cell strainer and rinsed with PBS containing 2% BSA. The methods for isolating, rinsing, counting, and quality control of the nuclei from cell suspensions adhered to the 10x Genomics user guide for complex tissues (CG000375; 10x Genomics, Pleasanton, CA, USA). In short, the tissues were treated with cold NP-40 lysis buffer in the presence of protease and RNase inhibitors to release nuclei from cells. Purification of the nuclei was carried out using 0.1× lysis buffer, followed by washing with a wash buffer that included RNase inhibitor and 0.1% TWEEN 20 before the permeabilization step. After the diluted nuclei buffer was resuspended, manual hemocytometry was employed to count the nuclei to achieve a targeted nuclei recovery of 10,000 nuclei.
The preparation of combined single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq) libraries was conducted following the manufacturer's guidelines using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit.

value: retina

value: Oxygen-Induced Retinopathy Model


title: snRNA, Mouse, OIR Model, retina, P17

description: Library name: OIR_P17_GTX


title: Bcatex3 HET, R26Notch.ICD HOM; AAV-Cre low dose; liver; Male; DP138

value: Hepatocellular carcinoma (HCC)


title: PRO_dTAG-3h_Gdown1-270D-OE_PNUTS-dTAG_DLD-1_Rep1

value: Gdown1-270D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26Notch.ICD HOM; AAV-Cre low dose; liver; Male; DP137


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Female; DP146


title: Bcatex3 HET, R26Notch.ICD HOM; AAV-Cre low dose; liver; Male; DP135


title: Bcatex3 HET, R26Notch.ICD HOM; AAV-Cre low dose; liver; Male; DP136


title: Bcatex3 HET, R26myc HET, R26Notch.ICD HET; AAV-Cre low dose; liver; Male; DP133


title: Bcatex3 HET, R26Notch.ICD HOM; AAV-Cre low dose; liver; Male; DP134


title: Bcatex3 HET, R26myc HET, R26Notch.ICD HET; AAV-Cre low dose; liver; Male; DP131


title: KO_day7_tumour_5

city: Cambridge

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

data_processing:
The Fastq files were then subjected to quality control using FastQC. Fastq files were aligned to the mouse reference genome (mm9) using STAR aligner and gene count tables were generated using STAR quantMode parameter
Differential gene expression analysis was performed on expressed genes using DESeq2
Assembly: mm9
Supplementary files format and content: tab-delimited text files of unnormalised gene counts

source_name: Lung

extract_protocol:
Cells were stored in RNAlater (Ambion/Sigma) and total RNA purified using Qiagen Rneasy Plus Mini kit. RNA quality was assessed using bioanalyser analysis
mRNA library preparation with polyA-enrichment

value: Lung

value: Intravenous B16 melanoma metastasis


title: Bcatex3 HET, R26myc HET, R26Notch.ICD HET; AAV-Cre low dose; liver; Male; DP132

value: Liver


title: Pancreatic islets, Spopfl/fl females, 12-weeks-old

city: Philadelphia

first: Doris

last: Stoffers

state: Pennsylvania

address: 3400 Civic Center Boulevard, TRC 12-166

institute: University of Pennsylvania

data_processing:
Data was processed using the Cell Ranger pipeline (10x Genomics, v.3.1.0) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome and creation of feature-barcode matrices.
The cell ranger output files were read into R (version 4.1.1) and processed utilizing the standard Seurat (version 4.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islets

extract_protocol:
Islets were isolated by collagenase digestion of the dissected pancreas as previously described (Good et al., 2019). After three rounds of hand-picking under a light microscope, islets were allowed to recover for 3 days in RPMI 1640 containing 10 mM glucose.washed with PBS, and dispersed to single cells with 0.25% trypsin at 37°C with gentle pipetting. 40% volume of FBS was added to the solution and the cell suspension was filtered through a 40 μm cell strainer to facilitate further breakup of cells (Corning). Debris and dead cells were then removed from the cell suspension using Dead Cell and Debris Removal kits (Miltenyi Biotec). Cells were counted and resuspended in 1x PBS with 0.04% BSA for library preparation
For library preparations, samples were loaded onto a Chromium 10X Genomics instrument to generate single-cell barcoded droplets according to the manufacturer’s instructions with 10X single-cell 3’ v3.1 Next GEM chemistry. Libraries were sequenced on a Novaseq 6000 instrument (Illumina) with the v1.5 SP 100 cycles reagent kit with parameters 28x10x10x90.

value: pancreatic islets

value: Spopfl/fl


title: KO_day7_tumour_4


title: Pancreatic islets, SpopβKO females, 12-weeks-old

value: Spop{beta}KO


title: KO_day7_tumour_3


title: Bcatex3 HET, R26myc HET, R26Notch.ICD HET; AAV-Cre low dose; liver; Male; DP129


title: PRO_dTAG-3h_MED1-1463A-OE_PNUTS-dTAG_DLD-1_Rep2

description: MED1-1463A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_NELFe-179-181D-OE_PNUTS-dTAG_DLD-1_Rep1

description: NELFe-179-181D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HET, R26Notch.ICD HET; AAV-Cre low dose; liver; Male; DP130


title: Bcatex3 HET, R26myc HET, R26Notch.ICD HET; AAV-Cre low dose; liver; Male; DP127


title: Bcatex3 HET, R26myc HET, R26Notch.ICD HET; AAV-Cre low dose; liver; Male; DP128


title: R26myc HOM, KRASG12D HET; AAV-Cre low dose; iRFP HEMI; liver; Male; DP126


title: KO_day7_tumour_2


title: R26myc HOM, KRASG12D HET; AAV-Cre low dose; iRFP HEMI; liver; Male; DP125


title: R26myc HOM, KRASG12D HET; AAV-Cre low dose; iRFP HEMI; liver; Male; DP124


title: PRO_dTAG-3h_MED1-1463A-OE_PNUTS-dTAG_DLD-1_Rep1

value: MED1-1463A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_MED1-1463D-OE_PNUTS-dTAG_DLD-1_Rep2

description: MED1-1463D overexpressed and treated with dTAG13 for 3h


title: KO_day7_tumour_1


title: WT_day7_tumour_5

value: WT


title: R26myc HOM, KRASG12D HET; AAV-Cre low dose; iRFP HEMI; liver; Male; DP122

value: male


title: PRO_dTAG-3h_NELFe-179-181A-OE_PNUTS-dTAG_DLD-1_Rep2

description: NELFe-179-181A overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line


title: PRO_dTAG-3h_NELFe-179-181A-OE_PNUTS-dTAG_DLD-1_Rep1

value: NELFe-179-181A overexpressed and treated with dTAG13 for 3h


title: R26myc HOM, KRASG12D HET; AAV-Cre low dose; iRFP HEMI; liver; Male; DP121


title: PRO_dTAG-3h_MED1-1463D-OE_PNUTS-dTAG_DLD-1_Rep1

value: PNUTS-dTAG

value: MED1-1463D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_NELFe-179-181D-OE_PNUTS-dTAG_DLD-1_Rep2

value: NELFe-179-181D overexpressed and treated with dTAG13 for 3h


title: WT_day7_tumour_4


title: Bcatex3 HET, R26myc HOM, p21KO HOM; AAV-Cre low dose; liver; Male; DP118


title: WT_day7_tumour_3


title: PRO_dTAG-3h_XRN2-470-487D-OE_PNUTS-dTAG_DLD-1_Rep2

description: XRN2-470-487D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p21KO HOM; AAV-Cre low dose; liver; Male; DP119


title: PRO_dTAG-3h_XRN2-470-487D-OE_PNUTS-dTAG_DLD-1_Rep1

value: XRN2-470-487D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p21KO HOM; AAV-Cre low dose; liver; Male; DP117

value: Hepatocellular carcinoma (HCC)


title: Bcatex3 HET, R26myc HOM, p21KO HOM; AAV-Cre low dose; liver; Male; DP116


title: WT_day7_tumour_2


title: PRO_dTAG-3h_XRN2-470-487A-OE_PNUTS-dTAG_DLD-1_Rep2

description: XRN2-470-487A overexpressed and treated with dTAG13 for 3h


title: WT_day7_tumour_1


title: Bcatex3 HET, R26myc HOM, p21KO HOM; AAV-Cre low dose; liver; Male; DP115


title: KO_d5_U46619_4

source_name: CD8 T cells

value: CD8 T cells

value: KO

value: anti-CD3/28 antibodies, rhIL-2 + U46619


title: Bcatex3 HET, R26myc HOM, p21KO HOM; AAV-Cre low dose; liver; Male; DP114

value: Liver


title: PRO_dTAG-3h_XRN2-470-487A-OE_PNUTS-dTAG_DLD-1_Rep1

value: XRN2-470-487A overexpressed and treated with dTAG13 for 3h


title: KO_d5_U46619_3


title: Bcatex3 HET, R26myc HOM, p21KO HOM; AAV-Cre low dose; liver; Male; DP113


title: R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP110


title: R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP111


title: R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP109


title: PRO_dTAG-3h_XRN2-439-448D-OE_PNUTS-dTAG_DLD-1_Rep2

description: XRN2-439-448D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_XRN2-439-448D-OE_PNUTS-dTAG_DLD-1_Rep1

value: XRN2-439-448D overexpressed and treated with dTAG13 for 3h


title: R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre low dose; TCF/LEF-GFP; liver; Male; DP108


title: R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP112


title: KO_d5_U46619_2


title: R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP107


title: R26myc HOM, KRASG12D HET; AAV-Cre low dose; iRFP HEMI; liver; Male; DP123


title: Bcatex3 HET, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP106


title: PRO_dTAG-3h_XRN2-439-448A-OE_PNUTS-dTAG_DLD-1_Rep2

description: XRN2-439-448A overexpressed and treated with dTAG13 for 3h


title: KO_d5_U46619_1


title: Bcatex3 HET, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP105


title: Bcatex3 HET, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP104


title: PRO_dTAG-3h_XRN2-439-448A-OE_PNUTS-dTAG_DLD-1_Rep1

value: XRN2-439-448A overexpressed and treated with dTAG13 for 3h


title: WT_d5_U46619_4


title: Bcatex3 HET, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP103


title: Bcatex3 HET, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP102


title: WT_d5_U46619_3


title: PRO_dTAG-3h_AFF4-222A-OE_PNUTS-dTAG_DLD-1_Rep2

description: AFF4-222A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP100


title: Bcatex3 HET, p53R172H HET, PTENfl HOM; AAV-Cre low dose; liver; Male; DP101


title: PRO_dTAG-3h_AFF4-222A-OE_PNUTS-dTAG_DLD-1_Rep1

value: AFF4-222A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP98


title: WT_d5_U46619_2

value: WT


title: WT_d5_U46619_1


title: PRO_dTAG-3h_AFF4-222D-OE_PNUTS-dTAG_DLD-1_Rep2

description: AFF4-222D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_AFF4-222D-OE_PNUTS-dTAG_DLD-1_Rep1

value: AFF4-222D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP97

value: male


title: Bcatex3 HET, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP95


title: Bcatex3 HET, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP96


title: Bcatex3 HET, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP94


title: PRO_dTAG-3h_CCNL1-342A-OE_PNUTS-dTAG_DLD-1_Rep2

description: CCNL1-342A overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line


title: KO_d5_Veh_2

value: anti-CD3/28 antibodies, rhIL-2 + Veh


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP92


title: PRO_dTAG-3h_CCNL1-342A-OE_PNUTS-dTAG_DLD-1_Rep1

value: PNUTS-dTAG

value: CCNL1-342A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP93


title: KO_d5_Veh_1


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP91


title: PRO_dTAG-3h_CCNL1-342D-OE_PNUTS-dTAG_DLD-1_Rep2

description: CCNL1-342D overexpressed and treated with dTAG13 for 3h


title: WT_d5_Veh_4


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP90


title: ChIP-FLAG_dTAG-3h_PNUTS-dTAG_DLD-1

description: treated with dTAG13 for 3h

data_processing:
The raw ChIP-Rx reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 with default parameters.
Low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 96 and Picard v2.23.3 (https:// broadinstitute.github.io/picard/).
We then collected the spike-in read number for each of the ChIP-Rx sample with SAMtools v1.9 96 and generated the normalization factor as 1e6/spike-in_count. Normalized bigwig files were generated by deeptools v3.5.0.
The ENCODE blacklist regions were removed using bedtools v2.29.2.98 Peak calling was performed by macs2 v2.2.6 with a q-value threshold of 0.05.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: Human DLD-1 , and murine MEF cells were grown in DMEM (Gibco) supplemented with 10% FBS (Yeasen) and 1 × Penicillin-Streptomycin (Thermo) at 37 °C, 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG 13 for 3 h,  the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution


title: Bcatex3 HET, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP99


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP86


title: WT_d5_Veh_3


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP87


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP85


title: PRO_dTAG-3h_CCNL1-342D-OE_PNUTS-dTAG_DLD-1_Rep1

value: CCNL1-342D overexpressed and treated with dTAG13 for 3h


title: ChIP-FLAG_DMSO-3h_PNUTS-dTAG_DLD-1

description: treated with DMSO for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP84

value: Hepatocellular carcinoma (HCC)


title: WT_d5_Veh_2

value: CD8 T cells


title: KO_d5_Veh_4

value: KO


title: WT_d5_Veh_1


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM; AAV-Cre low dose; TCF/LEF-GFP; liver; Male; DP82


title: PRO_dTAG-3h_CCNL1-374A-OE_PNUTS-dTAG_DLD-1_Rep2

description: CCNL1-374A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM; AAV-Cre low dose; TCF/LEF-GFP; liver; Male; DP83


title: Macrophages, BAL, Sig F KO Bleo day 21, mouse #3, run 2

city: Denver

first: Marika

last: Orlov

state: Colorado

address: 12700 East 19th Avenue  9C03

department: Medicine, Division of Pulmonary Sciences and Critical Care Medicine

institute: University of Colorado

description: Sample 24 (X21_494_KO_D21) Run 2

data_processing:
Raw sequencing reads were de-multiplexed using bcl2fastq and processed using the nf-core/rnaseq pipeline (3.12.0) with nextflow (23.04.1)
Resulting count data were transformed using variance stabilizing transformation (VST) (DESeq2, 1.42.0).
Differentially expressed genes (DEGS) were identified using limma (3.58.1) in R (4.3.1).
Multiple comparisons adjustments were done using the Benjamini-Hochberg method for controlling false discovery rates (FDRs), and an FDR threshold of 0.05 was used to determine statistical significance
Assembly: MM10
Supplementary files format and content: RNA-seq counts quantified by nextflow nf-core/rnaseq pipeline in comma-delimited format

source_name: Macrophages from BAL

extract_protocol:
Total RNA was extracted using RNeasy Micro Plus Kit from Qiagen per manufacturer's instructions.
The Universal Plus mRNA-Seq library preparation kit with NuQuant (Tecan, Männedorf, Switzerland) was used  with an input of 200 ng of total RNA to generate RNA-Seq libraries.
Paired-end sequencing reads of 150 bp was generated on NovaSeq 6000 (Illumina, La Jolla, CA) sequencer at a target depth of 80 million paired-end reads per sample.

treatment_protocol: mice were challenged with bleomycin (2.5 units/kg, IT) or saline vehicle and airspace macrophages were isolated 7, 14 and 21 days after challenge.

value: Macrophages from BAL

value: Male

value: Siglec F KO

value: Bleomycin Challenge

tag: time

value: Day 21


title: Macrophages, BAL, Sig F KO Bleo day 21, mouse #3, run 1

description: Sample 24 (X21_494_KO_D21) Run 1


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM; AAV-Cre low dose; TCF/LEF-GFP; liver; Male; DP81

value: Liver


title: ChIP-PNUTS_dTAG-3h_PNUTS-dTAG_DLD-1

description: treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP89


title: Bcatex3 HET, R26myc HOM, p53R172H HET; AAV-Cre low dose; liver; Male; DP78


title: Bcatex3 HET, R26myc HOM, p53R172H HET; AAV-Cre low dose; liver; Male; DP79


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP88


title: ChIP-PNUTS_DMSO-3h_PNUTS-dTAG_DLD-1

description: treated with DMSO for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET, p16KO HOM; AAV-Cre low dose; TCF/LEF-GFP; liver; Male; DP80


title: Bcatex3 HET, R26myc HOM, p53R172H HET; AAV-Cre low dose; liver; Male; DP77


title: PRO_dTAG-3h_CCNL1-374A-OE_PNUTS-dTAG_DLD-1_Rep1

value: CCNL1-374A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53R172H HET; AAV-Cre low dose; liver; Male; DP75


title: PRO_dTAG-3h_CCNL1-374D-OE_PNUTS-dTAG_DLD-1_Rep2

description: CCNL1-374D overexpressed and treated with dTAG13 for 3h


title: Macrophages, BAL, Sig F KO Bleo day 21, mouse #1, run 2

description: Sample 22 (X19_454_KO_D21) Run 2


title: Bcatex3 HET, R26myc HOM, p53R172H HET; AAV-Cre low dose; liver; Male; DP74


title: Bcatex3 HET, R26myc HOM, p53R172H HET; AAV-Cre low dose; liver; Male; DP73


title: ChIP-Input_dTAG-3h_PNUTS-dTAG_DLD-1_PNUTS-FLAG

description: treated with dTAG13 for 3h


title: Bcatex3 HET, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP71


title: Macrophages, BAL, Sig F KO Bleo day 21, mouse #1, run 1

description: Sample 22 (X19_454_KO_D21) Run 1


title: PRO_dTAG-3h_CCNL1-374D-OE_PNUTS-dTAG_DLD-1_Rep1

value: CCNL1-374D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP70

value: male


title: Macrophages, BAL, Sig F KO Bleo day 14, mouse #3, run 2

description: Sample 21 (X18_524_KO_D14) Run 2

value: Day 14


title: ChIP-Input_DMSO-3h_PNUTS-dTAG_DLD-1_PNUTS-FLAG

description: treated with DMSO for 3h

value: colorectal adenocarcinoma cell line


title: Bcatex3 HET, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP69


title: Macrophages, BAL, Sig F KO Bleo day 21, mouse #2, run 2

description: Sample 23 (X20_493_KO_D21) Run 2


title: Macrophages, BAL, Sig F KO Bleo day 14, mouse #3, run 1

description: Sample 21 (X18_524_KO_D14) Run 1


title: Bcatex3 HET, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP68


title: Bcatex3 HET, R26myc HOM, p53R172H HET; AAV-Cre low dose; liver; Male; DP76


title: PRO_dTAG-3h_SRSF3-5D-OE_PNUTS-dTAG_DLD-1_Rep2

description: SRSF3-5D overexpressed and treated with dTAG13 for 3h

value: PNUTS-dTAG


title: ChIP-PolII-pSer2_dTAG-3h_PNUTS-dTAG_DLD-1

description: treated with dTAG13 for 3h


title: Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP65


title: Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP64


title: Macrophages, BAL, Sig F KO Bleo day 21, mouse #2, run 1

description: Sample 23 (X20_493_KO_D21) Run 1


title: Macrophages, BAL, Sig F KO Bleo day 14, mouse #2, run 2

description: Sample  20 (X17_523_KO_D14) Run 2


title: Macrophages, BAL, Sig F KO Bleo day 14, mouse #2, run 1

description: Sample  20 (X17_523_KO_D14) Run 1


title: Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP62


title: Bcatex3 HET, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP66


title: PRO_dTAG-3h_SRSF3-5D-OE_PNUTS-dTAG_DLD-1_Rep1

value: SRSF3-5D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP63


title: Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP61


title: ChIP-PolII-pSer2_DMSO-3h_PNUTS-dTAG_DLD-1

description: treated with DMSO for 3h


title: Bcatex3 HET, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP72


title: Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP60


title: Macrophages, BAL, Sig F KO Bleo day 14, mouse #1, run 1

description: Sample 19 (X16_495_KO_D14) Run 1


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP57


title: Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP59


title: Bcatex3 HET, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre low dose; liver; Male; DP67


title: ChIP-PolII-pSer5_dTAG-3h_PNUTS-dTAG_DLD-1

description: treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP56


title: Macrophages, BAL, Sig F KO Bleo day 7, mouse #3, run 2

description: Sample 18 (X15_461_KO_D7) Run 2

value: Day 7


title: Macrophages, BAL, Sig F KO Bleo day 7, mouse #3, run 1

description: Sample 18 (X15_461_KO_D7) Run 1


title: Macrophages, BAL, Sig F KO Bleo day 7, mouse #2, run 2

description: Sample 17 (X14_456_KO_D7) Run 2


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP55

value: Hepatocellular carcinoma (HCC)


title: Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP52


title: Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP51


title: Macrophages, BAL, Sig F KO Bleo day 7, mouse #2, run 1

description: Sample 17 (X14_456_KO_D7) Run 1


title: Macrophages, BAL, Sig F KO Bleo day 14, mouse #1, run 2

description: Sample 19 (X16_495_KO_D14) Run 2


title: PRO_dTAG-3h_vector-OE_PNUTS-dTAG_DLD-1_Rep2

description: Vector overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP53


title: Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP50


title: Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP49


title: ChIP-PolII-pSer5_DMSO-3h_PNUTS-dTAG_DLD-1

description: treated with DMSO for 3h


title: Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP48


title: Macrophages, BAL, Sig F KO Bleo day 7, mouse #1, run 2

description: Sample 16 (X13_455_KO_D7) Run 2


title: Macrophages, BAL, Sig F KO Bleo day 7, mouse #1, run 1

description: Sample 16 (X13_455_KO_D7) Run 1


title: PRO_dTAG-3h_SRSF3-5A-OE_PNUTS-dTAG_DLD-1_Rep2

description: SRSF3-5A overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP58


title: Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP47


title: ChIP-PolII-NTD_dTAG-3h_PNUTS-dTAG_DLD-1

description: treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP46


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP45


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP44


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM, PTENfl HOM; AAV-Cre ultra low dose; liver; Male; DP54


title: PRO_dTAG-3h_SRSF3-5A-OE_PNUTS-dTAG_DLD-1_Rep1

value: SRSF3-5A overexpressed and treated with dTAG13 for 3h


title: Macrophages, BAL, Sig F KO Naïve, mouse #3, run 1

description: Sample 15 (X24_435_KO_Naive) Run 1

value: Saline Control

value: Day 0


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP43


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP42


title: ChIP-PolII-NTD_DMSO-3h_PNUTS-dTAG_DLD-1

description: treated with DMSO for 3h


title: Macrophages, BAL, Sig F KO Naïve, mouse #2, run 2

description: Sample 14 (X23_434_KO_Naive) Run 2

value: Macrophages from BAL

value: Male


title: Bcatex3 HET, R26myc HOM, p53fl HET, p16KO HOM; AAV-Cre low dose; liver; Male; DP41


title: PRO_DMSO_vector-OE_PNUTS-dTAG_DLD-1_Rep1

description: Vector overexpressed and treated with DMSO for 3 hours


title: Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre low dose; liver; Male; DP39


title: ChIP-Input_dTAG-3h_PNUTS-dTAG_DLD-1_PolII

description: treated with dTAG13 for 3h


title: PRO_dTAG-3h_vector-OE_PNUTS-dTAG_DLD-1_Rep1

value: Vector overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre low dose; liver; Male; DP37


title: Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre low dose; liver; Male; DP38


title: Macrophages, BAL, Sig F KO Naïve, mouse #2, run 1

description: Sample 14 (X23_434_KO_Naive) Run 1

value: Siglec F KO


title: Macrophages, BAL, Sig F KO Naïve, mouse #1, run 2

description: Sample 13 (X22_433_KO_Naive) Run 2


title: PRO_dTAG-3h_OE-MYC-12D-in-PNUTS-dTAG_DLD1

description: MYC-12D overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre low dose; liver; Male; DP36

value: Liver


title: Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre low dose; liver; Male; DP35


title: Macrophages, BAL, Sig F KO Naïve, mouse #1, run 1

description: Sample 13 (X22_433_KO_Naive) Run 1


title: Macrophages, BAL, Sig F KO Naïve, mouse #3, run 2

description: Sample 15 (X24_435_KO_Naive) Run 2


title: Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre low dose; liver; Male; DP34


title: ChIP-Input_DMSO-3h_PNUTS-dTAG_DLD-1_PolII

description: treated with DMSO for 3h


title: PRO_DMSO_vector-OE_PNUTS-dTAG_DLD-1_Rep2

value: Vector overexpressed and treated with DMSO for 3 hours


title: PRO_DMSO-3h_OE-MYC-12D-in-PNUTS-dTAG_DLD1

description: MYC-12D overexpressed and treated with DMSO for 3h


title: Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre low dose; liver; Male; DP33


title: treat

city: Wuhan

first: Xinyi

last: Li

address: Shuiguo street

department: Department of Anesthesiology

institute: Zhongnan hospital of Wuhan University

description: Library name: Sample 2

data_processing:
Firstly, the data is split according to the cell barcode and UMI markers using the official 10X software cellranger.
On this basis, the cells were filtered by Seurat for quality control before other analyses were performed.
Assembly: human NCBI genome build 36
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: The tsv file contains gene id and symbol information.
Supplementary files format and content: The tsv file contains the cell related barcode

source_name: lung

extract_protocol:
Cell Suspension Preparation include tissue disintegration, cell recovery, PBMC (peripheral blood mononuclear cell) separation, cell nuclear extraction from tissue and flow sorting, producing cells with high quality for single-cell library construction.
10x Genomics Single-cell 3’ Library Preparation include Microscope Assessment of the Cell or Nuclei, GEM Generation and Reverse Transcription, Breaking GEMs, cDNA Amplification, Fragmentation, end Repair & A-tailing, Adaptor Ligation, PCR, Library QC, Circularization, Sequencing.

value: lung


title: Macrophages, BAL, Sig F WT Bleo day 21, mouse #3, run 2

description: Sample 12 (X9_484_WT_D21) Run 2

value: Wild Type

value: Bleomycin Challenge

value: Day 21


title: Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre low dose; liver; Male; DP32

value: male


title: Macrophages, BAL, Sig F WT Bleo day 21, mouse #3, run 1

description: Sample 12 (X9_484_WT_D21) Run 1


title: control

description: Library name: Sample 1


title: Macrophages, BAL, Sig F WT Bleo day 21, mouse #2, run 2

description: Sample 11 (X8_483_WT_D21) Run 2


title: Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre low dose; liver; Male; DP30


title: ChIP_NELFe_dTAG-1h_PNUTS-dTAG_DLD-1

description: treated with dTAG13 for 1h

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG


title: PRO_dTAG-3h_OE-MYC-12A-in-PNUTS-dTAG_DLD1

description: MYC-12A overexpressed and treated with dTAG13 for 3h


title: iPSC-CS06

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

country: Germany

institute: Universitätsklinikum Bonn

description: 3' Poly(A) RNA-seq

data_processing:
For 3' Poly(A) RNA-seq, reads were trimmed with bbduk.sh following manufacturer's protocol. ref=/data/resources/polyA.fa.gz,/data/resources/truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20; For Ribo-Seq: trimGalore was used with options --length 17 --quality 20 --stringency 5 --cores 4
For 3' Poly(A) RNA-seq, Reads were aligned with STAR aligner following the manufacturer's protocol. STAR  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1   --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20   --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD  --outSAMtype BAM SortedByCoordinate --outFileNamePrefix. For Ribo-Seq, Star Aligner was used first to align against non-coding RNAs (retrieved from UCSC Table Browser) with options --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 1  --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outFilterMultimapNmax 100. Non-matched reads were then aligned with Star aligner against a transcriptome, recived from UCSC Table Browser with coding sequences including 3'- and 5'-UTR regions: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 1 --alignEndsType EndToEnd --seedSearchStartLmax 15 --outFileNamePrefix "$outName" --outSAMtype BAM Unsorted --scoreGap 1000000
For 3' Poly(A) RNA-seq, the amount of sequences aligned to transcripts was counted with cuffdiff and column for counts at the + strand was used for downstream analysis. For Ribo-Seq, reads with sizes 20, 21, 28 and 29 were used with an offset of 15nt form the 5' end to the A-site. Reads with A-site positions within the CDS of the corresponding transcript were counted and used for downstream analysis.
Genome_build: For 3' Poly(A) RNA-seq: GRCh38.101, for Ribo-Seq: hg38
Supplementary_files_format_and_content: table with 2 columns in .txt format, column1: Ensemble Gene Accession Number/Gene symbol, column2: corresponding counts

source_name: Induced pluripoent stem cells

extract_protocol:
total RNA was extracted using TRIzol Kit (Invitrogen) recommended by manufacturer.
Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.

value: MCT8 S194F


title: iPSC-CS01

description: 3' Poly(A) RNA-seq

value: MCT8 P321L


title: Macrophages, BAL, Sig F WT Bleo day 21, mouse #2, run 1

description: Sample 11 (X8_483_WT_D21) Run 1


title: Macrophages, BAL, Sig F WT Bleo day 21, mouse #1, run 2

description: Sample 10 (X7_482_WT_D21) Run 2


title: PRO_DMSO-3h_OE-MYC-12A-in-PNUTS-dTAG_DLD1

description: MYC-12A overexpressed and treated with DMSO for 3h


title: Macrophages, BAL, Sig F WT Bleo day 21, mouse #1, run 1

description: Sample 10 (X7_482_WT_D21) Run 1


title: Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre low dose; liver; Male; DP28

value: Hepatocellular carcinoma (HCC)


title: ChIP_NELFe_DMSO-1h_PNUTS-dTAG_DLD-1

description: treated with DMSO for 1h


title: Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre low dose; liver; Male; DP29


title: iPSC-2A2

description: 3' Poly(A) RNA-seq

value: MCT8 P321L-corr


title: Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre low dose; liver; Male; DP26


title: BMEC-CS06_2

description: 3' Poly(A) RNA-seq

source_name: Brain microvascular endothelial cells


title: ChIP_TAF3_dTAG-1h_PNUTS-dTAG_DLD-1_Rep2

description: treated with dTAG13 for 1h


title: Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre low dose; liver; Male; DP31


title: Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre low dose; liver; Male; DP24


title: PRO_DMSO-3h_OE-MYC-WT-in-PNUTS-dTAG_DLD1

description: MYC-WT overexpressed and treated with DMSO for 3h


title: Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre low dose; liver; Male; DP27


title: Macrophages, BAL, Sig F WT Bleo day 14, mouse 3, run 2

description: Sample 9 (X6_520_WT_D14) Run 2

value: Macrophages from BAL

value: Day 14


title: BMEC-CS01_2

description: 3' Poly(A) RNA-seq


title: PRO_dTAG-3h_OE-MYC-WT-in-PNUTS-dTAG_DLD1

description: MYC-WT overexpressed and treated with dTAG13 for 3h


title: BMEC-CS06_1

description: 3' Poly(A) RNA-seq


title: BMEC-CS03_1

description: 3' Poly(A) RNA-seq

value: MCT8 WT


title: Macrophages, BAL, Sig F WT Bleo day 14, mouse 3, run 1

description: Sample 9 (X6_520_WT_D14) Run 1

value: Male


title: Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre low dose; liver; Male; DP22

value: Liver


title: Macrophages, BAL, Sig F WT Bleo day 14, mouse #1, run 1

description: Sample 7 (X4_485_WT_D14) Run 1


title: BMEC-CR5_2

description: 3' Poly(A) RNA-seq


title: Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre low dose; liver; Male; DP25


title: ChIP_TAF3_dTAG-1h_PNUTS-dTAG_DLD-1_Rep1

description: treated with dTAG13 for 1h


title: BMEC-CS03_2

description: 3' Poly(A) RNA-seq


title: Macrophages, BAL, Sig F WT Bleo day 14, mouse #2, run 2

description: Sample 8 (X5_519_WT_D14) Run 2


title: Macrophages, BAL, Sig F WT Bleo day 14, mouse #2, run 1

description: Sample 8 (X5_519_WT_D14) Run 1


title: ChIP_TAF3_DMSO-1h_PNUTS-dTAG_DLD-1_Rep2

description: treated with DMSO for 1h


title: Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre low dose; liver; Male; DP20


title: PRO_DMSO-3h_vector-OE_PNUTS-dTAG_DLD-1_MYC

value: Vector overexpressed and treated with DMSO for 3 hours


title: BMEC-CS01_1

description: 3' Poly(A) RNA-seq


title: PRO_dTAG-3h_vector-OE_PNUTS-dTAG_DLD-1_MYC

description: Vector overexpressed and treated with dTAG13 for 3 hours


title: ChIP_TAF3_DMSO-1h_PNUTS-dTAG_DLD-1_Rep1

description: treated with DMSO for 1h


title: Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre low dose; liver; Male; DP21


title: BMEC-2A2_2

description: 3' Poly(A) RNA-seq


title: Macrophages, BAL, Sig F WT Bleo day 14, mouse #1, run 2

description: Sample 7 (X4_485_WT_D14) Run 2


title: Macrophages, BAL, Sig F WT Bleo day 7, mouse #3, run 2

description: Sample 6 (X3_473_WT_D7) Run 2

value: Day 7


title: Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre low dose; liver; Male; DP19


title: BMEC-CR5_1

description: 3' Poly(A) RNA-seq


title: PRO_dTAG-3h_OE-SPT5-T4A-in-PNUTS-DLD1

description: SPT5-T4A overexpressed and treated with dTAG13 for 3h


title: Macrophages, BAL, Sig F WT Bleo day 7, mouse #3, run 1

description: Sample 6 (X3_473_WT_D7) Run 1

value: Wild Type


title: R26myc HOM, Axin1fl HOM; AAV-Cre low dose; liver; Male; DP17


title: Macrophages, BAL, Sig F WT Bleo day 7, mouse #1, run 2

description: Sample 4 (X1_446_WT_D7) Run 2

value: Bleomycin Challenge


title: Macrophages, BAL, Sig F WT Bleo day 7, mouse #1, run 1

description: Sample 4 (X1_446_WT_D7) Run 1


title: R26myc HOM, Axin1fl HOM; AAV-Cre low dose; liver; Male; DP16


title: Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre low dose; liver; Male; DP23


title: ChIP_Input_dTAG-1h_PNUTS-dTAG_DLD-1_TAF3-NELF

description: treated with dTAG13 for 1h


title: BMEC-2A2_1

description: 3' Poly(A) RNA-seq


title: Macrophages, BAL, Sig F WT Bleo day 7, mouse #2, run 1

description: Sample 5 (X2_467_WT_D7) Run 1


title: R26myc HOM, Axin1fl HOM; AAV-Cre low dose; liver; Male; DP15


title: R26myc HOM, Axin1fl HOM; AAV-Cre low dose; liver; Male; DP18


title: Macrophages, BAL, Sig F WT Bleo day 7, mouse #2, run 2

description: Sample 5 (X2_467_WT_D7) Run 2


title: R26myc HOM, Axin1fl HOM; AAV-Cre low dose; liver; Male; DP14


title: R26myc HOM, Axin1fl HOM; AAV-Cre low dose; liver; Male; DP13


title: Macrophages, BAL, Sig F WT Naïve, mouse #2, run 2

description: Sample 2 (X11_474_WT_Naive) Run 2

value: Saline Control

value: Day 0


title: PRO_DMSO-3h_vector-OE_PNUTS-dTAG_DLD-1_SPT5

value: colorectal adenocarcinoma cell line


title: PRO_DMSO-3h_OE-SPT5-T4A-in-PNUTS-DLD1

description: SPT5-T4A overexpressed and treated with DMSO for 3h

value: PNUTS-dTAG


title: mcm23AhstD_H3K56ac_eSPAN_rep2

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
To improve mapping quality, raw sequencing reads were first processed with Trim Galore (v0.6.7) to remove low-quality reads and Illumina Prep Kit adaptors. The quality cutoff was set to 20, and the minimum required read length after trimming was 20 nt. Paired-end sequencing reads were mapped to yeast genome (sacCer3) using bowtie2 (V 2.2.4) with the following parameters: with --no-mixed --no-discordant --no-dovetail --no-contain --local --maxins 1000.
Sequence alignment map files, including uniquely mapped, PCR-duplicated, and multi-mapped reads, were transformed into BAM files using SAMtools (V 1.11).To obtain the accurate mapping reads, duplicate and multi-mapping reads were discarded and only paired-end reads with both ends aligning uniquely to the reference genome were used for further analysis.
Accurate early-firing region detection was achieved by using filtered paired-end reads of BrdU-IP-ssSeq signals to call broad peaks with MACS2 (V 2.2.5) for each replicate independently, applying a q-value cutoff of 0.001 and using the corresponding MNase-ssSeq Input samples as controls.
To calculate BrdU-IP-ssSeq and eSPAN strand bias, the filtered paired-end reads aligned to the Watson (W) and Crick (C) strands of the reference genome were partitioned using the bamtobed function of BEDTools (V 2.29.2) and custom Perl scripts. BrdU-IP-ssSeq and eSPAN bias was determined in 10bp bin from the segregated Watson and Crick reads using the formula Bias= (W-C)/(W + C) across the replicated regions. Bins with fewer than 10 sequencing reads were excluded. The eSPAN bias was furthermore normalized using the corresponding BrdU-IP-ssSeq strand bias.
Assembly: S. cerevisiae (UCSC sacCer3)
Supplementary files format and content: bigwig files were generated for plus strand, minus strand and both strands, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: They were grown in rich medium (1% yeast extract, 2% peptone) supplemented with 2% glucose (YPD) at 30 °C. Exponentially growing cells were arrested at the G1 phase with 5 μg/ml alpha-factor (EZBiolab) for 3 hours in YPD medium at 25 °C when the OD600 reached 0.4-0.5. Prior to completion, cell morphology was monitored to ensure the G1 arrest (bar-shaped).

extract_protocol:
All ChIP and eSPAN assays were performed as described previously (Yu et al., 2014). To carry out ChIP for H3K4me3 and H3K56ac, chromatin was pelleted and washed twice with NP buffer (1.6 M sorbitol, 5 mM MgCl2, 50 mM NaCl, 2 mM CaCl2, 14 mM β-mercaptoethanol, 0.075% NP-40, 10 mM Tris-HCl (pH 7.4), 5 mM spermidine). The chromatin was then resuspended in the same buffer and digested with 4U MNase (9013-53-0, Worthington Biochemical) for 20 minutes at 37°C, resulting in primarily mono- and di-nucleosome fragments. The digestion was terminated by adding 5 μl of 0.5 M EDTA and 1/5 volume of 5x ChIP lysis buffer, followed by incubation on ice for at least 30 minutes. Following MNase digestion, the chromatin was cleared by centrifugation and then immunoprecipitated using specific antibodies (anti-H3K4me3 (ab8580, Abcam) and homemade anti-H3K56ac along with protein G Sepharose beads (17-0618-02, GE Healthcare). The beads were extensively washed, and DNA from both Input and ChIP samples was extracted via the Chelex-100 protocol and utilized for BrdU IP/eSPAN or purified using the MinElute PCR Purification Kit (28004, Qiagen) for ChIP. BrdU immunoprecipitation was performed using either input DNA for BrdU-IP-ssSeq, and H3K4me3 or H3K56ac ChIP DNAs for eSPAN. Briefly, input or ChIP DNA obtained from the Chelex-100 extraction was incubated at 100°C for 10 minutes and then immediately cooled on ice for 10 minutes. BrdU immunoprecipitation was conducted by diluting the DNA ten-fold with BrdU IP buffer (PBS, 0.0625% Triton X-100 (v/v), 6.7 μg/ml Escherichia coli tRNA, 0.17 μg/ml BrdU antibody (555627, BD Bioscience)) and rotating for 2 hours at 4°C. Protein G Sepharose beads were added and incubated for another hour at 4°C. After extensive washing, the DNA was extracted with 100 μl of 1x TE buffer containing 1% SDS at 65°C for 15 minutes and then eluted again with 50 μl of 1x TE buffer containing 1% SDS. The collected supernatants were subsequently purified using the MinElute PCR Purification Kit (Qiagen, 28004). Quantitative PCR was performed to analyze Input, BrdU-IP, ChIP, or eSPAN DNA using primers for the early replication origin ARS607 and the distant site ARS607+14kb.
Single-stranded DNA sequencing libraries were prepared using the Accel-NGS 1S Plus DNA Library Kit (10096, Swift Biosciences).

treatment_protocol: Arrested cells were collected by centrifugation, washed twice with cold H2O, and then released into fresh medium (YPD) at 25°C with 400 μg/ml BrdU (B5002, Sigma).

value: whole cell

tag: strain

tag: chip antibody

value: anti-H3K56ac (Zhang Lab)

value: mcm2-3A mutant and Hst3-Hst4 KO

value: MNase


title: mcm23AhstD_H3K56ac_ChIP_rep2


title: mcm23AhstD_H3K4me3_eSPAN_rep1

value: anti-H3K4me3 (ab8580, Abcam)


title: PRO_dTAG-3h_OE-TET-PNUTS-W401A-in-PNUTS-DLD1-rtTA

description: PNUTS-W401A overexpressed and treated with dTAG13 for 3h


title: ChIP_Input_DMSO-1h_PNUTS-dTAG_DLD-1_TAF3-NELF

description: treated with DMSO for 1h


title: PRO_dTAG-3h_vector-OE_PNUTS-dTAG_DLD-1_SPT5

value: Vector overexpressed and treated with dTAG13 for 3 hours


title: Macrophages, BAL, Sig F WT Naïve, mouse #3, run 2

description: Sample 3 (X12_476_WT_Naive) Run 2

value: Macrophages from BAL


title: Macrophages, BAL, Sig F WT Naïve, mouse #3, run 1

description: Sample 3 (X12_476_WT_Naive) Run 1

value: Male


title: PRO_dTAG-3h_OE-TET-PNUTS-WT-in-PNUTS-DLD1-rtTA

description: PNUTS-WT overexpressed and treated with dTAG13 for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Male; DP11

value: Liver

value: male

value: Hepatocellular carcinoma (HCC)


title: mcm23AhstD_H3K56ac_ChIP_rep1


title: mcm23AhstD_H3K4me3_ChIP_rep1


title: PRO_DMSO-3h_OE-TET-PNUTS-W401A-in-PNUTS-DLD1-rtTA

description: PNUTS-W01A overexpressed and treated with DMSO for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Male; DP10


title: PRO_DMSO-3h_OE-TET-PNUTS-WT-in-PNUTS-DLD1-rtTA

description: PNUTS-WT overexpressed and treated with DMSO for 3h


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Male; DP12


title: Macrophages, BAL, Sig F WT Naïve, mouse #2, run 1

description: Sample 2 (X11_474_WT_Naive) Run 1

value: Wild Type


title: mcm23A_H3K56ac_eSPAN_rep3

value: mcm2-3A mutant


title: mcm23A_H3K4me3_ChIP_rep3


title: Macrophages, BAL, Sig F WT Naïve, mouse #1, run 1

description: Sample 1 (X10_445_WT_Naive) Run 1

value: Saline Control


title: mcm23A_H3K4me3_eSPAN_rep3


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Male; DP8


title: mcm23A_H3K56ac_ChIP_rep3


title: mcm23AhstD_H3K56ac_eSPAN_rep1


title: PRO_DMSO-3h_INTS8-PNUTS-dTAG_DLD-1_Rep2_noUMI

description: treated with DMSO for 3h

value: treated with DMSO for 3h


title: PRO_dTAG-3h_Plvx-vector-in-PNUTS-DLD1-rtTA

value: colorectal adenocarcinoma cell line


title: Macrophages, BAL, Sig F WT Naïve, mouse #1, run 2

description: Sample 1 (X10_445_WT_Naive) Run 2

value: Day 0


title: hstD_H3K56ac_ChIP

value: whole cell

value: Hst3 KO and Hst4 KO


title: hstD_H3K56ac_eSPAN

value: anti-H3K56ac (Zhang Lab)


title: Upd_tumor_magnifying

first: Amelie

last: Raz

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

data_processing:
Cell ranger mapping with default parameters
Assembly: DM6
Supplementary files format and content: Gene expression matrices, split into features, barcodes, and matrix

organism: Drosophila melanogaster

source_name: testis

extract_protocol:
Testes were dissected out and dissociated with trypsin and collagenase
3' 10X single-cell sequencing

value: testis

value: germline stem cells

value: Upd overexpression, low rDNA copy number


title: PRO_dTAG-3h_INTS8-PNUTS-dTAG_DLD-1_Rep2_noUMI

description: treated with dTAG13 for 3h

value: treated with dTAG13 for 3h


title: hstD_H3K4me3_eSPAN

value: anti-H3K4me3 (ab8580, Abcam)

value: MNase


title: hstD_H3K4me3_ChIP


title: Upd_tumor_control

value: nos>upd

value: Upd overexpression


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Male; DP6

value: Liver

value: male

value: Hepatocellular carcinoma (HCC)


title: PRO_dTAG-3h_PNUTS-dTAG_DLD1_Rep2_noUMI

description: treated with dTAG13 for 3h

value: PNUTS-dTAG


title: PRO_DMSO-3h_INTS8-PNUTS-dTAG_DLD-1_Rep1_noUMI

description: treated with DMSO for 3h

value: colorectal adenocarcinoma cell line

value: treated with DMSO for 3h


title: 72-SP-G2-1

city: Bei Jing

first: Hsiang-Ying

last: Lee

state: Bei Jing

address: Yiheyuan Road

institute: Peking University

data_processing:
The raw data of RNA-seq was first checked quality using FastQC.
Hisat2 was used to align the paired-end reads to hg19 version of human reference genome and estimate the reads counts with HTSeq.
Samtools was used to covert files format and generate index files.
Assembly: hg19
Supplementary files format and content: text

source_name: cord blood

growth_protocol: The erythroid culture medium is based on IMDM, and further supplemented with 10% FBS (Gibco, 10099141), 300 μg/mL human holo-transferrin (Sigma, T0665), 5% human AB serum (Wokavi Biotech, Beijing), 10 ng/mL heparin (Sigma, H3149), 10 μg/mL insulin (Sigma, I9278), 2 mM L-glutamine (Gibco, 25030081), 3 IU erythropoietin (Amgen, 55513-144-10), 50 ng/mL SCF (StemCell, 78062), and 10 ng/mL IL3 (StemCell, 78042). Medium and compounds were changed after centrifugation every 2–3 days.

extract_protocol:
Approximately 1 × 106 cells were used for RNA extraction. Cells were washed once with 1–2 mL pre-chilled PBS, resuspended in 1 mL TRIzol™, and incubated for 5 min at room temperature. Subsequently, 250 µL chloroform was added to the cell suspension, shaken vigorously for 15 s, and incubated for 5 min at room temperature. The cell suspension was centrifuged at 12,000 rpm for 15 min at 4°C, the aqueous phase was transferred to a clean 1.5-mL EP tube, 550 µL isopropanol was added and mixed gently, and the solution was incubated at room temperature for 5 min. The solution was centrifuged again at 4°C for 10 min at 12,000 rpm, the supernatant was discarded, and the RNA precipitate was resuspended in 1 mL pre-chilled 75% ethanol. The solution was centrifuged again at 7,500 rpm for 5 min, the supernatant was discarded, and the RNA precipitate was air-dried and resuspended in approximately 15-25 µL TE buffer or RNA-free water. The absorbance was measured at 260 nm and 280 nm to confirm that the 260/280 ratio was greater than 1.8 and the concentration was higher than 50 ng/µL.
Total RNA quality was assessed using Agilent 2100 bioanalyzer and then 1 μg of total RNA was quantified using the Qubit High-sensitivity kit (Life Technologies, Q32852), and the RNA-seq library was constructed by NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L).  There were two biological replicates per treatment were sequenced in a HiSeq X-Ten (Illumina, PE150) by Novogene Co. (Beijing)

treatment_protocol: We sorted human CD71+ CD235a- (single positive, SP) erythroblasts (erythroid progenitor cells) in the erythropoiesis culture system on day 9(starting with human cord blood derived CD34+ cells). Then culturing the sorted SP erythroblasts for 72h with DMSO(Ctrl) or 2 μM GDC-0879(G2), and each group has two biological replicates. Harvested the cells on day 12 with TRIzol™ and extracted the RNA.

value: cord blood

value: erythroblast

value: 2 μM GDC-0879 in DMSO(0.1% v/v)


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Male; DP9


title: PRO_DMSO-3h_Plvx-vector-in-PNUTS-DLD1-rtTA

value: Vector overexpressed and treated with DMSO for 3 hours


title: Bcatex3 HET, R26myc HOM; AAV-Cre low dose; liver; Male; DP7


title: WT_H3K4me3_eSPAN_rep2

value: whole cell

value: WT


title: WT_H3K4me3_ChIP_rep2


title: 72-SP-Ctrl-2


title: CD25neg, D7, Aged, 2

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

department: Department of Medicine I

country: Austria

institute: Medical University of Vienna

description: BSF_1396_H2GGMDRX3_1#S_39_19_S132881.bam

data_processing:
Convert BAM to FASTQ with picard SamToFastq (v2.25.5)
Pre-process with trimgalore (v0.6.6) --fastqc - length 15 and polyA --length 15 --aadapter A{20} -stringency 20 -e 0
Alignment to mm10 (GRCm39) with STAR (v2.7.9a) outFilterMismatchNoverLmax=0.1
Count matrix with Rsubread (v2.8.2) featureCounts countMultiMappingReads=FALSE GTF.featureType="gene"
Normalization with edgeR (3.36.0 calcNormFactors method="TMM" and cpm with normalized.lib.size=TRUE and log=FALSE
Assembly: mm10
Supplementary files format and content: tab-delimted text file includes raw counts
Supplementary files format and content: tab-delimted text file includes TMM normalized library size counts per million

extract_protocol:
RNA was isolated using the RNeasy Micro kit (Qiagen). Post isolation, RNA was precipitated with ice cold absolute ethanol, 3 M Sodium Acetate (NaOAc pH 5.2; ThermoFischer) and Linear Polyacrlamide (LPA; Sigma Aldrich) overnight and resuspended in 10 µl of 10 mM Tris buffer (pH 8.0; Invitrogen). RNA concentration was measured by fluorometric (Qubit) analysis
For Quant-seq, libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen) in combination with the PCR Add-on Kit for Illumina (Lexogen) and the UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen),

treatment_protocol: Mice were treated intratracheally with bleomycin (1U/Kg) . Cells (30,000-80,000) were sorted from the lungs into cold PBS 2% BSA, and the pellet resuspended in RLT Buffer (Qiagen).

value: Lung

value: Lung fibrosis


title: PRO_dTAG-3h_PNUTS-dTAG_DLD1_Rep1

description: treated with dTAG13 for 3h

data_processing:
The paired PRO-seq reads were subjected to trimming using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a read length threshold of >15 bp.
After removal of molecular barcode (UMI) with fastp v0.21.0,100 ribosomal RNA reads were discarded using Bowtie v2.3.5.1 with ‘‘--un-conc-gz’’.
Then the remaining reads were aligned to the hg19 or mm10 genome using Bowtie v2.3.5.1 with ‘‘--local --sensitive-local’’.
The mapped data were next deduplicated with UMI-tools to remove PCR duplicates based on the UMI sequences.
The normalization factor was generated following the approach used in ChIP-Rx, and strand-specific coverage tracks were created using deeptools v3.5.0.
Assembly: hg19
Supplementary files format and content: bigWig files
Library strategy: PRO-Seq

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.  Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

value: treated with dTAG13 for 3h


title: PRO_DMSO-3h_PNUTS-dTAG_DLD1_Rep2_noUMI

description: treated with DMSO for 3h


title: PRO_DMSO-3h_PNUTS-dTAG_DLD1_Rep1

description: treated with DMSO for 3h


title: 72-SP-Ctrl-1


title: mcm23A_BrdU_rep2

value: anti-BrdU (555627, BD Bioscience)

value: mcm2-3A mutant

value: MNase


title: ALIEX, replicate 2, scRNAseq

city: Seongnam-si

first: Young-Jae

last: Cho

address: 82, Gumi-ro 173 Beon-gil

country: South Korea

institute: Seoul National University Bundang Hospital

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
the cell suspension was obtained through the sequence steps corresponding to the cell preparation guide (CG00053 Rev C, 10X Genomics) and adjusted to up to 5,000 target cells with viability > 95%
By Chromium Next GEM Single Cell 3-Gen Expression v3.1 Dual Index (CG00315 Rev D, 10X Genomics) and Chromium Single Cell 3’ Reagent Kit (PN1000268, 10X Ge-nomics), we generated GEM from those cell suspensions. Subsequently, with continu-ous procedures, including cDNA amplification and clean-up, we produced the scRNA-seq libraries.

value: lung


title: mcm23A_Input_rep3


title: CD25neg, D7, Young, 4

description: BSF_1396_H2GGMDRX3_1#S_43_23_S132885.bam


title: PRO_dTAG-3h_INTS8-PNUTS-dTAG_DLD-1_Rep1_noUMI

description: treated with dTAG13 for 3h


title: CD25neg, D7, Aged, 1

description: BSF_1396_H2GGMDRX3_1#S_37_17_S132879.bam


title: EX, replicate 2, scRNAseq


title: SupT1 infected, DMS-Seq, 24hpi, ethanol, rep1

city: Würzburg

first: Neva

last: Caliskan

address: Josef-Schneider-Str. 2/D15

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description:
Library name: DMS_control_rep1
DMS_control_rep1

data_processing:
DMS-Seq: Reads were trimmed using cutadapt v 1.18 and aligned to the reference sequence using bowtie2. Further analysis was carried out using the rf-count and rf-norm modules of RNA Framework package v2.7.2.
Nanopore: Acquired Nanopore data was base called in “sup” mode with Guppy version 6.5.7 and filtered for minimal qscore of 10. Isoforms were identified with Isoquant version 3.3.0 using a GTF file containing all previously reported isoforms (HIVNL43_all_iso.gtf). Only uniquely identified isoforms were counted. To identify those isoforms that may express the novel peptides, the nucleotide sequence of all reported isoforms was searched for the iORFs or/and first AUG and in silico translated using Biopython 1.79 in a custom python script.
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: DMS-Seq: The mutationMap files are in RC (RNA Count) format according to the RNA framework standard (https://rnaframework-docs.readthedocs.io/en/latest/rf-count/).
Supplementary files format and content: Nanopore: The enclosed excel file contains a list of all potential HIV transcripts isoforms with Nanopore read-counts supporting each isoform. Furthermore, information on the two identified iORFs are indicated for each isoform. The enclosed fasta file, bed file and gtf file were used for the transcript isoform deconvolution.

molecule: cytoplasmic RNA

organism:
Homo sapiens
Human immunodeficiency virus 1

extract_protocol:
Nanopore: To analyze the HIV transcriptome in infected SupT1 cells at 8, 16 and 24 hpi 30 μg of Trizol extracted RNA was treated with 3 μL of Turbo DNase in 150 μL total volume for 30 min at 37 °C. RNA was purified with Macherey-Nagel PCR Clean-up kit using NTC buffer according to manufacturer’s instructions.
DMS-Seq: For in vivo DMS modification of HIV-1 gRNA, 40 mL of SupT1 cells were infected with VSV pseudotyped HIV-1 (ΔEnv). 24 h post infection, 5 mL of cells were probed with 85 mM of dimethyl sulfate (DMS) for 6 min at 37°C, placed immediately on ice and the reaction was quenched by addition of 100 mM of β-mercaptoethanol. Cells were pelleted by centrifugation for 5 min at 400 g, 4°C and washed with PBS. The cell pellet was directly resuspended in 1 mL of TRI reagent (Sigma-Aldrich) and total RNA was extracted according to the manufacturer’s instructions. Ten μg of total cellular RNA were treated with 4 U of TURBO DNase (ThermoFisher Scientific) for 30 min at 37°C. The RNA was purified using NucleoSpin Gel and PCR Clean- Up (Macherey-Nagel, NTC buffer), according to the manufacturer´s instructions.
Nanopore: 1 ug of RNA was reverse transcribed with SuperScript IV (Invitrogen) using primer GTACAGGCAAAAAGCAGCTGCT according to manufacturer’s instructions in a 10 μL reaction. The cDNA was purified with Macharey-Nagel PCR Clean-up kit using NTC buffer and eluted in 20 μL H2O. RNA was digested in a 10 μL reaction containing 3 μL cDNA product with 0.5 μL RNase A (NEB) and 0.5 μL RNase T1 (NEB) and incubation at 37 °C for 30 min, followed by column purification as described above. Next, PCR amplification of 20 μL of the RNase-digested, purified cDNA in a 100 μL reaction with Primestar GXL (Takara) using primers GGTCTCTCTGGTTAGACCAGATCTGAG and GTACAGGCAAAAAGCAGCTGCT was performed with 12 cycles of denaturation at 98 °C for 10 sec, annealing at 55 °C for 15 sec and extension at 68 °C for 2 min. PCR products were purified with a 1:1 ratio of Mag-Bind TotalPure NGS beads (Omega Bio-Tek) according to the manufacturer’s recommendations and eluted in 14 μL H2O. Next, 80 ng PCR product in 5 μ was end repaired by addition of 0.7 μL NEBNext End Repair buffer (NEB) and 0.3 μL NEBNext End Repair Enzyme Mix (NEB), mixed thoroughly by pipetting and incubated for 5 min at 25 °C followed by 5 min at 65 °C. Nanopore native ligation barcoding barcodes (ONT SQK-NBD114.96) were ligated by transfer of 3.5 μL of end-repaired product into a new well, followed by addition of 1.5 μL of barcode and 5 μL of Blunt/TA ligation master mix (NEB). After incubation at 25 °C for 20 min, 1 μL of EDTA (SQK802 NBD114.96) was added, samples were pooled and purified with 0.4 volumes of Ampure XP beads (SQK-NBD114.96). Barcoded DNA was eluted in 31 μL of H2O. To ligate the motor protein 30 μL of the barcoded DNA was mixed with 10 μ of 5x Quick Ligation Buffer (NEB), 5 μL of NA and 5 μL of high concentration T4 DNA ligase (NEB) was added. After incubation for 20 min at 25 °C, 0.4 volumes of Ampure XP beads (SQK-NBD114.96) were added, beads were washed twice with 125 μL Short Fragment Buffer (SFB, SQK-NBD114.96) and eluted in 14 μL of Elution Buffer (EB, SQK-NBD114.96). DNA concentration was quantified with AccuClear Ultra High Sensitivity dsDNA Quantitation Solution (Biotium) and 10 fmol was prepared for sequencing on a R10.4.1 Flongle flow cell (FLO-FLG114) by addition of 15 μL sequencing buffer (SB) and 10 μL loading beads (LIB). Data was acquired on a MinION Mk1b with MinKNOW version 23.04.3.
DMS-Seq: Reverse transcription was performed on 1 μg of purified RNA mixed with 0.5 mM dNTPs, 0.25 μM of RT primer (5´- CTT GTC TAT CGG CTC CTG CTT C - 3´) in a final volume of 12 μL. The RNA was denatured at 65°C for 5 min and placed on ice. The reverse transcription reaction was performed by addition of 1 mM of MnCl2, 1x MarathonRT buffer (Tris-HCl 50 mM, pH 8.3; KCl 200 mM; Glycerol 20%), 0.2 μL RNasin (Promega) and 40 U of MarathonRT 93 in 25 μL final volume. The reactions were incubated for 8 h at 42°C. Newly synthesized cDNAs were diluted 8 times and PCR amplified: 10 μL of diluted cDNA were mixed with 0.2 mM dNTPs, 0.25 μM of both Forward (5´ - TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CTA CCA TAA TGA TAC AGA AAG GC - 3´) and Reverse (5´ - GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGT CTC TTC CCC AAA CCT GAA G - 3´) primers, 10 μL of Q5 Buffer 5x, and 1 U Q5 polymerase (NEB) in 50 μL final volume. The initial denaturation was performed at 98 °C for 2 min, followed by 25 cycles of 10 sec at 98°C, 20 sec at 55°C and 30 sec 721 at 72°C before a final extension at 72°C for 5 min. Amplicon quality was controlled on an agarose gel 1%. DNA amplicons were purified by solid-phase reversible immobilization (SPRI) using Mag-Bind TotalPure NGS beads (Omega Biotek) following the manufacturer´s instruction, with a DNA to beads ratio of 1:0.8. Nextera indexes were added by PCR, 80 ng of purified DNA were mixed with 1x Q5 Buffer, 0.2 mM dNTPs, 0.02 U of Q5 polymerase and 2.5 μL of Nextera Index (Illumina) in a 14 μL reaction. The initial denaturation was performed at 98 °C for 2 min, followed by 5 cycles of 30 sec at 98°C, 30 sec at 62°C and 1 min at 72°C before a final extension at 72°C for 5 min. Quality of libraries was assessed by agarose gel electrophoresis. Equal amounts of each sample were pooled together followed by a final SPRI purification (DNA to beads ratio of 1:0.8). Paired-end PE150 sequencing was carried out on an Illumina Novaseq instrument (Novogene).

value: T-cell

value: Ethanol


title: 72-SP-G2-2


title: SupT1 infected, DMS-Seq, 24hpi, ethanol, rep2

description:
Library name: DMS_control_rep2
DMS_control_rep2


title: mcm23A_Input_rep2


title: SupT1 infected, DMS-Seq, 24hpi, DMS, rep2

description:
Library name: DMS_rep2
DMS_rep2

value: Dimethyl sulfate


title: CD25neg, D7, Young, 2

description: BSF_1396_H2GGMDRX3_1#S_41_21_S132883.bam


title: mcm23A_Input_rep1


title: O1, replicate 2, scRNAseq


title: O2, replicate 2, scRNAseq


title: mcm23A_BrdU_rep3


title: SupT1 infected, DMS-Seq, 24hpi, DMS, rep1

description:
Library name: DMS_rep1
DMS_rep1


title: mcm23AhstD_BrdU_rep2

value: mcm2-3A mutant and Hst3-Hst4 KO


title: CD25neg, D7, Young, 1

description: BSF_1396_H2GGMDRX3_1#S_40_20_S132884.bam


title: ALIEX, replicate 1, scRNAseq


title: CD25pos, D7, Aged, 3

description: BSF_1396_H2GGMDRX3_1#S_55_33_S132801.bam


title: mcm23AhstD_BrdU_rep1


title: Sorted EGFP+ population, replicate 4

city: Palo Also

first: Joanna

last: Wysocka

state: CA

address: 265 Campus Drive, rm G3065

department: Chemical and Systems Biology

institute: Standford University

description: count, trimmed sequence

data_processing:
*library strategy: CRISPR screen
We counted the occurrence of each unique guide sequence in the fastq files using the following command, "seqret fastq-sanger::$FILES[:20] fastq-sanger::stdout | awk 'NR%4==2' | sort | uniq -c > ${FILES}_count.txt"
Assembly: mm9
Supplementary files format and content: tab-delimited text files contains sequence counts and sequence for each population.

source_name: R1 mESCS

growth_protocol: mESCs were grown in serum-free 2i (GSK3 and MEK1 inhibitors) and LIF conditions on PLO/Laminin coated plates.

extract_protocol:
Genomic DNA was extracted from sorted and unsorted populations using Qiagen Puregene kit according to manuacture's protocol.
Total genomic DNA was amplified by PCR with Huclease II polymerase using guide-specific primers, oMCB_1562 5'-aggcttggatttctataacttcgtatagcatacattatac-3' and oMCB_1563 5'-ACATGCATGGCGGTAATACGGTTATC-3'. Like samples were pooled and used as template for a second PCR in which Illumina adaptors (5'-caagcagaagacggcatacgagatgcacaaaaggaaactcaccct-3') and barcodes were added to the samples.

treatment_protocol: Cells were infected at a low MOI with sgRNA tiling library on day 0. On days 1-4, cells were given fresh media supplemented with 2ug/ML doxycycline and 1ug/ml puromycin. On day 5, cells were given fresh media containing doxycycline several hours before sorting.

value: R1 mESCS

value: embryonic stem cells

value: doxcycline, 4 days

tag: cell population

value: Sorted EGFP+ population


title: EX, replicate 1, scRNAseq


title: hstD_BrdU_rep2

value: whole cell

value: Hst3 KO and Hst4 KO


title: CD25pos, D7, Aged, 1

description: BSF_1396_H2GGMDRX3_1#S_44_24_S132888.bam

value: Lung


title: Unsorted population, replicate 3

description: count, trimmed sequence

value: Unsorted population


title: O2, replicate 1, scRNAseq


title: mcm23A_BrdU_rep1


title: hstD_BrdU_rep1


title: O1, replicate 1, scRNAseq


title: CD25pos, D7, Young, 3

description: BSF_1396_H2GGMDRX3_1#S_60_38_S132808.bam

value: Lung fibrosis


title: Sorted EGFP+ population, replicate 3

description: count, trimmed sequence


title: CD25neg, D7, Young, 3

description: BSF_1396_H2GGMDRX3_1#S_42_22_S132886.bam


title: mcm23AhstD_Input_rep1


title: Unsorted population, replicate 4

description: count, trimmed sequence


title: CD25pos, D7, Young, 2

description: BSF_1396_H2GGMDRX3_1#S_59_37_S132805.bam


title: mcm23AhstD_Input_rep2


title: CD25pos, D7, Young, 1

description: BSF_1396_H2GGMDRX3_1#S_56_34_S132804.bam


title: hstD_Input_rep2


title: Unsorted population, replicate 2

description: count, trimmed sequence


title: Unsorted population, replicate 1

description: count, trimmed sequence


title: D8_ATAC

city: Madison

first: Igor

middle: I.

last: Slukvin

address: 1220 Capitol Court

institute: University of Wisconsin

description:
D8.filtered_feature_bc_matrix.h5
D8.per_barcode_metrics.csv

library_source: genomic single cell

data_processing:
Cell Ranger ARC (version 2.0.1) and a human genome reference (hg38 version 2020-A) downloaded from 10x Genomics were used to process single cell multiome RNA-seq and ATAC-seq FASTQ files.
Assembly: hg38
Supplementary files format and content: Cell Ranger ARC output files:
Supplementary files format and content: filtered_feature_bc_matrix.h5 (linked to the corresponding GEX sample records): HDF5 format, filtered feature, barcode, and count matrix
Supplementary files format and content: per_barcode_metrics.csv  (linked to the corresponding GEX sample records): CSV format, metrics by barcode
Supplementary files format and content: gex_molecule_info.h5: HDF5 format, gene expression molecule information
Supplementary files format and content: atac_fragments.tsv.gz: gzipped TSV format, ATAC-seq fragments

source_name: H9 hPSC

extract_protocol:
Nuclei extraction kit according manufacturer’s instructions (10X Genomics)
Library construction Kit 10XGenomics

value: H9 hPSC

value: Day 8 CD31+ cells.


title: D4_ATAC

description:
D4.filtered_feature_bc_matrix.h5
D4.per_barcode_metrics.csv

value: Day 4 KDR+ cells


title: D5_ATAC

description:
D5.filtered_feature_bc_matrix.h5
D5.per_barcode_metrics.csv

value: Day 5 CD31+ cells


title: AM, D14, Aged, 3

description: BSF_1218_HGM2WDRX2_2#S_66_25_S121507.bam

value: AM


title: Sorted EGFP+ population, replicate 1

description: count, trimmed sequence


title: D8_GEX


title: hstD_Input_rep1

value: MNase


title: Sorted EGFP+ population, replicate 2

description: count, trimmed sequence


title: AM, D14, Aged, 2

description: BSF_1218_HGM2WDRX2_2#S_62_19_S121503.bam


title: AM, D14, Aged, 1


title: mcm23AH3K56R_BrdU_S30_rep2

value: anti-BrdU (555627, BD Bioscience)

value: mcm2-3A and H3K56R mutant


title: D4_GEX


title: NK3_S18

city: Marseille

first: Anne-Marie

last: François-Bellan

address: 27 Bd Jean Moulin

department: Facute de Medecine

country: France

institute: CNRS-AMU

description: Paired-end strand-specific RNA-seq

data_processing:
HISAT2
FeatureCounts
Assembly: UCSC mm10
Supplementary files format and content: csv, counts

source_name: Hypothalamus

extract_protocol:
Nucleospin RNA Macherey-Nagel
RNA library preparation with rRNA depletion.

value: Hypothalamus

value: day

value: Hypothalamus cells

value: magel2/necdin knokdown


title: CD25pos, D7, Aged, 2

description: BSF_1396_H2GGMDRX3_1#S_48_26_S132892.bam


title: CD34plus_ATAC

description:
CD34plus.filtered_feature_bc_matrix.h5
CD34plus.per_barcode_metrics.csv

value: cord blood


title: WT_BrdU

value: whole cell

value: WT


title: AM, D14, Young, 2

value: Lung


title: CD34plus_GEX


title: NK5_S20

description: Paired-end strand-specific RNA-seq

value: night


title: AM, D14, Young, 1

value: Lung fibrosis


title: WT_Input


title: NK2_S17

description: Paired-end strand-specific RNA-seq


title: NK4_S19

description: Paired-end strand-specific RNA-seq


title: SK5_S15

description: Paired-end strand-specific RNA-seq


title: TT-seq_dTAG-3h_DRB-3h_release-20min_PNUTS-DLD1

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

data_processing:
The TT-seq raw reads were trimmed and then aligned to the hg19 or mm10 genome using STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate”.
Duplicate and low-quality reads were removed, retaining only properly paired reads for downstream analyses.
The spike-in mm10 reads were quantified to generate the normalization factor. Strand-specific normalized bigwigs were generated with deepTools v3.5.0.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: TT-seq

extract_protocol:
RNA was isolated with TRIzol. 100 μg RNA was fragmentated and  biotinylated. The biotinylated RNA  was immunoprecipitated and purified.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: For TT-seq, cells were treated with dTAG 13 for 3,12 h,  the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution. Cells were labeled by 4SU for 15min.  For DRB/TT-seq, cells were treated with dTAG 13 and DRB for 3h,  the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution. Cells were labeled by 4SU for 10min.

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG

value: treated with dTAG13&DRB for 3h


title: mcm23AH3K56R_H3K4me3_ChIP

value: anti-H3K4me3 (ab8580, Abcam)


title: D5_GEX

value: H9 hPSC

value: Day 5 CD31+ cells


title: AM, D14, Young, 3

description: BSF_1396_H2GGMDRX3_1#S_30_10_S132874.bam

value: AM


title: AM, D7, Aged, 3


title: DK4_S14

description: Paired-end strand-specific RNA-seq

value: Hypothalamus


title: mcm23AH3K56R_Input_S30_rep1

value: mcm2-3A and H3K56R mutant

value: MNase


title: mcm23AH3K56R_Input_S30_rep2


title: mcm23AH3K56R_BrdU_S30_rep1

value: anti-BrdU (555627, BD Bioscience)


title: NK1_S16

description: Paired-end strand-specific RNA-seq

value: day

value: Hypothalamus cells

value: magel2/necdin knokdown


title: TT-seq_dTAG-3h_DRB-3h_release-30min_PNUTS-DLD1


title: mcm23AH3K56R_H3K4me3_eSPAN

value: whole cell


title: DK3_S13

description: Paired-end strand-specific RNA-seq


title: AM, D7, Aged, 4

value: Lung


title: AM, D7, Aged, 2

value: Lung fibrosis


title: mcm23Aisw1D_H3K4me3_eSPAN

value: mcm2-3A mutant and Isw1 KO


title: mcm23Achd1D_H3K4me3_eSPAN

value: mcm2-3A mutant and Chd1 KO


title: TT-seq_DMSO-3h_DRB-3h_release-30min_PNUTS-DLD1

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG

value: treated with DMSO&DRB for 3h


title: TT-seq_dTAG-3h_DRB-3h_release-10min_PNUTS-DLD1

value: treated with dTAG13&DRB for 3h


title: DK2_S12

description: Paired-end strand-specific RNA-seq

value: night


title: TT-seq_DMSO-3h_DRB-3h_release-10min_PNUTS-DLD1


title: AM, D7, Young, 3

description: BSF_1396_H2GGMDRX3_1#S_36_16_S132880.bam

value: AM


title: AM, D7, Young, 2

description: BSF_1396_H2GGMDRX3_1#S_32_12_S132876.bam


title: NW5_S10

description: Paired-end strand-specific RNA-seq

value: Hypothalamus

value: WT