title: L03_3, KO_Tdp1, KO_Tdp1_G6, TPC_OL9, biol rep 4

city: Novosibirsk

first: Maxim

last: Ri

address: Lavrenteva st. 6

country: Russia

institute: LLC AcademGene

data_processing:
Quality control of raw reads were performed using FastQC  v0.11.9
Sequence reads were aligned to hg38 human genome using STAR v 2.7.8.
Quantification of reads was also performed using STAR, option –quantMode GeneCounts
Quality control of aligment were performed using module infer_experiment.py of RSeQC v4.0.0, module CollectRnaSeqMetrics from Picard v2.26.6
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: Cells were grown in DMEM/F12 medium supplemented with 1×GlutaMAX, 100 c.u./ml penicillin and 100 mg/ml streptomycin, in the presence of 10% fetal bovine serum in a 5% CO2 atmosphere.

extract_protocol:
RNA was isolated with the Trizol according to the manufacturer instructions.
RNA were enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module, libraries were prepared with MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd., China)

treatment_protocol: Cells were treated for 5-5,5 hours with following agents: 1) No treatment, 2) 0.1% DMSO, 3) 100 nM Tpc + 0.1% DMSO, 4) 5 μM OL9-119 solved in 0.1% DMSO, 5) 100 nM Tpc + 5 μM OL9-119.

value: human embryonic kidney cells

tag: clone


title: L03_48, KO_Tdp1, KO_Tdp1_F7, TPC_OL9, biol rep 4

status: Public on Nov 20 2023

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: L02_37, KO_Tdp1, KO_Tdp1_G6, TPC_OL9, biol rep 3


title: L01_127, KO_Tdp1, KO_Tdp1_G6, TPC_OL9, biol rep 1


title: Cell line Exon 25 batch2 Cis Pool2 Replicate 2

city: Frederick

first: Shyam

last: Sharan

state: MD

address: Building 560, Room 32-33

country: USA

institute: Mouse Cancer Genetics Program

library_source: genomic

data_processing:
The paired end reads were aligned to the reference sequence using the Needleman-Wunsch alignment algorithm after the reads were demultiplexed using bcl2fastq (Illumina), generation of fastq files, and merging using FLASH.
The total number of aligned reads were quantified using CRISPResso2 http://crispresso.pinellolab.org/submission. Iindividual unique alignments were annotated with a custom-made variant caller modified from ANNOVAR (64) (release 2019-10-21) and the R/Bioconductor Biostrings package in R version 4.1.2 https://bioconductor.org/packages/Biostrings. Merged reads containing “N” bases were removed from the analysis.
Abundances of SNVs were quantified when the reads contained a single-nucleotide substitution. Read counts for each SNVs were then normalized to the total read coverage of the sequencing library after adding a pseudocount of 1 to all reads for all conditions. Individual variants with a read count of more than 1 in 1,000 reads in the M15 condition were used for further analysis. Dropout or enrichment scores were calculated by taking the ratio of frequency of SNV after HAT, cisplatin, or olaparib treatment over that in M15.
The scores were expressed in log2 scale, which we define as the functional scores of SNVs in HAT, cisplatin, and olaparib. The functional scores, averaged between independent replicates (2-4), were used to calculate the the probabilities of impact on function (PIF) for all the variants in the data set.
Assembly: GRCh38
Supplementary files format and content: xlsx: Excel files include PIF and function scores for all variants.
Library strategy: Amplicon sequencing

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Genomic DNA was extracted from the cell pellets using Zymo Genomic DNA Extraction kit
DNA libraries were prepared using TruSeq Nano DNA Library Prep kit

value: Embryonic stem cell

value: Cisplatin


title: Late exponential mavR, biological rep 1

type: RNA

city: Pittsford

first: Paul

last: M Dunman

state: NY

address: 695 W. Bloomfield Rd

institute: University of Rochester

description: Gene expression data from stationary phase 2308 cells containing mavR mutation

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on a B. abortus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

label: Biotin

molecule: total RNA

organism: Brucella abortus

source_name: Brucella abortus late exponential phase

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to late exponential phase in brucella broth at 37C with aeration

extract_protocol: Total bacterial RNA was isolated using Trizol according to the manufacturer's recommendations (Invitrogen)

treatment_protocol: Once reaching late exponential phase (measured by colony forming unit counts) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: sample

value: Whole cell

value: mavR

tag: growth phase

value: Late exponential


title: L03_43, KO_Tdp1, KO_Tdp1_F7, TPC_OL9, biol rep 3


title: Cell line Exon 25 batch2 Ola Pool2 Replicate 2

value: Olaparib


title: Late exponential 2308, biological rep 1

description: Gene expression data from late exponential phase wildtype 2308 cells

value: Wildtype


title: L02_3, KO_Tdp1, KO_Tdp1_F7, TPC_OL9, biol rep 2


title: Large preB cell, WT, rep1

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Alignment to the mouse mm10 assembly was conducted by STAR 5.02 (Dobin et al., 2013) on the DNAnexus platform
Normalization and differential expression by  DESeq2 were performed through a HOMER v4.10.4 implementation of the package in R.
Assembly: mm10

source_name: mouse large pre-B cell (CD19+CD43+BP1+)

growth_protocol: Sorted wild-type and IkE5Δ/Δ large pre-B cells were cultured on OP9 stroma in DMEM ( D-5671; Sigma) supplemented with 10% FBS (2442; Sigma), 50 μM 2-mercaptoethanol, 100 μg/ml penicillin, 100 μg/ml streptomycin, 1× Glutamax (35050-062; Gibco), 10 mM HEPES (156-30-80; Gibco) and 1× sodium pyruvate (11360-070; Gibco) in the presence of 5ng/ml of IL-7. Stroma adherent large pre-B cells from WT or IKDN cultures were detached with 0.2% trypsin (EDTA free) for 2 minutes at room temperature. Large pre-B cells were ~ 99% of the cells in suspension as determined by flow cytometry.

extract_protocol:
Total RNAs were prepared using the Direct-zol RNA Miniprep (Zymo Research) and 1mg of total RNA was used for the construction of sequencing libraries.
The TruSeq Stranded mRNA Library prep kit was used for construction of cDNA libraries for RNA-sequencing (Illumina). The cDNA libraries were ligated with indexed primers and amplified by PCR for 10 cycles, multiplexed and sequenced in house with an Illumina NextSeq550 system.

value: mouse large pre-B cell (CD19+CD43+BP1+)

value: Wild-type (IKE5 fl/fl, Cre-)


title: Late exponential mavR, biological rep 2


title: Cell line Exon 25 batch2 Cis Pool2 Replicate 1


title: L01_38, KO_Tdp1, KO_Tdp1_G6, TPC_OL9, biol rep 2


title: Cell line Exon 25 batch2 HAT Pool2 Replicate 2

value: HAT


title: Cell line Exon 11partc M15 Pool1 Replicate 1


title: Cell line Exon 25 batch2 HAT Pool2 Replicate 1


title: L01_28, KO_Tdp1, KO_Tdp1_F7, TPC_OL9, biol rep 1


title: L03_122, KO_Tdp1, KO_Tdp1_C6, TPC_OL9, biol rep 4


title: L02_101, KO_Tdp1, KO_Tdp1_C6, TPC_OL9, biol rep 3


title: Cell line Exon 25 batch2 M15 Pool2 Replicate 2


title: Cell line Exon 25 batch2 M15 Pool2 Replicate 1


title: L01_43, KO_Tdp1, KO_Tdp1_C6, TPC_OL9, biol rep 1


title: Cell line Exon 25 batch2 Ola Pool1 Replicate 2


title: Cell line Exon 25 batch2 Cis Pool1 Replicate 2


title: L01_35, KO_Tdp1, KO_Tdp1_G6, TPC, biol rep 1

value: TPC


title: Cell line Exon 25 batch2 HAT Pool1 Replicate 2


title: L03_15, KO_Tdp1, KO_Tdp1_F7, TPC, biol rep 4


title: L02_39, KO_Tdp1, KO_Tdp1_G6, TPC, biol rep 3


title: L01_14, KO_Tdp1, KO_Tdp1_G6, TPC, biol rep 2


title: Cell line Exon 25 batch2 Cis Pool1 Replicate 1


title: L03_14, KO_Tdp1, KO_Tdp1_G6, TPC, biol rep 4


title: Cell line Exon 25 batch2 M15 Pool1 Replicate 2


title: Cell line Exon 25 batch2 M15 Pool1 Replicate 1


title: Cell line Exon 14 batch2 Ola Pool2 Replicate 2


title: Cell line Exon 25 batch2 HAT Pool1 Replicate 1


title: L02_13, KO_Tdp1, KO_Tdp1_F7, TPC, biol rep 2


title: L03_125, KO_Tdp1, KO_Tdp1_C6, TPC, biol rep 4


title: L01_30, KO_Tdp1, KO_Tdp1_F7, TPC, biol rep 1


title: MOLM14_InVivo_plusDox_Rep3

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
*library strategy: shRNA dropout screen
To calculate read counts from shRNA experiments, 75bp single-end reads in fastq format were first processed to remove the first and last 25bp from each sequence, corresponding to the regions flanking the shRNA sequence that are common across all reads.
The shRNA sequences were then compared to the library of oligonucleotide sequences used in the experiment, allowing for only a single base mismatch.
Assembly: hg38
Supplementary files format and content: Tab-delimited files of shRNA sequence IDs, target gete ID, shRNA sequences used and counts

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 1% L-glutamine and 20% heat-inactivated FBS. For culture maintenance cells were split to 0.5x106 cells/ml every 3 days to not exceed 1-2 x 106 cells/ml. For the in vitro screen after sorting the media was also supplemented with 1% Penicillin/Streptomycin. HEK293T cells (DSMZ, ACC305) were used to produce lentivirus. These cells are cultured in HEPES-modified DMEM medium supplemented with 10% FBS, 4mM L-glutamine and 1mM sodium pyruvate. Cells were split using trypsin every 3 days to not exceed a confluency of 70%. All cells were cultured and treated in an incubator at 37C with 5% CO2.

extract_protocol:
PCR of genomic DNA was performed using ExTaq (Takara) using custom designed primers with Nextera i5 and i7 index sequences (supplementary table X) to amplify the mir30 insert containing the shRNA. Amplicons were electrophoresed on an agarose gel and DNA was purified using the QIAquick gel extraction kit (QIAGEN) according to manufacturers instructions and further purified by ampure (Beckman Coulter).
Samples were pooled and analysed on a Next Seq 2000 75 using a NextSeq 500/550 High output kit

treatment_protocol: MV4-11 and MOLM-14 cells were transduced following the protocol described in Martinez et al 5. As a summary, cells at 106 cells/ml were transduced with the pooled library shRNA lentivirus particles present in the supernatant using Polybrene at a final concentration of 8 µg/ml. Afterwards, the plate was centrifuged at 34C for 50 min at 900xg. After centrifugation, cells were incubated for 3 days. The transduction was performed at a low MOI (0.3 TU/cell) to produce a population of cells with one integration event per cell.  Following lentiviral transduction, cells successfully carrying the fluorescent Venus constitutive expressed were purified using fluorescence activated cell sorting (FACS) in an ARIA II. Most cells that remained after selection carried a single copy of the inducible shRNA. Cells were then used to perform the screening as described.

value: plus Dox


title: L02_103, KO_Tdp1, KO_Tdp1_C6, TPC, biol rep 3


title: Cell line Exon 14 batch2 Cis Pool2 Replicate 2


title: L02_98, KO_Tdp1, KO_Tdp1_C6, TPC, biol rep 2


title: Cell line Exon 14 batch2 Cis Pool2 Replicate 1


title: Cell line Exon 14 batch2 HAT Pool2 Replicate 2


title: L02_48, KO_Tdp1, KO_Tdp1_C6, TPC_OL9, biol rep 2


title: L01_45, KO_Tdp1, KO_Tdp1_C6, TPC, biol rep 1


title: Cell line Exon 14 batch2 HAT Pool2 Replicate 1


title: Cell line Exon 14 batch2 Ola Pool2 Replicate 1


title: Cell line Exon 25 batch2 Ola Pool1 Replicate 1


title: L03_4, KO_Tdp1, KO_Tdp1_G6, OL9, biol rep 4


title: L03_45, KO_Tdp1, KO_Tdp1_F7, TPC, biol rep 3


title: L01_128, KO_Tdp1, KO_Tdp1_G6, OL9, biol rep 1


title: L01_39, KO_Tdp1, KO_Tdp1_G6, OL9, biol rep 2


title: L02_4, KO_Tdp1, KO_Tdp1_F7, OL9, biol rep 2


title: L01_29, KO_Tdp1, KO_Tdp1_F7, OL9, biol rep 1


title: Cell line Exon 14 batch2 Ola Pool1 Replicate 1


title: Forebrain, Dyrk1a<+/->, E15.5  bio rep 1

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

country: France

institute: IGBMC/PHENOMIN-ICS

description: Biol rep 1

data_processing:
The alignment was performed on the mouse GRCm38 release 93 using HISAT2 87 with the options -p 8 –dta, -t –summary-file –no-unal, --no-hd. Samtools version 1.9 (http://www.htslib.org/) was used to generate the bam file and index and the counts were generated using HTSeq-Count 0.9.1 88. Using RseQC 89 we checked that the percentage of mapped reads distributed in each genomic feature followed an optimal distribution (exon, 5’UTR exon, 3’ UTR exon, Intron, Intergenic…). Then differential expression analysis was done using FCROS 90. Representation of protein-protein interaction network was obtained from mysregulated genes using Cytoscape 91.
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: mm10
Supplementary files format and content: Text file with Total_counts_not_normalized

source_name: Forebrain

extract_protocol: Then RNA was extracted using Trizol and Qiagen RNeasy Minikit following the manufacturer protocol, and sent for single-end bulk RNA-Seq sequencing. The preparation of the libraries was done by the GenomEast platform, using the TruSeq Stranded Total RNA Sample Preparation Guide PN 15031048. Total RNA-Seq libraries were generated from 150-300 ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. The molecule extracted from the biological material were polyA RNA. The sequencing was performed by the platform using Illumina Hiseq 4000.

tag: tissue

value: Forebrain


title: L03_123, KO_Tdp1, KO_Tdp1_C6, OL9, biol rep 4


title: Forebrain, Dyrk1a<+/->, E15.5  bio rep 3

description: Biol rep 3


title: Forebrain, Dyrk1a<+/->, E15.5  bio rep 2

description: Biol rep 2


title: Cell line Exon 14 batch2 M15 Pool2 Replicate 2


title: L03_13, KO_Tdp1, KO_Tdp1_F7, OL9, biol rep 4


title: Forebrain, wt, E15.5 bio rep 2

description: Biol rep 2

value: wt


title: L02_97, KO_Tdp1, KO_Tdp1_C6, OL9, biol rep 2


title: Cell line Exon 14 batch2 Cis Pool1 Replicate 2


title: L02_35, KO_Tdp1, KO_Tdp1_G6, no, biol rep 3

value: no


title: Cell line Exon 14 batch2 Ola Pool1 Replicate 2


title: L03_1, KO_Tdp1, KO_Tdp1_G6, no, biol rep 4


title: Cell line Exon 14 batch2 M15 Pool2 Replicate 1


title: L02_102, KO_Tdp1, KO_Tdp1_C6, OL9, biol rep 3


title: Cell line Exon 14 batch2 HAT Pool1 Replicate 2


title: Forebrain, wt, E15.5 bio rep 3

description: Biol rep 3


title: L01_44, KO_Tdp1, KO_Tdp1_C6, OL9, biol rep 1


title: L03_44, KO_Tdp1, KO_Tdp1_F7, OL9, biol rep 3


title: L01_124, KO_Tdp1, KO_Tdp1_G6, no, biol rep 1


title: Cell line Exon 14 batch2 Cis Pool1 Replicate 1


title: Forebrain, Dyrk1a<Dlx/+>, E15.5 rep 3

description: G8Dlx Mut3

data_processing:
The alignment was performed on the mouse GRCm38 release 93 using HISAT2 87 with the options -p 8 –dta, -t –summary-file –no-unal, --no-hd. Samtools version 1.9 (http://www.htslib.org/) was used to generate the bam file and index and the counts were generated using HTSeq-Count 0.9.1 88. Using RseQC 89 we checked that the percentage of mapped reads distributed in each genomic feature followed an optimal distribution (exon, 5’UTR exon, 3’ UTR exon, Intron, Intergenic…). Then differential expression analysis was done using FCROS 90. Representation of protein-protein interaction network was obtained from mysregulated genes using Cytosca
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: mm10
Supplementary files format and content: Text file with Total_counts_not_normalized


title: L01_36, KO_Tdp1, KO_Tdp1_G6, no, biol rep 2


title: Forebrain, Dyrk1a<Dlx/+>, E15.5 rep 2

description: G8Dlx Mut2


title: L03_46, KO_Tdp1, KO_Tdp1_F7, no, biol rep 4


title: Cell line Exon 14 batch2 HAT Pool1 Replicate 1


title: Forebrain, Dyrk1a<Dlx/+>, E15.5 rep 1

description: G8Dlx Mut1


title: Forebrain, wt, E15.5 rep 3

description: G8Dlx WT3


title: L01_25, KO_Tdp1, KO_Tdp1_F7, no, biol rep 1


title: L02_38, KO_Tdp1, KO_Tdp1_G6, OL9, biol rep 3


title: L03_41, KO_Tdp1, KO_Tdp1_F7, no, biol rep 3


title: L02_1, KO_Tdp1, KO_Tdp1_F7, no, biol rep 2


title: Cell line Exon 14 batch2 M15 Pool1 Replicate 2


title: L03_104, KO_Tdp1, KO_Tdp1_C6, no, biol rep 4


title: Forebrain, wt, E15.5 bio rep 1

description: Biol rep 1


title: L02_46, KO_Tdp1, KO_Tdp1_C6, no, biol rep 2


title: Cell line Exon 25 Ola Pool1 Replicate 2


title: Forebrain, wt, E15.5 rep 2

description: G8Dlx WT2


title: Forebrain, wt, E15.5 rep 1

description: G8Dlx WT1


title: L01_41, KO_Tdp1, KO_Tdp1_C6, no, biol rep 1


title: Mycoplasma bovis HB0801 MbovGdpP knock-out mutant,T6_290_3

city: Zhengzhou

first: Xifang

last: Zhu

state: Henan

address: No. 100, Science Avenue

country: China

institute: Zhengzhou University

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated. Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads. Then the clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the M. bovis HB0801 genome using Rockhooper2. Rockhooper2 was used to obtain the number of reads aligned to the gene in each sample and then to calculate RPKM. Differential expression analysis was performed using the DESeq (2012) R package
Assembly: NC_018077.1
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Mycoplasmopsis bovis

growth_protocol: M. bovis HB0801 was grown in pleuropneumonia-like organism (PPLO) medium with or without 100 μg/mL gentamicin

extract_protocol:
Total RNA was isolated from M. bovis pellets using TRIzol reagent
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions

treatment_protocol: M. bovis MbovGdpP konck-out mutant T6.290 and wild type strain HB0801 were grown to the stationary phase

tag: strain

value: MbovGdpP knock-out

value: Grown to the stationary phase


title: Cell line Exon 25 Ola Pool1 Replicate 1

value: Embryonic stem cell


title: L02_36, KO_Tdp1, KO_Tdp1_G6, DMSO, biol rep 3

value: human embryonic kidney cells

value: DMSO


title: L03_2, KO_Tdp1, KO_Tdp1_G6, DMSO, biol rep 4


title: Mycoplasma bovis HB0801 MbovGdpP knock-out mutant,T6_290_1


title: L01_37, KO_Tdp1, KO_Tdp1_G6, DMSO, biol rep 2


title: Cell line Exon 25 Cis Pool1 Replicate 1

value: Cisplatin


title: hippocampus21d,sham,rep1

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.5.0c.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital gene expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
Drop-seq samples were processed using Drop-seq Tools  were processed using cell ranger.
Assembly: mm10 (GRCm38)
Supplementary files format and content: tsv and matix files
Supplementary files format and content: Digital gene expression matrices (genes x cells) in sparse matrix format. Compressed, flat text files with tab delimiters. Requires the corresponding features (genes) and barcodes (cell names) files. Meta Data files include the cell type labels.

source_name: hippocampus

growth_protocol: Ten-week-old male C57BL/6J (B6) mice from Jackson Laboratory weighing between 20 and -25g were maintained under standard housing conditions (room temperature 22-24 °C) with 12 hours (h) light/dark cycle. Mice were randomly divided into either the sham or TBI group.

extract_protocol:
Briefly, the hippocampus and frontal cortex were dissected from the ipsilateral side of the brain, sliced into thin pieces, and transferred into 4 ml HABG medium containing Hibernate A, B27 supplement, and 0.5 mM Glutamax (Fisher Scientific, Hampton, NH, USA) then incubated in a water bath at 30 °C for 8 mins. Subsequently, the HABG media was removed and prewarmed papain solution (2 mg/ml HA-Ca) was added to the tissues and incubated for 30 mins at 30 °C with shaking. The papain solution was then washed out with 2 ml prewarmed HABG. The tissue was triturated approximately ten times for 45s using a siliconized 9-in Pasteur pipette with a fire-polished tip. After 1 min, the supernatant was gently transferred to the top of the prepared OptiPrep density gradient  without breaking the gradient. After centrifugation of 800 g for 15 min at 22 °C, the top 6 ml containing cellular debris was discarded. The bottom fraction was collected and diluted with 5 ml HABG and centrifuged for 3 min at 22 °C at 200 g followed by removal of the supernatant containing the debris. Finally, the cell pellet was loosened by flicking the tube and re-suspended in 1 ml of 0.01% BSA in PBS. The cell suspension was filtered through a 40-micron strainer  followed by cell counting.
Barcoded single cells, or STAMPs (single-cell transcriptomes attached to microparticles), and cDNA libraries were generated following the drop seq protocol from Macosko et al11. and version 3.1 of the online Drop-seq protocol [http://mccarrolllab.com/download/905/]. Briefly, single cell suspensions at 100 cells/μl, EvaGreen droplet generation oil (BIO-RAD, Hercules, CA, USA), and ChemGenes barcoded microparticles (ChemGenes, Wilmington, MA, USA) were co-flowed through a FlowJEM aquapel-treated Drop-seq microfluidic device (FlowJEM, Toronto, Canada) at recommended flow speeds (oil: 15,000 μl/hr, cells: 4000 μl/hr, and beads 4000 μl/hr) to generate STAMPs. The following modifications were made to the online published protocol to obtain enough cDNA as quantified by a high sensitivity BioAnalyzer (Agilent, Santa Clara, CA, USA) to continue the protocol: (1) The number of beads in a single PCR tube was 4000. (2) The number of PCR cycles was 4 + 11 cycles. (3) Multiple PCR tubes were pooled. The libraries were then checked on a BioAnalyzer high sensitivity chip (Agilent, Santa Clara, CA, USA) for library quality, average size, and concentration estimation. The samples were then tagmented using the Nextera DNA Library Preparation kit (Illumina, San Diego, CA, USA) and multiplex indices were added. After another round of PCR, the samples were checked on a BioAnalyzer high sensitivity chip for library quality check before sequencing. A cell doublet rate of 5.6% was obtained by running the microfluidic device without the lysis buffer and counting the percentage of cell doublets through three separate runs.

treatment_protocol: Brain injury was induced using a fluid percussion injury technique. Craniotomy was performed under a microscope (Leica), where a 3.0-mm diameter hole was made 2.5mm posterior to the bregma and 2.0mm lateral (left) of the midline with a high-speed drill (Dremel, Racine, WI, USA). The animals with intact dura underwent the fluid percussion injury procedure. Specifically, a plastic cap was first fixed over the hole with adhesive and dental cement. When the dental cement hardened, the cap was filled with 0.9% saline solution. Anesthesia was discontinued, and the injury cap was connected to the fluid percussion device. A fluid percussion (1.5–1.7 atm) was administered and wake-up time was determined as the time when the hind limb responded to a paw pinch (wake-up time falls into range of 5 -12 min). The animals in the sham group also underwent an identical preparation except for the percussion. T4 (1.2 ug/100g bodyweight) or saline (control) was administered via i.p. injection at 1 h and 6 h post-FPI, based on previous studies where a therapeutic effect was observed

value: hippocampus

tag: Sex

value: male

tag: age

value: 10 weeks

value: sham

tag: time point


title: hippocampus21d,T4,rep2


title: L01_126, KO_Tdp1, KO_Tdp1_G6, DMSO, biol rep 1


title: Cell line Exon 25 HAT Pool1 Replicate 2


title: L03_47, KO_Tdp1, KO_Tdp1_F7, DMSO, biol rep 4


title: Mycoplasma bovis HB0801 wild type strain, HB0801_3

value: WT


title: Mycoplasma bovis HB0801 wild type strain, HB0801_2


title: hippocampus21d,TBI,rep3

value: TBI


title: hippocampus21d,T4,rep1


title: Cell line Exon 14 batch2 M15 Pool1 Replicate 1


title: L02_99, KO_Tdp1, KO_Tdp1_C6, no, biol rep 3


title: Mycoplasma bovis HB0801 wild type strain, HB0801_1


title: L03_42, KO_Tdp1, KO_Tdp1_F7, DMSO, biol rep 3


title: Cell line Exon 25 HAT Pool1 Replicate 1

value: HAT


title: blue catfish muscle, 10.8-month, replicate 3

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

data_processing:
The raw reads quality was assessed by FastQC (version 0.11.6)
Low-quality bases and adapter sequences were trimmed using Trimmomatic (version 0.39)
RNA-seq reads were aligned to the blue catfish (Ictalurus furcatus) reference genome using STAR aligner version 2.7.5c
The gene read counts of each sample were quantified and summarized using HTseq version1.0 (Anders et al. 2015)
Assembly: GCA_023701845.2
Supplementary files format and content: tab-delimited text file includes gene read counts for each sample

organism: Ictalurus furcatus

source_name: muscle

extract_protocol:
Total RNA were extracted from muscle, liver, intestine, mucus, and heart of blue catfish and channel catfish with three replicates using Quick RNA Microprep Kit (Zymo Research, Irvine, CA, USA).
The library for each tissue sample was constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA)

value: muscle

value: Ictalurus furcatus x Ictalurus furcatus

value: 10.8 month


title: Cell line Exon 25 M15 Pool1 Replicate 2


title: hippocampus21d,TBI,rep2


title: L02_2, KO_Tdp1, KO_Tdp1_F7, DMSO, biol rep 2


title: Cell line Exon 25 Cis Pool1 Replicate 2


title: Mycoplasma bovis HB0801 MbovGdpP knock-out mutant,T6_290_2


title: hippocampus21d,sham,rep3


title: blue catfish mucus, 10.8-month, replicate 3

source_name: mucus

value: mucus


title: Cell line Exon 25 Ola Pool2 Replicate 1

value: Olaparib


title: L01_26, KO_Tdp1, KO_Tdp1_F7, DMSO, biol rep 1


title: hippocampus21d,sham,rep2


title: blue catfish liver, 10.8-month, replicate 3

source_name: liver

value: liver


title: Cell line Exon 25 Cis Pool2 Replicate 2

value: Embryonic stem cell


title: L03_121, KO_Tdp1, KO_Tdp1_C6, DMSO, biol rep 4

value: human embryonic kidney cells


title: Cell line Exon 25 Cis Pool2 Replicate 1


title: blue catfish intestine, 10.8-month, replicate 3

source_name: intestine

value: intestine


title: hippocampus21d,T4,rep3


title: blue catfish heart, 10.8-month, replicate 3

source_name: heart

value: heart


title: Cell line Exon 25 HAT Pool2 Replicate 2


title: Cell line Exon 25 Ola Pool2 Replicate 2


title: blue catfish muscle, 10.8-month, replicate 2


title: Cell line Exon 25 HAT Pool2 Replicate 1


title: cortex21d,sham,rep2

source_name: cortex

value: cortex


title: L02_47, KO_Tdp1, KO_Tdp1_C6, DMSO, biol rep 2

value: DMSO


title: Cell line Exon 25 M15 Pool2 Replicate 2


title: cortex21d,TBI,rep2

value: male

value: 10 weeks


title: PAWNPG_Rel_scATAC

city: Vancouver

first: Marco

last: Marra

state: BC

address: 675 West 10th Avenue

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Research Centre

description: 10x Genomics

data_processing:
1. Raw scATAC sequencing data was processed using Cellranger-ATAC (V1.2) to generate fastq files using mkfastq and subsequently aligned to hg38 using Cellranger count using the default settings. Libraries with poor sequencing quality (as determined by Cellranger metrics: base quality, percentage of valid barcodes, insert size distribution, median insertions and cluster density) were discarded.
2. Cells were filtered out with less than 2000 fragments, and cells that had less than 10% of their fragments mapping to transcription start site (TSS) regions, as defined by regions 2000 base pairs upstream and downstream of each unique TSS. Doublets and multiplets were removed using ArchR by generating synthetic doublets and calculating the nearest neighbors, defining those cells as doublets
3. To find peaks of overlapping sequence reads, pseudobulk data were first generated. Pseudobulk data were formed from clusters assigned using Seurat findClusters after applying iterative LSI. Peak calling was performed using Model-based Analysis of CHIP-seq (MACS2) (V2.2.7.1) and a p-value cutoff of 1e-5, applied over two iterations of inferred pseudobulk data per identified cluster, normalized according to read depth. Peaks were subsequently combined between these two replicates using the iterative overlap function in ArchR in clusters with a minimum of 50 cells to generate a set of peaks of a uniform 500 bp length.
Assembly: HG38
Supplementary files format and content: Tab-separated values files and matrix files containing: unfiltered fragments, filtered fragments, filtered barcodes, filtered metadata, peaks and a matrix with fragments in peaks. Unfiltered fragments contain the fragments directly derived from cellranger described in 1. Barcodes, fragments and metadata are based on barcodes filtered by the processing steps described in 2. Peaks were called and insertions were quantified as described in 3. Metadata contains, in order: cell and sample IDs, Quality statistics (fragments, reads in peaks, reads in TSS), cell classification including celltype identified using scPRED (see manuscript for details), cluster identified using ArchR and Malignancy status (see manuscript for details), the linked scRNA barcode, sample and score and patient information.

source_name: Marrow

extract_protocol:
At diagnosis, remission or relapse, bone marrow or blood samples were taken and Ficoll-enrichment was performed followed by viable cryopreservation of the cells (in FBS + DMSO) and long-term storage in liquid nitrogen at the COG biorepository.Cryopreserved samples were taken from liquid nitrogen and thawed in thawing media (50% FBS (ThermoFisher Scientific) + 40% HBSS (Stemcell Technologies) + 100ug/ml DNAseI (Sigma)). Cells were centrifuged (300g for 5 minutes), and washed once with 10ml of ice-cold HBSS + 10% FBS. A second wash with 1ml of HBSS + 10% FBS was performed followed by passing the cell suspension through a 40µm FlowMi filter (SP Bel-Art) into a new 1.5ml Eppendorf tube.
Single-cell 3’ RNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.0 (10X Genomics) following the manufacturer’s protocol.Library quality was assessed using the Agilent High Sensitivity DNA kit and libraries were quantified using the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled and converted using the MGIEasy Universal Library Conversion Kit (MGI Americas) following the manufacturer's protocol

treatment_protocol: For this study, a cohort of 28 patients who were enrolled in the Children’s Oncology Group (COG) Phase III AAML1031 trial (clinicaltrials.gov, NCT01371981) were studied using single cell sequencing. For the generation of the single cell datasets, patients were selected from Arm B (Standard Chemotherapy (ADE 10+3+5) + Bortezomib (n=24)) or Arm C (Standard Chemotherapy (ADE 10+3) + Sorafenib (n=4)). Four patients that were taken from Arm B were long-term remission patients (no event for at least five years after treatment). None of the patients that were sequenced longitudinally underwent stem cell transplantation.

value: Bone marrow cells

value: Marrow

value: Arm B


title: hippocampus21d,TBI,rep1

value: hippocampus

value: TBI


title: blue catfish mucus, 10.8-month, replicate 2

value: Ictalurus furcatus x Ictalurus furcatus

value: 10.8 month


title: cortex21d,T4,rep3


title: cortex21d,sham,rep1

value: sham


title: blue catfish liver, 10.8-month, replicate 2

value: liver


title: blue catfish intestine, 10.8-month, replicate 2


title: PAWMKP_Rel_scATAC

description: 10x Genomics


title: PAWNPG_Dx_scATAC

description: 10x Genomics


title: Cell line Exon 25 M15 Pool1 Replicate 1

value: Embryonic stem cell


title: Cell line Exon 25 M15 Pool2 Replicate 1


title: L02_100, KO_Tdp1, KO_Tdp1_C6, DMSO, biol rep 3

value: human embryonic kidney cells


title: cortex21d,sham,rep3


title: L01_42, KO_Tdp1, KO_Tdp1_C6, DMSO, biol rep 1


title: blue catfish heart, 10.8-month, replicate 2


title: Cell line Exon 21 batch2 Ola Pool2 Replicate 2

value: Olaparib


title: PAWMKP_Dx_scATAC

description: 10x Genomics


title: Cell line Exon 21 batch2 Ola Pool2 Replicate 1


title: blue catfish muscle, 10.8-month, replicate 1

value: muscle


title: cortex21d,TBI,rep1

value: cortex


title: cortex21d,TBI,rep3


title: PAVGJG_Rel_scATAC

description: 10x Genomics


title: blue catfish mucus, 10.8-month, replicate 1

value: mucus


title: cortex21d,T4,rep2

value: male


title: Cell line Exon 21 batch2 Cis Pool2 Replicate 2

value: Cisplatin


title: Cell line Exon 21 batch2 Cis Pool2 Replicate 1


title: PAVGJG_Dx_scATAC

description: 10x Genomics

source_name: Blood

value: Blood cells

value: Blood


title: blue catfish liver, 10.8-month, replicate 1


title: blue catfish intestine, 10.8-month, replicate 1

value: intestine


title: PAUXCD_Rel_scATAC

description: 10x Genomics

value: Bone marrow cells

value: Marrow

value: Arm B


title: PAUXCD_Dx_scATAC

description: 10x Genomics


title: Cell line Exon 21 batch2 HAT Pool2 Replicate 1

value: HAT


title: blue catfish heart, 10.8-month, replicate 1

value: heart

value: Ictalurus furcatus x Ictalurus furcatus

value: 10.8 month


title: PAUVAT_Rem_scATAC

description: 10x Genomics


title: hippocampus,7d,T4,rep3

value: hippocampus

value: 10 weeks


title: channel catfish muscle, 10.8-month, replicate 3

organism: Ictalurus punctatus

value: muscle

value: Ictalurus punctatus x Ictalurus punctatus


title: Cell line Exon 21 batch2 HAT Pool2 Replicate 2

value: Embryonic stem cell


title: Cell line Exon 21 batch2 M15 Pool2 Replicate 2


title: hippocampus,7d,TBI,rep1

value: male

value: TBI


title: Cell line Exon 21 batch2 M15 Pool2 Replicate 1


title: channel catfish mucus, 10.8-month, replicate 3

value: mucus


title: PAUVAT_Dx_scATAC

description: 10x Genomics


title: PAUVAT_Rel_scATAC

description: 10x Genomics


title: Cell line Exon 21 batch2 Ola Pool1 Replicate 2

value: Olaparib


title: hippocampus,7d,TBI,rep3


title: hippocampus,7d,T4,rep1


title: hippocampus,7d,T4,rep2


title: channel catfish liver, 10.8-month, replicate 3

value: liver


title: hippocampus,24h,TBI,rep3


title: hippocampus,7d,TBI,rep2


title: PAUUWT_Rel_scATAC

description: 10x Genomics

value: Bone marrow cells


title: channel catfish heart, 10.8-month, replicate 3


title: Cell line Exon 21 batch2 Ola Pool1 Replicate 1


title: hippocampus,24h,TBI,rep2


title: Cell line Exon 21 batch2 Cis Pool1 Replicate 2

value: Cisplatin


title: PAUUWT_Dx_scATAC

description: 10x Genomics

value: Blood cells

value: Blood

value: Arm B


title: channel catfish muscle, 10.8-month, replicate 2


title: Cell line Exon 21 batch2 Cis Pool1 Replicate 1


title: hippocampus,24h,T4,rep3


title: channel catfish mucus, 10.8-month, replicate 2


title: hippocampus,24h,TBI,rep1


title: Cell line Exon 21 batch2 HAT Pool1 Replicate 2

value: HAT


title: Cell line Exon 21 batch2 HAT Pool1 Replicate 1


title: channel catfish liver, 10.8-month, replicate 2

value: 10.8 month


title: hippocampus,24h,T4,rep2

value: hippocampus


title: PAULDS_Dx_scATAC

description: 10x Genomics

value: Marrow

value: Arm B (long-term remission)


title: PAUUWT_Rem_scATAC

description: 10x Genomics


title: PAXLEE_Rem_scATAC

description: 10x Genomics

value: Arm C


title: hippocampus,24h,T4,rep1

value: 10 weeks


title: channel catfish intestine, 10.8-month, replicate 2

value: intestine

value: Ictalurus punctatus x Ictalurus punctatus


title: cortex,7d,TBI,rep3

value: cortex

value: male

value: TBI


title: Cell line Exon 21 batch2 M15 Pool1 Replicate 1

value: Embryonic stem cell


title: Cell line Exon 21 batch2 M15 Pool1 Replicate 2


title: channel catfish intestine, 10.8-month, replicate 3


title: PAXLEE_Rel_scATAC

description: 10x Genomics

value: Bone marrow cells


title: channel catfish heart, 10.8-month, replicate 2

value: heart


title: channel catfish muscle, 10.8-month, replicate 1

value: muscle


title: cortex,7d,TBI,rep2


title: PAWHFW_Rem_scATAC

description: 10x Genomics


title: PAULDS_Rem_scATAC

description: 10x Genomics


title: Cell line Exon 21 Ola Pool2 Replicate 1

value: Olaparib


title: channel catfish mucus, 10.8-month, replicate 1

value: mucus


title: PAXLEE_Dx_scATAC

description: 10x Genomics


title: cortex,7d,TBI,rep1


title: Cell line Exon 21 Cis Pool2 Replicate 2

value: Cisplatin


title: PAWHFW_Rel_scATAC

description: 10x Genomics


title: Cell line Exon 21 Ola Pool2 Replicate 2


title: channel catfish liver, 10.8-month, replicate 1

value: liver

value: 10.8 month


title: Cell line Exon 21 Cis Pool2 Replicate 1


title: PAWHFW_Dx_scATAC

description: 10x Genomics

value: Marrow


title: channel catfish intestine, 10.8-month, replicate 1


title: cortex,7d,T4,rep3


title: channel catfish heart, 10.8-month, replicate 1


title: cortex,7d,T4,rep2


title: Cell line Exon 21 HAT Pool2 Replicate 2

value: HAT


title: PAVBFN_Rem_scATAC

description: 10x Genomics

value: Arm C


title: PAVBFN_Rel_scATAC

description: 10x Genomics


title: PAVBFN_Dx_scATAC

description: 10x Genomics


title: cortex,7d,T4,rep1

value: 10 weeks


title: cortex,24h,TBI,rep1


title: ser-3

city: Anseong-si

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero, Daedeok-myeon,

department: plant biotechnology

country: South Korea

institute: Chung-Ang University

description: replicate 3

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software
The raw reads were trimmed and quality-filtered before alignment, and those with more than 90 % threshold (Q>30) were used for mapping. B. oleracea reference genome was obtained from Ensembl and were used using the STAR software with default parameters
Aligned reads were converted to digital counts using featureCounts and were analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a 0.05 p-value and a cutoff of two-fold difference in expression.
Supplementary files format and content: B. oleracea reference genome was obtained from Ensembl

organism: Brassica oleracea

source_name: whole plant

extract_protocol:
Two weeks old seedlings were harvested at ZT4 time point and used for extraction of total RNAs using RNeasy Plant Mini Kit (Qiagen, Germany).
Three biological replicates for each cultivar were used for the construction of RNA-seq libraries using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions.
paired-end sequencing

value: whole plant


title: Cell line Exon 21 HAT Pool2 Replicate 1


title: PAWHKK_Dx_scATAC

description: 10x Genomics

value: Arm B


title: cortex,24h,TBI,rep3

value: cortex

value: male


title: DBN-3

description: replicate 3


title: Cell line Exon 21 Ola Pool1 Replicate 2

value: Embryonic stem cell


title: cortex,24h,TBI,rep2

value: TBI


title: ser-2

description: replicate 2


title: PAWHKK_Rel_scATAC

description: 10x Genomics

value: Bone marrow cells


title: Cell line Exon 21 M15 Pool2 Replicate 1


title: Cell line Exon 21 Cis Pool1 Replicate 2


title: DBN-2

description: replicate 2


title: PAWWCW_Rem_scATAC

description: 10x Genomics

value: Blood cells

value: Blood


title: cortex,24h,T4,rep3


title: DBN-1

description: replicate 1


title: ser-1

description: replicate 1


title: BACHD, SPI-77, 4 days, bio rep3

city: Rehovot

first: Rivka

last: Dikstein

address: 234 Herzel

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mouse genome using STAR
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count
Normalization and differential expression was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: Excel file includes the normalized counts and DESEq2 output

source_name: brain

extract_protocol:
Following mice sacrification, brains were removed, sliced and small punch-size pieces of tissue from the striatum were immediately placed in Bio-Tri RNA. Total RNA was further extracted using Direct-zol™ RNA MiniPrep kit (Zymo Research).
The RNA-seq libraries were prepared with the TruSeq Stranded mRNA Library Prep (Cat #20020594; Illumina).

treatment_protocol: DMSO (control) or SPI-24 or SPI-77 were SC injected to BACHD mice for 4 subsequent days and 6 hours after the last administration the mice were sacrificed.

value: brain

value: BACHD

value: striatum cells

value: HD mutant


title: PAWWCW_Rel_scATAC

description: 10x Genomics


title: PAWTSD_Rem_scATAC

description: 10x Genomics

value: Marrow


title: BACHD, SPI-77, 4 days, bio rep2


title: RNA-seq_PigU_3

city: Dunedin

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

data_processing:
Base calling with Illumina Sequencer RTA version 1.18.64
FASTQ conversion with Bcl2fastq version 2.18.0.12
FASTQ quality assesment using FASTQC v0.11.5
Trimming of the TruSeq3 sequence from FASTQ files using the ILLUMINACLIP option of Trimmomatic version 0.39
Read alignment to the Serratia genome using Bowtie2 version 2.3.5.1 using default parameters
Conversion of SAM to BAM format using Samtools version 1.9
Differential expression analysis performed using DESeq2 (version 1.38.3) with FDR < 5% and |log2 fold change| > 0
Assembly: CP025085.1
Supplementary files format and content: Raw counts for each locus tag and sample (wildtype and pigU replicates) generated using the summarizeOverlaps() function of the R GenomicAlignments package (version 1.34.1), with counting mode="Union"
Supplementary files format and content: Normalized counts (median of ratios method) for each locus tag and sample (wildtype and pigU replicates), generated using the estimateSizeFactors() function of the R DESeq2 package (version 1.38.3)

organism: Prodigiosinella confusarubida

growth_protocol: PigU (HSPIG43) and WT (LacA) control strains were grown for 12 h and 2 ml samples harvested by centrifugation. Cell pellets were resuspended in RNAlater.

extract_protocol:
RNA extracted from cell pellets using the Qiagen Rneasy kit, Turbo DNase treatment was performed to remove any gDNA.
RNA samples were sequenced at Vertis Biotechnologie in Freising, Germany. Ribosomal RNA (rRNA) was depleted using a RiboZero kit (Illumina), and the remaining RNA species were fragmented by means of an ultrasound. Synthesis of antisense cDNA was initiated through ligation of a TruSeq adaptor sequence (Illumina) to the 3’ OH end of the fragmented RNA. Next, the antisense cDNA was purified, followed by a ligation of a 5’ sequencing adaptor to the 3’ end of the antisense cDNA. The cDNA was then amplified using PCR (the number of PCR cycles was dependent on the amount of starting product) and the resulting products were gel fractionated to satisfy the size requirements for Illumina sequencing. Lastly, cDNA libraries were sequenced with the Illumina NextSeq 500 System using a 'HIGH 75' sequencing kit to an average depth of around 10 million reads per library, generating an output in the form of 75 bp demultiplexed reads in FASTQ format.

treatment_protocol: No treatment applied during growth

value: LacA with pigUpro::mini-Tn5lacZ1, KmR

tag: time


title: cortex,24h,T4,rep1


title: Cell line Exon 21 M15 Pool2 Replicate 2


title: BACHD, SPI-77, 4 days, bio rep1


title: cortex,24h,T4,rep2


title: Cell line Exon 21 Cis Pool1 Replicate 1

value: Cisplatin


title: BACHD, SPI-24, 4 days, bio rep4


title: PAWTSD_Dx_scATAC

description: 10x Genomics


title: PAWTSD_Rel_scATAC

description: 10x Genomics


title: RNA-seq_PigU_2


title: RNA-seq_LacA_3

source_name: LacA

value: LacA


title: PAWWCW_Dx_scATAC

description: 10x Genomics


title: Cell line Exon 21 M15 Pool1 Replicate 2


title: Cell line Exon 21 HAT Pool1 Replicate 1

value: HAT


title: Cell line Exon 21 Ola Pool1 Replicate 1

value: Olaparib


title: Cell line Exon 21 HAT Pool1 Replicate 2


title: PAVBCV_Rem_scATAC

description: 10x Genomics

value: Arm B


title: BACHD, SPI-24, 4 days, bio rep2


title: BACHD, SPI-24, 4 days, bio rep3


title: RNA-seq_LacA_1


title: PAVBCV_Dx_scATAC

description: 10x Genomics


title: Cell line Exon 21 M15 Pool1 Replicate 1


title: PAVBCV_Rel_scATAC

description: 10x Genomics


title: RNA-seq_LacA_2


title: BACHD, SPI-24, 4 days, bio rep1


title: RNA-seq_PigU_1


title: Cell line Exon 20 Cis Pool2 Replicate 2


title: TL-Om1_H3k27ac_Hi-CHIP

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
Sequencing data of H3K27ac Hi-ChIP were processed with fastp to remove adapter sequence (CTGTCTCTTATACACA) and phred quality >=Q15. Then the sequenced reads were aligned, paired, and removed of duplicates using the HiC-Pro pipeline version (2.11.1) where the fastq files were aligned to hg19 genome using bowtie2 version 2.4.1.
The MboI restriction enzyme cutsite over the human genome were generated using HiC-Pro utilities python script digest_genome function by using ^GATC as the ligation site.
The aligned data were further processed using hichipper to call the interactions. Hichipper version 2.7.9 processed the valid interactions from HiC-Pro and generate the interaction bedpe file.
Hichipper processed the interactions using parameters as shown -l 50 -mi 5000 -ma 2000000.
Genome_build: hg19
Supplementary_files_format_and_content: ATL_allValidPairs: txt file output from HiC-Pro
Supplementary_files_format_and_content: ATL.filt.intra.loop_counts.bedpe: bedpe file output from hichipper
Supplementary_files_format_and_content: ATL.anchors.bed: anchor used by hichipper

source_name: TL-Om1 cells

growth_protocol: TL-Om1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

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

treatment_protocol: TL-Om1 cells were cross-linked with formaldehyde, lysed with Hi-C buffer and then sonicated. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. Post-ChIP DNA was tagmented with Tn5 enzyme follwed by PCR amplification library synthesis

value: ATL

tag: chip antibody

value: H3K27ac Antibody (abcam; ab4729)


title: Cell line Exon 20 Ola Pool2 Replicate 2

value: Embryonic stem cell


title: PAULSL_Rem_scATAC

description: 10x Genomics

value: Bone marrow cells

value: Arm B (long-term remission)


title: BACHD, DMSO, 4 days, bio rep4

value: DMSO (control)


title: BACHD, DMSO, 4 days, bio rep3

value: brain


title: TP73_ChIP-Seq

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is p-value < 1e-9, keep-dup=1, --SPMR were used to normalized the bedGraph output.
bigWig files were generated using MACS2 -B begGraph output. TP73 sample were normalized by subtracting corresponding background using MACS2 bdgcmp. The BEDGRAPH files were further floored to 0.1 and convert to bigWig using bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files of TP73 called with MACS2

extract_protocol:
Library construction from the TP73 ChIP-seq samples and sequencing of single-end 50-bp-long reads by the DNBseq were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single-end ChIP-Seq sequencing

treatment_protocol: TL-Om1 cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and TP73-DNA complexes were isolated with antibody.  A sample of whole cell extract (input) was sequenced and used as the background to determine enrichment.

value: TP73 Antibody (abcam; ab14430)


title: PAULSL_Dx_scATAC

description: 10x Genomics


title: Cell line Exon 20 Ola Pool2 Replicate 1


title: Cell line Exon 20 Cis Pool2 Replicate 1


title: TP73 ex2-3del_DOX_8wkcoculture_rep3

description: Replicate 3

data_processing:
RNA-seq reads were mapped to curated RefSeq transcripts (NM and NR transcripts) using salmon (version 1.1.0) with the options “--gcBias --seqBias –validateMappings”.
The salmon index file was created with default settings.
Transcript-level read counts were converted to gene-level read counts using tximport (version 1.18.0).
Differentially expressed genes were estimated using DESeq2 (version 1.30.0).
Supplementary_files_format_and_content: txt file for differentially expressed genes

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBseq were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: TL-Om1 cells were induced with doxycycline for 3 days to induce deletion.  The cells were also cultured with control cells in the same flask for 8 weeks.   In each condition, total RNA were harvested from sorted cells.

tag: knockdown

value: deletion (8 weeks co-culture)

value: Dox


title: PAXGDG_Rel_scATAC

description: 10x Genomics

value: Blood cells

value: Blood


title: BACHD, DMSO, 4 days, bio rep2

value: BACHD

value: striatum cells

value: HD mutant


title: Cell line Exon 20 HAT Pool2 Replicate 2

value: HAT


title: BACHD, DMSO, 4 days, bio rep1


title: Cell line Exon 20 HAT Pool2 Replicate 1


title: TP73 ex2-3del_DOX_8wkcoculture_rep1

description: Replicate 1


title: TP73 ex2-3del_DMSO_8wkcoculture_rep3

description: Replicate 3

value: control (8 weeks co-culture)

value: DMSO


title: ChIP_Input (TP73 control)

value: ATL


title: PAWUAE_Rel_scATAC

description: 10x Genomics

value: Marrow

value: Arm B


title: PAXGDG_Dx_scATAC

description: 10x Genomics

value: Bone marrow cells


title: TP73 ex2-3del_DMSO_8wkcoculture_rep2

description: Replicate 2


title: 6.2

city: Slough

first: Andrew

middle: James

last: Skelton

address: 208 Bath Road

department: Translational Bioinformatics

institute: UCB

data_processing:
Demultiplexing with bcl2fastq
Salmon quantification V1.3 with Seq and GC Bias Correction, 100 Gibbs Bootstraps
Import counts using tximport to the LengthScaledTPM unit
Voom Transformation
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_Counts_LengthScaledTPM.tsv.gz
Supplementary_files_format_and_content: VoomTransformed_LengthScaledTPM.tsv.gz; Salmon Counts as LengthScaledTPM via tximport

source_name: IL17F Postive Sorted Cells

growth_protocol: PBMCs were cultured in X-VIVO15 media with anti-CD3/CD28 stimulation with IL-1b and IL-23 for 72 hours.

extract_protocol:
RNA was extracted using RNeasy micro kit (Qiagen)
Input material was normalised to 100ng. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions

treatment_protocol: Activated, cytokine secreting cells were captured using bispecific antibodies to CD45/IL-17A or CD45/IL-17F to anchor the cytokine to the cell. Subsets were purified by FACS sorting

tag: seqid

tag: sampleID

tag: donor

value: F

tag: sampletype

tag: rnaconc

tag: prepdate

tag: numcells


title: Cell line Exon 20 Ola Pool1 Replicate 2

data_processing:
The paired end reads were aligned to the reference sequence using the Needleman-Wunsch alignment algorithm after the reads were demultiplexed using bcl2fastq (Illumina), generation of fastq files, and merging using FLASH.
The total number of aligned reads were quantified using CRISPResso2 http://crispresso.pinellolab.org/submission. Iindividual unique alignments were annotated with a custom-made variant caller modified from ANNOVAR (64) (release 2019-10-21) and the R/Bioconductor Biostrings package in R version 4.1.2 https://bioconductor.org/packages/Biostrings. Merged reads containing “N” bases were removed from the analysis.
Abundances of SNVs were quantified when the reads contained a single-nucleotide substitution. Read counts for each SNVs were then normalized to the total read coverage of the sequencing library after adding a pseudocount of 1 to all reads for all conditions. Individual variants with a read count of more than 1 in 1,000 reads in the M15 condition were used for further analysis. Dropout or enrichment scores were calculated by taking the ratio of frequency of SNV after HAT, cisplatin, or olaparib treatment over that in M15.
The scores were expressed in log2 scale, which we define as the functional scores of SNVs in HAT, cisplatin, and olaparib. The functional scores, averaged between independent replicates (2-4), were used to calculate the the probabilities of impact on function (PIF) for all the variants in the data set.
Assembly: GRCh38
Supplementary files format and content: xlsx: Excel files include PIF and function scores for all variants.
Library strategy: Amplicon sequencing

tag: cell line

tag: cell type

value: Embryonic stem cell

tag: treatment

value: Olaparib


title: TP73 ex2-3del_DOX_8wkcoculture_rep2

description: Replicate 2

value: deletion (8 weeks co-culture)


title: 6.1

source_name: IL17A Postive Sorted Cells


title: PAWUAE_Rem_scATAC

description: 10x Genomics

tag: tissue


title: 6.4

source_name: IL17AF Negative Sorted Cells

value: DN


title: 5.4

value: E


title: PAUURD_Dx_scATAC

description: 10x Genomics

value: Arm B (long-term remission)


title: Cell line Exon 20 Cis Pool1 Replicate 2

value: Cisplatin


title: TP73 ex2-3del_DOX_independentculture_rep2

description: Replicate 2

value: deletion (independent culture)

value: Dox


title: PAUURD_Rem_scATAC

description: 10x Genomics


title: Cell line Exon 20 M15 Pool2 Replicate 1


title: Cell line Exon 20 Ola Pool1 Replicate 1


title: Cell line Exon 20 Cis Pool1 Replicate 1


title: PAVJXG_Rem_scATAC

description: 10x Genomics


title: 6.3

source_name: IL17AF Postive Sorted Cells


title: PAVJXG_Rel_scATAC

description: 10x Genomics


title: TP73 ex2-3del_DOX_independentculture_rep1

description: Replicate 1


title: Cell line Exon 20 M15 Pool2 Replicate 2


title: Cell line Exon 20 HAT Pool1 Replicate 2

value: HAT


title: PAWUAE_Dx_scATAC

description: 10x Genomics


title: TP73 ex2-3del_DMSO_independentculture_rep2

description: Replicate 2

value: control (independent culture)


title: 5.2


title: 5.1


title: PAVJXG_Dx_scATAC

description: 10x Genomics


title: TP73 ex2-3del_DMSO_independentculture_rep1

description: Replicate 1

value: DMSO


title: Cell line Exon 20 HAT Pool1 Replicate 1


title: 4.4

value: D


title: PAWNPU_Rem_scATAC

description: 10x Genomics

value: Marrow


title: TP73 ex2-3del_DMSO_8wkcoculture_rep1

description: Replicate 1

value: ATL

value: control (8 weeks co-culture)


title: dCas9_TP73_DOX_rep2

description: Replicate 2

treatment_protocol: TL-Om1 cells were incubated with doxycycline for 3 days, after which total RNA were harvested.

value: knockdown


title: Cell line Exon 20 M15 Pool1 Replicate 2

value: Embryonic stem cell


title: 4.3


title: PAWNPU_Dx_scATAC

description: 10x Genomics

value: Bone marrow cells

value: Arm B


title: PAWNPU_Rel_scATAC

description: 10x Genomics


title: dCas9_TP73_DOX_rep1

description: Replicate 1


title: 4.2


title: 5.3


title: Cell line Exon 20 M15 Pool1 Replicate 1


title: dCas9_TP73_DMSO_rep1

description: Replicate 1

value: control


title: Cell line Exon 14 Ola Pool2 Replicate 2

value: Olaparib


title: ∆Np73_OE_DOX_rep2

description: Replicate 2

value: overexpression


title: 4.1


title: PAUWUZ_Rem_scATAC

description: 10x Genomics

value: Arm B (long-term remission)


title: Cell line Exon 14 Ola Pool2 Replicate 1


title: PAUWUZ_Dx_scATAC

description: 10x Genomics


title: PAWWXU_Rem_scATAC

description: 10x Genomics


title: Cell line Exon 14 Cis Pool2 Replicate 2

value: Cisplatin


title: 3.5

source_name: Naïve CD4 Positive cells

value: C


title: Cell line Exon 14 Cis Pool2 Replicate 1


title: ∆Np73_OE_DOX_rep1

description: Replicate 1

value: Dox


title: PAWWXU_Rel_scATAC

description: 10x Genomics


title: ∆Np73_OE_DMSO_rep2

description: Replicate 2


title: Cell line Exon 14 HAT Pool2 Replicate 2

value: HAT


title: 3.4

value: DN


title: dCas9_TP73_DMSO_rep2

description: Replicate 2

value: DMSO


title: 3.3


title: ∆Np73_OE_DMSO_rep1

description: Replicate 1


title: Cell line Exon 14 HAT Pool2 Replicate 1


title: PAVDYE_Rem_scATAC

description: 10x Genomics

value: Marrow


title: 3.6

source_name: Naïve Th17 Positive cells


title: PAVDYE_Rel_scATAC

description: 10x Genomics


title: TAp73_OE_DOX_rep2

description: Replicate 2

value: ATL


title: TAp73_OE_DOX_rep1

description: Replicate 1


title: Cell line Exon 14 M15 Pool2 Replicate 1


title: 3.1


title: 2.6

value: B


title: Cell line Exon 14 Ola Pool1 Replicate 2


title: TAp73_OE_DMSO_rep1

description: Replicate 1


title: 2.5


title: TAp73_OE_DMSO_rep2

description: Replicate 2


title: PAVDYE_Dx_scATAC

description: 10x Genomics


title: Cell line Exon 14 Cis Pool1 Replicate 2


title: PAWWXU_Dx_scATAC

description: 10x Genomics


title: KO6

city: Tianjin

first: Lei

last: Cao

address: 92 Weijin Road

institute: The School of Pharmaceutical Science and Technology (SPST)

data_processing:
BGISEQ-500 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using SOAPnuke v1.4.0 with parameters -l 5 -q 0.5 -n 0.1
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text file include TPM, count, and  FPKM values for each Sample

source_name: hepatocytes

growth_protocol: 10% FBS containing DMEM at 37°C with 5%CO2

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BGISEQ-500 standard protocols

treatment_protocol: Liver-derived WT and Fxr-/- mouse primary hepatocytes were cultured in 10% FBS containing DMEM and treated with FAC (100μM) or AC(100μM)  for 24 h.

value: liver-derived primary hepatocytes

tag: strain

tag: genotype

value: Fxr-/-

value: liver

value: treated with FAC for 24 hours


title: PAWNYX_Dx_scATAC

description: 10x Genomics

value: Blood cells

value: Blood

value: Arm B


title: 2.3


title: Cell line Exon 14 Ola Pool1 Replicate 1

extract_protocol:
Genomic DNA was extracted from the cell pellets using Zymo Genomic DNA Extraction kit
DNA libraries were prepared using TruSeq Nano DNA Library Prep kit

value: Embryonic stem cell

value: Olaparib


title: 2.4


title: Cell line Exon 14 Cis Pool1 Replicate 1

value: Cisplatin


title: PAUZRT_Rem_scATAC

description: 10x Genomics


title: KO5


title: 2.2


title: PAUZRT_Rel_scATAC

description: 10x Genomics

value: Bone marrow cells


title: KO4


title: 3.2

value: C


title: Cell line Exon 14 M15 Pool2 Replicate 2


title: Cell line Exon 14 HAT Pool1 Replicate 2

value: HAT


title: PAUZRT_Dx_scATAC

description: 10x Genomics


title: 2.1


title: Cell line Exon 14 HAT Pool1 Replicate 1


title: KO3

value: treated with AC for 24 hours


title: PAWNYX_Rel_scATAC

description: 10x Genomics

value: Marrow


title: PAWNPG_Rem_scRNA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
1. Raw sequencing data was processed using Cellranger (V3.1) mkfastq to generate fastq files. Fastq files were aligned to hg38 and quantified using CellRanger (V3.1) count applying standard settings. Libraries with poor sequencing quality (as determined by Cellranger metrics: e.g. base quality, percentage of valid barcodes, valid unique molecular identifiers (UMIs) and cluster density) were discarded.
2. Cells were filtered with less than 1000 UMIs, less than 500 covered genes or more than 15% mitochondrial reads.
3. Using Seurat (V4.0.1), data were log normalized to 10,000 counts and subsequently scaled. Considering the uniform treatment of the cohort and uniform processing of samples, batch effect correction was not applied to avoid overcorrection of patient-to-patient differences. The uwot implementation of Uniform Manifold Approximation and Projection (UMAP) (V0.1.1), was used to visualize scRNA-seq data after initialization using principal component analysis (PCA) and calculation of nearest neighbors (nn) by applying the annoy algorithm.
Assembly: HG38
Supplementary files format and content: Tab-separated values files and matrix files containing: unfiltered files that have not been processed after alignament using cellranger including genes, barcodes and matrix files with the raw counts and filtered files containing the matrices, genes and barcodes for filtered cells, having processed counts. Each sample also contains a metadata file for the processed cells containing, in order: cell and sample IDs, Quality statistics (counts, genes covered, mitochondiral reads) , cell classification including celltype identified using scPRED (see manuscript for details), cluster identified using Seurat and Malignancy status (see manuscript for details), and various patient information.

extract_protocol:
At diagnosis, remission or relapse, bone marrow or blood samples were taken and Ficoll-enrichment was performed followed by viable cryopreservation of the cells (in FBS + DMSO) and long-term storage in liquid nitrogen at the COG biorepository.Cryopreserved samples were taken from liquid nitrogen and thawed in thawing media (50% FBS (ThermoFisher Scientific) + 40% HBSS (Stemcell Technologies) + 100ug/ml DNAseI (Sigma)). Cells were centrifuged (300g for 5 minutes), and washed once with 10ml of ice-cold HBSS + 10% FBS. A second wash with 1ml of HBSS + 10% FBS was performed followed by passing the cell suspension through a 40µm FlowMi filter (SP Bel-Art) into a new 1.5ml Eppendorf tube
Single-cell 3’ RNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.0 (10X Genomics) following the manufacturer’s protocol.Library quality was assessed using the Agilent High Sensitivity DNA kit and libraries were quantified using the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled and converted using the MGIEasy Universal Library Conversion Kit (MGI Americas) following the manufacturer's protocol


title: PAWNPG_Rel_scRNA

description: 10x Genomics


title: PAWNPG_Dx_scRNA

description: 10x Genomics


title: KO2


title: 1.4

value: A

value: DN


title: WT5

value: liver-derived primary hepatocytes

value: wild type


title: WT6

value: liver


title: PAWMKP_Rem_scRNA

description: 10x Genomics


title: 1.6


title: WT4

value: treated with FAC for 24 hours


title: 1.5


title: 1.2


title: Cell line Exon 14 M15 Pool1 Replicate 1


title: PAWMKP_Dx_scRNA

description: 10x Genomics


title: 1.1


title: Cell line Exon 11partd Cis Pool2 Replicate 2


title: Cell line Exon 11partd Ola Pool2 Replicate 2


title: WT3


title: Cell line Exon 11partd Cis Pool2 Replicate 1


title: Cell line Exon 11partd Ola Pool2 Replicate 1


title: PAVGJG_Rel_scRNA

description: 10x Genomics


title: hFGF19_4

city: Jinan

first: Tianli

last: Chen

state: Shandong

address: 107 West Wenhua Road

department: Department of General Surgery

institute: Qilu Hospital of Shandong University

description: hFGF stimulation for 72 hours

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include FPKM values for each Sample

source_name: human colorectal cancer cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (allwegene, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human colorectal cancer cell


title: WT2


title: Cell line Exon 11partd HAT Pool2 Replicate 2


title: Cell line Exon 14 M15 Pool1 Replicate 2


title: PAVGJG_Dx_scRNA

description: 10x Genomics

value: Blood cells

value: Blood


title: KO1

value: Fxr-/-


title: WT1


title: 1.3


title: Cell line Exon 11partd HAT Pool2 Replicate 1

value: Embryonic stem cell


title: hFGF19_3

description: hFGF stimulation for 72 hours


title: PAWMKP_Rel_scRNA

description: 10x Genomics

value: Arm B


title: PAUXCD_Rel_scRNA

description: 10x Genomics

value: Bone marrow cells


title: PAUXCD_Dx_scRNA

description: 10x Genomics


title: hFGF19_1

description: hFGF stimulation for 72 hours


title: PAUVAT_Rem_scRNA

description: 10x Genomics


title: Cell line Exon 11partd M15 Pool2 Replicate 1


title: con_4

description: control group without hFGF19 stimulation


title: Sample 1, ADT

city: Gaithersburg

first: Yang

last: Song

address: 1 MedImmune Way

institute: AstraZeneca

description: 10X Genomics

library_source: other

data_processing:
FASTQ files were process with CellRanger v6.0.1 with feature barcode information to produce a count matrix with gene expression and labelled antibody data.
Raw count matrix was further processed using ScanPy (v1.9.1) for downstream analysis
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Lung

extract_protocol:
Neutrophils were enriched from the lung of Balb/c animals infected with NTHi using magnetic beads. Single cells from the enriched neutrophil fraction were stained with pooled BioLegend TotalSeq-B antibodies. Stained cells were diluted in PBS with a final concentration of 1000 cells per µL.
Stained cells were loaded into a single lane of 10X Chromium (Single Cell 3’ V3). Library construction for both polyA RNA and surface protin was done using 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcoding technology protocol

value: Lung

value: Neutrophils

value: Balb/c


title: Sample 1, GEX

description: 10X Genomics


title: Cell line Exon 11partd Ola Pool1 Replicate 1

city: Frederick

last: Sharan

address: Building 560, Room 32-33

institute: Mouse Cancer Genetics Program

value: Olaparib


title: PAUVAT_Rel_scRNA

description: 10x Genomics

value: Marrow


title: con_3


title: Cell line Exon 11partd Ola Pool1 Replicate 2


title: con_2


title: PAUUWT_Rem_scRNA

description: 10x Genomics


title: PAUVAT_Dx_scRNA

description: 10x Genomics


title: con_1


title: Cell line Exon 11partd Cis Pool1 Replicate 2

value: Cisplatin


title: Cell line Exon 11partd Cis Pool1 Replicate 1


title: PAUUWT_Rel_scRNA

description: 10x Genomics


title: HM-1-PCR-Control-R3

first: Benjamin

last: Edginton-White

address: Medical School

department: ICGS

description: Library from wild type HM-1 cells to control for PCR atrifacts

data_processing:
Paired end sequencing reads were trimmed using Trim Galore (Krueger F, 2021) with the parameters --nextera --length 70 –paired.
The reads were then aligned to the mm10 genome using bowtie2 using parameters --very-sensitive --fr --no-discordant -X 600 --no-mixed.
Aligned reads were filtered for only those which were properly paired and with a mapq score of over 40 using Samtools and output as a bedpe file.
This was further converted to a bed file of enhancer fragments by taking the first co-ordinate of read 1 and the final co-ordinate of read 2 for each pair. Duplicate fragments were removed using the uniq functionin bash and fragments were further filtered using the intersect function on Bedtools for any which had 100% overlap with an off target background fragment list which was created by producing a library from un-transfected cells. The fragments were further filtered by the same method against the input plasmid libraries.
The fragments were then filtered using Bedtools intersect for those which were found in open chromatin, defined by ATAC-Seq peaks in the correct differentiation stage in HM-1 cells.
Finally, the enhancer fragments were annotated using the annotatePeaks function of Homer for those within 1.5 kb of a TSS (promoter fragments) and distal fragments representing genuine enhancers.
Assembly: mm10
Supplementary files format and content: Bed files of filtered distal enhancer fragment co-ordinates
Supplementary files format and content: Bed files of filtered promoter fragment co-ordinates
Library strategy: Enhancer Reporter Sequencing

source_name: Embryonic Stem Cell (ES)

growth_protocol: A genome-wide enhancer reporter assay was designed based on an enhancer reporter system designed by Wilkinson et al. (2013). Briefly the enhancer reporter functions by inserting a fragment of interest upstream of a HSP68 minimal promoter and Venus-YFP reporter by Gateway® cloning. The reporter construct is then transfected into the HM-1 ES cell line which has a non-functional HPRT locus. Using HPRT homology arms the report cassette becomes integrated into the HPRT locus by homologous recombination, also repairing the locus, enabling selection of clones with successful recombination. This enhancer reporter system was modified and optimised for genome-wide screening. To obtain genome-wide enhancer fragments for cloning into the reporter we isolated tn5 tagmented open-chromatin fragments based on the ATAC-Seq protocol 33 from cells of the five differentiation stages. Cells were obtained (2.5x105) from each differentiation stage (ES, HB, HE1, HE2, HP) as detailed in the serum IVD method. Cells were pelleted in 5 aliquots of 50x103 cells and following the ATAC-Seq protocol each cell pellet had a transposition mix added (2x TD Buffer 25µl, TN5 Transposase 2.5 µl, PBS 16.5 µl, 1% Digitonin 0.5 µl, 10 % Tween-20 0.5 µl, H2O 5 µl) and cells were gently resuspended by pipetting. The transposition reaction was then incubated in a shaker at 700 RPM, 37°C for 30 minutes. The 5 reactions were then combined and DNA purified using the Qiagen MinElute® Reaction Clean-up kit and eluted in 26.5 µl H2O. One fifth of the purified reaction from each stage was used to produce ATAC-Seq libraries for direct sequencing and the remainder had linkers added incorporating AttB Gateway® cloning sites to enable insertion into a Gateway® donor vector (pDONR 221). The linkers were designed based on the tn5 transposase sequence and added by PCR in 2 steps. Initially 5 cycles of PCR were performed (Transposed DNA 20 µl, H2O 20 µl, 25 µM AttB tn5 Fwd primer 5 µl, 25 µM AttB tn5 Rev primer 5 µl, NEBNext Master Mix 50 µl) with the following conditions, 72°C for 5 minutes, 98°C for 30 seconds, 5 cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute and a final hold at 4°C.  To optimize the required cycle number, the material from the initial PCR reaction was split and a 5 µl was used for a separate qPCR reaction (0.125 µM AttB tn5 Fwd Primer, 0.125 µM AttB tn5 Rev Primer, 1 x SYBR Green I, NEBNext Master Mix) with the following conditions: 72°C for 5 minutes, 98°C for 30 seconds, 35 cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute using a StepOnePlus™ Real-Time PCR System (Thermo Fisher). Using the raw data from the cyan channel the number of cycles for 25% amplification was calculated. The number of cycles obtained from the qPCR side reaction was then used to amplify the remainder of the material as follows, 98°C for 30 seconds, cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute with a final hold at 4°C. The resulting material was size selected, to optimise for material originating from enhancers, for fragments between 350 and 650 bp by electrophoresis on a 1.2% agarose gel with ethidium bromide and gel extraction was performed using the Qiagen MinElute® Gel Extraction Kit following manufactures protocol. To generate attL-flanked entry clones compatible with cloning into the reporter vector the size selected material was cloned into the pDONR™221 (Thermo Fisher) by BP Gateway® reaction (100 fmol pDONR221, 100 fmol PCR material, 2 µl BP Clonase II, made up to 20µl with TE buffer (pH 8.0) the reaction was incubated for 18 hours at 25°C and ended by treatment with 0.2µg proteinase K and incubation at 37°C for 10 minutes. NEB 10-beta Electrocompetent cells were transformed with the plasmid by electroporation with a Bio-Rad GenePulser using program EC1 (2.0 kV, 200 Ohm, 25 µF), after addition of outgrowth media and incubation at 37°C, 250 rpm for 1 hour the bacteria were spread onto 150 mm agar plates containing 50 µg/ml kanamycin. Following overnight incubation at 37°C, 10 ml of LB was added to each plate and the bacterial lawn scraped off using a cell scraper. Plasmid DNA was extracted from the collected bacteria by Maxi-prep using the NucleoBond Xtra Midi EF kit following manufacturer’s instructions. The resulting product was eluted in 500 µl H2O.  The chromatin fragments were then transferred into the enhancer reporter cassette in the pSKB-GW-Hsp68-Venus vector 1 by Gateway® LR reaction (150ng Entry clone (pDONR), 150 ng pSKB, 2 µl LR Clonase II, made up to 10µl with TE buffer (pH 8.0) ) the reaction was incubated for 1 hour at 25°C and ended by treatment with 0.2 µg proteinase K and incubation at 37°C for 10 minutes. As with the BP reaction product, NEB 10-beta Electrocompetent cells were transformed with the material and after overnight incubation on agar plates containing 200 µg/ml ampicillin the bacteria were collected and the plasmid library extracted by Maxi-Prep. To obtain the highest possible diversity of fragments the cloning was carried out 10 times for material from each differentiation stage with the pDONR 221 library material  being combined before moving to the LR clonase reaction.  The HM-1 ES cell line was cultured on gelatinised culture plates in ES-Media (DMEM, 15% FCS, 1 mM Sodium pyruvate, 1x Pen/Strep, 1x L-glutamine, 0.15 mM MTG, 25 mM Hepes buffer and 1u/ml ESGRO LIF (Sigma-Aldrich)) at 37 °C, 10% CO2 and split every 48 hours to maintain healthy cells. Prior to transfection the cells were treated for 1 week with 1 x 6-TG to remove any cells with a functional HPRT locus. The plasmid libraries were mixed and digested with PmeI (NEB) to linearise the plasmids prior to transfection. To obtain optimum homologous recombination efficiency CRISPR guides were designed flanking the region and cloned into the PX458 Cas9 and sgRNA expression vector. For each experiment, 500x106 cells were transfected using a Nucleofector®-4D (Lonza) with the P3 Primary Cell X kit with 5x106 per cuvette 10 ug pSKB enhancer reporter plasmid and 10 ug of PX458-HPRT CRISPR plasmid using program CG-104. Following electroporation, the cells were plated on gelatinised plates in ES-media with the addition of 50 µM SCR7 pyrazine (Sigma) to inhibit Non-homologous end joining, promoting homologous recombination following cutting by Cas9. After 12 hours the media was changed and 1 x HAT (Hypoxanthine-Aminopterin-Thymidine (Sigma)) was added to select for clones with successful recombination. The cells were then maintained in media containing HAT for one week and HT (hypoxanthine and thymidine (Sigma)) for a further 2 passages to prevent the cells from dying after the withdrawal of HAT, whereby all cells were kept and replated after splitting. The selected cells were then put into IVD cultures and differentiated into HB, HE1, HE2 and HP (as described in Obier et al (2016)) and sorted by FACS. In addition to the previously mentioned gating for obtaining the cell populations the cells were also sorted into negative, low, medium and high Venus-YFP populations representing the activity of the enhancer fragment driven minimal promoter. The YFP-Venus negative population was gated based on a cell line containing a reporter construct with only the minimal promoter and reporter with no enhancer fragment.

extract_protocol:
Genomic DNA was extracted from the sorted cell populations using the Qiagen DNA Micro kit following manufacturer’s instructions.
To amplify the fragments contained in the reporter cassettes and add sequencing adaptors a PCR using indexed primers compatible with Illumina sequencing and targeted against the tn5 transposase sequence ((0.5 µM Nextera PCR Primer i5, 0.5 µM Nextera PCR Primer i7, 25 µl NEBNext Master Mix). Dependant on the amount of DNA obtained from the sorted cells between 25 and 30 PCR cycles were performed with the following conditions 98°C for 30 seconds, cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute with a final hold at 4°C. Libraries were quantified using a Bioanalyzer 2100 (Agilent) with a High Sensitivity DNA Chip and pooled at equal concentration for sequencing. The final pool concentration and size was then confirmed by Kappa Library Quantification Kit (Roche) and Bioanalyzer. The pooled libraries were sequenced on a Next-Seq 550 as a paired end run with a 150 cycle High Output kit by the Genomics Birmingham Sequencing Facility.

value: Embryonic Stem Cell (ES)

value: HM-1 ES cells


title: pSKB-Plasmid-HP

description: ATAC-Seq material cloned into the pSKB vector to create a plasmid library

source_name: Hematopeitic Porgenitor (HP)

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells

value: In Vitro Differentiation


title: HM-1-PCR-Control-R1


title: hFGF19_2

description: hFGF stimulation for 72 hours

value: human colorectal cancer cell


title: pSKB-Plasmid-HE2

source_name: Hemogenic Endothelium 2 (HE2)

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: Cell line Exon 11partd M15 Pool2 Replicate 2

value: Embryonic stem cell


title: HM-1-PCR-Control-R2


title: hmo1△ yeast, replicate 3

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

description: Hmo1 C

data_processing:
*library strategy: native elongating transcript sequencing (NET-seq)
Base-calling was performed using bcl2fastq software (version 2.20.00).
Fqtrim (version 0.9.7) with the "-C" option was used for deduplication of reads based on the UMI sequence.
Reads containing 5' sequence and UMI (5'-AGNNNNNNNNTG-3') were isolated, and this sequence was removed using cutadapt (version 3.4) with "-g -no-indels" parameters.
The 3' sequence 5'-CTGTAGGCACCAT-3' was removed from reads with cutadapt (version 3.4) and the parameters "-a -no-indels".
Alignment of the reads to the Saccharomyces cerevisiae genome was performed with STAR (version 2.7.1a). The STAR alignIntronMax parameter was set to 1.
Output BAM files were sorted and indexed using SAMtools (version 1.6).
BEDTools (version 2.28.0) was used to convert files to BED format.
Genome coverage files were generated using BEDTools (version 2.28.0) with the genomecov function and parameters "-strand" and "+strand"
Data processing and visualization was performed using R (version 4.0.2) and RStudio (1.3.959).
Assembly: S. cerevisiae R64-1-1
Supplementary files format and content: Processed data are included in a single .csv file (WT vs HMO1 sumnorm.csv). The header/column names specify which strain (wt = WT strain and mut = hmo1△ strain) and replicate that the values in the table represent.

organism: Saccharomyces cerevisiae

source_name: hmo1△ yeast

growth_protocol: Both strains of yeast were grown at 30ºC with nutation for all experiments.

extract_protocol:
Extraction methods was exactly the same as described in previously publications from our lab (data available at GSE142457, GSE166983, and GSE175553). In brief, cells were rapidly harvested and lysed under cryogenic conditions. An immunoprecipitation was performed to isolate Pol I and then an acidic phenol/chloroform extraction was used to extract total RNA.
The generation of NET-seq libraries was performed exactly as previously published. In brief, a DNA linker containing a UMI sequence was ligated onto the 3' end of RNA reads. After ligation, a reverse transcription was performed, and DNA was circularized. Circular DNAs were amplified, libraries were purified with PCRClean DX beads, and reads were sequenced.

value: yeast cells


title: PAUUWT_Dx_scRNA

description: 10x Genomics

source_name: Blood

value: Blood cells

value: Blood

value: Arm B


title: hmo1△ yeast, replicate 2

description: Hmo1 B


title: pSKB-Plasmid-HE1

source_name: Hemogenic Endothelium 1 (HE1)

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: Cell line Exon 11partd HAT Pool1 Replicate 1

first: Shyam

value: HAT


title: pSKB-Plasmid-HB

source_name: Hemangioblast Cell (HB)

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: Cell line Exon 11partd M15 Pool1 Replicate 2


title: PAULDS_Rem_scRNA

description: 10x Genomics

source_name: Marrow

value: Bone marrow cells

value: Marrow

value: Arm B (long-term remission)


title: PAULDS_Dx_scRNA

description: 10x Genomics


title: pSKB-Plasmid-ES

value: Embryonic Stem Cell (ES)

value: HM-1 ES cells


title: Cell line Exon 11partd M15 Pool1 Replicate 1


title: Tongue, OSCC, 1027

city: Fukuoka

first: Hu

address: 3-1-1 Maidashi, Higashi-ku

department: Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science

country: Japan

institute: Kyushu University

data_processing:
The 10x Genomics Cell Ranger 6.0 software suite was utilized for reads alignment and the creation of a gene-cell unique molecular identifier (UMI) matrix, employing the GRCh38 reference genome. Cells exhibiting an abnormally high level of mitochondrial gene expression were removed from the analysis.
Assembly: hg38
Supplementary files format and content: comma-separated values files and matrix market files include raw counts for each sample
Supplementary files format and content: comma-separated values files include TCR and BCR filtered contig annotations for each sample

source_name: Tongue

extract_protocol:
All fresh tissue samples of OSCC were collected at the time of surgical resection. Excised tongue specimens from three OSCC patients were preserved in Tissue Storage Solution (130-100-008, Miltenyi Biotec) for subsequent processing. The tissue samples were transferred to gentleMACS C Tubes (130-093-237, Miltenyi Biotec) and cut into small pieces in RPMI-1640 with L-glutamine and phenol red (189-02025, FUJIFILM). Multi Tissue Dissociation Kit I (130-110-201, Miltenyi Biotec) and a gentleMACS Octo Dissociator with Heaters (130-096-427, Miltenyi Biotec) were employed to gently isolate cells from the tongue samples while preserving cell surface epitopes. Following homogenization for 1 hour, the tissue sample was passed through a 100 µm MACS SmartStrainer (130-098-463, Miltenyi Biotec) and transferred into a 5 mL Round Bottom Polystyrene Test Tube with Cell Strainer Snap Cap (352235, Falcon). After washing twice with EasySep Buffer (20144, STEMCELL), erythrocytes were eliminated using a Red Blood Cell Lysis Solution (130-094-183, Miltenyi Biotec). For CD45+ cell isolation, the homogenized cell suspension was incubated with a PE anti-human CD45 antibody (304039, BioLegend) and FcR Blocking Reagent, human (130-059-901, Miltenyi Biotec) at room temperature (RT) for 15 min. Then, EasySep Human PE Positive Selection Kit II (17664, STEMCELL) was employed for positive selection of desired cells. Cells were labeled with anti-CD45+ antibody-coated magnetic particles and separated using an EasySep Magnet (18000, STEMCELL). After separation, the cells were preserved in CELLBANKER 1 plus (11912, ZENOGEN PHARMA) and stored at -80 °C for subsequent analysis.
The number and viability of isolated CD45+ cells were assessed using a LUNA-FX7 Automated Cell Counter (L70001, Logos Biosystems). The cell concentration was adjusted to 10,000 single cells per sample. Subsequently, the cells were processed using a Chromium Single Cell 5ʹ Reagent Kit (v2) in the 10x Genomics Chromium instrument in accordance with the manufacturer’s protocol. To construct libraries, 10x Genomics Chromium Single Cell V(D)J v2 (GEX + human TCR/BCR) reagents were used. The prepared libraries were subjected to sequencing on an Illumina Hiseq platform with the following configuration: Read 1 (26 bp) + i7 index (8 bp) + i5 index (8 bp) + Read 2 (91 bp). Additionally, Hiseq 350M read/lane and two lanes per sample were used to ensure a sequence depth of 100,000 reads per cell.

value: Tongue

value: CD45+ cells


title: Tongue, OSCC, 1122


title: pDONR-Plasmid-HP

institute: University of Birmingham

description: ATAC-Seq material cloned into the pDONR vector to create a plasmid library

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells

value: In Vitro Differentiation


title: PAVUBN_Rem_scRNA

description: 10x Genomics


title: Cell line Exon 11partd2 Ola Pool2 Replicate 2

value: Embryonic stem cell

value: Olaparib


title: Tongue, OSCC, R412


title: PAVUBN_Rel_scRNA

description: 10x Genomics

value: Arm B


title: Cell line Exon 11partd2 Ola Pool2 Replicate 1


title: Cell line Exon 11partd HAT Pool1 Replicate 2


title: pDONR-Plasmid-HE2

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: pDONR-Plasmid-HE1

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: PAXLWH_Rem_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Arm C


title: PAXLWH_Rel_scRNA

description: 10x Genomics

value: Marrow


title: Cell line Exon 11partd-2 Cis Pool2 Replicate 2

value: Cisplatin


title: pDONR-Plasmid-HB

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: PAXLWH_Dx_scRNA

description: 10x Genomics

value: Blood cells

value: Blood


title: pDONR-Plasmid-ES

value: Embryonic Stem Cell (ES)

value: HM-1 ES cells


title: MDA-MB-231 shKDM2B 2

city: Columbus

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

institute: The Ohio State University

data_processing:
Raw sequencing reads in FASTQ format were quality trimmed, and adapters were removed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were then used as input for RNAdetector (La Ferlita et al., 2021) which integrates alignment, read counting, differential expression analysis, and pathway analysis.
Trimmed reads were aligned to the human genome (GRCh38) using STAR (Dobin et al., 2013) and then quantified by featureCounts (Liao et al., 2014).
Differential expression analysis was ultimately performed using DESeq2 (Love et al. 2014), edgeR (Robinson et al., 2010), and LIMMA (Ritchie et al., 2015).
The differential expression results produced by these three tools were then combined and based on the consensus among all three, we calculated a meta-p-value using metaSeqR (Moulos et al., 2015). Genes with a |Log2FC| > 0.58 (|Linear FC| > 1.5) and a meta-adjusted p-value (Benjamini-Hochberg correction) < 0.05 (determined by metaSeqR) were considered differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited raw count matrix

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) (Millipore-Sigma, Cat. D5796) supplemented with penicillin/streptomycin (Corning, Cat. 30-002-CI), nonessential amino acids (Corning, Cat. 25-025-CI), l-glutamine (Corning, Cat. 25-005-CI), sodium pyruvate (Millipore-Sigma, Cat. S8636), plasmocin 2.5 ng/μL (Invivogen, Cat. ant-mpp), and 10% fetal bovine serum (Fisher Scientific, Cat. MT35010CV). Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted from MDA-MB-231 Empty Vector and shKDM2B cells (50-70% confluence) using the Total RNA Purification Plus Kit (Norgen Biotek Corp., Cat. 48300).
RNA purity and integrity were confirmed using the Agilent ScreenTape (Agilent Technologies Cat 5067-5576) before the preparation of the RNA-Seq libraries. Three biological replicates were used for library preparation. Libraries were prepared, using a KAPA RNA HyperPrep kit with RiboErase (Roche Cat KK8560)

value: MDA-MB-231 cells

value: triple negative breast cancer

value: KDM2B knockdown


title: MDA-MB-231 shKDM2B 1


title: PAXLEE_Rem_scRNA

description: 10x Genomics


title: MDA-MB-231 EMPTY VECTOR 3

value: WT


title: Cell line Exon 11partd-2 HAT Pool2 Replicate 1

value: Embryonic stem cell

value: HAT


title: HP-Medium/High-R5

city: Birmingham

description: Higher read depth sequencing than original experiments

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells

value: In Vitro Differentiation


title: MDA-MB-231 EMPTY VECTOR 2


title: PAXLEE_Rel_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Marrow

value: Arm C


title: Cell line Exon 11partd-2 M15 Pool2 Replicate 2


title: HP-Low-R5


title: PAXLEE_Dx_scRNA

description: 10x Genomics


title: MDA-MB-231 EMPTY VECTOR 1


title: Cell line Exon 11partd-2 Cis Pool2 Replicate 1

value: Cisplatin


title: MDA-MB-231 shKDM2B 3


title: PAWHFW_Rem_scRNA

description: 10x Genomics


title: Control ISC mature, rep3

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed of adapters and sequencing quality lower than 20 (using cutadapt and sickle)
The RNAseq reads were aligned to hg38 whole genome using Hisat2
Fragments Per Kilobase of transcript per Million (FPKM) was calculated using StringTie with gene level.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Human intestinal stem cells from human pluripotent stem cell-drived 3D intestinal organoids

extract_protocol:
Illumina TruSeq kit for paired-end reads, poly-A selection, non-strand-specific
The NEBNext RNA first-strand synthesis module and NEBNExt Ultra Directional second strand synthesis kit (New England BioLabs) were used for the preparation of RNA sequencing (RNA-Seq) libraries.

value: Human intestinal stem cells


title: Cell line Exon 11partd-2 M15 Pool2 Replicate 1


title: Cell line Exon 11partd-2 Ola Pool1 Replicate 2

value: Olaparib


title: Cell line Exon 11partd-2 HAT Pool2 Replicate 2


title: PAWHFW_Rel_scRNA

description: 10x Genomics


title: Control ISC mature, rep2

value: Human intestinal stem cells from human pluripotent stem cell-drived 3D intestinal organoids


title: Cell line Exon 11partd-2 Ola Pool1 Replicate 1


title: Control ISC mature, rep1


title: HE2-Medium/High-R5

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: Cell line Exon 11partd-2 Cis Pool1 Replicate 2


title: Control ISC immature, rep3


title: HE2-Low-R5


title: PAWHFW_Dx_scRNA

description: 10x Genomics


title: HE2-Negative-R5


title: PAVBFN_Rem_scRNA

description: 10x Genomics


title: Cell line Exon 11partd-2 Cis Pool1 Replicate 1


title: PAVBFN_Rel_scRNA

description: 10x Genomics


title: Control ISC immature, rep2


title: Cell line Exon 11partd-2 HAT Pool1 Replicate 2


title: HP-Negative-R5


title: HE1-Medium/High-R5

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: Control ISC immature, rep1


title: HE1-Low-R5


title: Cell line Exon 11partd-2 HAT Pool1 Replicate 1


title: PAVBFN_Dx_scRNA

description: 10x Genomics


title: Control ALI mature, rep3


title: PAWHKK_Rel_scRNA

description: 10x Genomics

value: Arm B


title: Cell line Exon 11partd-2 M15 Pool1 Replicate 2

value: Embryonic stem cell


title: PAWHKK_Dx_scRNA

description: 10x Genomics


title: PAWWCW_Rem_scRNA

description: 10x Genomics

value: Blood cells

value: Blood


title: HB-Medium/High-R5

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: Control ALI mature, rep1


title: Control ALI mature, rep2


title: HB-Low-R5

value: In Vitro Differentiation


title: Control ALI immature, rep3


title: Cell line Exon 11partc-2 Ola Pool2 Replicate 1


title: PAWWCW_Rel_scRNA

description: 10x Genomics


title: HB-Negative-R5


title: Control ALI immature, rep2


title: ES-Medium/High-R5

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell

value: HM-1 ES cell


title: ES-Low-R5


title: PAWTSD_Rem_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Marrow


title: PAWWCW_Dx_scRNA

description: 10x Genomics


title: HE1-Negative-R5


title: ES-Negative-R5


title: Control ALI immature, rep1

value: Human intestinal stem cells


title: Cell line Exon 11partd-2M15 Pool1 Replicate 1


title: Cell line Exon 11partc-2 Ola Pool2 Replicate 2

value: Olaparib


title: Cell line Exon 11partc-2 Cis Pool2 Replicate 2

value: Cisplatin


title: PAWTSD_Rel_scRNA

description: 10x Genomics


title: iPSCDA neuron Sol1, replicate 2

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the hg19 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: 39840 iPSC derived neurons

growth_protocol: Dopaminergic neurons were differentiated directly from iPSCs using the Kriks et al protocol https://www.nature.com/articles/nature10648

extract_protocol: Cells were dissociated using Trizol and the Zymo RNA clean and concentrate kit was used for RNA preparation

value: 39840 iPSC derived neurons

value: dopmainergic

value: alpha synuclein duplication

value: 45 days


title: HP-High-Rep4

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells


title: Cell line Exon 11partc-2 HAT Pool2 Replicate 2

value: Embryonic stem cell

value: HAT


title: iPSCDA neuron Sol1, replicate 1


title: Cell line Exon 11partc-2 Cis Pool2 Replicate 1


title: HP-Medium-Rep4


title: Cell line Exon 11partc-2 HAT Pool2 Replicate 1


title: Cell line Exon 11partc-2 M15 Pool2 Replicate 2


title: PAWRVC_Rem_scRNA

description: 10x Genomics

value: Arm B


title: hmo1△ yeast, replicate 1

description: Hmo1 A

value: yeast cells


title: PAWTSD_Dx_scRNA

description: 10x Genomics

value: Blood cells

value: Blood


title: iPSCDA neuron PET3, replicate 1

source_name: 39720 iPSC derived neurons

value: 39720 iPSC derived neurons

value: Parkin mutation


title: PAWRVC_Rel_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Marrow


title: Cell line Exon 11partc-2 M15 Pool2 Replicate 1


title: iPSCDA neuron Hu4-17, replicate 2

source_name: Hu.F4.17 iPSC derived neurons

value: Hu.F4.17 iPSC derived neurons

value: alpha synuclein triplication


title: HP-Low-Rep4

value: In Vitro Differentiation


title: HE2-High-Rep4

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: HE2-Medium-Rep4


title: iPSCDA neuron Hu4-17, replicate 1

value: dopmainergic

value: 45 days